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

Differentiating mechanism from outcome for ancestry-assortative mating in admixed human populations

Population genetic theory, and the empirical methods built upon it, often assume that individuals pair randomly for reproduction. However, natural populations frequently violate this assumption, which may potentially confound genome-wide association studies, selection scans, and demographic inference. Within several recently admixed human populations, empirical genetic studies have reported a correlation in global ancestry proportion between spouses, referred to as ancestry-assortative mating. Here, we use forward genomic simulations to link correlations in ancestry between mates to the underlying mechanistic mate-choice process. We consider the impacts of two types of mate-choice model, using either ancestry-based preferences or social groups as the basis for mate pairing. We find that multiple mate-choice models can produce the same correlations in ancestry proportion between spouses; however, we also highlight alternative analytic approaches and circumstances in which these models may be distinguished. With this work, we seek to highlight potential pitfalls when interpreting correlations in empirical data as evidence for a particular model of human mating practices, as well as to offer suggestions toward development of new best practices for analysis of human ancestry-assortative mating.

Counting the genetic ancestors from source populations in members of an admixed population

In a genetically admixed population, admixed individuals possess genealogical and genetic ancestry from multiple source groups. Under a mechanistic model of admixture, we study the number of distinct ancestors from the source populations that the admixture represents. Combining a mechanistic admixture model with a recombination model that describes the probability that a genealogical ancestor is a genetic ancestor, for a member of a genetically admixed population, we count genetic ancestors from the source populations-those genealogical ancestors from the source populations who contribute to the genome of the modern admixed individual. We compare patterns in the numbers of genealogical and genetic ancestors across the generations. To illustrate the enumeration of genetic ancestors from source populations in an admixed group, we apply the model to the African-American population, extending recent results on the numbers of African and European genealogical ancestors that contribute to the pedigree of an African-American chosen at random, so that we also evaluate the numbers of African and European genetic ancestors who contribute to random African-American genomes. The model suggests that the autosomal genome of a random African-American born in the interval 1960-1965 contains genetic contributions from a mean of 162 African (standard deviation 47, interquartile range 127-192) and 32 European ancestors (standard deviation 14, interquartile range 21-43). The enumeration of genetic ancestors can potentially be performed in other diploid species in which admixture and recombination models can be specified.

Genetic and molecular architecture of complex traits

Human genetics has emerged as one of the most dynamic areas of biology, with a broadening societal impact. In this review, we discuss recent achievements, ongoing efforts, and future challenges in the field. Advances in technology, statistical methods, and the growing scale of research efforts have all provided many insights into the processes that have given rise to the current patterns of genetic variation. Vast maps of genetic associations with human traits and diseases have allowed characterization of their genetic architecture. Finally, studies of molecular and cellular effects of genetic variants have provided insights into biological processes underlying disease. Many outstanding questions remain, but the field is well poised for groundbreaking discoveries as it increases the use of genetic data to understand both the history of our species and its applications to improve human health.

The genomic footprint of social stratification in admixing American populations

Cultural and socioeconomic differences stratify human societies and shape their genetic structure beyond the sole effect of geography. Despite mating being limited by sociocultural stratification, most demographic models in population genetics often assume random mating. Taking advantage of the correlation between sociocultural stratification and the proportion of genetic ancestry in admixed populations, we sought to infer the former process in the Americas. To this aim, we define a mating model where the individual proportions of the genome inherited from Native American, European, and sub-Saharan African ancestral populations constrain the mating probabilities through ancestry-related assortative mating and sex bias parameters. We simulate a wide range of admixture scenarios under this model. Then, we train a deep neural network and retrieve good performance in predicting mating parameters from genomic data. Our results show how population stratification, shaped by socially constructed racial and gender hierarchies, has constrained the admixture processes in the Americas since the European colonization and the subsequent Atlantic slave trade.

On the number of genealogical ancestors tracing to the source groups of an admixed population

Members of genetically admixed populations possess ancestry from multiple source groups, and studies of human genetic admixture frequently estimate ancestry components corresponding to fractions of individual genomes that trace to specific ancestral populations. However, the same numerical ancestry fraction can represent a wide array of admixture scenarios within an individual's genealogy. Using a mechanistic model of admixture, we consider admixture genealogically: how many ancestors from the source populations does the admixture represent? We consider African-Americans, for whom continent-level estimates produce a 75-85% value for African ancestry on average and 15-25% for European ancestry. Genetic studies together with key features of African-American demographic history suggest ranges for parameters of a simple three-epoch model. Considering parameter sets compatible with estimates of current ancestry levels, we infer that if all genealogical lines of a random African-American born during 1960-1965 are traced back until they reach members of source populations, the mean over parameter sets of the expected number of genealogical lines terminating with African individuals is 314 (interquartile range 240-376), and the mean of the expected number terminating in Europeans is 51 (interquartile range 32-69). Across discrete generations, the peak number of African genealogical ancestors occurs in birth cohorts from the early 1700s, and the probability exceeds 50% that at least one European ancestor was born more recently than 1835. Our genealogical perspective can contribute to further understanding the admixture processes that underlie admixed populations. For African-Americans, the results provide insight both on how many of the ancestors of a typical African-American might have been forcibly displaced in the Transatlantic Slave Trade and on how many separate European admixture events might exist in a typical African-American genealogy.

Challenges of accurately estimating sex-biased admixture from X chromosomal and autosomal ancestry proportions

Sex-biased admixture can be inferred from ancestry-specific proportions of X chromosome and autosomes. In a paper published in the American Journal of Human Genetics, Micheletti et al.1 used this approach to quantify male and female contributions following the transatlantic slave trade. Using a large dataset from 23andMe, they concluded that African and European contributions to gene pools in the Americas were much more sex biased than previously thought. We show that the reported extreme sex-specific contributions can be attributed to unassigned genetic ancestry as well as the limitations of simple models of sex-biased admixture. Unassigned ancestry proportions in the study by Micheletti et al. ranged from ∼1% to 21%, depending on the type of chromosome and geographic region. A sensitivity analysis illustrates how this unassigned ancestry can create false patterns of sex bias and that mathematical models are highly sensitive to slight sampling errors when inferring mean ancestry proportions, making confidence intervals necessary. Thus, unassigned ancestry and the sensitivity of the models effectively prohibit the interpretation of estimated sex biases for many geographic regions in Micheletti et al. Furthermore, Micheletti et al. assumed models of a single admixture event. Using simulations, we find that violations of demographic assumptions, such as subsequent gene flow and/or sex-specific assortative mating, may have confounded the analyses of Micheletti et al., but unassigned ancestry was likely the more important confounding factor. Our findings underscore the importance of using complete ancestry information, sufficiently large sample sizes, and appropriate models when inferring sex-biased patterns of demography. This Matters Arising paper is in response to Micheletti et al.,1 published in American Journal of Human Genetics. See also the response by Micheletti et al.,2 published in this issue.

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

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 genetic patterns. Notably, multiple population genetic tools that assume random mating underestimate the timing of admixture, but incorporating nonrandom mating produces estimates more consistent with historical records. We consider how admixture interrupts common summaries of genomic variation such as runs of homozygosity. While summaries of runs of homozygosity may be difficult to interpret in admixed populations, differentiating runs of homozygosity by length class shows that runs of homozygosity reflect historical differences between the islands in their contributions from the source populations and postadmixture 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.

Assortative mating enhances postzygotic barriers to gene flow via ancestry bundling

Hybridization and subsequent genetic introgression are now known to be common features of the histories of many species, including our own. Following hybridization, selection often purges introgressed DNA genome-wide. While assortative mating can limit hybridization in the first place, it is also known to play an important role in postzygotic selection against hybrids and, thus, the purging of introgressed DNA. However, this role is usually thought of as a direct one: a tendency for mates to be conspecific reduces the sexual fitness of hybrids, reducing the transmission of introgressed ancestry. Here, we explore a second, indirect role of assortative mating as a postzygotic barrier to gene flow. Under assortative mating, parents covary in their ancestry, causing ancestry to be "bundled" in their offspring and later generations. This bundling effect increases ancestry variance in the population, enhancing the efficiency with which postzygotic selection purges introgressed DNA. Using whole-genome simulations, we show that the bundling effect can comprise a substantial portion of mate choice's overall effect as a postzygotic barrier to gene flow. We then derive a simple method for estimating the impact of the bundling effect from standard metrics of assortative mating. Applying this method to data from a diverse set of hybrid zones, we find that the bundling effect increases the purging of introgressed DNA by between 1.2-fold (in a baboon system with weak assortative mating) and 14-fold (in a swordtail system with strong assortative mating). Thus, assortative mating's bundling effect contributes substantially to the genetic isolation of species.

Human genetic admixture through the lens of population genomics

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'.

Why do we pick similar mates, or do we?

Humans often mate with those resembling themselves, a phenomenon described as positive assortative mating (PAM). The causes of this attract broad interest, but there is little agreement on the topic. This may be because empirical studies and reviews sometimes focus on just a few explanations, often based on disciplinary conventions. This review presents an interdisciplinary conceptual framework on the causes of PAM in humans, drawing on human and non-human biology, the social sciences, and the humanities. Viewing causality holistically, we first discuss the proximate causes (i.e. the 'how') of PAM, considering three mechanisms: stratification, convergence and mate choice. We also outline methods to control for confounders when studying mate choice. We then discuss ultimate explanations (i.e. 'the why') for PAM, including adaptive and non-adaptive processes. We conclude by suggesting a focus on interdisciplinarity in future research.

Skin deep: The decoupling of genetic admixture levels from phenotypes that differed between source populations

OBJECTIVES

In genetic admixture processes, source groups for an admixed population possess distinct patterns of genotype and phenotype at the onset of admixture. Particularly in the context of recent and ongoing admixture, such differences are sometimes taken to serve as markers of ancestry for individuals-that is, phenotypes initially associated with the ancestral background in one source population are assumed to continue to reflect ancestry in that population. Such phenotypes might possess ongoing significance in social categorizations of individuals, owing in part to perceived continuing correlations with ancestry. However, genotypes or phenotypes initially associated with ancestry in one specific source population have been seen to decouple from overall admixture levels, so that they no longer serve as proxies for genetic ancestry. Here, we aim to develop an understanding of the joint dynamics of admixture levels and phenotype distributions in an admixed population.

METHODS

We devise a mechanistic model, consisting of an admixture model, a quantitative trait model, and a mating model. We analyze the behavior of the mechanistic model in relation to the model parameters.

RESULTS

We find that it is possible for the decoupling of genetic ancestry and phenotype to proceed quickly, and that it occurs faster if the phenotype is driven by fewer loci. Positive assortative mating attenuates the process of dissociation relative to a scenario in which mating is random with respect to genetic admixture and with respect to phenotype.

CONCLUSIONS

The mechanistic framework suggests that in an admixed population, a trait that initially differed between source populations might serve as a reliable proxy for ancestry for only a short time, especially if the trait is determined by few loci. It follows that a social categorization based on such a trait is increasingly uninformative about genetic ancestry and about other traits that differed between source populations at the onset of admixture.