The Making of the African mtDNA Landscape

Salas, Antonio; Richards, Martin B.; Fé, T De La; Lareu, M.V.; Sobrino, Beatriz; Sánchez-Diz, Paula; Macaulay, Vincent; Carracedo, Ángel

doi:10.1086/344348

Cited by 437 publications

(684 citation statements)

References 68 publications

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“…The network obtained for the HVS-I weighty variation presented some secondary reticulation that was basically due to the presence of alternative transversions in sites 114, 265 and 286. The two different transversions in those three sites have already been described in other African data sets (Graven et al 1995;Pereira et al 2001;Salas et al 2002), and so they are not private in our sequences. When these three non-binary sites were treated as binary we obtained the tree displayed in Fig.…”

Section: Checking For Phantom Mutationssupporting

confidence: 73%

“…The haplogroup classification was according to Watson et al (1997), Rando et al (1998), Macaulay et al (1999), Richards & Macaulay (2000), Bandelt et al (2001), Pereira et al (2001) and Salas et al (2002).…”

Section: Genetic Analysis and Population Comparisonsmentioning

confidence: 99%

“…Likely due to drift effects -the haplogroup reaches particularly high frequency among Biaka, the western group of Pygmies from Republic Central African, and among the Bubi from Bioko. Recently, Salas et al (2002) noticed that more than one-third of L1c haplotypes in their database belonged to African Americans, and only a few showed matches with continental Africans. These findings, together with the geographical distribution of L1c, led the authors to suggest that the origin of the cluster could probably be somewhere in Central Africa, towards the Atlantic west coast.…”

Section: Haplogroups Profilesmentioning

confidence: 99%

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Pattern of mtDNA Variation in Three Populations from São Tomé e Príncipe

Trovoada

Pereira

Gusmão

et al. 2004

Annals of Human Genetics

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SummaryWe have analysed the matrilineal genetic composition of three self-reported ethnic groups from São Tomé e Príncipe (Gulf of Guinea), an African archipelago whose settlement begun in the late fifteenth century. Sequence data from the hypervariable segments I (HVS-I) and II (HVS-II) were obtained for 30 Angolares, 35 Forros and 38 Tongas. The repertory of mtDNA lineages in São Tomé e Príncipe denoted a fully African maternal pool, primarily arisen from a Central/Southwestern substratum. The absence of any lineages of putative European descent means that the European impact at the mitochondrial pool was virtually nil. Angolares showed a clear reduction of mtDNA diversity and a slight genetic differentiation relative to Tongas or Forros, whereas the latter two groups did not present any signs of genetic boundaries between each other. The data obtained here reinforce the depiction of genetic substructuring in São Tomé e Príncipe previously derived from Y-chromosome STRs. In addition, the crossing of mtDNA and Y-STR information led to the inference that the female mediated gene flow within the archipelago was less restricted than the male, a pattern that could be framed in the cultural traditions and socio-historical interactions among the groups.

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Section: Checking For Phantom Mutationssupporting

confidence: 73%

Section: Genetic Analysis and Population Comparisonsmentioning

confidence: 99%

Section: Haplogroups Profilesmentioning

confidence: 99%

See 1 more Smart Citation

Pattern of mtDNA Variation in Three Populations from São Tomé e Príncipe

Trovoada

Pereira

Gusmão

et al. 2004

Annals of Human Genetics

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“…Secondly, it has been argued by some to be the place of origin of modern Homo sapiens. Whilst the main line of evidence is that the earliest transitional/modern fossil skeletal remains have been found in Ethiopia (McDougall et al 2005;White et al 2003), Eastern Africa also harbours deep branches in the mtDNA and Ychromosome phylogenies, and genetic diversity estimated here is often higher than anywhere else in the world Hassan et al 2008;Pagani et al 2012;Poloni et al 2009;Salas et al 2002) -although Central Africa has become an increasingly plausible candidate (Cruciani et al 2011;Rito et al 2013). On the other hand, Tishkoff et al (2009) suggested, on the basis of genome-wide autosomal studies, that Southwest Africa, rather than Eastern Africa, might be the most likely place for the geographical origin of modern humans within the continent.…”

Section: Introductionmentioning

confidence: 82%

Mosaic maternal ancestry in the Great Lakes region of East Africa

et al. 2015

Self Cite

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The Great Lakes lie within a region of East Africa with very high human genetic diversity, home of many ethno-linguistic groups usually assumed to be the product of a small number of major dispersals. However, our knowledge of these dispersals relies primarily on the inferences of historical linguistics and oral traditions, with attempts to match up the archaeological evidence where possible. This is an obvious area to which archaeogenetics can contribute, yet Uganda, at the heart of these developments, has not been studied for mitochondrial DNA (mtDNA) variation. Here, we compare mtDNA lineages at this putative genetic crossroads across 409 representatives of the major language groups: Bantu speakers and Eastern and Western Nilotic speakers. We show that Uganda harbours one of the highest mtDNA diversities within and between linguistic groups, with the various groups significantly differentiated from each other. Despite an inferred linguistic origin in South Sudan, the data from the two Nilotic-speaking groups point to a much more complex history, involving not only possible dispersals from Sudan and the Horn but also large-scale assimilation of autochthonous lineages within East Africa and even Uganda itself. The Eastern Nilotic group also carries signals characteristic of West-Central Africa, primarily due to Bantu influence, whereas a much stronger signal in the Western Nilotic group suggests direct West-Central African ancestry. Bantu speakers share lineages with both Nilotic groups, and also harbour East African lineages not found in Western Nilotic speakers, likely due to assimilating indigenous populations since arriving in the region ~3000 years ago.

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“…However, we identified a minor contribution of 9.3% of haplogroups L2 and L3 within the Khoe-San. The absence of lineages L1, L5, L6, and L4 in our dataset corresponds to their documented main dispersals within North/East -Africa (L5, L6, L4) and Central to Southeast Africa (L1) [20][21][22]. The intrapopulation probability for a random match (RMP) was calculated 0.09 for the entire control region when disregarding length variants at positions 16193, 309 and 573.…”

Section: Observed Cr Haplotypes and Diversity Indicesmentioning

confidence: 99%

Mitochondrial DNA control region data from indigenous Angolan Khoe-San lineages

Fendt

Huber

Röck

et al. 2012

Forensic Science International: Genetics

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Here we provide 129 complete mitochondrial control region sequences of indigenous KhoeSan individuals from Angola to contribute to the still underrepresented pool of data from Africa. The dataset consists of exclusively African lineages with a majority of Sub-Saharan haplogroups. The probability of a random match was calculated as 0.09. The data set comprises 21 haplotypes occurring more than once and 17 unique haplotypes. Upon publication, haplotypes were incorporated in the EMPOP database (www.empop.org; Only few Angolan mtDNA sequences were available in the literature, which were typed for the first and second hypervariable segment of the control region [11][12][13]. The blood samples for this study came from 129 healthy randomly drawn volunteer donors of to our knowledge unrelated individuals collected in the Schmidtsdrift community. Individuals identified themselves as !Xu (113) and Khwe (13). Ethnicities of three individuals remained unknown.Informed written/oral consent was obtained from all human subjects. Ethic approval was obtained by the Hans Snykers Institute for the collection of samples for both biochemical and genetic studies on the Bushmen from the Faculty of Medicine, University of Pretoria Ethics Committee. DNA extraction, amplification and sequencingGenomic DNA was extracted from peripheral blood as described in [14]. Full mitochondrial control region (CR) was amplified, sequenced and interpreted as reported in [15]. 3 Data analysisAccording to our in-house data quality management process, the resulting consensus sequences were inspected independently by two different analysts using the sequence analysis software Sequencher (Version 4.8) and reviewed by a third scientist. Consensus sequences covered a common reading frame from position 16024 to 576 and were reported as differences to the rCRS [16] following updated nomenclature guidelines for mtDNA [17].Haplogroups were assigned according to Phylotree, build 12 [18]. Within our Khoe-San sample set the random match probability was calculated as the sum of squared CR frequencies, disregarding length variants at positions 16193, 309 and 573. The haplotypes from this study will be available on the EMPOP database (www.empop.org) upon publication (EMPOP accession number EMP00069). Results Observed CR haplotypes and diversity indicesThe entire control region analysis revealed exclusively typical Africa-specific L lineages with a majority of Sub-Saharan origin (Table S1). Within our dataset, we found 90.7% L0 haplotypes, hence it is remarkable that 97.4% of all L0 haplotypes (or 88.4% of the observed Khoe-San dataset) belonged to the Khoe-San specific L0d/L0k cluster which is reported to account for ~ 60% in observed Khoe-San populations [19]. Among these, the most frequent haplogroups within the Angolan Khoe-San samples were L0d1c1 (33.3%) as well as L0k1 (27.1%). However, we identified a minor contribution of 9.3% of haplogroups L2 and L3 within the Khoe-San. The absence of lineages L1, L5, L6, and L4 in our dataset corresponds to their docu...

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The Making of the African mtDNA Landscape

Cited by 437 publications

References 68 publications

Pattern of mtDNA Variation in Three Populations from São Tomé e Príncipe

Pattern of mtDNA Variation in Three Populations from São Tomé e Príncipe

Mosaic maternal ancestry in the Great Lakes region of East Africa

Mitochondrial DNA control region data from indigenous Angolan Khoe-San lineages

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