Inferring the mode of origin of polyploid species from next‐generation sequence data

Abstract

Many eukaryote organisms are polyploid. However, despite their importance, evolutionary inference of polyploid origins and modes of inheritance has been limited by a need for analyses of allele segregation at multiple loci using crosses. The increasing availability of sequence data for nonmodel species now allows the application of established approaches for the analysis of genomic data in polyploids. Here, we ask whether approximate Bayesian computation (ABC), applied to realistic traditional and next-generation sequence data, allows correct inference of the evolutionary and demographic history of polyploids. Using simulations, we evaluate the robustness of evolutionary inference by ABC for tetraploid species as a function of the number of individuals and loci sampled, and the presence or absence of an outgroup. We find that ABC adequately retrieves the recent evolutionary history of polyploid species on the basis of both old and new sequencing technologies. The application of ABC to sequence data from diploid and polyploid species of the plant genus Capsella confirms its utility. Our analysis strongly supports an allopolyploid origin of C. bursa-pastoris about 80 000 years ago. This conclusion runs contrary to previous findings based on the same data set but using an alternative approach and is in agreement with recent findings based on whole-genome sequencing. Our results indicate that ABC is a promising and powerful method for revealing the evolution of polyploid species, without the need to attribute alleles to a homeologous chromosome pair. The approach can readily be extended to more complex scenarios involving higher ploidy levels.

Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence

“…Multilocus analyses of the process of population divergence have been achieved in various groups of animals [26,27] and plants [28–30] for which genome-wide data are available, revealing a diversity of patterns. These case studies, however, are limited in number and have taken different approaches, such that we still lack a unifying picture of the prevalence of gene flow during early divergence between gene pools.…”

Shedding light on the grey zone of speciation along a continuum of genomic divergence

“…Multi-locus analyses of the process of population divergence has been achieved in various groups of animals [25,26] and plants [27][28][29] in which genome-wide data are available, revealing a diversity of patterns. These case studies, however, are limited in number and have taken different approaches, so that we still lack a unifying picture of the prevalence of gene flow during early divergence between gene pools.…”

Genome-specific histories of divergence and introgression between an allopolyploid unisexual salamander lineage and two sexual species

“…Thus, the high levels of observed genetic diversity in this lineage is best explained by a combination of mitotic recombination and preservation of the initial genetic diversity from backcrossing. Until recently, inferences about the historical timing of ingression in polyploid animals were not possible not only due to a lack of genomic resources, but also the difficulty in distinguishing incomplete lineage sorting from hybridization (Choleva et al 2014) and the bioinformatics challenges associated with identifying genomespecific variation in polyploids (Roux and Pannell 2015). However, recent methodological and analytic developments now approach these challenges directly.…”