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.txt