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 1) ascertain their origins and 2) 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 sequences from Kauai that predate European contact. The more prevalent mtDNA clade also 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 recent increases in G. gallus density on Kauai.
SNPs obtained from whole genome sequencing provided evidence of admixture between Kauai’s divergent G. gallus lineages. Feral plumage, skin color, and vocalizations overlapped with traits of domestic chickens and Red Junglefowl, further suggesting hybrid origins. Together, our data support the hypotheses that 1) Kauai’s feral G. gallus descend from recent invasion(s) of domestic chickens into an ancient Red Junglefowl reservoir, and 2) feral chickens exhibit greater phenotypic diversity than candidate source populations. These findings complicate management objectives for Pacific feral chickens, while highlighting the potential of these, and other feral systems for evolutionary studies of invasions.