Model‐based genotype and ancestry estimation for potential hybrids with mixed‐ploidy

Abstract

Species are distributed across geographic ranges and potentially heterogeneous environments and experience barriers to dispersal, leading to clinal genetic differentiation, genetic subdivisions into local populations or 'demes', or some combination of both (Bradburd et al., 2013;Endler, 1977;Gompert & Buerkle, 2016). Even species with high rates of dispersal can have geographic ranges that are large relative to dispersal distances (e.g., Novembre et al., 2008; Phifer-Rixey et al., 2018), such that the distribution of traits and alleles is commonly heterogeneous and stratified among geographic locations. Quantifying this population heterogeneity and stratification is a fundamental component of empirical population genetics, both as a context for the study of evolutionary dynamics and as a component of learning about trait genetics in natural populations. Information about population structure and mixtures can reveal aspects of the underlying evolutionary processes and has played a significant role in shaping our understanding of the nature of hybridization, speciation and adaptation. This includes knowledge of the prevalence of gene flow

Multigenerational backcrossing and introgression between two woodrat species at an abrupt ecological transition

“…See Figure S2 for estimates of uncertainty. (c) Individual ancestry classes were assigned based on estimates of ancestry coefficients (q) and interspecific ancestry (Q 12 ) generated with entropy (Gompert et al, 2014;Shastry et al, 2021). Pure parental N. lepida and N. bryanti individuals have ancestry coefficients of zero and one, respectively.…”

“…Pure parental N. lepida and N. bryanti individuals have ancestry coefficients of zero and one, respectively. All individuals residing on the dashed lines, which depict the theoretical maximum value of Q 12 for a given q, have at least one parent with pure parental ancestry (e.g., pure parentals, F 1 hybrids, backcrosses), whereas individuals in the centre of the triangle have two parents with admixed ancestry (e.g., F 2 and F 3 hybrids) (Gompert et al, 2014;Shastry et al, 2021). Points were jittered to avoid overplotting.…”

When do autopolyploids need poly‐sequencing data?

“…for inferring population structure for mixed ploidy populations using low sequencing depth data (Shastry et al, 2021).…”

Tracing evolutionary history and admixture in mixed‐ploidy systems

“…By addressing these two challenges via designing a Bayesian hierarchical model assuming variation in ploidy and inference from genotype likelihoods, Shastry et al, (2021) present a novel tool specifically designated to analyse polyploid ancestry, and demonstrate its utility on an extensive genomic data set of ~300 accessions of outcrossing di-polyploid Arabidopsis (Figure 1). The model is implemented in the program entropy which represents the very first program allowing such analysis in populations and species of varying ploidy using both high-and low-depth sequencing data.…”

“…In this issue of Molecular Ecology Resources, Shastry et al (2021) develops the first software specifically designed to infer population structure and ancestry in large genome-wide mixed-ploidy data sets, opening novel opportunities for polyploid population genomic analysis.…”