Data from: Exploring conflicts in whole genome phylogenetics: A case study within Manakins (Aves: Pipridae)

<p>Some phylogenetic problems remain unresolved even when large amounts of sequence data are analyzed and methods that accommodate processes such as incomplete lineage sorting are employed. In addition to investigating biological sources of phylogenetic incongruence, it is also important to reduce noise in the phylogenomic dataset by using an appropriate filtering approach that addresses gene tree estimation errors. We present the results of a case study in manakins, focusing on the very difficult clade comprising the genera <em>Antilophia</em> and <em>Chiroxiphia</em>. Previous studies suggest that <em>Antilophia</em> is nested within <em>Chiroxiphia</em>, though relationships among <em>Antilophia</em>+<em>Chiroxiphia</em> species have been highly unstable. We extracted more than 11,000 loci (ultra-conserved elements and introns) from whole genomes and conducted analyses using concatenation and multi-species coalescent methods. Topologies resulting from analyses using all loci differed depending on the data type and analytical method, with two clades (<em>Antilophia</em>+<em>Chiroxiphia</em> and <em>Manacus</em>+<em>Pipra</em>+<em>Machaeopterus</em>) in the manakin tree showing incongruent results. We hypothesized that gene trees that conflicted with a long coalescent branch (e.g., the branch uniting <em>Antilophia</em>+<em>Chiroxiphia</em>) might be enriched for cases of gene tree estimation error, so we conducted analyses that either constrained those gene trees to include monophyly of <em>Antilophia</em>+<em>Chiroxiphia</em> or excluded these loci. While constraining trees reduced some incongruence, excluding the trees led to completely congruent species trees, regardless of the data type or model of sequence evolution used. We found that a suite of gene metrics (most importantly the number of informative sites and likelihood of intralocus recombination) collectively explained the loci that resulted in non-monophyly of <em>Antilophia</em>+<em>Chiroxiphia</em>. We also found evidence for introgression that may have contributed to the discordant topologies we observe in <em>Antilophia</em>+<em>Chiroxiphia</em> and led to deviations from expectations given the multi-species coalescent model. Our study highlights the importance of identifying factors that can obscure phylogenetic signal when dealing with recalcitrant phylogenetic problems, such as gene tree estimation error, incomplete lineage sorting and reticulation events.</p>