Viewport Size Code:
Login | Create New Account
picture

  MENU

About | Classical Genetics | Timelines | What's New | What's Hot

About | Classical Genetics | Timelines | What's New | What's Hot

icon

Bibliography Options Menu

icon
QUERY RUN:
HITS:
PAGE OPTIONS:
Hide Abstracts   |   Hide Additional Links
NOTE:
Long bibliographies are displayed in blocks of 100 citations at a time. At the end of each block there is an option to load the next block.

Bibliography on: Paleontology Meets Genomics — Sequencing Ancient DNA

The Electronic Scholarly Publishing Project: Providing world-wide, free access to classic scientific papers and other scholarly materials, since 1993.

More About:  ESP | OUR CONTENT | THIS WEBSITE | WHAT'S NEW | WHAT'S HOT

ESP: PubMed Auto Bibliography 05 Jun 2020 at 01:47 Created: 

Paleontology Meets Genomics — Sequencing Ancient DNA

The ideas behind Jurassic Park have become real, kinda sorta. It is now possible to retrieve and sequence DNA from ancient specimens. Although these sequences are based on poor quality DNA and thus have many inferential steps (i,e, the resulting sequence is not likely to be a perfect replica of the living DNA), the insights to be gained from paleosequentcing are nonetheless great. For example, paleo-sequencing has shown that Neanderthal DNA is sufficiently different from human DNA as to be reasonably considered as coming from a different species.

Created with PubMed® Query: "ancient DNA" OR "ancient genome" OR paleogenetic OR paleogenetics NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

RevDate: 2020-06-04

Díez-Del-Molino D, L Dalén (2020)

Unroll Please: Deciphering the Genetic Code in Scrolls and Other Ancient Materials.

Cell pii:S0092-8674(20)30626-7 [Epub ahead of print].

The unrelenting development of ancient DNA methods now allows researchers to obtain archaeogenetic data from increasingly diverse sources. In a new study in this issue of Cell, researchers apply the latest DNA technologies to unravel the mysteries of the Dead Sea Scrolls, one of the world's most famous and influential sets of ancient parchments.

RevDate: 2020-06-04

Coutinho A, Günther T, Munters AR, et al (2020)

The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders.

American journal of physical anthropology [Epub ahead of print].

OBJECTIVES: In order to understand contacts between cultural spheres in the third millennium BC, we investigated the impact of a new herder culture, the Battle Axe culture, arriving to Scandinavia on the people of the sub-Neolithic hunter-gatherer Pitted Ware culture. By investigating the genetic make-up of Pitted Ware culture people from two types of burials (typical Pitted Ware culture burials and Battle Axe culture-influenced burials), we could determine the impact of migration and the impact of cultural influences.

METHODS: We sequenced and analyzed the genomes of 25 individuals from typical Pitted Ware culture burials and from Pitted Ware culture burials with Battle Axe culture influences in order to determine if the different burial types were associated with different gene-pools.

RESULTS: The genomic data show that all individuals belonged to one genetic population-a population associated with the Pitted Ware culture-irrespective of the burial style.

CONCLUSION: We conclude that the Pitted Ware culture communities were not impacted by gene-flow, that is, via migration or exchange of mates. These different cultural expressions in the Pitted Ware culture burials are instead a consequence of cultural exchange.

RevDate: 2020-06-04

Buckley M, Harvey VL, Orihuela J, et al (2020)

Collagen sequence analysis reveals evolutionary history of extinct West Indies Nesophontes ('island-shrews').

Molecular biology and evolution pii:5851441 [Epub ahead of print].

Ancient biomolecule analyses are proving increasingly useful in the study of evolutionary patterns, including extinct organisms. Proteomic sequencing techniques complement genomic approaches, having the potential to examine lineages further back in time than achievable using ancient DNA, given the less stringent preservation requirements. In this study, we demonstrate the ability to use collagen sequence analyses via proteomics to provide species delimitation as a foundation for informing evolutionary patterns. We uncover biogeographic information of an enigmatic and recently extinct lineage of Nesophontes across their range on the Caribbean islands. First, evolutionary relationships reconstructed from collagen sequences reaffirm the affinity of Nesophontes and Solenodon as sister taxa within Solenodonota. This relationship helps lay the foundation for testing geographical isolation hypotheses across islands within the Greater Antilles, including movement from Cuba towards Hispaniola. Second, our results are consistent with Cuba having just two species of Nesophontes (N. micrus and N. major) that exhibit intrapopulation morphological variation. Finally, analysis of the recently described species from the Cayman Islands (N. hemicingulus) indicates that it is a closer relative to the Cuban species, N. major rather than N. micrus as previously speculated. Our proteomic sequencing improves our understanding of the origin, evolution, and distribution of this extinct mammal lineage, particularly with respect to approximate timing of speciation. Such knowledge is vital for this biodiversity hotspot, where the magnitude of recent extinctions may obscure true estimates of species richness in the past.

RevDate: 2020-06-03

Anava S, Neuhof M, Gingold H, et al (2020)

Illuminating Genetic Mysteries of the Dead Sea Scrolls.

Cell pii:S0092-8674(20)30552-3 [Epub ahead of print].

The discovery of the 2,000-year-old Dead Sea Scrolls had an incomparable impact on the historical understanding of Judaism and Christianity. "Piecing together" scroll fragments is like solving jigsaw puzzles with an unknown number of missing parts. We used the fact that most scrolls are made from animal skins to "fingerprint" pieces based on DNA sequences. Genetic sorting of the scrolls illuminates their textual relationship and historical significance. Disambiguating the contested relationship between Jeremiah fragments supplies evidence that some scrolls were brought to the Qumran caves from elsewhere; significantly, they demonstrate that divergent versions of Jeremiah circulated in parallel throughout Israel (ancient Judea). Similarly, patterns discovered in non-biblical scrolls, particularly the Songs of the Sabbath Sacrifice, suggest that the Qumran scrolls represent the broader cultural milieu of the period. Finally, genetic analysis divorces debated fragments from the Qumran scrolls. Our study demonstrates that interdisciplinary approaches enrich the scholar's toolkit.

RevDate: 2020-06-03

Seersholm FV, Werndly DJ, Grealy A, et al (2020)

Rapid range shifts and megafaunal extinctions associated with late Pleistocene climate change.

Nature communications, 11(1):2770 pii:10.1038/s41467-020-16502-3.

Large-scale changes in global climate at the end of the Pleistocene significantly impacted ecosystems across North America. However, the pace and scale of biotic turnover in response to both the Younger Dryas cold period and subsequent Holocene rapid warming have been challenging to assess because of the scarcity of well dated fossil and pollen records that covers this period. Here we present an ancient DNA record from Hall's Cave, Texas, that documents 100 vertebrate and 45 plant taxa from bulk fossils and sediment. We show that local plant and animal diversity dropped markedly during Younger Dryas cooling, but while plant diversity recovered in the early Holocene, animal diversity did not. Instead, five extant and nine extinct large bodied animals disappeared from the region at the end of the Pleistocene. Our findings suggest that climate change affected the local ecosystem in Texas over the Pleistocene-Holocene boundary, but climate change on its own may not explain the disappearance of the megafauna at the end of the Pleistocene.

RevDate: 2020-06-02

Lord E, Collins C, deFrance S, et al (2020)

Ancient DNA of Guinea Pigs (Cavia spp.) Indicates a Probable New Center of Domestication and Pathways of Global Distribution.

Scientific reports, 10(1):8901 pii:10.1038/s41598-020-65784-6.

Guinea pigs (Cavia spp.) have a long association with humans. From as early as 10,000 years ago they were a wild food source. Later, domesticated Cavia porcellus were dispersed well beyond their native range through pre-Columbian exchange networks and, more recently, widely across the globe. Here we present 46 complete mitogenomes of archaeological guinea pigs from sites in Peru, Bolivia, Colombia, the Caribbean, Belgium and the United States to elucidate their evolutionary history, origins and paths of dispersal. Our results indicate an independent centre of domestication of Cavia in the eastern Colombian Highlands. We identify a Peruvian origin for the initial introduction of domesticated guinea pigs (Cavia porcellus) beyond South America into the Caribbean. We also demonstrate that Peru was the probable source of the earliest known guinea pigs transported, as part of the exotic pet trade, to both Europe and the southeastern United States. Finally, we identify a modern reintroduction of guinea pigs to Puerto Rico, where local inhabitants use them for food. This research demonstrates that the natural and cultural history of guinea pigs is more complex than previously known and has implications for other studies regarding regional to global-scale studies of mammal domestication, translocation, and distribution.

RevDate: 2020-05-31

Barquera R, Collen E, Di D, et al (2020)

Binding affinities of 438 HLA proteins to complete proteomes of seven pandemic viruses and distributions of strongest and weakest HLA peptide binders in populations worldwide.

HLA [Epub ahead of print].

We report detailed peptide binding affinities between 438 HLA Class I and Class II proteins and complete proteomes of seven pandemic human viruses, including coronaviruses, influenza viruses and HIV-1. We contrast these affinities with HLA allele frequencies across hundreds of human populations worldwide. Statistical modelling shows that peptide binding affinities classified into four distinct categories depend on the HLA locus but that the type of virus is only a weak predictor, except in the case of HIV-1. Amongst the strong HLA binders (IC50 ≤ 50), we uncovered 16 alleles (the top ones being A*02:02, B*15:03 and DRB1*01:02) binding more than 1% of peptides derived from all viruses, 9 (top ones including HLA-A*68:01, B*15:25, C*03:02 and DRB1*07:01) binding all viruses except HIV-1, and 15 (top ones A*02:01 and C*14:02) only binding coronaviruses. The frequencies of strongest and weakest HLA peptide binders differ significantly among populations from different geographic regions, with Indigenous peoples of America showing both higher frequencies of strongest and lower frequencies of weakest binders. As many HLA proteins are strong binders of peptides from distinct viral families, we discuss this result in relation to possible signatures of natural selection on HLA promiscuous alleles due to undetermined past pathogenic infections. Although highly relevant for evolutionary genetics and the development of vaccine therapies, these results should not lead to forget that individual resistance and vulnerability to diseases go beyond the sole HLA allelic affinity and depend on multiple, complex and often unknown biological, environmental and other variables. This article is protected by copyright. All rights reserved.

RevDate: 2020-05-29

Skourtanioti E, Erdal YS, Frangipane M, et al (2020)

Genomic History of Neolithic to Bronze Age Anatolia, Northern Levant, and Southern Caucasus.

Cell, 181(5):1158-1175.e28.

Here, we report genome-wide data analyses from 110 ancient Near Eastern individuals spanning the Late Neolithic to Late Bronze Age, a period characterized by intense interregional interactions for the Near East. We find that 6th millennium BCE populations of North/Central Anatolia and the Southern Caucasus shared mixed ancestry on a genetic cline that formed during the Neolithic between Western Anatolia and regions in today's Southern Caucasus/Zagros. During the Late Chalcolithic and/or the Early Bronze Age, more than half of the Northern Levantine gene pool was replaced, while in the rest of Anatolia and the Southern Caucasus, we document genetic continuity with only transient gene flow. Additionally, we reveal a genetically distinct individual within the Late Bronze Age Northern Levant. Overall, our study uncovers multiple scales of population dynamics through time, from extensive admixture during the Neolithic period to long-distance mobility within the globalized societies of the Late Bronze Age. VIDEO ABSTRACT.

RevDate: 2020-05-29

Agranat-Tamir L, Waldman S, Martin MAS, et al (2020)

The Genomic History of the Bronze Age Southern Levant.

Cell, 181(5):1146-1157.e11.

We report genome-wide DNA data for 73 individuals from five archaeological sites across the Bronze and Iron Ages Southern Levant. These individuals, who share the "Canaanite" material culture, can be modeled as descending from two sources: (1) earlier local Neolithic populations and (2) populations related to the Chalcolithic Zagros or the Bronze Age Caucasus. The non-local contribution increased over time, as evinced by three outliers who can be modeled as descendants of recent migrants. We show evidence that different "Canaanite" groups genetically resemble each other more than other populations. We find that Levant-related modern populations typically have substantial ancestry coming from populations related to the Chalcolithic Zagros and the Bronze Age Southern Levant. These groups also harbor ancestry from sources we cannot fully model with the available data, highlighting the critical role of post-Bronze-Age migrations into the region over the past 3,000 years.

RevDate: 2020-05-23

Gonzalez A, Cannet C, Zvénigorosky V, et al (2020)

The petrous bone: Ideal substrate in legal medicine?.

Forensic science international. Genetics, 47:102305 pii:S1872-4973(20)30078-8 [Epub ahead of print].

Over the last few years, palaeogenomic studies of the petrous bone (the densest part of the temporal bone) have shown that it is a source of DNA in both larger quantities and of better quality than other bones. This dense bone around the otic capsule has therefore been called the choice substrate in palaeogenomics. Because the practice of forensic genetics responds to different imperatives, we implemented a study aimed at (i) understanding how and why the petrous bone is an advantageous substrate in ancient DNA studies and (ii) establishing whether it is advantageous in forensic STR typing. We selected 50 individual skeletal remains and extracted DNA from one tooth and one petrous bone from each. We then amplified 24 STR markers commonly used in forensic identification and compared the quality of that amplification using the RFU intensities of the signal as read on the STR profiles. We also performed histological analyses to compare (i) the microscopic structure of a petrous bone and of a tooth and (ii) the microscopic structure of fresh petrous bone and of an archaeological or forensic sample. We show that the RFU intensities read on STR profiles are systematically higher in experiments using DNA extracted from petrous bones rather than teeth. For this reason, we were more likely to obtain a complete STR profile from petrous bone material, increasing the chance of identification in a forensic setting. Histological analyses revealed peculiar microstructural characteristics (tissue organization), unique to the petrous bone, that might explain the good preservation of DNA in that substrate. Therefore, it appears that despite the necessity of analysing longer fragments in forensic STR typing compared to NGS palaeogenomics, the use of petrous bones in forensic genetics could prove valuable, especially in cases involving infants, toothless individuals or very degraded skeletal remains.

RevDate: 2020-05-20

Gryseels S, Watts TD, Kabongo Mpolesha JM, et al (2020)

A near full-length HIV-1 genome from 1966 recovered from formalin-fixed paraffin-embedded tissue.

Proceedings of the National Academy of Sciences of the United States of America pii:1913682117 [Epub ahead of print].

With very little direct biological data of HIV-1 from before the 1980s, far-reaching evolutionary and epidemiological inferences regarding the long prediscovery phase of this pandemic are based on extrapolations by phylodynamic models of HIV-1 genomic sequences gathered mostly over recent decades. Here, using a very sensitive multiplex RT-PCR assay, we screened 1,645 formalin-fixed paraffin-embedded tissue specimens collected for pathology diagnostics in Central Africa between 1958 and 1966. We report the near-complete viral genome in one HIV-1 positive specimen from Kinshasa, Democratic Republic of Congo (DRC), from 1966 ("DRC66")-a nonrecombinant sister lineage to subtype C that constitutes the oldest HIV-1 near full-length genome recovered to date. Root-to-tip plots showed the DRC66 sequence is not an outlier as would be expected if dating estimates from more recent genomes were systematically biased; and inclusion of the DRC66 sequence in tip-dated BEAST analyses did not significantly alter root and internal node age estimates based on post-1978 HIV-1 sequences. There was larger variation in divergence time estimates among datasets that were subsamples of the available HIV-1 genomes from 1978 to 2014, showing the inherent phylogenetic stochasticity across subsets of the real HIV-1 diversity. Our phylogenetic analyses date the origin of the pandemic lineage of HIV-1 to a time period around the turn of the 20th century (1881 to 1918). In conclusion, this unique archival HIV-1 sequence provides direct genomic insight into HIV-1 in 1960s DRC, and, as an ancient-DNA calibrator, it validates our understanding of HIV-1 evolutionary history.

RevDate: 2020-05-19

Aoki K (2020)

A three-population wave-of-advance model for the European early Neolithic.

PloS one, 15(5):e0233184 pii:PONE-D-20-01744.

Ancient DNA studies have shown that early farming spread through most of Europe by the range expansion of farmers of Anatolian origin rather than by the conversion to farming of the local hunter-gatherers, and have confirmed that these hunter-gatherers continued to coexist with the incoming farmers. In this short report, I extend a previous three-population wave-of-advance model to accommodate these new findings, and derive the conditions supportive of such a scenario in terms of the relative magnitudes of the parameters. The revised model predicts that the conversion rate must, not surprisingly, be low, but also that the hunter-gatherers must compete more strongly with the converted farmers than with the alien farmers. Moreover, competition with the hunter-gatherers diminishes the speed of the wave-of advance of the farmers. In addition, I briefly consider how the wave-of-advance approach may contribute to interpreting the results of archaeological studies using the summed probability distribution of radiocarbon dates.

RevDate: 2020-05-19

Schweizer RM, RK Wayne (2020)

Illuminating the mysteries of wolf history.

One of the most enduring surprises about the genetic history of Late Pleistocene populations is that continuity is often disturbed by upheaval. In fact, studies that support population continuity are increasingly rare in humans, a variety of vertebrate taxa, and vascular plants (Hofreiter & Stewart 2009; Burbrink et al. 2016). Perhaps such continuity should not be expected as the Pleistocene is marked by episodes of climate change, glaciation and the invasions of humans into previously isolated areas. Although fossils are one of the primary sources for inferring population continuity, a problem with fossil material is that, even if similar morphological forms might exist in a place over time, they may not be from the same genetic lineage. There are now readily available methods to assess genetic continuity solely from DNA found in fossil material, provided the record is fairly continuous. In a From the Cover article in this issue of Molecular Ecology, Loog et al. (2020) apply some of these readily available methods to analyse mitochondrial genomes and model the demography of wolves over the last 50,000 years.

RevDate: 2020-05-18

Peña-Ahumada B, Saldarriaga-Córdoba M, Kardailsky O, et al (2020)

A tale of textiles: Genetic characterization of historical paper mulberry barkcloth from Oceania.

PloS one, 15(5):e0233113 pii:PONE-D-19-31840.

Humans introduced paper mulberry (Broussonetia papyrifera) from Taiwan into the Pacific over 5000 years ago as a fiber source to make barkcloth textiles that were, and still are, important cultural artifacts throughout the Pacific. We have used B. papyrifera, a species closely associated to humans, as a proxy to understand the human settlement of the Pacific Islands. We report the first genetic analysis of paper mulberry textiles from historical and archaeological contexts (200 to 50 years before present) and compare our results with genetic data obtained from contemporary and herbarium paper mulberry samples. Following stringent ancient DNA protocols, we extracted DNA from 13 barkcloth textiles. We confirmed that the fiber source is paper mulberry in nine of the 13 textiles studied using the nuclear ITS-1 marker and by statistical estimates. We detected high genetic diversity in historical Pacific paper mulberry barkcloth with a set of ten microsatellites, showing new alleles and specific genetic patterns. These genetic signatures allow tracing connections to plants from the Asian homeland, Near and Remote Oceania, establishing links not observed previously (using the same genetic tools) in extant plants or herbaria samples. These results show that historic barkcloth textiles are cultural materials amenable to genetic analysis to reveal human history and that these artifacts may harbor evidence of greater genetic diversity in Pacific B. papyrifera in the past.

RevDate: 2020-05-14
CmpDate: 2020-05-14

Raveane A, Aneli S, Montinaro F, et al (2019)

Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe.

Science advances, 5(9):eaaw3492.

European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non-steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.

RevDate: 2020-05-15

Amankwaa AO, Nsiah Amoako E, Mensah Bonsu DO, et al (2019)

Forensic science in Ghana: A review.

Forensic Science International (Online), 1:151-160 pii:S2589-871X(19)30138-X.

The use of forensic science continues to grow across the world. In Ghana, major advancements took off in 2011, including the introduction of modern DNA profiling and the establishment of an automated fingerprint identification system. These developments have led to some positive impacts on the delivery of justice, including the exoneration of a wrongly incarcerated individual. However, a review of the policy-related aspects of forensic science shows gaps in legislation, governance, service provision, quality assurance and accreditation, education and research. An important recommendation to improve forensic science in Ghana is the creation of a "national policy strategy", a blueprint informed by relevant stakeholders, best practice from other countries and the status of the field. Resolutions to the policy issues identified in this review will ensure a more robust application of forensic science in delivering safe justice and enhancing public security.

RevDate: 2020-05-15

Yang MA, Fan X, Sun B, et al (2020)

Ancient DNA indicates human population shifts and admixture in northern and southern China.

Science (New York, N.Y.) pii:science.aba0909 [Epub ahead of print].

Human genetic history in East Asia is poorly understood. To clarify population relationships, we obtained genome wide data from 26 ancient individuals from northern and southern East Asia spanning 9,500-300 years ago. Genetic differentiation was higher in the past than the present, reflecting a major episode of admixture involving northern East Asian ancestry spreading across southern East Asia after the Neolithic, transforming the genetic ancestry of southern China. Mainland southern East Asian and Taiwan Strait island samples from the Neolithic show clear connections with modern and ancient samples with Austronesian-related ancestry, supporting a southern China origin for proto-Austronesians. Connections among Neolithic coastal groups from Siberia and Japan to Vietnam indicate that migration and gene flow played an important role in the prehistory of coastal Asia.

RevDate: 2020-05-14

Li J, Cai D, Zhang Y, et al (2020)

Ancient DNA reveals two paternal lineages C2a1a1b1a/F3830 and C2b1b/F845 in past nomadic peoples distributed on the Mongolian Plateau.

American journal of physical anthropology [Epub ahead of print].

OBJECTIVES: Since the third century CE, a series of nomadic tribes have been active on the eastern part of the Mongolian Plateau. Characterizing the genetic compositions of past nomadic people is significant for research on the nomadic cultures of the Eurasian Steppe region. Ancient DNA analysis facilitates a deeper understanding of the relationship between historical and modern nomadic populations.

MATERIALS AND METHODS: Whole-genome shotgun sequencing and capture sequencing of the nonrecombining region of the Y chromosome were performed for six ancient Hg C2/M217 individuals. The individuals were interred at six separate sites on the Mongolian Plateau and represent dates spanning the late Neolithic to Yuan Dynasty (~3,500-700 BP).

RESULTS: After NRY capture sequencing, three of the six ancient samples were attributed to C2b1b/F845 and the other three ancient samples belonged to C2a1a1b1a/F3830. Analysis of whole-genome shotgun sequencing data shows that the ancient C2b1b/F845 individuals are closely related to She, Han and other East Asian populations, while the ancient C2a1a1b1a/F3830 individuals are more similar to modern Northeast Asian peoples, such as the Ulchi and Yakut.

DISCUSSION: Hg C2/M217, widely distributed in the eastern part of the Eurasian continent, was discovered in the ancient Central Steppe and Baikal region. This study shows that there were two important subclades of Hg C2/M217 among the ancient nomadic peoples: C2a1a1b1a/F3830, which has made important genetic contributions to modern Mongolic- and Manchu-speaking populations, and C2b1b/F845, which probably originated in the farming populations of southern East Asia and made certain genetic contributions to past nomadic peoples on the Mongolian Plateau.

RevDate: 2020-05-14

Samida S (2020)

[About Media Presence and Prominence of DNA-Supported Research of the Past].

NTM pii:10.1007/s00048-020-00249-5 [Epub ahead of print].

In recent years molecular genetics has provided a completely new approach/access to the human past. The still new and quite dynamic research field of archaeogenetics (also known as palaeogenetics or genetic history) claims to be able to write history using ancient DNA. Through numerous remarkable publications it has generated and received much interest not only in scientific discourse but also in the media. So far, however, scientists have not paid much attention to this coverage-a research desideratum this paper cannot resolve. But by looking at selected press clippings it seeks to capture first trends according to the following three theses: telling success stories, drawing boundaries, and writing in a conformist manner.

RevDate: 2020-05-14

Charlton S, Booth T, I Barnes (2019)

The problem with petrous? A consideration of the potential biases in the utilization of pars petrosa for ancient DNA analysis.

World archaeology, 51(4):574-585 pii:1694062.

Advances in NGS sequencing technologies, improved laboratory protocols and new bioinformatic workflows have seen huge increases in ancient DNA (aDNA) research on archaeological materials. A large proportion of aDNA work now utilizes the petrous portion of the temporal bone (pars petrosa), which is recognized as an excellent skeletal element for long-term ancient endogenous (host) DNA survival. This has been significant due to the often low endogenous content of other skeletal elements, meaning that large amounts of sequencing are frequently required to obtain sufficient genetic coverage. However, exclusive sampling of the petrous for aDNA analysis introduces a new set of potential biases into our scientific studies - and these issues are yet to be considered by ancient DNA researchers. This paper aims to outline the possible biases of utilizing petrous bones to undertake aDNA analyses and highlight how these complications may potentially be overcome in future research.

RevDate: 2020-05-11

Carr SM (2020)

Evidence for the persistence of ancient Beothuk and Maritime Archaic mitochondrial DNA genome lineages among modern Native American peoples.

Genome [Epub ahead of print].

The Beothuk were a Native American people who formerly occupied the island of Newfoundland, and who are generally accepted to have become culturally extinct in 1829. The Beothuk succeeded the Maritime Archaic people on the island after a hiatus of ca. 1.4 ka, and were themselves succeeded by the extant Mi'kmaq within historic times. Genetic continuity between ancient and modern Native Americans remains of interest. Complete aDNA mitogenomes from ancient Beothuk and Maritime Archaic were compared with the most closely related modern mitogenomes as obtained by BLAST search of GenBank. Beothuk mitogenomes in five clades are in one case identical to and otherwise differ by minima of three to eight SNPs from the most closely related modern mitogenomes. Maritime Archaic mitogenomes in 12 clades are in one case identical to and otherwise differ by minima of one to nine SNPs from the most similar modern mitogenomes. The single available modern Mi'kmaq mitogenome differs from the most similar Beothuk and Maritime Archaic mitogenomes by 12 and 22 SNPs, respectively. Phylogenetic analysis and sequence similarities imply lineage extinction of most ancient clades, as well as continuity of two Beothuk and at least one Maritime Archaic lineages in modern Native Americans and their descendants.

RevDate: 2020-05-12

Rees JS, Castellano S, AM Andrés (2020)

The Genomics of Human Local Adaptation.

Trends in genetics : TIG, 36(6):415-428.

Modern humans inhabit a variety of environments and are exposed to a plethora of selective pressures, leading to multiple genetic adaptations to local environmental conditions. These include adaptations to climate, UV exposure, disease, diet, altitude, or cultural practice and have generated important genetic and phenotypic differences amongst populations. In recent years, new methods to identify the genomic signatures of natural selection underlying these adaptations, combined with novel types of genetic data (e.g., ancient DNA), have provided unprecedented insights into the origin of adaptive alleles and the modes of adaptation. As a result, numerous instances of local adaptation have been identified in humans. Here, we review the most exciting recent developments and discuss, in our view, the future of this field.

RevDate: 2020-05-12

Fewlass H, Mitchell PJ, Casanova E, et al (2020)

Chemical evidence of dairying by hunter-gatherers in highland Lesotho in the late first millennium AD.

Nature human behaviour pii:10.1038/s41562-020-0859-0 [Epub ahead of print].

The recovery of Early Iron Age artefacts and domestic animal remains from hunter-gatherer contexts at Likoaeng, Lesotho, has been argued to indicate contact between highland hunter-gatherers and Early Iron Age agropastoralist communities settled in lowland areas of southeastern Africa during the second half of the first millennium AD. However, disagreement between archaeozoological studies and ancient DNA means that the possibility that those hunter-gatherers kept livestock themselves remains controversial. Here we report analyses of pottery-absorbed organic residues from two hunter-gatherer sites and one agriculturalist site in highland Lesotho to reconstruct prehistoric subsistence practices. Our results demonstrate the exploitation of secondary products from domestic livestock by hunter-gatherers in Lesotho, directly dated to the seventh century AD at Likoaeng and the tenth century AD at the nearby site of Sehonghong. The data provide compelling evidence for the keeping of livestock by hunter-gatherer groups and their probable incorporation as ancillary resources into their subsistence strategies.

RevDate: 2020-05-11

Ahmed AE, Mpangase PT, Panji S, et al (2018)

Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience.

AAS open research, 1:9.

The need for portable and reproducible genomics analysis pipelines is growing globally as well as in Africa, especially with the growth of collaborative projects like the Human Health and Heredity in Africa Consortium (H3Africa). The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized the need for portable, reproducible pipelines adapted to heterogeneous computing environments, and for the nurturing of technical expertise in workflow languages and containerization technologies. Building on the network's Standard Operating Procedures (SOPs) for common genomic analyses, H3ABioNet arranged its first Cloud Computing and Reproducible Workflows Hackathon in 2016, with the purpose of translating those SOPs into analysis pipelines able to run on heterogeneous computing environments and meeting the needs of H3Africa research projects. This paper describes the preparations for this hackathon and reflects upon the lessons learned about its impact on building the technical and scientific expertise of African researchers. The workflows developed were made publicly available in GitHub repositories and deposited as container images on Quay.io.

RevDate: 2020-05-10

Nakatsuka N, Lazaridis I, Barbieri C, et al (2020)

A Paleogenomic Reconstruction of the Deep Population History of the Andes.

Cell pii:S0092-8674(20)30477-3 [Epub ahead of print].

There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today's genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000-500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin. VIDEO ABSTRACT.

RevDate: 2020-03-09
CmpDate: 2020-02-14

Sikora M, Pitulko VV, Sousa VC, et al (2019)

The population history of northeastern Siberia since the Pleistocene.

Nature, 570(7760):182-188.

Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of 'Ancient North Siberians' who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to 'Ancient Palaeo-Siberians' who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name 'Neo-Siberians', and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.

RevDate: 2020-05-08

Bonsu DOM, Higgins D, JJ Austin (2020)

Forensic touch DNA recovery from metal surfaces - A review.

Science & justice : journal of the Forensic Science Society, 60(3):206-215.

Trace evidence such as touch (also known as contact) DNA has probative value as a vital forensic investigative tool that can lead to the identification and apprehension of a criminal. While the volume of touch DNA evidence items submitted to forensic laboratories has significantly increased, recovery and amplification of DNA from these items, especially from metal surfaces, remains challenging. Currently little is understood with regards to the underlying mechanisms of metal-DNA interactions in the context of forensic science and how this may impact on DNA recovery. An increased understanding of these mechanisms would allow optimisation of methods to improve outcomes when sampling these materials. This paper reviews the basis of DNA binding to metal substrates, the merits and limitations of current methods and future perspectives of improving recovery and amplification of touch DNA from metal surfaces of forensic interest.

RevDate: 2020-05-07

Rifkin RF, Vikram S, Ramond JB, et al (2020)

Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the 'ancestral' sub-Saharan African intestinal microbiome.

Microbiome, 8(1):62 pii:10.1186/s40168-020-00832-x.

BACKGROUND: The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen.

METHODS: Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. The extraction of ancient DNA from the specimen and its subsequent shotgun metagenomic sequencing facilitated the taxonomic and metabolic characterisation of this ancient human IM.

RESULTS: Our results indicate that the distal IM of the Neolithic 'Middle Iron Age' (c. AD 1460) Bantu-speaking individual exhibits features indicative of a largely mixed forager-agro-pastoralist diet. Subsequent comparison with the IMs of the Tyrolean Iceman (Ötzi) and contemporary Hadza hunter-gatherers, Malawian agro-pastoralists and Italians reveals that this IM precedes recent adaptation to 'Western' diets, including the consumption of coffee, tea, chocolate, citrus and soy, and the use of antibiotics, analgesics and also exposure to various toxic environmental pollutants.

CONCLUSIONS: Our analyses reveal some of the causes and means by which current human IMs are likely to have responded to recent dietary changes, prescription medications and environmental pollutants, providing rare insight into human IM evolution following the advent of the Neolithic c. 12,000 years ago. Video Abtract.

RevDate: 2020-05-07
CmpDate: 2020-05-07

Velsko IM, Fellows Yates JA, Aron F, et al (2019)

Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage.

Microbiome, 7(1):102.

BACKGROUND: Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses. Dental calculus does not typically accumulate as much today as historically, and clinical oral microbiome research studies focus primarily on living dental plaque biofilm. However, plaque and calculus reflect different conditions of the oral biofilm, and the differences in microbial characteristics between the sample types have not yet been systematically explored. Here, we compare the microbial profiles of modern dental plaque, modern dental calculus, and historic dental calculus to establish expected differences between these substrates.

RESULTS: Metagenomic data was generated from modern and historic calculus samples, and dental plaque metagenomic data was downloaded from the Human Microbiome Project. Microbial composition and functional profile were assessed. Metaproteomic data was obtained from a subset of historic calculus samples. Comparisons between microbial, protein, and metabolomic profiles revealed distinct taxonomic and metabolic functional profiles between plaque, modern calculus, and historic calculus, but not between calculus collected from healthy teeth and periodontal disease-affected teeth. Species co-exclusion was related to biofilm environment. Proteomic profiling revealed that healthy tooth samples contain low levels of bacterial virulence proteins and a robust innate immune response. Correlations between proteomic and metabolomic profiles suggest co-preservation of bacterial lipid membranes and membrane-associated proteins.

CONCLUSIONS: Overall, we find that there are systematic microbial differences between plaque and calculus related to biofilm physiology, and recognizing these differences is important for accurate data interpretation in studies comparing dental plaque and calculus.

RevDate: 2020-05-05

Liu X (2020)

Human prehistoric demography revealed by the polymorphic pattern of CpG transitions.

Molecular biology and evolution pii:5830537 [Epub ahead of print].

The prehistoric demography of human populations is an essential piece of information for illustrating our evolution. Despite its importance and the advancement of ancient DNA studies, our knowledge of human evolution is still limited, which is also the case for relatively recent population dynamics during and around the Holocene. Here, we inferred detailed demographic histories from 1 to 40 thousand years ago (kya) for 24 population samples using an improved model-flexible method with 36 million genome-wide non-coding CpG sites. Our results showed many population growth events that were likely due to the Neolithic Revolution (i.e., the shift from hunting and gathering to agriculture and settlement). Our results help to provide a clearer picture of human prehistoric demography, confirming the significant impact of agriculture on population expansion, and provide new hypotheses and directions for future research.

RevDate: 2020-05-03

Barquera R, Lamnidis TC, Lankapalli AK, et al (2020)

Origin and Health Status of First-Generation Africans from Early Colonial Mexico.

Current biology : CB pii:S0960-9822(20)30482-6 [Epub ahead of print].

The forced relocation of several thousand Africans during Mexico's historic period has so far been documented mostly through archival sources, which provide only sparse detail on their origins and lived experience. Here, we employ a bioarchaeological approach to explore the life history of three 16th century Africans from a mass burial at the San José de los Naturales Royal Hospital in Mexico City. Our approach draws together ancient genomic data, osteological analysis, strontium isotope data from tooth enamel, δ13C and δ15N isotope data from dentine, and ethnohistorical information to reveal unprecedented detail on their origins and health. Analyses of skeletal features, radiogenic isotopes, and genetic data from uniparental, genome-wide, and human leukocyte antigen (HLA) markers are consistent with a Sub-Saharan African origin for all three individuals. Complete genomes of Treponema pallidum sub. pertenue (causative agent of yaws) and hepatitis B virus (HBV) recovered from these individuals provide insight into their health as related to infectious disease. Phylogenetic analysis of both pathogens reveals their close relationship to strains circulating in current West African populations, lending support to their origins in this region. The further relationship between the treponemal genome retrieved and a treponemal genome previously typed in an individual from Colonial Mexico highlights the role of the transatlantic slave trade in the introduction and dissemination of pathogens into the New World. Putting together all lines of evidence, we were able to create a biological portrait of three individuals whose life stories have long been silenced by disreputable historical events.

RevDate: 2020-05-04

Mathieson I, Abascal F, Vinner L, et al (2020)

An Ancient Baboon Genome Demonstrates Long-Term Population Continuity in Southern Africa.

Genome biology and evolution, 12(4):407-412.

Baboons are one of the most abundant large nonhuman primates and are widely studied in biomedical, behavioral, and anthropological research. Despite this, our knowledge of their evolutionary and demographic history remains incomplete. Here, we report a 0.9-fold coverage genome sequence from a 5800-year-old baboon from the site of Ha Makotoko in Lesotho. The ancient baboon is closely related to present-day Papio ursinus individuals from southern Africa-indicating a high degree of continuity in the southern African baboon population. This level of population continuity is rare in recent human populations but may provide a good model for the evolution of Homo and other large primates over similar timespans in structured populations throughout Africa.

RevDate: 2020-05-01

Pierini F, Nutsua M, Böhme L, et al (2020)

Targeted analysis of polymorphic loci from low-coverage shotgun sequence data allows accurate genotyping of HLA genes in historical human populations.

Scientific reports, 10(1):7339 pii:10.1038/s41598-020-64312-w.

The highly polymorphic human leukocyte antigen (HLA) plays a crucial role in adaptive immunity and is associated with various complex diseases. Accurate analysis of HLA genes using ancient DNA (aDNA) data is crucial for understanding their role in human adaptation to pathogens. Here, we describe the TARGT pipeline for targeted analysis of polymorphic loci from low-coverage shotgun sequence data. The pipeline was successfully applied to medieval aDNA samples and validated using both simulated aDNA and modern empirical sequence data from the 1000 Genomes Project. Thus the TARGT pipeline enables accurate analysis of HLA polymorphisms in historical (and modern) human populations.

RevDate: 2020-04-28

Guiry E, Royle TCA, Matson RG, et al (2020)

Differentiating salmonid migratory ecotypes through stable isotope analysis of collagen: Archaeological and ecological applications.

PloS one, 15(4):e0232180 pii:PONE-D-20-03408.

The ability to distinguish between different migratory behaviours (e.g., anadromy and potamodromy) in fish can provide important insights into the ecology, evolution, and conservation of many aquatic species. We present a simple stable carbon isotope (δ13C) approach for distinguishing between sockeye (anadromous ocean migrants) and kokanee (potamodromous freshwater residents), two migratory ecotypes of Oncorhynchus nerka (Salmonidae) that is applicable throughout most of their range across coastal regions of the North Pacific Ocean. Analyses of kokanee (n = 239) and sockeye (n = 417) from 87 sites spanning the North Pacific (Russia to California) show that anadromous and potamodromous ecotypes are broadly distinguishable on the basis of the δ13C values of their scale and bone collagen. We present three case studies demonstrating how this approach can address questions in archaeology, archival, and conservation research. Relative to conventional methods for determining migratory status, which typically apply chemical analyses to otoliths or involve genetic analyses of tissues, the δ13C approach outlined here has the benefit of being non-lethal (when applied to scales), cost-effective, widely available commercially, and should be much more broadly accessible for addressing archaeological questions since the recovery of otoliths at archaeological sites is rare.

RevDate: 2020-04-27
CmpDate: 2020-04-27

Gibbons A (2020)

Strange bedfellows for human ancestors.

Science (New York, N.Y.), 367(6480):838-839.

RevDate: 2020-04-23

Cai Y, Fu W, Cai D, et al (2020)

Ancient genomes reveal the evolutionary history and origin of cashmere producing goats in China.

Molecular biology and evolution pii:5824306 [Epub ahead of print].

Goats are one of the most widespread farmed animals across the world; however, their migration route to East Asia and local evolutionary history remain poorly understood. Here, we sequenced 27 ancient Chinese goat genomes dating from the Late Neolithic period to the Iron Age. We found close genetic affinities between ancient and modern Chinese goats, demonstrating their genetic continuity. We found that Chinese goats originated from the eastern regions around the Fertile Crescent, and we estimated that the ancestors of Chinese goats diverged from this population in the Chalcolithic period. Modern Chinese goats were divided into a northern and a southern group, coinciding with the most prominent climatic division in China, and two genes related to hair follicle development, FGF5 and EDA2R, were highly divergent between these populations. We identified a likely causal de novo deletion near FGF5 in northern Chinese goats that increased to high frequency over time, whereas EDA2R harbored standing variation dating to the Neolithic. Our findings add to our understanding of the genetic composition and local evolutionary process of Chinese goats.

RevDate: 2020-04-23

Ferrando-Bernal M, Morcillo-Suarez C, de-Dios T, et al (2020)

Mapping co-ancestry connections between the genome of a Medieval individual and modern Europeans.

Scientific reports, 10(1):6843 pii:10.1038/s41598-020-64007-2.

Historical genetic links among similar populations can be difficult to establish. Identity by descent (IBD) analyses find genomic blocks that represent direct genealogical relationships among individuals. However, this method has rarely been applied to ancient genomes because IBD stretches are progressively fragmented by recombination and thus not recognizable after few tens of generations. To explore such genealogical relationships, we estimated long IBD blocks among modern Europeans, generating networks to uncover the genetic structures. We found that Basques, Sardinians, Icelanders and Orcadians form, each of them, highly intraconnected sub-clusters in a European network, indicating dense genealogical links within small, isolated populations. We also exposed individual genealogical links -such as the connection between one Basque and one Icelandic individual- that cannot be uncovered with other, widely used population genetics methods such as PCA or ADMIXTURE. Moreover, using ancient DNA technology we sequenced a Late Medieval individual (Barcelona, Spain) to high genomic coverage and identified IBD blocks shared between her and modern Europeans. The Medieval IBD blocks are statistically overrepresented only in modern Spaniards, which is the geographically closest population. This approach can be used to produce a fine-scale reflection of shared ancestry across different populations of the world, offering a direct genetic link from the past to the present.

RevDate: 2020-04-22

Zvénigorosky V, Sabbagh A, Gonzalez A, et al (2020)

The limitations of kinship determinations using STR data in ill-defined populations.

International journal of legal medicine pii:10.1007/s00414-020-02298-w [Epub ahead of print].

The likelihood ratio (LR) method is commonly used to determine kinship in civil, criminal, or forensic cases. For the past 15 years, our research group has also applied LR to ancient STR data and obtained kinship results for collections of graves or necropolises. Although we were able to reconstruct large genealogies, some pairs of individuals showed ambiguous results. Second-degree relationships, half-sibling pairs for example, were often inconsistent with detected first-degree relationships, such as parent/child or brother/sister pairs. We therefore set about providing empirical estimations of the error rates for the LR method in living populations with STR allelic diversities comparable to that of the ancient populations we had previously studied. We collected biological samples in the field in North-Eastern Siberia and West Africa and studied more than 800 pairs of STR profiles from individuals with known relationships. Because commercial STR panels were constructed for specific regions (namely Europe and North America), their allelic makeup showed a significant deficit in diversity when compared to European populations, replicating a situation often faced in ancient DNA studies. We assessed the capacity of the LR method to confirm known relationships (effectiveness) and its capacity to detect those relationships (reliability). Concerns over the effectiveness of LR determinations are mostly an issue in forensic studies, while the reliability of the detection of kinship is an issue for the study of necropolises or other large gatherings of unidentified individuals, such as disaster victims or mass graves. We show that the application of LR to both test populations highlights specific issues (both false positives and false negatives) that prevent the confirmation of second-degree kinship or even full siblingship in small populations. Up to 29% of detected full sibling relationships were either overestimated half-sibling relationships or underestimated parent-offspring relationships. The error rate for detected half-sibling relationships was even higher, reaching 41%. Only parent-offspring pairs were reliably detected or confirmed. This implies that, in populations that are small, ill-defined, or for which the STR loci analyzed are inappropriate, an examiner might not be able to distinguish a pair of full siblings from a pair of half-siblings. Furthermore, half-sibling pairs might be overlooked altogether, an issue that is exacerbated by the common confusion, in many languages and cultures, between half-siblings and full siblings. Consequently, in the study of ancient populations, human remains of unknown origins, or poorly surveyed modern populations, we recommend a conservative approach to kinship determined by LR. Next-generation sequencing data should be used when possible, but the costs and technology involved might be prohibitive. Therefore, in potentially contentious situations or cases lacking sufficient external information, uniparental markers should be analyzed: ideally, complete mitochondrial genomes and Y-chromosome haplotypes (STR, SNP, and/or sequencing).

RevDate: 2020-04-21

Dehasque M, Ávila-Arcos MC, Díez-Del-Molino D, et al (2020)

Inference of natural selection from ancient DNA.

Evolution letters, 4(2):94-108 pii:EVL3165.

Evolutionary processes, including selection, can be indirectly inferred based on patterns of genomic variation among contemporary populations or species. However, this often requires unrealistic assumptions of ancestral demography and selective regimes. Sequencing ancient DNA from temporally spaced samples can inform about past selection processes, as time series data allow direct quantification of population parameters collected before, during, and after genetic changes driven by selection. In this Comment and Opinion, we advocate for the inclusion of temporal sampling and the generation of paleogenomic datasets in evolutionary biology, and highlight some of the recent advances that have yet to be broadly applied by evolutionary biologists. In doing so, we consider the expected signatures of balancing, purifying, and positive selection in time series data, and detail how this can advance our understanding of the chronology and tempo of genomic change driven by selection. However, we also recognize the limitations of such data, which can suffer from postmortem damage, fragmentation, low coverage, and typically low sample size. We therefore highlight the many assumptions and considerations associated with analyzing paleogenomic data and the assumptions associated with analytical methods.

RevDate: 2020-04-19

Lang PLM, Weiß CL, Kersten S, et al (2020)

Hybridization ddRAD-sequencing for population genomics of non-model plants using highly degraded historical specimen DNA.

Molecular ecology resources [Epub ahead of print].

Species' responses at the genetic level are key to understanding the long-term consequences of anthropogenic global change. Herbaria document such responses, and, with contemporary sampling, provide high-resolution time-series of plant evolutionary change. Characterizing genetic diversity is straightforward for model species with small genomes and a reference sequence. For non-model species - with small or large genomes - diversity is traditionally assessed using restriction-enzyme based sequencing. However, age-related DNA damage and fragmentation preclude the use of this approach for ancient herbarium DNA. Here, we combine reduced representation sequencing and hybridization-capture to overcome this challenge and efficiently compare contemporary and historical specimens. Specifically, we describe how homemade DNA baits can be produced from reduced representation libraries of fresh samples, and used to efficiently enrich historical libraries for the same fraction of the genome to produce compatible sets of sequence data from both types of material. Applying this approach to both Arabidopsis thaliana and the non-model plant Cardamine bulbifera, we discovered polymorphisms de novo in an unbiased, reference-free manner. We show that the recovered genetic variation recapitulates known genetic diversity in A. thaliana, and recovers geographic origin in both species and over time, independent of bait diversity. Hence, our method enables fast, cost-efficient, large-scale integration of contemporary and historical specimens for assessment of genome-wide genetic trends over time, independent of genome size and presence of a reference genome.

RevDate: 2020-04-18

Zhang X, Li C, Zhou Y, et al (2020)

A Matrilineal Genetic Perspective of Hanging Coffin Custom in Southern China and Northern Thailand.

iScience, 23(4):101032 pii:S2589-0042(20)30216-9 [Epub ahead of print].

Hanging Coffin is a unique and ancient burial custom that has been practiced in southern China, Southeast Asia, and near Oceania regions for more than 3,000 years. Here, we conducted mitochondrial whole-genome analyses of 41 human remains sampled from 13 Hanging Coffin sites in southern China and northern Thailand, which were dated between ∼2,500 and 660 years before present. We found that there were genetic connections between the Hanging Coffin people living in different geographic regions. Notably, the matrilineal genetic diversity of the Hanging Coffin people from southern China is much higher than those from northern Thailand, consistent with the hypothesized single origin of the Hanging Coffin custom in southern China about 3,600 years ago, followed by its dispersal in southern China through demic diffusion, whereas the major dispersal pattern in Southeast Asia is cultural assimilation in the past 2,000 years.

RevDate: 2020-04-16

Sanchez-Mazas A (2020)

A review of HLA allele and SNP associations with highly prevalent infectious diseases in human populations.

Swiss medical weekly, 150:w20214 pii:Swiss Med Wkly. 2020;150:w20214.

Human leucocyte antigen (HLA) alleles and single nucleotide polymorphisms (SNPs) lying in the HLA region are known to be associated with several infectious diseases among which acquired immunodeficiency syndrome, hepatitis B, hepatitis C, tuberculosis, leprosy and malaria are highly prevalent in many human populations worldwide. Distinct approaches such as case-control comparisons, immunogenetic analyses, bioinformatic peptide-binding predictions, ancient DNA and genome-wide association studies (GWAS) have contributed to improving this knowledge during the last decade, although many results still need stronger statistical and/or functional support. The present review updates the information regarding the main HLA allele and SNP associations observed to date for six of the most widespread and some other infectious diseases, and provides a synthetic illustration of these findings on a schematic HLA genomic map. It then discusses these results by stressing the importance of integrating information on HLA population diversity in disease-association studies.

RevDate: 2020-04-16

Juras A, Makarowicz P, Chyleński M, et al (2020)

Mitochondrial genomes from Bronze Age Poland reveal genetic continuity from the Late Neolithic and additional genetic affinities with the steppe populations.

American journal of physical anthropology [Epub ahead of print].

OBJECTIVE: In this work we aim to investigate the origins and genetic affinities of Bronze Age populations (2,400-1,100 BC) from the region of southern Poland and to trace maternal kinship patterns present in the burials of those populations by the use of complete mitochondrial genomes.

MATERIALS AND METHODS: We performed ancient DNA analyses for Bronze Age individuals from present-day Poland associated with the Strzyżow culture, the Mierzanowice culture, and the Trzciniec Cultural circle. To obtain complete mitochondrial genomes, we sequenced genomic libraries using Illumina platform. Additionally, hybridization capture was used to enrich some of the samples for mitochondrial DNA. AMS 14 C-dating was conducted for 51 individuals to verify chronological and cultural attribution of the analyzed samples.

RESULTS: Complete ancient mitochondrial genomes were generated for 80 of the Bronze Age individuals from present-day Poland. The results of the population genetic analyses indicate close maternal genetic affinity between Mierzanowice, Trzciniec, and Corded Ware culture-associated populations. This is in contrast to the genetically more distant Strzyżów people that displayed closer maternal genetic relation to steppe populations associated with the preceding Yamnaya culture and Catacomb culture, and with later Scythians. Potential maternal kinship relations were identified in burials of Mierzanowice and Trzciniec populations analyzed in this study.

DISCUSSION: Results revealed genetic continuity from the Late Neolithic Corded Ware groups to Bronze Age Mierzanowice and Trzciniec-associated populations, and possible additional genetic contribution from the steppe to the formation of the Strzyżów-associated group at the end of 3rd millennium BC. Mitochondrial patterns indicated several pairs of potentially maternally related individuals mostly in Trzciniec-associated group.

RevDate: 2020-04-11

Armbrecht L, Herrando-Pérez S, Eisenhofer R, et al (2020)

An optimized method for the extraction of ancient eukaryote DNA from marine sediments.

Molecular ecology resources [Epub ahead of print].

Marine sedimentary ancient DNA (sedaDNA) provides a powerful means to reconstruct marine palaeo-communities across the food web. However, currently there are few optimized sedaDNA extraction protocols available to maximize the yield of small DNA fragments typical of ancient DNA (aDNA) across a broad diversity of eukaryotes. We compared seven combinations of sedaDNA extraction treatments and sequencing library preparations using marine sediments collected at a water depth of 104 m off Maria Island, Tasmania, in 2018. These seven methods contrasted frozen versus refrigerated sediment, bead-beating induced cell lysis versus ethylenediaminetetraacetic acid (EDTA) incubation, DNA binding in silica spin columns versus in silica-solution, diluted versus undiluted DNA in shotgun library preparations to test potential inhibition issues during amplification steps, and size-selection of low molecular-weight (LMW) DNA to increase the extraction efficiency of sedaDNA. Maximum efficiency was obtained from frozen sediments subjected to a combination of EDTA incubation and bead-beating, DNA binding in silica-solution, and undiluted DNA in shotgun libraries, across 45 marine eukaryotic taxa. We present an optimized extraction protocol integrating these steps, with an optional post-library LMW size-selection step to retain DNA fragments of ≤500 base pairs. We also describe a stringent bioinformatic filtering approach for metagenomic data and provide a comprehensive list of contaminants as a reference for future sedaDNA studies. The new extraction and data-processing protocol should improve quantitative paleo-monitoring of eukaryotes from marine sediments, as well as other studies relying on the detection of highly fragmented and degraded eukaryote DNA in sediments.

RevDate: 2020-04-09

Barbato M, Reichel MP, Passamonti M, et al (2020)

A genetically unique Chinese cattle population shows evidence of common ancestry with wild species when analysed with a reduced ascertainment bias SNP panel.

PloS one, 15(4):e0231162 pii:PONE-D-19-33024.

In Hong Kong, there is a cattle population of ~1,200 individuals of uncertain origin and genetic diversity. This population shows heterogeneous morphology, both in body type and pigmentation. Once used as draught animals by the local farmers, they were abandoned around the 1970s due to changes in the economy, and since then have lived as feral populations. To explore the origins of these cattle, we analysed ~50k genotype data of 21 Hong Kong feral cattle, along with data from 703 individuals of 36 cattle populations of European, African taurine, and Asian origin, the wild x domestic hybrid gayal, plus two wild bovine species, gaur and banteng. To reduce the effect of ascertainment bias ~4k loci that are polymorphic in the two wild species were selected for further analysis. The stringent SNP selection we applied resulted in increased heterozygosity across all populations studies, compared with the full panel of SNP, thus reducing the impact of ascertainment bias and facilitating the comparison of divergent breeds of cattle. Our results showed that Hong Kong feral cattle have relatively high levels of genetic distinctiveness, possibly due to the low level of artificial selection, and a likely common ancestry with wild species. We found signs of a putative taurine introgression, probably dating to the import of north European breeds during the British colonialism of Hong Kong. We showed that Hong Kong feral cattle, are distinct from Bos taurus and Bos indicus breeds. Our results highlight the distinctiveness of Hong Kong feral cattle and stress the conservation value of this indigenous breed that is likely to harbour adaptive genetic variation, which is a fundamental livestock resource in the face of climate change and diversifying market demands.

RevDate: 2020-04-09

Welker F, Ramos-Madrigal J, Gutenbrunner P, et al (2020)

The dental proteome of Homo antecessor.

Nature, 580(7802):235-238.

The phylogenetic relationships between hominins of the Early Pleistocene epoch in Eurasia, such as Homo antecessor, and hominins that appear later in the fossil record during the Middle Pleistocene epoch, such as Homo sapiens, are highly debated1-5. For the oldest remains, the molecular study of these relationships is hindered by the degradation of ancient DNA. However, recent research has demonstrated that the analysis of ancient proteins can address this challenge6-8. Here we present the dental enamel proteomes of H. antecessor from Atapuerca (Spain)9,10 and Homo erectus from Dmanisi (Georgia)1, two key fossil assemblages that have a central role in models of Pleistocene hominin morphology, dispersal and divergence. We provide evidence that H. antecessor is a close sister lineage to subsequent Middle and Late Pleistocene hominins, including modern humans, Neanderthals and Denisovans. This placement implies that the modern-like face of H. antecessor-that is, similar to that of modern humans-may have a considerably deep ancestry in the genus Homo, and that the cranial morphology of Neanderthals represents a derived form. By recovering AMELY-specific peptide sequences, we also conclude that the H. antecessor molar fragment from Atapuerca that we analysed belonged to a male individual. Finally, these H. antecessor and H. erectus fossils preserve evidence of enamel proteome phosphorylation and proteolytic digestion that occurred in vivo during tooth formation. Our results provide important insights into the evolutionary relationships between H. antecessor and other hominin groups, and pave the way for future studies using enamel proteomes to investigate hominin biology across the existence of the genus Homo.

RevDate: 2020-04-08

Frantz LAF, Bradley DG, Larson G, et al (2020)

Animal domestication in the era of ancient genomics.

Nature reviews. Genetics pii:10.1038/s41576-020-0225-0 [Epub ahead of print].

The domestication of animals led to a major shift in human subsistence patterns, from a hunter-gatherer to a sedentary agricultural lifestyle, which ultimately resulted in the development of complex societies. Over the past 15,000 years, the phenotype and genotype of multiple animal species, such as dogs, pigs, sheep, goats, cattle and horses, have been substantially altered during their adaptation to the human niche. Recent methodological innovations, such as improved ancient DNA extraction methods and next-generation sequencing, have enabled the sequencing of whole ancient genomes. These genomes have helped reconstruct the process by which animals entered into domestic relationships with humans and were subjected to novel selection pressures. Here, we discuss and update key concepts in animal domestication in light of recent contributions from ancient genomics.

RevDate: 2020-04-08
CmpDate: 2020-04-08

Mittnik A, Massy K, Knipper C, et al (2019)

Kinship-based social inequality in Bronze Age Europe.

Science (New York, N.Y.), 366(6466):731-734.

Revealing and understanding the mechanisms behind social inequality in prehistoric societies is a major challenge. By combining genome-wide data, isotopic evidence, and anthropological and archaeological data, we have gone beyond the dominating supraregional approaches in archaeogenetics to shed light on the complexity of social status, inheritance rules, and mobility during the Bronze Age. We applied a deep microregional approach and analyzed genome-wide data of 104 human individuals deriving from farmstead-related cemeteries from the Late Neolithic to the Middle Bronze Age in southern Germany. Our results reveal individual households, lasting several generations, that consisted of a high-status core family and unrelated low-status individuals; a social organization accompanied by patrilocality and female exogamy; and the stability of this system over 700 years.

RevDate: 2020-04-07

Herrera MB, Kraitsek S, Alcalde JA, et al (2020)

European and Asian contribution to the genetic diversity of mainland South American chickens.

Royal Society open science, 7(2):191558 pii:rsos191558.

Chickens (Gallus gallus domesticus) from the Americas have long been recognized as descendants of European chickens, transported by early Europeans since the fifteenth century. However, in recent years, a possible pre-Columbian introduction of chickens to South America by Polynesian seafarers has also been suggested. Here, we characterize the mitochondrial control region genetic diversity of modern chicken populations from South America and compare this to a worldwide dataset in order to investigate the potential maternal genetic origin of modern-day chicken populations in South America. The genetic analysis of newly generated chicken mitochondrial control region sequences from South America showed that the majority of chickens from the continent belong to mitochondrial haplogroup E. The rest belongs to haplogroups A, B and C, albeit at very low levels. Haplogroup D, a ubiquitous mitochondrial lineage in Island Southeast Asia and on Pacific Islands is not observed in continental South America. Modern-day mainland South American chickens are, therefore, closely allied with European and Asian chickens. Furthermore, we find high levels of genetic contributions from South Asian chickens to those in Europe and South America. Our findings demonstrate that modern-day genetic diversity of mainland South American chickens appear to have clear European and Asian contributions, and less so from Island Southeast Asia and the Pacific Islands. Furthermore, there is also some indication that South Asia has more genetic contribution to European chickens than any other Asian chicken populations.

RevDate: 2020-04-02

Racimo F, Woodbridge J, Fyfe RM, et al (2020)

The spatiotemporal spread of human migrations during the European Holocene.

Proceedings of the National Academy of Sciences of the United States of America pii:1920051117 [Epub ahead of print].

The European continent was subject to two major migrations of peoples during the Holocene: the northwestward movement of Anatolian farmer populations during the Neolithic and the westward movement of Yamnaya steppe peoples during the Bronze Age. These movements changed the genetic composition of the continent's inhabitants. The Holocene was also characterized by major changes in vegetation composition, which altered the environment occupied by the original hunter-gatherer populations. We aim to test to what extent vegetation change through time is associated with changes in population composition as a consequence of these migrations, or with changes in climate. Using ancient DNA in combination with geostatistical techniques, we produce detailed maps of ancient population movements, which allow us to visualize how these migrations unfolded through time and space. We find that the spread of Neolithic farmer ancestry had a two-pronged wavefront, in agreement with similar findings on the cultural spread of farming from radiocarbon-dated archaeological sites. This movement, however, did not have a strong association with changes in the vegetational landscape. In contrast, the Yamnaya migration speed was at least twice as fast and coincided with a reduction in the amount of broad-leaf forest and an increase in the amount of pasture and natural grasslands in the continent. We demonstrate the utility of integrating ancient genomes with archaeometric datasets in a spatiotemporal statistical framework, which we foresee will enable future studies of ancient populations' movements, and their putative effects on local fauna and flora.

RevDate: 2020-04-02
CmpDate: 2020-04-02

Lipson M, Ribot I, Mallick S, et al (2020)

Ancient West African foragers in the context of African population history.

Nature, 577(7792):665-670.

Our knowledge of ancient human population structure in sub-Saharan Africa, particularly prior to the advent of food production, remains limited. Here we report genome-wide DNA data from four children-two of whom were buried approximately 8,000 years ago and two 3,000 years ago-from Shum Laka (Cameroon), one of the earliest known archaeological sites within the probable homeland of the Bantu language group1-11. One individual carried the deeply divergent Y chromosome haplogroup A00, which today is found almost exclusively in the same region12,13. However, the genome-wide ancestry profiles of all four individuals are most similar to those of present-day hunter-gatherers from western Central Africa, which implies that populations in western Cameroon today-as well as speakers of Bantu languages from across the continent-are not descended substantially from the population represented by these four people. We infer an Africa-wide phylogeny that features widespread admixture and three prominent radiations, including one that gave rise to at least four major lineages deep in the history of modern humans.

RevDate: 2020-04-01

Mai BHA, Drancourt M, G Aboudharam (2020)

Ancient dental pulp: Masterpiece tissue for paleomicrobiology.

Molecular genetics & genomic medicine [Epub ahead of print].

INTRODUCTION: Dental pulp with special structure has become a good reference sample in paleomicrobiology-related blood-borne diseases, many pathogens were detected by different methods based on the diagnosis of nucleic acids and proteins.

OBJECTIVES: This review aims to propose the preparation process from ancient teeth collection to organic molecule extraction of dental pulp and summary, analyze the methods that have been applied to detect septicemic pathogens through ancient dental pulps during the past 20 years following the first detection of an ancient microbe.

METHODS: The papers used in this review with two main objectives were obtained from PubMed and Google scholar with combining keywords: "ancient," "dental pulp," "teeth," "anatomy," "structure," "collection," "preservation," "selection," "photography," "radiography," "contamination," "decontamination," "DNA," "protein," "extraction," "bone," "paleomicrobiology," "bacteria," "virus," "pathogen," "molecular biology," "proteomics," "PCR," "MALDI-TOF," "LC/MS," "ELISA," "immunology," "immunochromatography," "genome," "microbiome," "metagenomics."

RESULTS: The analysis of ancient dental pulp should have a careful preparation process with many different steps to give highly accurate results, each step complies with the rules in archaeology and paleomicrobiology. After the collection of organic molecules from dental pulp, they were investigated for pathogen identification based on the analysis of DNA and protein. Actually, DNA approach takes a principal role in diagnosis while the protein approach is more and more used. A total of seven techniques was used and ten bacteria (Yersinia pestis, Bartonella quintana, Salmonella enterica serovar Typhi, Salmonella enterica serovar Paratyphi C, Mycobacterium leprae, Mycobacterium tuberculosis, Rickettsia prowazeki, Staphylococcus aureus, Borrelia recurrentis, Bartonella henselae) and one virus (Anelloviridae) were identified. Y. pestis had the most published in quantity and all methods were investigated for this pathogen, S. aureus and B. recurrentis were identified by three different methods and others only by one. The combining methods interestingly increase the positive rate with ELISA, PCR and iPCR in Yersinia pestis diagnosis. Twenty-seven ancient genomes of Y. pestis and one ancient genome of B. recurrentis were reconstructed. Comparing to the ancient bone, ancient teeth showed more advantage in septicemic diagnosis. Beside pathogen identification, ancient pulp help to distinguish species.

CONCLUSIONS: Dental pulp with specific tissue is a suitable sample for detection of the blood infection in the past through DNA and protein identification with the correct preparation process, furthermore, it helps to more understand the pathogens of historic diseases and epidemics.

RevDate: 2020-04-01

Cortázar-Chinarro M, Meyer-Lucht Y, Van der Valk T, et al (2020)

Antimicrobial peptide and sequence variation along a latitudinal gradient in two anurans.

BMC genetics, 21(1):38 pii:10.1186/s12863-020-00839-1.

BACKGROUND: While there is evidence of both purifying and balancing selection in immune defense genes, large-scale genetic diversity in antimicrobial peptides (AMPs), an important part of the innate immune system released from dermal glands in the skin, has remained uninvestigated. Here we describe genetic diversity at three AMP loci (Temporin, Brevinin and Palustrin) in two ranid frogs (Rana arvalis and R. temporaria) along a 2000 km latitudinal gradient. We amplified and sequenced part of the Acidic Propiece domain and the hypervariable Mature Peptide domain (~ 150-200 bp) in the three genes using Illumina Miseq and expected to find decreased AMP genetic variation towards the northern distribution limit of the species similarly to studies on MHC genetic patterns.

RESULTS: We found multiple loci for each AMP and relatively high gene diversity, but no clear pattern of geographic genetic structure along the latitudinal gradient. We found evidence of trans-specific polymorphism in the two species, indicating a common evolutionary origin of the alleles. Temporin and Brevinin did not form monophyletic clades suggesting that they belong to the same gene family. By implementing codon evolution models we found evidence of strong positive selection acting on the Mature Peptide. We also found evidence of diversifying selection as indicated by divergent allele frequencies among populations and high Theta k values.

CONCLUSION: Our results suggest that AMPs are an important source of adaptive diversity, minimizing the chance of microorganisms developing resistance to individual peptides.

RevDate: 2020-03-31

Zhang L, Liu M, Long H, et al (2020)

Tung Tree (Vernicia fordii) Genome Provides A Resource for Understanding Genome Evolution and Improved Oil Production.

Genomics, proteomics & bioinformatics pii:S1672-0229(18)30216-X [Epub ahead of print].

Tung tree (Vernicia fordii) is an economically important woody oil plant that produces tung oil rich in eleostearic acid. Here, we report a high-quality chromosome-scale genome sequence of tung tree. The genome sequence was assembled by combining Illumina short reads, Pacific Biosciences single-molecule real-time long reads, and Hi-C sequencing data. The size of tung tree genome is 1.12 Gb, with 28,422 predicted genes and over 73% repeat sequences. The V. fordii underwent an ancient genome triplication event shared by core eudicots but no further whole-genome duplication in the subsequent ca. 34.55 million years of evolutionary history of the tung tree lineage. Insertion time analysis revealed that repeat-driven genome expansion might have arisen as a result of long-standing long terminal repeat retrotransposon bursts and lack of efficient DNA deletion mechanisms. The genome harbors 88 resistance genes encoding nucleotide-binding sites; 17 of these genes may be involved in early-infection stage of Fusarium wilt resistance. Further, 651 oil-related genes were identified, 88 of which are predicted to be directly involved in tung oil biosynthesis. Relatively few phosphoenolpyruvate carboxykinase genes, and synergistic effects between transcription factors and oil biosynthesis-related genes might contribute to the high oil content of tung seed. The tung tree genome constitutes a valuable resource for understanding genome evolution, as well as for molecular breeding and genetic improvements for oil production.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Voosen P (2019)

DNA from Arctic lakes traces past climate impacts.

Science (New York, N.Y.), 366(6471):1296-1297.

RevDate: 2020-03-30
CmpDate: 2020-03-30

Vogel G (2019)

Seeing fossils in a new light.

Science (New York, N.Y.), 366(6462):176-178.

RevDate: 2020-03-25
CmpDate: 2020-03-25

Gibbons A (2019)

DNA reveals European roots of the ancient Philistines.

Science (New York, N.Y.), 365(6448):17.

RevDate: 2020-03-24
CmpDate: 2020-03-24

Frantz LAF, Haile J, Lin AT, et al (2019)

Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe.

Proceedings of the National Academy of Sciences of the United States of America, 116(35):17231-17238.

Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.

RevDate: 2020-03-18

Utge J, Sévêque N, Lartigot-Campin AS, et al (2020)

A mobile laboratory for ancient DNA analysis.

PloS one, 15(3):e0230496 pii:PONE-D-19-17921.

Mobile devices for on-field DNA analysis have been used for medical diagnostics at the point-of-care, forensic investigations and environmental surveys, but still have to be validated for ancient DNA studies. We report here on a mobile laboratory that we setup using commercially available devices, including a compact real-time PCR machine, and describe procedures to perform DNA extraction and analysis from a variety of archeological samples within 4 hours. The process is carried out on 50 mg samples that are identified at the species level using custom TaqMan real-time PCR assays for mitochondrial DNA fragments. We evaluated the potential of this approach in museums lacking facilities for DNA studies by analyzing samples from the Enlène (MIS 2 layer) and the Portel-Ouest cave (MIS 3 deposits), and also performed experiments during an excavation campaign at the Roc-en-Pail (MIS 5) open-air site. Enlène Bovinae bone samples only yielded DNA for the extinct steppe bison (Bison priscus), whereas Portel-Ouest cave coprolites contained cave hyena (Crocuta crocuta spelaea) DNA together, for some of them, with DNA for the European bison sister species/subspecies (Bison schoetensacki/Bb1-X), thus highlighting the cave hyena diet. Roc-en-Pail Bovinae bone and tooth samples also contained DNA for the Bison schoetensacki/Bb1-X clade, and Cervidae bone samples only yielded reindeer (Rangifer tarandus) DNA. Subsequent DNA sequencing analyses confirmed that correct species identification had been achieved using our TaqMan assays, hence validating these assays for future studies. We conclude that our approach enables the rapid genetic characterization of tens of millennia-old archeological samples and is expected to be useful for the on-site screening of museums and freshly excavated samples for DNA content. Because our mobile laboratory is made up of commercially available instruments, this approach is easily accessible to other investigators.

RevDate: 2020-03-18

Moore G, Tessler M, Cunningham SW, et al (2020)

Paleo-metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA.

Ecology and evolution, 10(5):2530-2544 pii:ECE36082.

Fossil rodent middens are powerful tools in paleoecology. In arid parts of western North America, packrat (Neotoma spp.) middens preserve plant and animal remains for tens of thousands of years. Midden contents are so well preserved that fragments of endogenous ancient DNA (aDNA) can be extracted and analyzed across millennia. Here, we explore the use of shotgun metagenomics to study the aDNA obtained from packrat middens up to 32,000 C14 years old. Eleven Illumina HiSeq 2500 libraries were successfully sequenced, and between 0.11% and 6.7% of reads were classified using Centrifuge against the NCBI "nt" database. Eukaryotic taxa identified belonged primarily to vascular plants with smaller proportions mapping to ascomycete fungi, arthropods, chordates, and nematodes. Plant taxonomic diversity in the middens is shown to change through time and tracks changes in assemblages determined by morphological examination of the plant remains. Amplicon sequencing of ITS2 and rbcL provided minimal data for some middens, but failed at amplifying the highly fragmented DNA present in others. With repeated sampling and deep sequencing, analysis of packrat midden aDNA from well-preserved midden material can provide highly detailed characterizations of past communities of plants, animals, bacteria, and fungi present as trace DNA fossils. The prospects for gaining more paleoecological insights from aDNA for rodent middens will continue to improve with optimization of laboratory methods, decreasing sequencing costs, and increasing computational power.

RevDate: 2020-03-18

Ding M, Wang T, Ko AM, et al (2020)

Ancient mitogenomes show plateau populations from last 5200 years partially contributed to present-day Tibetans.

Proceedings. Biological sciences, 287(1923):20192968.

The clarification of the genetic origins of present-day Tibetans requires an understanding of their past relationships with the ancient populations of the Tibetan Plateau. Here we successfully sequenced 67 complete mitochondrial DNA genomes of 5200 to 300-year-old humans from the plateau. Apart from identifying two ancient plateau lineages (haplogroups D4j1b and M9a1a1c1b1a) that suggest some ancestors of Tibetans came from low-altitude areas 4750 to 2775 years ago and that some were involved in an expansion of people moving between high-altitude areas 2125 to 1100 years ago, we found limited evidence of recent matrilineal continuity on the plateau. Furthermore, deep learning of the ancient data incorporated into simulation models with an accuracy of 97% supports that present-day Tibetan matrilineal ancestry received partial contribution rather than complete continuity from the plateau populations of the last 5200 years.

RevDate: 2020-03-15

Emery MV, Bolhofner K, Winingear S, et al (2020)

Reconstructing full and partial STR profiles from severely burned human remains using comparative ancient and forensic DNA extraction techniques.

Forensic science international. Genetics, 46:102272 pii:S1872-4973(20)30043-0 [Epub ahead of print].

Thermal degeneration of the DNA molecule presents a special challenge to medico-legal investigations since low DNA yields, fragmented DNA molecules, and damaged nucleotide bases hinder accurate STR genotyping. As a consequence, fragments of severely burned human remains are often not amenable to standard DNA recovery. However, current ancient DNA (aDNA) extraction methods have proven highly effective at obtaining ultrashort DNA fragments (∼50 bp) from degraded palaeontological and archaeological specimens. In this study, we compare DNA yields and STR results obtained from two established aDNA and forensic DNA extraction protocols by sampling multiple skeletal elements recovered from victims (n = 23) involved in fire-related incidents. DNA yields and STR results suggest an inverse correlation between DNA yield and STR quality and increasing temperature. Despite the rapid thermal destruction of DNA at high temperatures, we generated higher quality full and partial STR profiles using the aDNA extraction protocol across all burn categories than the forensic total bone demineralization extraction method. Our analysis suggests adopting aDNA extraction methods as an alternative to current forensic practices to improve DNA yields from challenging human remains.

RevDate: 2020-03-15

Rahmat RA, Humphries MA, Austin JJ, et al (2020)

Integrating spectrophotometric and XRD analyses in the investigation of burned dental remains.

Forensic science international, 310:110236 pii:S0379-0738(20)30098-0 [Epub ahead of print].

Heat alters colour and crystallinity of teeth by destruction of the organic content and inducing hydroxyapatite crystal growth. The colour and crystallite changes can be quantified using spectrophotometric and x-ray diffraction analyses, however these analyses are not commonly used in combination to evaluate burned dental remains. In this study, thirty-nine teeth were incinerated at 300-1000 °C for 15 and 30 min and then measured using a spectrophotometer and an x-ray diffractometer. Response variables used were lightness, L*, and chromaticity a* and b* and luminance (whiteness and yellowness) for colour, and crystal size for crystallinity. Statistical analysis to determine the attribution of these variables revealed yellowness and crystal size were significantly affected by temperature (p < 0.05), whilst duration of heat-exposure showed no significant effect. This study suggests the inclusion of both spectrophotometric and x-ray diffraction in investigating thermal-heated teeth is useful to accurately estimate the temperature teeth are exposed to.

RevDate: 2020-03-12

Li L, Zou X, Zhang G, et al (2020)

Population genetic analysis of Shaanxi male Han Chinese population reveals genetic differentiation and homogenization of East Asians.

Molecular genetics & genomic medicine [Epub ahead of print].

BACKGROUND: Shaanxi province, located in the upper Yellow River, has been evidenced as the geographic origin of Chinese civilization, Sino-Tibetan-speaking language, and foxtail or broomcorn millet farmers via the linguistic phylogenetic spectrum, archeological documents, and genetic evidence. Nowadays, Han Chinese is the dominant population in this area. The formation process of modern Shaanxi Han population reconstructed via the ancient DNA is on the way, however, the patterns of genetic relationships of modern Shaanxi Han, allele frequency distributions of high mutated short tandem repeats (STRs) and corresponding forensic parameters are remained to be explored.

METHODS: Here, we successfully genotyped 23 autosomal STRs in 630 unrelated Shaanxi male Han individuals using the recently updated Huaxia Platinum PCR amplification system. Forensic allele frequency and parameters of all autosomal STRs were assessed. And comprehensive population genetic structure was explored via various typical statistical technologies.

RESULTS: Population genetic analysis based on the raw-genotype dataset among 15,803 Eurasian individuals and frequency datasets among 56 populations generally illustrated that linguistic stratification is significantly associated with the genetic substructure of the East Asian population. Principal component analysis, multidimensional scaling plots and phylogenetic tree further demonstrated that Shaanxi Han has a close genetic relationship with geographically close Shanxi Han, and showed that Han Chinese is a homogeneous population during the historic and recent admixture from the STR variations. Except for Sinitic-speaking populations, Shaanxi Han harbored more alleles sharing with Tibeto-Burman-speaking populations than with other reference populations. Focused on the allele frequency correlation and forensic parameters, all loci are in accordance with the minimum requirements of HWE and LD. The observed combined probability of discrimination of 8.2201E-28 and the cumulative power of exclusion of 0.9999999995 in Shaanxi Han demonstrated that the studied STR loci are informative and polymorphic, and this system can be used as a powerful routine forensic tool in personal identification and parentage testing.

CONCLUSION: Both the geographical and linguistic divisions have shaped the genetic structure of modern East Asian. And more forensic reference data should be obtained for ethnically, culturally, geographically and linguistically different populations for better routine forensic practice and population genetic studies.

RevDate: 2020-03-12
CmpDate: 2020-03-12

Peterson A (2019)

On Reconstruction of ancestral footfalls in South Asia using genomic data By Saikat Chakraborty and Analabha Basu.

Journal of biosciences, 44(3):.

RevDate: 2020-03-12
CmpDate: 2020-03-12

Pitchappan R (2019)

On Historic migration to South Asia in the last two millennia: A case of Jewish and Parsi populations By Ajai Kumar Pathak, et al.

Journal of biosciences, 44(3):.

RevDate: 2020-03-12
CmpDate: 2020-03-12

Silva M, Koch JT, Pala M, et al (2019)

On Methodological issues in the Indo-European debate By Michel Danino.

Journal of biosciences, 44(3):.

RevDate: 2020-03-07

Thang TN, Vázquez-Prieto S, Vilas R, et al (2020)

Genetic diversity of Fasciola hepatica in Spain and Peru.

Parasitology international pii:S1383-5769(20)30050-7 [Epub ahead of print].

In the present study, molecular characterization of Fasciola flukes from Spain was performed to reveal the relation with the previously reported Peruvian F. hepatica population. The nuclear DNA markers, phosphoenolpyruvate carboxykinase (pepck) and DNA polymerase delta (pold), were used for species identification of Fasciola flukes. A total of 196 Fasciola flukes were identified as F. hepatica by pepck and pold, and 26 haplotypes were detected in mitochondrial NADH dehydrogenase subunit 1 (nad1). Only one of them was previously found in Spanish samples; which indicates the existence of high genetic diversity and population structure in F. hepatica from Spain. Three haplotypes were identical to those from Peruvian F. hepatica. The pairwise fixation index value confirmed a relatively close relationship between the Spanish and Peruvian F. hepatica samples. The Spanish samples showed clearly higher genetic variability than the Peruvian population. These results are discussed in relation with the hypothesis of the introduction of the parasite in America from Europe and recent evidence of pre-Hispanic F. hepatica from Argentina revealed by ancient DNA.

RevDate: 2020-03-07

Mathieson I (2020)

Limited evidence for selection at the FADS locus in Native American populations.

Molecular biology and evolution pii:5799087 [Epub ahead of print].

The FADS locus contains the genes FADS1 and FADS2 that encode enzymes involved in the synthesis of long-chain polyunsaturated fatty acids (LC-PUFA). This locus appears to have been a repeated target of selection in human evolution, likely because dietary input of LC-PUFA varied over time depending on environment and subsistence strategy. Several recent studies have identified selection at the FADS locus in Native American populations, interpreted as evidence for adaptation during or subsequent to the passage through Beringia. Here, we show that these signals are confounded by independent selection-postdating the split from Native Americans-in the European and, possibly, the East Asian populations used in the population branch statistic (PBS) test. This is supported by direct evidence from ancient DNA that one of the putatively selected haplotypes was already common in Northern Eurasia at the time of the separation of Native American ancestors. An explanation for the present-day distribution of the haplotype that is more consistent with the data is that Native Americans retain the ancestral state of Paleolithic Eurasians. Another haplotype at the locus may reflect a secondary selection signal, although its functional impact is unknown.

RevDate: 2020-03-07

Popitsch N, Huber CD, Buchumenski I, et al (2020)

A-to-I RNA editing uncovers hidden signals of adaptive genome evolution in animals.

Genome biology and evolution pii:5799079 [Epub ahead of print].

In animals, the most common type of RNA editing is the deamination of adenosines (A) into inosines (I). Because inosines base-pair with cytosines (C), they are interpreted as guanosines (G) by the cellular machinery and genomically encoded G alleles at edited sites mimic the function of edited RNAs. The contribution of this hardwiring effect on genome evolution remains obscure. We looked for population genomics signatures of adaptive evolution associated with A-to-I RNA edited sites in humans and Drosophila melanogaster. We found that single nucleotide polymorphisms at edited sites occur 3 (humans) to 15 times (Drosophila) more often than at unedited sites, the nucleotide G is virtually the unique alternative allele at edited sites and G alleles segregate at higher frequency at edited sites than at unedited sites. Our study reveals that a significant fraction of coding synonymous and nonsynonymous as well as silent and intergenic A-to-I RNA editing sites are likely adaptive in the distantly related human and Drosophila lineages.

RevDate: 2020-03-06

Zhang J, Lees DC, Shen J, et al (2020)

The mitogenome of a Malagasy butterfly Malaza fastuosus (Mabille, 1884) recovered from the holotype collected over 140 years ago adds support for a new subfamily of Hesperiidae (Lepidoptera).

Genome [Epub ahead of print].

Malaza fastuosus is a lavishly patterned skipper butterfly from a genus that has three described species, all endemic to the mainland of Madagascar. To our knowledge, M. fastuosus has not been collected for nearly 50 years. To evaluate the power of our techniques to recover DNA, we used a single foreleg of an at least 140-year-old holotype specimen from the collection of the Natural History Museum London with no destruction of external morphology to extract DNA and assemble a complete mitogenome from next generation sequencing reads. The resulting 15 540 bp mitogenome contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and an A+T rich region, similarly to other Lepidoptera mitogenomes. Here we provide the first mitogenome also for Trapezitinae (Rachelia extrusus). Phylogenetic analysis of available skipper mitogenomes places Malaza outside of Trapezitinae and Barcinae + Hesperiinae, with a possible sister relationship to Heteropterinae. Of these, at least Heteropterinae, Trapezitinae, and almost all Hesperiinae have monocot-feeding caterpillars. Malaza appears to be an evolutionarily highly distinct ancient lineage, morphologically with several unusual hesperiid features. The monotypic subfamily Malazinae Lees & Grishin subfam. nov. (type genus Malaza) is proposed to reflect this morphological and molecular evidence.

RevDate: 2020-03-05

Gokhman D, Nissim-Rafinia M, Agranat-Tamir L, et al (2020)

Differential DNA methylation of vocal and facial anatomy genes in modern humans.

Nature communications, 11(1):1189 pii:10.1038/s41467-020-15020-6.

Changes in potential regulatory elements are thought to be key drivers of phenotypic divergence. However, identifying changes to regulatory elements that underlie human-specific traits has proven very challenging. Here, we use 63 reconstructed and experimentally measured DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that likely emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes associated with face and vocal tract anatomy went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-associated genes (SOX9, ACAN, COL2A1, NFIX and XYLT1). We propose that these repression patterns appeared after the split from Neanderthals and Denisovans, and that they might have played a key role in shaping the modern human face and vocal tract.

RevDate: 2020-03-04

Sawafuji R, Saso A, Suda W, et al (2020)

Ancient DNA analysis of food remains in human dental calculus from the Edo period, Japan.

PloS one, 15(3):e0226654 pii:PONE-D-19-25288.

Although there are many methods for reconstructing diets of the past, detailed taxon identification is still challenging, and most plants hardly remain at a site. In this study, we applied DNA metabarcoding to dental calculus of premodern Japan for the taxonomic identification of food items. DNA was extracted from 13 human dental calculi from the Unko-in site (18th-19th century) of the Edo period, Japan. Polymerase chain reaction (PCR) and sequencing were performed using a primer set specific to the genus Oryza because rice (Oryza sativa) was a staple food and this was the only member of this genus present in Japan at that time. DNA metabarcoding targeting plants, animals (meat and fish), and fungi were also carried out to investigate dietary diversity. We detected amplified products of the genus Oryza from more than half of the samples using PCR and Sanger sequencing. DNA metabarcoding enabled us to identify taxa of plants and fungi, although taxa of animals were not detected, except human. Most of the plant taxonomic groups (family/genus level) are present in Japan and include candidate species consumed as food at that time, as confirmed by historical literature. The other groups featured in the lifestyle of Edo people, such as for medicinal purposes and tobacco. The results indicate that plant DNA analysis from calculus provides information about food diversity and lifestyle habits from the past and can complement other analytical methods such as microparticle analysis and stable isotope analysis.

RevDate: 2020-03-04

Racimo F, Sikora M, Vander Linden M, et al (2020)

Beyond broad strokes: sociocultural insights from the study of ancient genomes.

Nature reviews. Genetics pii:10.1038/s41576-020-0218-z [Epub ahead of print].

In the field of human history, ancient DNA has provided answers to long-standing debates about major movements of people and has begun to inform on other important facets of the human experience. The field is now moving from mostly large-scale supraregional studies to a more local perspective, shedding light on socioeconomic processes, inheritance rules, marriage practices and technological diffusion. In this Review, we summarize recent studies showcasing these types of insights, focusing on methods used to infer sociocultural aspects of human behaviour. This approach often involves working across disciplines - such as anthropology, archaeology, linguistics and genetics - that have until recently evolved in separation. Multidisciplinary dialogue is important for an integrated reconstruction of human history, which can yield extraordinary insights about past societies, reproductive behaviours and even lifestyle habits that would not be possible to obtain otherwise.

RevDate: 2020-03-02

Kistler L, Bieker VC, Martin MD, et al (2020)

Ancient Plant Genomics in Archaeology, Herbaria, and the Environment.

Annual review of plant biology [Epub ahead of print].

The ancient DNA revolution of the past 35 years has driven an explosion in the breadth, nuance, and diversity of questions that are approachable using ancient biomolecules, and plant research has been a constant, indispensable facet of these developments. Using archaeological, paleontological, and herbarium plant tissues, researchers have probed plant domestication and dispersal, plant evolution and ecology, paleoenvironmental composition and dynamics, and other topics across related disciplines. Here, we review the development of the ancient DNA discipline and the role of plant research in its progress and refinement. We summarize our understanding of long-term plant DNA preservation and the characteristics of degraded DNA. In addition, we discuss challenges in ancient DNA recovery and analysis and the laboratory and bioinformatic strategies used to mitigate them. Finally, we review recent applications of ancient plant genomic research. Expected final online publication date for the Annual Review of Plant Biology, Volume 71 is April 29, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

RevDate: 2020-03-02
CmpDate: 2020-03-02

Fox K, J Hawks (2019)

Use ancient remains more wisely.

Nature, 572(7771):581-583.

RevDate: 2020-02-26

Anonymous (2018)

On the use and abuse of ancient DNA.

Nature, 555(7698):559.

RevDate: 2020-02-26

Sirak KA, Fernandes DM, Cheronet O, et al (2020)

Human auditory ossicles as an alternative optimal source of ancient DNA.

Genome research pii:gr.260141.119 [Epub ahead of print].

DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provide optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluate the ossicles as an alternative source of ancient DNA. We demonstrate that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quantity and minimal differences in data quality across preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that they should be utilized when available to reduce damage to human remains. Our results identify another optimal skeletal element for ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that ancient DNA analysis will produce useable results.

RevDate: 2020-02-25

Anonymous (2018)

UK university strike, quark pioneer and the ancient-genome boom.

Nature, 555(7694):10-11.

RevDate: 2020-02-25

King T (2018)

Sex, power and ancient DNA.

Nature, 555(7696):307-308.

RevDate: 2020-02-25

Fernandes DM, Mittnik A, Olalde I, et al (2020)

The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean.

Nature ecology & evolution pii:10.1038/s41559-020-1102-0 [Epub ahead of print].

Steppe-pastoralist-related ancestry reached Central Europe by at least 2500 BC, whereas Iranian farmer-related ancestry was present in Aegean Europe by at least 1900 BC. However, the spread of these ancestries into the western Mediterranean, where they have contributed to many populations that live today, remains poorly understood. Here, we generated genome-wide ancient-DNA data from the Balearic Islands, Sicily and Sardinia, increasing the number of individuals with reported data from 5 to 66. The oldest individual from the Balearic Islands (~2400 BC) carried ancestry from steppe pastoralists that probably derived from west-to-east migration from Iberia, although two later Balearic individuals had less ancestry from steppe pastoralists. In Sicily, steppe pastoralist ancestry arrived by ~2200 BC, in part from Iberia; Iranian-related ancestry arrived by the mid-second millennium BC, contemporary to its previously documented spread to the Aegean; and there was large-scale population replacement after the Bronze Age. In Sardinia, nearly all ancestry derived from the island's early farmers until the first millennium BC, with the exception of an outlier from the third millennium BC, who had primarily North African ancestry and who-along with an approximately contemporary Iberian-documents widespread Africa-to-Europe gene flow in the Chalcolithic. Major immigration into Sardinia began in the first millennium BC and, at present, no more than 56-62% of Sardinian ancestry is from its first farmers. This value is lower than previous estimates, highlighting that Sardinia, similar to every other region in Europe, has been a stage for major movement and mixtures of people.

RevDate: 2020-02-25

Marcus JH, Posth C, Ringbauer H, et al (2020)

Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia.

Nature communications, 11(1):939 pii:10.1038/s41467-020-14523-6.

The island of Sardinia has been of particular interest to geneticists for decades. The current model for Sardinia's genetic history describes the island as harboring a founder population that was established largely from the Neolithic peoples of southern Europe and remained isolated from later Bronze Age expansions on the mainland. To evaluate this model, we generate genome-wide ancient DNA data for 70 individuals from 21 Sardinian archaeological sites spanning the Middle Neolithic through the Medieval period. The earliest individuals show a strong affinity to western Mediterranean Neolithic populations, followed by an extended period of genetic continuity on the island through the Nuragic period (second millennium BCE). Beginning with individuals from Phoenician/Punic sites (first millennium BCE), we observe spatially-varying signals of admixture with sources principally from the eastern and northern Mediterranean. Overall, our analysis sheds light on the genetic history of Sardinia, revealing how relationships to mainland populations shifted over time.

RevDate: 2020-02-24

van Dorp L, Gelabert P, Rieux A, et al (2020)

Plasmodium vivax Malaria Viewed through the Lens of an Eradicated European Strain.

Molecular biology and evolution, 37(3):773-785.

The protozoan Plasmodium vivax is responsible for 42% of all cases of malaria outside Africa. The parasite is currently largely restricted to tropical and subtropical latitudes in Asia, Oceania, and the Americas. Though, it was historically present in most of Europe before being finally eradicated during the second half of the 20th century. The lack of genomic information on the extinct European lineage has prevented a clear understanding of historical population structuring and past migrations of P. vivax. We used medical microscope slides prepared in 1944 from malaria-affected patients from the Ebro Delta in Spain, one of the last footholds of malaria in Europe, to generate a genome of a European P. vivax strain. Population genetics and phylogenetic analyses placed this strain basal to a cluster including samples from the Americas. This genome allowed us to calibrate a genomic mutation rate for P. vivax, and to estimate the mean age of the last common ancestor between European and American strains to the 15th century. This date points to an introduction of the parasite during the European colonization of the Americas. In addition, we found that some known variants for resistance to antimalarial drugs, including Chloroquine and Sulfadoxine, were already present in this European strain, predating their use. Our results shed light on the evolution of an important human pathogen and illustrate the value of antique medical collections as a resource for retrieving genomic information on pathogens from the past.

RevDate: 2020-02-21

Guedes L, Borba VH, Camacho M, et al (2020)

African helminth infection out of Africa: paleoparasitological and paleogenetic investigations in Pretos Novos cemetery, Rio de Janeiro, Brazil (1769-1830).

Acta tropica pii:S0001-706X(19)30474-7 [Epub ahead of print].

Pretos Novos cemetery (PNC), Rio de Janeiro, Brazil (1769-1830) was created exclusively to bury enslaved Africans who died upon arrival at the city or before being sold in the slave market. The PNC site may be unique in the Americas in allowing the study of African parasite infections acquired in Africa. We aimed to identify parasites infecting PNC individuals through paleoparasitological and paleogenetic analyses. The bodies had been dismembered, placed in mass graves, and burned, and most human remains collected from the site are highly fragmented and show extensive degradation. Sacrum and pelvic sediments were collected from five individuals along with seven samples of sediment from other areas of the body, as controls. Samples were submitted to three parasitological techniques and, in paleogenetic analysis, to four molecular targets. Larvae, mites, pollen grains, and structure suggestive of plants and fungus were observed, but we found no evidence of helminth infection. Ascaris sp. cytb sequence was recovered in one individual. We emphasize that, even with the extensive degradation of PNC human remains and the process of curation of samples, it was possible to recover helminth aDNA. The origin of PNC individuals confirms that these infections were brought to Brazil from western and central Africa during the colonial era.

RevDate: 2020-02-19

Wu X, Ning C, Bao Q, et al (2019)

Mitochondrial Genome of an 8,400-Year-Old Individual from Northern China Reveals a Novel Subclade Under C5d.

Human biology, 91(1):21-30.

Ancient DNA studies have always refreshed our understanding of the human past that cannot be tracked by modern DNA alone. Until recently, ancient mitochondrial genomic studies in East Asia were still very limited. Here, we retrieved the whole mitochondrial genome of an 8,400-year-old individual from Inner Mongolia, China. Phylogenetic analyses show that the individual belongs to a previously undescribed clade under haplogroup C5d that most probably originated in northern Asia and may have a very low frequency in extant populations that have not yet been sampled. We further characterized the demographic history of mitochondrial haplogroups C5 and C5d and found that C5 experienced a sharp increase in population size starting around 4,000 years before present, the time when intensive millet farming was developed by populations who are associated with the Lower Xiajiadian culture and was widely adopted in northern China. We caution that people related to haplogroup C5 may have added this farming technology to their original way of life and that the various forms of subsistence may have provided abundant food sources and further contributed to the increase in population size.

RevDate: 2020-02-17

Harding T, Milot E, Moreau C, et al (2020)

Historical human remains identification through maternal and paternal genetic signatures in a founder population with extensive genealogical record.

American journal of physical anthropology [Epub ahead of print].

OBJECTIVES: We describe a method to identify human remains excavated from unmarked graves in historical Québec cemeteries by combining parental-lineage genetic markers with the whole-population genealogy of Québec contained in the BALSAC database.

MATERIALS AND METHODS: The remains of six men were exhumed from four historical cemeteries in the province of Québec, Canada. DNA was extracted from the remains and genotyped to reveal their mitochondrial and Y-chromosome haplotypes, which were compared to a collection of haplotypes of genealogically-anchored modern volunteers. Maternal and paternal genealogies were searched in the BALSAC genealogical record for parental couples matching the mitochondrial and the Y-chromosome haplotypic signatures, to identify candidate sons from whom the remains could have originated.

RESULTS: Analysis of the matching genealogies identified the parents of one man inhumed in the cemetery of the investigated parish during its operating time. The candidate individual died in 1833 at the age of 58, a plausible age at death in light of osteological analysis of the remains.

DISCUSSION: This study demonstrates the promising potential of coupling genetic information from living individuals to genealogical data in BALSAC to identify historical human remains. If genetic coverage is increased, the genealogical information in BALSAC could enable the identification of 87% of the men (n = 178,435) married in Québec before 1850, with high discriminatory power in most cases since >75% of the parental couples have unique biparental signatures in most regions. Genotyping and identifying Québec's historical human remains are a key to reconstructing the genomes of the founders of Québec and reinhuming archeological remains with a marked grave.

RevDate: 2020-02-13
CmpDate: 2020-02-13

Warren M (2019)

Move over, DNA: ancient proteins are starting to reveal humanity's history.

Nature, 570(7762):433-436.

RevDate: 2020-02-07

Pérez V, Cortés J, Marchant F, et al (2020)

Aquatic Thermal Reservoirs of Microbial Life in a Remote and Extreme High Andean Hydrothermal System.

Microorganisms, 8(2): pii:microorganisms8020208.

Hydrothermal systems are ideal to understand how microbial communities cope with challenging conditions. Lirima, our study site, is a polyextreme, high-altitude, hydrothermal ecosystem located in the Chilean Andean highlands. Herein, we analyze the benthic communities of three nearby springs in a gradient of temperature (42-72 °C represented by stations P42, P53, and P72) and pH, and we characterize their microbial diversity by using bacteria 16S rRNA (V4) gene metabarcoding and 16S rRNA gene clone libraries (bacteria and archaea). Bacterial clone libraries of P42 and P53 springs showed that the community composition was mainly represented by phototrophic bacteria (Chlorobia, 3%, Cyanobacteria 3%, at P42; Chlorobia 5%, and Chloroflexi 5% at P53), Firmicutes (32% at P42 and 43% at P53) and Gammaproteobacteria (13% at P42 and 29% at P53). Furthermore, bacterial communities that were analyzed by 16S rRNA gene metabarcoding were characterized by an overall predominance of Chloroflexi in springs with lower temperatures (33% at P42), followed by Firmicutes in hotter springs (50% at P72). The archaeal diversity of P42 and P53 were represented by taxa belonging to Crenarchaeota, Diapherotrites, Nanoarchaeota, Hadesarchaeota, Thaumarchaeota, and Euryarchaeota. The microbial diversity of the Lirima hydrothermal system is represented by groups from deep branches of the tree of life, suggesting this ecosystem as a reservoir of primitive life and a key system to study the processes that shaped the evolution of the biosphere.

RevDate: 2020-02-12

Turney CSM, Fogwill CJ, Golledge NR, et al (2020)

Early Last Interglacial ocean warming drove substantial ice mass loss from Antarctica.

Proceedings of the National Academy of Sciences of the United States of America pii:1902469117 [Epub ahead of print].

The future response of the Antarctic ice sheet to rising temperatures remains highly uncertain. A useful period for assessing the sensitivity of Antarctica to warming is the Last Interglacial (LIG) (129 to 116 ky), which experienced warmer polar temperatures and higher global mean sea level (GMSL) (+6 to 9 m) relative to present day. LIG sea level cannot be fully explained by Greenland Ice Sheet melt (∼2 m), ocean thermal expansion, and melting mountain glaciers (∼1 m), suggesting substantial Antarctic mass loss was initiated by warming of Southern Ocean waters, resulting from a weakening Atlantic meridional overturning circulation in response to North Atlantic surface freshening. Here, we report a blue-ice record of ice sheet and environmental change from the Weddell Sea Embayment at the periphery of the marine-based West Antarctic Ice Sheet (WAIS), which is underlain by major methane hydrate reserves. Constrained by a widespread volcanic horizon and supported by ancient microbial DNA analyses, we provide evidence for substantial mass loss across the Weddell Sea Embayment during the LIG, most likely driven by ocean warming and associated with destabilization of subglacial hydrates. Ice sheet modeling supports this interpretation and suggests that millennial-scale warming of the Southern Ocean could have triggered a multimeter rise in global sea levels. Our data indicate that Antarctica is highly vulnerable to projected increases in ocean temperatures and may drive ice-climate feedbacks that further amplify warming.

RevDate: 2020-02-05

Macleod R, Sinding MS, Olsen MT, et al (2020)

DNA preserved in jetsam whale ambergris.

Biology letters, 16(2):20190819.

Jetsam ambergris, found on beaches worldwide, has always been assumed to originate as a natural product of sperm whales (Physeteroidea). However, only indirect evidence has ever been produced for this, such as the presence of whale prey remains in ambergris. Here, we extracted and analysed DNA sequences from jetsam ambergris from beaches in New Zealand and Sri Lanka, and sequences from ambergris of a sperm whale beached in The Netherlands. The lipid-rich composition of ambergris facilitated high preservation-quality of endogenous DNA, upon which we performed shotgun Illumina sequencing. Alignment of mitochondrial and nuclear genome sequences with open-access reference data for multiple whale species confirms that all three jetsam samples derived originally from sperm whales (Physeter macrocephalus). Shotgun sequencing here also provides implications for metagenomic insights into ambergris-preserved DNA. These results demonstrate significant implications for elucidating the origins of jetsam ambergris as a prized natural product, and also for the understanding of sperm whale metabolism and diet, and the ecological mechanisms underlying these coproliths.

RevDate: 2020-02-04

Xenikoudakis G, Ahmed M, Harris JC, et al (2020)

Ancient DNA reveals twenty million years of aquatic life in beavers.

Current biology : CB, 30(3):R110-R111.

Xenikoudakis et al. report a partial mitochondrial genome of the extinct giant beaver Castoroides and estimate the origin of aquatic behavior in beavers to approximately 20 million years. This time estimate coincides with the extinction of terrestrial beavers and raises the question whether the two events had a common cause.

RevDate: 2020-02-04

Tabares X, Zimmermann H, Dietze E, et al (2020)

Vegetation state changes in the course of shrub encroachment in an African savanna since about 1850 CE and their potential drivers.

Ecology and evolution, 10(2):962-979 pii:ECE35955.

Shrub encroachment has far-reaching ecological and economic consequences in many ecosystems worldwide. Yet, compositional changes associated with shrub encroachment are often overlooked despite having important effects on ecosystem functioning.We document the compositional change and potential drivers for a northern Namibian Combretum woodland transitioning into a Terminalia shrubland. We use a multiproxy record (pollen, sedimentary ancient DNA, biomarkers, compound-specific carbon (δ13C) and deuterium (δD) isotopes, bulk carbon isotopes (δ13Corg), grain size, geochemical properties) from Lake Otjikoto at high taxonomical and temporal resolution.We provide evidence that state changes in semiarid environments may occur on a scale of one century and that transitions between stable states can span around 80 years and are characterized by a unique vegetation composition. We demonstrate that the current grass/woody ratio is exceptional for the last 170 years, as supported by n-alkane distributions and the δ13C and δ13Corg records. Comparing vegetation records to environmental proxy data and census data, we infer a complex network of global and local drivers of vegetation change. While our δD record suggests physiological adaptations of woody species to higher atmospheric pCO2 concentration and drought, our vegetation records reflect the impact of broad-scale logging for the mining industry, and the macrocharcoal record suggests a decrease in fire activity associated with the intensification of farming. Impact of selective grazing is reflected by changes in abundance and taxonomical composition of grasses and by an increase of nonpalatable and trampling-resistant taxa. In addition, grain-size and spore records suggest changes in the erodibility of soils because of reduced grass cover. Synthesis. We conclude that transitions to an encroached savanna state are supported by gradual environmental changes induced by management strategies, which affected the resilience of savanna ecosystems. In addition, feedback mechanisms that reflect the interplay between management legacies and climate change maintain the encroached state.

RevDate: 2020-01-31

De-Dios T, van Dorp L, Charlier P, et al (2020)

Metagenomic analysis of a blood stain from the French revolutionary Jean-Paul Marat (1743-1793).

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases pii:S1567-1348(20)30041-1 [Epub ahead of print].

The French revolutionary Jean-Paul Marat (1743-1793) was assassinated in 1793 in his bathtub, where he was trying to find relief from the debilitating skin disease he was suffering from. At the time of his death, Marat was annotating newspapers, which got stained with his blood and were subsequently preserved by his sister. We extracted and sequenced DNA from the blood stain and also from another section of the newspaper, which we used for comparison. Results from the human DNA sequence analyses were compatible with a heterogeneous ancestry of Marat, with his mother being of French origin and his father born in Sardinia. Metagenomic analyses of the non-human reads uncovered the presence of fungal, bacterial and low levels of viral DNA. Relying on the presence/absence of microbial species in the samples, we could cast doubt on several putative infectious agents that have been previously hypothesised as the cause of his condition but for which we detect not a single sequencing read. Conversely, some of the species we detect are uncommon as environmental contaminants and may represent plausible infective agents. Based on all the available evidence, we hypothesize that Marat may have suffered from a fungal infection (seborrheic dermatitis), possibly superinfected with bacterial opportunistic pathogens.

RevDate: 2020-01-29

Oswald JA, Allen JM, LeFebvre MJ, et al (2020)

Ancient DNA and high-resolution chronometry reveal a long-term human role in the historical diversity and biogeography of the Bahamian hutia.

Scientific reports, 10(1):1373 pii:10.1038/s41598-020-58224-y.

Quaternary paleontological and archaeological evidence often is crucial for uncovering the historical mechanisms shaping modern diversity and distributions. We take an interdisciplinary approach using multiple lines of evidence to understand how past human activity has shaped long-term animal diversity in an island system. Islands afford unique opportunities for such studies given their robust fossil and archaeological records. Herein, we examine the only non-volant terrestrial mammal endemic to the Bahamian Archipelago, the hutia Geocapromys ingrahami. This capromyine rodent once inhabited many islands but is now restricted to several small cays. Radiocarbon dated fossils indicate that hutias were present on the Great Bahama Bank islands before humans arrived at AD ~800-1000; all dates from other islands post-date human arrival. Using ancient DNA from a subset of these fossils, along with modern representatives of Bahamian hutia and related taxa, we develop a fossil-calibrated phylogeny. We found little genetic divergence among individuals from within either the northern or southern Bahamas but discovered a relatively deep North-South divergence (~750 ka). This result, combined with radiocarbon dating and archaeological evidence, reveals a pre-human biogeographic divergence, and an unexpected human role in shaping Bahamian hutia diversity and biogeography across islands.

RevDate: 2020-01-29

Barbato M, Hailer F, Upadhyay M, et al (2020)

Adaptive introgression from indicine cattle into white cattle breeds from Central Italy.

Scientific reports, 10(1):1279 pii:10.1038/s41598-020-57880-4.

Cattle domestication occurred at least twice independently and gave rise to the modern taurine and indicine cattle breeds. European cattle diversity is generally dominated by taurine cattle, although elevated levels of indicine ancestry have been recorded in several breeds from southern Europe. Here we use genome-wide high-density SNP genotyping data to investigate the taurine and indicine ancestry in southern European cattle, based on a dataset comprising 508 individuals from 23 cattle breeds of taurine, indicine and mixed ancestry, including three breeds from Central Italy known to exhibit the highest levels of indicine introgression among southern European breeds. Based on local genomic ancestry analyses, we reconstruct taurine and indicine ancestry genome-wide and along chromosomes. We scrutinise local genomic introgression signals and identify genomic regions that have introgressed from indicine into taurine cattle under positive selection, harbouring genes with functions related to body size and feed efficiency. These findings suggest that indicine-derived traits helped enhance Central Italian cattle through adaptive introgression. The identified genes could provide genomic targets for selection for improved cattle performance. Our findings elucidate the key role of adaptive introgression in shaping the phenotypic features of modern cattle, aided by cultural and livestock exchange among historic human societies.

RevDate: 2020-01-28

Gismondi A, Baldoni M, Gnes M, et al (2020)

A multidisciplinary approach for investigating dietary and medicinal habits of the Medieval population of Santa Severa (7th-15th centuries, Rome, Italy).

PloS one, 15(1):e0227433 pii:PONE-D-19-21430.

A multidisciplinary approach, combining stable isotope analysis from bone proteins and investigations on dental calculus using DNA analysis, light microscopy, and gas chromatography coupled with mass spectrometry, was applied to reconstruct dietary and medicinal habits of the individuals recovered in the cemetery of the Castle of Santa Severa (7th-15th centuries CE; Rome, Italy). Stable isotope analysis was performed on 120 humans, 41 faunal specimens and 8 charred seeds. Dental calculus analyses were carried out on 94 samples. Overall, isotope data indicated an omnivorous diet based on C3-terrestrial protein, although some individuals possessed carbon values indicative of C4 plant consumption. In terms of animal protein, the diet was probably based on cattle, sheep, pig and chicken products, as witnessed by the archaeozoological findings. Evidence from calculus suggested the consumption of C3 cereals, Fabaceae, Fagaceae, milk and dairy products. Secondary metabolites of herbs and wine were also detected. The detection of marine fish ancient DNA, as well as of ω3 fatty acids in calculus, hypothesized the consumption of marine foodstuffs for this coastal population, despite the lack of a clear marine isotopic signal and the presence of polyunsaturated fatty acids in plant tissues. Moreover, the knowledge of ethnopharmacological tradition and the application of medicinal plants (e.g. Punica granatum L., Ephedra sp. L.) were also identified. The detection of artemisinin, known to have antimalarial properties, led to hypothesize the presence of malaria in the area. Altogether, the combined application of microscopy and biomolecular techniques provided an innovative reconstruction of Medieval lifeways in Central Italy.

RevDate: 2020-01-27

Segawa T, T Yonezawa (2020)

Evaluation of reported sediment samples from 20 Ma using a molecular phylogenetic approach: Comment on Liu et al. (2017).

Environmental microbiology [Epub ahead of print].

Liu et al. (2017) reported the cultivation and DNA sequencing of 69 fungal isolates (Ascomycota and Basidiomycota) from ancient subseafloor sediments, suggesting that they represent living fungal populations that have persisted for over 20 million years. Because these findings could bring about a paradigm shift in our understanding of the spatial breadth of the deep subsurface biosphere as well as the longevity of ancient DNA, it is extremely important to verify that their samples represent pure ancient fungi from 20 million years ago without contamination by modern species. For this purpose, we estimated the divergence times among Dikarya fungi (Ascomycete + Basidiomycete) assuming that the fungal isolates were actually sampled from 20 Ma (mega-annum) sediments and evaluated the validity of the sample ages. Using this approach, we estimate that the age of the last common ancestor of Dikarya fungi greatly exceeds the age of the Earth. Our finding emphasizes the importance of using reliable approaches to confirm the dating of ancient samples. This article is protected by copyright. All rights reserved.

RevDate: 2020-01-23

Taylor WTT, Clark J, Bayarsaikhan J, et al (2020)

Early Pastoral Economies and Herding Transitions in Eastern Eurasia.

Scientific reports, 10(1):1001 pii:10.1038/s41598-020-57735-y.

While classic models for the emergence of pastoral groups in Inner Asia describe mounted, horse-borne herders sweeping across the Eurasian Steppes during the Early or Middle Bronze Age (ca. 3000-1500 BCE), the actual economic basis of many early pastoral societies in the region is poorly characterized. In this paper, we use collagen mass fingerprinting and ancient DNA analysis of some of the first stratified and directly dated archaeofaunal assemblages from Mongolia's early pastoral cultures to undertake species identifications of this rare and highly fragmented material. Our results provide evidence for livestock-based, herding subsistence in Mongolia during the late 3rd and early 2nd millennia BCE. We observe no evidence for dietary exploitation of horses prior to the late Bronze Age, ca. 1200 BCE - at which point horses come to dominate ritual assemblages, play a key role in pastoral diets, and greatly influence pastoral mobility. In combination with the broader archaeofaunal record of Inner Asia, our analysis supports models for widespread changes in herding ecology linked to the innovation of horseback riding in Central Asia in the final 2nd millennium BCE. Such a framework can explain key broad-scale patterns in the movement of people, ideas, and material culture in Eurasian prehistory.

RevDate: 2020-01-22

Nelson EA, Buikstra JE, Herbig A, et al (2020)

Advances in the molecular detection of tuberculosis in pre-contact Andean South America.

International journal of paleopathology pii:S1879-9817(19)30153-6 [Epub ahead of print].

Andean paleopathological research has significantly enhanced knowledge about the geographical distribution and evolution of tuberculosis (TB) in pre-Columbian South America. In this paper, we review the history and progress of research on ancient tuberculosis (TB) in the Andean region, focusing on the strengths and limitations of current approaches for the molecular detection of ancient pathogens, with special attention to TB. As a case study, we describe a molecular screening approach for the detection of ancient Mycobacterium tuberculosis in individuals from Late Intermediate Period (1000-1400 CE) contexts at the site of Huari, Peru. We evaluate 34 commingled human vertebrae and combine morphological assessments of pathology with high throughput sequencing and a non-selective approach to ancient pathogen DNA screening. Our method enabled the simultaneous detection of ancient M. tuberculosis DNA and an evaluation of the environmental microbial composition of each sample. Our results show that despite the dominance of environmental DNA, molecular signatures of M. tuberculosis were identified in eight vertebrae, six of which had no observable skeletal pathology classically associated tuberculosis infection. This screening approach will assist in the identification of candidate samples for downstream genomic analyses. The method permits higher resolution disease identification in cases where pathology may be absent, or where the archaeological context may necessitate a broad differential diagnosis based on morphology alone.

RevDate: 2020-01-21

Napier JD, de Lafontaine G, ML Chipman (2020)

The Evolution of Paleoecology.

Trends in ecology & evolution pii:S0169-5347(19)30351-9 [Epub ahead of print].

While the interplay between migration and adaptation dictates species response to climate change, technological limitations have obfuscated explicit tests on past adaptive responses. However, a surge in technology-driven advances in paleoecological methods coincides with breakthroughs in processing ancient DNA, providing the first opportunity to assess adaptation to past climate shifts.

LOAD NEXT 100 CITATIONS

ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

Electronic Scholarly Publishing
961 Red Tail Lane
Bellingham, WA 98226

E-mail: RJR8222 @ gmail.com

Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin (and even a collection of poetry — Chicago Poems by Carl Sandburg).

Timelines

ESP now offers a much improved and expanded collection of timelines, designed to give the user choice over subject matter and dates.

Biographies

Biographical information about many key scientists.

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are now being automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )