10.5061/DRYAD.VT4B8GTN1
FitzGerald, Alyssa
0000-0002-9850-2003
University at Albany, State University of New York
Weir, Jason
University of Toronto
University of Toronto
Ralston, Joel
Saint Mary's College
Notre Dame College
Warkentin, Ian
Memorial University of Newfoundland
Whitaker, Darroch
Parks Canada
Kirchman, Jeremy
New York State Museum
Genetic structure and biogeographic history of the Bicknell’s Thrush/
Gray-cheeked Thrush species complex
Dryad
dataset
2020
Natural Sciences and Engineering Research Council
https://ror.org/01h531d29
RGPIN-2016-06538
Natural Sciences and Engineering Research Council
https://ror.org/01h531d29
492890
American Museum of Natural History Frank Chapman
Centre for Forest Science and Innovation
University at Albany Benevolent Association
2020-10-17T00:00:00Z
2020-10-17T00:00:00Z
en
https://doi.org/10.1093/auk/ukz066
1670496 bytes
3
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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 >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.
DNA extracts were sent to the Institute of Genomic Diversity at Cornell
University for genotyping-by-sequencing. High quality DNA extracts
(>20 ng/μL) were digested with the restriction enzyme PstI 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).
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.