DOI: 10.5061/dryad.cnp5hqc30
title: The population genetics of non-migratory Allen's Hummingbird (Selasphorus sasin sedentarius) following a recent mainland colonization

description: 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.
description: 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).