Rheindt, F. E., Fujita, M. K., Wilton, P. R., and S. V. Edwards. (2014). Introgression and Phenotypic Assimilation in Zimmerius Flycatchers (Tyrannidae): Population Genetic and Phylogenetic Inferences from Genome-Wide SNPs. Systematic Biology doi: 10.1093/sysbio/syt070.
This 19-page paper investigates the relationship between genomic markers and putative phenotypic admixture in a “mosaic” population of Andean flycatchers. The mosaic birds exhibit similarity in vocalizations and mtDNA sequence to southern Zimmerius viridiflavus but sport the plumage color of northern Z. chrysops. Why?
The authors obtain RADseq-like data from 2 viridiflavus, 3 chrysops, 5 mosaic, and 2 outgroup Zimmerius. They use STRUCTURE, FST, principle components analysis, parsimony, SNAPP, and the ABBA-BABA test to evaluate 5 alternative hypotheses (Figure 2) explaining the observed genomic and phenotypic patterns. They unequivocally show that mosaic shares genomic affinities with viridiflavus.
But why then does mosaic share plumage coloration with chrysops? Introgression from chrysops is one possible explanation, which they evaluate with the ABBA-BABA test. Since significantly more of the species-tree-discordant SNP trees had chrysops sister to mosaic than had viridiflavus sister to mosaic, the authors inferred gene flow between chrysops and mosaic.
They also mapped their contigs to the Zebra Finch (Taeniopygia guttata) genome, tallying chromosomal position and nearby gene annotations to SNPs showing the ABBA-BABA pattern. They noticed a possible selective sweep at the Z-chromosome and possible prevalence of membrane and cell projection proteins near ABBA-BABA-like SNPs. The suggestion was that these protein types might be associated with carotenoid plumage pigmentation pathways in Zimmerius, but this functional link between SNP trees and phenotype seemed tenuous at best.
We enjoyed this data-heavy paper’s demonstration of interesting new methods and appreciated the hypothesis-testing framework. However, we came up with another hypothesis (H6?) that is supported by their data, whereby 1) viridiflavus and mosaic are sister species with apomorphous voice and mtDNA, 2) a single plumage change occurs on the branch to viridiflavus, and 3) some neutral gene flow happens between mosaic and chrysops across the narrow Rio Marañòn valley. [UW Phylogenetics Seminar, 2/6/14; Dave Slager]