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Thread: New DNA Papers

  1. #1081
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    An unidentified population admixed with modern humans within Africa

    Models of archaic admixture and recent history from two-locus statistics

    Abstract
    We learn about population history and underlying evolutionary biology through patterns of genetic polymorphism. Many approaches to reconstruct evolutionary histories focus on a limited number of informative statistics describing distributions of allele frequencies or patterns of linkage disequilibrium. We show that many commonly used statistics are part of a broad family of two-locus moments whose expectation can be computed jointly and rapidly under a wide range of scenarios, including complex multi-population demographies with continuous migration and admixture events. A full inspection of these statistics reveals that widely used models of human history fail to predict simple patterns of linkage disequilibrium. To jointly capture the information contained in classical and novel statistics, we implemented a tractable likelihood-based inference framework for demographic history. Using this approach, we show that human evolutionary models that include archaic admixture in Africa, Asia, and Europe provide a much better description of patterns of genetic diversity across the human genome. We estimate that an unidentified, deeply diverged population admixed with modern humans within Africa both before and after the split of African and Eurasian populations, contributing 4 − 8% genetic ancestry to individuals in world-wide populations.

    Author summary
    Throughout human history, populations have expanded and contracted, split and merged, and exchanged migrants. Because these events affected genetic diversity, we can learn about human history by comparing predictions from evolutionary models to genetic data. Here, we show how to rapidly compute such predictions for a wide range of diversity measures within and across populations under complex demographic scenarios. While widely used models of human history accurately predict common measures of diversity, we show that they strongly underestimate the co-occurence of low frequency mutations within human populations in Asia, Europe, and Africa. Models allowing for archaic admixture, the relatively recent mixing of human populations with deeply diverged human lineages, resolve this discrepancy. We use such models to infer demographic models that include both recent and ancient features of human history. We recover the well-characterized admixture of Neanderthals in Eurasian populations, as well as admixture from an as-yet unknown diverged human population within Africa, further suggesting that admixture with deeply diverged lineages occurred multiple times in human history. By simultaneously testing model predictions for a broad range of diversity statistics, we can assess the robustness of common evolutionary models, identify missing historical events, and build more informed models of human demography.
    YFull: YF14620 (Dante Labs 2018)

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  3. #1082
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    East Asia origin of Modern Human Y and mtDNA?

    And now for something completely different ...

    Modern human origins: multiregional evolution of autosomes and East Asia origin of Y and mtDNA

    Abstract
    The neutral theory has been used as a null model for interpreting nature and produced the Recent Out of Africa model of anatomically modern humans. Recent studies, however, have established that genetic diversities are mostly at maximum saturation levels maintained by selection, therefore challenging the explanatory power of the neutral theory and rendering the present molecular model of human origins untenable. Using improved methods and public data, we have revisited human evolution and found sharing of genetic variations among racial groups to be largely a result of parallel mutations rather than recent common ancestry and admixture as commonly assumed. We derived an age of 1.86-1.92 million years for the first split in modern human populations based on autosomal diversity data. We found evidence of modern Y and mtDNA originating in East Asia and dispersing via hybridization with archaic humans. Analyses of autosomes, Y and mtDNA all suggest that Denisovan and Neanderthal were archaic Africans with Eurasian admixtures and ancestors of South Asia Negritos and Aboriginal Australians. Verifying our model, we found more ancestry of Southern Chinese from Hunan in Africans relative to other East Asian groups examined. These results suggest multiregional evolution of autosomes and replacements of archaic Y and mtDNA by modern ones originating in East Asia, thereby leading to a coherent account of modern human origins.
    YFull: YF14620 (Dante Labs 2018)

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  5. #1083
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    Via Iosif Lazaridis:

    https://twitter.com/iosif_lazaridis/...64204575813632

    The paper:

    https://onlinelibrary.wiley.com/doi/...1111/ahg.12328

    ORIGINAL ARTICLE Open Access

    Genetic history of the population of Crete

    Petros Drineas, Fotis Tsetsos, Anna Plantinga, Iosif Lazaridis, Evangelia Yannaki, Anna Razou, Katerina Kanaki, Manolis Michalodimitrakis, Francisco Perez‐Jimenez, Giustina De Silvestro, Maria C. Renda, John A. Stamatoyannopoulos, Kenneth K Kidd, Brian L. Browning, Peristera Paschou, George Stamatoyannopoulos

    First published: 13 June 2019

    https://doi.org/10.1111/ahg.12328

    Abstract

    The medieval history of several populations often suffers from scarcity of contemporary records resulting in contradictory and sometimes biased interpretations by historians. This is the situation with the population of the island of Crete, which remained relatively undisturbed until the Middle Ages when multiple wars, invasions, and occupations by foreigners took place. Historians have considered the effects of the occupation of Crete by the Arabs (in the 9th and 10th centuries C.E.) and the Venetians (in the 13th to the 17th centuries C.E.) to the local population. To obtain insights on such effects from a genetic perspective, we studied representative samples from 17 Cretan districts using the Illumina 1 million or 2.5 million arrays and compared the Cretans to the populations of origin of the medieval conquerors and settlers. Highlights of our findings include (1) small genetic contributions from the Arab occupation to the extant Cretan population, (2) low genetic contribution of the Venetians to the extant Cretan population, and (3) evidence of a genetic relationship among the Cretans and Central, Northern, and Eastern Europeans, which could be explained by the settlement in the island of northern origin tribes during the medieval period. Our results show how the interaction between genetics and the historical record can help shed light on the historical record.

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  7. #1084
    ADMIN

    As a reminder to our regulars - This thread serves as a 'news listing' for the latest DNA papers, abstracts or pre-prints that are published online.

    This thread is not intended as a discussion thread for said papers - There is a dedicated thread which facilitates this HERE.

    All the discussion posts going back to page 100 / Jan 2019 have been moved to the discussion thread above. Let's keep this one nice and tidy friends.

    Thanks!
    Forum Reminders - Please remember to:
    Report any problematic content • Adhere to Anthrogenica Hidden Content • Discuss respectfully • Be mindful of sharing user data (both yours and others) • English language only in main forum area • PM 'Moderator' for basic maintenance tasks or information about member suspensions or bans

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  9. #1085
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    https://www.genetics.org/content/ear...ics.119.302368

    A Rare Deep-Rooting D0 African Y-Chromosomal Haplogroup and Its Implications for the Expansion of Modern Humans out of Africa

    Marc Haber, Abigail L. Jones, Bruce A. Connell, Asan, Elena Arciero, Huanming Yang, Mark G. Thomas, Yali Xue and Chris Tyler-Smith

    Genetics Early online June 13, 2019; https://doi.org/10.1534/genetics.119.302368

    Abstract

    Present-day humans outside Africa descend mainly from a single expansion out ∼50,000-70,000 years ago, but many details of this expansion remain unclear, including the history of the male-specific Y chromosome at this time. Here, we re-investigate a rare deep-rooting African Y-chromosomal lineage by sequencing the whole genomes of three Nigerian men described in 2003 as carrying haplogroup DE* Y-chromosomes, and analyzing them in the context of a calibrated worldwide Y-chromosomal phylogeny. We confirm that these three chromosomes do represent a deep-rooting DE lineage, branching close to the DE bifurcation, but place them on the D branch as an outgroup to all other known D chromosomes, and designate the new lineage D0. We consider three models for the expansion of Y lineages out of Africa ∼50,000-100,000 years ago, incorporating migration back to Africa where necessary to explain present-day Y-lineage distributions. Considering both the Y-chromosomal phylogenetic structure incorporating the D0 lineage, and published evidence for modern humans outside Africa, the most favored model involves an origin of the DE lineage within Africa with D0 and E remaining there, and migration out of the three lineages (C, D and FT) that now form the vast majority of non-African Y chromosomes. The exit took place 50,300-81,000 years ago (latest date for FT lineage expansion outside Africa - earliest date for the D/D0 lineage split inside Africa), and most likely 50,300-59,400 years ago (considering Neanderthal admixture). This work resolves a long-running debate about Y-chromosomal out-of-Africa/back-to-Africa migrations, and provides insights into the out-of-Africa expansion more generally.

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  11. #1086
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    Australia Italy Veneto Friuli Italy Trentino Alto Adige Austria Tirol Australia Eureka
    https://www.academia.edu/39222183/Ha...ine_Bronze_Age

    Haplogroup J-Z640-Genetic Insight into the Levantine Bronze Age

    This article aims at researching the evolution of J-Z640 using an interdisciplinary approach in order to clarify the leading historical and anthropological events that shaped this particular branch of the human Y chromosome. We compiled a STR (short tandem repeat) and SNP (single nucleotide polymorphism) dataset of 145 known or predicted J-Z640 samples among the customers of Family Tree DNA and Full Genomes Corporation, as well as publicly available samples. Amongst these, we analyzed the results of 41 samples that had undergone Next-Generation Sequencing (NGS) and 32 samples that had undergone SNP testing using Sanger Sequencing. From this data, we constructed a J-Z640 phylogenetic tree that was dated using the method. Our data revealed that Haplogroup J-Z640 is a Y chromosome lineage found most notably, in several minority groups within the Near East such as the Samaritans, Druze, Armenians and Jews. J-Z640 originated during the Bronze Age, most likely in the Levant. During the Bronze Age the haplogroup rapidly expanded with multiple ancient branches surviving to the present, evidencing population growth. Further population expansion, and contraction, was also observed in later periods. Based on its geographic dispersal and age of the haplogroup and its subclades, the founder population most likely belonged to Canaanites found in the Levant. Following the collapse of the late Bronze age system, from the Iron Age onwards there followed a period of “differentiation by culture”, with many of the ancient branches surviving to the present separated along ethno-religious lines.

    Father's Mtdna .........T2b17
    Grandfather's Mtdna .......T1a1e
    Sons Mtdna .......K1a4o
    Maternal Grandfather paternal......I1d1-P109
    Maternal side Grandfather .......R1b-S8172
    Wife's Ydna .....R1a-Z282

    My Path = ( K-M9+, TL-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS3767+, CTS8862+, Z19945+, Y70078+ )

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  13. #1087
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    https://www.nature.com/articles/s41598-019-45746-3

    Article | Open | Published: 24 June 2019

    Patterns of genetic structure and adaptive positive selection in the Lithuanian population from high-density SNP data

    A. Urnikyte, A. Flores-Bello, M. Mondal, A. Molyte, D. Comas, F. Calafell, E. Bosch & V. Kučinskas

    Scientific Reportsvolume 9, Article number: 9163 (2019) | Download Citation

    Abstract

    The analysis of geographically specific regions and the characterization of fine-scale patterns of genetic diversity may facilitate a much better understanding of the microevolutionary processes affecting local human populations. Here we generated genome-wide high-density SNP genotype data in 425 individuals from six geographical regions in Lithuania and combined our dataset with available ancient and modern data to explore genetic population structure, ancestry components and signatures of natural positive selection in the Lithuanian population. Our results show that Lithuanians are a homogenous population, genetically differentiated from neighbouring populations but within the general expected European context. Moreover, we not only confirm that Lithuanians preserve one of the highest proportions of western, Scandinavian and eastern hunter-gather ancestry components found in European populations but also that of an steppe Early to Middle Bronze Age pastoralists, which together configure the genetic distinctiveness of the Lithuanian population. Finally, among the top signatures of positive selection detected in Lithuanians, we identified several candidate genes related with diet (PNLIP, PPARD), pigmentation (SLC24A5, TYRP1 and PPARD) and the immune response (BRD2, HLA-DOA, IL26 and IL22).

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  15. #1088
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    United States of America Palestine Germany Ireland
    Haven't seen this linked yet, it's not ancient DNA but a very large sweeping modern autosomal study. Lazaridis tweeted it:

    The genomic impact of European colonization of the Americas

    The human genetic diversity of the Americas has been shaped by several events of gene flow that have continued since the Colonial Era and the Atlantic slave trade. Moreover, multiple waves of migration followed by local admixture occurred in the last two centuries, the impact of which has been largely unexplored.

    Here we compiled a genome-wide dataset of ∼12,000 individuals from twelve American countries and ∼6,000 individuals from worldwide populations and applied haplotype-based methods to investigate how historical movements from outside the New World affected i) the genetic structure, ii) the admixture profile, iii) the demographic history and iv) sex-biased gene-flow dynamics, of the Americas.

    We revealed a high degree of complexity underlying the genetic contribution of European and African populations in North and South America, from both geographic and temporal perspectives, identifying previously unreported sources related to Italy, the Middle East and to specific regions of Africa.

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  17. #1089
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    https://www.nature.com/articles/s415...#disqus_thread


    Article | Open | Published: 21 June 2019
    Estimating Y-Str Mutation Rates and Tmrca Through Deep-Rooting Italian Pedigrees

    Alessio Boattini, Stefania Sarno, Alessandra M. Mazzarisi, Cinzia Viroli, Sara De Fanti, Carla Bini, Maarten H. D. Larmuseau, Susi Pelotti & Donata Luiselli


    In the population genomics era, the study of Y-chromosome variability is still of the greatest interest for several fields ranging from molecular anthropology to forensics and genetic genealogy. In particular, mutation rates of Y-chromosomal Short Tandem Repeats markers (Y-STRs) are key parameters for different interdisciplinary applications. Among them, testing the patrilineal relatedness between individuals and calculating their Time of Most Recent Common Ancestors (TMRCAs) are of the utmost importance. To provide new valuable estimates and to address these issues, we typed 47 Y-STRs (comprising Yfiler, PowerPlex23 and YfilerPlus loci, the recently defined Rapidly Mutating [RM] panel and 11 additional markers often used in genetic genealogical applications) in 135 individuals belonging to 66 deep-rooting paternal genealogies from Northern Italy. Our results confirmed that the genealogy approach is an effective way to obtain reliable Y-STR mutation rate estimates even with a limited number of samples. Moreover, they showed that the impact of multi-step mutations and backmutations is negligible within the temporal scale usually adopted by forensic and genetic genealogy analyses. We then detected a significant association between the number of mutations within genealogies and observed TMRCAs. Therefore, we compared observed and expected TMRCAs by implementing a Bayesian procedure originally designed by Walsh (2001) and showed that the method yields a good performance (up to 96.72%), especially when using the Infinite Alleles Model (IAM).



    HAPLOGROUP ABS. FREQ. REL. FREQ.
    E-V13 5 3.70
    E-M34 1 0.74
    G2a-U1 2 1.48
    G2a-U8 9 6.67
    I1-M253 5 3.70
    I1-P109 1 0.74
    J1-P58 4 2.96
    J2a-M410 3 2.22
    J2b-M241 12 8.89
    LT-P326 1 0.74
    T-L131 10 7.41
    R1a-M198 6 4.44
    R1b-M269 4 2.96
    R1b-M412 6 4.44
    R1b-Z381 1 0.74
    R1b-L48 2 1.48
    R1b-P312 4 2.96
    R1b-Z195 2 1.48
    R1b-U152 33 24.44
    R1b-L2 24 17.78

    Father's Mtdna .........T2b17
    Grandfather's Mtdna .......T1a1e
    Sons Mtdna .......K1a4o
    Maternal Grandfather paternal......I1d1-P109
    Maternal side Grandfather .......R1b-S8172
    Wife's Ydna .....R1a-Z282

    My Path = ( K-M9+, TL-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS3767+, CTS8862+, Z19945+, Y70078+ )

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  19. #1090
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    Insights into human genetic variation and population history from 929 diverse genomes

    Insights into human genetic variation and population history from 929 diverse genomes

    Anders Bergström, View ORCID ProfileShane A. McCarthy, Ruoyun Hui, Mohamed A. Almarri, Qasim Ayub, Petr Danecek, Yuan Chen, Sabine Felkel, Pille Hallast, Jack Kamm, Hélène Blanché, Jean-François Deleuze, Howard Cann, Swapan Mallick, David Reich, Manjinder S. Sandhu, Pontus Skoglund, Aylwyn Scally, Yali Xue, Richard Durbin, Chris Tyler-Smith

    Abstract
    Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented private genetic variation in southern and central Africa and in Oceania and the Americas, but an absence of fixed, private variants between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the last 10,000 years, a potentially major population growth episode after the peopling of the Americas, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations. We also demonstrate benefits to the study of population relationships of genome sequences over ascertained array genotypes. These genome sequences are freely available as a resource with no access or analysis restrictions.
    YFull: YF14620 (Dante Labs 2018)

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