Refining the Y chromosome phylogeny with southern African sequences

Barbieri, Chiara; Hübner, Alexander; Macholdt, Enrico; Ni, Shengyu; Lippold, Sebastian; Schröder, Roland; Mpoloka, Sununguko Wata; Purps, Josephine; Roewer, Lutz; Stoneking, Mark; Pakendorf, Brigitte

doi:10.1101/034983

Cited by 14 publications

(44 citation statements)

References 49 publications

(85 reference statements)

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“…We identified single nucleotide variants (SNVs) using GATK UnifiedGenotyper v3.3-0 across all samples simultaneously setting the parameter ploidy to 1 and using DBSNP build 138 as a prior position list. The identified SNVs were further filtered as previously described 54 . We imputed all samples with missing genotype information at any of these variant sites using BEAGLE 55 .…”

Section: Y Chromosomementioning

confidence: 99%

Contrasting maternal and paternal genetic variation of hunter-gatherer groups in Thailand

Kutanan

Kampuansai

Changmai

et al. 2017

Preprint

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The Maniq and Mlabri are the only recorded nomadic hunter-gatherer groups in Thailand.Here, we sequenced complete mitochondrial (mt) DNA genomes and ~2.364 Mbp of nonrecombining Y chromosome (NRY) to learn more about the origins of these two enigmatic populations. Both groups exhibited low genetic diversity compared to other Thai populations, and contrasting patterns of mtDNA and NRY diversity: there was greater mtDNA diversity in the Maniq than in the Mlabri, while the converse was true for the NRY. We found basal uniparental lineages in the Maniq, namely mtDNA haplogroups M21a, R21 and M17a, and NRY haplogroup

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Section: Y Chromosomementioning

confidence: 99%

Contrasting maternal and paternal genetic variation of hunter-gatherer groups in Thailand

Kutanan

Kampuansai

Changmai

et al. 2017

Preprint

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“…In this study, we compare new data on MSY sequence variation with our previous findings on whole mtDNA genomes [9] to investigate whether the histories of these groups fit the expectations of earlier anthropological and linguistic hypotheses, and to study the causes and consequences of sex-biased processes for their genetic variation. [7,27,30]. Main haplogroup clades and their labels are shown with different colors.…”

Section: Introductionmentioning

confidence: 99%

The role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola

et al. 2018

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Southwestern Angola is a region characterized by contact between indigenous foragers and incoming food-producers, involving genetic and cultural exchanges between peoples speaking Kx'a, Khoe-Kwadi, and Bantu languages. Although present-day Bantu speakers share a patrilocal residence pattern and matrilineal principle of clan and group membership, a highly stratified social setting divides dominant pastoralists from marginalized groups that subsist on alternative strategies and have previously been thought to have pre-Bantu origins. Here, we compare new high-resolution sequence data from 2.3 Mb of the male-specific region of the Y chromosome (MSY) from 170 individuals with previously reported mitochondrial DNA (mtDNA) genomes, to investigate the population history of seven representative southwestern Angolan groups (Himba, Kuvale, Kwisi, Kwepe, Twa, Tjimba, !Xun), and to study the causes and consequences of sex-biased processes in their genetic variation. We found no clear link between the formerly Kwadi-speaking Kwepe and pre-Bantu eastern African migrants, and no pre-Bantu MSY lineages among Bantu-speaking groups, except for small amounts of "Khoisan" introgression. We therefore propose that irrespective of their subsistence strategies, all Bantu-speaking groups of the area share a male Bantu origin. Additionally, we show that in Bantu-speaking groups, the levels of among-group and between-group variation are higher for mtDNA than for MSY. These results, together with our previous demonstration that the matriclanic systems of southwestern Angolan Bantu groups are genealogically consistent, suggest that matrilineality strongly enhances both female population sizes and interpopulation mtDNA variation.

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“…We identified single nucleotide variants (SNVs) using GATK UnifiedGenotyper v3.3-0 across all samples simultaneously, setting the parameter ploidy to 1 and using DBSNP build 138 as a prior position list. The identified SNVs were further filtered as previously described by Barbieri et al (2016) (Barbieri et al 2016) and we obtained a set of 2969 SNVs. We imputed all samples with missing genotype information at any of these variant sites using BEAGLE (Browning and Browning 2013) and assigned Y chromosome haplogroups using yhaplo (Poznik et al 2016).…”

Section: Dna Sequencing and Sequence Analysismentioning

confidence: 99%

Cultural Innovations Influence Patterns of Genetic Diversity in Northwestern Amazonia

Arias

Schroeder

Huebner

et al. 2018

Preprint

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Human populations often exhibit contrasting patterns of genetic diversity in the mtDNA and the nonrecombining portion of the Y-chromosome (NRY), which reflect sex-specific cultural behaviors and population histories. Here, we sequenced 2.3 Mb of the NRY from 284 individuals representing more than 30 Native-American groups from Northwestern Amazonia (NWA) and compared these data to previously generated mtDNA genomes from the same groups, to investigate the impact of cultural practices on genetic diversity and gain new insights about NWA population history. Relevant cultural practices in NWA include postmarital residential rules and linguistic-exogamy, a marital practice in which men are required to marry women speaking a different language.We identified 2,969 SNPs in the NRY sequences; only 925 SNPs were previously described. The NRY and mtDNA data showed that males and females experienced different demographic histories:the female effective population size has been larger than that of males through time, and both markers show an increase in lineage diversification beginning ~5,000 years ago, with a male-specific expansion occurring ~3,500 years ago. These dates are too recent to be associated with agriculture, therefore we propose that they reflect technological innovations and the expansion of regional trade networks documented in the archaeological evidence. Furthermore, our study provides evidence of the impact of postmarital residence rules and linguistic exogamy on genetic diversity patterns. Finally, we highlight the importance of analyzing high-resolution mtDNA and NRY sequences to reconstruct demographic history, since this can differ considerably between males and females.

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Refining the Y chromosome phylogeny with southern African sequences

Cited by 14 publications

References 49 publications

Contrasting maternal and paternal genetic variation of hunter-gatherer groups in Thailand

Contrasting maternal and paternal genetic variation of hunter-gatherer groups in Thailand

The role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola

Cultural Innovations Influence Patterns of Genetic Diversity in Northwestern Amazonia

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