Rapid adaptation to malaria facilitated by admixture in the human population of Cabo Verde

Hamid, Iman; Korunes, Katharine L; Beleza, Sandra; Goldberg, Amy

doi:10.1101/2020.09.01.278226

Cited by 3 publications

(4 citation statements)

References 91 publications

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“…We then called local ancestry with RFMix v1.5.4 ( Maples et al 2013 ) PopPhased under a 2-way admixture model using the West African and European reference genotypes described above. These local ancestry calls are publicly available via Zenodo ( Hamid et al 2020 ). Ancestry proportions estimated with ADMIXTURE and RFMix here are highly correlated with results from Beleza et al (2013) , using the same genotype data but with different software [ frappe ( Tang et al 2005 ) and SABER ( Tang et al 2006 )] and an older reference dataset ( Supplementary Fig.…”

Section: Methodsmentioning

confidence: 99%

Sex-biased admixture and assortative mating shape genetic variation and influence demographic inference in admixed Cabo Verdeans

Korunes

Souza

Bobrek

et al. 2022

G3 Genes|Genomes|Genetics

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Genetic data can provide insights into population history, but first we must understand the patterns that complex histories leave in genomes. Here, we consider the admixed human population of Cabo Verde to understand the patterns of genetic variation left by social and demographic processes. First settled in the late 1400s, Cabo Verdeans are admixed descendants of Portuguese colonizers and enslaved West African people. We consider Cabo Verde’s well-studied historical record alongside genome-wide SNP data from 563 individuals from 4 regions within the archipelago. We use genetic ancestry to test for patterns of nonrandom mating and sex-specific gene flow, and we examine the consequences of these processes for common demographic inference methods and for genetic patterns. Notably, multiple population genetic tools that assume random mating underestimate the timing of admixture, but incorporating non-random mating produces estimates more consistent with historical records. We consider how admixture interrupts common summaries of genomic variation such as runs-of-homozygosity (ROH). While summaries of ROH may be difficult to interpret in admixed populations, differentiating ROH by length class shows that ROH reflect historical differences between the islands in their contributions from the source populations and post-admixture population dynamics. Finally, we find higher African ancestry on the X chromosome than on the autosomes, consistent with an excess of European males and African females contributing to the gene pool. Considering these genomic insights into population history in the context of Cabo Verde’s historical record, we can identify how assumptions in genetic models impact inference of population history more broadly.

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Section: Methodsmentioning

confidence: 99%

Sex-biased admixture and assortative mating shape genetic variation and influence demographic inference in admixed Cabo Verdeans

Korunes

Souza

Bobrek

et al. 2022

G3 Genes|Genomes|Genetics

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“…For example, the Duffy-null allele at the DARC locus is protective against malaria-causing Plasmodium vivax infection, which is estimated to be one of the strongest selective pressures in recent human history. The Duffy-null allele is nearly fixed in sub-Saharan African populations and mostly absent in non-African populations, producing a classic signal in which the DARC locus is an outlier in its proportion of local African ancestry in multiple admixed populations [21][22][23][24][25]. However, the strength of selection at the DARC locus is not typical of human adaptation.…”

Section: Phenotypically Important Loci and Regions Under Selectionmentioning

confidence: 99%

“…https://doi.org/10.1371/journal.pgen.1009374.g001 or adaptive [18][19][20][21][22][23][24][25][26] alleles. In this context, we use ancestry to describe "genetic ancestry"-the population origins of material within a genome.…”

Section: Introductionmentioning

confidence: 99%

Human genetic admixture

Korunes

Goldberg

2021

PLoS Genet

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Throughout human history, large-scale migrations have facilitated the formation of populations with ancestry from multiple previously separated populations. This process leads to subsequent shuffling of genetic ancestry through recombination, producing variation in ancestry between populations, among individuals in a population, and along the genome within an individual. Recent methodological and empirical developments have elucidated the genomic signatures of this admixture process, bringing previously understudied admixed populations to the forefront of population and medical genetics. Under this theme, we present a collection of recent PLOS Genetics publications that exemplify recent progress in human genetic admixture studies, and we discuss potential areas for future work.

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“…Results from these studies have also demonstrated that admixture between modern human populations following a period of isolation can result in the adaptive introgression of previously population‐specific advantageous alleles. This phenomenon has occurred repeatedly in recent human history, for example for alleles associated with malaria resistance, 54–58 skin depigmentation, 59 and lactase persistence 9 …”

Section: Genome‐wide “Scans” For Signatures Of Positive Selection In mentioning

confidence: 99%

Scanning the human genome for “signatures” of positive selection: Transformative opportunities and ethical obligations

Hernandez

Perry

2021

Evolutionary Anthropology

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The relationship history of evolutionary anthropology and genetics is complex. At best, genetics is a beautifully integrative part of the discipline. Yet this integration has also been fraught, with punctuated, disruptive challenges to dogma, periodic reluctance by some members of the field to embrace results from analyses of genetic data, and occasional over‐assertions of genetic definitiveness by geneticists. At worst, evolutionary genetics has been a tool for reinforcing racism and colonialism. While a number of genetics/genomics papers have disproportionately impacted evolutionary anthropology, here we highlight the 2002 presentation of an elegantly powerful approach for identifying “signatures” of past positive selection from haplotype‐based patterns of genetic variation. Together with technological advances in genotyping methods, this article transformed our field by facilitating genome‐wide “scans” for signatures of past positive selection in human populations. This approach helped researchers test longstanding evolutionary anthropology hypotheses while simultaneously providing opportunities to develop entirely new ones. Genome‐wide scans for signatures of positive selection have since been conducted in diverse worldwide populations, with striking findings of local adaptation and convergent evolution. Yet there are ethical considerations with respect to the ubiquity of these studies and the cross‐application of the genome‐wide scan approach to existing datasets, which we also discuss.

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Rapid adaptation to malaria facilitated by admixture in the human population of Cabo Verde

Cited by 3 publications

References 91 publications

Sex-biased admixture and assortative mating shape genetic variation and influence demographic inference in admixed Cabo Verdeans

Sex-biased admixture and assortative mating shape genetic variation and influence demographic inference in admixed Cabo Verdeans

Human genetic admixture

Scanning the human genome for “signatures” of positive selection: Transformative opportunities and ethical obligations

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