DOI: 10.5061/dryad.vt4b8gtn1
title: Genetic structure and biogeographic history of the Bicknell’s Thrush/ Gray-cheeked Thrush species complex

description: Abstract We examined species limits, admixture, and genetic structure
 among populations in the Bicknell’s Thrush (Catharus
 bicknelli)–Gray-cheeked Thrush (C. minimus) species complex to establish
 the geographic and temporal context of speciation in this group, which is
 a model system in ecology and a high conservation priority. We obtained
 mitochondrial ND2 sequences from 186 Bicknell’s Thrushes, 77 Gray-cheeked
 Thrushes, and 55 individuals of their closest relative, the Veery (C.
 fuscescens), and genotyped a subset of individuals (n = 72) at 5,633
 anonymous single nucleotide polymorphic (SNP) loci. Between-species
 sequence divergence was an order of magnitude greater than divergence
 within each species, divergence was dated to the late Pleistocene (420
 kbp) based on Bayesian coalescence estimation, and a coalescent model
 (IMa) revealed almost no gene flow between species based on ND2. SNP data
 were consistent with mitochondrial results and revealed low levels of
 admixture among species (3 of 37 Bicknell’s Thrushes, no Gray-cheeked
 Thrushes, and no Veeries were &gt;2% admixed). Species
 distribution models projected to the Last Glacial Maximum suggest that
 Bicknell’s Thrush and Gray-cheeked Thrush resided in primarily allopatric
 refugia in the late Pleistocene, consistent with the genetic data that
 support reproductive isolation over an extended period of time. Our
 genetic data suggest that both species underwent demographic expansions,
 possibly as they expanded out of Pleistocene refugia into their current
 ranges. We conclude that Bicknell’s Thrush and Gray-cheeked Thrush are 2
 distinct species-level lineages despite low levels of Gray-cheeked Thrush
 introgression in Bicknell’s Thrushes, and divergence has been maintained
 by a long history of allopatry in subtly different habitats. Their unique
 phylogeography among boreal forest birds indicates that either cryptic
 species breaks in eastern North America are still undiscovered, or another
 factor, such as divergent natural selection, high migratory connectivity,
 or interspecific competition, played a role in their divergence.
description: DNA extracts were sent to the Institute of Genomic Diversity at
 Cornell University for genotyping-by-sequencing. High quality DNA extracts
 (&gt;20 ng/μL) were digested with the restriction enzyme
 <i>PstI</i> and a unique barcode/adapter combination was
 ligated to each sample prior to pooling and amplification by PCR.
 Fragments were pooled with amplicons from other bird species to create
 three sequencing libraries, with 95 barcoded individuals per library, and
 sequenced on multiple lanes of a Hi-Seq 2000 Illumina sequencer (Illumina,
 San Digeo, CA). Each library resulted in ~200 Gbp of raw data. The 100
 base pair reads were filtered using the Universal Network Enabled Analysis
 Kit (UNEAK) pipeline implemented in TASSEL 3.0. Adapter dimers and
 sequences with an ambiguous base were removed and all reads were trimmed
 to 64 bp. Identical reads were merged into “tags” within each barcoded
 individual. Using a pairwise alignment, tags with 1 bp mismatch were
 retained as candidate SNPs. Candidate SNP loci that were present in fewer
 than 75% of individuals were removed, and then individuals possessing
 fewer than 50% of candidate SNPs were removed. To construct genotypes
 based on sequencing coverage, a maximum-likelihood method with an updated
 version of the script from White et al. (2013) was implemented; this
 method retained SNPs with an AIC ≥ 4 units lower than the next best
 reconstructed genotype. To remove paralogs (duplicated regions within the
 genome), SNPs with observed heterozygosities ≥ 0.75 were removed. Finally,
 SNPs present in fewer than 25% of individuals and individuals with fewer
 than 70% of SNPs were excluded. Following filtering, we retained a dataset
 of 5633 SNPs from 72 birds, including 37 Bicknell’s Thrushes from
 locations spanning the species’ entire breeding range, 23 Gray-cheeked
 Thrushes representing both subspecies and including individuals from
 Siberia, Alaska, and eastern Canada, a probable late migrating
 Gray-cheeked Thrush, and a small sample of eastern and western Veeries (n
 = 11).
description: The first column lists the sample identification number; all
 samples are museum accession numbers; date of collection, location of
 collection, and species type are listed in FitzGerald et al. (2019) The
 Auk. Each individual has two rows. The first row is the SNP name. A
 '0' indicates an uncalled allele.