Mapping the genomic architecture of adaptive traits with interspecific introgressive origin: a coalescent-based approach.

Hussein A Hejase,Kevin J Liu

doi:10.1186/s12864-015-2298-2

Abstract

Recent studies of eukaryotes including human and Neandertal, mice, and butterflies have highlighted the major role that interspecific introgression has played in adaptive trait evolution. A common question arises in each case: what is the genomic architecture of the introgressed traits? One common approach that can be used to address this question is association mapping, which looks for genotypic markers that have significant statistical association with a trait. It is well understood that sample relatedness can be a confounding factor in association mapping studies if not properly accounted for. Introgression and other evolutionary processes (e.g., incomplete lineage sorting) typically introduce variation among local genealogies, which can also differ from global sample structure measured across all genomic loci. In contrast, state-of-the-art association mapping methods assume fixed sample relatedness across the genome, which can lead to spurious inference. We therefore propose a new association mapping method called Coal-Map, which uses coalescent-based models to capture local genealogical variation alongside global sample structure. Using simulated and empirical data reflecting a range of evolutionary scenarios, we compare the performance of Coal-Map against EIGENSTRAT, a leading association mapping method in terms of its popularity, power, and type I error control. Our empirical data makes use of hundreds of mouse genomes for which adaptive interspecific introgression has recently been described. We found that Coal-Map’s performance is comparable or better than EIGENSTRAT in terms of statistical power and false positive rate. Coal-Map’s performance advantage was greatest on model conditions that most closely resembled empirically observed scenarios of adaptive introgression. These conditions had: (1) causal SNPs contained in one or a few introgressed genomic loci and (2) varying rates of gene flow – from high rates to very low rates where incomplete lineage sorting dominated as a primary cause of local genealogical variation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2298-2) contains supplementary material, which is available to authorized users.

Highlights

Adaptive interspecific introgression has played a key role in the evolution of novel traits in many eukaryotic organisms
The performance improvement was significant in terms of area under receiver operating characteristic (ROC) curve (AUROC) for all model conditions (Delong et al test [33], α = 0.05), with P values of 2 ∗ 10−14, 5 ∗ 10−5, and .006 for the single-causallocus, two-causal-loci, and all-causal-loci model conditions, respectively
The performance improvement was significant in terms of area under ROC curve (AUROC) for the single-causal-locus and two-causal-loci model conditions but not for the all-causal-loci model conditions (Delong et al test [33], α = 0.05)

Summary

Introduction

Adaptive interspecific introgression has played a key role in the evolution of novel traits in many eukaryotic organisms. Species A and B diverged from a most recent common ancestor at time t1. At time t2, a new hybrid population was formed by hybridization between species A and B. We assume that ploidy is preserved across the phylogeny. In a first generation hybrid offspring, half of the alleles in its genome are expected to come from a parent individual in species A and the other half from a parent individual in species B. A locus in a first-generation hybrid genome has ancestry either

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Discussion

Conclusion