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Bibliography on: History of Genetics

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ESP: PubMed Auto Bibliography 21 Sep 2023 at 01:48 Created: 

History of Genetics

Created with PubMed® Query: genetics (classical OR mendelian) genetics history[mesh] NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)


RevDate: 2023-08-23
CmpDate: 2023-08-23

Schioldann J (2023)

Classic Text No. 135: 'On inheritance of the insanities', by Jens Chr. Smith (1924).

History of psychiatry, 34(3):350-362.

Serious and realistic research into the inheritance of the psychoses started in earnest at the beginning of the twentieth century. This was encouraged by both the acceptance of the Kraepelinian classification and the rediscovery of the Mendelian model of inheritance. The application of Mendelian rules to the very complex genetics of the psychoses led to agonizing debate. The Classic Text is a translation of the introduction of the doctoral thesis of Jens Chr. Smith, a little-known Danish psychiatrist who was able to summarize, with the enthusiasm typical to his youth and with surprising accuracy, the early stages of the debate mentioned above.

RevDate: 2023-08-04
CmpDate: 2023-08-03

Chyleński M, Makarowicz P, Juras A, et al (2023)

Patrilocality and hunter-gatherer-related ancestry of populations in East-Central Europe during the Middle Bronze Age.

Nature communications, 14(1):4395.

The demographic history of East-Central Europe after the Neolithic period remains poorly explored, despite this region being on the confluence of various ecological zones and cultural entities. Here, the descendants of societies associated with steppe pastoralists form Early Bronze Age were followed by Middle Bronze Age populations displaying unique characteristics. Particularly, the predominance of collective burials, the scale of which, was previously seen only in the Neolithic. The extent to which this re-emergence of older traditions is a result of genetic shift or social changes in the MBA is a subject of debate. Here by analysing 91 newly generated genomes from Bronze Age individuals from present Poland and Ukraine, we discovered that Middle Bronze Age populations were formed by an additional admixture event involving a population with relatively high proportions of genetic component associated with European hunter-gatherers and that their social structure was based on, primarily patrilocal, multigenerational kin-groups.

RevDate: 2023-06-26
CmpDate: 2023-06-26

Simões LG, Günther T, Martínez-Sánchez RM, et al (2023)

Northwest African Neolithic initiated by migrants from Iberia and Levant.

Nature, 618(7965):550-556.

In northwestern Africa, lifestyle transitioned from foraging to food production around 7,400 years ago but what sparked that change remains unclear. Archaeological data support conflicting views: (1) that migrant European Neolithic farmers brought the new way of life to North Africa[1-3] or (2) that local hunter-gatherers adopted technological innovations[4,5]. The latter view is also supported by archaeogenetic data[6]. Here we fill key chronological and archaeogenetic gaps for the Maghreb, from Epipalaeolithic to Middle Neolithic, by sequencing the genomes of nine individuals (to between 45.8- and 0.2-fold genome coverage). Notably, we trace 8,000 years of population continuity and isolation from the Upper Palaeolithic, via the Epipaleolithic, to some Maghrebi Neolithic farming groups. However, remains from the earliest Neolithic contexts showed mostly European Neolithic ancestry. We suggest that farming was introduced by European migrants and was then rapidly adopted by local groups. During the Middle Neolithic a new ancestry from the Levant appears in the Maghreb, coinciding with the arrival of pastoralism in the region, and all three ancestries blend together during the Late Neolithic. Our results show ancestry shifts in the Neolithization of northwestern Africa that probably mirrored a heterogeneous economic and cultural landscape, in a more multifaceted process than observed in other regions.

RevDate: 2023-05-09
CmpDate: 2023-04-19

Cohen P, Bacilieri R, Ramos-Madrigal J, et al (2023)

Ancient DNA from a lost Negev Highlands desert grape reveals a Late Antiquity wine lineage.

Proceedings of the National Academy of Sciences of the United States of America, 120(17):e2213563120.

Recent excavations of Late Antiquity settlements in the Negev Highlands of southern Israel uncovered a society that established commercial-scale viticulture in an arid environment [D. Fuks et al., Proc. Natl. Acad. Sci. U.S.A. 117, 19780-19791 (2020)]. We applied target-enriched genome-wide sequencing and radiocarbon dating to examine grapevine pips that were excavated at three of these sites. Our analyses revealed centuries long and continuous grape cultivation in the Southern Levant. The genetically diverse pips also provided clues to ancient cultivation strategies aimed at improving agricultural productivity and ensuring food security. Applying genomic prediction analysis, a pip dated to the eighth century CE was determined to likely be from a white grape, to date the oldest to be identified. In a kinship analysis, another pip was found to be descendant from a modern Greek cultivar and was thus linked with several popular historic wines that were once traded across the Byzantine Empire. These findings shed light on historical Byzantine trading networks and on the genetic contribution of Levantine varieties to the classic Aegean landscape.

RevDate: 2023-05-08
CmpDate: 2023-05-08

Ptushenko VV, EV Ramensky (2023)

Biologist Nikolai K. Koltzoff: the forgotten genius.

Genetics, 224(1):.

Nikolai K. Koltzoff (Koltsov) (1872-1940) is one of the key figures in Russian biology. He essentially initiated Russian physicochemical biology and established a large scientific school in the area. Among his disciples, there are the geneticists B.L. Astaurov, S.S. Chetverikov, N.P. Dubinin, V.P. Efroimson, I.A. Rapoport, V.V. Sakharov, and N.V. Timofeeff-Ressovsky; histologist G.I. Roskin, experimental surgeon A.G. Lapchinsky, developmental biologist M.M. Zavadovsky, physiologist L.V. Krushinsky, microbiologist S.M. Gershenson, biochemist V.A. Engelhardt, hydrobiologist G.G. Vinberg, cytologist M.A. Peshkov, and many other famous Soviet biologists. He made several fundamental discoveries; the first of them was the discovery of the cytoskeleton (1903). He was the first to formulate the idea of a crystal-like mechanism for copying inherited information (1927) and the principles of epigenetics (as well as the term itself, in 1934; it seems astonishing, but as early as 1915, he hypothesized that the gene methylation might be a mechanism of genetic variability). He started the work which later led his disciples V.V. Sakharov and I.A. Rapoport to the discovery of chemical mutagenesis. His research on sex regulation in silkworms was later successfully continued by B.L. Astaurov. Koltzoff encouraged S.S. Chetverikov, the entomologist, to study the genetics of natural Drosophila populations, which went on to form the basis of the Modern Synthesis reconciling Darwinian evolutionary theory and the Mendelian laws of heredity. Unfortunately, the name of N.K. Koltzoff has almost sunk into oblivion. This is largely due to the fact that mentioning his name was prohibited in the USSR over a long period of time, since he was a staunch opponent of Lysenko. In this paper dedicated to the 150th anniversary of Koltzoff, we briefly describe the milestones of the life and scientific research of this outstanding biologist and his scientific school.

RevDate: 2023-06-01
CmpDate: 2023-05-29

van Dijk PJ, TH Noel Ellis (2023)

Gregor Mendel and the theory of species multiplication.

Genetics, 224(2):.

According to the revisionist interpretation of Mendel's pea crosses, his primary aim was not to study the inheritance of traits. Instead, he was interested in the question raised by Linnaeus as to whether new species could arise from the hybridization of existing species. The genetic interpretation is therefore seen as ahistorical by the revisionists. This view goes back to the 1979 article "Mendel no Mendelian?" by the historian of science R.C. Olby. A closer analysis shows that Olby implicitly assumed Mendel adhered to the unusual strictest species definition for Pisum. However, we argue that Mendel only mentions the hypothetical application of this strict definition in his 1866 paper. Like most of his contemporaries, Mendel accepted variation within species where the differences between varieties and species were a matter of degree. After researching variable hybrids in peas (Pisum; 1854-1863), Mendel also studied constant hybrids in hawkweeds (Hieracium; 1866-1873), which he considered to be new species. There is no debate about the latter, but the matter becomes muddled because Olby lumps Pisum and Hieracium together, despite their having completely different reproduction systems. Based on newly discovered historical sources, we also dispute several other assumptions made by Olby. We do not consider Olby's claim that Mendel conducted the Pisum experiments to investigate species multiplication to be tenable.

RevDate: 2023-04-25
CmpDate: 2023-03-14

Kendler KS, A Klee (2023)

The era of the Dawn of Mendelian research in the field of psychiatry: Rüdin's 1922 review paper "regarding the heredity of mental disturbances".

American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics, 192(3-4):53-61.

On September 27, 1922, Ernst Rüdin gave an address to the Annual Conference of the German Society of Genetics entitled "Regarding the Heredity of Mental Disturbances." Published in a 37-page article, Rüdin reviewed the progress in the field of Mendelian psychiatric genetics, then hardly more than a decade old. Topics included (a) the status of Mendelian analyses of dementia praecox and manic-depressive insanity which had expanded to include two and three locus and early polygenic models and sometimes included, respectively, schizoid and cyclothymic personalities; (b) a critique of theories for the explanation of co-occurrence of different psychiatric disorders within families; and (c) a sharp methodologic critique of Davenport and Rosanoff's contemporary work which emphasized Rüdin's commitment to careful, expert phenotyping, a primary focus on well-validated psychiatric disorders and not broad spectra of putatively inter-related conditions, and an emphasis on rigorous statistical modeling as seen in his continued collaboration with Wilhelm Weinberg.

RevDate: 2023-03-05
CmpDate: 2023-01-19

Pearson J, Evans J, Lamb A, et al (2023)

Mobility and kinship in the world's first village societies.

Proceedings of the National Academy of Sciences of the United States of America, 120(4):e2209480119.

Around 10,000 y ago in southwest Asia, the cessation of a mobile lifestyle and the emergence of the first village communities during the Neolithic marked a fundamental change in human history. The first communities were small (tens to hundreds of individuals) but remained semisedentary. So-called megasites appeared soon after, occupied by thousands of more sedentary inhabitants. Accompanying this shift, the material culture and ancient ecological data indicate profound changes in economic and social behavior. A shift from residential to logistical mobility and increasing population size are clear and can be explained by either changes in fertility and/or aggregation of local groups. However, as sedentism increased, small early communities likely risked inbreeding without maintaining or establishing exogamous relationships typical of hunter-gatherers. Megasites, where large populations would have made endogamy sustainable, could have avoided this risk. To examine the role of kinship practices in the rise of megasites, we measured strontium and oxygen isotopes in tooth enamel from 99 individuals buried at Pınarbaşı, Boncuklu, and Çatalhöyük (Turkey) over 7,000 y. These sites are geographically proximate and, critically, span both early sedentary behaviors (Pınarbaşı and Boncuklu) and the rise of a local megasite (Çatalhöyük). Our data are consistent with the presence of only local individuals at Pınarbaşı and Boncuklu, whereas at Çatalhöyük, several nonlocals are present. The Çatalhöyük data stand in contrast to other megasites where bioarchaeological evidence has pointed to strict endogamy. These different kinship behaviors suggest that megasites may have arisen by employing unique, community-specific kinship practices.

RevDate: 2023-02-05
CmpDate: 2023-01-12

Koptekin D, Yüncü E, Rodríguez-Varela R, et al (2023)

Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean.

Current biology : CB, 33(1):41-57.e15.

We present a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, a broad region that experienced the earliest Neolithic transition and the emergence of complex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 ancient and 23 present-day published genomes, we found that genetic diversity within each region steadily increased through the Holocene. We further observed that the inferred sources of gene flow shifted in time. In the first half of the Holocene, Southwest Asian and the East Mediterranean populations homogenized among themselves. Starting with the Bronze Age, however, regional populations diverged from each other, most likely driven by gene flow from external sources, which we term "the expanding mobility model." Interestingly, this increase in inter-regional divergence can be captured by outgroup-f3-based genetic distances, but not by the commonly used FST statistic, due to the sensitivity of FST, but not outgroup-f3, to within-population diversity. Finally, we report a temporal trend of increasing male bias in admixture events through the Holocene.

RevDate: 2022-10-27
CmpDate: 2022-10-25

Kendler KS, A Klee (2022)

Hermann Hoffmann's 1921 Monograph: "The Offspring of Endogenous Psychoses: Genealogical-Characterological Examinations".

Schizophrenia bulletin, 48(Suppl 1):S20-S27.

Five years after the publication of Rüdin's major sibling study, Hermann Hoffmann, working with Rüdin, performed the first systematic study of the risk for dementia praecox (DP) in offspring of DP probands. Field work was limited to 3 months. Hoffmann ascertained families with at least one parent with certain DP, after Kraepelin, with children the youngest of whom were at least 30 years old. These families contained 103 offspring 30 years or older of whom 7 had definite DP and two possible DP for an estimated risk of 6.8%-8.7%. Hoffmann assessed schizoidia in these children, reporting the quite high risk figure of 47.6%. Hoffmann explored a wide range of two and three locus recessive models in his modest sample. He finds Rüdin's two locus recessive model at the boundary of his results and then reviews three additional more complex models. The simplest is a three-locus recessive model which fits his data better. He also explores an oligogenic three locus model with risk classes of individuals with 1 to 6 risk alleles and an epistatic model where two loci form a di-recessive model for schizoidia, and the third locus is a dominant required for the expression of psychosis. Hoffman questioned whether DP was a "unit-character" appropriate for Mendelian analysis and advocated for a much larger study of offspring. His work should be appreciated in light of his enthusiastic endorsement of Nazi eugenic goals.

RevDate: 2022-10-27
CmpDate: 2022-10-21

Kendler KS, A Klee (2022)

Rüdin's 1916 Monograph: On the Inheritance and Primary Origin of Dementia Praecox.

Schizophrenia bulletin, 48(Suppl 1):S8-S19.

In 1916, Ernst Rüdin published the first modern family study in the history of psychiatric genetics, the major goal of which was to test whether the pattern of risk in the siblings of dementia praecox (DP) probands followed Mendelian expectations. He utilized systematic ascertainment of probands and multisourced diagnostic assessments of probands and relatives, applying the narrow Kraepelinian concept of DP. In a novel step, he collaborated closely with a statistical geneticist-Wilhelm Weinberg-and applied his sibling, proband, and age correction methods. In his key sample-701 sibships when neither parent had DP-the morbid risk for DP in siblings was 4.48%, much lower than 25% expected for a recessive disorder. Risk for DP was increased by alcoholism or other mental disorders in parents. Other non-DP psychoses were common in both siblings and parents of DP probands. Rüdin discussed several alternative genetic models for DP including a 2-locus recessive, incomplete penetrance, and an oligogenic model. The high rates of other psychoses and psychopathic personalities in relatives might arise, he suggested, because these disorders shared genetic risks with DP. Rüdin established that DP, when carefully studied, ran in families, did not have a simple Mendelian genetic transmission pattern, and appeared likely to be genetically related to other non-DP psychotic disorders and perhaps some kinds of psychopathic personalities. This study, the most important in Rüdin's career, should be viewed in the context of his later extensive support of and collaboration with Nazi eugenic policies.

RevDate: 2023-02-22
CmpDate: 2022-10-05

Reitsema LJ, Mittnik A, Kyle B, et al (2022)

The diverse genetic origins of a Classical period Greek army.

Proceedings of the National Academy of Sciences of the United States of America, 119(41):e2205272119.

Trade and colonization caused an unprecedented increase in Mediterranean human mobility in the first millennium BCE. Often seen as a dividing force, warfare is in fact another catalyst of culture contact. We provide insight into the demographic dynamics of ancient warfare by reporting genome-wide data from fifth-century soldiers who fought for the army of the Greek Sicilian colony of Himera, along with representatives of the civilian population, nearby indigenous settlements, and 96 present-day individuals from Italy and Greece. Unlike the rest of the sample, many soldiers had ancestral origins in northern Europe, the Steppe, and the Caucasus. Integrating genetic, archaeological, isotopic, and historical data, these results illustrate the significant role mercenaries played in ancient Greek armies and highlight how participation in war contributed to continental-scale human mobility in the Classical world.

RevDate: 2022-10-15
CmpDate: 2022-09-13

Löwy I (2022)

Precision Medicine: Historiography of Life Sciences and the Geneticization of the Clinics.

Berichte zur Wissenschaftsgeschichte, 45(3):487-498.

In 2013, Hans Jörg Rheinberger proposed that Mendelian genetics and molecular biology were "scientific ideologies," that is, for him they are systems of thought whose objects are hyperbolic; they are not, or not yet, in the realm of and not, or not yet, under the control of that system. This article proposes that precision medicine today is a scientific ideology and analyses the implications of this statement for historians of biology, genetics, and medicine.

RevDate: 2023-04-03
CmpDate: 2022-08-29

Lazaridis I, Alpaslan-Roodenberg S, Acar A, et al (2022)

The genetic history of the Southern Arc: A bridge between West Asia and Europe.

Science (New York, N.Y.), 377(6609):eabm4247.

By sequencing 727 ancient individuals from the Southern Arc (Anatolia and its neighbors in Southeastern Europe and West Asia) over 10,000 years, we contextualize its Chalcolithic period and Bronze Age (about 5000 to 1000 BCE), when extensive gene flow entangled it with the Eurasian steppe. Two streams of migration transmitted Caucasus and Anatolian/Levantine ancestry northward, and the Yamnaya pastoralists, formed on the steppe, then spread southward into the Balkans and across the Caucasus into Armenia, where they left numerous patrilineal descendants. Anatolia was transformed by intra-West Asian gene flow, with negligible impact of the later Yamnaya migrations. This contrasts with all other regions where Indo-European languages were spoken, suggesting that the homeland of the Indo-Anatolian language family was in West Asia, with only secondary dispersals of non-Anatolian Indo-Europeans from the steppe.

RevDate: 2023-03-06
CmpDate: 2022-08-29

Lazaridis I, Alpaslan-Roodenberg S, Acar A, et al (2022)

Ancient DNA from Mesopotamia suggests distinct Pre-Pottery and Pottery Neolithic migrations into Anatolia.

Science (New York, N.Y.), 377(6609):982-987.

We present the first ancient DNA data from the Pre-Pottery Neolithic of Mesopotamia (Southeastern Turkey and Northern Iraq), Cyprus, and the Northwestern Zagros, along with the first data from Neolithic Armenia. We show that these and neighboring populations were formed through admixture of pre-Neolithic sources related to Anatolian, Caucasus, and Levantine hunter-gatherers, forming a Neolithic continuum of ancestry mirroring the geography of West Asia. By analyzing Pre-Pottery and Pottery Neolithic populations of Anatolia, we show that the former were derived from admixture between Mesopotamian-related and local Epipaleolithic-related sources, but the latter experienced additional Levantine-related gene flow, thus documenting at least two pulses of migration from the Fertile Crescent heartland to the early farmers of Anatolia.

RevDate: 2023-03-17
CmpDate: 2022-08-29

Lazaridis I, Alpaslan-Roodenberg S, Acar A, et al (2022)

A genetic probe into the ancient and medieval history of Southern Europe and West Asia.

Science (New York, N.Y.), 377(6609):940-951.

Literary and archaeological sources have preserved a rich history of Southern Europe and West Asia since the Bronze Age that can be complemented by genetics. Mycenaean period elites in Greece did not differ from the general population and included both people with some steppe ancestry and others, like the Griffin Warrior, without it. Similarly, people in the central area of the Urartian Kingdom around Lake Van lacked the steppe ancestry characteristic of the kingdom's northern provinces. Anatolia exhibited extraordinary continuity down to the Roman and Byzantine periods, with its people serving as the demographic core of much of the Roman Empire, including the city of Rome itself. During medieval times, migrations associated with Slavic and Turkic speakers profoundly affected the region.

RevDate: 2022-10-19
CmpDate: 2022-08-09

Silva NM, Kreutzer S, Souleles A, et al (2022)

Ancient mitochondrial diversity reveals population homogeneity in Neolithic Greece and identifies population dynamics along the Danubian expansion axis.

Scientific reports, 12(1):13474.

The aim of the study is to investigate mitochondrial diversity in Neolithic Greece and its relation to hunter-gatherers and farmers who populated the Danubian Neolithic expansion axis. We sequenced 42 mitochondrial palaeogenomes from Greece and analysed them together with European set of 328 mtDNA sequences dating from the Early to the Final Neolithic and 319 modern sequences. To test for population continuity through time in Greece, we use an original structured population continuity test that simulates DNA from different periods by explicitly considering the spatial and temporal dynamics of populations. We explore specific scenarios of the mode and tempo of the European Neolithic expansion along the Danubian axis applying spatially explicit simulations coupled with Approximate Bayesian Computation. We observe a striking genetic homogeneity for the maternal line throughout the Neolithic in Greece whereas population continuity is rejected between the Neolithic and present-day Greeks. Along the Danubian expansion axis, our best-fitting scenario supports a substantial decrease in mobility and an increasing local hunter-gatherer contribution to the gene-pool of farmers following the initial rapid Neolithic expansion. Οur original simulation approach models key demographic parameters rather than inferring them from fragmentary data leading to a better understanding of this important process in European prehistory.

RevDate: 2022-09-07
CmpDate: 2022-07-22

Barton NH (2022)

The "New Synthesis".

Proceedings of the National Academy of Sciences of the United States of America, 119(30):e2122147119.

When Mendel's work was rediscovered in 1900, and extended to establish classical genetics, it was initially seen in opposition to Darwin's theory of evolution by natural selection on continuous variation, as represented by the biometric research program that was the foundation of quantitative genetics. As Fisher, Haldane, and Wright established a century ago, Mendelian inheritance is exactly what is needed for natural selection to work efficiently. Yet, the synthesis remains unfinished. We do not understand why sexual reproduction and a fair meiosis predominate in eukaryotes, or how far these are responsible for their diversity and complexity. Moreover, although quantitative geneticists have long known that adaptive variation is highly polygenic, and that this is essential for efficient selection, this is only now becoming appreciated by molecular biologists-and we still do not have a good framework for understanding polygenic variation or diffuse function.

RevDate: 2022-08-17
CmpDate: 2022-07-21

McLysaght A (2022)

The deceptive simplicity of mendelian genetics.

PLoS biology, 20(7):e3001691.

Mendel, a genius experimentalist, meticulously uncovered the genetic basis of heredity in work that transformed the science of biology. But does the alluring simplicity of Mendel's laws sometimes obscure the true complexity of genetics?

RevDate: 2022-08-15
CmpDate: 2022-08-09

Pence CH (2022)

Of stirps and chromosomes: Generality through detail.

Studies in history and philosophy of science, 94:177-190.

One claim found in the received historiography of the biometrical school (comprised primarily of Francis Galton, Karl Pearson, and W. F. R. Weldon) is that one of the biometricians' great flaws was their inability to look past their population-focused, statistical, gradualist understanding of evolutionary change - which led, in part, to their ignoring developments in cellular biology around 1900. I will argue, on the contrary, that the work of the biometricians was, from its earliest days, fundamentally concerned with connections between statistical patterns of inheritance and the underlying cellular features that gave rise to them. Such work remained current with contemporary knowledge of chromosomes, cytology, and development; in this article, I explore the first case. The biometricians were thus well positioned to understand the relationship between the patterns of Mendelian inheritance and the statistical distributions with which they primarily occupied themselves. Ignorance of this connection, then, is not the reason why they rejected Mendelism. Further, both Galton and Weldon - though each in their own unique way - decided to turn to biological detail as a way to better justify the generality of their statistical approaches to heredity. Perhaps paradoxically, then, for these biometricians, detail offered an approach to theoretical generality.

RevDate: 2022-09-16
CmpDate: 2022-07-12

Cilia G, Flaminio S, M Quaranta (2022)

A novel and non-invasive method for DNA extraction from dry bee specimens.

Scientific reports, 12(1):11679.

In recent years molecular techniques have been used on museum material as integrative support for classic taxonomy. This cumulative systematics approach is especially for rare or extinct specimens, and genetic analysis may be useful to discern information that is not possible to glean from live materials or morphology. To date, the extraction of DNA required at least a partial destruction of the specimens, which is not possible for all individuals, especially the types. In this study, we described a novel method to extract mitochondrial DNA (mtDNA) from pinned museum bee individuals to avoid any external morphological damage. This method was able to amplify the mtDNA Cytochrome C oxidase subunit I (COI) gene in bee samples collected up to 27 years ago. We tested the efficacy of this method on 72 preserved be specimens belonging to nine species among four families, it could be used on many museums' rare and/or extinct bee species because it does not provide external morphological damages. The method could be helpful for providing ecological, taxonomic, and phylogenetic information about specimens preserved in museum collections.

RevDate: 2023-03-29
CmpDate: 2022-06-23

Ariano B, Mattiangeli V, Breslin EM, et al (2022)

Ancient Maltese genomes and the genetic geography of Neolithic Europe.

Current biology : CB, 32(12):2668-2680.e6.

Archaeological consideration of maritime connectivity has ranged from a biogeographical perspective that considers the sea as a barrier to a view of seaways as ancient highways that facilitate exchange. Our results illustrate the former. We report three Late Neolithic human genomes from the Mediterranean island of Malta that are markedly enriched for runs of homozygosity, indicating inbreeding in their ancestry and an effective population size of only hundreds, a striking illustration of maritime isolation in this agricultural society. In the Late Neolithic, communities across mainland Europe experienced a resurgence of hunter-gatherer ancestry, pointing toward the persistence of different ancestral strands that subsequently admixed. This is absent in the Maltese genomes, giving a further indication of their genomic insularity. Imputation of genome-wide genotypes in our new and 258 published ancient individuals allowed shared identity-by-descent segment analysis, giving a fine-grained genetic geography of Neolithic Europe. This highlights the differentiating effects of seafaring Mediterranean expansion and also island colonization, including that of Ireland, Britain, and Orkney. These maritime effects contrast profoundly with a lack of migratory barriers in the establishment of Central European farming populations from Anatolia and the Balkans.

RevDate: 2022-07-16
CmpDate: 2022-05-06

Gelabert P, Schmidt RW, Fernandes DM, et al (2022)

Genomes from Verteba cave suggest diversity within the Trypillians in Ukraine.

Scientific reports, 12(1):7242.

The transition to agriculture occurred relatively late in Eastern Europe, leading researchers to debate whether it was a gradual, interactive process or a colonisation event. In the forest and forest-steppe regions of Ukraine, farming appeared during the fifth millennium BCE, associated with the Cucuteni-Trypillia cultural complex (CTCC, ~ 5000-3000 BCE). Across Europe, the Neolithisation process was highly variable across space and over time. Here, we investigate the population dynamics of early agriculturalists from the eastern forest-steppe region based on the analyses of 20 ancient genomes from the site of Verteba Cave (3935-825 cal BCE). Results reveal that the CTCC individuals' ancestry is related to both western hunter-gatherers and Near Eastern farmers, has no local ancestry associated with Ukrainian Neolithic hunter-gatherers and has steppe ancestry. An Early Bronze Age individual has an ancestry profile related to the Yamnaya expansions but with 20% of ancestry related to the other Trypillian individuals, which suggests admixture between the Trypillians and the incoming populations carrying steppe-related ancestry. A Late Bronze Age individual dated to 980-825 cal BCE has a genetic profile indicating affinity to Beaker-related populations, detected close to 1000 years after the end of the Bell Beaker phenomenon during the third millennium BCE.

RevDate: 2022-06-24
CmpDate: 2022-06-16

Roll-Hansen N (2022)

A special role for the genotype? Some comments on Keith Baverstock: "The gene: An appraisal".

Progress in biophysics and molecular biology, 172:82-89.

There is at present uneasiness about the conceptual basis of genetics. The gene concept has become blurred and there are problems with the distinction between genotype and phenotype. In the present paper I go back to their role in the creation of modern genetics in the early twentieth century. The terms were introduced by the Danish botanist and geneticist Wilhelm Johannsen in his big textbook of 1909. Historical accounts usually concentrate on this book and his 1911 paper "The Genotype Conception of Heredity." His bean selection experiment of 1900-1903 is generally assumed to be the source of his genotype theory. The present paper examines the scientific context and meaning of this experiment, how it was received, and how the genotype theory became securely established by the early 1910s. I argue in conclusion that the genotype/phenotype distinction, which provides the empirical basis for Johannsen's gene, was scientifically well founded when introduced and still is. Keith Baverstock's criticism does not consider the force of the bean selection experiment at the time and as a paradigm for following investigations of heredity.

RevDate: 2022-05-12
CmpDate: 2022-05-12

Carlson SJ, Bauer CE, G Govindjee (2022)

Remembering Robert (Bob) Togasaki (1932-2019): A leader in Chlamydomonas genetics and in plant biology, as well as a teacher par excellence.

Photosynthesis research, 152(1):73-86.

Robert (Bob) K. Togasaki was devoted to science and the people in the scientific community. He elucidated some of the most fundamental aspects of photosynthesis and carbon metabolism through classic genetic approaches and later using the tools of modern biotechnology. Along the way, he freely shared his ideas and enthusiasm with established scientists, junior researchers, graduate students, and even elementary students. His career trajectory led him to work with some of the leaders in the field, including the late Martin Gibbs and R. Paul Levine. His dedicated research has led to a more complete understanding of some of the core biochemical functions relating to photosynthesis of the green alga Chlamydomonas; this has included carbon-concentrating mechanisms, hydrogenases, and superoxide dismutase to name just a few. The focus of this Tribute is personal reminiscences by his postdoctoral advisor R. Paul Levine; his collaborators Teruo Ogawa, Jean-David Rochaix, Hidehiro Sakurai, Michael Seibert; and by his students William Belknap, Susan Carlson, Charlene Forest, Arthur Grossman, Gregory Katzman, Masahiko Kitayama, and Jon Suzuki. All remember Bob Togasaki for his intellect, dedication to science education, and his unwavering goodwill and optimism towards his fellow human beings.

RevDate: 2022-05-02
CmpDate: 2022-05-02

Kendler KS, A Klee (2022)

The place of Franz Kallmann's 1938 "the genetics of schizophrenia" in the history of psychiatric genetics.

American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics, 189(1-2):26-36.

This essay provides the historical context and key findings of one of the largest fieldwork-based family studies ever done in the history of psychiatric genetics conducted in Berlin by Franz Kallmann from 1929 to 1933. It included over 1,000 schizophrenic probands and 12,500 of their relatives including siblings, offspring, nieces/nephews and grandchildren. The work was analyzed in close collaboration with Rüdin, Schulz, and Luxenburger in Munich. Born of Jewish parents, Kallmann had to leave Germany in 1936, completing and publishing the monograph in the United States in 1938. This study included a number of methodologic advances over the classic 1916 sibling study of Rüdin: (a) joint analysis of multiple classes of relatives; (b) subdivision of schizophrenia into four subtypes; (c) a focus on schizoid personality [schizoidia]; (d) examination of the familial aggregation of schizophrenia; and (e) a more complex genetic model-with schizophrenia arising from a single-recessive gene with 70% penetrance and background polygenic influences, and schizoidia from heterozygotes. Kallmann found important differences in risk of relatives in nuclear versus peripheral subtypes and concluded that schizoidia was a part of schizophrenia disease complex while other psychopathies, feeblemindedness, and organic brain disorders were not. Kallmann was strongly invested in the eugenic implications of his results.

RevDate: 2022-02-23
CmpDate: 2022-02-23

Anonymous (2022)

A very Mendelian year.

Nature genetics, 54(1):1.

RevDate: 2022-05-02
CmpDate: 2022-05-02

Kendler KS (2022)

The beginnings of biometrical psychiatric genetics: Studies of the insane diathesis 1905-1909.

American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics, 189(1-2):6-15.

The year 1900 saw not only the rediscovery of Mendel's hybridization studies but also the publication by Karl Pearson of his newly developed tetrachoric correlation which he used to study the parent-offspring resemblance for the "insane diathesis" in 1905. This was followed by more detailed reports by two of his students/associates: Heron in 1907 and Goring in 1909. Both calculated the tetrachoric correlation for insanity in parent-offspring and Heron for sib-sib pairs. Estimates ranged from approximately +0.30 to +0.60. These papers were statistically sophisticated but demonstrated minimal interest in the phenotype being studied. They are of historical interest because they laid the groundwork for biometrical psychiatric genetics which emerged as a major research paradigm in latter third of the 20th century. In a biting critique of Heron's paper by a young Ernst Rüdin, we see the beginnings of a long-running argument in psychiatric genetics about the relative value of detailed phenotyping versus novel statistical methods and of Mendelian versus Biometrical methods. While much interest has focused on the eugenic orientation of German psychiatric genetics in the early 20th century, these early British biometrical geneticists, like the majority of geneticists of that day, were also ardent advocates of the eugenic application of their research results.

RevDate: 2022-05-02
CmpDate: 2022-05-02

Kendler KS (2022)

The beginnings of the debate between the Mendelians and the Biometricians in psychiatric genetics: David Heron, Karl Pearson, Abraham Rosanoff, and Charles Davenport 1913-1914.

American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics, 189(1-2):16-25.

The world learned of the heated dispute about the methodology of the early works by Davenport and Rosanoff claiming Mendelian transmission patterns for mental handicap and psychiatric illness in a bold headline in the New York Times on Sunday, November 9, 1913: ENGLISH EXPERT ATTACKS AMERICAN EUGENIC WORK. I here focus on the debate surrounding Rosanoff's 1911 study where he presented evidence that the neuropathic constitution, including, among its manifestations, dementia praecox, and manic-depressive illness, was an autosomal recessive trait. The "English expert," David Heron, a student of Pearson's, launched the debate in his 1913 paper which argued that Rosanoff's field work methods were biased, his clinical assessments sloppy, his phenotype far too broad, and his statistical approach flawed. Both Davenport, Rosanoff's mentor, and Rosanoff vigorously defended their methods. Behind this sometimes personal debate was the long simmering controversy about the relative validity of Biometrical genetic (represented by Heron and Pearson) and Mendelian genetic (represented by Rosanoff and Davenport) models for genetic transmission in plants, animals and, especially, humans. A review suggests that most of Heron's criticisms were valid. This episode presages later controversies within psychiatric genetics, for example between twin and linkage researchers in the 1980s and 1990s.

RevDate: 2022-12-07
CmpDate: 2021-10-15

Kocher A, Papac L, Barquera R, et al (2021)

Ten millennia of hepatitis B virus evolution.

Science (New York, N.Y.), 374(6564):182-188.

Hepatitis B virus (HBV) has been infecting humans for millennia and remains a global health problem, but its past diversity and dispersal routes are largely unknown. We generated HBV genomic data from 137 Eurasians and Native Americans dated between ~10,500 and ~400 years ago. We date the most recent common ancestor of all HBV lineages to between ~20,000 and 12,000 years ago, with the virus present in European and South American hunter-gatherers during the early Holocene. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for ~4000 years, declining around the end of the 2nd millennium BCE. The only remnant of this prehistoric HBV diversity is the rare genotype G, which appears to have reemerged during the HIV pandemic.

RevDate: 2022-02-24
CmpDate: 2022-02-24

Puffenberger EG (2021)

Mendelian disease research in the Plain populations of Lancaster County, Pennsylvania.

American journal of medical genetics. Part A, 185(11):3322-3333.

Founder populations have long contributed to our knowledge of rare disease genes and phenotypes. From the pioneering work of Dr. Victor McKusick to today, research in these groups has shed light on rare recessive phenotypes, expanded the clinical spectrum of disease, and facilitated disease gene identification. Current clinical and research studies in these special groups augment the wealth of knowledge already gained, provide new insights into emerging problems such as variant interpretation and reduced penetrance, and contribute to the development of novel therapies for rare genetic diseases. Clinical developments over the past 30 years have altered the fundamental relationship with the Lancaster Plain communities: research has become more collaborative, and the knowledge imparted by these studies is now being harnessed to provide cutting-edge translational medicine to the very community of vulnerable individuals who need it most.

RevDate: 2022-02-24
CmpDate: 2022-02-24

Francomano CA (2021)

Victor Almon McKusick: In the footsteps of Mendel and Osler.

American journal of medical genetics. Part A, 185(11):3193-3201.

Victor Almon McKusick (VAM) is widely recognized as the father of the field of medical genetics. He established one of the first medical genetics clinics in the United States at Johns Hopkins in 1957 and developed a robust training program with the tripartite mission of education, research, and clinical care. Thousands of clinicians and scientists were educated over the years through the Short Course in Medical and Molecular Genetics, which VAM founded with Dr. Thomas Roderick in 1960. His Online Mendelian Inheritance in Man (OMIM), a catalog of human genes and genetic disorders, serves as the authoritative reference for geneticists around the globe. Throughout his career he was an advocate for mapping the human genome. He collaborated with Dr. Frank Ruddle in founding the International Human Gene Mapping Workshops in the early 70's and was an avid proponent of the Human Genome Project. He was the founding President of the Human Genome Organization and a founding editor of the journal Genomics. His prodigious contributions to the field of medical genetics were recognized by multiple honors, culminating with the Japan Prize in 2008.

RevDate: 2022-04-05
CmpDate: 2022-04-05

Shan Y (2021)

Beyond Mendelism and Biometry.

Studies in history and philosophy of science, 89:155-163.

Historiographical analyses of the development of genetics in the first decade of the 20th century have been to a great extent framed in the context of the Mendelian-Biometrician controversy. Much has been discussed on the nature, origin, development, and legacy of the controversy. However, such a framework is becoming less useful and fruitful. This paper challenges the traditional historiography framed by the Mendelian-Biometrician distinction. It argues that the Mendelian-Biometrician distinction fails to reflect the theoretical and methodological diversity in the controversy. It also argues that the Mendelian-Biometrician distinction is not helpful to make a full understanding of the development of genetics in the first decade of the twentieth century.

RevDate: 2022-01-13
CmpDate: 2022-01-13

Kendler KS (2021)

Ernst Rüdin's, 1911 vision of a Mendelian psychiatric genetics research program: His paper "Methods and goals of family research in psychiatry".

American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics, 186(5):279-288.

While working under Kraepelin in Munich, Ernst Rüdin, a Swiss-born Psychiatrist, at the age of 26, outlined in a 1911 98-page article, a detailed plan for a future Mendelian-informed family research program for psychiatry. Rüdin would go on to head the Department of Genealogical and Demographic Studies at Kraepelin's Research Institute which became one of the world's leading programs in psychiatric genetics. I here summarize this article, providing a complete translation online. Rüdin's review outlined a paradigm shift in psychiatric genetics research moving from calculations of aggregate hereditary burden, as they applied to the proband, to examining patterns of transmission within family pedigrees which involved careful individual assessments of relatives. He references widely clinical and statistical genetic studies, many focusing on the newly discovered Mendelian laws. However, Rüdin was no genetic reductionist but recognized the contribution of environmental risk factors to psychiatric illness arguing that they should be studied as part of a comprehensive research program. As a committed eugenicist, Rüdin also explored the implications of such a program for "racial hygiene." Rüdin's contributions should be viewed in the context of his extensive collaboration from 1933 to 1945 with the National Socialists and his support for their eugenics program, including involuntary sterilizations.

RevDate: 2021-10-11
CmpDate: 2021-10-11

Meza-Peñaloza A, Zertuche F, C Morehart (2021)

Population level comparisons in central Mexico using cranial nonmetric traits.

American journal of physical anthropology, 176(2):237-248.

OBJECTIVES: We study the genetic diversity between Classic Teotihuacan and its neighboring towns trying to understand how far or close they are at the genetic level.

MATERIALS AND METHODS: We use cranial nonmetric traits to study a sample of 280 adult skulls from archaeological sites running from the late Preclassic to the early Postclassic. Samples of Classic Teotihuacan were studied for La Ventilla and San Sebastián Xolalpan neighbors. For the Epiclassic period, samples from Xaltocan, Toluca valley, Mogotes and Xico were used. For the Preclassic and Postclassic samples from Xico were also used. We used a parametric bootstrap for the mean measure of divergence for the statistical analysis.

RESULTS: Samples from Xico have small biodistance from Preclassic to Postclassic. Samples from Los Mogotes differ depending on the functional context of deposition, with individuals from household burials (funerary) differing from non-funerary, ceremonial interments and exhibiting affinities to Epiclassic samples from Toluca valley. Epiclassic populations from Xaltocan vary significantly from any samples analyzed. Samples from Classic period Teotihuacan vary considerably among them but form a separate genetic group from all the other populations under study.

CONCLUSIONS: The great biodistance separation among Classic Teotihuacan and its neighbor villages of central Mexico let us conclude that, contrary from the classical idea that those villages were confirmed by the inhabitants of Teotihuacan's collapse: They indeed remain as separate populations by themselves.

RevDate: 2022-07-31
CmpDate: 2021-12-13

Rakotoambinina B, Hiffler L, F Gomes (2021)

Pediatric thiamine deficiency disorders in high-income countries between 2000 and 2020: a clinical reappraisal.

Annals of the New York Academy of Sciences, 1498(1):57-76.

Often thought to be a nutritional issue limited to low- and middle-income countries (LMICs), pediatric thiamine deficiency (PTD) is perceived as being eradicated or anecdotal in high-income countries (HICs). In HICs, classic beriberi cases in breastfed infants by thiamine-deficient mothers living in disadvantaged socioeconomic conditions are thought to be rare. This study aims to assess PTD in HICs in the 21st century. Literature searches were conducted to identify case reports of PTD observed in HICs and published between 2000 and 2020. The analyzed variables were age, country, underlying conditions, clinical manifestations of PTD, and response to thiamine supplementation. One hundred and ten articles were identified, totaling 389 PTD cases that were classified into four age groups: neonates, infants, children, and adolescents. Eleven categories of PTD-predisposing factors were identified, including genetic causes, lifestyle (diabetes, obesity, and excessive consumption of sweetened beverages), eating disorders, cancer, gastrointestinal disorders/surgeries, critical illness, and artificial nutrition. TD-associated hyperlactatemia and Wernicke encephalopathy were the most frequent clinical manifestations. The circumstances surrounding PTD in HICs differ from classic PTD observed in LMICs and this study delineates its mutiple predisposing factors. Further studies are required to estimate its magnitude. Awareness is of utmost importance in clinical practice.

RevDate: 2022-12-07
CmpDate: 2021-10-11

Juras A, Ehler E, Chyleński M, et al (2021)

Maternal genetic origin of the late and final Neolithic human populations from present-day Poland.

American journal of physical anthropology, 176(2):223-236.

OBJECTIVE: We aim to identify maternal genetic affinities between the Middle to Final Neolithic (3850-2300 BC) populations from present-day Poland and possible genetic influences from the Pontic steppe.

MATERIALS AND METHODS: We conducted ancient DNA studies from populations associated with Złota, Globular Amphora, Funnel Beaker, and Corded Ware cultures (CWC). We sequenced genomic libraries on Illumina platform to generate 86 complete ancient mitochondrial genomes. Some of the samples were enriched for mitochondrial DNA using hybridization capture.

RESULTS: The maternal genetic composition found in Złota-associated individuals resembled that found in people associated with the Globular Amphora culture which indicates that both groups likely originated from the same maternal genetic background. Further, these two groups were closely related to the Funnel Beaker culture-associated population. None of these groups shared a close affinity to CWC-associated people. Haplogroup U4 was present only in the CWC group and absent in Złota group, Globular Amphora, and Funnel Beaker cultures.

DISCUSSION: The prevalence of mitochondrial haplogroups of Neolithic farmer origin identified in Early, Middle and Late Neolithic populations suggests a genetic continuity of these maternal lineages in the studied area. Although overlapping in time - and to some extent - in cultural expressions, none of the studied groups (Złota, Globular Amphora, Funnel Beaker), shared a close genetic affinity to CWC-associated people, indicating a larger extent of cultural influence from the Pontic steppe than genetic exchange. The higher frequency of haplogroup U5b found in populations associated with Funnel Beaker, Globular Amphora, and Złota cultures suggest a gradual maternal genetic influx from Mesolithic hunter-gatherers. Moreover, presence of haplogroup U4 in Corded Ware groups is most likely associated with the migrations from the Pontic steppe at the end of the Neolithic and supports the observed genetic distances.

RevDate: 2022-02-24
CmpDate: 2022-02-24

Hamosh A, Amberger JS, Bocchini C, et al (2021)

Online Mendelian Inheritance in Man (OMIM®): Victor McKusick's magnum opus.

American journal of medical genetics. Part A, 185(11):3259-3265.

Victor McKusick's many contributions to medicine are legendary, but his magnum opus is Mendelian Inheritance in Man (MIM), his catalog of Mendelian phenotypes and their associated genes. The catalog, originally published in 1966 in book form, became available on the internet as Online Mendelian Inheritance in Man (OMIM®) in 1987. The first of 12 editions of MIM included 1486 entries; this number has increased to over 25,000 entries in OMIM as of April 2021, which demonstrates the growth of knowledge about Mendelian phenotypes and their genes through the years. OMIM now has over 20,000 unique users a day, including users from every country in the world. Many of the early decisions made by McKusick, such as to maintain MIM data in a computer-readable format, to separate phenotype entries from those for genes, and to give phenotypes and genes MIM numbers, have proved essential to the long-term utility and flexibility of his catalog. Based on his extensive knowledge of genetics and vision of its future in the field of medicine, he developed a framework for the capture and summary of information from the published literature on phenotypes and their associated genes; this catalog continues to serve as an indispensable resource to the genetics community.

RevDate: 2022-11-02
CmpDate: 2022-02-24

Rasmussen SA, Pomputius A, Amberger JS, et al (2021)

Viewing Victor McKusick's legacy through the lens of his bibliography.

American journal of medical genetics. Part A, 185(11):3212-3223.

Victor McKusick's contributions to the field of medical genetics are legendary and include his contributions as a mentor, as creator of Mendelian Inheritance in Man (now Online Mendelian Inheritance in Man [OMIM®]), and as a leader in the field of medical genetics. McKusick's full bibliography includes 772 publications. Here we review the 453 papers authored by McKusick and indexed in PubMed, from his earliest paper published in the New England Journal of Medicine in 1949 to his last paper published in American Journal of Medical Genetics Part A in 2008. This review of his bibliography chronicles McKusick's evolution from an internist and cardiologist with an interest in genetics to an esteemed leader in the growing field of medical genetics. Review of his bibliography also provides a historical perspective of the development of the discipline of medical genetics. This field came into its own during his lifetime, transitioning from the study of interesting cases and families used to codify basic medical genetics principles to an accredited medical specialty that is expected to transform healthcare. Along the way, he helped to unite the fields of medical and human genetics to focus on mapping the human genome, culminating in completion of the Human Genome Project. This review confirms the critical role played by Victor McKusick as the founding father of medical genetics.

RevDate: 2022-02-24
CmpDate: 2022-02-24

Antonarakis SE (2021)

History of the methodology of disease gene identification.

American journal of medical genetics. Part A, 185(11):3266-3275.

The past 45 years have witnessed a triumph in the discovery of genes and genetic variation that cause Mendelian disorders due to high impact variants. Important discoveries and organized projects have provided the necessary tools and infrastructure for the identification of gene defects leading to thousands of monogenic phenotypes. This endeavor can be divided in three phases in which different laboratory strategies were employed for the discovery of disease-related genes: (i) the biochemical phase, (ii) the genetic linkage followed by positional cloning phase, and (iii) the sequence identification phase. However, much more work is needed to identify all the high impact genomic variation that substantially contributes to the phenotypic variation.

RevDate: 2023-02-03
CmpDate: 2021-10-29

Lentz DL, Hamilton TL, Dunning NP, et al (2021)

Environmental DNA reveals arboreal cityscapes at the Ancient Maya Center of Tikal.

Scientific reports, 11(1):12725.

Tikal, a major city of the ancient Maya world, has been the focus of archaeological research for over a century, yet the interactions between the Maya and the surrounding Neotropical forests remain largely enigmatic. This study aimed to help fill that void by using a powerful new technology, environmental DNA analysis, that enabled us to characterize the site core vegetation growing in association with the artificial reservoirs that provided the city water supply. Because the area has no permanent water sources, such as lakes or rivers, these reservoirs were key to the survival of the city, especially during the population expansion of the Classic period (250-850 CE). In the absence of specific evidence, the nature of the vegetation surrounding the reservoirs has been the subject of scientific hypotheses and artistic renderings for decades. To address these hypotheses we captured homologous sequences of vascular plant DNA extracted from reservoir sediments by using a targeted enrichment approach involving 120-bp genetic probes. Our samples encompassed the time before, during and after the occupation of Tikal (1000 BCE-900 CE). Results indicate that the banks of the ancient reservoirs were primarily fringed with native tropical forest vegetation rather than domesticated species during the Maya occupation.

RevDate: 2022-07-16
CmpDate: 2022-01-03

Rohatgi A, Westerterp M, von Eckardstein A, et al (2021)

HDL in the 21st Century: A Multifunctional Roadmap for Future HDL Research.

Circulation, 143(23):2293-2309.

Low high-density lipoprotein cholesterol (HDL-C) characterizes an atherogenic dyslipidemia that reflects adverse lifestyle choices, impaired metabolism, and increased cardiovascular risk. Low HDL-C is also associated with increased risk of inflammatory disorders, malignancy, diabetes, and other diseases. This epidemiologic evidence has not translated to raising HDL-C as a viable therapeutic target, partly because HDL-C does not reflect high-density lipoprotein (HDL) function. Mendelian randomization analyses that have found no evidence of a causal relationship between HDL-C levels and cardiovascular risk have decreased interest in increasing HDL-C levels as a therapeutic target. HDLs comprise distinct subpopulations of particles of varying size, charge, and composition that have several dynamic and context-dependent functions, especially with respect to acute and chronic inflammatory states. These functions include reverse cholesterol transport, inhibition of inflammation and oxidation, and antidiabetic properties. HDLs can be anti-inflammatory (which may protect against atherosclerosis and diabetes) and proinflammatory (which may help clear pathogens in sepsis). The molecular regulation of HDLs is complex, as evidenced by their association with multiple proteins, as well as bioactive lipids and noncoding RNAs. Clinical investigations of HDL biomarkers (HDL-C, HDL particle number, and apolipoprotein A through I) have revealed nonlinear relationships with cardiovascular outcomes, differential relationships by sex and ethnicity, and differential patterns with coronary versus noncoronary events. Novel HDL markers may also have relevance for heart failure, cancer, and diabetes. HDL function markers (namely, cholesterol efflux capacity) are associated with coronary disease, but they remain research tools. Therapeutics that manipulate aspects of HDL metabolism remain the holy grail. None has proven to be successful, but most have targeted HDL-C, not metrics of HDL function. Future therapeutic strategies should focus on optimizing HDL function in the right patients at the optimal time in their disease course. We provide a framework to help the research and clinical communities, as well as funding agencies and stakeholders, obtain insights into current thinking on these topics, and what we predict will be an exciting future for research and development on HDLs.

RevDate: 2021-08-19
CmpDate: 2021-08-19

McGovern MF (2021)

Genes go digital: Mendelian Inheritance in Man and the genealogy of electronic publishing in biomedicine.

British journal for the history of science, 54(2):213-231.

Mendelian Inheritance in Man (MIM), a computerized catalogue of human genetic disorders authored and maintained by cardiologist and medical genetics pioneer Victor A. McKusick, played a major part in demarcating between a novel biomedical science and the eugenic projects of racial betterment which existed prior to its emergence. Nonetheless, it built upon prior efforts to systematize genetic knowledge tied to individuals and institutions invested in eugenics. By unpacking the process of digitizing a homespun cataloguing project and charting its development into an online database, this article aims to illuminate how the institution-building efforts of one individual created an 'information order' for accessing genetic information that tacitly shaped the norms and priorities of the field toward the pursuit of specific genes associated with discernible genetic disorders. This was not by design, but rather arose through negotiation with the catalogue's users; it accommodated further changes as biomedical research displaced the Mendelian paradigm. While great effort was expended toward making sequence data available to investigators during the Human Genome Project, MIM was largely taken for granted as a 'legacy system', McKusick's own labour of love. Drawing on recent histories of biomedical data, the article suggests that the bibliographical work of curation and translation is a central feature of value production in the life sciences meriting attention in its own right.

RevDate: 2021-09-17
CmpDate: 2021-09-17

Battaglia A, JC Carey (2021)

Reflections on observing faces in art.

American journal of medical genetics. Part C, Seminars in medical genetics, 187(2):144-147.

The experience of art provides the visitor of a museum or gallery with the opportunity to contemplate and share the human condition both from the physical and psychological point of view. Because of the accessibility and the number of museums throughout Europe, classical European art as both sculpture and painting, affords the viewer the opportunity to experience life from one part of the world over centuries of history. These museums occasionally exhibit pieces showing a person with a human disorder and physical differences. On viewing such artwork, practitioners of health care, especially dysmorphologists, usually find themselves observing such pieces within the context of their practice. In this essay, the coauthors reflect on paintings and sculptures which remind us of our patients with similar physical and medical conditions. Various works of art also provide the opportunity to observe and view the human face from many vantage points and times in history. Several paintings are cited to illustrate the central themes of the Commentary: the human circumstance of disease and differences and the skill of observing and describing the human face.

RevDate: 2022-02-24
CmpDate: 2022-02-24

Saupe T, Montinaro F, Scaggion C, et al (2021)

Ancient genomes reveal structural shifts after the arrival of Steppe-related ancestry in the Italian Peninsula.

Current biology : CB, 31(12):2576-2591.e12.

Across Europe, the genetics of the Chalcolithic/Bronze Age transition is increasingly characterized in terms of an influx of Steppe-related ancestry. The effect of this major shift on the genetic structure of populations in the Italian Peninsula remains underexplored. Here, genome-wide shotgun data for 22 individuals from commingled cave and single burials in Northeastern and Central Italy dated between 3200 and 1500 BCE provide the first genomic characterization of Bronze Age individuals (n = 8; 0.001-1.2× coverage) from the central Italian Peninsula, filling a gap in the literature between 1950 and 1500 BCE. Our study confirms a diversity of ancestry components during the Chalcolithic and the arrival of Steppe-related ancestry in the central Italian Peninsula as early as 1600 BCE, with this ancestry component increasing through time. We detect close patrilineal kinship in the burial patterns of Chalcolithic commingled cave burials and a shift away from this in the Bronze Age (2200-900 BCE) along with lowered runs of homozygosity, which may reflect larger changes in population structure. Finally, we find no evidence that the arrival of Steppe-related ancestry in Central Italy directly led to changes in frequency of 115 phenotypes present in the dataset, rather that the post-Roman Imperial period had a stronger influence, particularly on the frequency of variants associated with protection against Hansen's disease (leprosy). Our study provides a closer look at local dynamics of demography and phenotypic shifts as they occurred as part of a broader phenomenon of widespread admixture during the Chalcolithic/Bronze Age transition.

RevDate: 2021-12-21
CmpDate: 2021-12-21

Clemente F, Unterländer M, Dolgova O, et al (2021)

The genomic history of the Aegean palatial civilizations.

Cell, 184(10):2565-2586.e21.

The Cycladic, the Minoan, and the Helladic (Mycenaean) cultures define the Bronze Age (BA) of Greece. Urbanism, complex social structures, craft and agricultural specialization, and the earliest forms of writing characterize this iconic period. We sequenced six Early to Middle BA whole genomes, along with 11 mitochondrial genomes, sampled from the three BA cultures of the Aegean Sea. The Early BA (EBA) genomes are homogeneous and derive most of their ancestry from Neolithic Aegeans, contrary to earlier hypotheses that the Neolithic-EBA cultural transition was due to massive population turnover. EBA Aegeans were shaped by relatively small-scale migration from East of the Aegean, as evidenced by the Caucasus-related ancestry also detected in Anatolians. In contrast, Middle BA (MBA) individuals of northern Greece differ from EBA populations in showing ∼50% Pontic-Caspian Steppe-related ancestry, dated at ca. 2,600-2,000 BCE. Such gene flow events during the MBA contributed toward shaping present-day Greek genomes.

RevDate: 2023-01-31
CmpDate: 2021-05-03

von Seth J, Dussex N, Díez-Del-Molino D, et al (2021)

Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations.

Nature communications, 12(1):2393.

Small populations are often exposed to high inbreeding and mutational load that can increase the risk of extinction. The Sumatran rhinoceros was widespread in Southeast Asia, but is now restricted to small and isolated populations on Sumatra and Borneo, and most likely extinct on the Malay Peninsula. Here, we analyse 5 historical and 16 modern genomes from these populations to investigate the genomic consequences of the recent decline, such as increased inbreeding and mutational load. We find that the Malay Peninsula population experienced increased inbreeding shortly before extirpation, which possibly was accompanied by purging. The populations on Sumatra and Borneo instead show low inbreeding, but high mutational load. The currently small population sizes may thus in the near future lead to inbreeding depression. Moreover, we find little evidence for differences in local adaptation among populations, suggesting that future inbreeding depression could potentially be mitigated by assisted gene flow among populations.

RevDate: 2022-02-11
CmpDate: 2022-02-11

Yaka R, Mapelli I, Kaptan D, et al (2021)

Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes.

Current biology : CB, 31(11):2455-2468.e18.

The social organization of the first fully sedentary societies that emerged during the Neolithic period in Southwest Asia remains enigmatic,[1] mainly because material culture studies provide limited insight into this issue. However, because Neolithic Anatolian communities often buried their dead beneath domestic buildings,[2] household composition and social structure can be studied through these human remains. Here, we describe genetic relatedness among co-burials associated with domestic buildings in Neolithic Anatolia using 59 ancient genomes, including 22 new genomes from Aşıklı Höyük and Çatalhöyük. We infer pedigree relationships by simultaneously analyzing multiple types of information, including autosomal and X chromosome kinship coefficients, maternal markers, and radiocarbon dating. In two early Neolithic villages dating to the 9th and 8th millennia BCE, Aşıklı Höyük and Boncuklu, we discover that siblings and parent-offspring pairings were frequent within domestic structures, which provides the first direct indication of close genetic relationships among co-burials. In contrast, in the 7th millennium BCE sites of Çatalhöyük and Barcın, where we study subadults interred within and around houses, we find close genetic relatives to be rare. Hence, genetic relatedness may not have played a major role in the choice of burial location at these latter two sites, at least for subadults. This supports the hypothesis that in Çatalhöyük,[3-5] and possibly in some other Neolithic communities, domestic structures may have served as burial location for social units incorporating biologically unrelated individuals. Our results underscore the diversity of kin structures in Neolithic communities during this important phase of sociocultural development.

RevDate: 2022-10-05
CmpDate: 2021-08-26

Masiuk S, Chepurny M, Buderatska V, et al (2021)

Thyroid doses in Ukraine due to [131]I intake after the Chornobyl accident. Report I: revision of direct thyroid measurements.

Radiation and environmental biophysics, 60(2):267-288.

The increased risk of thyroid cancer among individuals exposed during childhood and adolescence to Iodine-131 ([131]I) is the main statistically significant long-term effect of the Chornobyl accident. Several radiation epidemiological studies have been carried out or are currently in progress in Ukraine, to assess the risk of radiation-related health effects in exposed populations. About 150,000 measurements of [131]I thyroid activity, so-called 'direct thyroid measurements', performed in May-June 1986 in the Ukrainian population served as the main sources of data used to estimate thyroid doses to the individuals of these studies. However, limitations in the direct thyroid measurements have been recently recognized including improper measurement geometry and unknown true values of calibration coefficients for unchecked thyroid detectors. In the present study, a comparative analysis of [131]I thyroid activity measured by calibrated and unchecked devices in residents of the same neighboring settlements was conducted to evaluate the correct measurement geometry and calibration coefficients for measuring devices. As a result, revised values of [131]I thyroid activity were obtained. On average, in Vinnytsia, Kyiv, Lviv and Chernihiv Oblasts and in the city of Kyiv, the revised values of the [131]I thyroid activities were found to be 10-25% higher than previously reported, while in Zhytomyr Oblast, the values of the revised activities were found to be lower by about 50%. New sources of shared and unshared errors associated with estimates of [131]I thyroid activity were identified. The revised estimates of thyroid activity are recommended to be used to develop an updated Thyroid Dosimetry system (TD20) for the entire population of Ukraine as well as to revise the thyroid doses for the individuals included in post-Chornobyl radiation epidemiological studies: the Ukrainian-American cohort of individuals exposed during childhood and adolescence, the Ukrainian in utero cohort and the Chornobyl Tissue Bank.

RevDate: 2021-04-26
CmpDate: 2021-04-26

Kendler KS (2021)

Kraepelin's final views on manic-depressive Illness.

Journal of affective disorders, 282:979-990.

At the age of 65, 8 years after finishing his last textbook edition, Emil Kraepelin completed the final edition of his "Introduction to Clinical Psychiatry" which included a mini-textbook for students with a 7-page section on manic-depressive insanity (MDI), a disorder he had formally proposed 22 years earlier, and a series of new detailed case histories, 9 of which examined MDI. This text distills, near the end of his life, Kraepelin's perspective of the key features of MDI. The text and case histories are here translated into English for the first time. Kraepelin's views of the symptoms and signs of melancholia and mania closely aligned to those proposed by DSM-5. He emphasized the importance both of mixed features and the constitutional/personality foundations of MDI suggesting that a particular emotional disposition is often seen both inter-episodically in affected individuals (where they "fill the entire life") and in their unaffected relatives. He illustrates both these points in his case reports. His cases also made clear that for Kraepelin, classical Schneiderian psychotic symptoms and a full catatonic syndrome were consistent with a diagnosis of MDI.

RevDate: 2023-01-29
CmpDate: 2021-03-09

Bergström A, Stringer C, Hajdinjak M, et al (2021)

Origins of modern human ancestry.

Nature, 590(7845):229-237.

New finds in the palaeoanthropological and genomic records have changed our view of the origins of modern human ancestry. Here we review our current understanding of how the ancestry of modern humans around the globe can be traced into the deep past, and which ancestors it passes through during our journey back in time. We identify three key phases that are surrounded by major questions, and which will be at the frontiers of future research. The most recent phase comprises the worldwide expansion of modern humans between 40 and 60 thousand years ago (ka) and their last known contacts with archaic groups such as Neanderthals and Denisovans. The second phase is associated with a broadly construed African origin of modern human diversity between 60 and 300 ka. The oldest phase comprises the complex separation of modern human ancestors from archaic human groups from 0.3 to 1 million years ago. We argue that no specific point in time can currently be identified at which modern human ancestry was confined to a limited birthplace, and that patterns of the first appearance of anatomical or behavioural traits that are used to define Homo sapiens are consistent with a range of evolutionary histories.

RevDate: 2021-04-22
CmpDate: 2021-04-22

Mineta K, Goto K, Gojobori T, et al (2021)

Population structure of indigenous inhabitants of Arabia.

PLoS genetics, 17(1):e1009210.

Modern day Saudi Arabia occupies the majority of historical Arabia, which may have contributed to ancient waves of migration out of Africa. This ancient history has left a lasting imprint in the genetics of the region, including the diverse set of tribes that call Saudi Arabia their home. How these tribes relate to each other and to the world's major populations remains an unanswered question. In an attempt to improve our understanding of the population structure of Saudi Arabia, we conducted genomic profiling of 957 unrelated individuals who self-identify with 28 large tribes in Saudi Arabia. Consistent with the tradition of intra-tribal unions, the subjects showed strong clustering along tribal lines with the distance between clusters correlating with their geographical proximities in Arabia. However, these individuals form a unique cluster when compared to the world's major populations. The ancient origin of these tribal affiliations is supported by analyses that revealed little evidence of ancestral origin from within the 28 tribes. Our results disclose a granular map of population structure and have important implications for future genetic studies into Mendelian and common diseases in the region.

RevDate: 2021-03-15
CmpDate: 2021-03-15

Scharf ME, BF Peterson (2021)

A Century of Synergy in Termite Symbiosis Research: Linking the Past with New Genomic Insights.

Annual review of entomology, 66:23-43.

Termites have long been studied for their symbiotic associations with gut microbes. In the late nineteenth century, this relationship was poorly understood and captured the interest of parasitologists such as Joseph Leidy; this research led to that of twentieth-century biologists and entomologists including Cleveland, Hungate, Trager, and Lüscher. Early insights came via microscopy, organismal, and defaunation studies, which led to descriptions of microbes present, descriptions of the roles of symbionts in lignocellulose digestion, and early insights into energy gas utilization by the host termite. Focus then progressed to culture-dependent microbiology and biochemical studies of host-symbiont complementarity, which revealed specific microhabitat requirements for symbionts and noncellulosic mechanisms of symbiosis (e.g., N2 fixation). Today, knowledge on termite symbiosis has accrued exponentially thanks to omic technologies that reveal symbiont identities, functions, and interdependence, as well as intricacies of host-symbiont complementarity. Moving forward, the merging of classical twentieth-century approaches with evolving omic tools should provide even deeper insights into host-symbiont interplay.

RevDate: 2021-10-08
CmpDate: 2021-10-08

Mishcheniuk OY, Kostiukevych OM, Benkovska LK, et al (2020)


Problemy radiatsiinoi medytsyny ta radiobiolohii, 25:502-515.

UNLABELLED: Thrombosis triggers, in addition to «classic» risk factors (RFs) of cardiovascular events, includes the reactive changesof peripheral blood (RCPB), markers of the hereditary thrombophilia and radiation anamnesis. However, results ofmost studies suggest the «classic» RFs are able to neutralize the prothrombogenic potential of the hereditary thrombophilia and other, less powerful predictors of thrombosis.

OBJECTIVE: to determine the influence of the G1691A allele of the proaccelerin gene carrying to the thrombosis development, taking into account the vascular type of their occurrence, the presence of RFs in individuals with RCPB (reactive leukocytosis and thrombocytosis, and secondary erythrocytosis), as well as with and without radiation anamnesis.

MATERIAL AND METHODS: In general, it was analyzed the results of clinical and molecular-genetic data of 152 patientswith RCPB, 19 patients had radiation anamnesis, 133 - did not have. The thrombotic complications were detected in5 (26.31 %) of radiation-exposer patients and 25 (18.79 %) patients without radiation anamneses. The carrying ofthe G1691A allele proaccelerin gene (APG) (Leiden mutation (LM)) was detected using the allele-specific polymerasechain reaction.

RESULTS: The LM was found in 5.9 % (9 carriers) of the general cohort (GC) of RPBC patients. There were no differencein the LM frequency between the groups of patients with and without radiation anamnesis (р = 0.312). In the groupof radiation-exposer patients (р = 0.017), as well as in the group without its (р = 0.031), venous thromboses only weremore frequently in the LM carriers. In the presence of a radiation anamnesis, G1691A APG carriers with RFs have thehigher frequency (р = 0.008) and the probability of the occurrence (relative risk [RR] = 25.00; CI 95 %: 1.56-399.68)of venous thrombosis. In the group without radiation anamnesis, the frequency of venues thrombosis in the LMcarriers is higher in the younger age subgroup (р = 0.001), without RFs (p = 0.044) and without RFs under 60 years(р = 0.023). The risk of venous thrombosis in the G1691A APG carriers of the group without radiation anamnesis is5.78 (95 % CI: 1.58-21.13). In LM carriers without radiation anamnesis and RFs, as well as under the 60 years of age,the probability of venous thrombosis was 6.85 (95 % CI: 1.86-25.22) and 19.40 (95 % CI: 4.64-81.09), respectively,and in the absence of both criteria - 9.57 (95 % CI: 2.49-36.73).

CONCLUSIONS: In patients with and without radiation anamnesis, the risk of venues thrombosis are observed moreoften in carriers of LM. The carrying of the G1691A APG in patients with RPBC and without RA increased the risk ofvenues thrombosis development in subjects without FRs and below 60 years of age. In the radiation-exposure group,the frequency and the risk of venues thrombosis in the G1691A APG carriers was higher in the subgroup with RFs. It isprobably due to the peculiarity of the samples, or prothrombogenic interaction between LM and radiation-associated endothelial damage.

RevDate: 2021-10-08
CmpDate: 2021-10-08

Dyagil IS, Dmytrenko IV, Sholoiko VV, et al (2020)


Problemy radiatsiinoi medytsyny ta radiobiolohii, 25:443-455.

OBJECTIVE: Describe and characterize the peculiarities of the chronic myeloid leukemia (CML) course and responseto treatment in patients irradiated as a result of the Chornobyl nuclear power plant (ChNPP) accident based on theassessment of clinical-laboratory and clinical parameters.

MATERIALS AND METHODS: The CML patients (n = 33) exposed to ionizing radiation as a result of the ChNPP accidentwere enrolled. The comparison group consisted of CML patients (n = 725) with no history of radiation exposure. Allpatients were in the chronic phase of the disease. Clinical, hematological and molecular genetic research methodswere applied.

RESULTS: Patients exposed to ionizing radiation as a result of the ChNPP accident had no differences in CML manifestation, as well as in classical genetic markers at the onset of the disease compared with patients with no historyof radiation exposure. Reduction of tumor clone on imatinib therapy was significantly less effective in the patientsexposed to ionizing radiation than in cases of no history of radiation exposure. Cases of primary resistance were statistically significantly prevalent in the ChNPP accident consequences clean-up workers while in the residents ofradiologically contaminated areas a statistically significant increase in probability of loss of complete cytogeneticresponse (development of secondary resistance) to imatinib therapy was found. An association was found betweenthe radiation exposure and probability of loss of complete cytogenetic response to imatinib therapy in this group ofpatients.

CONCLUSION: The radiation exposure in the history even many years before the onset of CML is an unfavorable exogenous factor responsible for the development of resistance to imatinib therapy.

RevDate: 2021-10-12
CmpDate: 2021-03-18

Hoyal Cuthill JF, Guttenberg N, GE Budd (2020)

Impacts of speciation and extinction measured by an evolutionary decay clock.

Nature, 588(7839):636-641.

The hypothesis that destructive mass extinctions enable creative evolutionary radiations (creative destruction) is central to classic concepts of macroevolution[1,2]. However, the relative impacts of extinction and radiation on the co-occurrence of species have not been directly quantitatively compared across the Phanerozoic eon. Here we apply machine learning to generate a spatial embedding (multidimensional ordination) of the temporal co-occurrence structure of the Phanerozoic fossil record, covering 1,273,254 occurrences in the Paleobiology Database for 171,231 embedded species. This facilitates the simultaneous comparison of macroevolutionary disruptions, using measures independent of secular diversity trends. Among the 5% most significant periods of disruption, we identify the 'big five' mass extinction events[2], seven additional mass extinctions, two combined mass extinction-radiation events and 15 mass radiations. In contrast to narratives that emphasize post-extinction radiations[1,3], we find that the proportionally most comparable mass radiations and extinctions (such as the Cambrian explosion and the end-Permian mass extinction) are typically decoupled in time, refuting any direct causal relationship between them. Moreover, in addition to extinctions[4], evolutionary radiations themselves cause evolutionary decay (modelled co-occurrence probability and shared fraction of species between times approaching zero), a concept that we describe as destructive creation. A direct test of the time to over-threshold macroevolutionary decay[4] (shared fraction of species between two times ≤ 0.1), counted by the decay clock, reveals saw-toothed fluctuations around a Phanerozoic mean of 18.6 million years. As the Quaternary period began at a below-average decay-clock time of 11 million years, modern extinctions further increase life's decay-clock debt.

RevDate: 2021-08-30
CmpDate: 2021-08-30

Tunlid A, Kristoffersson U, F Åström (2020)

A century of Hereditas: from local publication to international journal.

Hereditas, 157(1):50.

BACKGROUND: The Mendelian Society of Lund launched Hereditas in 1920. The purpose of this article is to give an overview of Hereditas's hundred-year existence, focusing on the conditions for a learned society to publish a scientific journal, and the journal's importance for the publication and dissemination of genetic research. The article focuses on the historical development of the journal and analyses how the content and orientation of research published in Hereditas have changed over the years.

METHODS: The historical study is based on the collation and interpretation of archival material, mainly held in the Mendelian Society's archive, which includes the Hereditas archive. The bibliometric analyses are based on bibliographic metadata from Web of Science (WoS). Together with descriptive statistics, co-citation analyses were performed by using BibExcel, in combination with the clustering and visualisation tool VOSviewer. Journals with articles citing Hereditas articles were identified as a complement to the co-citation analyses.

RESULTS: The history of the journal falls into three main periods: a local period, 1920-1959, when Hereditas was primarily intended for Swedish geneticists; a Scandinavian period, 1960-1988, when Hereditas was the official journal of the Scandinavian Association of Geneticists; and an international period from 1989 onwards. The original decision that Hereditas should cover genetic research with no particular specialisation was retained throughout. Its publications demonstrate the continuing presence of genetic research on plants and animals, albeit with a shifting focus, while human genetics emerged slowly and reached its peak in the period 1960-1988.

CONCLUSION: In the hundred years of Hereditas's existence, the publishing landscape has changed dramatically, including a far greater number of specialist journals, changes to the academic merit system, new commercial models for publishing, and digitalisation. Over the years, the journal's survival has therefore been dependent on the strong commitment of its owners and an ability to adapt to changing conditions.

RevDate: 2021-06-17
CmpDate: 2021-06-17

Nicholas FW (2021)

Online Mendelian Inheritance in Animals (OMIA): a record of advances in animal genetics, freely available on the Internet for 25 years.

Animal genetics, 52(1):3-9.

For the last 25 years, Online Mendelian Inheritance in Animals (OMIA) has been providing free global access to an ever-increasing record of discoveries made by animal geneticists around the world. To mark this 25-year milestone, this document provides a brief account (including some pre-history) of how OMIA came to be; some timelines of important discoveries and advances in the genetics of the animal species covered by OMIA, gleaned from the OMIA database; and an analysis of the current state of knowledge regarding likely causal variants of single-locus traits in OMIA species, also gleaned from the OMIA database.

RevDate: 2021-01-27
CmpDate: 2021-01-27

Gombeau K, Bonzom JM, Cavalié I, et al (2020)

Dose-dependent genomic DNA hypermethylation and mitochondrial DNA damage in Japanese tree frogs sampled in the Fukushima Daiichi area.

Journal of environmental radioactivity, 225:106429.

The long-term consequences of the nuclear disaster at the Fukushima Daiichi Nuclear Power Plant (FDNPP) that occurred on March 2011, have been scarcely studied on wildlife. We sampled Japanese tree frogs (Dryophytes japonicus), in a 50 -km area around the FDNPP to test for an increase of DNA damages and variation of DNA methylation level. The ambient dose rate ranged between 0.4 and 2.8 μGy h[-1] and the total estimated dose rate absorbed by frogs ranged between 0.3 and 7.7 μGy h[-1]. Frogs from contaminated sites exhibited a dose-dependent increase of global genomic DNA methylation level (5-mdC and 5-hmdC) and of mitochondrial DNA damages. Such DNA damages may indicate a genomic instability, which may induce physiological adaptations governed by DNA methylation changes. This study stresses the need for biological data combining targeted molecular methods and classic ecotoxicology, in order to better understand the impacts on wildlife of long term exposure to low ionizing radiation levels.

RevDate: 2021-12-21
CmpDate: 2021-02-26

Kitahara CM, Sosa JA, MS Shiels (2020)

Influence of Nomenclature Changes on Trends in Papillary Thyroid Cancer Incidence in the United States, 2000 to 2017.

The Journal of clinical endocrinology and metabolism, 105(12):e4823-30.

CONTEXT: US papillary thyroid carcinoma (PTC) incidence recently declined for the first time in decades, for reasons that remain unclear.

OBJECTIVE: This work aims to evaluate PTC incidence trends, including by histologic subtype and size, and noninvasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP).

DESIGN: This descriptive study uses US Surveillance, Epidemiology, and End Results-18 cancer registry data (2000-2017).

PATIENTS: Participants included individuals diagnosed with PTC (2000-2017) or NIFTP (2016-2017).

RESULTS: During 2000 to 2015, PTC incidence increased an average 7.3% per year, (95% CI, 6.9% to 7.8%) during 2000 to 2009, and 3.7% per year (95% CI, 0.2% to 7.3%) during 2009 to 2012, before stabilizing in 2012 to 2015 (annual percentage change [APC] = 1.4% per year, 95% CI, -1.8% to 4.7%) and declining in 2015 to 2017 (APC = -4.6% per year, 95% CI, -7.6% to -1.4%). The recent declines were observed for all sizes of PTC at diagnosis. Incidence of follicular variant of PTC (FVPTC) sharply declined in 2015 to 2017, overall (APC = -21.1% per year; 95% CI, -26.5% to -15.2%) and for all tumor sizes. Observed increases in encapsulated papillary carcinoma (classical PTC subtype) and NIFTP each accounted for 10% of the decline in FVPTC. Classical PTC incidence continuously increased (2000-2009, APC = 8.7% per year, 95% CI, 8.1% to 9.4%; 2009-2017, APC = 1.0% per year, 95% CI, 0.4% to 1.5%), overall and for all sizes except smaller than 1 cm, as did incidence of other PTC variants combined (2000-2017, APC = 5.9% per year, 95% CI, 4.0% to 7.9%).

CONCLUSION: The reasons underlying PTC incidence trends were multifactorial. Sharp declines in FVPTC incidence during 2015 to 2017 coincided with clinical practice and diagnostic coding changes, including reclassification of noninvasive encapsulated FVPTC from a malignant to in situ neoplasm (NIFTP). Observed increases in NIFTP accounted for 10% of the decline in FVPTC.

RevDate: 2021-06-03
CmpDate: 2021-06-03

Kendler KS, A Klee (2020)

The turn to controls and the refinement of the concept of hereditary burden: The 1895 study of Jenny Koller.

American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics, 183(7):433-442.

Throughout the 19th century, many alienists reported the proportion of their patients who were "hereditarily burdened," meaning they had a positive family history for mental illness. The rates of such burden differed widely because different authors used divergent definition of illness and investigated different groups of relatives. Most importantly, no authors compared rates of burden with those seen in a nonpatient control group. The first such study in the history of psychiatric genetics was published in 1895, the doctoral dissertation of a Swiss physician Jenny Koller working under Auguste Forel. She obtained histories of a range of mental/neurologic disorders in the parents, aunts/uncles, grandparents and siblings of 370 hospitalized psychiatric patients and 370 controls. Rates of any hereditary burden were only modestly higher in cases (78%) than controls (59%). However, when examining individual syndromes, only major mental illness and eccentricities, but not apoplexy, nervous disorders or dementia, were more common in proband than control families. Furthermore, the rates of mental illness and eccentricities were substantially elevated in the first-degree relatives of cases versus controls but not in the second-degree relatives. Koller's study represented a major methodological advance in psychiatric genetics, helping to define which disorders coaggregated with major mental illness.

RevDate: 2021-08-18
CmpDate: 2021-08-18

Huminiecki Ł (2020)

A Contemporary Message from Mendel's Logical Empiricism.

BioEssays : news and reviews in molecular, cellular and developmental biology, 42(9):e2000120.

The gene is one of the most fundamental concepts in life sciences, having been developed in the mold of the Mendelian paradigm of heredity, which shaped genetics across 150 years. How could Mendel possibly be so prophetic in the middle of 19[th] century, using only the small garden of the monastery as his experimental breeding field? I believe that we are indebted to Mendel's mastery of the scientific method, which was far ahead of his time. Although his experimental technology was literally garden-variety, Mendel's excellence in the method of science, algebra, and logical analysis helped him in designing the right experiment and in interpreting the results insightfully. This may be valuable to recall in today's technology-focused culture, where the center of interest tends to be on the generation and description of high-throughput datasets from specialized genomics screens. As Mendel's story suggests, progress in 21[st] century genetics may also depend on the development of robust concepts and generalizations.

RevDate: 2020-10-07
CmpDate: 2020-10-07

Hegele RA, JS Dron (2020)

2019 George Lyman Duff Memorial Lecture: Three Decades of Examining DNA in Patients With Dyslipidemia.

Arteriosclerosis, thrombosis, and vascular biology, 40(9):1970-1981.

Dyslipidemias include both rare single gene disorders and common conditions that have a complex underlying basis. In London, ON, there is fortuitous close physical proximity between the Lipid Genetics Clinic and the London Regional Genomics Centre. For >30 years, we have applied DNA sequencing of clinical samples to help answer scientific questions. More than 2000 patients referred with dyslipidemias have participated in an ongoing translational research program. In 2013, we transitioned to next-generation sequencing; our targeted panel is designed to concurrently assess both monogenic and polygenic contributions to dyslipidemias. Patient DNA is screened for rare variants underlying 25 mendelian dyslipidemias, including familial hypercholesterolemia, hepatic lipase deficiency, abetalipoproteinemia, and familial chylomicronemia syndrome. Furthermore, polygenic scores for LDL (low-density lipoprotein) and HDL (high-density lipoprotein) cholesterol, and triglycerides are calculated for each patient. We thus simultaneously document both rare and common genetic variants, allowing for a broad view of genetic predisposition for both individual patients and cohorts. For instance, among patients referred with severe hypertriglyceridemia, defined as ≥10 mmol/L (≥885 mg/dL), <1% have a mendelian disorder (ie, autosomal recessive familial chylomicronemia syndrome), ≈15% have heterozygous rare variants (a >3-fold increase over normolipidemic individuals), and ≈35% have an extreme polygenic score (a >3-fold increase over normolipidemic individuals). Other dyslipidemias show a different mix of genetic determinants. Genetic results are discussed with patients and can support clinical decision-making. Integrating DNA testing into clinical care allows for a bidirectional flow of information, which facilitates scientific discoveries and clinical translation.

RevDate: 2021-07-29
CmpDate: 2020-12-16

Chessa D, Murgia M, Sias E, et al (2020)

Metagenomics and microscope revealed T. trichiura and other intestinal parasites in a cesspit of an Italian nineteenth century aristocratic palace.

Scientific reports, 10(1):12656.

This study evidenced the presence of parasites in a cesspit of an aristocratic palace of nineteenth century in Sardinia (Italy) by the use of classical paleoparasitological techniques coupled with next-generation sequencing. Parasite eggs identified by microscopy included helminth genera pathogenic for humans and animals: the whipworm Trichuris sp., the roundworm Ascaris sp., the flatworm Dicrocoelium sp. and the fish tapeworm Diphyllobothrium sp. In addition, 18S rRNA metabarcoding and metagenomic sequencing analysis allowed the first description in Sardinia of aDNA of the human specific T. trichiura species and Ascaris genus. Their presence is important for understanding the health conditions, hygiene habits, agricultural practices and the diet of the local inhabitants in the period under study.

RevDate: 2021-03-24
CmpDate: 2021-03-24

Sadhukhan D, Biswas A, Bhaduri A, et al (2020)

Role of LRRK2 variant p.Gly2019Ser in patients with Parkinsonism.

The Indian journal of medical research, 151(6):592-597.

BACKGROUND & OBJECTIVES: Parkinsonian disorder, including Parkinson's disease (PD), is an aetiologically complex neurodegenerative disorder. Mutations in leucine-rich repeat kinase 2 (LRRK2) gene have been implicated in an autosomal dominant form of PD with variable penetrance. The identification of a common LRRK2 variant (p.Gly2019Ser) in dementia with Lewy bodies indicated its potential role in Parkinsonian disorder. The current study was aimed to identify the p.Gly2019Ser variant in Indian patients with Parkinsonian disorder.

METHODS: The patient group consisting of 412 classical PD patients, 107 PD patients with cognitive impairment, 107 patients with Parkinson plus syndrome and 200 unrelated controls were recruited from eastern part of India. The allele representing p.Gly2019Ser variant was screened by polymerase chain reaction followed by restriction fragment length polymorphism analysis.

RESULTS: The p.Gly2019Ser variant was identified in an East Indian young-onset female PD patient in a heterozygous state having several motor and autonomic problems without disturbed cognition. Her younger brother, sister and elder son harbouring the same mutation were asymptomatic carriers for the variant. However, the influence of DNM3 on decreased disease onset in this family was not clear.

Identification of the p.Gly2019Ser variant in only one patient among a large number of Indian patients (n=626) with Parkinsonian disorder in our study suggests a limited role of the LRRK2 variant towards disease pathogenesis.

RevDate: 2021-07-09
CmpDate: 2021-01-22

Haruda AF, Ventresca Miller AR, Paijmans JLA, et al (2020)

The earliest domestic cat on the Silk Road.

Scientific reports, 10(1):11241.

We present the earliest evidence for domestic cat (Felis catus L., 1758) from Kazakhstan, found as a well preserved skeleton with extensive osteological pathologies dating to 775-940 cal CE from the early medieval city of Dzhankent, Kazakhstan. This urban settlement was located on the intersection of the northern Silk Road route which linked the cities of Khorezm in the south to the trading settlements in the Volga region to the north and was known in the tenth century CE as the capital of the nomad Oghuz. The presence of this domestic cat, presented here as an osteobiography using a combination of zooarchaeological, genetic, and isotopic data, provides proxy evidence for a fundamental shift in the nature of human-animal relationships within a previously pastoral region. This illustrates the broader social, cultural, and economic changes occurring within the context of rapid urbanisation during the early medieval period along the Silk Road.

RevDate: 2021-05-04
CmpDate: 2021-05-04

Eaves L (2020)

Birmingham and Beyond.

Twin research and human genetics : the official journal of the International Society for Twin Studies, 23(2):68-71.

Nick Martin was a doctoral student of mine at the University of Birmingham in the mid 1970s. In this review, I discuss two of Nick's earliest and most seminal contributions to the field of behavior genetics. First, Martin and Eaves' (1977) extension of the model-fitting approach to multivariate data, which laid the theoretical groundwork for a generation of multivariate behavior genetic studies. Second, the Martin et al.'s (1978) manuscript on the power of the classical twin design, which showed that thousands of twin pairs would be required in order to reliably estimate components of variance, and has served as impetus for the formation of large-scale twin registries across the world. I discuss these contributions against the historical backdrop of a time when we and others were struggling with the challenge of figuring out how to incorporate gene-by-environment interaction, gene-environment correlation, mate selection and cultural transmission into more complex genetic models of human behavior.

RevDate: 2021-05-04
CmpDate: 2021-05-04

Sham PC, Purcell SM, Cherny SS, et al (2020)

Statistical Power and the Classical Twin Design.

Twin research and human genetics : the official journal of the International Society for Twin Studies, 23(2):87-89.

Dr Nick Martin has made enormous contributions to the field of behavior genetics over the past 50 years. Of his many seminal papers that have had a profound impact, we focus on his early work on the power of twin studies. He was among the first to recognize the importance of sample size calculation before conducting a study to ensure sufficient power to detect the effects of interest. The elegant approach he developed, based on the noncentral chi-squared distribution, has been adopted by subsequent researchers for other genetic study designs, and today remains a standard tool for power calculations in structural equation modeling and other areas of statistical analysis. The present brief article discusses the main aspects of his seminal paper, and how it led to subsequent developments, by him and others, as the field of behavior genetics evolved into the present era.

RevDate: 2020-12-19
CmpDate: 2020-07-08

Düx A, Lequime S, Patrono LV, et al (2020)

Measles virus and rinderpest virus divergence dated to the sixth century BCE.

Science (New York, N.Y.), 368(6497):1367-1370.

Many infectious diseases are thought to have emerged in humans after the Neolithic revolution. Although it is broadly accepted that this also applies to measles, the exact date of emergence for this disease is controversial. We sequenced the genome of a 1912 measles virus and used selection-aware molecular clock modeling to determine the divergence date of measles virus and rinderpest virus. This divergence date represents the earliest possible date for the establishment of measles in human populations. Our analyses show that the measles virus potentially arose as early as the sixth century BCE, possibly coinciding with the rise of large cities.

RevDate: 2021-02-26
CmpDate: 2021-02-26

Capelli I, Aiello V, Gasperoni L, et al (2020)

Kidney Transplant in Fabry Disease: A Revision of the Literature.

Medicina (Kaunas, Lithuania), 56(6):.

Fabry disease is classified as a rare X-linked disease caused by a complete or partial defect of enzyme alpha-galactosidase, due to GLA gene mutations. This disorder leads to intracellular globotriaosylceramide (Gb3) deposition associated with increased Gb3 plasma levels. Most of the symptoms of the disease, involving kidneys, heart and nervous system, result from this progressive Gb3 deposition. The incidence is estimated in 1/50,000 to 1/117,000 in males. Fabry nephropathy begins with microalbuminuria and/or proteinuria, which, in the classic form, appear from childhood. Thus, a progressive decline of renal function can start at a young age, and evolve to kidney failure, requiring dialysis or renal transplantation. Enzyme replacement therapy (ERT), available since 2001 for Fabry disease, has been increasingly introduced into the clinical practice, with overall positive short-term and long-term effects in terms of ventricular hypertrophy and renal function. Kidney transplantation represents a relevant therapeutic option for Fabry nephropathy management, for patients reaching end-stage renal disease, but little is known about long-term outcomes, overall patient survival or the possible role of ERT after transplant. The purpose of this review is to analyze the literature on every aspect related to kidney transplantation in patients with Fabry nephropathy: from the analysis of transplant outcomes, to the likelihood of disease recurrence, up to the effects of ERT and its possible interference with immunosuppression.

RevDate: 2022-12-07
CmpDate: 2021-02-11

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, 172(4):638-649.

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: 2021-05-04
CmpDate: 2021-05-04

Verhulst B (2020)

Sociopolitical Attitudes Through the Lens of Behavioral Genetics: Contributions from Dr Nicholas Martin.

Twin research and human genetics : the official journal of the International Society for Twin Studies, 23(2):125-126.

Professor Nicholas (Nick) Martin spearheaded initial investigations into the genetic basis of political attitudes and behaviors, demonstrating that behaviors that are perceived as socially constructed could have a biological basis. As he showed, the typical mode of inheritance for political attitudes consists of approximately equal proportions of variance from additive genetic, shared environmental and unique environmental sources. This differs from other psychological variables, such as personality traits, which tend to be characterized by genetic and unique environmental sources of variation. By treating political attitudes as a model phenotype, Nick Martin was able to leverage the unique pattern of observed intergenerational transmission for political attitudes to reexamine the quintessential assumptions of the classical twin model. Specifically, by creatively leveraging the nuances of the genetic architecture of political attitudes, he was able to demonstrate the robustness of the equal environments assumption and suggest corrections to account for assortative mating. These advances have had a substantial impact on both the fields of political science, as well as behavioral and quantitative genetics.

RevDate: 2021-12-04
CmpDate: 2020-12-16

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 6[th] 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: 2021-12-04
CmpDate: 2020-10-13

Haber M, Nassar J, Almarri MA, et al (2020)

A Genetic History of the Near East from an aDNA Time Course Sampling Eight Points in the Past 4,000 Years.

American journal of human genetics, 107(1):149-157.

The Iron and Classical Ages in the Near East were marked by population expansions carrying cultural transformations that shaped human history, but the genetic impact of these events on the people who lived through them is little-known. Here, we sequenced the whole genomes of 19 individuals who each lived during one of four time periods between 800 BCE and 200 CE in Beirut on the Eastern Mediterranean coast at the center of the ancient world's great civilizations. We combined these data with published data to traverse eight archaeological periods and observed any genetic changes as they arose. During the Iron Age (∼1000 BCE), people with Anatolian and South-East European ancestry admixed with people in the Near East. The region was then conquered by the Persians (539 BCE), who facilitated movement exemplified in Beirut by an ancient family with Egyptian-Lebanese admixed members. But the genetic impact at a population level does not appear until the time of Alexander the Great (beginning 330 BCE), when a fusion of Asian and Near Easterner ancestry can be seen, paralleling the cultural fusion that appears in the archaeological records from this period. The Romans then conquered the region (31 BCE) but had little genetic impact over their 600 years of rule. Finally, during the Ottoman rule (beginning 1516 CE), Caucasus-related ancestry penetrated the Near East. Thus, in the past 4,000 years, three limited admixture events detectably impacted the population, complementing the historical records of this culturally complex region dominated by the elite with genetic insights from the general population.

RevDate: 2021-07-22
CmpDate: 2021-07-22

Roberts J (2020)

A Tale of Good Fortune in the Era of DNA.

Annual review of microbiology, 74:1-19.

Two strains of good fortune in my career were to stumble upon the Watson-Gilbert laboratory at Harvard when I entered graduate school in 1964, and to study gene regulation in bacteriophage λ when I was there. λ was almost entirely a genetic item a few years before, awaiting biochemical incarnation. Throughout my career I was a relentless consumer of the work of previous and current generations of λ geneticists. Empowered by this background, my laboratory made contributions in two areas. The first was regulation of early gene transcription in λ, the study of which began with the discovery of the Rho transcription termination factor, and the regulatory mechanism of transcription antitermination by the λ N protein, subjects of my thesis work. This was developed into a decades-long program during my career at Cornell, studying the mechanism of transcription termination and antitermination. The second area was the classic problem of prophage induction in response to cellular DNA damage, the study of which illuminated basic cellular processes to survive DNA damage.

RevDate: 2021-05-04
CmpDate: 2021-05-04

Visscher PM (2020)

Musings on Visscher et al. (2006).

Twin research and human genetics : the official journal of the International Society for Twin Studies, 23(2):107-108.

The classical twin design relies on a number of strong number of assumptions in order to yield unbiased estimates of heritability. This includes the equal environments assumption - that monozygotic and dizygotic twins experience similar degrees of environmental similarity - an assumption that is likely to be violated in practice for many traits of interest. An alternative method of estimating heritability that does not suffer from many of these limitations is to model trait similarity between sibling pairs as a function of their empirical genome-wide identity by descent sharing, estimated from genetic markers. In this review, I recount the story behind Nick Martin's and my development of this method, our first attempts at applying it in a human population and more recent studies using the original and related methods to estimate trait heritability.

RevDate: 2021-04-14
CmpDate: 2020-12-16

Linderholm A, Kılınç GM, Szczepanek A, et al (2020)

Corded Ware cultural complexity uncovered using genomic and isotopic analysis from south-eastern Poland.

Scientific reports, 10(1):6885.

During the Final Eneolithic the Corded Ware Complex (CWC) emerges, chiefly identified by its specific burial rites. This complex spanned most of central Europe and exhibits demographic and cultural associations to the Yamnaya culture. To study the genetic structure and kin relations in CWC communities, we sequenced the genomes of 19 individuals located in the heartland of the CWC complex region, south-eastern Poland. Whole genome sequence and strontium isotope data allowed us to investigate genetic ancestry, admixture, kinship and mobility. The analysis showed a unique pattern, not detected in other parts of Poland; maternally the individuals are linked to earlier Neolithic lineages, whereas on the paternal side a Steppe ancestry is clearly visible. We identified three cases of kinship. Of these two were between individuals buried in double graves. Interestingly, we identified kinship between a local and a non-local individual thus discovering a novel, previously unknown burial custom.

RevDate: 2022-12-07
CmpDate: 2021-02-03

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, 172(2):176-188.

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: 2020-03-23
CmpDate: 2020-03-23

Anonymous (2020)


JAMA, 323(9):898.

RevDate: 2023-05-17
CmpDate: 2021-06-24

Davies KE (2020)

The Long Journey from Diagnosis to Therapy.

Annual review of genomics and human genetics, 21:1-13.

I was honored to be asked by the Editorial Committee of the Annual Review of Genomics and Genetics to write an autobiographical account of my life in science and in genetics in particular. The field has moved from mapping Mendelian disorders 40 years ago to the delivery of effective therapies for some monogenic disorders today. My 40-year journey from diagnosis to therapy for Duchenne muscular dystrophy has depended on collaborations among basic scientists, clinicians, medical charities, genetic counselors, biotech companies, and affected families. The future of human genetics looks even more exciting, with techniques such as single-cell sequencing and somatic cell CRISPR editing opening up opportunities for precision medicine and accelerating progress.

RevDate: 2021-02-25
CmpDate: 2021-02-25

Lanciego JL, FG Wouterlood (2020)

Neuroanatomical tract-tracing techniques that did go viral.

Brain structure & function, 225(4):1193-1224.

Neuroanatomical tracing methods remain fundamental for elucidating the complexity of brain circuits. During the past decades, the technical arsenal at our disposal has been greatly enriched, with a steady supply of fresh arrivals. This paper provides a landscape view of classical and modern tools for tract-tracing purposes. Focus is placed on methods that have gone viral, i.e., became most widespread used and fully reliable. To keep an historical perspective, we start by reviewing one-dimensional, standalone transport-tracing tools; these including today's two most favorite anterograde neuroanatomical tracers such as Phaseolus vulgaris-leucoagglutinin and biotinylated dextran amine. Next, emphasis is placed on several classical tools widely used for retrograde neuroanatomical tracing purposes, where Fluoro-Gold in our opinion represents the best example. Furthermore, it is worth noting that multi-dimensional paradigms can be designed by combining different tracers or by applying a given tracer together with detecting one or more neurochemical substances, as illustrated here with several examples. Finally, it is without any doubt that we are currently witnessing the unstoppable and spectacular rise of modern molecular-genetic techniques based on the use of modified viruses as delivery vehicles for genetic material, therefore, pushing the tract-tracing field forward into a new era. In summary, here, we aim to provide neuroscientists with the advice and background required when facing a choice on which neuroanatomical tracer-or combination thereof-might be best suited for addressing a given experimental design.

RevDate: 2020-05-27
CmpDate: 2020-05-27

Kolobova KA, Roberts RG, Chabai VP, et al (2020)

Archaeological evidence for two separate dispersals of Neanderthals into southern Siberia.

Proceedings of the National Academy of Sciences of the United States of America, 117(6):2879-2885.

Neanderthals were once widespread across Europe and western Asia. They also penetrated into the Altai Mountains of southern Siberia, but the geographical origin of these populations and the timing of their dispersal have remained elusive. Here we describe an archaeological assemblage from Chagyrskaya Cave, situated in the Altai foothills, where around 90,000 Middle Paleolithic artifacts and 74 Neanderthal remains have been recovered from deposits dating to between 59 and 49 thousand years ago (age range at 95.4% probability). Environmental reconstructions suggest that the Chagyrskaya hominins were adapted to the dry steppe and hunted bison. Their distinctive toolkit closely resembles Micoquian assemblages from central and eastern Europe, including the northern Caucasus, more than 3,000 kilometers to the west of Chagyrskaya Cave. At other Altai sites, evidence of earlier Neanderthal populations lacking associated Micoquian-like artifacts implies two or more Neanderthal incursions into this region. We identify eastern Europe as the most probable ancestral source region for the Chagyrskaya toolmakers, supported by DNA results linking the Neanderthal remains with populations in northern Croatia and the northern Caucasus, and providing a rare example of a long-distance, intercontinental population movement associated with a distinctive Paleolithic toolkit.

RevDate: 2021-07-06
CmpDate: 2021-07-06

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, 29:128-140.

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: 2020-09-29
CmpDate: 2020-09-29

Gabbianelli F, Alhaique F, Romagnoli G, et al (2020)

Was the Cinta Senese Pig Already a Luxury Food in the Late Middle Ages? Ancient DNA and Archaeozoological Evidence from Central Italy.

Genes, 11(1):.

The Cinta senese is a pig breed, highly esteemed for its meat and derived products, characterized by a black coat with a typical white "belt" and documented by scant iconography, since the 13[th]-14[th] century in Italy. A piece of pottery showing a Cinta pig was found in the Graffignano castle (Northern Latium, Italy) dated 15th-16th centuries, spurring us to investigate the diet of the inhabitants. Ancient DNA analysis was carried out on 21 pig specimens on three nuclear SNPs: (1) g.43597545C>T, on the KIT gene, informative for the identification of the Cinta senese breed; (2) rs81460129, on an intergenic region in chr. 16, which discriminates between domestic pigs and wild boars, and; (3) a SNP on the ZFY/ZFX homologous genes, to determine the sex of the individuals. Our results indicate that the Cinta senese was present in Northern Latium in Late Medieval time, although it was not the only breed, and that pigs, including Cinta, interbred with wild boars, suggesting free-range breeding for all types of pigs. Moreover, the unexpected high proportion of young females may be considered as evidence for the wealth of the family inhabiting the castle.

RevDate: 2020-07-20
CmpDate: 2020-07-20

Trenholm S, A Krishnaswamy (2020)

An Annotated Journey through Modern Visual Neuroscience.

The Journal of neuroscience : the official journal of the Society for Neuroscience, 40(1):44-53.

Recent advances in microscopy, genetics, physiology, and data processing have expanded the scope and accelerated the pace of discovery in visual neuroscience. However, the pace of discovery and the ever increasing number of published articles can present a serious issue for both trainees and senior scientists alike: with each passing year the fog of progress thickens, making it easy to lose sight of important earlier advances. As part of this special issue of the Journal of Neuroscience commemorating the 50th anniversary of SfN, here, we provide a variation on Stephen Kuffler's Oldies but Goodies classic reading list, with the hope that by looking back at highlights in the field of visual neuroscience we can better define remaining gaps in our knowledge and thus guide future work. We also hope that this article can serve as a resource that will aid those new to the field to find their bearings.

RevDate: 2020-06-30
CmpDate: 2020-06-30

Du ZY, Harris AJ, QJ Xiang (2020)

Phylogenomics, co-evolution of ecological niche and morphology, and historical biogeography of buckeyes, horsechestnuts, and their relatives (Hippocastaneae, Sapindaceae) and the value of RAD-Seq for deep evolutionary inferences back to the Late Cretaceous.

Molecular phylogenetics and evolution, 145:106726.

In this study, we used RAD-seq data to resolve the phylogeny of the tribe Hippocastaneae (Sapindaceae) and conducted comparative analyses to gain insights into the evolution and biogeography of the group that had fossils dating back to the late Cretaceous. Hippocastaneae, including the horsechestnuts and buckeyes, is a well-supported clade in Sapindaceae that comprises 12-14 species in Aesculus, two in Billia, and one in Handeliodendron. Most species in the tribe are distributed in Eurasia and North America and exhibit a classic pattern of intercontinental disjunction in the Northern Hemisphere, while Billia occurs from southern Mexico to northern South America. The earliest fossils of Aesculus date back to at least the earliest Paleocene of eastern Asia and western North America, where there are also putative occurrences from the latest Cretaceous. The group provides an excellent system for understanding floristic disjunction in the Northern Hemisphere extending to the Neotropics. However, a strongly supported and well resolved phylogeny is presently lacking for the tribe. Previous phylogenetic studies using several gene regions revealed five well-supported clades in Aesculus, largely corresponding to five recognized taxonomic sections, but relationships among these clades and among Aesculus, Billia, and Handeliodendron were not well supported. In this study, we used RAD-seq data from 68 samples representing all clades and species of Hippocastaneae except Billia, for which we used one of two species, to further resolve relationships within the tribe. Our phylogenomic analyses showed strong support for a sister relationship between Aesculus and Handeliodendron, in contrast to previous findings which supported Billia as sister to Aesculus. Within Aesculus, relationships among sections were strongly supported as (sect. Calothyrsus, (sect. Aesculus, (sect. Macrothyrsus, (sect. Parryana, sect. Pavia)))). We found that the traditionally recognized section Calothyrsus was monophyletic, with all eastern Asian species sister to the western North American species, A. californica. Analyses of divergence times combined with biogeographic analyses suggested a Late Cretaceous origin of Hippocastaneae, in eastern Asia, western North America, and Central America (including southern Mexico), followed by isolation of Billia in Central America, extinction of the tribe ancestor in western North America, and divergence of Aesculus from Handeliodendron in eastern Asia. A Late Cretaceous origin of the common ancestor of Aesculus in eastern Asia was followed by dispersals into western North America, Europe, and eastern North America during the Late Cretaceous and the Paleogene. Our results support Aesculus as a relic of the boreotropical flora and subsequent intercontinental spread of the genus through the Bering and North Atlantic land bridges. We performed character mapping analyses, which revealed that biogeographic isolation and niche divergence may have played important roles in driving morphological evolution and lineage divergence in Aesculus. Our study demonstrates the value of RAD-seq data for reconstructing phylogeny back to the Late Cretaceous.

RevDate: 2021-10-14
CmpDate: 2021-01-25

Gómez-Olivencia A, López-Onaindia D, Sala N, et al (2020)

The human remains from Axlor (Dima, Biscay, northern Iberian Peninsula).

American journal of physical anthropology, 172(3):475-491.

OBJECTIVES: We provide the description and comparative analysis of all the human fossil remains found at Axlor during the excavations carried out by J. M. de Barandiarán from 1967 to 1974: a cranial vault fragment and seven teeth, five of which likely belonged to the same individual, although two are currently lost. Our goal is to describe in detail all these human remains and discuss both their taxonomic attribution and their stratigraphic context.

MATERIALS AND METHODS: We describe external and internal anatomy, and use classic and geometric morphometrics. The teeth from Axlor are compared to Neandertals, Upper Paleolithic, and recent modern humans.

RESULTS: Two teeth (a left dm[2] , a left di[1]) and the parietal fragment show morphological features consistent with a Neandertal classification, and were found in an undisturbed Mousterian context. The remaining three teeth (plus the two lost ones), initially classified as Neandertals, show morphological features and a general size that are more compatible with their classification as modern humans.

DISCUSSION: A left parietal fragment (Level VIII) from a single probably adult Neandertal individual was recovered during the old excavations performed by Barandiarán. Additionally, two different Neandertal children lost deciduous teeth during the formations of levels V (left di[1]) and IV (right dm[2]). In addition, a modern human individual is represented by five remains (two currently lost) from a complex stratigraphic setting. Some of the morphological features of these remains suggest that they may represent one of the scarce examples of Upper Paleolithic modern human remains in the northern Iberian Peninsula, which should be confirmed by direct dating.

RevDate: 2022-11-18
CmpDate: 2021-05-19

Fairbanks DJ (2020)

Mendel and Darwin: untangling a persistent enigma.

Heredity, 124(2):263-273.

Mendel and Darwin were contemporaries, with much overlap in their scientifically productive years. Available evidence shows that Mendel knew much about Darwin, whereas Darwin knew nothing of Mendel. Because of the fragmentary nature of this evidence, published inferences regarding Mendel's views on Darwinian evolution are contradictory and enigmatic, with claims ranging from enthusiastic acceptance to outright rejection. The objective of this review is to examine evidence from Mendel's published and private writings on evolution and Darwin, and the influence of the scientific environment in which he was immersed. Much of this evidence lies in Mendel's handwritten annotations in his copies of Darwin's books, which this review scrutinises in detail. Darwin's writings directly influenced Mendel's classic 1866 paper, and his letters to Nägeli. He commended and criticised Darwin on specific issues pertinent to his research, including the provisional hypothesis of pangenesis, the role of pollen in fertilisation, and the influence of "conditions of life" on heritable variation. In his final letter to Nägeli, Mendel proposed a Darwinian scenario for natural selection using the same German term for "struggle for existence" as in his copies of Darwin's books. His published and private scientific writings are entirely objective, devoid of polemics or religious allusions, and address evolutionary questions in a manner consistent with that of his scientific contemporaries. The image that emerges of Mendel is of a meticulous scientist who accepted the tenets of Darwinian evolution, while privately pinpointing aspects of Darwin's views of inheritance that were not supported by Mendel's own experiments.

RevDate: 2020-07-08
CmpDate: 2020-07-08

Nanjundiah V (2019)

Individual and collective behaviour in cellular slime mould development: contributions of John Bonner (1920-2019).

The International journal of developmental biology, 63(8-9-10):333-342.

John Bonner used the cellular slime moulds to address issues that lie at the heart of evolutionary and developmental biology. He did so mostly by combining acute observation and a knack for asking the right questions with the methods of classical embryology. The present paper focusses on his contributions to understanding two phenomena that are characteristic of development in general: chemotaxis of single cells to an external attractant, and spatial patterning and proportioning of cell types in the multicellular aggregate. Brief mention is also made of other areas of slime mould biology where he made significant inputs. He saw cellular slime moulds as exemplars of development and worthy of study in their own right. His ideas continue to inspire researchers.

RevDate: 2020-04-13
CmpDate: 2020-04-13

DiMauro S (2019)

A Brief History of Mitochondrial Pathologies.

International journal of molecular sciences, 20(22):.

The history of "mitochondrial pathologies", namely genetic pathologies affecting mitochondrial metabolism because of mutations in nuclear DNA-encoded genes for proteins active inside mitochondria or mutations in mitochondrial DNA-encoded genes, began in 1988. In that year, two different groups of researchers discovered, respectively, large-scale single deletions of mitochondrial DNA (mtDNA) in muscle biopsies from patients with "mitochondrial myopathies" and a point mutation in the mtDNA gene for subunit 4 of NADH dehydrogenase (MTND4), associated with maternally inherited Leber's hereditary optic neuropathy (LHON). Henceforth, a novel conceptual "mitochondrial genetics", separate from mendelian genetics, arose, based on three features of mtDNA: (1) polyplasmy; (2) maternal inheritance; and (3) mitotic segregation. Diagnosis of mtDNA-related diseases became possible through genetic analysis and experimental approaches involving histochemical staining of muscle or brain sections, single-fiber polymerase chain reaction (PCR) of mtDNA, and the creation of patient-derived "cybrid" (cytoplasmic hybrid) immortal fibroblast cell lines. The availability of the above-mentioned techniques along with the novel sensitivity of clinicians to such disorders led to the characterization of a constantly growing number of pathologies. Here is traced a brief historical perspective on the discovery of autonomous pathogenic mtDNA mutations and on the related mendelian pathology altering mtDNA integrity.

RevDate: 2020-01-29
CmpDate: 2020-01-29

Lowe JWE, A Bruce (2019)

Genetics without genes? The centrality of genetic markers in livestock genetics and genomics.

History and philosophy of the life sciences, 41(4):50 pii:10.1007/s40656-019-0290-x.

In this paper, rather than focusing on genes as an organising concept around which historical considerations of theory and practice in genetics are elucidated, we place genetic markers at the heart of our analysis. This reflects their central role in the subject of our account, livestock genetics concerning the domesticated pig, Sus scrofa. We define a genetic marker as a (usually material) element existing in different forms in the genome, that can be identified and mapped using a variety (and often combination) of quantitative, classical and molecular genetic techniques. The conjugation of pig genome researchers around the common object of the marker from the early-1990s allowed the distinctive theories and approaches of quantitative and molecular genetics concerning the size and distribution of gene effects to align (but never fully integrate) in projects to populate genome maps. Critical to this was the nature of markers as ontologically inert, internally heterogeneous and relational. Though genes as an organising and categorising principle remained important, the particular concatenation of limitations, opportunities, and intended research goals of the pig genetics community, meant that a progressively stronger focus on the identification and mapping of markers rather than genes per se became a hallmark of the community. We therefore detail a different way of doing genetics to more gene-centred accounts. By doing so, we reveal the presence of practices, concepts and communities that would otherwise be hidden.

RevDate: 2020-04-23
CmpDate: 2020-04-23

Veuille M (2019)

Chance, Variation and Shared Ancestry: Population Genetics After the Synthesis.

Journal of the history of biology, 52(4):537-567.

Chance has been a focus of attention ever since the beginning of population genetics, but neutrality has not, as natural selection once appeared to be the only worthwhile issue. Neutral change became a major source of interest during the neutralist-selectionist debate, 1970-1980. It retained interest beyond this period for two reasons that contributed to its becoming foundational for evolutionary reasoning. On the one hand, neutral evolution was the first mathematical prediction to emerge from Mendelian inheritance: until then evolution by natural selection was considered the alternative to the fixity of species; now it appears to be the alternative to continuous change. Second, neutral change generated a set of clear predictions on standing variation. These could be used as a reference for detecting more elusive alternative mechanisms of evolution including natural selection. In the wake of the transition from Mendelism to genomics, the combination of coalescent theory, DNA sequence variation, and numerical analysis made it possible to integrate contingent aspects of the history of species into a new null model, thus opening a new dimension in the concept of population that the Modern Synthesis formerly considered as a mere gene pool.

RevDate: 2022-12-07
CmpDate: 2020-05-28

Malmström H, Günther T, Svensson EM, et al (2019)

The genomic ancestry of the Scandinavian Battle Axe Culture people and their relation to the broader Corded Ware horizon.

Proceedings. Biological sciences, 286(1912):20191528.

The Neolithic period is characterized by major cultural transformations and human migrations, with lasting effects across Europe. To understand the population dynamics in Neolithic Scandinavia and the Baltic Sea area, we investigate the genomes of individuals associated with the Battle Axe Culture (BAC), a Middle Neolithic complex in Scandinavia resembling the continental Corded Ware Culture (CWC). We sequenced 11 individuals (dated to 3330-1665 calibrated before common era (cal BCE)) from modern-day Sweden, Estonia, and Poland to 0.26-3.24× coverage. Three of the individuals were from CWC contexts and two from the central-Swedish BAC burial 'Bergsgraven'. By analysing these genomes together with the previously published data, we show that the BAC represents a group different from other Neolithic populations in Scandinavia, revealing stratification among cultural groups. Similar to continental CWC, the BAC-associated individuals display ancestry from the Pontic-Caspian steppe herders, as well as smaller components originating from hunter-gatherers and Early Neolithic farmers. Thus, the steppe ancestry seen in these Scandinavian BAC individuals can be explained only by migration into Scandinavia. Furthermore, we highlight the reuse of megalithic tombs of the earlier Funnel Beaker Culture (FBC) by people related to BAC. The BAC groups likely mixed with resident middle Neolithic farmers (e.g. FBC) without substantial contributions from Neolithic foragers.

RevDate: 2020-02-18
CmpDate: 2020-02-18

Löwy I (2019)

How diseases became "genetic".

Ciencia & saude coletiva, 24(10):3607-3617 pii:S1413-81232019001003607.

This article examines the origins of the term "genetic disease." In the late 19 and early 20th century, an earlier idea that diseases that occur in families reflect a vague familiar "predisposition" was replaced by the view that such diseases have specific causes, while Mendelian genetics provided then clues to the patterns of their transmission. The genetictisation of inborn pathologies took a decisive turn with the redefinition, in 1959, of Down syndrome as a chromosomal anomaly, then the development of tests for the diagnosis of other hereditary pathologies. At that time, geneticists distinguished "hereditary" diseases that run in families, from "genetic" conditions that are the result of new mutations during the production of egg and sperm cells. In the latter case, the inborn impairment is produced by an anomaly in the genetic material of the cell, but is not hereditary, because it is not transmitted from one or both parents. In the late 20th and early 21st century, new genomic technologies blurred the distinction between hereditary and genetic impairments, extended the concept of genetic disease, and modified the experience of people living with such a disease.

RevDate: 2022-01-29
CmpDate: 2019-11-12

Cappellini E, Welker F, Pandolfi L, et al (2019)

Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny.

Nature, 574(7776):103-107.

The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa[1]. However, the irreversible post-mortem degradation[2] of ancient DNA has so far limited its recovery-outside permafrost areas-to specimens that are not older than approximately 0.5 million years (Myr)[3]. By contrast, tandem mass spectrometry has enabled the sequencing of approximately 1.5-Myr-old collagen type I[4], and suggested the presence of protein residues in fossils of the Cretaceous period[5]-although with limited phylogenetic use[6]. In the absence of molecular evidence, the speciation of several extinct species of the Early and Middle Pleistocene epoch remains contentious. Here we address the phylogenetic relationships of the Eurasian Rhinocerotidae of the Pleistocene epoch[7-9], using the proteome of dental enamel from a Stephanorhinus tooth that is approximately 1.77-Myr old, recovered from the archaeological site of Dmanisi (South Caucasus, Georgia)[10]. Molecular phylogenetic analyses place this Stephanorhinus as a sister group to the clade formed by the woolly rhinoceros (Coelodonta antiquitatis) and Merck's rhinoceros (Stephanorhinus kirchbergensis). We show that Coelodonta evolved from an early Stephanorhinus lineage, and that this latter genus includes at least two distinct evolutionary lines. The genus Stephanorhinus is therefore currently paraphyletic, and its systematic revision is needed. We demonstrate that sequencing the proteome of Early Pleistocene dental enamel overcomes the limitations of phylogenetic inference based on ancient collagen or DNA. Our approach also provides additional information about the sex and taxonomic assignment of other specimens from Dmanisi. Our findings reveal that proteomic investigation of ancient dental enamel-which is the hardest tissue in vertebrates[11], and is highly abundant in the fossil record-can push the reconstruction of molecular evolution further back into the Early Pleistocene epoch, beyond the currently known limits of ancient DNA preservation.

RevDate: 2021-01-10
CmpDate: 2020-04-02

Geber J, Tromp M, Scott A, et al (2019)

Relief food subsistence revealed by microparticle and proteomic analyses of dental calculus from victims of the Great Irish Famine.

Proceedings of the National Academy of Sciences of the United States of America, 116(39):19380-19385.

Food and diet were class markers in 19th-century Ireland, which became evident as nearly 1 million people, primarily the poor and destitute, died as a consequence of the notorious Great Famine of 1845 to 1852. Famine took hold after a blight (Phytophthora infestans) destroyed virtually the only means of subsistence-the potato crop-for a significant proportion of the population. This study seeks to elucidate the variability of diet in mid-19th-century Ireland through microparticle and proteomic analysis of human dental calculus samples (n = 42) from victims of the famine. The samples derive from remains of people who died between August 1847 and March 1851 while receiving poor relief as inmates in the union workhouse in the city of Kilkenny (52°39' N, -7°15' W). The results corroborate the historical accounts of food provisions before and during the famine, with evidence of corn (maize), potato, and cereal starch granules from the microparticle analysis and milk protein from the proteomic analysis. Unexpectedly, there is also evidence of egg protein-a food source generally reserved only for export and the better-off social classes-which highlights the variability of the prefamine experience for those who died. Through historical contextualization, this study shows how the notoriously monotonous potato diet of the poor was opportunistically supplemented by other foodstuffs. While the Great Irish Famine was one of the worst subsistence crises in history, it was foremost a social disaster induced by the lack of access to food and not the lack of food availability.

RevDate: 2020-05-18
CmpDate: 2020-05-18

Duboule D (2019)

Commentary on paper by Leroy C.

Developmental biology, 454(1):1-14.

RevDate: 2019-12-19
CmpDate: 2019-12-19

Buś MM, Lembring M, Kjellström A, et al (2019)

Mitochondrial DNA analysis of a Viking age mass grave in Sweden.

Forensic science international. Genetics, 42:268-274.

In 1998, a Viking Age mass grave was discovered and excavated at St. Laurence´s churchyard in Sigtuna, Sweden. The excavated bones underwent osteoarchaeological analysis and were assigned to at least 19 individuals. Eleven skeletons showed sharp force trauma from bladed weapons. Mass graves are an unusual finding from this time period, making the burial context extraordinary. To investigate a possible maternal kinship among the individuals, bones and teeth from the skeletal remains were selected for mitochondrial DNA (mtDNA) analysis. Sanger sequencing of short stretches of the hypervariable segments I and II (HVS-I and HVS-II) was performed. A subset of the samples was also analysed by massively parallel sequencing analysis (MPS) of the entire mtDNA genome using the Precision ID mtDNA Whole Genome Panel. A total of 15 unique and three shared mtDNA profiles were obtained. Based on a combination of genetic and archaeological data, we conclude that a minimum of 20 individuals was buried in the mass grave. The majority of the individuals were not maternally related. However, two possible pairs of siblings or mother-child relationships were identified. All individuals were assigned to West Eurasian haplogroups, with a predominance of haplogroup H. Although the remains showed an advanced level of DNA degradation, the combined use of Sanger sequencing and MPS with the Precision ID mtDNA Whole Genome Panel revealed at least partial mtDNA data for all samples.

RevDate: 2021-07-15
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: 2020-05-05
CmpDate: 2020-05-04

Wirtz J, T Wiehe (2019)

The Evolving Moran Genealogy.

Theoretical population biology, 130:94-105.

We study the evolution of the population genealogy in the classic neutral Moran Model of finite size n∈N and in discrete time. The stochastic transformations that shape a Moran population can be realized directly on its genealogy and give rise to a process on a state space consisting of n-sized binary increasing trees. We derive a number of properties of this process, and show that they are in agreement with existing results on the infinite-population limit of the Moran Model. Most importantly, this process admits time reversal, which makes it possible to simplify the mechanisms determining state changes, and allows for a thorough investigation of the Most Recent Common Ancestorprocess.


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 @

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).


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


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 )