Food and pathogen adaptations in the Angolan Namib desert: Tracing the spread of lactase persistence and human African trypanosomiasis resistance into southwestern Africa

Pinto, Joana Costa; Oliveira, Sandra; Teixeira, Sérgio Amaro Antunes; Martins, Dayana; Fehn, Anne-Maria; Aço, Teresa; Gayà-Vidal, Magdalena; Rocha, Jorge

doi:10.1002/ajpa.23042

Cited by 60 publications

(19 citation statements)

References 48 publications

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“…gambiense- endemic West Africa (Figure 2D), raising speculation about the evolutionary history of these two variants. Studies of genetic diversity at the APOL1 locus are consistent with a older (2,000–7,000 years), less intensively selected allele (Genovese et al, 2010; Pinto et al, 2016) for G2, and a more recent, rapid sweep for the G1 allele in West Africa (Genovese et al, 2010; Pinto et al, 2016; Limou et al, 2015). One possible interpretation of the available data is that T.b.…”

Section: Discussionmentioning

confidence: 83%

APOL1 renal risk variants have contrasting resistance and susceptibility associations with African trypanosomiasis

Cooper

Ilboudo

Alibu

et al. 2017

eLife

111

118

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Reduced susceptibility to infectious disease can increase the frequency of otherwise deleterious alleles. In populations of African ancestry, two apolipoprotein-L1 (APOL1) variants with a recessive kidney disease risk, named G1 and G2, occur at high frequency. APOL1 is a trypanolytic protein that confers innate resistance to most African trypanosomes, but not Trypanosoma brucei rhodesiense or T.b. gambiense, which cause human African trypanosomiasis. In this case-control study, we test the prevailing hypothesis that these APOL1 variants reduce trypanosomiasis susceptibility, resulting in their positive selection in sub-Saharan Africa. We demonstrate a five-fold dominant protective association for G2 against T.b. rhodesiense infection. Furthermore, we report unpredicted strong opposing associations with T.b. gambiense disease outcome. G2 associates with faster progression of T.b. gambiense trypanosomiasis, while G1 associates with asymptomatic carriage and undetectable parasitemia. These results implicate both forms of human African trypanosomiasis in the selection and persistence of otherwise detrimental APOL1 kidney disease variants.DOI: http://dx.doi.org/10.7554/eLife.25461.001

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Section: Discussionmentioning

confidence: 83%

APOL1 renal risk variants have contrasting resistance and susceptibility associations with African trypanosomiasis

Cooper

Ilboudo

Alibu

et al. 2017

eLife

111

118

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“…1; Table S1), and eight additional sequences from Bantu-speaking individuals with other ethnic affiliations used exclusively in haplotypebased analysis. The samples were collected as described previously 16 , with the donors' written informed consent, the ethical clearance of ISCED and CIBIO/InBIO-University of Porto boards, and the support and permission of the Provincial Governments of Namibe and Kunene.…”

Section: Samplesmentioning

confidence: 99%

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

Oliveira

Hübner

Fehn

et al. 2018

Preprint

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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 presentday 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.

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Section: Samplesmentioning

confidence: 99%

“…Given the intrinsic social structure of these highly endogamous groups, we only avoided including siblings and mother-offspring pairs in the final dataset (see Pinto et al 2016 for details). The linguistic analyses were based on lexical data collected from individuals belonging to each sampled group, including two elder community members of the Kwepe community, who still remember Kwadi (see Pinto et al 2016). As previously described (Pinto et al 2016), the saliva samples, as well as the linguistic and the personal information, were collected with the donors' written informed consent in the framework of a collaboration between the Portuguese-Angolan TwinLab established between CIBIO/InBio and ISCED/Huíla Angola, with the ethical clearance of ISCED and the CIBIO/InBIO-University of Porto boards, and the support and permission of the Provincial Governments of Namibe and Kunene.…”

Section: Samplesmentioning

confidence: 99%

“…The genetic similarity of the Kwepe to immediate geographic neighbors displaying Bantu-related mtDNA profiles, rather than to other Khoe-Kwadi-speaking groups, suggests that their former use of Kwadi resulted from language shift after contact with a group of migrants that brought the Kwadi language to the Angolan Namib. So far the only available evidence for a possible genetic contribution of any Khoe-Kwadi migrants to the area is the occurrence in all Namib populations of the lactase persistence -14010*C allele (Pinto et al 2016), which is found with elevated frequencies in several Khoe-Kwadi-speaking peoples of southern Africa (Macholdt et al 2014). This evidence suggests that there might have been a measurable genetic impact associated with the original Kwadispeakers that is not captured in the maternal lineages, and might be revealed by Y-chromosome markers and autosomal genome-wide data (currently under analysis).…”

Section: The Southwestern African Pastoral Scene: Herero Himba Damamentioning

confidence: 99%

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

Oliveira

Fehn

et al. 2017

Preprint

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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 Kx’a-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.

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Food and pathogen adaptations in the Angolan Namib desert: Tracing the spread of lactase persistence and human African trypanosomiasis resistance into southwestern Africa

Cited by 60 publications

References 48 publications

APOL1 renal risk variants have contrasting resistance and susceptibility associations with African trypanosomiasis

APOL1 renal risk variants have contrasting resistance and susceptibility associations with African trypanosomiasis

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

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

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