Biology subjects

Pakendorf, B.

Publications and source records attributed to Pakendorf, B..

5 recordsLinked to original sources

bioRxiv2018

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

Southwestern Angola is a region characterized by contact between indigenous foragers and incoming food-producers, involving genetic and cultural exchanges between peoples speaking Kxa, 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 though to have pre-Bantu origins. Here, we compare new high-resolution sequence data from 2.3 Mb of the non-recombining Y chromosome (NRY) from 170 individuals with previously reported mitochondrial genomes (mtDNA), 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 NRY 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 NRY. 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.

genetics↗

bioRxiv2018

Cultural Innovations influence patterns of genetic diversity in Northwestern Amazonia

Human populations often exhibit contrasting patterns of genetic diversity in the mtDNA and the non-recombining 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.\n\nWe 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.

genetics↗

bioRxiv2017

Genetic structure and sex-biased gene flow in the history of southern African populations

ObjectivesWe investigated the genetic history of southern African populations with a special focus on their paternal history. We reexamined previous claims that the Y-chromosome haplogroup E1b1b was brought to southern Africa by pastoralists from eastern Africa, and investigated patterns of sex-biased gene flow in southern Africa.\n\nMaterial and MethodsWe analyzed previously published complete mtDNA genome sequences and ~900 kb of NRY sequences from 23 populations from Namibia, Botswana and Zambia, as well as haplogroup frequencies from a large sample of southern African populations and 23 newly genotyped Y-linked STR loci for samples assigned to haplogroup E1b1b.\n\nResultsOur results support an eastern African origin for Y-chromosome haplogroup E1b1b; however, its current distribution in southern Africa is not strongly associated with pastoralism, suggesting a more complex origin for pastoralism in this region. We confirm that the Bantu expansion had a notable genetic impact in southern Africa, and that in this region it was probably a rapid, male-dominated expansion. Furthermore, we find a significant increase in the intensity of sex-biased gene flow from north to south, which may reflect changes in the social dynamics between Khoisan and Bantu groups over time.\n\nConclusionsOur study shows that the population history of southern Africa has been very complex, with different immigrating groups mixing to different degrees with the autochthonous populations. The Bantu expansion led to heavily sex-biased admixture as a result of interactions between Khoisan females and Bantu males, with a geographic gradient which may reflect changes in the social dynamics between Khoisan and Bantu groups over time.

genetics↗

bioRxiv2017

The maternal genetic history of the Angolan Namib Desert: a key region for understanding the peopling of southern Africa

Southern Angola is a poorly studied region, inhabited by populations that have been associated with different migratory movements into southern Africa. Besides the long-standing presence of indigenous Kxa-speaking foragers and the more recent arrival of Bantu-speaking pastoralists, ethnographic and linguistic studies have suggested that other pre-Bantu communities were also present in the Namib desert, including peripatetic groups like the Kwepe (formerly Kwadi speakers), Twa and Kwisi. Here we evaluate previous peopling hypotheses by analyzing the relationships between seven groups from the Namib desert (Kuvale, Himba, Tjimba, Kwisi, Twa, Kwepe) and Kunene Province (!Xun), based on newly collected linguistic data and 295 complete mtDNA genomes. We found that: i) all groups from the Namib desert have genealogically-consistent matriclanic systems that had a strong impact on their maternal genetic structure by enhancing genetic drift and population differentiation; ii) the dominant pastoral groups represented by the Kuvale and Himba were part of a Bantu proto-population that also included the ancestors of present-day Damara and Herero peoples from Namibia; iii) Tjimba are closely related to the Himba; iv) the Kwepe, Twa and Kwisi have a divergent Bantu-related mtDNA profile and probably stem from a single population that does not show clear signs of being a pre-Bantu indigenous group. Taken together, our results suggest that the maternal genetic structure of the different groups from the Namib desert is largely derived from endogamous Bantu peoples, and that their social stratification and different subsistence patterns are not indicative of remnant groups, but reflect Bantu-internal variation and ethnogenesis.

genetics↗

bioRxiv2017

High Resolution Mitochondrial DNA Analysis Sheds Light On Human Diversity, Cultural Interactions And Population Mobility In Northwestern Amazonia

ObjectivesNorthwestern Amazonia (NWA) is a center of high linguistic and cultural diversity. Several language families and linguistic isolates occur in this region, as well as different subsistence patterns: some groups are foragers while others are agriculturalists. In addition, speakers of Eastern Tukanoan languages are known for practicing linguistic exogamy, a marriage system in which partners must come from different language groups. In this study, we use high resolution mitochondrial DNA sequencing to investigate the impact of this linguistic and cultural diversity on the genetic relationships and structure of NWA groups.\n\nMethodsWe collected saliva samples from individuals representing 40 different NWA ethnolinguistic groups and sequenced 439 complete mitochondrial genomes to an average coverage of 1030x.\n\nResultsThe mtDNA data revealed that NWA populations have high genetic diversity with extensive sharing of haplotypes among groups. Moreover, groups who practice linguistic exogamy have higher mtDNA diversity, while the foraging Nukak have lower diversity. We also find that rivers play a more important role than either geography or language affiliation in structuring the genetic relationships of populations.\n\nDiscussionContrary to the view of NWA as a pristine area inhabited by small human populations living in isolation, our data support a view of high diversity and contact among different ethnolinguistic groups; movement along rivers has probably facilitated this contact. Additionally, we provide evidence for the impact of cultural practices, such as linguistic exogamy, on patterns of genetic variation. Overall, this study provides new data and insights into a remote and little-studied region of the world.

evolutionary biology↗