Résumé
Many eucaryote 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 non-model
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. 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 dataset
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.