Assessing ant taxonomy and hidden diversity using morphology and genetic data in the southern Atlantic Forest

CAMPAGNA L.; REPENNING, MÁRCIO; SILVEIRA, LUÍS FÁBIO; FONTANA, CARLA SUERTEGARAY; TUBARO, P. L.; LOVETTE, IRBY J.

Austin

Congreso; Evolution 2016; 2016

Society for the Study of Evolution, the Society of Systematic Biologists, and the American Society of Naturalists

Recent radiations can offer insight into the genetic architecture of the phenotypes that are important in the early stages of speciation. Incipient species have a weakly differentiated genomic background, facilitating the search for highly diverged outlier loci. These loci are candidate targets of selection and may resist crossing species barriers in the face of gene flow.  Here we explore patterns of genomic divergence among southern capuchino seedeaters, a group of recently radiated sympatric passerine birds in the genus Sporophila. Capuchino seedeaters can be identified by male plumage and song, traits that are important for generating reproductive isolation in birds, yet show high levels of shared polymorphisms in different genetic (mtDNA and DNA microsatellite loci) and genomic markers (restriction-site associated DNA sequences). To date, species-diagnostic genetic markers are not available and the phylogenetic affinities within the capuchinos remain unresolved. This lack of differentiation is possibly the consequence of a combination of a recent origin during the Pleistocene, large effective population sizes, and perhaps gene flow. We first combined short-read Illumina sequences with long-read Pacific Biosciences sequence data to obtain a high coverage reference genome for an S. hypoxantha individual. We subsequently sequenced the genomes of 48 adult males belonging to four different capuchino species (S. melanogaster, S. nigrorufa, S. pileata, and S. hypoxantha) at lower coverage. We used these data to search for outlier regions across the genomes of these four species, and discovered a small number of unlinked, highly differentiated peaks. Collectively these outlier regions encompass