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

Abstract

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.