Introgressed variants obscure phylogenetic relationships but are not subject to positive selection in Australasian long-tailed parrots

Gene flow often obscures phylogenetic relationships, but the evolutionary significance of introgressed variants is unclear. Here, we examine the Australasian long-tailed parrots (Psittaculinae: Polytelini), in which an unexpected sister relationship between Polytelis alexandrae and the genus Aprosmictus, and not the other Polytelis species, has been observed. We tested whether this relationship was due to ancient introgression in whole genomes and found that the majority of gene trees had Ap. erythropterus and P. alexandrae as sister taxa, whereas network analysis indicated monophyly of Polytelis, and 48% of gene trees were in phylogenetic conflict due to introgression from Ap. erythropterus into P. alexandrae. Some 4–8% of the genome of P. alexandrae was introgressed from Ap. erythropterus, with signals of gene flow occurring throughout the genome. These findings indicate that topologies with P. alexandrae and the genus Ap. erythropterus as sister taxa were biased by gene flow and affirm that Polytelis is monophyletic. Next, we assessed the evolutionary outcomes for introgressed variants and found that, among introgressed protein-coding genes, only two (0.8%) were under positive selection, in comparison to 99 (1.7%) of non-introgressed genes. Our results indicate that, despite the ubiquity of genetic introgression across a given phylogeny, many genetic variants flowing between species may play a small role in molecular adaptations, with selection most frequently acting on existing variation.

Methods
The data was generated using the methods described herein and in the manuscript Smith et al. "Introgressed variants obscure phylogenetic relationships but are not subject to positive selection in Australasian long-tailed parrots."