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The Genomics of Feralisation

Periodic Reporting for period 2 - FERALGEN (The Genomics of Feralisation)

Reporting period: 2019-10-01 to 2021-03-31

The aim of this project is to understand the phenomenon of feralisation, and the trade-offs and genes that are selected during this process. Feralisation is a complex process that occurs when a domestic population is returned to the wild. By understanding feralisation we can use it as a model for evolution, especially in comparison to domestication. Although domestication has been previously heralded as an excellent model for evolution, in fact the reverse of this process, feralisation, is much superior in this regard. Domestication is more precisely a model of strong artificial selection on a few key traits. In contrast, feralisation will involve the whole gamut of natural and sexual selection pressures associated with the new natural environments the feral animals find themselves in. In addition, any changes can be far more accurately gauged, coming as they do from a known (domestic) stand-point, with a great deal already known about the genetics of the domesticated system. This gives us far more power to exactly how the phenotypic changes associated with feralisation are actually formed at a genetic level. This can then enable us to answer many of the important questions currently predominating the field of biology. How do gene polymorphisms affect small-scale quantitative variation, particularly in wild population? How does the genome respond to selection, and how can (cryptic) variation be maintained and increased in the face of this selection? What mechanisms underlie gene and organismal trait variation? The overall aim with this project is thus to identify the genes and polymorphisms that respond to feralisation, and to understand the complex trade-offs that occur during this selection. This in turn allows us to see exactly how feralisation is maintained and what happens to feral populations, with these results having impacts on topics including species invasion biology, speciation, conservation and hybridisation
We have now successfully completed five field trips – three to Hawaii and two to Bermuda. We have collected samples from over 500 chickens, and have also already obtained the DNA sequences from all 500+ samples, as well as gene expression profiles from a further 1400 samples (comb, bone and the hypothalamus region in the brain). Furthermore, we have sampled three separate Hawaiian islands (Kauai, Oahu, Hawaii), as well as the large number of birds from Bermuda. In addition, we have built an aviary and testing facility on the island of Kauai, and tested over 100 birds in this. These tests have included a variety of different measures of fear and anxiety related behaviour, ranging from predator avoidance behaviour, to socialisation and anxiety responses. In this way, we are now ready to begin the actual analysis to identify genomic regions that have responded to feralisation selection (i.e. the selection that occurs when domestic birds are reintroduced to a natural environment). We will also now map the expression QTL (that is to say the regions that regulate gene expression) in these genomic regions responding to feralisation, as well as throughout the genome. Another important aspect is to compare these feral samples with a controlled wild-domestic lab intercross population based in Sweden. To that end we have performed a methylation-based QTL analysis to identify the genetic elements responsible for the control of local methylation levels in the laboratory population, with this work being published in Nature Ecology and Evolution. We will now be doing a similar analysis in the feral Hawaiian and Bermudian birds. Finally we have also now ordered the reagents required for single cell sequence and epigenome analysis, with this being first conducted in the laboratory population, before we also conduct this on the feral birds.
We have now performed the bulk of the data collection, allowing progress on all work packages to now be achieved. In terms of the initial results, we have performed reviews highlighting feralisation in Trends in Ecology and Evolution, as well as publishing work on the laboratory aspects of the work using methylation-based data in our laboratory intercross, and we are also about to submit for publication a study on the genetic basis of structural coloration in chickens, using the feral birds as a mapping population. Further to this, genomic studies for the regulation of expression in feral birds over three different tissue types will also be performed, as well as how methylation is regulated in these feral populations. In this way, we will be able to identify the genes and even the polymorphisms that are responding to feralisation selection, as well as assessing the corresponding phenotypic trade-offs that these genomic changes control. We are currently on-track to perform all of the objectives set out in the work packages.