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Thread: New DNA Papers

  1. #801
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    Ayyubid Dynasty Zand Dynasty Ararat Republic Mahabad Republic Kurdistan Rojavaya Kurdistane
    Archaeogenetics of Late Iron Age Çemialo Sırtı, Batman: Investigating maternal genetic continuity in North Mesopotamia since the Neolithic
    Reyhan Yaka, Ayşegül Birand, Yasemin Yılmaz, Ceren Caner, Sinan Can Açan, Sidar Gündüzalp, Poorya Parvizi, Aslı Erim Özdoğan, Zehra İnci Togan, Mehmet Somel
    doi: https://doi.org/10.1101/172890

    Abstract

    North Mesopotamia has witnessed dramatic political and social change since the Bronze Age, but the impact of these events on its demographic history is little understood. Here we study this question by analysing the recently excavated Late Iron Age settlement of Çemialo Sırtı in Batman, southeast Turkey. Archaeological and/or radiocarbon evidence indicate that the site was inhabited during two main periods: the first half of the 2nd millennium BCE and the first millennium BCE. Çemialo Sırtı reveals nomadic items of the Early Iron Age, as well as items associated with the Late Achaemenid and subsequent Hellenistic Periods. Mitochondrial DNA (mtDNA) haplotypes from 12 Çemialo Sırtı individuals reveal high genetic diversity in this population, conspicuously higher than early Holocene west Eurasian populations, which supports the notion of increasing population admixture in west Eurasia through the Holocene. Still, in its mtDNA composition, Çemialo Sırtı shows highest affinity to Neolithic north Syria and Neolithic Anatolia among ancient populations studied, and to modern-day southwest Asian populations. Population genetic simulations do not reject continuity between Neolithic and Iron Age, nor between Iron Age and present-day populations of the region. Despite the region's complex political history and indication for increased genetic diversity over time, we find no evidence for sharp shifts in north Mesopotamian maternal genetic composition within the last 10,000 years.
    E-M84>Y5435>Y5412>FGC18389>FGC18401>FGC18388 tMRCA 3000ybp

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  3. #802
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    High Y-chromosomal Differentiation Among Ethnic Groups of Dir and Swat Districts, Pakistan
    http://onlinelibrary.wiley.com/doi/1...ahg.12204/full
    "Summary

    The ethnic groups that inhabit the mountainous Dir and Swat districts of northern Pakistan are marked by high levels of cultural and phenotypic diversity. To obtain knowledge of the extent of genetic diversity in this region, we investigated Y-chromosomal diversity in five population samples representing the three main ethnic groups residing within these districts, including Gujars, Pashtuns and Kohistanis. A total of 27 Y-chromosomal short tandem repeats (Y-STRs) and 331 Y-chromosomal single nucleotide polymorphisms (Y-SNPs) were investigated. In the Y-STRs, we observed very high and significant levels of genetic differentiation in nine of the 10 pairwise between-group comparisons (RST 0.179–0.746), and the differences were mirrored in the Y-SNP haplogroup frequency distribution. No genetic differences were found between the two Pashtun subethnic groups Tarklanis and Yusafzais (RST = 0.000). Utmankhels, also considered Pashtuns culturally, were not closely related to any of the other population samples (RST 0.451–0.746). Thus, our findings provide examples of both associations and dissociations between cultural and genetic legacies. When analyzed within a larger continental-scale context, these five ethnic groups fall mostly outside the previously characterized Y-chromosomal gene pools of the Indo-Pakistani subcontinent. Male founder effects, coupled with culturally and topographically based constraints upon marriage and movement, are likely responsible for the high degree of genetic structure in this region."

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  5. #803
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    Early history of Neanderthals and Denisovans
    http://www.pnas.org/content/early/2017/08/01/1706426114
    "
    Significance

    Neanderthals and Denisovans were human populations that separated from the modern lineage early in the Middle Pleistocene. Many modern humans carry DNA derived from these archaic populations by interbreeding during the Late Pleistocene. We develop a statistical method to study the early history of these archaic populations. We show that the archaic lineage was very small during the 10,000 y that followed its separation from the modern lineage. It then split into two regional populations, the Neanderthals and the Denisovans. The Neanderthal population grew large and separated into largely isolated local groups.
    Abstract

    Extensive DNA sequence data have made it possible to reconstruct human evolutionary history in unprecedented detail. We introduce a method to study the past several hundred thousand years. Our results show that (i) the Neanderthal–Denisovan lineage declined to a small size just after separating from the modern lineage, (ii) Neanderthals and Denisovans separated soon thereafter, and (iii) the subsequent Neanderthal population was large and deeply subdivided. They also (iv) support previous estimates of gene flow from Neanderthals into modern Eurasians. These results suggest an archaic human diaspora early in the Middle Pleistocene."

    an interesting interview on the daily mail about it:

    http://www.dailymail.co.uk/sciencete...evolution.html

    The genes that rewrite the history of human evolution: DNA mutations reveal 'tens of thousands' more Neanderthals walked the Earth than first thought




    "The study claims that the number of Neanderthals that walked the Earth could have been tens of thousands more than scientists first thought.

    It also suggests Neanderthals and Denisovans diverged from each other around 744,000 years ago - around 300,000 earlier than previously believed.

    This implies that Homo heidelbergensis - which lived in Africa, Europe and western Asia between 600,000 and 200,000 years ago - was an early Neanderthal"



    "Professor Rogers added: 'There's a rich Neanderthal fossil record - there are lots of Neanderthal sites."
    "It's hard to imagine that there would be so many of them if there were only 1,000 individuals in the whole world."

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  7. #804
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    Genomic landscape of human diversity across Madagascar
    http://www.pnas.org/content/114/32/E6498.abstract
    "
    Significance

    The origins of the Malagasy raise questions about ancient connections between continents; moreover, because ancestors are fundamental to Malagasy society, Malagasy origins is also a heated topic around the country, with numerous proposed hypotheses. This study provides a comprehensive view of genomic diversity (including maternal lineages, paternal lineages, and genome-wide data) based on a sampling of 257 villages across Madagascar. The observed spatial patterns lead to a scenario of a recent and sex-biased admixture between Bantu and Austronesian ancestors across the island. Moreover, we find geographical influences creating subtle signals of genetic structure that are independent of the Bantu/Austronesian admixture, suggesting that recent history has a role in the genomic diversity of the Malagasy.
    Abstract

    Although situated ∼400 km from the east coast of Africa, Madagascar exhibits cultural, linguistic, and genetic traits from both Southeast Asia and Eastern Africa. The settlement history remains contentious; we therefore used a grid-based approach to sample at high resolution the genomic diversity (including maternal lineages, paternal lineages, and genome-wide data) across 257 villages and 2,704 Malagasy individuals. We find a common Bantu and Austronesian descent for all Malagasy individuals with a limited paternal contribution from Europe and the Middle East. Admixture and demographic growth happened recently, suggesting a rapid settlement of Madagascar during the last millennium. However, the distribution of African and Asian ancestry across the island reveals that the admixture was sex biased and happened heterogeneously across Madagascar, suggesting independent colonization of Madagascar from Africa and Asia rather than settlement by an already admixed population. In addition, there are geographic influences on the present genomic diversity, independent of the admixture, showing that a few centuries is sufficient to produce detectable genetic structure in human populations."

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  9. #805
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    Cultural diffusion of Indo-Aryan languages into Bangladesh: A perspective from mitochondrial DNA
    Yu-Chun Lia, Hua-Wei Wanga, Jiao-Yang Tiana, Rui-Lei Lia, Zia Ur Rahmana, Qing-Peng Konga

    Abstract
    Although both linguistic and historical studies indicated only a small group of Aryans had been involved into the diffusion of Indo-Aryan languages into Bangladesh, no genetic studies had been carried out to prove this notion. By studying mitochondrial DNA variants of 240 Bengali speakers in Bangladesh, among which 23 mitogenomes are completely sequenced, we found a high proportion of South Asian components in this group. By contrast, only a small proportion of lineages can be traced back to western Eurasia, which could be attributed to recent gene flow. Our results implied a cultural diffusion of the Indo-Aryan languages into Bangladesh.

    http://www.sciencedirect.com/science...67724916302896
    J1 FGC5987 to FGC6175 (188 new SNPs)
    MDKAs before Colonial Brazil
    Y-DNA - Milhazes, Barcelos, Minho, Portugal.
    mtDNA - Ilha Terceira, Azores, Portugal

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  11. #806
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    open access

    mtDNA structure: the women who formed the Brazilian Northeast
    https://bmcevolbiol.biomedcentral.co...862-017-1027-7
    "Abstract
    Background

    The distribution of mitochondrial DNA (mtDNA) lineages in Brazil is heterogeneous due to different regional colonization dynamics. Northeastern Brazil, although being an important region in terms of human imigration and ethnic admixture, has little information regarding its population mtDNA composition. Here, we determine which mitochondrial lineages contributed to the formation of the Northeastern Brazilian population. Our sample consisted of 767 individuals distributed as follows i) 550 individuals from eight Northeastern states (Piauí, Ceará, Rio Grande do Norte, Paraíba, Pernambuco, Alagoas, Sergipe, and Bahia) which were sequenced for mtDNA hypervariable segments I, II, and III; ii) 217 individuals from Alagoas and Pernambuco (previously published data). Data analysis was performed through sequence alignment and Haplogrep 2.0 haplogroup assignment tools. Furthermore, maternal ancestry distribution was contextualized and, when possible, related to historical events to better understand the biological interactions and population dynamics that occurred in this region since the beginning of colonization"

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  13. #807
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    http://www.nature.com/nature/journal...ture23452.html
    Westaway et al.
    An early modern human presence in Sumatra 73,000–63,000 years ago

    "Genetic evidence for anatomically modern humans (AMH) out of Africa before 75 thousand years ago (ka)1 and in island southeast Asia (ISEA) before 60 ka (93–61 ka)2 predates accepted archaeological records of occupation in the region3. Claims that AMH arrived in ISEA before 60 ka (ref. 4) have been supported only by equivocal5 or non-skeletal evidence6. AMH evidence from this period is rare and lacks robust chronologies owing to a lack of direct dating applications7, poor preservation and/or excavation strategies8 and questionable taxonomic identifications9. Lida Ajer is a Sumatran Pleistocene cave with a rich rainforest fauna associated with fossil human teeth7, 10. The importance of the site is unclear owing to unsupported taxonomic identification of these fossils and uncertainties regarding the age of the deposit, therefore it is rarely considered in models of human dispersal. Here we reinvestigate Lida Ajer to identify the teeth confidently and establish a robust chronology using an integrated dating approach. Using enamel–dentine junction morphology, enamel thickness and comparative morphology, we show that the teeth are unequivocally AMH. Luminescence and uranium-series techniques applied to bone-bearing sediments and speleothems, and coupled uranium-series and electron spin resonance dating of mammalian teeth, place modern humans in Sumatra between 73 and 63 ka. This age is consistent with biostratigraphic estimations7, palaeoclimate and sea-level reconstructions, and genetic evidence for a pre-60 ka arrival of AMH into ISEA2. Lida Ajer represents, to our knowledge, the earliest evidence of rainforest occupation by AMH, and underscores the importance of reassessing the timing and environmental context of the dispersal of modern humans out of Africa."

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  15. #808
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    Quote Originally Posted by parasar View Post
    http://www.nature.com/nature/journal...ture23452.html
    Westaway et al.
    An early modern human presence in Sumatra 73,000–63,000 years ago

    "Genetic evidence for anatomically modern humans (AMH) out of Africa before 75 thousand years ago (ka)1 and in island southeast Asia (ISEA) before 60 ka (93–61 ka)2 predates accepted archaeological records of occupation in the region3. Claims that AMH arrived in ISEA before 60 ka (ref. 4) have been supported only by equivocal5 or non-skeletal evidence6. AMH evidence from this period is rare and lacks robust chronologies owing to a lack of direct dating applications7, poor preservation and/or excavation strategies8 and questionable taxonomic identifications9. Lida Ajer is a Sumatran Pleistocene cave with a rich rainforest fauna associated with fossil human teeth7, 10. The importance of the site is unclear owing to unsupported taxonomic identification of these fossils and uncertainties regarding the age of the deposit, therefore it is rarely considered in models of human dispersal. Here we reinvestigate Lida Ajer to identify the teeth confidently and establish a robust chronology using an integrated dating approach. Using enamel–dentine junction morphology, enamel thickness and comparative morphology, we show that the teeth are unequivocally AMH. Luminescence and uranium-series techniques applied to bone-bearing sediments and speleothems, and coupled uranium-series and electron spin resonance dating of mammalian teeth, place modern humans in Sumatra between 73 and 63 ka. This age is consistent with biostratigraphic estimations7, palaeoclimate and sea-level reconstructions, and genetic evidence for a pre-60 ka arrival of AMH into ISEA2. Lida Ajer represents, to our knowledge, the earliest evidence of rainforest occupation by AMH, and underscores the importance of reassessing the timing and environmental context of the dispersal of modern humans out of Africa."
    How is this DNA paper?

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  17. #809
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    http://journals.plos.org/plosone/art...l.pone.0178882
    Prehistoric mitochondrial DNA of domesticate animals supports a 13th century exodus from the northern US southwest
    Kemp et al.
    "The 13th century Puebloan depopulation of the Four Corners region of the US Southwest is an iconic episode in world prehistory. Studies of its causes, as well as its consequences, have a bearing not only on archaeological method and theory, but also social responses to climate change, the sociology of social movements, and contemporary patterns of cultural diversity. Previous research has debated the demographic scale, destinations, and impacts of Four Corners migrants. Much of this uncertainty stems from the substantial differences in material culture between the Four Corners vs. hypothesized destination areas. Comparable biological evidence has been difficult to obtain due to the complete departure of farmers from the Four Corners in the 13th century CE and restrictions on sampling human remains. As an alternative, patterns of genetic variation among domesticated species were used to address the role of migration in this collapse. We collected mitochondrial haplotypic data from dog (Canis lupus familiaris) and turkey (Meleagris gallopavo) remains from archaeological sites in the most densely-populated portion of the Four Corners region, and the most commonly proposed destination area for that population under migration scenarios. Results are consistent with a large-scale migration of humans, accompanied by their domestic turkeys, during the 13th century CE. These results support scenarios that suggest contemporary Pueblo peoples of the Northern Rio Grande are biological and cultural descendants of Four Corners populations."

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  19. #810
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    http://onlinelibrary.wiley.com/doi/1...jpa.23291/full

    The genetic admixture in Tibetan-Yi Corridor

    Yao et al.

    First published: 7 August 2017

    DOI: 10.1002/ajpa.23291

    Abstract

    Objectives

    The Tibetan-Yi Corridor located on the eastern edge of Tibetan Plateau is suggested to be the key region for the origin and diversification of Tibeto-Burman speaking populations and the main route of the peopling of the Plateau. However, the genetic history of the populations in the Corridor is far from clear due to limited sampling in the northern part of the Corridor.

    Materials and methods

    We collected blood samples from 10 Tibetan and 10 Han Chinese individuals from Gansu province and genotyped about 600,000 genome-wide single nucleotide polymorphisms (SNPs).

    Results

    Our data revealed that the populations in the Corridor are all admixed on a genetic cline of deriving ancestry from Tibetans on the Plateau and surrounding lowland East Asians. The Tibetan and Han Chinese groups in the north of the Plateau show significant evidence of low-level West Eurasian admixture that could be probably traced back to 600∼900 years ago.

    Discussion

    We conclude that there have been huge population migrations from surrounding lowland onto the Tibetan Plateau via the Tibetan-Yi Corridor since the initial formation of Tibetans probably in Neolithic Time, which leads to the current genetic structure of Tibeto-Burman speaking populations.

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