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.

File Descriptions:

sample_information.csv: location data (approximate) where each sample was collected, date collected, USGS band number (if banded), sex

VoucherNumbers&Acknowledgements.csv: Voucher numbers for samples donated by the San Diego State University Museum of Biodiversity and the San Diego Natural History Museum; and acknowledgements

alhu_nomigrate_final.vcf: 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.

dDocent_allalhu_0.98.fa.zip: 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

FST_function.R: function in R to calculate Hudson's F_ST from allele frequencies for population differentiation

PCA_function.R: function in R to generate Principal Component Analysis from genotype point estimates

parse_barcodes.pl: 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.

splitfastq.pl: Script in perl to create a separate fastq file for each individual's reads

vcf2mpgl.pl: 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)

gl2genest.pl: 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