Data from: Mixed-ancestry and admixture in Kaua'i's feral chickens: invasion of domestic genes into ancient Red Junglefowl reservoirs?

A major goal of invasion genetics is to determine how establishment histories shape non-native organisms' genotypes and phenotypes. While domesticated species commonly escape cultivation to invade feral habitats, few studies have examined how this process shapes feral gene pools and traits. We collected genomic and phenotypic data from feral chickens (Gallus gallus) on the Hawaiian island of Kauai to (i) ascertain their origins and (ii) measure standing variation in feral genomes, morphology and behaviour. Mitochondrial phylogenies (D-loop & whole Mt genome) revealed two divergent clades within our samples. The rare clade also contains sequences from Red Junglefowl (the domestic chicken's progenitor) and ancient DNA sequences from Kauai that predate European contact. This lineage appears to have been dispersed into the east Pacific by ancient Polynesian colonists. The more prevalent MtDNA clade occurs worldwide and includes domesticated breeds developed recently in Europe that are farmed within Hawaii. We hypothesize this lineage originates from recently feralized livestock and found supporting evidence for increased G. gallus density on Kauai within the last few decades. SNPs obtained from whole-genome sequencing were consistent with historic admixture between Kauai's divergent (G. gallus) lineages. Additionally, analyses of plumage, skin colour and vocalizations revealed that Kauai birds' behaviours and morphologies overlap with those of domestic chickens and Red Junglefowl, suggesting hybrid origins. Together, our data support the hypotheses that (i) Kauai's feral G. gallus descend from recent invasion(s) of domestic chickens into an ancient Red Junglefowl reservoir and (ii) feral chickens exhibit greater phenotypic diversity than candidate source populations. These findings complicate management objectives for Pacific feral chickens, while highlighting the potential of this and other feral systems for evolutionary studies of invasions.Mitochondrial DNA alignmentsSequences and alignments used for whole mitochondrial and control region phylogenies. Sequences files in FASTA format contain Kauai sequences from this work (consensus sequences from mapping short reads against the chicken reference genome) and previously published sequences from Genbank. Sequences were aligned with ClustalW and are stored in nexus format.alignment.tar.gzMitochondrial DNA phylogeniesBayesian whole mitochondrial genome and control region phylogenies in nexus format.phylogeny.tar.gzNuclear variantsNuclear variants used for population genetic analyses (PCA, STRUCTURE and ADMIXTURE). One dataset contains 3000 randomly selected variants, and the other SNPs that were typed both in this study and Wragg et al (2012).variants.tar.gzSupplementary table 2Supplementary table 2 in tab-delimited text format, containing vocalization data and links to YouTube and database entry IDs for Xeno Canto sources.supplementary_vocalization_data.tx