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The genomic signals of feralisation: Not just domestication in reverse?
Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.ORCID iD: 0000-0003-1262-4585
Department of Zoology, Michigan University, Michigan, USA.
Department of Biology, University of Victoria, Victoria, British Columbia, Canada.
UCL Genetics Institute, University College London, London, UK.
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Feralisation occurs when a domestic population is returned to the wild, escaping the cultivated settings it has been selected for, and has been considered as the reverse of domestication. The radical shifts in social, biotic and abiotic environments results in greatly increased natural and sexual selection. However, it is currently unknown if (and how) feral populations evolve in response to these altered selection regimes. Feralisation can therefore provide a unique opportunity to observe how natural and sexual selection acts on a domestic population returned to natural conditions, and especially how the genome responds to the reintroduction of such strong selective forces.

We have previously shown that Kauai Island’s feral chickens are a highly variable population with both domestic and ancient Polynesian origins. Here, we map selective sweeps in feral Kauai chickens using whole genome sequencing. 37 putative Kauai sweep regions were identified, with 26 being unique to feralisation (i.e. not present among the genomic regions that have previously been associated with domestication). To ascribe potential phenotypic functions to these genes, we utilised a laboratory-controlled equivalent to the Kauai population – an eighth generation advanced intercross between Red Junglefowl and domestic layer birds that has been used previously for both QTL and expression QTL studies of male ornaments and female reproductive traits (comb mass and fecundity). Certain sweep genes exhibited significant correlations with comb mass, maternal brooding behaviour and fecundity.

Together, our analyses of feral and intercrossed genomes indicate that adaptations to feral and domestic environments involve different genome regions and feral chickens show some evidence of adaptation at genes associated with sexual selection and reproduction. At the genomic level, feralisation is not simply a reversal of the domestication process.  A comprehensive understanding of feralisation will thus bring unique evolutionary insights, while facilitating ‘evolutionarily-enlightened’ management practices for animals and crops.

National Category
Genetics
Identifiers
URN: urn:nbn:se:liu:diva-122279OAI: oai:DiVA.org:liu-122279DiVA: diva2:865191
Available from: 2015-10-27 Created: 2015-10-27 Last updated: 2015-11-05Bibliographically approved
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.
Series
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1708
National Category
Genetics
Identifiers
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)
Opponent
Supervisors
Available from: 2015-11-02 Created: 2015-10-27 Last updated: 2015-11-05Bibliographically approved

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