DOI: 10.5061/dryad.5dv41nsb5
title: Lineage diversity in a widely distributed New World songbird, the House Wren

description: We explored the evolutionary radiation in the House Wren complex
 (Troglodytes aedon and allies), the most widely distributed
 passerine species in the New World. The complex, classified into
 as many as 25 subspecies and five species, has been the source of ongoing
 taxonomic debate. To evaluate this extensive phenotypic variation
 in the House Wren complex from a genomic perspective, we
 collected 81,182 single nucleotide polymorphisms (SNPs)
 from restriction site associated loci (RADseq) and mtDNA from
 samples representing the taxonomic and geographic diversity of
 the complex. Both datasets reveal deep phylogeographic
 structuring across the complex, but topological relationships
 revealed several major discrepancies. The trees highlight the
 evolutionary distinctiveness of eastern and western T.
 aedon, which were sister in the SNP tree and paraphyletic on the
 mtDNA tree. The RADseq data reveal a distinct T.brunneicollis
 group, although STRUCTURE plots show putative admixture
 between western T. aedon and northern Mexican samples of T.
 brunneicollis. In the mtDNA tree this introgression resulted in
 paraphyly of T. brunneicollis/western T. aedon. mtDNA data
 further show a paraphyletic arrangement of T. musculus on the
 tree, whereas the SNP tree portrays them as monophyletic. Island
 taxa are distinct in both data sets, including T. beani (Isla
 Cozumel), which appears derived from T. musculus in eastern Mexico, and T.
 sissonii (Isla Socorro) and T. tanneri (Isla Clarión) although
 the two data sets disagree on their overall phylogenetic
 placement. Although we had only mtDNA data for T. martinicensis
 from the Lesser Antilles, we found at least four distinct and
 paraphyletic taxa from Trinidad, Granada, St. Vincent islands,
 and Dominica. The House Wren complex showed strong
 differentiation in both mtDNA and RADseq datasets, with
 conflicting patterns likely having arisen due to some combination
 of sex-biased dispersal or selection on mtDNA. The most glaring
 discrepancies between these two 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.
description: # Lineage diversity in a widely distributed New World songbird, the House
 Wren raw_data.zip: Contains all the raw data from the sequencing facility
 along with the barcode files to demultiplex the data. The barcodes contain
 the study number, also called "RadSeq Tip ID", for the
 individual specimen the data corresponds to. See
 Wren_specimen_data_submit.xlsm for the meta information corresponding to
 each individual. ipyrad_demultiplexed_data.zip: Contains the raw data for
 each individual demultiplexed using ipyrad. The name of each file contains
 the study number, also called "RadSeq Tip ID", for the
 individual specimen the data corresponds to. See
 Wren_specimen_data_submit.xlsm for the meta information corresponding to
 each individual. .str files: Datamatrices containing SNPS from the RADseq
 data for each dataset used in the study in STRUCTURE format.
 '.u.pi.str' or '_u_pi.str' stand for datamatrices
 containing only unlinked, parsimony informative SNPs. *
 Trog_ALL_NO_OG_u_pi.str: contains all specimens except those from the
 outgroup. * Trog_ade_bru.u.pi.str: Contains only the T. aedon and
 brunneicollis specimens. * Trog_ade_bru.u.str: Contains only the T. aedon
 and brunneicollis specimens. Has all the unlinked SNPs, not just the
 parsimony informative ones. * Trog_mus_C_AM_u_pi.str: Contains only the T.
 musculus specimens from Central America. * Trog_mus_S_AM_u_pi.str:
 Contains only the T. musculus specimens from South America. .nex files:
 Datamatrices in the NEXUS format containing the concatenated loci for each
 ND2 mitochondrial dataset used in the study. * Trog_ALL.nex: Contains all
 individuals for which ND2 data existed. * Trog_ade_bru.nex: Contains only
 the T. aedon and brunneicollis specimens. * Trog_mus_C_AM.nex: Contains
 only the T. musculus specimens from Central America. * Trog_mus_S_AM.nex:
 Contains only the T. musculus specimens from South America.
 Wren_specimen_data_submit.xlsm: Spreadsheet containing all the information
 for the specimens used in the study including study number, museum number,
 locality and date collected, etc. Fields containing "null" mean
 that the original data associated with the specimens contained a
 "?" in this field. Blank fields mean that data does not exist
 for that specific specimen. #### Variables: * Taxon: Species of the
 specimen. All of are Genus Troglodytes unless otherwise noted. * Prep/
 Genbank No: The perpetrator or Genbank number associated with the
 specimen, if it exists. * ND2 349: Whether this specimen is in the
 mitochondrial ND2 gene datasets or not. "X" means it is in the
 dataset, blank means it is not. * RAD: Whether this specimen is in the
 RADseq datasets or not. "X" means it is in the dataset, blank
 means it is not. * RadSeq Tip ID: This is the RADseq study number used for
 the specimen. If the field is blank that specimen was not included in the
 RADseq dataset. * CAT No.: The museum catalog number for the specimen. The
 institution is listed where known along with the catalog number. If there
 is no number it means the specimen was not officially cataloged at time of
 publishing. See "Prep/Genbank No" for unique identifier in this
 case. * Collect Date: the date the specimen was collected in
 day/month/year format. * Country: Abbreviation for the country the
 specimen was collected in. * State/Dpto/Prov: The state, department or
 providence in which the specimen was collected. * County/Prov: The county
 or providence in which the specimen was collected. * Specific Locality:
 The named place where or near where the specimen was collected, in the
 format provided in the original information associated with the specimen.
 * Lat: Latitude where the specimen was located in decimal degrees format.
 * Long: Longitude where the specimen was collected in decimal degrees
 format. * Altitude: Altitude at which the specimen was collected in
 meters.