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Thread: New DNA Papers

  1. #1161
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    Removing reference bias in ancient DNA data analysis

    Removing reference bias in ancient DNA data analysis by mapping to a sequence variation graph

    Rui Martiniano, Erik Garrison, Eppie R Jones, Andrea Manica, Richard Durbin


    Abstract
    During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA sequencing reads are short, single-ended and frequently mutated by post-mortem chemical modifications. All these features decrease read mapping accuracy and increase reference bias, in which reads containing non-reference alleles are less likely to be mapped than those containing reference alleles. Recently, alternative approaches for read mapping and genetic variation analysis have been developed that replace the linear reference by a variation graph which includes all the alternative variants at each genetic locus. Here, we evaluate the use of variation graph software vg to avoid reference bias for ancient DNA. We used vg to align multiple previously published aDNA samples to a variation graph containing 1000 Genome Project variants, and compared these with the same data aligned with bwa to the human linear reference genome. We show that use of vg leads to a much more balanced allelic representation at polymorphic sites and better variant detection in comparison with bwa, especially in the presence of post-mortem changes, effectively removing reference bias. A recently published approach that filters bwa alignments using modified reads also removes bias, but has lower sensitivity than vg. Our findings demonstrate that aligning aDNA sequences to variation graphs allows recovering a higher fraction of non-reference variation and effectively mitigates the impact of reference bias in population genetics analyses using aDNA, while retaining mapping sensitivity.
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  3. #1162
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    DNA Testing Reveals the Putative Identity of JB55, a 19th Century Vampire

    DNA Testing Reveals the Putative Identity of JB55, a 19th Century Vampire Buried in Griswold, Connecticut.

    Daniels-Higginbotham J, Gorden EM, Farmer SK, Spatola B, Damann F, Bellantoni N, Gagnon KS, de la Puente M, Xavier C, Walsh S, Parson W, McMahon TP, Marshall C.

    Abstract
    In 1990 in Griswold, Connecticut, archaeologists excavated a burial found in a "skull and crossbones" orientation. The lid of the 19th century coffin had brass tacks that spelled "JB55", the initials of the person lying there and age at death. JB55 had evidence of chronic pulmonary infection, perhaps tuberculosis. It is possible that JB55 was deemed a vampire due to his disease, and therefore had to be "killed" by mutilating his corpse. In an attempt to reveal the identity of JB55, DNA testing was performed. Ancestry informative single nucleotide polymorphism (SNP) analysis using the Precision ID Ancestry Panel indicated European ancestry. A full Y-chromosomal short tandem repeat (Y-STR) profile was obtained, belonging to haplogroup R1b. When the Y-STR profile was searched in the publicly accessible FamilyTreeDNA R1b Project website, the two closest matches had the surname "Barber". A search of historical records led to a death notice mentioning John Barber, whose son Nathan Barber was buried in Griswold in 1826. The description of Nathan Barber closely fits the burial of "NB13," found near JB55. By applying modern forensic DNA tools to a historical mystery, the identity of JB55 as John Barber, the 19th century Connecticut vampire, has been revealed.
    YFull: YF14620 (Dante Labs 2018)

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  5. #1163
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    Quote Originally Posted by pmokeefe View Post
    DNA Testing Reveals the Putative Identity of JB55, a 19th Century Vampire Buried in Griswold, Connecticut.

    Daniels-Higginbotham J, Gorden EM, Farmer SK, Spatola B, Damann F, Bellantoni N, Gagnon KS, de la Puente M, Xavier C, Walsh S, Parson W, McMahon TP, Marshall C.

    Abstract
    In 1990 in Griswold, Connecticut, archaeologists excavated a burial found in a "skull and crossbones" orientation. The lid of the 19th century coffin had brass tacks that spelled "JB55", the initials of the person lying there and age at death. JB55 had evidence of chronic pulmonary infection, perhaps tuberculosis. It is possible that JB55 was deemed a vampire due to his disease, and therefore had to be "killed" by mutilating his corpse. In an attempt to reveal the identity of JB55, DNA testing was performed. Ancestry informative single nucleotide polymorphism (SNP) analysis using the Precision ID Ancestry Panel indicated European ancestry. A full Y-chromosomal short tandem repeat (Y-STR) profile was obtained, belonging to haplogroup R1b. When the Y-STR profile was searched in the publicly accessible FamilyTreeDNA R1b Project website, the two closest matches had the surname "Barber". A search of historical records led to a death notice mentioning John Barber, whose son Nathan Barber was buried in Griswold in 1826. The description of Nathan Barber closely fits the burial of "NB13," found near JB55. By applying modern forensic DNA tools to a historical mystery, the identity of JB55 as John Barber, the 19th century Connecticut vampire, has been revealed.
    OMG poor vampire

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    The Parallel Lives of Human Y Chromosome Lineages Across the Strait of Gibraltar


    Abstract
    The patrilineal transmission of the Y chromosome and the fact that diversity in it accumulates along a strict genealogy imply that, by observing the current Y chromosome diversity in men, inferences can be made about the male-mediated history of humans (exactly like the female-mediated history is traced by mitochondrial DNA). By resequencing the non-recombining portion of the Y chromosome, it has been recently recognized that many branches of the Y chromosome genealogy (the so-called haplogroups) have expanded recently in bursts often tied to lifestyle changes or technological innovations. We have analysed two such bursting haplogroups: R1b-DF27 and E-M183. R1b-DF27 is prevalent in the Iberian Peninsula (40–70%), while its frequency drops to <15% north of the Pyrenees. We have estimated its age at ~4000 years ago, in line with ancient DNA discoveries and pointing to the population upheaval of the Bronze Age as a plausible agent in its origin and dispersion. Similarly, across the Strait of Gibraltar, E-M183 (equivalent to E-M81) dominates the Y chromosome landscape in NW Africa (up to 70%) and is much rarer elsewhere. However, its origins are more recent, at ~2000 years ago, and more difficult to pin down to a particular historical event. In conclusion, either in Iberia or the Maghreb, most men share a common ancestor that lived just a few hundred generations ago.
    https://link.springer.com/chapter/10...030-30363-1_11

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  9. #1165
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    HELLENIC ORIGIN OF EUROPE: Formation of the Greeks 4600–2600 BC

    HELLENIC ORIGIN OF EUROPE: Formation of the Greeks 4600–2600 BC and the first Greek states 2600–1450 BC in Cretan Hieroglyphs and Linear A Script

    Foreword
    The author, Iurii Leonidovych Mosenkis, is PhD in general linguistics, DrSc in the Ukrainian language and general linguistics, Professor of the Kyiv National Taras Shevchenko University (Ukraine), member of thePresidium of the Ukraine Higher Education Academy of Sciences, member of the European Academy of Sciences, Arts, and Literary (France), Bulgarian Academy of Sciences and Arts, and PEN club (Belgian francophonesection).The author proposes reconstruction of three unknown Greek-like ancient dialects and decipherment of CretanHieroglyphic and Linear A in Greek. Greek mythical events are interpreted historically and archaeologically.
    https://www.academia.edu/28968300/HE...inear_A_Script
    Y-DNA R-Z49>Z142>Z12222>FGC12378>FGC12401>FGC12384
    Ancestry: 37% English, 26% Scot/Ulster Scot, 14% Welsh, 14% German 3% Ireland, 3% Nordic, 2% French & Dutch, 1% India

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  11. #1166
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    ASHG 2019 PgmNr 84: Recent population history inferred from more than 5,000 high-coverage South Asian genomes

    Jeffrey Wall et al.

    South Asia contains hundreds of different ethnic or caste groups, many of which are thought to be mostly or completely endogamous. However, the age of this extreme population structure (and the underlying caste system) is unknown, with estimates ranging from hundreds to thousands of years. We analyzed high-coverage whole-genome sequence data from 6,610 individuals, including 1,812 from Pakistan, 500 from Bangladesh, 1,356 from urban South India and 1,180 from the Birbhum district of West Bengal. We used these data to estimate recent changes in population size and split times between caste groups. We do not observe the huge excess of extremely rare variants that has been observed in multiple studies of European and African-American populations. This observation cannot be fully explained by recent inbreeding: simulations suggest that the estimated levels of consanguinity (7.7% are the offspring of 1st cousin marriages, and 27.8% are the offspring of 2nd cousin marriages) will have a modest effect on the site frequency spectrum. Inbreeding with longstanding endogamy though may mostly explain our results.
    Next, we developed a novel method for estimating the genome-wide average divergence time between a single individual and a focal group. This method focuses on extremely rare variants, which should be the most informative about very recent demographic events, and is robust to demographic events affecting the particular individual studied. We focused this work on samples from Birbhum district, West Bengal due to the presence of additional metadata on caste and religion. We used 704 general-caste individuals from Birbhum as the focal group, and estimated divergence times for all other individuals. Mean divergence times ranged from ~2,600 years for the Santal, an Austro-Asiatic language speaking tribal group, to 850 years for "scheduled castes" (i.e., Dalits), 625 years for Bangladeshis and 225 years for "Other Backward Castes" (OBC) individuals. The recent divergence times for OBC individuals confirms that this category is more of a political construct than a long-lived social grouping, while the other divergence times suggest a substantial amount of gene flow between groups. Finally, we extended our approach to thousands of other genomes from around the world. We show how patterns of rare variation can be used to detect asymmetrical migration, and document evidence for more migration from East Asia into Bengal than the converse.


    PgmNr 2352/W: Reconstructing the peopling of old world South Asia: From modern to ancient genomes

    Niraj Rai et al.

    South Asia was one of the first geographic regions to be peopled by modern humans after their African exodus. Today, the diverse ethnic groups of South Asia comprise an array of tribes, castes, and religious groups, who are largely endogamous and have hence developed complex, multi-layered genetic differentiation. From such a complex structure, several questions have stood out from the research of our group and others that are only beginning to be resolved using modern sequencing techniques and targeted sampling of populations and archaeological specimens. In this forum, I will discuss the complex population structure of the Indian subcontinent and future research directions to understand the deep ancestry components of South Asians and Eurasians in the global context, patterns of admixture, and migrations, as revealed by the study of ancient and modern genomes.

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  13. #1167
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    ASHG 2019 PgmNr 2338/T: Exploring the demographic history of tribal and caste groups from West Maharashtra (India) using dense genome-wide data

    Manjari Jonnalagadda et al.

    The South Asian subcontinent has a complex history of human migrations and interactions, which is reflected in an extensive cultural and genetic diversity. One of the defining characteristics of the Indian human landscape is the presence of endogamous tribal and non-tribal groups. Additionally, non-tribal groups are hierarchically arranged in social classes termed castes. Recent studies based on genomic data for ancient and modern South Asian populations have indicated that the genetic diversity in this region is derived primarily from three population sources: i) Ancient Ancestral South Indians (AASI), which represent an early South Asian hunter-gatherer lineage, ii) Iranian agriculturalists, which started to expand from West Asia to South Asia via the Iranian Plateau in the 7th and 8th millennia BCE , and iii) Steppe pastoralists, which arrived in the region in the 2nd millennium BCE. In this study, we characterized the population diversity and demographic history of six populations from West Maharashtra (WM), India using dense genome-wide SNP data. The dataset includes 331 individuals from four Indo-European tribal groups (Kokana, Warli, Bhil and Pawara) and 125 individuals from two castes (Deshastha Brahmins and Kunbi Marathas). Comparisons of the six WM samples with other available ancient and modern DNA samples indicate that the WM tribal groups are characterized by some of the highest proportions of AASI ancestry reported in South Asia. The relative contributions of Steppe pastoralists and in particular Iranian agriculturalists have been very small in the tribal groups. In contrast, in the two caste samples both the Steppe and agriculturalist contributions are substantially higher, in line what has been described in other Indian caste groups. The Deshastha Brahmin sample has a higher Steppe contribution than the Kunbi Maratha sample, also in agreement with previous reports indicating relatively high Steppe proportions in Brahmins. Overall, this study highlights the complex demographic histories of tribal and castes groups from India.

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  15. #1168
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    ASHG 2019 PgmNr 2335/T: Paternal diversity in different ethnic groups of Jammu and Kashmir

    Ekta Rai et al.

    Background: Jammu and Kashmir is located on the crossroads of Eurasia, it has been believed that this region might have acted as corridor to various migrations and immigrations to and from mainland India, Eurasia or northeast Asia. These migrations and immigrations have impacted the cultural and social structure of society. Ethnically and linguistically this region is diverse.

    Objective: To find out the paternal diversity among different ethnic groups of Jammu and Kashmir.

    Methodology: 133 markers of non-recombining (NRY) region of Y chromosome belonging to major haplogroups from A to R, were genotyped for 291 samples. Genotyping was done by using Agena Massarray Platform.

    Results: A total of twenty one different haplogroups: C, G2, H1, H1a, H1b, J, J2, J2b, K, L, P, Q, R, R1a1a, R1a1a1, R2, E1, F, G and H1a3 were found after genotyping. The frequent haplogroup found was R1a1a1, H1b was the second frequent and R2 was the third frequent haplogroup found in the present study. Huge paternal diversity is indicated in the population studied by the presence of diverse paternal haplogroups.

    Conclusion: Multiple lines of paternal ancestry and geographic origins is highlighted by the presence of more than one haplogroup in each of the ethnic groups in the present study. Even these ethnic groups are presently endogamous, yet their genetic architecture suggests their genetic relations. This unifies populations of the region genetically as the presence of haplogroups was not observed as caste specific.

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  17. #1169
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    Human Reference Genome and a High Contiguity Ethnic Genome AK1

    Human Reference Genome and a High Contiguity Ethnic Genome AK1
    Jina Kim, Joohon Sung, Kyudong Han, Wooseok Lee, Seyoung Mun, Jooyeon Lee, Kunhyung Bahk, Inchul Yang, Young-Kyung Bae, Changhoon Kim, Jong-il Kim, Jeongsun Seo


    Abstract
    Studies have shown that the current human reference genome (GRCh38) might miss information for some populations, but 'exactly what we miss' is still elusive due to the lower contiguity of non-reference genomes. We juxtaposed the GRCh38 with high contiguity genome assemblies, AK1, to show that ~1.8% (~53.4 Mbp) of AK1 sequences missed in GRCh38 with ~0.76% (~22.2 Mbp) of ectopic chromosomes. The unique AK1 sequences harbored ~1,390 putative coding elements. We found that ~5.3Mb (~0.2%) of the AK1 sequences aligned and recovered the 'unmapped' reads of fourteen individuals (5 East-Asians, 4 Europeans, and 5 Africans) as a reference. The regions that 'unmapped' reads aligned included 110 common (shared between ≥2 individuals) and 38 globally (≥7 individuals) missing regions with 25 candidate coding elements. We verified that many of the common missing regions exist in multiple populations and chimpanzee's DNA. Our study illuminates not only the discovery of missing information but the use of highly precise ethnic genomes in understanding human genetics.
    YFull: YF14620 (Dante Labs 2018)

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  19. #1170
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    Genetic contributions to variation in human stature in prehistoric Europe

    Genetic contributions to variation in human stature in prehistoric Europe
    Samantha L. Cox, Christopher B. Ruff, Robert M. Maier, and Iain Mathieson

    Significance
    Measurements of prehistoric human skeletal remains provide a record of changes in height and other anthropometric traits over time. Often, these changes are interpreted in terms of plastic developmental response to shifts in diet, climate, or other environmental factors. These changes can also be genetic in origin, but, until recently, it has been impossible to separate the effects of genetics and environment. Here, we use ancient DNA to directly estimate genetic changes in phenotypes and to identify changes driven not by genetics, but by environment. We show that changes over the past 35,000 y are largely predicted by genetics but also identify specific shifts that are more likely to be environmentally driven.

    Abstract
    The relative contributions of genetics and environment to temporal and geographic variation in human height remain largely unknown. Ancient DNA has identified changes in genetic ancestry over time, but it is not clear whether those changes in ancestry are associated with changes in height. Here, we directly test whether changes over the past 38,000 y in European height predicted using DNA from 1,071 ancient individuals are consistent with changes observed in 1,159 skeletal remains from comparable populations. We show that the observed decrease in height between the Early Upper Paleolithic and the Mesolithic is qualitatively predicted by genetics. Similarly, both skeletal and genetic height remained constant between the Mesolithic and Neolithic and increased between the Neolithic and Bronze Age. Sitting height changes much less than standing height—consistent with genetic predictions—although genetics predicts a small post-Neolithic increase that is not observed in skeletal remains. Geographic variation in stature is also qualitatively consistent with genetic predictions, particularly with respect to latitude. Finally, we hypothesize that an observed decrease in genetic heel bone mineral density in the Neolithic reflects adaptation to the decreased mobility indicated by decreased femoral bending strength. This study provides a model for interpreting phenotypic changes predicted from ancient DNA and demonstrates how they can be combined with phenotypic measurements to understand the relative contribution of genetic and developmentally plastic responses to environmental change.
    YFull: YF14620 (Dante Labs 2018)

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