@article {pmid37239354,
year = {2023},
author = {Thomas, JT and Cavagnino, C and Kjelland, K and Anderson, E and Sturk-Andreaggi, K and Daniels-Higginbotham, J and Amory, C and Spatola, B and Moran, K and Parson, W and Marshall, C},
title = {Evaluating the Usefulness of Human DNA Quantification to Predict DNA Profiling Success of Historical Bone Samples.},
journal = {Genes},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/genes14050994},
pmid = {37239354},
issn = {2073-4425},
abstract = {This study assessed the usefulness of DNA quantification to predict the success of historical samples when analyzing SNPs, mtDNA, and STR targets. Thirty burials from six historical contexts were utilized, ranging in age from 80 to 800 years postmortem. Samples underwent library preparation and hybridization capture with two bait panels (FORCE and mitogenome), and STR typing (autosomal STR and Y-STR). All 30 samples generated small (~80 bp) autosomal DNA target qPCR results, despite mean mappable fragments ranging from 55-125 bp. The qPCR results were positively correlated with DNA profiling success. Samples with human DNA inputs as low as 100 pg resulted in ≥80% FORCE SNPs at 10X coverage. All 30 samples resulted in mitogenome coverage ≥100X despite low human DNA input (as low as 1 pg). With PowerPlex Fusion, ≥30 pg human DNA input resulted in >40% of auSTR loci. At least 59% of Y-STR loci were recovered with Y-target qPCR-based inputs of ≥24 pg. The results also indicate that human DNA quantity is a better predictor of success than the ratio of human to exogenous DNA. Accurate quantification with qPCR is feasible for historical bone samples, allowing for the screening of extracts to predict the success of DNA profiling.},
}

@article {pmid37224187,
year = {2023},
author = {Gibbon, VE and Feris, L and Gretzinger, J and Smith, K and Hall, S and Penn, N and Mutsvangwa, TEM and Heale, M and Finaughty, DA and Karanja, YW and Esterhuyse, J and Kotze, D and Barnes, N and Gunston, G and May, J and Krause, J and Wilkinson, CM and Schiffels, S and Februarie, D and Alves, S and Sealy, JC},
title = {Confronting historical legacies of biological anthropology in South Africa-Restitution, redress and community-centered science: The Sutherland Nine.},
journal = {PloS one},
volume = {18},
number = {5},
pages = {e0284785},
pmid = {37224187},
issn = {1932-6203},
mesh = {Humans ; South Africa ; *Anthropology ; *Archaeology ; Cemeteries ; DNA, Ancient ; },
abstract = {We describe a process of restitution of nine unethically acquired human skeletons to their families, together with attempts at redress. Between 1925-1927 C.E., the skeletonised remains of nine San or Khoekhoe people, eight of them known-in-life, were removed from their graves on the farm Kruisrivier, near Sutherland in the Northern Cape Province of South Africa. They were donated to the Anatomy Department at the University of Cape Town. This was done without the knowledge or permission of their families. The donor was a medical student who removed the remains from the labourers' cemetery on his family farm. Nearly 100 years later, the remains are being returned to their community, accompanied by a range of community-driven interdisciplinary historical, archaeological and analytical (osteobiographic, craniofacial, ancient DNA, stable isotope) studies to document, as far as possible, their lives and deaths. The restitution process began by contacting families living in the same area with the same surnames as the deceased. The restitution and redress process prioritises the descendant families' memories, wishes and desire to understand the situation, and learn more about their ancestors. The descendant families have described the process as helping them to reconnect with their ancestors. A richer appreciation of their ancestors' lives, gained in part from scientific analyses, culminating with reburial, is hoped to aid the descendant families and wider community in [re-]connecting with their heritage and culture, and contribute to restorative justice, reconciliation and healing while confronting a traumatic historical moment. While these nine individuals were exhumed as specimens, they will be reburied as people.},
}

Humans
South Africa
*Anthropology
*Archaeology
Cemeteries
DNA, Ancient

@article {pmid37141357,
year = {2023},
author = {Gibbons, A},
title = {The woman with the deer pendant.},
journal = {Science (New York, N.Y.)},
volume = {380},
number = {6644},
pages = {446},
doi = {10.1126/science.adi5371},
pmid = {37141357},
issn = {1095-9203},
mesh = {Animals ; Female ; Humans ; Deer ; *DNA, Ancient/isolation & purification ; },
abstract = {Pioneering technique gleans DNA from a Stone Age ornament, revealing its last wearer.},
}

Animals
Female
Humans
Deer
*DNA, Ancient/isolation & purification

@article {pmid37220274,
year = {2023},
author = {Tobler, R and Souilmi, Y and Huber, CD and Bean, N and Turney, CSM and Grey, ST and Cooper, A},
title = {The role of genetic selection and climatic factors in the dispersal of anatomically modern humans out of Africa.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {22},
pages = {e2213061120},
doi = {10.1073/pnas.2213061120},
pmid = {37220274},
issn = {1091-6490},
abstract = {The evolutionarily recent dispersal of anatomically modern humans (AMH) out of Africa (OoA) and across Eurasia provides a unique opportunity to examine the impacts of genetic selection as humans adapted to multiple new environments. Analysis of ancient Eurasian genomic datasets (~1,000 to 45,000 y old) reveals signatures of strong selection, including at least 57 hard sweeps after the initial AMH movement OoA, which have been obscured in modern populations by extensive admixture during the Holocene. The spatiotemporal patterns of these hard sweeps provide a means to reconstruct early AMH population dispersals OoA. We identify a previously unsuspected extended period of genetic adaptation lasting ~30,000 y, potentially in the Arabian Peninsula area, prior to a major Neandertal genetic introgression and subsequent rapid dispersal across Eurasia as far as Australia. Consistent functional targets of selection initiated during this period, which we term the Arabian Standstill, include loci involved in the regulation of fat storage, neural development, skin physiology, and cilia function. Similar adaptive signatures are also evident in introgressed archaic hominin loci and modern Arctic human groups, and we suggest that this signal represents selection for cold adaptation. Surprisingly, many of the candidate selected loci across these groups appear to directly interact and coordinately regulate biological processes, with a number associated with major modern diseases including the ciliopathies, metabolic syndrome, and neurodegenerative disorders. This expands the potential for ancestral human adaptation to directly impact modern diseases, providing a platform for evolutionary medicine.},
}

@article {pmid37216609,
year = {2023},
author = {Ciecierski, L and Stolarek, I and Figlerowicz, M},
title = {Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkad428},
pmid = {37216609},
issn = {1362-4962},
abstract = {Archeogenomics is a rapidly growing interdisciplinary research field driven by the development of techniques that enable the acquisition and analysis of ancient DNA (aDNA). Recent advances in aDNA studies have contributed significantly to increasing our understanding of the natural history of humans. One of the most significant challenges facing archeogenomics is the integration of highly heterogeneous genomic, archeological, and anthropological data and their comprehensive analysis, considering changes that occur in time and space. Only this complex approach can explain the relationship between past populations in the context of migration or cultural development. To address these challenges, we developed a Human AGEs web server. It focuses on creating comprehensive spatiotemporal visualizations of genomic, archeogenomic, and archeological information, which can be provided by the user or loaded from a graph database. The interactive map application at the center of Human AGEs can display multiple layers of data in various forms, such as bubble charts, pie charts, heatmaps, or tag clouds. These visualizations can be modified using various clustering, filtering, and styling options, and the map state can be exported to a high-resolution image or saved as a session file for later use. Human AGEs, along with their tutorial, are accessible at https://archeogenomics.eu/.},
}

@article {pmid37215481,
year = {2023},
author = {Mármol-Sánchez, E and Heidemann, PL and Gredal, H and Cirera, S},
title = {MicroRNA profiling of cerebrospinal fluid from dogs with steroid responsive meningitis-arteritis and meningoencephalitis of unknown origin.},
journal = {Frontiers in veterinary science},
volume = {10},
number = {},
pages = {1144084},
doi = {10.3389/fvets.2023.1144084},
pmid = {37215481},
issn = {2297-1769},
abstract = {INTRODUCTION: Non-infectious inflammatory diseases of the central nervous system in dogs, such as steroid responsive meningitis-arteritis (SRMA) and meningoencephalitis of unknown origin (MUO), represent a common clinical challenge that needs extensive and multimodal work-up to reach a presumptive diagnosis. Both diseases are presumably caused by dysregulations of the immune system, but further research is needed in order to understand the molecular mechanisms behind each disease and to optimize treatment.

METHODS: By next-generation sequencing and subsequent quantitative real-time PCR (qPCR) verification, we designed a prospective case-control pilot study to analyze the small RNA profiles of cerebrospinal fluid from dogs suffering from MUO (N = 5), dogs suffering from SRMA (N = 8), and healthy dogs (N = 5) presented for elective euthanasia used as the Control group.

RESULTS: Our results showed an overall enrichment in Y-RNA fragments across all samples, followed by microRNAs (miRNAs) and ribosomal RNAs as the major findings. Additional traces of short RNA reads mapped to long non-coding RNAs and protein-coding genes were also found. From the detected canine miRNAs, miR-21, miR-486, miR-148a, miR-99a, miR-191 and miR-92a were among the most abundant. Dogs with SRMA showed higher differences in miRNA abundance than dogs with MUO when compared to healthy dogs, and miR-142-3p was consistently detected as differentially upregulated in both diseases, although at a low concentration. Moreover, miR-405-5p and miR-503-5p showed different profiles between SRMA and MUO dogs. Subsequent qPCR analyses confirmed miR-142-5p, miR-191-5p and miR-92a-3p as significantly upregulated miRNAs in dogs with SRMA and/or MUO.

DISCUSSION: Cerebrospinal fluid is a challenging biological material to use for profiling miRNAs due to the low content of circulating RNAs. Despite this, we could confirm several miRNAs being differentially abundant when comparing healthy dogs and dogs with MUO and SRMA, respectively. The results of this study indicate a potential role of miRNAs in the underlying molecular mechanisms of these diseases and establish the basis for further studies.},
}

@article {pmid37212188,
year = {2023},
author = {Bunce, M},
title = {It is time for ancient DNA to sweat the small stuff.},
journal = {Molecular ecology},
volume = {32},
number = {11},
pages = {2689-2691},
doi = {10.1111/mec.16970},
pmid = {37212188},
issn = {1365-294X},
abstract = {When one thinks of the field of ancient DNA it conjures images of extinct megafauna, from mammoths and woolly rhinos, through to the giant, flightless elephant bird (but hopefully not dinosaurs - despite the pervasive idea of 'dino DNA' from Jurassic park). These taxa have fascinating evolutionary histories, and their extinction stories need to be told. At the other end of the vertebrate scale, however, is the often neglected 'small stuff' - lizards, frogs, and other herpetofauna. But here's the rub - extracting DNA from the bones of this 'small stuff' is not only difficult, it often destroys the sample. In this issue, Scarsbrook et al. (2023) describe a new way to study the ancient (or historical) DNA of small vertebrates that is minimally destructive. The authors use the method to reconstruct the dynamic evolutionary history of New Zealand geckos and make new insights into how remnant populations should be managed. This work provides some key insights into New Zealand geckos but also opens up opportunities of biomolecular research on the smallest of vouchered vertebrate samples held within museum collections.},
}

@article {pmid37207647,
year = {2023},
author = {Fleskes, RE and Owsley, DW and Bruwelheide, KS and Barca, KG and Griffith, DR and Cabana, GS and Schurr, TG},
title = {Historical genomes elucidate European settlement and the African diaspora in Delaware.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2023.04.069},
pmid = {37207647},
issn = {1879-0445},
abstract = {The 17[th]-century colonization of North America brought thousands of Europeans to Indigenous lands in the Delaware region, which comprises the eastern boundary of the Chesapeake Bay in what is now the Mid-Atlantic region of the United States.[1] The demographic features of these initial colonial migrations are not uniformly characterized, with Europeans and European-Americans migrating to the Delaware area from other countries and neighboring colonies as single persons or in family units of free persons, indentured servants, or tenant farmers.[2] European colonizers also instituted a system of racialized slavery through which they forcibly transported thousands of Africans to the Chesapeake region. Historical information about African-descended individuals in the Delaware region is limited, with a population estimate of less than 500 persons by 1700 CE.[3][,][4] To shed light on the population histories of this period, we analyzed low-coverage genomes of 11 individuals from the Avery's Rest archaeological site (circa 1675-1725 CE), located in Delaware. Previous osteological and mitochondrial DNA (mtDNA) sequence analyses showed a southern group of eight individuals of European maternal descent, buried 15-20 feet from a northern group of three individuals of African maternal descent.[5] Autosomal results further illuminate genomic similarities to Northwestern European reference populations or West and West-Central African reference populations, respectively. We also identify three generations of maternal kin of European ancestry and a paternal parent-offspring relationship between an adult and child of African ancestry. These findings expand our understanding of the origins and familial relationships in late 17[th] and early 18[th] century North America.},
}

@article {pmid37187366,
year = {2023},
author = {Wilke, T and Kehlmaier, C and Stelbrink, B and Albrecht, C and Bouchet, P},
title = {Historical DNA solves century-old mystery on sessility in freshwater gastropods.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {107813},
doi = {10.1016/j.ympev.2023.107813},
pmid = {37187366},
issn = {1095-9513},
abstract = {Extinction rates are increasing unabatedly but resources available for conservation action are limited. Therefore, some conservationists are pushing for ecology- and evolution-based conservation choices, prioritizing taxa with phylogenetic and trait-based originality. Extinction of original taxa may result in a disproportionate loss of evolutionary innovations and potentially prevent transformative changes in living systems. Here, we generated historical DNA data from an almost 120-year-old syntype of the enigmatic sessile snail Helicostoa sinensis from the Three Gorges region of the Yangtze River (PR China), using a next-generation sequencing protocol developed for ancient DNA. In a broader phylogenetic context, we assessed the phylogenetic and trait-based originality of this enigmatic taxon to solve the century-old puzzle of sessility in freshwater gastropods. Our multi-locus data confirm the phylogenetic and trait-based originality of H. sinensis. It is an ultra-rare, subfamily-level taxon (Helicostoinae stat. nov.) within the family Bithyniidae, which exhibits the evolutionary innovation of sessility. While we conservatively classify H. sinensis as "Critically Endangered", there is mounting evidence of the biological annihilation of this endemic species. Although rapidly rising extinction rates in invertebrates are increasingly recognized, the potential loss of originality in these "little things that run the world" has received little attention. We therefore call for comprehensive surveys of originality in invertebrates, particularly from extreme environments such as rapids of large rivers, as a basis for urgently needed ecology- and evolution-based conservation decisions.},
}

@article {pmid37185708,
year = {2023},
author = {Abondio, P and Bruno, F and Luiselli, D},
title = {Apolipoprotein E (APOE) Haplotypes in Healthy Subjects from Worldwide Macroareas: A Population Genetics Perspective for Cardiovascular Disease, Neurodegeneration, and Dementia.},
journal = {Current issues in molecular biology},
volume = {45},
number = {4},
pages = {2817-2831},
doi = {10.3390/cimb45040184},
pmid = {37185708},
issn = {1467-3045},
abstract = {Human APOE is a 299-amino acid long protein expressed and secreted in several tissues and body districts, where it exerts different functions mainly related to lipid metabolism, with specific activities around cholesterol transport and absorption/elimination. It has three main isoforms, determined by the pair of mutations rs7412-C/T and rs429358-C/T, which gives rise to the functionally different APOE variants ε2, ε3, and ε4. These have a distinct impact on lipid metabolism and are differentially implicated in Alzheimer's disease and neurodegeneration, cardiovascular disease, and dyslipidemia. A plethora of other single nucleotide variants along the sequence of the APOE gene have been studied in cohorts of affected individuals, where they also modulate the influence of the three main isoforms to determine the risk of developing the disease. However, no contextual analysis of gene-long haplotypes has been carried out so far, and never extensively in cohorts of healthy individuals from different worldwide populations. Leveraging a rich population genomics dataset, this study elucidates the distribution of APOE variants and haplotypes that are shared across populations and to specific macroareas, revealing a variety of risk-allele associations that distinguish specific ancestral backgrounds and can be leveraged for specific ancestry-informed screenings in medicine and public health.},
}

@article {pmid37167404,
year = {2023},
author = {Llamas, B and Roca-Rada, X},
title = {Paleogenomic study of the Mexican past.},
journal = {Science (New York, N.Y.)},
volume = {380},
number = {6645},
pages = {578-579},
doi = {10.1126/science.adh7902},
pmid = {37167404},
issn = {1095-9203},
mesh = {Humans ; *DNA, Ancient ; Mexico ; },
abstract = {Ancient DNA analysis of ancestral Mexicans reveals a complex demographic history.},
}

Humans
*DNA, Ancient
Mexico

@article {pmid37163039,
year = {2023},
author = {Pandey, D and Harris, M and Garud, NR and Narasimhan, VM},
title = {Understanding natural selection in Holocene Europe using multi-locus genotype identity scans.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.04.24.538113},
pmid = {37163039},
abstract = {Ancient DNA (aDNA) has been a revolutionary technology in understanding human history but has not been used extensively to study natural selection as large sample sizes to study allele frequency changes over time have thus far not been available. Here, we examined a time transect of 708 published samples over the past 7,000 years of European history using multi-locus genotype-based selection scans. As aDNA data is affected by high missingness, ascertainment bias, DNA damage, random allele calling, and is unphased, we first validated our selection scan, G12 ancient , on simulated data resembling aDNA under a demographic model that captures broad features of the allele frequency spectrum of European genomes as well as positive controls that have been previously identified and functionally validated in modern European datasets on data from ancient individuals from time periods very close to the present time. We then applied our statistic to the aDNA time transect to detect and resolve the timing of natural selection occurring genome wide and found several candidates of selection across the different time periods that had not been picked up by selection scans using single SNP allele frequency approaches. In addition, enrichment analysis discovered multiple categories of complex traits that might be under adaptation across these periods. Our results demonstrate the utility of applying different types of selection scans to aDNA to uncover putative selection signals at loci in the ancient past that might have been masked in modern samples.},
}

@article {pmid37157914,
year = {2023},
author = {Whitehouse, LS and Schrider, DR},
title = {Timesweeper: Accurately Identifying Selective Sweeps Using Population Genomic Time Series.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyad084},
pmid = {37157914},
issn = {1943-2631},
abstract = {Despite decades of research, identifying selective sweeps, the genomic footprints of positive selection, remains a core problem in population genetics. Of the myriad methods that have been developed to tackle this task, few are designed to leverage the potential of genomic time-series data. This is because in most population genetic studies of natural populations only a single period of time can be sampled. Recent advancements in sequencing technology, including improvements in extracting and sequencing ancient DNA, have made repeated samplings of a population possible, allowing for more direct analysis of recent evolutionary dynamics. Serial sampling of organisms with shorter generation times has also become more feasible due to improvements in the cost and throughput of sequencing. With these advances in mind, here we present Timesweeper, a fast and accurate convolutional neural network-based tool for identifying selective sweeps in data consisting of multiple genomic samplings of a population over time. Timesweeper population genomic time-series data by first simulating training data under a demographic model appropriate for the data of interest, training a one-dimensional Convolutional Neural Network on said simulations, and inferring which polymorphisms in this serialized dataset were the direct target of a completed or ongoing selective sweep. We show that Timesweeper is accurate under multiple simulated demographic and sampling scenarios, identifies selected variants with high resolution, and estimates selection coefficients more accurately than existing methods. In sum, we show that more accurate inferences about natural selection are possible when genomic time-series data are available; such data will continue to proliferate in coming years due to both the sequencing of ancient samples and repeated samplings of extant populations with faster generation times, as well as experimentally evolved populations where time-series data are often generated. Methodological advances such as Timesweeper thus have the potential to help resolve the controversy over the role of positive selection in the genome. We provide Timesweeper as a Python package for use by the community.},
}

@article {pmid37153511,
year = {2023},
author = {Sharko, FS and Zhur, KV and Trifonov, VA and Prokhortchouk, EB},
title = {Distortion of Population Statistics due to the Use of Different Methodological Approaches to the Construction of Genomic DNA Libraries.},
journal = {Acta naturae},
volume = {15},
number = {1},
pages = {87-96},
pmid = {37153511},
issn = {2075-8251},
abstract = {Several different methods of DNA library preparation for paleogenetic studies are now available. However, the chemical reactions underlying each of them can affect the primary sequence of ancient DNA (aDNA) in the libraries and taint the results of a statistical analysis. In this paper, we compare the results of a sequencing of the aDNA libraries of a Bronze Age sample from burials of the Caucasian burial ground Klady, prepared using three different approaches: (1) shotgun sequencing, (2) strategies for selecting target genomic regions, and (3) strategies for selecting target genomic regions, including DNA pre-treatment with a mixture of uracil-DNA glycosylase (UDG) and endonuclease VIII. The impact of the studied approaches to genomic library preparation on the results of a secondary analysis of the statistical data, namely F4 statistics, ADMIXTURE, and principal component analysis (PCA), was analyzed. It was shown that preparation of genomic libraries without the use of UDG can result in distorted statistical data due to postmortem chemical modifications of the aDNA. This distortion can be alleviated by analyzing only the single nucleotide polymorphisms caused by transversions in the genome.},
}

@article {pmid37141673,
year = {2023},
author = {Zupanič Pajnič, I and Leskovar, T and Zupanc, T and Podovšovnik, E},
title = {A fast and highly efficient automated DNA extraction method from small quantities of bone powder from aged bone samples.},
journal = {Forensic science international. Genetics},
volume = {65},
number = {},
pages = {102882},
doi = {10.1016/j.fsigen.2023.102882},
pmid = {37141673},
issn = {1878-0326},
abstract = {An efficient extraction method is important for obtaining high-quality DNA from degraded aged bone samples. An automated full-demineralization method using the EDTA and DNA Investigator Kit (Qiagen) combined with Qiagen's biorobots was optimized in our laboratory in the past to extract the DNA from 500 mg of aged bone samples. The purpose of this research was to further improve the method with the aim of reducing the required sample material, shortening the extraction time, and achieving higher throughput. To process extremely small samples, the amount of bone powder was reduced to 75 mg, EDTA was replaced with reagents from the Bone DNA Extraction Kit (Promega), and decalcification was shortened from overnight to 2.5 h. Instead of 50 ml tubes, 2 ml tubes were used, which allows higher throughput. The DNA Investigator Kit (Qiagen) and EZ1 Advanced XL biorobot (Qiagen) was used for DNA purification. A comparison between both extraction methods was made on 29 Second World War bones and 22 archaeological bone samples. The differences between both methods were explored by measuring nuclear DNA yield and STR typing success. After cleaning the samples, 500 mg of bone powder was processed using EDTA, and 75 mg of powder from the same bone was processed using the Bone DNA Extraction Kit (Promega). DNA content and DNA degradation were determined using PowerQuant (Promega), and the PowerPlex ESI 17 Fast System (Promega) was used for STR typing. The results showed that the full-demineralization protocol using 500 mg of bone was efficient for Second World War and archaeological samples, and the partial-demineralization protocol using 75 mg of bone powder was only efficient for the Second World War bones. The improved extraction method-for which significantly lower amounts of bone powder can be used, the extraction process is faster, and higher throughput of bone samples is possible-is applicable for genetic identification of relatively well-preserved aged bone samples in routine forensic analyses.},
}

@article {pmid37095409,
year = {2023},
author = {Callaway, E},
title = {'Truly gobsmacked': Ancient-human genome count surpasses 10,000.},
journal = {Nature},
volume = {617},
number = {7959},
pages = {20},
pmid = {37095409},
issn = {1476-4687},
mesh = {Humans ; *Anthropology/trends ; *Archaeology/trends ; *Genome, Human/genetics ; *DNA, Ancient ; },
}

Humans
*Anthropology/trends
*Archaeology/trends
*Genome, Human/genetics
*DNA, Ancient

@article {pmid37141315,
year = {2023},
author = {Klapper, M and Hübner, A and Ibrahim, A and Wasmuth, I and Borry, M and Haensch, VG and Zhang, S and Al-Jammal, WK and Suma, H and Fellows Yates, JA and Frangenberg, J and Velsko, IM and Chowdhury, S and Herbst, R and Bratovanov, EV and Dahse, HM and Horch, T and Hertweck, C and González Morales, MR and Straus, LG and Vilotijevic, I and Warinner, C and Stallforth, P},
title = {Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic.},
journal = {Science (New York, N.Y.)},
volume = {},
number = {},
pages = {eadf5300},
doi = {10.1126/science.adf5300},
pmid = {37141315},
issn = {1095-9203},
abstract = {Major advances over the past decade in the field of ancient DNA are providing access to past paleogenomic diversity, but the diverse functions and biosynthetic capabilities of this growing paleome remain largely elusive. Here, we investigated the dental calculus of 12 Neanderthals and 52 anatomically modern humans spanning 100 kya to the present and reconstructed 459 bacterial metagenome-assembled genomes (MAGs). We identified a biosynthetic gene cluster (BGC) shared by seven Middle and Upper Paleolithic individuals that allows for the heterologous production of a class of previously unknown metabolites we name paleofurans. This paleobiotechnological approach demonstrates that viable biosynthetic machinery can be produced from the preserved genetic material of ancient organisms, allowing access to natural products from the Pleistocene and providing a promising area for natural product exploration.},
}

@article {pmid37137206,
year = {2023},
author = {Zupanič Pajnič, I and Geršak, ŽM and Leskovar, T and Črešnar, M},
title = {Kinship analysis of 5th- to 6th-century skeletons of Romanized indigenous people from the Bled-Pristava archaeological site.},
journal = {Forensic science international. Genetics},
volume = {65},
number = {},
pages = {102886},
doi = {10.1016/j.fsigen.2023.102886},
pmid = {37137206},
issn = {1878-0326},
abstract = {The familial relationship between skeletons buried together in a shared grave is important for understanding the burial practices of past human populations. Four skeletons were excavated from the Late Antiquity part of the Bled-Pristava burial site in Slovenia, dated to the 5th to 6th century. They were anthropologically characterized as two adults (a middle-aged man and a young woman) and two non-adults (of unknown sex). Based on stratigraphy, the skeletons were considered to be buried simultaneously in one grave. Our aim was to determine whether the skeletons were related. Petrous bones and teeth were used for genetic analysis. Specific precautions were followed to prevent contamination of ancient DNA with contemporary DNA, and an elimination database was established. Bone powder was obtained using a MillMix tissue homogenizer. Prior to extracting the DNA using Biorobot EZ1, 0.5 g of powder was decalcified. The PowerQuant System was used for quantification, various autosomal kits for autosomal short tandem repeat (STR) typing, and the PowerPlex Y23 kit for Y-STR typing. All analyses were performed in duplicate. Up to 28 ng DNA/g of powder was extracted from the samples analyzed. Almost full autosomal STR profiles obtained from all four skeletons and almost full Y-STR haplotypes obtained from two male skeletons were compared, and the possibility of a familial relationship was evaluated. No amplification was obtained in the negative controls, and no match was found in the elimination database. Autosomal STR statistical calculations confirmed that the adult male was the father of two non-adult individuals and one young adult individual from the grave. The relationship between the males (father and son) was additionally confirmed by an identical Y-STR haplotype that belonged to the E1b1b haplogroup, and a combined likelihood ratio for autosomal and Y-STRs was calculated. Kinship analysis confirmed with high confidence (kinship probability greater than 99.9% was calculated for all three children) that all four skeletons belonged to the same family (a father, two daughters, and a son). Through genetic analysis, the burial of members of the same family in a shared grave was confirmed as a burial practice of the population living in the Bled area in Late Antiquity.},
}

@article {pmid37127762,
year = {2023},
author = {Zupanič Pajnič, I and Leskovar, T and Črešnar, M},
title = {Improving kinship probability in analysis of ancient skeletons using identity SNPs and MPS technology.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {37127762},
issn = {1437-1596},
abstract = {In forensic kinship analysis and human identification cases, analysis of STRs is the gold standard. When badly preserved ancient DNA is used for kinship analysis, short identity SNPs are more promising for successful amplification. In this work, kinship analysis was performed on two skeletons from the Early Middle Ages. The surface contaminants of petrous bones were removed by chemical cleaning and UV irradiation; DNA was isolated through full demineralization and purified in an EZ1 Advanced XL machine. The PowerQuant kit was used to analyze DNA yield and degradation, and on average, 17 ng DNA/g of petrous bone was obtained. Both skeletons were typed in duplicate for STR markers using the Investigator EssplexPlus SE QS kit, and comparison of partial consensus genotypes showed shared allelic variants at most loci amplified, indicating close kinship. After statistical calculation, the full-sibling kinship probability was too low for kinship confirmation, and additional analyses were performed with PCR-MPS using the Precision ID Identity Panel. The HID Ion Chef Instrument was used to prepare the libraries and for templating and the Ion GeneStudio S5 System for sequencing. Analysis of identity SNPs produced full genetic profiles from both skeletons. For combined likelihood ratio (LR) calculation, the product rule was used, combining LR for STRs and LR for SNPs, and a combined LR of 3.3 × 10[7] (corresponding to a full-sibling probability of 99.999997%) was calculated. Through the SNP PCR-MPS that followed the STR analysis, full-sibling kinship between the ancient skeletons excavated from an early medieval grave was confirmed.},
}

@article {pmid37117261,
year = {2023},
author = {Ferrando-Bernal, M},
title = {Ancient DNA suggests anaemia and low bone mineral density as the cause for porotic hyperostosis in ancient individuals.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {6968},
pmid = {37117261},
issn = {2045-2322},
mesh = {Humans ; Skull ; DNA, Ancient ; Paleopathology ; *Anemia/complications ; *Hyperostosis/genetics ; *Bone Diseases, Metabolic/complications ; },
abstract = {Porotic hyperostosis (PH) is a disease that had high prevalence during the Neolithic. Several hypotheses have been suggested to explain the origin of the disease, such as an iron deficiency diet, low B12 intake, malaria caused by Plasmodium spp., low haemoglobin levels or low vitamin D levels. None of these hypotheses have been tested genetically. Here, I calculated different genetic scores to test each hypothesis. Additionally, I calculated a genetic score of bone mineral density as it is a phenotype that seems to be selected in ancient Europeans. I apply these genetic scores on 80 ancient samples, 33 with diagnosed PH. The results seem to suggest anaemia and low bone mineral density as the main cause for this disease. Additionally, Neolithic individuals show the lowest genetic risk score for bone mineral density of all other periods tested here, which may explain the highest prevalence of the porotic hyperostosis during this age.},
}

Humans
Skull
DNA, Ancient
Paleopathology
*Anemia/complications
*Hyperostosis/genetics
*Bone Diseases, Metabolic/complications

@article {pmid37101579,
year = {2023},
author = {Kowal, E and Weyrich, LS and Argüelles, JM and Bader, AC and Colwell, C and Cortez, AD and Davis, JL and Figueiro, G and Fox, K and Malhi, RS and Matisoo-Smith, E and Nayak, A and Nelson, EA and Nicholas, G and Nieves-Colón, MA and Russell, L and Ulm, S and Vergara-Silva, F and Villanea, FA and Wagner, JK and Yracheta, JM and Tsosie, KS},
title = {Community partnerships are fundamental to ethical ancient DNA research.},
journal = {HGG advances},
volume = {4},
number = {2},
pages = {100161},
pmid = {37101579},
issn = {2666-2477},
mesh = {Humans ; *DNA, Ancient ; *Ethics, Research ; Population Groups ; Family ; Research Personnel ; },
abstract = {The ethics of the scientific study of Ancestors has long been debated by archaeologists, bioanthropologists, and, more recently, ancient DNA (aDNA) researchers. This article responds to the article "Ethics of DNA research on human remains: five globally applicable guidelines" published in 2021 in Nature by a large group of aDNA researchers and collaborators. We argue that these guidelines do not sufficiently consider the interests of community stakeholders, including descendant communities and communities with potential, but yet unestablished, ties to Ancestors. We focus on three main areas of concern with the guidelines. First is the false separation of "scientific" and "community" concerns and the consistent privileging of researcher perspectives over those of community members. Second, the commitment of the guidelines' authors to open data ignores the principles and practice of Indigenous Data Sovereignty. Further, the authors argue that involving community members in decisions about publication and data sharing is unethical. We argue that excluding community perspectives on "ethical" grounds is convenient for researchers, but it is not, in fact, ethical. Third, we stress the risks of not consulting communities that have established or potential ties to Ancestors, using two recent examples from the literature. Ancient DNA researchers cannot focus on the lowest common denominator of research practice, the bare minimum that is legally necessary. Instead, they should be leading multidisciplinary efforts to create processes to ensure communities from all regions of the globe are identified and engaged in research that affects them. This will often present challenges, but we see these challenges as part of the research, rather than a distraction from the scientific endeavor. If a research team does not have the capacity to meaningfully engage communities, questions must be asked about the value and benefit of their research.},
}

Humans
*DNA, Ancient
*Ethics, Research
Population Groups
Family
Research Personnel

@article {pmid37097268,
year = {2023},
author = {Rogers, NM and Zammit, N and Nguyen-Ngo, D and Souilmi, Y and Minhas, N and Meijles, DN and Self, E and Walters, SN and Warren, J and Cultrone, D and El-Rashid, M and Li, J and Chtanova, T and O'Connell, PJ and Grey, ST},
title = {The impact of the cytoplasmic ubiquitin ligase TNFAIP3 gene variation on transcription factor NF-κB activation in acute kidney injury.},
journal = {Kidney international},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.kint.2023.02.030},
pmid = {37097268},
issn = {1523-1755},
abstract = {Nuclear factor κB (NF-κB) activation is a deleterious molecular mechanism that drives acute kidney injury (AKI) and manifests in transplanted kidneys as delayed graft function. The TNFAIP3 gene encodes A20, a cytoplasmic ubiquitin ligase and a master negative regulator of the NF- κB signaling pathway. Common population-specific TNFAIP3 coding variants that reduce A20's enzyme function and increase NF- κB activation have been linked to heightened protective immunity and autoimmune disease, but have not been investigated in AKI. Here, we functionally identified a series of unique human TNFAIP3 coding variants linked to the autoimmune genome-wide association studies single nucleotide polymorphisms of F127C; namely F127C;R22Q, F127C;G281E, F127C;W448C and F127C;N449K that reduce A20's anti-inflammatory function in an NF- κB reporter assay. To investigate the impact of TNFAIP3 hypomorphic coding variants in AKI we tested a mouse Tnfaip3 hypomorph in a model of ischemia reperfusion injury (IRI). The mouse Tnfaip3 coding variant I325N increases NF- κB activation without overt inflammatory disease, providing an immune boost as I325N mice exhibit enhanced innate immunity to a bacterial challenge. Surprisingly, despite exhibiting increased intra-kidney NF- κB activation with inflammation in IRI, the kidney of I325N mice was protected. The I325N variant influenced the outcome of IRI by changing the dynamic expression of multiple cytoprotective mechanisms, particularly by increasing NF- κB-dependent anti-apoptotic factors BCL-2, BCL-XL, c-FLIP and A20, altering the active redox state of the kidney with a reduction of superoxide levels and the enzyme super oxide dismutase-1, and enhancing cellular protective mechanisms including increased Foxp3[+] T cells. Thus, TNFAIP3 gene variants represent a kidney and population-specific molecular factor that can dictate the course of IRI.},
}

@article {pmid37096383,
year = {2023},
author = {da Silva Coelho, FA and Gill, S and Tomlin, CM and Papavassiliou, M and Farley, SD and Cook, JA and Sonsthagen, SA and Sage, GK and Heaton, TH and Talbot, SL and Lindqvist, C},
title = {Ancient bears provide insights into Pleistocene ice age refugia in Southeast Alaska.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.16960},
pmid = {37096383},
issn = {1365-294X},
abstract = {During the Late Pleistocene, major parts of North America were periodically covered by ice sheets. However, there are still questions about whether ice-free refugia were present in the Alexander Archipelago along the Southeast (SE) Alaska coast during the last glacial maximum (LGM). Numerous subfossils have been recovered from caves in SE Alaska, including American black (Ursus americanus) and brown (U. arctos) bears, which today are found in the Alexander Archipelago but are genetically distinct from mainland bear populations. Hence, these bear species offer an ideal system to investigate long-term occupation, potential refugial survival and lineage turnover. Here, we present genetic analyses based on 99 new complete mitochondrial genomes from ancient and modern brown and black bears spanning the last ~45,000 years. Black bears form two SE Alaskan subclades, one preglacial and another postglacial, that diverged >100,000 years ago. All postglacial ancient brown bears are closely related to modern brown bears in the archipelago, while a single preglacial brown bear is found in a distantly related clade. A hiatus in the bear subfossil record around the LGM and the deep split of their pre- and postglacial subclades fail to support a hypothesis of continuous occupancy in SE Alaska throughout the LGM for either species. Our results are consistent with an absence of refugia along the SE Alaska coast, but indicate that vegetation quickly expanded after deglaciation, allowing bears to recolonize the area after a short-lived LGM peak.},
}

@article {pmid37094265,
year = {2023},
author = {Demeure, CE and Poinar, H and Barreiro, L and Pizarro-Cerdá, J},
title = {[The Black Death, natural selection and susceptibility to auto-immune disorders].},
journal = {Medecine sciences : M/S},
volume = {39},
number = {4},
pages = {331-333},
doi = {10.1051/medsci/2023050},
pmid = {37094265},
issn = {1958-5381},
support = {R01-GM134376/NH/NIH HHS/United States ; },
}

@article {pmid37072186,
year = {2023},
author = {Fernandes, DM and Sirak, KA and Cheronet, O and Novak, M and Brück, F and Zelger, E and Llanos-Lizcano, A and Wagner, A and Zettl, A and Mandl, K and Duffett Carlson, KS and Oberreiter, V and Özdoğan, KT and Sawyer, S and La Pastina, F and Borgia, E and Coppa, A and Dobeš, M and Velemínský, P and Reich, DE and Bell, LS and Pinhasi, R},
title = {Density separation of petrous bone powders for optimized ancient DNA yields.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.277714.123},
pmid = {37072186},
issn = {1549-5469},
abstract = {Density separation is a process routinely used to segregate minerals, organic matter, and even microplastics, from soils and sediments. Here we apply density separation to archaeological bone powders prior to DNA extraction to increase endogenous DNA recovery relative to a standard control extraction of the same powders. Using nontoxic heavy liquid solutions we separated powders from the petrous bones of 10 individuals of similar archaeological preservation into 8 density intervals (2.15 to 2.45 g/cm3, in 0.05 increments). We found that the 2.30-2.35 and 2.35-2.40 g/cm3 intervals yielded up to 5.28-fold more endogenous unique DNA than the corresponding standard extraction (and up to 8.53-fold before duplicate read removal), while maintaining signals of ancient DNA authenticity and not reducing library complexity. Although small 0.05 g/cm3 intervals may maximally optimize yields, a single separation to remove materials with a density above 2.40 g/cm3 yielded up to 2.57-fold more endogenous DNA on average, which enables the simultaneous separation of samples that vary in preservation or in the type of material analyzed. While requiring no new ancient DNA lab equipment and fewer than 30 minutes of extra lab work, the implementation of density separation prior to DNA extraction can substantially boost endogenous DNA yields without decreasing library complexity. Although subsequent studies are required, we present theoretical and practical foundations that may prove useful when applied to other ancient DNA substrates such as teeth, other bones, and sediments.},
}

@article {pmid37071008,
year = {2023},
author = {Vassallo, A and Modi, A and Quagliariello, A and Bacci, G and Faddetta, T and Gallo, M and Provenzano, A and La Barbera, A and Lombardo, G and Maggini, V and Firenzuoli, F and Zaccaroni, M and Gallo, G and Caramelli, D and Aleo Nero, C and Baldi, F and Fani, R and Palumbo Piccionello, A and Pucciarelli, S and Puglia, AM and Sineo, L},
title = {Novel Sources of Biodiversity and Biomolecules from Bacteria Isolated from a High Middle Ages Soil Sample in Palermo (Sicily, Italy).},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0437422},
doi = {10.1128/spectrum.04374-22},
pmid = {37071008},
issn = {2165-0497},
abstract = {The urban plan of Palermo (Sicily, Italy) has evolved throughout Punic, Roman, Byzantine, Arab, and Norman ages until it stabilized within the borders that correspond to the current historic center. During the 2012 to 2013 excavation campaign, new remains of the Arab settlement, directly implanted above the structures of the Roman age, were found. The materials investigated in this study derived from the so-called Survey No 3, which consists of a rock cavity of subcylindrical shape covered with calcarenite blocks: it was probably used to dispose of garbage during the Arabic age and its content, derived from daily activities, included grape seeds, scales and bones of fish, small animal bones, and charcoals. Radiocarbon dating confirmed the medieval origin of this site. The composition of the bacterial community was characterized through a culture-dependent and a culture-independent approach. Culturable bacteria were isolated under aerobic and anaerobic conditions and the total bacterial community was characterized through metagenomic sequencing. Bacterial isolates were tested for the production of compounds with antibiotic activity: a Streptomyces strain, whose genome was sequenced, was of particular interest because of its inhibitory activity, which was due to the Type I polyketide aureothin. Moreover, all strains were tested for the production of secreted proteases, with those belonging to the genus Nocardioides having the most active enzymes. Finally, protocols commonly used for ancient DNA studies were applied to evaluate the antiquity of isolated bacterial strains. Altogether these results show how paleomicrobiology might represent an innovative and unexplored source of novel biodiversity and new biotechnological tools. IMPORTANCE One of the goals of paleomicrobiology is the characterization of the microbial community present in archaeological sites. These analyses can usually provide valuable information about past events, such as occurrence of human and animal infectious diseases, ancient human activities, and environmental changes. However, in this work, investigations about the composition of the bacterial community of an ancient soil sample (harvested in Palermo, Italy) were carried out aiming to screen ancient culturable strains with biotechnological potential, such as the ability to produce bioactive molecules and secreted hydrolytic enzymes. Besides showing the biotechnological relevance of paleomicrobiology, this work reports a case of germination of putatively ancient bacterial spores recovered from soil rather than extreme environments. Moreover, in the case of spore-forming species, these results raise questions about the accuracy of techniques usually applied to estimate antiquity of DNA, as they could lead to its underestimation.},
}

@article {pmid37068234,
year = {2023},
author = {Cohen, P and Bacilieri, R and Ramos-Madrigal, J and Privman, E and Boaretto, E and Weber, A and Fuks, D and Weiss, E and Erickson-Gini, T and Bucking, S and Tepper, Y and Cvikel, D and Schmidt, J and Gilbert, MTP and Wales, N and Bar-Oz, G and Meiri, M},
title = {Ancient DNA from a lost Negev Highlands desert grape reveals a Late Antiquity wine lineage.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {17},
pages = {e2213563120},
doi = {10.1073/pnas.2213563120},
pmid = {37068234},
issn = {1091-6490},
abstract = {Recent excavations of Late Antiquity settlements in the Negev Highlands of southern Israel uncovered a society that established commercial-scale viticulture in an arid environment [D. Fuks et al., Proc. Natl. Acad. Sci. U.S.A. 117, 19780-19791 (2020)]. We applied target-enriched genome-wide sequencing and radiocarbon dating to examine grapevine pips that were excavated at three of these sites. Our analyses revealed centuries long and continuous grape cultivation in the Southern Levant. The genetically diverse pips also provided clues to ancient cultivation strategies aimed at improving agricultural productivity and ensuring food security. Applying genomic prediction analysis, a pip dated to the eighth century CE was determined to likely be from a white grape, to date the oldest to be identified. In a kinship analysis, another pip was found to be descendant from a modern Greek cultivar and was thus linked with several popular historic wines that were once traded across the Byzantine Empire. These findings shed light on historical Byzantine trading networks and on the genetic contribution of Levantine varieties to the classic Aegean landscape.},
}

@article {pmid37066305,
year = {2023},
author = {Mallick, S and Micco, A and Mah, M and Ringbauer, H and Lazaridis, I and Olalde, I and Patterson, N and Reich, D},
title = {The Allen Ancient DNA Resource (AADR): A curated compendium of ancient human genomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.04.06.535797},
pmid = {37066305},
abstract = {More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases since it first was made available and crossed the threshold of >10,000 ancient individuals with genome-wide data at the end of 2022. This note is intended as a citable description of the AADR.},
}

@article {pmid37065506,
year = {2023},
author = {Gancz, AS and Weyrich, LS},
title = {Studying ancient human oral microbiomes could yield insights into the evolutionary history of noncommunicable diseases.},
journal = {F1000Research},
volume = {12},
number = {},
pages = {109},
pmid = {37065506},
issn = {2046-1402},
abstract = {Noncommunicable diseases (NCDs) have played a critical role in shaping human evolution and societies. Despite the exceptional impact of NCDs economically and socially, little is known about the prevalence or impact of these diseases in the past as most do not leave distinguishing features on the human skeleton and are not directly associated with unique pathogens. The inability to identify NCDs in antiquity precludes researchers from investigating how changes in diet, lifestyle, and environments modulate NCD risks in specific populations and from linking evolutionary processes to modern health patterns and disparities. In this review, we highlight how recent advances in ancient DNA (aDNA) sequencing and analytical methodologies may now make it possible to reconstruct NCD-related oral microbiome traits in past populations, thereby providing the first proxies for ancient NCD risk. First, we review the direct and indirect associations between modern oral microbiomes and NCDs, specifically cardiovascular disease, diabetes mellitus, rheumatoid arthritis, and Alzheimer's disease. We then discuss how oral microbiome features associated with NCDs in modern populations may be used to identify previously unstudied sources of morbidity and mortality differences in ancient groups. Finally, we conclude with an outline of the challenges and limitations of employing this approach, as well as how they might be circumvented. While significant experimental work is needed to verify that ancient oral microbiome markers are indeed associated with quantifiable health and survivorship outcomes, this new approach is a promising path forward for evolutionary health research.},
}

@article {pmid37059363,
year = {2023},
author = {Kattner, AA},
title = {When it doesn't run in the blood(vessels) - events involved in vascular disorders.},
journal = {Biomedical journal},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bj.2023.03.004},
pmid = {37059363},
issn = {2320-2890},
abstract = {In the current issue of the Biomedical Journal the underlying pathology of hemodynamic compromise in acute small subcortical infarction are elucidated. A follow-up study in patients with childhood Kawasaki disease is presented, as well as an insight into the gradually decreasing antigen expression in cases of acute myeloid leukemia. Furthermore this issue provides an exciting update concerning COVID-19 and the use of CRISPR-Cas, a review about computational approaches in the research of kidney stone formation, factors connected to central precocious puberty, and why a rock star of paleogenetics recently received a Nobel Prize. Additionally, this issue contains an article proposing the repurposing of the lung cancer drug Capmatinib, a study of how the gut microbiome develops in neonates, an impulse about the role of the transmembrane protein TMED3 in esophageal carcinoma, and the revelation about how competing endogenous RNA influences ischemic stroke. Lastly, genetic reasons for male infertility are discussed, as well as the relation between non-alcoholic fatty liver disease and chronic kidney disease.},
}

@article {pmid37057308,
year = {2023},
author = {Ķimsis, J and Pokšāne, A and Kazarina, A and Vilcāne, A and Petersone-Gordina, E and Zayakin, P and Gerhards, G and Ranka, R},
title = {Tracing microbial communities associated with archaeological human samples in Latvia, 7-11th centuries AD.},
journal = {Environmental microbiology reports},
volume = {},
number = {},
pages = {},
doi = {10.1111/1758-2229.13157},
pmid = {37057308},
issn = {1758-2229},
abstract = {In the grave environment, microorganisms are major ecological participants in the successional decomposition of vertebrates and could infiltrate the skeleton/skeletal material during taphonomic processes. The diversity of archaeological skeleton-associated microbial assemblages and the impact of various factors are poorly understood. This study aimed to evaluate the taxonomic microbial composition of archaeological human bone and teeth samples from the 7th to 11th centuries AD from two burial sites in Latvia. Samples were analysed by a shotgun metagenomics-based approach. The results showed a strong presence of the environmental DNA in the samples, and variability in microbial community structure between individual samples. Differences in microbial composition were observed between bone and tooth samples, as well as between different burial sites. Furthermore, the presence of endogenous ancient DNA (aDNA) in tooth samples was detected. Overall, compositions of microbial communities associated with archaeological human remains in Latvia dated 7-11th century AD were influenced by the sample type and burial location. These findings indicate that, while the content of historical DNA in archaeological samples is low, the comparison of archaeological skeleton-associated microbial assemblages across time and space, along with aDNA damage profile analysis, is important and could help to reveal putative ancient microorganisms.},
}

@article {pmid37043523,
year = {2023},
author = {Rümpler, F and Tessari, C and Gramzow, L and Gafert, C and Blohs, M and Theißen, G},
title = {The origin of floral quartet formation - Ancient exon duplications shaped the evolution of MIKC-type MADS-domain transcription factor interactions.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msad088},
pmid = {37043523},
issn = {1537-1719},
abstract = {During development of flowering plants, some MIKC-type MADS-domain transcription factors (MTFs) exert their regulatory function as heterotetrameric complexes bound to two sites on the DNA of target genes. This way they constitute "floral quartets"or related "floral quartet-like complexes"(FQCs), involving a unique multimeric system of paralogous protein interactions. Tetramerisation of MTFs is brought about mainly by interactions of keratin-like (K) domains. The K-domain associated with the more ancient DNA-binding MADS-domain during evolution in the stem group of extant streptophytes (charophyte green algae + land plants). However, whether this was sufficient for MTF tetramerisation and FQC formation to occur, remains unknown. Here, we provide biophysical and bioinformatic data indicating that FQC formation likely originated in the stem group of land plants in a sublineage of MIKC-type genes termed MIKCC-type genes. In the stem group of this gene lineage, the duplication of the most downstream exon encoding the K-domain led to a C-terminal elongation of the second K-domain helix, thus, generating the tetramerisation interface found in extant MIKCC type proteins. In the stem group of the sister lineage of the MIKCC-type genes, termed MIKC*-type genes, the duplication of two other K-domain exons occurred, extending the K-domain at its N-terminal end. Our data indicate that this structural change prevents heterodimerisation between MIKCC-type and MIKC*-type proteins. This way, two largely independent gene regulatory networks could be established, featuring MIKCC-type or MIKC*-type proteins, respectively, that control different aspects of plant development.},
}

@article {pmid37040705,
year = {2023},
author = {Wegmann, D and Eckel, R},
title = {Human evolution: When admixture met selection.},
journal = {Current biology : CB},
volume = {33},
number = {7},
pages = {R259-R261},
doi = {10.1016/j.cub.2023.02.077},
pmid = {37040705},
issn = {1879-0445},
abstract = {Admixture has been a major force during human evolution. Two new studies using ancient DNA now show how two key admixture events in the evolutionary history of Europeans altered their adaptive trajectories and facilitated rapid evolution.},
}

@article {pmid37002784,
year = {2023},
author = {Honap, TP and Monroe, CR and Johnson, SJ and Jacobson, DK and Abin, CA and Austin, RM and Sandberg, P and Levine, M and Sankaranarayanan, K and Lewis, CM},
title = {Oral metagenomes from Native American Ancestors reveal distinct microbial lineages in the pre-contact era.},
journal = {American journal of biological anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.24735},
pmid = {37002784},
issn = {2692-7691},
abstract = {OBJECTIVES: Limited studies have focused on how European contact and colonialism impacted Native American oral microbiomes, specifically, the diversity of commensal or opportunistically pathogenic oral microbes, which may be associated with oral diseases. Here, we studied the oral microbiomes of pre-contact Wichita Ancestors, in partnership with the Descendant community, The Wichita and Affiliated Tribes, Oklahoma, USA.

MATERIALS AND METHODS: Skeletal remains of 28 Wichita Ancestors from 20 archeological sites (dating approximately to 1250-1450 CE) were paleopathologically assessed for presence of dental calculus and oral disease. DNA was extracted from calculus, and partial uracil deglycosylase-treated double-stranded DNA libraries were shotgun-sequenced using Illumina technology. DNA preservation was assessed, the microbial community was taxonomically profiled, and phylogenomic analyzes were conducted.

RESULTS: Paleopathological analysis revealed signs of oral diseases such as caries and periodontitis. Calculus samples from 26 Ancestors yielded oral microbiomes with minimal extraneous contamination. Anaerolineaceae bacterium oral taxon 439 was found to be the most abundant bacterial species. Several Ancestors showed high abundance of bacteria typically associated with periodontitis such as Tannerella forsythia and Treponema denticola. Phylogenomic analyzes of Anaerolineaceae bacterium oral taxon 439 and T. forsythia revealed biogeographic structuring; strains present in the Wichita Ancestors clustered with strains from other pre-contact Native Americans and were distinct from European and/or post-contact American strains.

DISCUSSION: We present the largest oral metagenome dataset from a pre-contact Native American population and demonstrate the presence of distinct lineages of oral microbes specific to the pre-contact Americas.},
}

@article {pmid37002389,
year = {2023},
author = {Callaway, E},
title = {Ancient DNA illuminates Swahili culture's origins.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {37002389},
issn = {1476-4687},
}

@article {pmid36996223,
year = {2023},
author = {Curry, A},
title = {'Persian princes' helped found early African trade power.},
journal = {Science (New York, N.Y.)},
volume = {379},
number = {6639},
pages = {1284-1285},
doi = {10.1126/science.adi0093},
pmid = {36996223},
issn = {1095-9203},
abstract = {Ancient DNA reflects foreign influx to Swahili coast, but its culture is largely local.},
}

@article {pmid36994803,
year = {2023},
author = {He, Z and Dai, X and Lyu, W and Beaumont, M and Yu, F},
title = {Estimating temporally variable selection intensity from ancient DNA data with the flexibility of modelling linkage and epistasis.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13790},
pmid = {36994803},
issn = {1755-0998},
abstract = {Innovations in ancient DNA (aDNA) preparation and sequencing technologies have exponentially increased the quality and quantity of aDNA data extracted from ancient biological materials. The additional temporal component from the incoming aDNA data can provide improved power to address fundamental evolutionary questions like characterising selection processes that shape the phenotypes and genotypes of contemporary populations or species. However, utilising aDNA to study past selection processes still involves considerable hurdles like how to eliminate the confounding factor of genetic interactions in the inference of selection. To address this issue, we extend the approach of He et al. (2022) to infer temporally variable selection from the aDNA data in the form of genotype likelihoods with the flexibility of modelling linkage and epistasis in this work. Our posterior computation is carried out by a robust adaptive version of the particle marginal Metropolis-Hastings algorithm with a coerced acceptance rate. Our extension inherits the desirable features of He et al. (2022) such as modelling sample uncertainty resulting from the damage and fragmentation of aDNA molecules and reconstructing underlying gamete frequency trajectories of the population. We evaluate its performance through extensive simulations and show its utility with an application to the aDNA data from pigmentation loci in horses.},
}

@article {pmid36993413,
year = {2023},
author = {Barton, AR and Santander, CG and Skoglund, P and Moltke, I and Reich, D and Mathieson, I},
title = {Insufficient evidence for natural selection associated with the Black Death.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.03.14.532615},
pmid = {36993413},
abstract = {Klunk et al. analyzed ancient DNA data from individuals in London and Denmark before, during and after the Black Death [1], and argued that allele frequency changes at immune genes were too large to be produced by random genetic drift and thus must reflect natural selection. They also identified four specific variants that they claimed show evidence of selection including at ERAP2 , for which they estimate a selection coefficient of 0.39â€"several times larger than any selection coefficient on a common human variant reported to date. Here we show that these claims are unsupported for four reasons. First, the signal of enrichment of large allele frequency changes in immune genes comparing people in London before and after the Black Death disappears after an appropriate randomization test is carried out: the P value increases by ten orders of magnitude and is no longer significant. Second, a technical error in the estimation of allele frequencies means that none of the four originally reported loci actually pass the filtering thresholds. Third, the filtering thresholds do not adequately correct for multiple testing. Finally, in the case of the ERAP2 variant rs2549794, which Klunk et al. show experimentally may be associated with a host interaction with Y. pestis , we find no evidence of significant frequency change either in the data that Klunk et al. report, or in published data spanning 2,000 years. While it remains plausible that immune genes were subject to natural selection during the Black Death, the magnitude of this selection and which specific genes may have been affected remains unknown.},
}

@article {pmid36991187,
year = {2023},
author = {Brielle, ES and Fleisher, J and Wynne-Jones, S and Sirak, K and Broomandkhoshbacht, N and Callan, K and Curtis, E and Iliev, L and Lawson, AM and Oppenheimer, J and Qiu, L and Stewardson, K and Workman, JN and Zalzala, F and Ayodo, G and Gidna, AO and Kabiru, A and Kwekason, A and Mabulla, AZP and Manthi, FK and Ndiema, E and Ogola, C and Sawchuk, E and Al-Gazali, L and Ali, BR and Ben-Salem, S and Letellier, T and Pierron, D and Radimilahy, C and Rakotoarisoa, JA and Raaum, RL and Culleton, BJ and Mallick, S and Rohland, N and Patterson, N and Mwenje, MA and Ahmed, KB and Mohamed, MM and Williams, SR and Monge, J and Kusimba, S and Prendergast, ME and Reich, D and Kusimba, CM},
title = {Entwined African and Asian genetic roots of medieval peoples of the Swahili coast.},
journal = {Nature},
volume = {615},
number = {7954},
pages = {866-873},
pmid = {36991187},
issn = {1476-4687},
abstract = {The urban peoples of the Swahili coast traded across eastern Africa and the Indian Ocean and were among the first practitioners of Islam among sub-Saharan people[1,2]. The extent to which these early interactions between Africans and non-Africans were accompanied by genetic exchange remains unknown. Here we report ancient DNA data for 80 individuals from 6 medieval and early modern (AD 1250-1800) coastal towns and an inland town after AD 1650. More than half of the DNA of many of the individuals from coastal towns originates from primarily female ancestors from Africa, with a large proportion-and occasionally more than half-of the DNA coming from Asian ancestors. The Asian ancestry includes components associated with Persia and India, with 80-90% of the Asian DNA originating from Persian men. Peoples of African and Asian origins began to mix by about AD 1000, coinciding with the large-scale adoption of Islam. Before about AD 1500, the Southwest Asian ancestry was mainly Persian-related, consistent with the narrative of the Kilwa Chronicle, the oldest history told by people of the Swahili coast[3]. After this time, the sources of DNA became increasingly Arabian, consistent with evidence of growing interactions with southern Arabia[4]. Subsequent interactions with Asian and African people further changed the ancestry of present-day people of the Swahili coast in relation to the medieval individuals whose DNA we sequenced.},
}

@article {pmid36980999,
year = {2023},
author = {Toncheva, D and Marinova, M and Chobanov, T and Serbezov, D},
title = {Pathogenic Variants Associated with Rare Monogenic Diseases Established in Ancient Neanderthal and Denisovan Genome-Wide Data.},
journal = {Genes},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/genes14030727},
pmid = {36980999},
issn = {2073-4425},
abstract = {Ancient anatomically modern humans (AMHs) encountered other archaic human species, most notably Neanderthals and Denisovans, when they left Africa and spread across Europe and Asia ~60,000 years ago. They interbred with them, and modern human genomes retain DNA inherited from these interbreeding events. High quality (high coverage) ancient human genomes have recently been sequenced allowing for a direct estimation of individual heterozygosity, which has shown that genetic diversity in these archaic human groups was very low, indicating low population sizes. In this study, we analyze ten ancient human genome-wide data, including four sequenced with high-coverage. We screened these ancient genome-wide data for pathogenic mutations associated with monogenic diseases, and established unusual aggregation of pathogenic mutations in individual subjects, including quadruple homozygous cases of pathogenic variants in the PAH gene associated with the condition phenylketonuria in a ~120,000 years old Neanderthal. Such aggregation of pathogenic mutations is extremely rare in contemporary populations, and their existence in ancient humans could be explained by less significant clinical manifestations coupled with small community sizes, leading to higher inbreeding levels. Our results suggest that pathogenic variants associated with rare diseases might be the result of introgression from other archaic human species, and archaic admixture thus could have influenced disease risk in modern humans.},
}

@article {pmid36980972,
year = {2023},
author = {Sharko, F and Slobodova, N and Boulygina, E and Cheprasov, M and Gladysheva-Azgari, M and Tsygankova, S and Rastorguev, S and Novgorodov, G and Boeskorov, G and Grigorieva, L and Hwang, WS and Tikhonov, A and Nedoluzhko, A},
title = {Ancient DNA of the Don-Hares Assumes the Existence of Two Distinct Mitochondrial Clades in Northeast Asia.},
journal = {Genes},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/genes14030700},
pmid = {36980972},
issn = {2073-4425},
abstract = {Paleoclimatic changes during the Pleistocene-Holocene transition is suggested as a main factor that led to species extinction, including the woolly mammoth (Mammuthus primigenius), Steller's sea cow (Hydrodamalis gigas) and the Don-hare (Lepus tanaiticus). These species inhabited the territory of Eurasia during the Holocene, but eventually went extinct. The Don-hare is an extinct species of the genus Lepus (Leporidae, Lagomorpha), which lived in the Late Pleistocene-Early Holocene in Eastern Europe and Northern Asia. For a long time, the Don-hare was considered a separate species, but at the same time, its species status was disputed, taking into account both morphological data and mitochondrial DNA. In this study, mitochondrial genomes of five Don-hares, whose remains were found on the territory of Northeastern Eurasia were reconstructed. Firstly, we confirm the phylogenetic proximity of the "young" specimens of Don-hare and mountain or white hare, and secondly, that samples older than 39 Kya form a completely distinct mitochondrial clade.},
}

@article {pmid36968599,
year = {2023},
author = {Yu, HX and Ao, C and Wang, XP and Zhang, XP and Sun, J and Li, H and Liu, KJ and Wei, LH},
title = {The impacts of bronze age in the gene pool of Chinese: Insights from phylogeographics of Y-chromosomal haplogroup N1a2a-F1101.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1139722},
pmid = {36968599},
issn = {1664-8021},
abstract = {Objectives: Previous studies of archaeology and history suggested that the rise and prosperity of Bronze Age culture in East Asia had made essential contribution to the formation of early state and civilization in this region. However, the impacts in perspective of genetics remain ambiguous. Previous genetic researches indicated the Y-chromosome Q1a1a-M120 and N1a2a-F1101 may be the two most important paternal lineages among the Bronze Age people in ancient northwest China. Here, we investigated the 9,000-years history of haplogroup N1a2a-F1101 with revised phylogenetic tree and spatial autocorrelation analysis. Materials and Methods: In this study, 229 sequences of N1a2a-F1101 were analyzed. We developed a highly-revised phylogenetic tree with age estimates for N1a2a-F1101. In addition, we also explored the geographical distribution of sub-lineages of N1a2a-F1101, and spatial autocorrelation analysis was conducted for each sub-branch. Results: The initial differentiation location of N1a2a-F1101 and its most closely related branch, N1a2b-P43, a major lineage of Uralic-speaking populations in northern Eurasia, is likely the west part of northeast China. After ~4 thousand years of bottleneck effect period, haplgroup N1a2a-F1101 experienced continuous expansion during the Chalcolithic age (~ 4.5 kya to 4 kya) and Bronze age (~ 4 kya to 2.5 kya) in northern China. Ancient DNA evidence supported that this haplogroup is the lineage of ruling family of Zhou Dynasty (~ 3 kya-2.2 kya) of ancient China. Discussion: In general, we proposed that the Bronze Age people in the border area between the eastern Eurasian steppe and northern China not only played a key role in promoting the early state and civilization of China, but also left significant traces in the gene pool of Chinese people.},
}

@article {pmid36967935,
year = {2023},
author = {Sen, A and Andersen, LW and Kjeldsen, KU and Michel, LN and Hong, WL and Choquet, M and Rasmussen, TL},
title = {The phylogeography and ecology of Oligobrachia frenulate species suggest a generalist chemosynthesis-based fauna in the arctic.},
journal = {Heliyon},
volume = {9},
number = {3},
pages = {e14232},
pmid = {36967935},
issn = {2405-8440},
abstract = {We used ancient DNA (aDNA) extraction methods to sequence museum voucher samples of Oligobrachia webbi, a frenulate siboglinid polychaete described from a northern Norwegian fjord over fifty years ago. Our sequencing results indicate a genetic match with the cryptic seep species, Oligobrachia haakonmosbiensis (99% pairwise identity for 574 bp mtCOI fragments). Due to its similarity with O. webbi, the identity of O. haakonmosbiensis has been a matter of debate since its description, which we have now resolved. Furthermore, our results demonstrate that chemosynthesis-based siboglinids, that constitute the bulk of the biomass at Arctic seeps are not seep specialists. Our data on sediment geochemistry and carbon and nitrogen content reveal reduced conditions in fjords/sounds, similar to those at seep systems. Accumulation and decomposition of both terrestrial and marine organic matter results in the buildup of methane and sulfide that apparently can sustain chemosymbiotic fauna. The occurrence of fjords and by extension, highly reducing habitats, could have led to Arctic chemosymbiotic species being relatively generalist with their habitat, as opposed to being seep or vent specialists. Our stable isotope analyses indicate the incorporation of photosynthetically derived carbon in some individuals, which aligns with experiments conducted on frenulates before the discovery of chemosynthesis that demonstrated their ability to take up organic molecules from the surrounding sediment. Since reduced gases in non-seep environments are ultimately sourced from photosynthetic processes, we suggest that the extreme seasonality of the Arctic has resulted in Arctic chemosymbiotic animals seasonally changing their degree of reliance on chemosynthetic partners. Overall, the role of chemosynthesis in Arctic benthos and marine ecosystems and links to photosynthesis may be complex, and more extensive than currently known.},
}

@article {pmid36966434,
year = {2023},
author = {Hixson, KK and Fajardo, DA and Devitt, NP and Sena, JA and Costa, MA and Meng, Q and Boschiero, C and Zhao, PX and Baack, E and Paurus, VL and Davin, LB and Lewis, NG and Bell, CJ},
title = {Annotated genome sequence of a fast-growing diploid clone of red alder (Alnus rubra Bong.).},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkad060},
pmid = {36966434},
issn = {2160-1836},
abstract = {Red alder (Alnus rubra Bong.) is an ecologically significant and important, fast-growing commercial tree species native to western coastal and riparian regions of North America, having highly desirable wood, pigment and medicinal properties. We have sequenced the genome of a rapidly growing clone. The assembly is nearly complete, containing the full complement of expected genes. This supports our objectives of identifying and studying genes and pathways involved in nitrogen fixing symbiosis, and those related to secondary metabolites that underlie red alder's many interesting defense, pigmentation and wood quality traits. We established that this clone is most likely diploid, and identified a set of SNPs that will have utility in future breeding and selection endeavors, as well as in ongoing population studies. We have added a well-characterized genome to others from the order Fagales. In particular, it improves significantly upon the only other published alder genome sequence, that of Alnus glutinosa. Our work initiated a detailed comparative analysis of members of the order Fagales, and established some similarities with previous reports in this clade suggesting biased retention of certain gene functions in the vestiges of an ancient genome duplication as compared to more recent tandem duplications.},
}

@article {pmid36964154,
year = {2023},
author = {Zimmermann, HH and Stoof-Leichsenring, KR and Dinkel, V and Harms, L and Schulte, L and Hütt, MT and Nürnberg, D and Tiedemann, R and Herzschuh, U},
title = {Marine ecosystem shifts with deglacial sea-ice loss inferred from ancient DNA shotgun sequencing.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {1650},
pmid = {36964154},
issn = {2041-1723},
abstract = {Sea ice is a key factor for the functioning and services provided by polar marine ecosystems. However, ecosystem responses to sea-ice loss are largely unknown because time-series data are lacking. Here, we use shotgun metagenomics of marine sedimentary ancient DNA off Kamchatka (Western Bering Sea) covering the last ~20,000 years. We traced shifts from a sea ice-adapted late-glacial ecosystem, characterized by diatoms, copepods, and codfish to an ice-free Holocene characterized by cyanobacteria, salmon, and herring. By providing information about marine ecosystem dynamics across a broad taxonomic spectrum, our data show that ancient DNA will be an important new tool in identifying long-term ecosystem responses to climate transitions for improvements of ocean and cryosphere risk assessments. We conclude that continuing sea-ice decline on the northern Bering Sea shelf might impact on carbon export and disrupt benthic food supply and could allow for a northward expansion of salmon and Pacific herring.},
}

@article {pmid36963383,
year = {2023},
author = {Davy, T and Ju, D and Mathieson, I and Skoglund, P},
title = {Hunter-gatherer admixture facilitated natural selection in Neolithic European farmers.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2023.02.049},
pmid = {36963383},
issn = {1879-0445},
abstract = {Ancient DNA has revealed multiple episodes of admixture in human prehistory during geographic expansions associated with cultural innovations. One important example is the expansion of Neolithic agricultural groups out of the Near East into Europe and their consequent admixture with Mesolithic hunter-gatherers.[1][,][2][,][3][,][4] Ancient genomes from this period provide an opportunity to study the role of admixture in providing new genetic variation for selection to act upon, and also to identify genomic regions that resisted hunter-gatherer introgression and may thus have contributed to agricultural adaptations. We used genome-wide DNA from 677 individuals spanning Mesolithic and Neolithic Europe to infer ancestry deviations in the genomes of admixed individuals and to test for natural selection after admixture by testing for deviations from a genome-wide null distribution. We find that the region around the pigmentation-associated gene SLC24A5 shows the greatest overrepresentation of Neolithic local ancestry in the genome (|Z| = 3.46). In contrast, we find the greatest overrepresentation of Mesolithic ancestry across the major histocompatibility complex (MHC; |Z| = 4.21), a major immunity locus, which also shows allele frequency deviations indicative of selection following admixture (p = 1 × 10[-56]). This could reflect negative frequency-dependent selection on MHC alleles common in Neolithic populations or that Mesolithic alleles were positively selected for and facilitated adaptation in Neolithic populations to pathogens or other environmental factors. Our study extends previous results that highlight immune function and pigmentation as targets of adaptation in more recent populations to selection processes in the Stone Age.},
}

@article {pmid36958333,
year = {2023},
author = {Begg, TJA and Schmidt, A and Kocher, A and Larmuseau, MHD and Runfeldt, G and Maier, PA and Wilson, JD and Barquera, R and Maj, C and Szolek, A and Sager, M and Clayton, S and Peltzer, A and Hui, R and Ronge, J and Reiter, E and Freund, C and Burri, M and Aron, F and Tiliakou, A and Osborn, J and Behar, DM and Boecker, M and Brandt, G and Cleynen, I and Strassburg, C and Prüfer, K and Kühnert, D and Meredith, WR and Nöthen, MM and Attenborough, RD and Kivisild, T and Krause, J},
title = {Genomic analyses of hair from Ludwig van Beethoven.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2023.02.041},
pmid = {36958333},
issn = {1879-0445},
abstract = {Ludwig van Beethoven (1770-1827) remains among the most influential and popular classical music composers. Health problems significantly impacted his career as a composer and pianist, including progressive hearing loss, recurring gastrointestinal complaints, and liver disease. In 1802, Beethoven requested that following his death, his disease be described and made public. Medical biographers have since proposed numerous hypotheses, including many substantially heritable conditions. Here we attempt a genomic analysis of Beethoven in order to elucidate potential underlying genetic and infectious causes of his illnesses. We incorporated improvements in ancient DNA methods into existing protocols for ancient hair samples, enabling the sequencing of high-coverage genomes from small quantities of historical hair. We analyzed eight independently sourced locks of hair attributed to Beethoven, five of which originated from a single European male. We deemed these matching samples to be almost certainly authentic and sequenced Beethoven's genome to 24-fold genomic coverage. Although we could not identify a genetic explanation for Beethoven's hearing disorder or gastrointestinal problems, we found that Beethoven had a genetic predisposition for liver disease. Metagenomic analyses revealed furthermore that Beethoven had a hepatitis B infection during at least the months prior to his death. Together with the genetic predisposition and his broadly accepted alcohol consumption, these present plausible explanations for Beethoven's severe liver disease, which culminated in his death. Unexpectedly, an analysis of Y chromosomes sequenced from five living members of the Van Beethoven patrilineage revealed the occurrence of an extra-pair paternity event in Ludwig van Beethoven's patrilineal ancestry.},
}

@article {pmid36951219,
year = {2023},
author = {Kolbe, D and da Silva, NA and Dose, J and Torres, GG and Caliebe, A and Krause-Kyora, B and Nebel, A},
title = {Current allele distribution of the human longevity gene APOE in Europe can mainly be explained by ancient admixture.},
journal = {Aging cell},
volume = {},
number = {},
pages = {e13819},
doi = {10.1111/acel.13819},
pmid = {36951219},
issn = {1474-9726},
abstract = {Variation in apolipoprotein E (APOE) has been shown to have the strongest genetic effect on human longevity. The aim of this study was to unravel the evolutionary history of the three major APOE alleles in Europe by analysing ancient samples up to 12,000 years old. We detected significant allele frequency shifts between populations and over time. Our analyses indicated that selection led to large frequency differences between the earliest European populations (i.e., hunter-gatherers vs. first farmers), possibly due to changes in diet/lifestyle. In contrast, the allele distributions in populations from ~4000 BCE onward can mainly be explained by admixture, suggesting that it also played an important role in shaping current APOE variation. In any case, the resulting allele frequencies strongly influence the predisposition for longevity today, likely as a consequence of past adaptations and demographic processes.},
}

@article {pmid36945531,
year = {2023},
author = {Ringbauer, H and Huang, Y and Akbari, A and Mallick, S and Patterson, N and Reich, D},
title = {ancIBD - Screening for identity by descent segments in human ancient DNA.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.03.08.531671},
pmid = {36945531},
abstract = {Long DNA sequences shared between two individuals, known as Identical by descent (IBD) segments, are a powerful signal for identifying close and distant biological relatives because they only arise when the pair shares a recent common ancestor. Existing methods to call IBD segments between present-day genomes cannot be straightforwardly applied to ancient DNA data (aDNA) due to typically low coverage and high genotyping error rates. We present ancIBD, a method to identify IBD segments for human aDNA data implemented as a Python package. Our approach is based on a Hidden Markov Model, using as input genotype probabilities imputed based on a modern reference panel of genomic variation. Through simulation and downsampling experiments, we demonstrate that ancIBD robustly identifies IBD segments longer than 8 centimorgan for aDNA data with at least either 0.25x average whole-genome sequencing (WGS) coverage depth or at least 1x average depth for in-solution enrichment experiments targeting a widely used aDNA SNP set ('1240k'). This application range allows us to screen a substantial fraction of the aDNA record for IBD segments and we showcase two downstream applications. First, leveraging the fact that biological relatives up to the sixth degree are expected to share multiple long IBD segments, we identify relatives between 10,156 ancient Eurasian individuals and document evidence of long-distance migration, for example by identifying a pair of two approximately fifth-degree relatives who were buried 1410km apart in Central Asia 5000 years ago. Second, by applying ancIBD, we reveal new details regarding the spread of ancestry related to Steppe pastoralists into Europe starting 5000 years ago. We find that the first individuals in Central and Northern Europe carrying high amounts of Steppe-ancestry, associated with the Corded Ware culture, share high rates of long IBD (12-25 cM) with Yamnaya herders of the Pontic-Caspian steppe, signaling a strong bottleneck and a recent biological connection on the order of only few hundred years, providing evidence that the Yamnaya themselves are a main source of Steppe ancestry in Corded Ware people. We also detect elevated sharing of long IBD segments between Corded Ware individuals and people associated with the Globular Amphora culture (GAC) from Poland and Ukraine, who were Copper Age farmers not yet carrying Steppe-like ancestry. These IBD links appear for all Corded Ware groups in our analysis, indicating that individuals related to GAC contexts must have had a major demographic impact early on in the genetic admixtures giving rise to various Corded Ware groups across Europe. These results show that detecting IBD segments in aDNA can generate new insights both on a small scale, relevant to understanding the life stories of people, and on the macroscale, relevant to large-scale cultural-historical events.},
}

@article {pmid36933795,
year = {2023},
author = {Zhang, G and Cui, C and Wangdue, S and Lu, H and Chen, H and Xi, L and He, W and Yuan, H and Tsring, T and Chen, Z and Yang, F and Tsering, T and Li, S and Tashi, N and Yang, T and Tong, Y and Wu, X and Li, L and He, Y and Cao, P and Dai, Q and Liu, F and Feng, X and Wang, T and Yang, R and Ping, W and Zhang, M and Gao, X and Liu, Y and Wang, W and Fu, Q},
title = {Maternal genetic history of ancient Tibetans over the past 4000 years.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2023.03.007},
pmid = {36933795},
issn = {1673-8527},
abstract = {The settlement of the Tibetan Plateau epitomizes human adaptation to a high-altitude environment that poses great challenges to human activity. Here, we reconstructed a 4000-year maternal genetic history of Tibetans using 128 ancient mitochondrial genome data from 37 sites in Tibet. The phylogeny of haplotypes M9a1a, M9a1b, D4g2, G2a'c, and D4i show ancient Tibetans shared the most recent common ancestor (TMRCA) with ancient Middle and Upper Yellow River populations around the Early and Middle Holocene. In addition, the connections between Tibetans and Northeastern Asians varied over the past 4000 years, with a stronger matrilineal connection between the two during 4000-3000 BP, and a weakened connection after 3000 BP, that coincident with climate change, followed by a reinforced connection after the Tubo period (1400-1100 BP). Besides, an over 4000-year matrilineal continuity was observed in some of the maternal lineages. We also found the maternal genetic structure of ancient Tibetans is correlated to the geography and interactions between ancient Tibetans and ancient Nepal and Pakistan populations. Overall, the maternal genetic history of Tibetans can be characterized as a long-term matrilineal continuity with frequent internal and external population interactions that were dynamically shaped by geography, climate changes, as well as historical events.},
}

@article {pmid36930997,
year = {2023},
author = {Schats, R},
title = {Developing an archaeology of malaria. A critical review of current approaches and a discussion on ways forward.},
journal = {International journal of paleopathology},
volume = {41},
number = {},
pages = {32-42},
doi = {10.1016/j.ijpp.2023.03.002},
pmid = {36930997},
issn = {1879-9825},
abstract = {OBJECTIVE: This paper presents the current state of the art in the investigation of past malaria by providing an extensive review of previous studies and identifying research possibilities for the future.

MATERIALS: All previous research on the detection of malaria in human skeletal material using macroscopic and biomolecular approaches is considered.

METHODS: The approaches and methods used by scholars and the results they obtained are evaluated and the limitations discussed.

RESULTS: There is a link between malaria and porous lesions with significantly higher prevalence in malaria-endemic areas, however, they are not pathognomonic or specific for malaria. Malaria can be identified using biomolecular techniques, yet, to date there is no completely satisfactory method that is able to consistently diagnose the disease.

CONCLUSIONS: Using macroscopic and biomolecular techniques, malaria can be investigated in past populations and the impact of the disease studied. Yet, this is not a straightforward process and the use of multiple lines of evidence is necessary to obtain the best results.

SIGNIFICANCE: The extensive discussion on ways malaria can and cannot be identified in past populations and the suggestions for new approaches provide a steppingstone for future research into this debilitating, global disease.

LIMITATIONS: Malaria is a difficult disease to study archaeologically and successful identification depends on many intrinsic and extrinsic factors.

More large-scale spatial analyses of porous lesions as well as targeting different tissues or molecules for biomolecular identification may improve the archaeological understanding of malaria.},
}

@article {pmid36930529,
year = {2023},
author = {de-Dios, T and Scheib, CL and Houldcroft, CJ},
title = {An adagio for viruses, played out on ancient DNA.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evad047},
pmid = {36930529},
issn = {1759-6653},
abstract = {Studies of ancient DNA have transformed our understanding of human evolution. Palaeogenomics can also reveal historic and prehistoric agents of disease, including endemic, epidemic and pandemic pathogens. Viruses - and in particular those with single or double-stranded DNA genomes - are an important part of the palaeogenomic revolution, preserving within some remains or environmental samples for tens of thousands of years. The results of these studies capture the public imagination, as well as giving scientists a unique perspective on some of the more slowly-evolving viruses which cause disease. In this review, we will revisit the first studies of historical virus genetic material in the 1990s, through to the genomic revolution of recent years. We will look at how palaeogenomics works for viral pathogens, such as the need for careful precautions against modern contamination, and robust computational pipelines to identify and analyse authenticated viral sequences. We will discuss the insights into virus evolution which have been gained through palaeogenomics, concentrating on three DNA viruses in particular: parvovirus B19, herpes simplex virus 1, and smallpox. As we consider recent worldwide transmission of monkeypox and synthetic biology tools that allow the potential reconstruction of extinct viruses, we show that studying historical and ancient virus evolution has never been more topical.},
}

@article {pmid36922577,
year = {2023},
author = {Kerner, G and Choin, J and Quintana-Murci, L},
title = {Ancient DNA as a tool for medical research.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {36922577},
issn = {1546-170X},
}

@article {pmid36919783,
year = {2023},
author = {Motti, JMB and Pauro, M and Scabuzzo, C and García, A and Aldazábal, V and Vecchi, R and Bayón, C and Pastor, N and Demarchi, DA and Bravi, CM and Reich, D and Cabana, GS and Nores, R},
title = {Ancient mitogenomes from the Southern Pampas of Argentina reflect local differentiation and limited extra-regional linkages after rapid initial colonization.},
journal = {American journal of biological anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.24727},
pmid = {36919783},
issn = {2692-7691},
support = {/HHMI/Howard Hughes Medical Institute/United States ; },
abstract = {OBJECTIVE: This study aims to contribute to the recovery of Indigenous evolutionary history in the Southern Pampas region of Argentina through an analysis of ancient complete mitochondrial genomes.

MATERIALS AND METHODS: We generated DNA data for nine complete mitogenomes from the Southern Pampas, dated to between 2531 and 723 cal BP. In combination with previously published ancient mitogenomes from the region and from throughout South America, we documented instances of extra-regional lineage-sharing, and estimated coalescent ages for local lineages using a Bayesian method with tip calibrations in a phylogenetic analysis.

RESULTS: We identified a novel mitochondrial haplogroup, B2b16, and two recently defined haplogroups, A2ay and B2ak1, as well as three local haplotypes within founder haplogroups C1b and C1d. We detected lineage-sharing with ancient and contemporary individuals from Central Argentina, but not with ancient or contemporary samples from North Patagonian or Littoral regions of Argentina, despite archeological evidence of cultural interactions with the latter regions. The estimated coalescent age of these shared lineages is ~10,000 years BP.

DISCUSSION: The history of the human populations in the Southern Pampas is temporally deep, exhibiting long-term continuity of mitogenome lineages. Additionally, the identification of highly localized mtDNA clades accords with a model of relatively rapid initial colonization of South America by Indigenous communities, followed by more local patterns of limited gene flow and genetic drift in various South American regions, including the Pampas.},
}

@article {pmid36918761,
year = {2023},
author = {Marsh, WA and Brace, S and Barnes, I},
title = {Inferring biological kinship in ancient datasets: comparing the response of ancient DNA-specific software packages to low coverage data.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {111},
pmid = {36918761},
issn = {1471-2164},
abstract = {BACKGROUND: The inference of biological relations between individuals is fundamental to understanding past human societies. Caregiving, resource sharing and sexual behaviours are often mediated by biological kinship and yet the identification and interpretation of kin relationships in prehistoric human groups is difficult. In recent years, the advent of archaeogenetic techniques have offered a fresh approach, and when combined with more traditional osteological and interpretive archaeological methods, allows for improved interpretation of the burial practices, cultural behaviours, and societal stratification in ancient societies. Although archaeogenetic techniques are developing at pace, questions remain as to their accuracy, particularly when applied to the low coverage datasets that results from the sequencing of DNA derived from highly degraded ancient material.

RESULTS: The performance of six of the most commonly used kinship identifcation software methods was explored at a range of low and ultra low genome coverages. An asymmetrical response was observed across packages, with decreased genome coverage resulting in differences in both direction and degree of change of calculated kinship scores and thus pairwise relatedness estimates are dependant on both package used and genome coverage. Methods reliant upon genotype likelihoods methods (lcMLkin, NGSrelate and NGSremix) show a decreased level of prediction at coverage below 1x, although were consistent in the particular relationships identified at these coverages when compared to the pseudohaploid reliant methods tested (READ, the Kennett 2017 method and TKGWV2.0). The three pseudohaploid methods show predictive potential at coverages as low as 0.05x, although the accuracy of the relationships identified is questionable given the increase in the number of relationships identifIed at the low coverage (type I errors).

CONCLUSION: Two pseudohaploid methods (READ and Kennett 2017) show relatively consistent inference of kin relationships at low coverage (0.5x), with READ only showing a significant performance drop off at ultralow coverages (< 0.2x). More generally, our results reveal asymmetrical kinship classifications in some software packages even at high coverages, highlighting the importance of applying multiple methods to authenticate kin relationships in ancient material, along with the continuing need to develop laboratory methods that maximise data output for downstream analyses.},
}

@article {pmid36859677,
year = {2023},
author = {Callaway, E},
title = {Ancient genomes show how humans escaped Europe's deep freeze.},
journal = {Nature},
volume = {615},
number = {7951},
pages = {197-198},
pmid = {36859677},
issn = {1476-4687},
mesh = {Humans ; Europe ; *Genome, Human ; *DNA, Ancient/analysis ; *Human Migration/history ; Freezing ; *Cold Temperature ; History, Ancient ; },
}

Humans
Europe
*Genome, Human
*DNA, Ancient/analysis
*Human Migration/history
Freezing
*Cold Temperature
History, Ancient

@article {pmid36890036,
year = {2023},
author = {Johnson, OL and Tobler, R and Schmidt, JM and Huber, CD},
title = {Fluctuating selection and the determinants of genetic variation.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2023.02.004},
pmid = {36890036},
issn = {0168-9525},
abstract = {Recent studies of cosmopolitan Drosophila populations have found hundreds to thousands of genetic loci with seasonally fluctuating allele frequencies, bringing temporally fluctuating selection to the forefront of the historical debate surrounding the maintenance of genetic variation in natural populations. Numerous mechanisms have been explored in this longstanding area of research, but these exciting empirical findings have prompted several recent theoretical and experimental studies that seek to better understand the drivers, dynamics, and genome-wide influence of fluctuating selection. In this review, we evaluate the latest evidence for multilocus fluctuating selection in Drosophila and other taxa, highlighting the role of potential genetic and ecological mechanisms in maintaining these loci and their impacts on neutral genetic variation.},
}

@article {pmid36869137,
year = {2023},
author = {Rifkin, RF and Vikram, S and Alcorta, J and Ramond, JB and Cowan, DA and Jakobsson, M and Schlebusch, CM and Lombard, M},
title = {Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {240},
pmid = {36869137},
issn = {2399-3642},
abstract = {The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, e.g., the sickle cell trait which provides protection against malaria, there is inadequate direct human genomic evidence for ancient human-pathogen infection in the region. Here, we analysed shotgun metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, c. 2000 years ago. This resulted in the identification of ancient DNA sequence reads homologous to Rickettsia felis, the causative agent of typhus-like flea-borne rickettsioses, and the reconstruction of an ancient R. felis genome.},
}

@article {pmid36862777,
year = {2023},
author = {Curry, A},
title = {Ancient DNA upends European prehistory.},
journal = {Science (New York, N.Y.)},
volume = {379},
number = {6635},
pages = {865-866},
doi = {10.1126/science.adh3912},
pmid = {36862777},
issn = {1095-9203},
abstract = {Genes reveal striking diversity within similar ice age cultures.},
}

@article {pmid36855115,
year = {2023},
author = {Nyerki, E and Kalmár, T and Schütz, O and Lima, RM and Neparáczki, E and Török, T and Maróti, Z},
title = {correctKin: an optimized method to infer relatedness up to the 4th degree from low-coverage ancient human genomes.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {38},
pmid = {36855115},
issn = {1474-760X},
abstract = {Kinship analysis from very low-coverage ancient sequences has been possible up to the second degree with large uncertainties. We propose a new, accurate, and fast method, correctKin, to estimate the kinship coefficient and the confidence interval using low-coverage ancient data. We perform simulations and also validate correctKin on experimental modern and ancient data with widely different genome coverages (0.12×-11.9×) using samples with known family relations and known/unknown population structure. Based on our results, correctKin allows for the reliable identification of relatedness up to the 4th degree from variable/low-coverage ancient or badly degraded forensic whole genome sequencing data.},
}

@article {pmid36458990,
year = {2023},
author = {Flohr, S},
title = {Canine dimensions for estimation of sex in adult and non-adult individuals with external validation by aDNA.},
journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur},
volume = {80},
number = {2},
pages = {225-231},
doi = {10.1127/anthranz/2022/1653},
pmid = {36458990},
issn = {0003-5548},
mesh = {Humans ; Female ; *Tooth ; DNA, Ancient ; Discriminant Analysis ; Germany ; *Sex Determination by Skeleton/methods ; },
abstract = {Using discriminant functions obtained from canine dimensions for sex estimation in human skeletons has frequently been proposed as a promising approach within assemblages, even when used in non-adult individuals. However, applicability of this method to adult and non-adult individuals from other assemblages was rarely investigated, probably due to frequently observed inter-population differences in tooth dimensions. In the present study, discriminant functions obtained for permanent canine dimensions at the cemento-enamel junction in a previous study of the early medieval assemblage from Greding, were applied to individuals from a late medieval Jewish cemetery at Erfurt, Germany. The results were validated by aDNA analyses. Prior to the application of the functions, canine dimensions of the assemblages were compared. The comparison showed largely corresponding canine dimensions between the two assemblages. The application of the formulae obtained on the early medieval assemblage to the late medieval assemblage at Erfurt revealed a 100 % correct classification rate in the adult individuals. In non-adults, the correct classification rate was poorer, with 7 of 9 (77.8 %) individuals correctly classified. The study showed that the application of discriminant functions for sex estimation from canine measurements to assemblages other than those for which the functions were developed can lead to high correct classification rates in adults if the average canine dimensions are similar in the respective assemblages. An application to non-adult individuals should only be made with caution as canine dimensions in the "non-survivors" can lead to an over-estimation of the proportion of female non-adults.},
}

Humans
Female
*Tooth
DNA, Ancient
Discriminant Analysis
Germany
*Sex Determination by Skeleton/methods

@article {pmid33267568,
year = {2023},
author = {Gerussi, A and Halliday, N and Carbone, M and Invernizzi, P and Thorburn, D},
title = {Open challenges in the management of autoimmune hepatitis.},
journal = {Minerva gastroenterology},
volume = {69},
number = {1},
pages = {61-83},
doi = {10.23736/S2724-5895.20.02805-6},
pmid = {33267568},
issn = {2724-5365},
abstract = {Autoimmune hepatitis (AIH) is a rare autoimmune disease of the liver with many open questions as regards its etiopathogenesis, natural history and clinical management. The classical picture of AIH is chronic hepatitis with fluctuating elevation of serum transaminases and Immunoglobulin G levels, the presence of circulating autoantibodies and typical histological features. However, atypical presentations do occur and are not well captured by current diagnostic scores, with important consequences in terms of missed diagnoses and delayed treatments. AIH is treated with corticosteroids and immunosuppressive drugs but up to 40% of patients do not achieve full biochemical response and are at risk of progressing to cirrhosis and liver failure. Moreover, standard therapies are associated by significant side-effects which may impair the quality of life of patients living with AIH. However, advances in the understanding of the underlying immunology of AIH is raising the prospect of novel therapies and optimization of existing therapeutic approaches to reduce side-effect burdens and potentially restore immunological tolerance. In this review we outlined the clinical characteristics, etiopathogenesis and management of AIH and current challenges in the diagnosis and management of AIH and provided evidence underlying the evolution of diagnostic and clinical management protocols.},
}

@article {pmid36853456,
year = {2023},
author = {Ayling, C},
title = {TA Cloning Approaches to Cloning DNA with Damaged Ends DNA.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2633},
number = {},
pages = {55-64},
pmid = {36853456},
issn = {1940-6029},
abstract = {DNA ends can become damaged for various reasons making them unsuitable for TA cloning techniques, the easiest and most common of the DNA cloning technologies. Examples of end-damaged DNA include ancient DNA and those produced by laboratory methods such as sonication. In this chapter, we discuss how to deal with end-damaged DNA prior to cloning with either the popular pGEM[®]-T Easy Vector Systems Kit and TOPO™ TA Cloning™ Kits.},
}

@article {pmid36853452,
year = {2023},
author = {Mikić, A and Alomari, A and Gowers, DM},
title = {Classical Recombinant DNA Cloning.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2633},
number = {},
pages = {1-24},
pmid = {36853452},
issn = {1940-6029},
abstract = {Traditional molecular cloning involves a series of linked experimental steps performed with the overall goal of isolating ("cloning") a specific DNA sequence-often a gene. The main purpose of cloning is to study either that DNA sequence or the RNA or protein product it encodes. Building on key enzymatic discoveries in the late 1960s, gene cloning was pioneered in the early 1970s. Since then, DNA cloning and manipulation have been used in every area of biological and biomedical research, from molecular genetics, structural biology, and developmental biology to neurobiology, ancient DNA studies, and immunology. It is a versatile technique that can be applied to a variety of starting DNA types and lengths, including cDNAs, genes, gene fragments, chromosomal regions, or shorter fragments such as PCR products and functional control regions such as enhancers or promoters. The starting DNA can originate from any cell, tissue, or organism. In this chapter we will cover traditional ("classic") molecular cloning strategy. This comprises six linked stages in which (1) PCR is used to amplify a DNA region of interest that is then (2) digested with restriction enzymes, alongside a selected vector, to produce complementary ends crucial for the two molecules to be (3) ligated by an ATP-dependent DNA ligase, creating a recombinant DNA molecule. The recombinant DNA is then (4) introduced into competent bacterial cells by transformation and (5) grown on a selective agar media, followed by (6) colony-PCR for screening purposes. We provide a worked example to demonstrate the cloning of an average-size gene (in this case the 2 kb DNA ligase A gene) from E. coli into a common plasmid expression vector. We have included six color figures and two tables to depict the key stages of a classical molecular cloning protocol. If you are cloning a segment of DNA or a gene, remember that each DNA cloning experiment is unique in terms of sequence, length, and experimental purpose. However, the principles of traditional cloning covered in this chapter are the same for any DNA sequence; we have included a detailed notes section, so you should easily be able to transfer them to your own work. Some of the following chapters in this volume will cover other, more recently developed, cloning protocols.},
}

@article {pmid36847465,
year = {2022},
author = {Hublin, JJ and Changeux, JP},
title = {Paleoanthropology of cognition: an overview on Hominins brain evolution.},
journal = {Comptes rendus biologies},
volume = {345},
number = {2},
pages = {57-75},
doi = {10.5802/crbiol.92},
pmid = {36847465},
issn = {1768-3238},
abstract = {Recent advances in neurobiology, paleontology, and paleogenetics allow us to associate changes in brain size and organization with three main "moments" of increased behavioral complexity and, more speculatively, language development. First, Australopiths display a significant increase in brain size relative to the great apes and an incipient extension of postnatal brain development. However, their cortical organization remains essentially similar to that of apes. Second, over the last 2 My, with two notable exceptions, brain size increases dramatically, partly in relation to changes in body size. Differential enlargements and reorganizations of cortical areas lay the foundation for the "language-ready" brain and cumulative culture of later Homo species. Third, in Homo sapiens, brain size remains fairly stable over the last 300,000 years but an important cerebral reorganization takes place. It affects the frontal and temporal lobes, the parietal areas and the cerebellum and resulted in a more globular shape of the brain. These changes are associated, among others, with an increased development of long-distance-horizontal-connections. A few regulatory genetic events took place in the course of this hominization process with, in particular, enhanced neuronal proliferation and global brain connectivity.},
}

@article {pmid36821583,
year = {2023},
author = {Schmid, C and Schiffels, S},
title = {Estimating human mobility in Holocene Western Eurasia with large-scale ancient genomic data.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {9},
pages = {e2218375120},
doi = {10.1073/pnas.2218375120},
pmid = {36821583},
issn = {1091-6490},
mesh = {Humans ; History, Ancient ; *Genomics ; *DNA, Ancient/analysis ; Europe ; },
abstract = {The recent increase in openly available ancient human DNA samples allows for large-scale meta-analysis applications. Trans-generational past human mobility is one of the key aspects that ancient genomics can contribute to since changes in genetic ancestry-unlike cultural changes seen in the archaeological record-necessarily reflect movements of people. Here, we present an algorithm for spatiotemporal mapping of genetic profiles, which allow for direct estimates of past human mobility from large ancient genomic datasets. The key idea of the method is to derive a spatial probability surface of genetic similarity for each individual in its respective past. This is achieved by first creating an interpolated ancestry field through space and time based on multivariate statistics and Gaussian process regression and then using this field to map the ancient individuals into space according to their genetic profile. We apply this algorithm to a dataset of 3138 aDNA samples with genome-wide data from Western Eurasia in the last 10,000 y. Finally, we condense this sample-wise record with a simple summary statistic into a diachronic measure of mobility for subregions in Western, Central, and Southern Europe. For regions and periods with sufficient data coverage, our similarity surfaces and mobility estimates show general concordance with previous results and provide a meta-perspective of genetic changes and human mobility.},
}

Humans
History, Ancient
*Genomics
*DNA, Ancient/analysis
Europe

@article {pmid36841239,
year = {2023},
author = {Eaton, K and Sidhu, RK and Klunk, J and Gamble, JA and Boldsen, JL and Carmichael, AG and Varlık, N and Duchene, S and Featherstone, L and Grimes, V and Golding, GB and DeWitte, SN and Holmes, EC and Poinar, HN},
title = {Emergence, continuity, and evolution of Yersinia pestis throughout medieval and early modern Denmark.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2023.01.064},
pmid = {36841239},
issn = {1879-0445},
abstract = {The historical epidemiology of plague is controversial due to the scarcity and ambiguity of available data.[1][,][2] A common source of debate is the extent and pattern of plague re-emergence and local continuity in Europe during the 14th-18th century CE.[3] Despite having a uniquely long history of plague (∼5,000 years), Scandinavia is relatively underrepresented in the historical archives.[4][,][5] To better understand the historical epidemiology and evolutionary history of plague in this region, we performed in-depth (n = 298) longitudinal screening (800 years) for the plague bacterium Yersinia pestis (Y. pestis) across 13 archaeological sites in Denmark from 1000 to 1800 CE. Our genomic and phylogenetic data captured the emergence, continuity, and evolution of Y. pestis in this region over a period of 300 years (14th-17th century CE), for which the plague-positivity rate was 8.3% (3.3%-14.3% by site). Our phylogenetic analysis revealed that the Danish Y. pestis sequences were interspersed with those from other European countries, rather than forming a single cluster, indicative of the generation, spread, and replacement of bacterial variants through communities rather than their long-term local persistence. These results provide an epidemiological link between Y. pestis and the unknown pestilence that afflicted medieval and early modern Europe. They also demonstrate how population-scale genomic evidence can be used to test hypotheses on disease mortality and epidemiology and help pave the way for the next generation of historical disease research.},
}

@article {pmid36834612,
year = {2023},
author = {Bruno, F and Abondio, P and Montesanto, A and Luiselli, D and Bruni, AC and Maletta, R},
title = {The Nerve Growth Factor Receptor (NGFR/p75[NTR]): A Major Player in Alzheimer's Disease.},
journal = {International journal of molecular sciences},
volume = {24},
number = {4},
pages = {},
doi = {10.3390/ijms24043200},
pmid = {36834612},
issn = {1422-0067},
abstract = {Alzheimer's disease (AD) represents the most prevalent type of dementia in elderly people, primarily characterized by brain accumulation of beta-amyloid (Aβ) peptides, derived from Amyloid Precursor Protein (APP), in the extracellular space (amyloid plaques) and intracellular deposits of the hyperphosphorylated form of the protein tau (p-tau; tangles or neurofibrillary aggregates). The Nerve growth factor receptor (NGFR/p75[NTR]) represents a low-affinity receptor for all known mammalians neurotrophins (i.e., proNGF, NGF, BDNF, NT-3 e NT-4/5) and it is involved in pathways that determine both survival and death of neurons. Interestingly, also Aβ peptides can blind to NGFR/p75[NTR] making it the "ideal" candidate in mediating Aβ-induced neuropathology. In addition to pathogenesis and neuropathology, several data indicated that NGFR/p75[NTR] could play a key role in AD also from a genetic perspective. Other studies suggested that NGFR/p75[NTR] could represent a good diagnostic tool, as well as a promising therapeutic target for AD. Here, we comprehensively summarize and review the current experimental evidence on this topic.},
}

@article {pmid36833406,
year = {2023},
author = {Dalal, V and Pasupuleti, N and Chaubey, G and Rai, N and Shinde, V},
title = {Advancements and Challenges in Ancient DNA Research: Bridging the Global North-South Divide.},
journal = {Genes},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/genes14020479},
pmid = {36833406},
issn = {2073-4425},
abstract = {Ancient DNA (aDNA) research first began in 1984 and ever since has greatly expanded our understanding of evolution and migration. Today, aDNA analysis is used to solve various puzzles about the origin of mankind, migration patterns, and the spread of infectious diseases. The incredible findings ranging from identifying the new branches within the human family to studying the genomes of extinct flora and fauna have caught the world by surprise in recent times. However, a closer look at these published results points out a clear Global North and Global South divide. Therefore, through this research, we aim to emphasize encouraging better collaborative opportunities and technology transfer to support researchers in the Global South. Further, the present research also focuses on expanding the scope of the ongoing conversation in the field of aDNA by reporting relevant literature published around the world and discussing the advancements and challenges in the field.},
}

@article {pmid36833230,
year = {2023},
author = {Wiscovitch-Russo, RA and Santiago-Rodriguez, TM and Toranzos, GA},
title = {Deciphering Diets and Lifestyles of Prehistoric Humans through Paleoparasitology: A Review.},
journal = {Genes},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/genes14020303},
pmid = {36833230},
issn = {2073-4425},
abstract = {Parasites have affected and coevolved with humans and animals throughout history. Evidence of ancient parasitic infections, particularly, reside in archeological remains originating from different sources dating to various periods of times. The study of ancient parasites preserved in archaeological remains is known as paleoparasitology, and it initially intended to interpret migration, evolution, and dispersion patterns of ancient parasites, along with their hosts. Recently, paleoparasitology has been used to better understand dietary habits and lifestyles of ancient human societies. Paleoparasitology is increasingly being recognized as an interdisciplinary field within paleopathology that integrates areas such as palynology, archaeobotany, and zooarchaeology. Paleoparasitology also incorporates techniques such as microscopy, immunoassays, PCR, targeted sequencing, and more recently, high-throughput sequencing or shotgun metagenomics to understand ancient parasitic infections and thus interpret migration and evolution patterns, as well as dietary habits and lifestyles. The present review covers the original theories developed in the field of paleoparasitology, as well as the biology of some parasites identified in pre-Columbian cultures. Conclusions, as well as assumptions made during the discovery of the parasites in ancient samples, and how their identification may aid in better understanding part of human history, ancient diet, and lifestyles are discussed.},
}

@article {pmid36819665,
year = {2023},
author = {Kerner, G and Neehus, AL and Philippot, Q and Bohlen, J and Rinchai, D and Kerrouche, N and Puel, A and Zhang, SY and Boisson-Dupuis, S and Abel, L and Casanova, JL and Patin, E and Laval, G and Quintana-Murci, L},
title = {Genetic adaptation to pathogens and increased risk of inflammatory disorders in post-Neolithic Europe.},
journal = {Cell genomics},
volume = {3},
number = {2},
pages = {100248},
pmid = {36819665},
issn = {2666-979X},
abstract = {Ancient genomics can directly detect human genetic adaptation to environmental cues. However, it remains unclear how pathogens have exerted selective pressures on human genome diversity across different epochs and affected present-day inflammatory disease risk. Here, we use an ancestry-aware approximate Bayesian computation framework to estimate the nature, strength, and time of onset of selection acting on 2,879 ancient and modern European genomes from the last 10,000 years. We found that the bulk of genetic adaptation occurred after the start of the Bronze Age, <4,500 years ago, and was enriched in genes relating to host-pathogen interactions. Furthermore, we detected directional selection acting on specific leukocytic lineages and experimentally demonstrated that the strongest negatively selected candidate variant in immunity genes, lipopolysaccharide-binding protein (LBP) D283G, is hypomorphic. Finally, our analyses suggest that the risk of inflammatory disorders has increased in post-Neolithic Europeans, possibly because of antagonistic pleiotropy following genetic adaptation to pathogens.},
}

@article {pmid36812666,
year = {2023},
author = {Bľandová, G and Patlevičová, A and Palkovičová, J and Pavlíková, Š and Beňuš, R and Repiská, V and Baldovič, M},
title = {Pilot study of correlation of selected genetic factors with cribra orbitalia in individuals from a medieval population from Slovakia.},
journal = {International journal of paleopathology},
volume = {41},
number = {},
pages = {1-7},
doi = {10.1016/j.ijpp.2023.02.001},
pmid = {36812666},
issn = {1879-9825},
abstract = {OBJECTIVE: The aim of this study is to investigate the potential genetic etiology of cribra orbitalia noted on human skeletal remains.

MATERIALS: We obtained and analyzed ancient DNA of 43 individuals with cribra orbitalia. The analyzed set represented medieval individuals from two cemeteries in western Slovakia, Castle Devín (11th-12th century AD) and Cífer-Pác (8th-9th century AD).

METHODS: We performed a sequence analysis of 5 variants in 3 genes associated with anemia (HBB, G6PD, PKLR), which are the most common pathogenic variants in present day of European populations, and one variant MCM6:c.1917 + 326 C>T (rs4988235) associated with lactose intolerance.

RESULTS: DNA variants associated with anemia were not found in the samples. The allele frequency of MCM6:c.1917 + 326 C was 0.875. This frequency is higher but not statistically significant in individuals displaying cribra orbitalia compared to individuals without the lesion.

SIGNIFICANCE: This study seeks to expand our knowledge of the etiology of cribra orbitalia by exploring the potential association between the lesion and the presence of alleles linked to hereditary anemias and lactose intolerance.

LIMITATIONS: A relatively small set of individuals were analyzed, so an unequivocal conclusion cannot be drawn. Hence, although it is unlikely, a genetic form of anemia caused by rare variants cannot be ruled out.

Genetic research based on larger sample sizes and in more diverse geographical regions.},
}

@article {pmid36812179,
year = {2023},
author = {Kalisher, R and Cradic, MS and Adams, MJ and Martin, MAS and Finkelstein, I},
title = {Cranial trephination and infectious disease in the Eastern Mediterranean: The evidence from two elite brothers from Late Bronze Megiddo, Israel.},
journal = {PloS one},
volume = {18},
number = {2},
pages = {e0281020},
doi = {10.1371/journal.pone.0281020},
pmid = {36812179},
issn = {1932-6203},
abstract = {Here we present the paleopathological profiles of two young adult males, identified as brothers through ancient DNA analysis, who were buried together beneath the floor of an elite early Late Bronze Age I (ca. 1550-1450 BC) domestic structure at the urban center of Megiddo (modern Israel). Both individuals displayed uncommon morphological variants related to developmental conditions, and each exhibited extensive bone remodeling consistent with chronic infectious disease. Additionally, one brother had a healed fracture of the nose, as well as a large square piece of bone cut from the frontal bone (cranial trephination). We consider the potential etiologies for the appearance of the skeletal anomalies and lesions. Based on the bioarchaeological context, we propose that a shared epigenetic landscape predisposed the brothers to acquiring an infectious disease and their elite status privileged them enough to endure it. We then contextualize these potential illnesses and disorders with the trephination procedure. The infrequency of trephination in the region indicates that only selected individuals could access such a procedure, and the severity of the pathological lesions suggests the procedure was possibly intended as curative to deteriorating health. Ultimately, both brothers were buried with the same rites as others in their community, thus demonstrating their continued integration in society even after death.},
}

@article {pmid36799477,
year = {2023},
author = {Cortez, AD and Lippert, D and Davis, JL and Nicholas, G and Malhi, RS and Weyrich, LS and Claw, KG and Bader, AC and Colwell, C},
title = {Extracting the practices of paleogenomics: A study of ancient DNA labs and research in relation to Native Americans and Indigenous peoples.},
journal = {American journal of biological anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.24714},
pmid = {36799477},
issn = {2692-7691},
abstract = {OBJECTIVES: The field of paleogenomics has rapidly grown, influencing a range of scientific fields and drawing notice from the public. In the United States, this work is especially salient for Native Americans, who are frequently the subject of ancient DNA analyses, but are less frequently included as researchers, collaborators, or advisors. This article seeks to deepen our understanding of the current state of paleogenomics so that the field can center Indigenous peoples and their experiences, knowledges, and stakes in the research process.

MATERIALS AND METHODS: We conducted 31 semi-structured interviews with researchers from three paleogenomics labs located in North America and Europe. We used a responsive interviewing technique where the interview resembled a conversation around a set of questions that could change depending upon the interviewee's answers and experiences. We then employed a theme-based analysis of the interviews.

RESULTS: Through this analysis, we are able to identify practices in the field related to training, the structuring of labs and projects, consent, data control, Ancestor care, and funding that influence various forms of engagement with Indigenous peoples, and which foster or delimit ethical commitments to descendant communities.

DISCUSSION: This research not only elucidates contemporary practices in paleogenomics labs but also identifies specific areas of potential intervention to help researchers work toward ethical and collaborative paleogenomic research with Indigenous peoples. Using these results, researchers and community advocates can work toward reorienting the field of paleogenomics toward ethical research with Indigenous peoples.},
}

@article {pmid36796758,
year = {2023},
author = {Min-Shan Ko, A},
title = {The 2022 Nobel Prize in Physiology or Medicine awarded for the decoding of the complete ancient human genome.},
journal = {Biomedical journal},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bj.2023.02.004},
pmid = {36796758},
issn = {2320-2890},
abstract = {Since the publication of the first ancient DNA sequence in 1984, experimental methods used to recover ancient DNA have advanced greatly, illuminating previously unknown branches of the human family tree and opening up several promising new avenues for future studies of human evolution. The 2022 Nobel Prize in Physiology or Medicine was awarded to Svante Pääbo, director of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, for his work on ancient DNA and human evolution. On his first day back at work, he was thrown in the pond as part of his institute's tradition of celebrating award winners.},
}

@article {pmid36790695,
year = {2022},
author = {Rayo, E and Neukamm, J and Tomoum, N and Eppenberger, P and Breidenstein, A and Bouwman, AS and Schuenemann, VJ and Rühli, FJ},
title = {Metagenomic analysis of Ancient Egyptian canopic jars.},
journal = {American journal of biological anthropology},
volume = {179},
number = {2},
pages = {307-313},
doi = {10.1002/ajpa.24600},
pmid = {36790695},
issn = {2692-7691},
abstract = {UNLABELLED: Ancient Egyptian remains have been of interest for anthropological research for decades. Despite many investigations, the ritual vessels for the internal organs removed during body preparation-liver, lungs, stomach, and intestines, of Egyptian mummies are rarely used for palaeopathological or medical investigations. These artifacts, commonly referred to as canopic jars, are the perfect combination of cultural and biological material and present an untapped resource for both Egyptological and medical fields. Nevertheless, technical challenges associated with this archeological material have prevented the application of current ancient DNA techniques for both the characterization of human and pathogenic DNA. We present shotgun-sequenced metagenomic profiles and ancient DNA degradation patterns from multiple canopic jars sampled from several European museum collections and enumerate current limitations and possible solutions for the future analysis of similar material. This is the first-ever recorded evidence of ancient human DNA found in Ancient Egyptian canopic jars and the first associated metagenomic description of bacterial taxa in these funerary artifacts.

OBJECTIVES: In this study, our objectives were to characterize the metagenomic profile of the Ancient Egyptian funerary vessels known as canopic jars to retrieve endogenous ancient human DNA, reconstruct ancient microbial communities, and identify possible pathogens that could shed light on disease states of individuals from the past.

METHODS: We applied ancient DNA techniques on 140 canopic jars to extract DNA and generate whole-genome sequencing libraries for the analysis of both human and bacterial DNA. The samples were obtained from museum collections in Berlin (DE), Burgdorf (DE), Leiden (NE), Manchester (UK), Munich (DE), St. Gallen (CH), Turin (IT), and Zagreb (HR).

RESULTS: Here we describe the first isolated DNA from the Egyptian artifacts that hold human viscera. No previous work was ever conducted on such material, which led to the first characterization of human DNA from Ancient Egyptian canopic jars and the profiling of the complex bacterial composition of this highly degraded, challenging, organic material. However, the DNA recovered was not of enough quality to confidently characterize bacterial taxa associated with infectious diseases, nor exclusive bacterial members of the human microbiome.

DISCUSSION: In summary, we present the first genomic survey of the visceral content of Ancient Egyptian funerary artifacts and demonstrate the limitations of current molecular methods to analyze canopic jars, such as the incomplete history of the objects or the presence of uncharacterized compounds that can hamper the recovery of DNA. Our work highlights the main challenges and caveats when working with such complicated archeological material - and offers sampling recommendations for similarly complex future studies, such as incrementing the amount of starting material and sampling from the less exposed parts of the jar content. This is the first-ever recorded evidence of ancient human DNA found in Ancient Egyptian canopic jars, and our results open new avenues in the study of neglected archeological artifacts.},
}

@article {pmid36790664,
year = {2022},
author = {Vigeant, J and Ribot, I and Hélie, JF},
title = {Investigating individual migration life histories: An isotopic case study from 17th to 18th century Nouvelle France.},
journal = {American journal of biological anthropology},
volume = {177},
number = {2},
pages = {232-248},
doi = {10.1002/ajpa.24455},
pmid = {36790664},
issn = {2692-7691},
abstract = {OBJECTIVES: This isotopic study explores the mobility patterns of a growing urban population from Notre Dame's Catholic cemetery (1691-1796), located in Montreal (Canada). The site offers a unique opportunity to investigate early colonial settlement in Nouvelle France through individual life patterns.

MATERIALS AND METHODS: Stable oxygen isotopic compositions (δ[18]O) were measured on the enamel of 32 individuals from the Notre Dame collection. Premolars and third molars were selected, as they reflected the δ[18]O of the drinking water during childhood (2.5-5.5 years) and pre-adulthood (9.5-15.5 years). Firstly, premolars from three children (4-8 years of age) allowed us to provide a mean δ[18]O for the water consumed locally (22.7 ±  1.0 ‰ vs. VSMOW). Then, our δ[18]O were compared with published data from various geographical regions in North America (Eastern Canada and the United States) and Europe (France and the British Isles) to highlight mobility patterns of each individual.

RESULTS: Forty-eight percent of our sample (14 out of 29 individuals) did not reflect any long-distance mobility, as all their δ[18]O reflected Montreal's variation during their lifetime. The remaining (15 out of 29 individuals) experienced mobility within (n = 8) and outside (n = 7) North America and at different phases of their life (five at pre-adulthood, six at adulthood and four during both phases). Their migration patterns were analyzed according to age, sex, diet and possible ancestry in order to propose some "biographies."

DISCUSSION: This study highlights high population diversity in early colonial Montreal. Historians wrote that the city was growing, not only with the arrival of Europeans (e.g., young male workers, sailors), but also other groups (e.g., Indigenous people, slaves from North America). Additional analyses (e.g., ancient DNA) will be needed to explore further this phenomenon.},
}

@article {pmid36790637,
year = {2023},
author = {Balentine, CM and Alfonso-Durruty, M and Reynolds, AW and Vilar, M and Morello, F and Román, MS and Springs, LC and Smith, RWA and Archer, SM and Mata-Míguez, J and Wing, N and Bolnick, DA},
title = {Evaluating population histories in Patagonia and Tierra del Fuego, Chile, using ancient mitochondrial and Y-chromosomal DNA.},
journal = {American journal of biological anthropology},
volume = {180},
number = {1},
pages = {144-161},
doi = {10.1002/ajpa.24638},
pmid = {36790637},
issn = {2692-7691},
abstract = {OBJECTIVES: This study aims to characterize the genetic histories of ancient hunter-gatherer groups in Fuego-Patagonia (Chile) with distinct Marine, Terrestrial, and Mixed Economy subsistence strategies. Mitochondrial (mtDNA) and Y-chromosome data were generated to test three hypotheses. H0: All individuals were drawn from the same panmictic population; H1: Terrestrial groups first populated the region and gave rise to highly specialized Marine groups by ~7,500 cal BP; or H2: Marine and Terrestrial groups represent distinct ancestral lineages who migrated independently into the region.

METHODS: Ancient DNA was extracted from the teeth of 50 Fuegian-Patagonian individuals dating from 6,895 cal BP to after European arrival, and analyzed alongside other individuals from previous studies. Individuals were assigned to Marine, Terrestrial, and Mixed Economy groups based on archeological context and stable isotope diet inferences, and mtDNA (HVR1/2) and Y-chromosome variation was analyzed.

RESULTS: Endogenous aDNA was obtained from 49/50 (98%) individuals. Haplotype diversities, FST comparisons, and exact tests of population differentiation showed that Marine groups were significantly different from Terrestrial groups based on mtDNA (p < 0.05). No statistically significant differences were found between Terrestrial and Mixed Economy groups. Demographic simulations support models in which Marine groups diverged from the others by ~14,000 cal BP. Y-chromosome results showed similar patterns but were not statistically significant due to small sample sizes and allelic dropout.

DISCUSSION: These results support the hypothesis that Marine and Terrestrial economic groups represent distinct ancestral lineages who diverged during the time populations were expanding in the Americas, and may represent independent migrations into Fuego-Patagonia.},
}

@article {pmid36787794,
year = {2023},
author = {Baca, M and Popović, D and Agadzhanyan, AK and Baca, K and Conard, NJ and Fewlass, H and Filek, T and Golubiński, M and Horáček, I and Knul, MV and Krajcarz, M and Krokhaleva, M and Lebreton, L and Lemanik, A and Maul, LC and Nagel, D and Noiret, P and Primault, J and Rekovets, L and Rhodes, SE and Royer, A and Serdyuk, NV and Soressi, M and Stewart, JR and Strukova, T and Talamo, S and Wilczyński, J and Nadachowski, A},
title = {Ancient DNA of narrow-headed vole reveal common features of the Late Pleistocene population dynamics in cold-adapted small mammals.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {1993},
pages = {20222238},
doi = {10.1098/rspb.2022.2238},
pmid = {36787794},
issn = {1471-2954},
abstract = {The narrow-headed vole, collared lemming and common vole were the most abundant small mammal species across the Eurasian Late Pleistocene steppe-tundra environment. Previous ancient DNA studies of the collared lemming and common vole have revealed dynamic population histories shaped by climatic fluctuations. To investigate the extent to which species with similar adaptations share common evolutionary histories, we generated a dataset comprised the mitochondrial genomes of 139 ancient and 6 modern narrow-headed voles from several sites across Europe and northwestern Asia covering approximately the last 100 thousand years (kyr). We inferred Bayesian time-aware phylogenies using 11 radiocarbon-dated samples to calibrate the molecular clock. Divergence of the main mtDNA lineages across the three species occurred during marine isotope stages (MIS) 7 and MIS 5, suggesting a common response of species adapted to open habitat during interglacials. We identified several time-structured mtDNA lineages in European narrow-headed vole, suggesting lineage turnover. The timing of some of these turnovers was synchronous across the three species, allowing us to identify the main drivers of the Late Pleistocene dynamics of steppe- and cold-adapted species.},
}

@article {pmid36787792,
year = {2022},
author = {Broccard, N and Silva, NM and Currat, M},
title = {Simulated patterns of mitochondrial diversity are consistent with partial population turnover in Bronze Age Central Europe.},
journal = {American journal of biological anthropology},
volume = {177},
number = {1},
pages = {134-146},
doi = {10.1002/ajpa.24431},
pmid = {36787792},
issn = {2692-7691},
abstract = {OBJECTIVES: The analysis of ancient mitochondrial DNA from osteological remains has challenged previous conclusions drawn from the analysis of mitochondrial DNA from present populations, notably by revealing an absence of genetic continuity between the Neolithic and modern populations in Central Europe. Our study investigates how to reconcile these contradictions at the mitochondrial level using a modeling approach.

MATERIALS AND METHODS: We used a spatially explicit computational framework to simulate ancient and modern DNA sequences under various evolutionary scenarios of post Neolithic demographic events and compared the genetic diversity of the simulated and observed mitochondrial sequences. We investigated which-if any-scenarios were able to reproduce statistics of genetic diversity similar to those observed, with a focus on the haplogroup N1a, associated with the spread of early Neolithic farmers.

RESULTS: Demographic fluctuations during the Neolithic transition or subsequent demographic collapses after this period, that is, due to epidemics such as plague, are not sufficient to explain the signal of population discontinuity detected on the mitochondrial DNA in Central Europe. Only a scenario involving a substantial genetic input due to the arrival of migrants after the Neolithic transition, possibly during the Bronze Age, is compatible with observed patterns of genetic diversity.

DISCUSSION: Our results corroborate paleogenomic studies, since out of the alternative hypotheses tested, the best one that was able to recover observed patterns of mitochondrial diversity in modern and ancient Central European populations was one were immigration of populations from the Pontic steppes during the Bronze Age was explicitly simulated.},
}

@article {pmid36762361,
year = {2022},
author = {Riedel, A},
title = {Nine new species of Trigonopterus Fauvel (Coleoptera, Curculionidae) from Sundaland.},
journal = {ZooKeys},
volume = {1124},
number = {},
pages = {109-130},
pmid = {36762361},
issn = {1313-2989},
abstract = {The DNA of Trigonopterus specimens from the Sundaland region stored between ten and 32 years in museums could be used for next-generation sequencing. The availability of their cox1 sequence allowed the description of the following nine new species: Trigonopterusgrimmi sp. nov., T.johorensis sp. nov., T.lambirensis sp. nov., T.linauensis sp. nov., T.microreticulatus Riedel, Trnka & Wahab sp. nov., T.mulensis sp. nov., T.sarawakensis sp. nov., T.siamensis sp. nov., and T.singaporensis sp. nov. The alternative original spelling of the name T.tounensis Narakusumo & Riedel is chosen to prevail over T.tounaensis Narakusumo & Riedel. The new species represent the first country records of Trigonopterus for Brunei, Singapore, and Thailand. Thus, the genus´ known area of distribution in the Sundaland region is significantly extended. A key and a catalogue are provided to the Trigonopterus species from Borneo, W-Malaysia, Singapore, and Thailand.},
}

@article {pmid36760997,
year = {2023},
author = {Chang, X and Pamjav, H and Zhabagin, M and Wen, S},
title = {Editorial: The genetic history of human populations along the ancient silk road.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1130104},
pmid = {36760997},
issn = {1664-8021},
}

@article {pmid36755065,
year = {2021},
author = {Armbrecht, L and Eisenhofer, R and Utge, J and Sibert, EC and Rocha, F and Ward, R and Pierella Karlusich, JJ and Tirichine, L and Norris, R and Summers, M and Bowler, C},
title = {Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics.},
journal = {ISME communications},
volume = {1},
number = {1},
pages = {66},
pmid = {36755065},
issn = {2730-6151},
abstract = {Sedimentary ancient DNA (sedaDNA) analyses are increasingly used to reconstruct marine ecosystems. The majority of marine sedaDNA studies use a metabarcoding approach (extraction and analysis of specific DNA fragments of a defined length), targeting short taxonomic marker genes. Promising examples are 18S-V9 rRNA (~121-130 base pairs, bp) and diat-rbcL (76 bp), targeting eukaryotes and diatoms, respectively. However, it remains unknown how 18S-V9 and diat-rbcL derived compositional profiles compare to metagenomic shotgun data, the preferred method for ancient DNA analyses as amplification biases are minimised. We extracted DNA from five Santa Barbara Basin sediment samples (up to ~11 000 years old) and applied both a metabarcoding (18S-V9 rRNA, diat-rbcL) and a metagenomic shotgun approach to (i) compare eukaryote, especially diatom, composition, and (ii) assess sequence length and database related biases. Eukaryote composition differed considerably between shotgun and metabarcoding data, which was related to differences in read lengths (~112 and ~161 bp, respectively), and overamplification of short reads in metabarcoding data. Diatom composition was influenced by reference bias that was exacerbated in metabarcoding data and characterised by increased representation of Chaetoceros, Thalassiosira and Pseudo-nitzschia. Our results are relevant to sedaDNA studies aiming to accurately characterise paleo-ecosystems from either metabarcoding or metagenomic data.},
}

@article {pmid36750197,
year = {2023},
author = {Tiwari, J and Sur, S and Yadav, A and Kumar, R and Rai, N and Rani, S and Malik, S},
title = {Photoperiod-driven concurrent changes in hypothalamic and brainstem transcription of sleep and immune genes in migratory redheaded bunting.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {1992},
pages = {20222374},
doi = {10.1098/rspb.2022.2374},
pmid = {36750197},
issn = {1471-2954},
abstract = {The molecular regulation of sleep in avian migrants is still obscure. We thus investigated this in migratory redheaded buntings, where four life-history states (LHS; i.e. non-migratory, pre-migratory, migratory and refractory states) were induced. There was increased night-time activity (i.e. Zugunruhe) during the migratory state with reduced daytime activity. The recordings of the sleep-wake cycle in buntings showed increased night-time active wakefulness coupled with drastically reduced front and back sleep during migratory phase. Interestingly, we found the buntings to feed and drink even after lights-off during migration. Gene expression studies revealed increased hypothalamic expression of glucocorticoid receptor (nr3c1), and pro-inflammatory cytokines (il1b and il6) in pre-migratory and migratory states, respectively, whereas in brainstem Ca[2+]/calmodulin-dependent protein kinase 2 (camk2) was upregulated during the migratory state. This suggested a heightened pro-inflammatory state during migration which is a feature of chronic sleep loss, and a possible role of Ca[2+] signalling in promoting wakefulness. In both the hypothalamus and brainstem, the expression of melatonin receptors (mel1a and mel1b) was increased in the pre-migratory state, and growth hormone-releasing hormone (ghrh, known to induce sleep) was reduced during the migratory state. The current results demonstrate key molecules involved in the regulation of sleep-wake cycle across LHS in migratory songbirds.},
}

@article {pmid36748324,
year = {2023},
author = {Wagner, S and Seguin-Orlando, A and Leplé, JC and Leroy, T and Lalanne, C and Labadie, K and Aury, JM and Poirier, S and Wincker, P and Plomion, C and Kremer, A and Orlando, L},
title = {Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.16859},
pmid = {36748324},
issn = {1365-294X},
abstract = {Whole genome characterizations of crop plants based on ancient DNA have provided unique keys for a better understanding of the evolutionary origins of modern cultivars, the pace and mode of selection underlying their adaptation to new environments and the production of phenotypes of interest. Although forests are among the most biologically rich ecosystems on earth and represent a fundamental resource for human societies, no ancient genome sequences have been generated for trees. This contrasts with the generation of multiple ancient reference genomes for important crops. Here, we sequenced the first ancient tree genomes using two white oak wood remains from Germany dating to the Last Little Ice Age (15th century CE, 7.3× and 4.0×) and one from France dating to the Bronze Age (1700 BCE, 3.4×). We assessed the underlying species and identified one medieval remains as a hybrid between two common oak species (Quercus robur and Q. petraea) and the other two remains as Q. robur. We found that diversity at the global genome level had not changed over time. However, exploratory analyses suggested that a reduction of diversity took place at different time periods. Finally, we determined the timing of leaf unfolding for ancient trees for the first time. The study extends the application of ancient wood beyond the classical proxies of dendroclimatology, dendrochronology, dendroarchaeology and dendroecology, thereby enhancing resolution of inferences on the responses of forest ecosystems to past environmental changes, epidemics and silvicultural practices.},
}

@article {pmid36747166,
year = {2023},
author = {Sarhan, MS and Wurst, C and Tzankov, A and Bircher, AJ and Wittig, H and Briellmann, T and Augsburger, M and Hotz, G and Zink, A and Maixner, F},
title = {A nontuberculous mycobacterium could solve the mystery of the lady from the Franciscan church in Basel, Switzerland.},
journal = {BMC biology},
volume = {21},
number = {1},
pages = {9},
pmid = {36747166},
issn = {1741-7007},
abstract = {BACKGROUND: In 1975, the mummified body of a female has been found in the Franciscan church in Basel, Switzerland. Molecular and genealogic analyses unveiled her identity as Anna Catharina Bischoff (ACB), a member of the upper class of post-reformed Basel, who died at the age of 68 years, in 1787. The reason behind her death is still a mystery, especially that toxicological analyses revealed high levels of mercury, a common treatment against infections at that time, in different body organs. The computed tomography (CT) and histological analysis showed bone lesions in the femurs, the rib cage, and the skull, which refers to a potential syphilis case.

RESULTS: Although we could not detect any molecular signs of the syphilis-causing pathogen Treponema pallidum subsp. pallidum, we realized high prevalence of a nontuberculous mycobacterium (NTM) species in brain tissue sample. The genome analysis of this NTM displayed richness of virulence genes and toxins, and similarity to other infectious NTM, known to infect immunocompromised patients. In addition, it displayed potential resistance to mercury compounds, which might indicate a selective advantage against the applied treatment. This suggests that ACB might have suffered from an atypical mycobacteriosis during her life, which could explain the mummy's bone lesion and high mercury concentrations.

CONCLUSIONS: The study of this mummy exemplifies the importance of employing differential diagnostic approaches in paleopathological analysis, by combining classical anthropological, radiological, histological, and toxicological observations with molecular analysis. It represents a proof-of-concept for the discovery of not-yet-described ancient pathogens in well-preserved specimens, using de novo metagenomic assembly.},
}

@article {pmid36721228,
year = {2023},
author = {Wang, J and Yang, L and Duan, S and Sun, Q and Li, Y and Wu, J and Wu, W and Wang, Z and Liu, Y and Tang, R and Yang, J and Liu, C and Yuan, B and Wang, D and Xu, J and Wang, M and He, G},
title = {Genome-wide allele and haplotype-sharing patterns suggested one unique Hmong-Mein-related lineage and biological adaptation history in Southwest China.},
journal = {Human genomics},
volume = {17},
number = {1},
pages = {3},
doi = {10.1186/s40246-023-00452-0},
pmid = {36721228},
issn = {1479-7364},
abstract = {BACKGROUND: Fine-scale genetic structure of ethnolinguistically diverse Chinese populations can fill the gap in the missing diversity and evolutionary landscape of East Asians, particularly for anthropologically informed Chinese minorities. Hmong-Mien (HM) people were one of the most significant indigenous populations in South China and Southeast Asia, which were suggested to be the descendants of the ancient Yangtze rice farmers based on linguistic and archeological evidence. However, their deep population history and biological adaptative features remained to be fully characterized.

OBJECTIVES: To explore the evolutionary and adaptive characteristics of the Miao people, we genotyped genome-wide SNP data in Guizhou HM-speaking populations and merged it with modern and ancient reference populations via a comprehensive population genetic analysis and evolutionary admixture modeling.

RESULTS: The overall genetic admixture landscape of Guizhou Miao showed genetic differentiation between them and other linguistically diverse Guizhou populations. Admixture models further confirmed that Miao people derived their primary ancestry from geographically close Guangxi Gaohuahua people. The estimated identity by descent and effective population size confirmed a plausible population bottleneck, contributing to their unique genetic diversity and population structure patterns. We finally identified several natural selection candidate genes associated with several biological pathways.

CONCLUSIONS: Guizhou Miao possessed a specific genetic structure and harbored a close genetic relationship with geographically close southern Chinese indigenous populations and Guangxi historical people. Miao people derived their major ancestry from geographically close Guangxi Gaohuahua people and experienced a plausible population bottleneck which contributed to the unique pattern of their genetic diversity and structure. Future ancient DNA from Shijiahe and Qujialing will provide new insights into the origin of the Miao people.},
}

@article {pmid36714834,
year = {2022},
author = {Velsko, IM and Semerau, L and Inskip, SA and García-Collado, MI and Ziesemer, K and Ruber, MS and Benítez de Lugo Enrich, L and Molero García, JM and Valle, DG and Peña Ruiz, AC and Salazar-García, DC and Hoogland, MLP and Warinner, C},
title = {Ancient dental calculus preserves signatures of biofilm succession and interindividual variation independent of dental pathology.},
journal = {PNAS nexus},
volume = {1},
number = {4},
pages = {pgac148},
pmid = {36714834},
issn = {2752-6542},
abstract = {Dental calculus preserves oral microbes, enabling comparative studies of the oral microbiome and health through time. However, small sample sizes and limited dental health metadata have hindered health-focused investigations to date. Here, we investigate the relationship between tobacco pipe smoking and dental calculus microbiomes. Dental calculus from 75 individuals from the 19th century Middenbeemster skeletal collection (Netherlands) were analyzed by metagenomics. Demographic and dental health parameters were systematically recorded, including the presence/number of pipe notches. Comparative data sets from European populations before and after the introduction of tobacco were also analyzed. Calculus species profiles were compared with oral pathology to examine associations between microbiome community, smoking behavior, and oral health status. The Middenbeemster individuals exhibited relatively poor oral health, with a high prevalence of periodontal disease, caries, heavy calculus deposits, and antemortem tooth loss. No associations between pipe notches and dental pathologies, or microbial species composition, were found. Calculus samples before and after the introduction of tobacco showed highly similar species profiles. Observed interindividual microbiome differences were consistent with previously described variation in human populations from the Upper Paleolithic to the present. Dental calculus may not preserve microbial indicators of health and disease status as distinctly as dental plaque.},
}

@article {pmid36712342,
year = {2022},
author = {Brown, T and Rijal, DP and Heintzman, PD and Clarke, CL and Blankholm, HP and Høeg, HI and Lammers, Y and Bråthen, KA and Edwards, M and Alsos, IG},
title = {Paleoeconomy more than demography determined prehistoric human impact in Arctic Norway.},
journal = {PNAS nexus},
volume = {1},
number = {5},
pages = {pgac209},
pmid = {36712342},
issn = {2752-6542},
abstract = {Population size has increasingly been taken as the driver of past human environmental impact worldwide, and particularly in the Arctic. However, sedimentary ancient DNA (sedaDNA), pollen and archaeological data show that over the last 12,000 years, paleoeconomy and culture determined human impacts on the terrestrial ecology of Arctic Norway. The large Mortensnes site complex (Ceavccageađgi, 70°N) has yielded the most comprehensive multiproxy record in the Arctic to date. The site saw occupation from the Pioneer period (c. 10,000 cal. years BP) with more intensive use from c. 4,200 to 2,000 cal. years BP and after 1,600 cal. years BP. Here, we combine on-site environmental archaeology with a near-site lake record of plant and animal sedaDNA. The rich animal sedaDNA data (42 taxa) and on-site faunal analyses reveal switches in human dietary composition from early-Holocene fish + marine mammals, to mixed marine + reindeer, then finally to marine + reindeer + domesticates (sheep, cattle, pigs), with highest reindeer concentrations in the last millennium. Archaeological evidence suggests these changes are not directly driven by climate or variation in population densities at the site or in the region, but rather are the result of changing socio-economic activities and culture, probably reflecting settlers' origins. This large settlement only had discernable effects on its hinterland in the last 3,600 years (grazing) and more markedly in the last 1,000 years through reindeer keeping/herding and, possibly domestic stock. Near-site sedaDNA can be linked to and validate the faunal record from archaeological excavations, demonstrating that environmental impacts can be assessed at a landscape scale.},
}

@article {pmid36691623,
year = {2023},
author = {de March, CA and Matsunami, H and Abe, M and Cobb, M and Hoover, KC},
title = {Genetic and functional odorant receptor variation in the Homo lineage.},
journal = {iScience},
volume = {26},
number = {1},
pages = {105908},
pmid = {36691623},
issn = {2589-0042},
abstract = {Humans, Neanderthals, and Denisovans independently adapted to a wide range of geographic environments and their associated food odors. Using ancient DNA sequences, we explored the in vitro function of thirty odorant receptor genes in the genus Homo. Our extinct relatives had highly conserved olfactory receptor sequence, but humans did not. Variations in odorant receptor protein sequence and structure may have produced variation in odor detection and perception. Variants led to minimal changes in specificity but had more influence on functional sensitivity. The few Neanderthal variants disturbed function, whereas Denisovan variants increased sensitivity to sweet and sulfur odors. Geographic adaptations may have produced greater functional variation in our lineage, increasing our olfactory repertoire and expanding our adaptive capacity. Our survey of olfactory genes and odorant receptors suggests that our genus has a shared repertoire with possible local ecological adaptations.},
}

@article {pmid36672975,
year = {2023},
author = {Danielewski, M and Żuraszek, J and Zielińska, A and Herzig, KH and Słomski, R and Walkowiak, J and Wielgus, K},
title = {Methodological Changes in the Field of Paleogenetics.},
journal = {Genes},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/genes14010234},
pmid = {36672975},
issn = {2073-4425},
abstract = {Paleogenetics has significantly changed since its inception almost forty years ago. Initially, molecular techniques available to the researchers offered minimal possibilities for ancient DNA analysis. The subsequent expansion of the scientific tool cabinet allowed for more remarkable achievements, combined has with the newfound popularity of this budding field of science. Finally, a breakthrough was made with the development of next-generation sequencing (NGS) technologies and the update of DNA isolation protocols, through which even very fragmented aDNA samples could be used to sequence whole genomes. In this paper, we review the achievements made thus far and compare the methodologies utilized in this field of science, discussing their benefits and challenges.},
}

@article {pmid36672874,
year = {2023},
author = {Borbély, N and Székely, O and Szeifert, B and Gerber, D and Máthé, I and Benkő, E and Mende, BG and Egyed, B and Pamjav, H and Szécsényi-Nagy, A},
title = {High Coverage Mitogenomes and Y-Chromosomal Typing Reveal Ancient Lineages in the Modern-Day Székely Population in Romania.},
journal = {Genes},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/genes14010133},
pmid = {36672874},
issn = {2073-4425},
abstract = {Here we present 115 whole mitogenomes and 92 Y-chromosomal Short Tandem Repeat (STR) and Single Nucleotide Polymorphism (SNP) profiles from a Hungarian ethnic group, the Székelys (in Romanian: Secuii, in German: Sekler), living in southeast Transylvania (Romania). The Székelys can be traced back to the 12th century in the region, and numerous scientific theories exist as to their origin. We carefully selected sample providers that had local ancestors inhabiting small villages in the area of Odorheiu Secuiesc/Székelyudvarhely in Romania. The results of our research and the reported data signify a qualitative leap compared to previous studies since it presents the first complete mitochondrial DNA sequences and Y-chromosomal profiles of 23 STRs from the region. We evaluated the results with population genetic and phylogenetic methods in the context of the modern and ancient populations that are either geographically or historically related to the Székelys. Our results demonstrate a predominantly local uniparental make-up of the population that also indicates limited admixture with neighboring populations. Phylogenetic analyses confirmed the presumed eastern origin of certain maternal (A, C, D) and paternal (Q, R1a) lineages, and, in some cases, they could also be linked to ancient DNA data from the Migration Period (5th-9th centuries AD) and Hungarian Conquest Period (10th century AD) populations.},
}

@article {pmid36672816,
year = {2022},
author = {Salado, I and Preick, M and Lupiáñez-Corpas, N and Fernández-Gil, A and Vilà, C and Hofreiter, M and Leonard, JA},
title = {Loss of Mitochondrial Genetic Diversity despite Population Growth: The Legacy of Past Wolf Population Declines.},
journal = {Genes},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/genes14010075},
pmid = {36672816},
issn = {2073-4425},
abstract = {Gray wolves (Canis lupus) in the Iberian Peninsula declined substantially in both range and population size in the last few centuries due to human persecution and habitat fragmentation. However, unlike many other western European populations, gray wolves never went extinct in Iberia. Since the minimum number was recorded around 1970, their numbers have significantly increased and then stabilized in recent decades. We analyzed mitochondrial genomes from 54 historical specimens of Iberian wolves from across their historical range using ancient DNA methods. We compared historical and current mitochondrial diversity in Iberian wolves at the 5' end of the control region (n = 17 and 27) and the whole mitochondrial genome excluding the control region (n = 19 and 29). Despite an increase in population size since the 1970s, genetic diversity declined. We identified 10 whole mitochondrial DNA haplotypes in 19 historical specimens, whereas only six of them were observed in 29 modern Iberian wolves. Moreover, a haplotype that was restricted to the southern part of the distribution has gone extinct. Our results illustrate a lag between demographic and genetic diversity changes, and show that after severe population declines, genetic diversity can continue to be lost in stable or even expanding populations. This suggests that such populations may be of conservation concern even after their demographic trajectory has been reversed.},
}

@article {pmid36669262,
year = {2023},
author = {Dzehverovic, M and Jusic, B and Pilav, A and Lukic, T and Cakar, J},
title = {Kinship analysis of skeletal remains from the Middle Ages.},
journal = {Forensic science international. Genetics},
volume = {63},
number = {},
pages = {102829},
doi = {10.1016/j.fsigen.2023.102829},
pmid = {36669262},
issn = {1878-0326},
abstract = {Medieval cemeteries Klisa-Guca Gora, Alihodze and Glavica-Han Bila located in the Travnik area (Travnik, Bosnia and Herzegovina) were archaeologically examined in the period 2011-2014, revealing human skeletal remains of 11 individuals in total. Archaeological skeletal samples, previously deposited in Travnik Homeland Museum (Travnik, Bosnia and Herzegovina) were subjected to genetic analysis. The aim of this research was to test familiar relationship of 11 individuals excavated from three medieval cemeteries and to predict Y-haplogroup for male individuals. In order to perform molecular-genetic characterisation of collected human skeletal remains, two systems of genetic markers were analysed: autosomal and Y-STR loci. Complete or partial data obtained by autosomal STR typing of 11 individuals were subjected to kinship analysis. Male sex was determined in eight samples out of 11. Direct relatives of the "brother-brother" type were detected in one case with high kinship probability (KP) value of 99.99996 %. Complete or nearly complete and usable Y-STR profiles were obtained for six out of eight male individuals. The presence of identical haplotypes at Y-STR loci and results of Y-haplogroup prediction suggest that all male individuals share the same paternal lineage and belong to J2a haplogroup. Overall, this study emphasises the usefulness, efficiency and sensitivity of STR markers in the molecular-genetic characterisation of old skeletal remains as well as the importance of employing additional markers like Y-STRs in archaeogenetic studies, besides traditionally used autosomal STR markers, in order to get a comprehensive information about close and distant relatives, and ancestry.},
}

@article {pmid36661852,
year = {2023},
author = {He, Z and Dai, X and Lyu, W and Beaumont, M and Yu, F},
title = {Estimating temporally variable selection intensity from ancient DNA Data.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msad008},
pmid = {36661852},
issn = {1537-1719},
abstract = {Novel technologies for recovering DNA information from archaeological and historical specimens have made available an ever-increasing amount of temporally spaced genetic samples from natural populations. These genetic time series permit the direct assessment of patterns of temporal changes in allele frequencies, and hold the promise of improving power for the inference of selection. Increased time resolution can further facilitate testing hypotheses regarding the drivers of past selection events such as the incidence of plant and animal domestication. However, studying past selection processes through ancient DNA (aDNA) still involves considerable obstacles such as postmortem damage, high fragmentation, low coverage and small samples. To circumvent these challenges, we introduce a novel Bayesian framework for the inference of temporally variable selection based on genotype likelihoods instead of allele frequencies, thereby enabling us to model sample uncertainties resulting from the damage and fragmentation of aDNA molecules. Also, our approach permits the reconstruction of the underlying allele frequency trajectories of the population through time, which allows for a better understanding of the drivers of selection. We evaluate its performance through extensive simulations and demonstrate its utility with an application to the ancient horse samples genotyped at the loci for coat colouration. Our results reveal that incorporating sample uncertainties can further improve the inference of selection.},
}

@article {pmid36661298,
year = {2023},
author = {Henriksen, RA and Zhao, L and Korneliussen, TS},
title = {NGSNGS: Next generation simulator for next generation sequencing data.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btad041},
pmid = {36661298},
issn = {1367-4811},
abstract = {SUMMARY: With the rapid expansion of the capabilities of the DNA sequencers throughout the different sequencing generations, the quantity of generated data has likewise increased. This evolution has also led to new bioinformatical methods, for which in silico data has become crucial when verifying the accuracy of a model or the robustness of a genomic analysis pipeline. Here we present a multithreaded next-generation simulation tool for next-generation sequencing data (NGSNGS), which simulates reads faster than currently available methods and programs. NGSNGS can simulate reads with platform specific characteristics based on nucleotide quality score profiles, as well as including a post-mortem damage model which is relevant for simulating ancient DNA (aDNA). The simulated sequences are sampled (with replacement) from a reference DNA genome, which can represent a haploid genome, polyploid assemblies, or even population haplotypes and allows the user to simulate known variable sites directly. The program is implemented in a multithreading framework and is factors faster than currently available tools while extending their feature set and possible output formats.

AVAILABILITY: The method and associated programs are released as open-source software, code and user manual are available at https://github.com/RAHenriksen/NGSNGS.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid36658311,
year = {2023},
author = {Eaton, K and Featherstone, L and Duchene, S and Carmichael, AG and Varlık, N and Golding, GB and Holmes, EC and Poinar, HN},
title = {Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {23},
pmid = {36658311},
issn = {2399-3642},
abstract = {Plague has an enigmatic history as a zoonotic pathogen. This infectious disease will unexpectedly appear in human populations and disappear just as suddenly. As a result, a long-standing line of inquiry has been to estimate when and where plague appeared in the past. However, there have been significant disparities between phylogenetic studies of the causative bacterium, Yersinia pestis, regarding the timing and geographic origins of its reemergence. Here, we curate and contextualize an updated phylogeny of Y. pestis using 601 genome sequences sampled globally. Through a detailed Bayesian evaluation of temporal signal in subsets of these data we demonstrate that a Y. pestis-wide molecular clock is unstable. To resolve this, we developed a new approach in which each Y. pestis population was assessed independently, enabling us to recover substantial temporal signal in five populations, including the ancient pandemic lineages which we now estimate may have emerged decades, or even centuries, before a pandemic was historically documented from European sources. Despite this methodological advancement, we only obtain robust divergence dates from populations sampled over a period of at least 90 years, indicating that genetic evidence alone is insufficient for accurately reconstructing the timing and spread of short-term plague epidemics.},
}

@article {pmid36656838,
year = {2023},
author = {Wu, MY and Forcina, G and Low, GW and Sadanandan, KR and Gwee, CY and van Grouw, H and Wu, S and Edwards, SV and Baldwin, MW and Rheindt, FE},
title = {Historic samples reveal loss of wild genotype through domestic chicken introgression during the Anthropocene.},
journal = {PLoS genetics},
volume = {19},
number = {1},
pages = {e1010551},
doi = {10.1371/journal.pgen.1010551},
pmid = {36656838},
issn = {1553-7404},
abstract = {Human activities have precipitated a rise in the levels of introgressive gene flow among animals. The investigation of conspecific populations at different time points may shed light on the magnitude of human-mediated introgression. We used the red junglefowl Gallus gallus, the wild ancestral form of the chicken, as our study system. As wild junglefowl and domestic chickens readily admix, conservationists fear that domestic introgression into junglefowl may compromise their wild genotype. By contrasting the whole genomes of 51 chickens with 63 junglefowl from across their natural range, we found evidence of a loss of the wild genotype across the Anthropocene. When comparing against the genomes of junglefowl from approximately a century ago using rigorous ancient-DNA protocols, we discovered that levels of domestic introgression are not equal among and within modern wild populations, with the percentage of domestic ancestry around 20-50%. We identified a number of domestication markers in which chickens are deeply differentiated from historic junglefowl regardless of breed and/or geographic provenance, with eight genes under selection. The latter are involved in pathways dealing with development, reproduction and vision. The wild genotype is an allelic reservoir that holds most of the genetic diversity of G. gallus, a species which is immensely important to human society. Our study provides fundamental genomic infrastructure to assist in efforts to prevent a further loss of the wild genotype through introgression of domestic alleles.},
}

@article {pmid36653523,
year = {2023},
author = {Nwosu, EC and Brauer, A and Monchamp, ME and Pinkerneil, S and Bartholomäus, A and Theuerkauf, M and Schmidt, JP and Stoof-Leichsenring, KR and Wietelmann, T and Kaiser, J and Wagner, D and Liebner, S},
title = {Early human impact on lake cyanobacteria revealed by a Holocene record of sedimentary ancient DNA.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {72},
pmid = {36653523},
issn = {2399-3642},
abstract = {Sedimentary DNA-based studies revealed the effects of human activity on lake cyanobacteria communities over the last centuries, yet we continue to lack information over longer timescales. Here, we apply high-resolution molecular analyses on sedimentary ancient DNA to reconstruct the history of cyanobacteria throughout the Holocene in a lake in north-eastern Germany. We find a substantial increase in cyanobacteria abundance coinciding with deforestation during the early Bronze Age around 4000 years ago, suggesting increased nutrient supply to the lake by local communities settling on the lakeshore. The next substantial human-driven increase in cyanobacteria abundance occurred only about a century ago due to intensified agricultural fertilisation which caused the dominance of potentially toxic taxa (e.g., Aphanizomenon). Our study provides evidence that humans began to locally impact lake ecology much earlier than previously assumed. Consequently, managing aquatic systems today requires awareness of the legacy of human influence dating back potentially several millennia.},
}

@article {pmid36654346,
year = {2021},
author = {Liu, J and Zeng, W and Sun, B and Mao, X and Zhao, Y and Wang, F and Li, Z and Luan, F and Guo, J and Zhu, C and Wang, Z and Wei, C and Zhang, M and Cao, P and Liu, F and Dai, Q and Feng, X and Yang, R and Hou, W and Ping, W and Wu, X and Andrew Bennett, E and Liu, Y and Fu, Q},
title = {Maternal genetic structure in ancient Shandong between 9500 and 1800 years ago.},
journal = {Science bulletin},
volume = {66},
number = {11},
pages = {1129-1135},
doi = {10.1016/j.scib.2021.01.029},
pmid = {36654346},
issn = {2095-9281},
abstract = {Archaeological and ancient DNA studies revealed that Shandong, a multi-culture center in northern coastal China, was home to ancient populations having ancestry related to both northern and southern East Asian populations. However, the limited temporal and geographical range of previous studies have been insufficient to describe the population history of this region in greater detail. Here, we report the analysis of 86 complete mitochondrial genomes from the remains of 9500 to 1800-year-old humans from 12 archaeological sites across Shandong. For samples older than 4600 years before present (BP), we found haplogroups D4, D5, B4c1, and B5b2, which are observed in present-day northern and southern East Asians. For samples younger than 4600 BP, haplogroups C (C7a1 and C7b), M9 (M9a1), and F (F1a1, F2a, and F4a1) begin to appear, indicating changes in the Shandong maternal genetic structure starting from the beginning of the Longshan cultural period. Within Shandong, the genetic exchange is possible between the coastal and inland regions after 3100 BP. We also discovered the B5b2 lineage in Shandong populations, with the oldest Bianbian individual likely related to the ancestors of some East Asians and North Asians. By reconstructing a maternal genetic structure of Shandong populations, we provide greater resolution of the population dynamics of the northern coastal East Asia over the past nine thousand years.},
}