Phylogenetics of a recent radiation in the mallards and allies (Aves: Anas) : inferences from a genomic transect and the multispecies coalescent / Philip Lavretsky, Kevin G. McCracken, and Jeffrey L. Peters.

Includes bibliographical references (pages 410-411).

Reconstructing species trees by incorporating information from many independent gene trees reduces
the confounding influence of stochastic lineage sorting. Such analyses are particularly important for taxa
that share polymorphisms due to incomplete lineage sorting or introgressive hybridization. We investigated
phylogenetic relationships among 14 closely related taxa from the mallard (Anas spp.) complex
using the multispecies coalescent and 20 nuclear loci sampled from a genomic transect. We also examined
how treating recombining loci and hybridizing species influences results by partitioning the data
using various protocols. In general, topologies were similar among the various species trees, with major
clades consistently composed of the same taxa. However, relationships among these clades and among
taxa within clades changed among partitioned data sets. Posterior support generally decreased when filtering
for recombination, whereas excluding mallards (Anas platyrhynchos) increased posterior support
for taxa known to hybridize with them. Furthermore, branch lengths decreased substantially for recombination-
filtered data. Finally, concordance between nuclear and morphometric topologies conflicted
with those in the mitochondrial tree, particularly with regard to the placement of the Hawaiian duck
(A. wyvilliana), Philippine duck (A. luzonica), and two spot-billed ducks (A. zonorhyncha and A. poecilorhyncha).
These results demonstrate the importance of maximizing sequence length and taxon sampling
when inferring taxonomic relationships that are confounded by extensive allele sharing.