A Genomic Comparison Between Flycatchers Only Distinguishable by Innate Song Differences

GARCÍA, NATALIA C.; LEONARDO CAMPAGNA; ANDREW C. RUSH; RAURI BOWIE; IRBY LOVETTE

Congreso; American Ornithology Society Meeting; 2019

Comparing the genomes of different species can help identify genomic regions linked to variation in phenotype, one of the great challenges of evolutionary biology. Here, we applied a whole-genome sequencing and re-sequencing approach to analyze the levels of differentiation between the Alder and Willow flycatchers (Empidonax alnorum and E. traillii) and between the Pacific Slope and Cordilleran flycatchers (Empidonax difficilis and E. occidentalis). Each pair of sister species was taxonomically separated less than 50 years ago, mainly due to differences in vocalizations, as they are mostly indistinguishable based on plumage coloration and morphology. Analyses of mitochondrial DNA suggest that the Alder and Willow flycatchers have been diverging from each other for a longer period (2.3 millions of years) than the Pacific Slope and Cordilleran flycatchers (350,000 years), which still hybridize in areas of sympatry, resulting in individuals with intermediate songs. We recovered 21 million SNPs (single nucleotide polymorphisms) between the Alder and Willow flycatchers, with a mean Fst of 0.25, and a large proportion of SNPs with very high Fst values. Between the Pacific Slope and Cordilleran flycatcher we found 7 million SNPs, and a lower mean Fst of 0.06, with only a small number of SNPs with Fst > 0.7. These results are congruent with the previously estimated divergence times for these sister taxa. The shallow genomic differentiation between the Pacific Slope and Cordilleran flycatchers opens the possibility of detecting candidate areas of the genome related to innate song variation, the primary mean of mate recognition between these taxa.