At the southeast fringe of the Bantu expansion: genetic diversity and phylogenetic relationships to other sub-Saharan tribes

Rowold, Diane J.; Garcia-Bertrand, Ralph; Calderon, Silvia; Rivera, Luis; Benedico, David Perez; Alfonso‐Sánchez, Miguel Á.; Chennakrishnaiah, Shilpa; Varela, Mangela; Herrera, René J.

doi:10.1016/j.mgene.2014.08.003

Cited by 9 publications

(7 citation statements)

References 42 publications

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“…The STM1 individual bore the M343 mutation characteristic of haplogroup R1b, consistent with the back-to-Africa R1b1c-V88 haplogroup reported in [ 24 ]; however, we did not observe any of the SNPs specific to the V88 branch. Whereas for STM2, we identified a common and widespread African haplogroup characteristic of the Bantu expansion [ 42 ], E1b1a1a1-M80, consistent with the results from the analyses of the autosomal chromosomes [ 24 ]. For the remaining individuals, we could not resolve haplogroups due to the reduced complexity and endogenous content of the libraries.…”

Section: Discussionsupporting

confidence: 86%

In-solution Y-chromosome capture-enrichment on ancient DNA libraries

et al. 2018

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BackgroundAs most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One approach—in-solution capture-enrichment—retrieves sequences of interest and reduces the fraction of microbial DNA. In this work, we implement a capture-enrichment approach targeting informative regions of the Y chromosome in six human archaeological remains excavated in the Caribbean and dated between 200 and 3000 years BP. We compare the recovery rate of Y-chromosome capture (YCC) alone, whole-genome capture followed by YCC (WGC + YCC) versus non-enriched (pre-capture) libraries.ResultsThe six samples show different levels of initial endogenous content, with very low (< 0.05%, 4 samples) or low (0.1–1.54%, 2 samples) percentages of sequenced reads mapping to the human genome. We recover 12–9549 times more targeted unique Y-chromosome sequences after capture, where 0.0–6.2% (WGC + YCC) and 0.0–23.5% (YCC) of the sequence reads were on-target, compared to 0.0–0.00003% pre-capture. In samples with endogenous DNA content greater than 0.1%, we found that WGC followed by YCC (WGC + YCC) yields lower enrichment due to the loss of complexity in consecutive capture experiments, whereas in samples with lower endogenous content, the libraries’ initial low complexity leads to minor proportions of Y-chromosome reads. Finally, increasing recovery of informative sites enabled us to assign Y-chromosome haplogroups to some of the archeological remains and gain insights about their paternal lineages and origins.ConclusionsWe present to our knowledge the first in-solution capture-enrichment method targeting the human Y-chromosome in aDNA sequencing libraries. YCC and WGC + YCC enrichments lead to an increase in the amount of Y-DNA sequences, as compared to libraries not enriched for the Y-chromosome. Our probe design effectively recovers regions of the Y-chromosome bearing phylogenetically informative sites, allowing us to identify paternal lineages with less sequencing than needed for pre-capture libraries. Finally, we recommend considering the endogenous content in the experimental design and avoiding consecutive rounds of capture, as clonality increases considerably with each round.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4945-x) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 86%

In-solution Y-chromosome capture-enrichment on ancient DNA libraries

et al. 2018

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“…Nevertheless, recent studies showed that haplogroup B2a was already present in Khoisan groups before their contact with Bantu-speaking populations 43 , 45 . We identified three samples belonging to B2a-M150* in Palenque (5.17% of the African lineages), all lacking the M109-derived allele usually present in southwest, southeast and south African Bantu populations 40 , 46 , 47 . Subclade B2a is widely dispersed throughout sub-Saharan Africa 44 , 45 .…”

Section: Resultsmentioning

confidence: 99%

“…In this study, we detected three chromosomes classified as Y-MRCA* (xM13, SRY10831.1), which includes samples from haplogroup A. Haplogroup A is virtually restricted to the African continent, reaching the highest frequencies in Khoisan-speaking populations. It is also frequent in the Nilotic groups from east and northeast Africa 23,[36][37][38] , and it was sporadically observed in the southeast and southwest populations 39,40 . Some lineages inside clade A have geographic specificity.…”

Section: Phylogeographic Analysis Of Thementioning

confidence: 99%

Searching for the roots of the first free African American community

Martínez

Simão

Gomes

et al. 2020

Sci Rep

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San Basilio de Palenque is an Afro-descendant community near Cartagena, Colombia, founded in the sixteenth century. The recognition of the historical and cultural importance of Palenque has promoted several studies, namely concerning the African roots of its first inhabitants. To deepen the knowledge of the origin and diversity of the Palenque parental lineages, we analysed a sample of 81 individuals for the entire mtDNA Control Region as well as 92 individuals for 27 Y-STRs and 95 for 51 Y-SNPs. The results confirmed the strong isolation of the Palenque, with some degree of influx of Native American maternal lineages, and a European admixture exclusively mediated by men. Due to the high genetic drift observed, a pairwise FST analysis with available data on African populations proved to be inadequate for determining population affinities. In contrast, when a phylogenetic approach was used, it was possible to infer the phylogeographic origin of some lineages in Palenque. Contradicting previous studies indicating a single African origin, our results evidence parental genetic contributions from widely different African regions.

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“…The STM1 individual bore the M343 mutation characteristic of haplogroup R1b, consistent with the back-to-Africa R1b1c-V88 haplogroup reported in [22]; however, we did not observe any of the SNPs specific to the V88 branch. Whereas for STM2, we identified a common and widespread African haplogroup characteristic of the Bantu expansion [40], E1b1a1a1-M80, consistent with the results from the analyses of the autosomal chromosomes [22]. For the remaining individuals, we could not resolve haplogroups due to the low depth at which they were sequenced due to limited budget, although our results might be impacted by the paucity of Y-SNPs that define the tips of the Native American haplogroups versus haplogroups from other well-characterized populations in the database employed.…”

Section: Factors Influencing Enrichmentmentioning

confidence: 87%

In-solution Y-chromosome capture-enrichment on ancient DNA libraries

Dávalos

Nieves-Colón

Sockell

et al. 2017

Preprint

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Background: As most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One approach -in-solution capture-enrichment -retrieves sequences of interest and reduces the fraction of microbial DNA. In this work, we implement a capture-enrichment approach targeting informative regions of the Y chromosome in six human archaeological remains excavated in the Caribbean and dated between 200 and 3,000 years BP. We compare the recovery rate of Y-chromosome capture (YCC) alone, whole-genome capture followed by YCC (WGC+Y) versus non-enriched (pre-capture) libraries.

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At the southeast fringe of the Bantu expansion: genetic diversity and phylogenetic relationships to other sub-Saharan tribes

Cited by 9 publications

References 42 publications

In-solution Y-chromosome capture-enrichment on ancient DNA libraries

In-solution Y-chromosome capture-enrichment on ancient DNA libraries

Searching for the roots of the first free African American community

In-solution Y-chromosome capture-enrichment on ancient DNA libraries

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