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The population genetics of non-migratory Allen's Hummingbird (Selasphorus sasin sedentarius) following a recent mainland colonization

Citation

Myers, Brian; Burns, Kevin; Clark, Christopher; Brelsford, Alan (2021), The population genetics of non-migratory Allen's Hummingbird (Selasphorus sasin sedentarius) following a recent mainland colonization, Dryad, Dataset, https://doi.org/10.5061/dryad.cnp5hqc30

Abstract

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.

Methods

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).

Funding

National Science Foundation, Award: IOS-1656867

National Science Foundation, Award: IOS-1656708