Assortative mating by population of origin in a mechanistic model of admixture

G3 Genes|Genomes|Genetics

Souza

Bobrek

et al. 2022

Self Cite

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.

Section: Discussionsupporting

confidence: 88%

Section: Discussionmentioning

confidence: 99%

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

G3 Genes|Genomes|Genetics

Souza

Bobrek

et al. 2022

Self Cite

“…In contrast, ancestry-assortative mating can keep ancestral haplotypes more intact, leading to underestimation of the number of generations of admixture when estimating admixture timing. Zaitlen et al (2017) and Goldberg et al (2020) theoretically demonstrate that certain models of non-random mating in admixed populations drive variation in the ancestry proportion and maintain linkage over time— summary statistics that will make admixture appear more recent than it is when mating patterns are not considered (Zaitlen et al 2017; Goldberg et al 2020). Our evidence of ancestry-assortative mating in Cabo Verde underscores the importance of accounting for nonrandom mating in understanding admixture and inferring demographic history.…”

Section: Discussionmentioning

confidence: 99%

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

Souza

Bobrek³

et al. 2020

Preprint

Self Cite

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.

“…Recent methods have sought to test for ancestry-based assortative mating by developing frameworks to infer parental ancestries from phased haplotypes within a single individual [73][74][75]. When not accounted for, nonrandom mating patterns can bias inference of admixture parameters [62,76].…”

Section: Inferring Population Historymentioning

confidence: 99%

Human genetic admixture through the lens of population genomics

Patillo

Hamid

et al. 2022

Phil. Trans. R. Soc. B

Self Cite

Over the past 50 years, geneticists have made great strides in understanding how our species' evolutionary history gave rise to current patterns of human genetic diversity classically summarized by Lewontin in his 1972 paper, ‘The Apportionment of Human Diversity’. One evolutionary process that requires special attention in both population genetics and statistical genetics is admixture: gene flow between two or more previously separated source populations to form a new admixed population. The admixture process introduces ancestry-based structure into patterns of genetic variation within and between populations, which in turn influences the inference of demographic histories, identification of genetic targets of selection and prediction of complex traits. In this review, we outline some challenges for admixture population genetics, including limitations of applying methods designed for populations without recent admixture to the study of admixed populations. We highlight recent studies and methodological advances that aim to overcome such challenges, leveraging genomic signatures of admixture that occurred in the past tens of generations to gain insights into human history, natural selection and complex trait architecture. This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.