Lineage diversity in a widely distributed New World passerine bird, the House Wren

Lay Summary center dot The House Wren (Troglodytes) complex consists of at least 5 distinct evolutionary groups distributed from Canada to southern South America. center dot Morphological variation led taxonomists to name over 25 subspecies. center dot We used mitochondrial DNA (mtDNA; 349 individuals) and a genome-wide survey of single nucleotide polymorphisms (RADseq; 184 individuals) to evaluate evolutionary patterns and determine their relationship to current taxonomy. center dot The mtDNA data showed considerable differentiation, especially in island forms T. sissonii (Isla Socorro), T. a. beani (Isla Cozumel), and T. tanneri (Isla Clarion), and T. martinicensis, the latter of which includes several clades that were not monophyletic. center dot MtDNA suggested that eastern and western samples of T. aedon were not monophyletic, whereas they were in the RADseq analyses; the cause of the discordance is unclear. center dot We suggest that the RADseq data provide the most appropriate basis for classification and understanding House Wren evolution, and they show a high degree of phylogeographic differentiation and support for these taxonomic groups: eastern and western T. aedon, T. sissonii, T. tanneri, T. beani, and T. a. musculus. We explored the evolutionary radiation in the House Wren complex (Troglodytes aedon and allies), the New World's most widely distributed passerine species. The complex has been the source of ongoing taxonomic debate. To evaluate phenotypic variation in the House Wren complex, we collected 81,182 single-nucleotide polymorphisms (SNPs) from restriction site associated loci (RADseq) and mitochondrial DNA (mtDNA) from samples representing the taxonomic and geographic diversity of the complex. Both datasets reveal deep phylogeographic structuring, with several topological discrepancies. The trees highlight the evolutionary distinctiveness of eastern and western T. aedon, which were sister taxa in the SNP tree and paraphyletic on the mtDNA tree. The RADseq data reveal a distinct T. a. brunneicollis group, although STRUCTURE plots suggest admixture between western T. aedon and northern Mexican samples of T. a. brunneicollis. MtDNA data show a paraphyletic arrangement of T. a. musculus on the tree, whereas the SNP tree portrays them as monophyletic. Island taxa are distinct in both datasets, including T. a. beani (Isla Cozumel), which appears derived from T. a. musculus in eastern Mexico, and T. sissonii (Isla Socorro) and T. tanneri (Isla Clarion) although the 2 datasets disagree on their overall phylogenetic placement. Although we had only mtDNA data for T. a. martinicensis from the Lesser Antilles, we found at least 4 distinct and paraphyletic taxa from Trinidad, Granada, St. Vincent islands, and Dominica. The House Wren complex showed strong differentiation in mtDNA and RADseq datasets, with conflicting patterns likely arising from some combination of sex-biased dispersal, incomplete lineage sorting, or selection on mtDNA. The most glaring discrepancies between these 2 datasets, such as the paraphyly of eastern and western North American House Wrens in the mtDNA tree, present excellent opportunities for follow-up studies on evolutionary mechanisms that underpin phylogeographic patterns.