10.5061/DRYAD.CNP5HQC30
Myers, Brian
0000-0001-6485-8127
San Diego State University
Burns, Kevin
San Diego State University
Clark, Christopher
University of California, Riverside
Brelsford, Alan
University of California, Riverside
The population genetics of non-migratory Allen's Hummingbird
(Selasphorus sasin sedentarius) following a recent mainland colonization
Dryad
dataset
2020
National Science Foundation
https://ror.org/021nxhr62
IOS-1656867
National Science Foundation
https://ror.org/021nxhr62
IOS-1656708
2021-12-21T00:00:00Z
2021-12-21T00:00:00Z
en
18463411059 bytes
3
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Allen's Hummingbird comprises two subspecies, one migratory
(Selasphorus sasin sasin) and one non-migratory (S. s. sedentarius). The
non-migratory subspecies, previously endemic to the California Channel
Islands, apparently colonized the California mainland on the Palos Verdes
Peninsula some time before 1970, and now breeds throughout coastal
southern California. We sequenced and compared populations of mainland
non-migratory Allen's Hummingbird to Channel Island populations from
Santa Catalina, San Clemente, and Santa Cruz Island. We found no evidence
of founder effects on the mainland population. Values of nucleotide
diversity on the Channel Islands were lower than those on the mainland.
There were low levels of divergence between the Channel Islands and the
mainland, although Santa Cruz Island was the most genetically distinct.
Ecological niche models showed that rainfall and temperature variables on
the Channel Islands are similar in the Los Angeles basin, and predicted
continued expansion of non-migratory Allen's Hummingbird north along
the coast and inland. We also reviewed previous genetic studies of
vertebrate species found on the Channel Islands and mainland, and showed
that broad conclusions regarding island-mainland patterns remain elusive.
Challenges include the idiosyncratic nature of colonization itself as well
as the lack of a comprehensive approach that incorporates similar markers
and sampling strategies across taxa, which, within the context of a
comparative study of island-mainland relationships, may lead to
inconsistent results.
We collected tissue (N=17) and blood samples (N=5) from the Channel
Islands (N=10 individuals) and the southern California mainland (N=12
individuals). All data in the current study were acquired from
non-migratory Allen’s Hummingbird. Individuals included in the present
study were gathered from the mainland in Los Angeles County (N=5), as far
south as San Diego County (N=1), as far north as Santa Barbara County
(N=4), as far inland as Riverside County (N=2), and from San Clemente
(N=1), Santa Catalina (N=2), and Santa Cruz (N=7) islands. Collection of
all samples in the dataset occurred from March through May. All sampling
we conducted was in compliance with the IACUC at the University of
California, Riverside (protocols 20130018 and 20160039), USFWS permit
#MB087454-1, USGS Bird Banding Permit #23516, California Department of
Fish and Wildlife permit #SC006598, and California State Parks permit
#17-820-01. Genomic DNA from tissues and dried blood spots were extracted
using a Qiagen DNeasy Blood and Tissue Kit, following the recommendations
of the manufacturer (Qiagen, Valencia, California, USA). Library
preparation was based on a modified version from Baym et al. (2015). Whole
genomes of all individuals were sequenced using an Illumina NextSeq 500 at
the University of California, Riverside Genomics Core or an Illumina HiSeq
X at Novogene, Inc. with an average coverage of 3.7x per sample. Reads
were aligned to the Anna’s Hummingbird reference genome available on NCBI
using the software package BWA v0.7 (Burrows-Wheeler Aligner, Li and
Durbin 2009, NCBI Resource Coordinators 2018). Variants were called using
SAMtools v1.9 and BCFtools v1.9 (Li et al. 2009, Narasimhan et al. 2016).