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Mixed ancestry and admixture in Kauai's feral chickens: invasion of domestic genes into ancient Red Junglefowl reserviors
Kellogg Biological Station, Michigan State Universiry, 3700 East Gull Lake Road, Hickory Corners, MI 49060, USA.
Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.ORCID iD: 0000-0003-1262-4585
Department of Biology, University of Victoria, Cunningham 202, 3800 Finnerty Road, Victoria, BC V8P 5C2, Canada.
Kellogg Biological Station, Michigan State Universiry, 3700 East Gull Lake Road, Hickory Corners, MI 49060, USA.
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2015 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, no 9, 2112-2124 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
John Wiley & Sons, 2015. Vol. 24, no 9, 2112-2124 p.
Keyword [en]
conservation genetics, Gallius gallus, hybridization, invasive species
National Category
Evolutionary Biology
URN: urn:nbn:se:liu:diva-117160DOI: 10.1111/mec.13096ISI: 000353928200014PubMedID: 25655399OAI: diva2:806439
Available from: 2015-04-20 Created: 2015-04-20 Last updated: 2015-11-02
In thesis
1. Genomics of chicken domestication and feralisation
Open this publication in new window or tab >>Genomics of chicken domestication and feralisation
2015 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Domestication can serve as a study system of rapid evolutionary change with wide-ranging effects on traits in animals. The chicken was domesticated from the Red Junglefowl and has diverged in behaviour, morphology and life history traits. Conversely, feralisation is a more recent process when domestic animals are again exposed and respond to an environment outside of human husbandry. Linkage-based quantitative trait locus (QTL) mapping has been used to localise genetic variants that affect domestication traits in the chicken genome. Because of the limited resolution of linkage mapping, the QTL regions associated with domestication traits are often broad and contain many genes. One approach to help sort out potential causative genes is to measure gene expression as an intermediary molecular phenotype. In this dissertation, expression quantitative trait locus (eQTL) mapping of gene expression traits is used to search for potential causative genes for domestication traits in the chicken. Expression quantitative trait loci were mapped across the whole genome in bone and hypothalamus samples, and targeted at QTL regions in the base of the comb. These studies have resulted in candidate quantitative trait genes, supported by genetic and gene expression evidence, for relative comb mass, bone allocation, egg production and fearful behaviour as measured in an open field test. Secondly, a population genomics approach was used to study the molecular basis of feralisation in a free-range feral chicken population from the Pacific island of Kauai. Mitochondrial DNA sequences and phenotypic observations establish the hybrid origin of this population as a mixture of wild and domestic chickens. Genome-wide mapping of pooled heterozygosity highlight regions that may be involved in adaptation to the feral environment. The expression QTL results bring us closer to knowledge about the molecular basis of domestication traits in the chicken, suggesting plausible candidate genes and opening up for functional studies of individual loci. The population genomic study shows that feralisation has a mostly different genomic architecture than domestication, and suggests phenotypic effects, based on overlap with domestication QTL regions, for some of the identified regions.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2015. 28 p.
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1708
National Category
urn:nbn:se:liu:diva-122280 (URN)10.3384/diss.diva-122280 (DOI)978-91-7685-932-2 (Print) (ISBN)
Public defence
2015-12-18, Planck, Fysikhuset, Campus Valla, Linköping, 10:15 (English)
Available from: 2015-11-02 Created: 2015-10-27 Last updated: 2015-11-05Bibliographically approved

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