Periodic Reporting for period 4 - FERALGEN (The Genomics of Feralisation)
Reporting period: 2022-10-01 to 2023-03-31
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
Årevious report summary
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.
Previous report summary (3rd report period)
During the current reporting period we have now extracted methylated DNA from the feral hypothalamus samples, sequenced these and are now conducting the analysis for these. We have also completed the selective sweep analysis on the DNA taken from the feral samples, and are finalising the expression QTL (the loci responsible for regulating gene expression). We have also now submitted two papers on the feral populations, with both of these currently in revision. These papers look at admixture effects and their likely dating in Hawaii, and feral selective sweeps that are present in Bermuda and their effects. One final manuscript to be submitted concerns the methylation of the Z chromosome in the laboratory population. This is due to be submitted before the end of November 2022.
The last major piece of laboratory-based work has also been finalised now. This involved single-cell based sequencing to identify gene expression and regions of open chromatin (causal regions) in hypothalamus samples from the laboratory-based intercross. These samples have been prepared and sequenced, and the results are now being analysed. In total 45 samples were sequenced, with 718000 transcriptomes and ATAC-seq genomes generated and now being analysed. To facilitate the analyses, a small server computer was purchased and is now being used.
Current report summary (4th report period)
During this stage of the project, the final analyses are now ongoing. In particular we are working through the feral final association analyses, and with the single cell data we have now generated tissue specific single cell data and are continuing with these analyses. Final manuscripts are also now being worked on, whilst a small amount of single cell data is also being finalised in the lab. We have two publications under review currently, and are preapring the single cell and feral GWAS analyses for publication.
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.
Previous report summary (3rd report period)
During the current reporting period we have now extracted methylated DNA from the feral hypothalamus samples, sequenced these and are now conducting the analysis for these. We have also completed the selective sweep analysis on the DNA taken from the feral samples, and are finalising the expression QTL (the loci responsible for regulating gene expression). We have also now submitted two papers on the feral populations, with both of these currently in revision. These papers look at admixture effects and their likely dating in Hawaii, and feral selective sweeps that are present in Bermuda and their effects. One final manuscript to be submitted concerns the methylation of the Z chromosome in the laboratory population. This is due to be submitted before the end of November 2022.
The last major piece of laboratory-based work has also been finalised now. This involved single-cell based sequencing to identify gene expression and regions of open chromatin (causal regions) in hypothalamus samples from the laboratory-based intercross. These samples have been prepared and sequenced, and the results are now being analysed. In total 45 samples were sequenced, with 718000 transcriptomes and ATAC-seq genomes generated and now being analysed. To facilitate the analyses, a small server computer was purchased and is now being used.
Current report summary (4th report period)
During this stage of the project, the final analyses are now ongoing. In particular we are working through the feral final association analyses, and with the single cell data we have now generated tissue specific single cell data and are continuing with these analyses. Final manuscripts are also now being worked on, whilst a small amount of single cell data is also being finalised in the lab. We have two publications under review currently, and are preapring the single cell and feral GWAS analyses for publication.
Previous report summary
The final data has now all been generated, with mapping of expression QTL, mapping of methylation QTL and the single-cell analysis now on-going. We expect to have a first draft of the feral sweep and expression analyses ready by the end of the year (2022). Currently, we have identified feralasation-specific sweeps that exist between the disparate populations of Hawaii and Bermuda, we have also identified the traits that these regions appear to regulating, with these mainly being related to parasite resistance, behaviour and brain composition. We are now investigating the methylation patterns that exist in these regions as well. Subsequent work will now focus on the causation analyses between morphological QTL and expression QTL that will identify causal genes in the feral populations. The single cell based laboratory work has also now been finished, with the analysis now underway. We currently have 718000 transcriptomes and epigenomes for analysis and to combine with the feral data.
Current report summary
We are now pushing on with the final analyses to get these finished up ready for publication. The data is looking very exciting. In particular, the single cell data appears to show multiple large trans-acting hotspots that are highly cell-type specific. These can revolutionise how we consider the mechanisms for domestication are regulated, and in particular how individual cell types are regulated.
The final data has now all been generated, with mapping of expression QTL, mapping of methylation QTL and the single-cell analysis now on-going. We expect to have a first draft of the feral sweep and expression analyses ready by the end of the year (2022). Currently, we have identified feralasation-specific sweeps that exist between the disparate populations of Hawaii and Bermuda, we have also identified the traits that these regions appear to regulating, with these mainly being related to parasite resistance, behaviour and brain composition. We are now investigating the methylation patterns that exist in these regions as well. Subsequent work will now focus on the causation analyses between morphological QTL and expression QTL that will identify causal genes in the feral populations. The single cell based laboratory work has also now been finished, with the analysis now underway. We currently have 718000 transcriptomes and epigenomes for analysis and to combine with the feral data.
Current report summary
We are now pushing on with the final analyses to get these finished up ready for publication. The data is looking very exciting. In particular, the single cell data appears to show multiple large trans-acting hotspots that are highly cell-type specific. These can revolutionise how we consider the mechanisms for domestication are regulated, and in particular how individual cell types are regulated.