Identifying Darwinian Selection Acting on Different Human APOL1 Variants among Diverse African Populations

Ko, Wen Ya; Rajan, Prianka; Gomez, Felicia; Scheinfeldt, Laura B.; An, Ping; Winkler, Cheryl A.; Froment, Alain; Nyambo, Thomas; Omar, Sabah A.; Wambebe, Charles; Ranciaro, Alessia; Hirbo, Jibril; Tishkoff, Sarah A.

doi:10.1016/j.ajhg.2013.06.021

Cited by 12 publications

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“…The G1 form, defined by amino acids Gly342 and Met384, and the G2 allele, defined by a 6 bp deletion encompassing Asn388 and Tyr389, are both associated with HAT resistance and are geographically restricted to Africa (Genovese et al, ; Thomson et al, ). The G3 protein variant is defined by amino acids Met228 and Arg255, and is associated with a highly divergent haplotype that is found in European and African populations (Ko et al, ; Thomson et al, ).…”

Section: Resultsmentioning

confidence: 99%

“…Crosses: Nilo‐Saharian‐speaking populations; triangles: non‐Bantu Niger‐Congo‐speaking populations; rectangles: Afro‐Asiatic speaking populations; full circles: Bantu‐speaking populations; circle: Hazda‐speaking group; diamond: Sandawe‐speaking group; full diamond: Kx'a‐speaking group; full triangle: linguistically undefined San sample. Sources: this work; Ko et al (); Thomson et al (). Note that the predicted frequency is not shown for the northernmost part of the continent due to lack of data…”

Section: Resultsmentioning

confidence: 99%

“…To further assess the influence of the subsistence pattern in the distribution of HAT‐resistance alleles in Africa, we combined our data with available information from other regions of the continent (Ko et al, ; Thomson et al, ) and compared the frequencies of the G1 and G2 alleles among hunter‐gatherers, agriculturalists and pastoralists. The frequencies of G1 are highest in agriculturists/agro‐pastoralists (21.7%) intermediate in pastoralists (15.7%) and lowest in hunter‐gatherers (10.5%) ( p < 0.02 in all pairwise comparisons).…”

Section: Resultsmentioning

confidence: 99%

“…To reconstruct the relationships between APOL1 sequences from different African regions, we performed a network analysis including all inferred haplotypes from the resequenced 920 bp fragment and overlapping sequence data previously reported by Ko et al () (Figure A; Supporting Information Table 6).…”

Section: Resultsmentioning

confidence: 99%

“…However, although the distribution of G1 and G2 variants has been studied in several African regions (Ko et al, ; Thomson et al, ), there is still a dearth of data about southern African populations. Moreover, despite the use of linkage‐disequilibrium patterns to assess genetic signatures of selection (Genovese et al, ; Ko et al, ; Limou et al, ), currently available data remain insufficient to investigate the origin and spread of HAT‐resistance variants based on patterns of haplotype sharing across different regions of Africa. Therefore, to obtain a better understanding of the consequences of migration and Trypanosoma exposure on the distribution of APOL1 variants, both the range of studied populations and the resolution of haplotype analyses must be significantly increased.…”

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confidence: 99%

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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

Pinto¹,

Oliveira

Teixeira³

et al. 2016

American J Phys Anthropol

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The LP adaptation was carried to southern Africa by non-Bantu speaking pastoralists from eastern Africa, but an obvious link between its presence in southern Angola and groups speaking languages of the Khoe-Kwadi family, as previously found in other areas, could not be confirmed. The presence of APOL1 variants G1 and G2 is linked to the Bantu expansions. Our results suggest that the G3 variant was retained in modern humans by incomplete lineage sorting.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

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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

Pinto¹,

Oliveira

Teixeira³

et al. 2016

American J Phys Anthropol

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Runs of homozygosity in sub-Saharan African populations provide insights into complex demographic histories

2019

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The study of runs of homozygosity (ROH), contiguous regions in the genome where an individual is homozygous across all sites, can shed light on the demographic history and cultural practices. We present a fine-scale ROH analysis of 1679 individuals from 28 sub-Saharan African (SSA) populations along with 1384 individuals from 17 world-wide populations. Using high-density SNP coverage, we could accurately obtain ROH as low as 300Kb using PLINK software. The analyses showed a heterogeneous distribution of autozygosity across SSA, revealing a complex demographic history. They highlight differences between African groups and can differentiate between the impact of consanguineous practices (e.g. among the Somali) and endogamy (e.g. among several Khoe-San groups 1 ). The genomic distribution of ROH was analysed through the identification of ROH islands and regions of heterozygosity (RHZ). These 1 The term Khoe-San is often used in the literature, but is regarded by some as offensive as it conflates two distinct groups. The impact of colonialism had a very traumatic effect on population size and structure. We use the phrase Khoe and San to describe people who have either Khoe and/or San ancestry as a neutral term to describe people who live in similar regions and have had some shared history in the last centuries.

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Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia

Galinsky

Bhatia

Loh

et al. 2016

The American Journal of Human Genetics

378

394

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Searching for genetic variants with unusual differentiation between subpopulations is an established approach for identifying signals of natural selection. However, existing methods generally require discrete subpopulations. We introduce a method that infers selection using principal components (PCs) by identifying variants whose differentiation along top PCs is significantly greater than the null distribution of genetic drift. To enable the application of this method to large datasets, we developed the FastPCA software, which employs recent advances in random matrix theory to accurately approximate top PCs while reducing time and memory cost from quadratic to linear in the number of individuals, a computational improvement of many orders of magnitude. We apply FastPCA to a cohort of 54,734 European Americans, identifying 5 distinct subpopulations spanning the top 4 PCs. Using the PC-based test for natural selection, we replicate previously known selected loci and identify three new genome-wide significant signals of selection, including selection in Europeans at ADH1B. The coding variant rs1229984(∗)T has previously been associated to a decreased risk of alcoholism and shown to be under selection in East Asians; we show that it is a rare example of independent evolution on two continents. We also detect selection signals at IGFBP3 and IGH, which have also previously been associated to human disease.

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Identifying Darwinian Selection Acting on Different Human APOL1 Variants among Diverse African Populations

Abstract: Within the Material and Methods and within the Acknowledgments, references to primers and suggestions provided by Cheryl Ann Winkler have been removed given that she is now included in the author list.

Cited by 12 publications

References 0 publications

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

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

Runs of homozygosity in sub-Saharan African populations provide insights into complex demographic histories

Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia

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