DOI: 10.5061/dryad.zgmsbcc84
title: Novel hybrid finds a peri-urban niche: Allen’s Hummingbirds in southern California

description: Species range expansions and contractions can have ecological and genetic
 consequences, and thus are important areas of study for conservation.
 Hybridization and introgression are not uncommon in closely related
 populations that experience secondary contact during a range expansion.
 Allen’s Hummingbird (Selasphorus sasin) in California comprises two
 subspecies: the migratory S. s. sasin, which winters in central Mexico and
 breeds in central and northern California, and the resident S. s.
 sedentarius, which lives and breeds year-round on several of the Channel
 Islands off the California coast. Within recent decades, Allen’s
 Hummingbirds have been found living and breeding year-round in the
 southern California peri-urban mainland near Los Angeles. Ornithologists
 assumed that the L.A. birds were an expansion of the island subspecies, S.
 s. sedentarius due to similar but very subtle morphological
 characteristics. However, the genetic relationships among the three
 putative populations of Allen's hummingbird—migratory, southern
 California mainland, and island—are unknown. We investigated these
 relationships by analyzing variation of single nucleotide polymorphisms
 from the three geographic regions where S. sasin are present. Our
 population genomic analyses indicate that S. sasin hummingbirds inhabiting
 mainland southern California are a hybrid population resulting from
 admixture between S. s. sasin and S. s. sedentarius. From one perspective,
 these results may be interpreted as a positive development for S. s. sasin
 as the growing population represent an overall increase in the S. sasin
 population, and the expanding population contains a significant
 representation of S. s. sasin alleles.
description: File Descriptions:
 <strong>sample_information.csv:</strong> location
 data (approximate) where each sample was collected, date collected, USGS
 band number (if banded), sex
 <strong>VoucherNumbers&Acknowledgements.csv</strong>: Voucher numbers for samples donated by the San Diego State University Museum of Biodiversity and the San Diego Natural History Museum; and acknowledgements <strong>alhu_nomigrate_final.vcf: </strong>Reads from each individual was mapped to the de novo reference.We filtered for sites with minimum base and mapping quality scores (Q-score) of 20, kept a max-depth of 100 reads per site per individual, and omitted insertions and deletions. Sites were thinned to one SNP per 136 bp sequence read. In addition, we removed SNPs with a minor allele frequency less than 0.05, individuals missing more than 75% of data, or a minimum read depth per site per individual less than 3. <strong>dDocent_allalhu_0.98.fa.zip: </strong>synthetic reference from our data created with the cd-hit-est package in CD-HIT to cluster sequences. We used the sequences from all 102 individuals and a 0.95 sequence identity threshold, resulting in 504,892 unique contigs <strong>FST_function.R:</strong> function in R to calculate Hudson's F<sub>ST</sub> from allele frequencies for population differentiation <strong>PCA_function.R</strong>: function in R to generate Principal Component Analysis from genotype point estimates <strong>parse_barcodes.pl: </strong>Script in perl to demultiplex pooled libraries into individual samples by unique barcodes. This script allows and corrects for one mismatch in the barcode and removes the adapter sequences from the reads, leaving only genomic DNA sequences. <strong>splitfastq.pl</strong>: Script in perl to create a separate fastq file for each individual's reads <strong>vcf2mpgl.pl: </strong>Script in perl to convert a vcf file to 'multiple population genotype likelihoods', outputting the probabilty that the individual at that site is a heterozygote and each of the homozygotes (3 likelihoods) <strong>gl2genest.pl: </strong>Script in perl to convert genotype likelihoods to genotype point estimates, on a scale of 0-2. If all genotypes are equally likely, NA is returned