Use of genomic data to resolve gene tree discordance in a Southeast Asian genus: Readdressing paraphyly in the spiderhunter (Nectariniidae, Arachnothera) phylogeny

Reduced representation genomic sequencing methods provide a fast and relatively inexpensive way to gather sequence data from thousands of loci throughout the genome. These data can be used to test previous phylogenetic hypotheses produced from limited numbers of mitochondrial and nuclear loci that often revealed intriguing, but conflicting results. In this paper, we use phylogenomic data to revisit molecular phylogenetic work that while clarifying taxonomic relationships within spiderhunters (Aves: Arachnothera), also questioned monophyly of this distinctive genus. Previous phylogenetic analysis of two molecular markers (one mitochondrial and one nuclear locus) produced conflicting topologies, yet both strongly supported non-monophyly of Arachnothera. This present study assesses the nature of pervasive gene tree discordance in these birds and investigates phylogenetic relationships within spiderhunters. To accomplish this, we used target-capture of ultra conserved elements (UCEs) to produce a phylogenomic data matrix used to infer the evolutionary history of Arachnothera. Although we recovered many gene tree topologies, concatenated and species-tree methods of analysis converged on a phylogeny with strong support for monophyly of Arachnothera. The consistency in analytical results confers confidence that gene tree conflict has been resolved in this enigmatic genus

Comparison of Target-Capture and Restriction-Site Associated DNA Sequencing for Phylogenomics: A Test in Cardinalid Tanagers (Aves, Genus: Piranga)

This is a pre-copyedited, author-produced version of an article accepted for publication in Systematic Biology following peer review. The version of record, Joseph D. Manthey, Luke C. Campillo, Kevin J. Burns, Robert G. Moyle; Comparison of Target-Capture and Restriction-Site Associated DNA Sequencing for Phylogenomics: A Test in Cardinalid Tanagers (Aves, Genus: Piranga), Systematic Biology, Volume 65, Issue 4, 1 July 2016, Pages 640–650, is available online at: ttps://doi.org/10.1093/sysbio/syw005.Restriction-site associated DNA sequencing (RAD-seq) and target capture of specific genomic regions, such as ultraconserved elements (UCEs), are emerging as two of the most popular methods for phylogenomics using reduced-representation genomic data sets. These two methods were designed to target different evolutionary timescales: RAD-seq was designed for population-genomic level questions and UCEs for deeper phylogenetics. The utility of both data sets to infer phylogenies across a variety of taxonomic levels has not been adequately compared within the same taxonomic system. Additionally, the effects of uninformative gene trees on species tree analyses (for target capture data) have not been explored. Here, we utilize RAD-seq and UCE data to infer a phylogeny of the bird genus Piranga. The group has a range of divergence dates (0.5–6 myr), contains 11 recognized species, and lacks a resolved phylogeny. We compared two species tree methods for the RAD-seq data and six species tree methods for the UCE data. Additionally, in the UCE data, we analyzed a complete matrix as well as data sets with only highly informative loci. A complete matrix of 189 UCE loci with 10 or more parsimony informative (PI) sites, and an approximately 80% complete matrix of 1128 PI single-nucleotide polymorphisms (SNPs) (from RAD-seq) yield the same fully resolved phylogeny of Piranga. We inferred non-monophyletic relationships of Pirangalutea individuals, with all other a priori species identified as monophyletic. Finally, we found that species tree analyses that included predominantly uninformative gene trees provided strong support for different topologies, with consistent phylogenetic results when limiting species tree analyses to highly informative loci or only using less informative loci with concatenation or methods meant for SNPs alone