Sexually antagonistic genes in wild flies; searching for twin peaks.

Overview

Ever since Darwin it has been thought that sexual selection has a great influence on the process of speciation, and many animal species differ primarily in traits that are sexual dimorphic, such as behaviours and morphologies thought to have evolved by sexual selection. Sexual selection is also thought to influence genomic divergence, but the evidence is often indirect and less clear, and relies on examining divergence patterns of genes thought o be under divergent selection in males and females, i.e. genes showing sexual antagonism. For example genes that show sex-biased gene expression are often the most divergent between species, and this is sometimes more pronounced in sexually dimorphic species. Currently there is extensive debate about what patterns robustly and reliably reflect sexual selection and sexual conflict in genomic data. Identifying the precise targets of sexual selection, and the signature this leaves in the genome, is critical to understanding the importance of this form of selection in evolutionary divergence and speciation.

The proposed work will take advantage of new collections of flies from wild populations to examine signatures of sexually antagonistic selection in action, in a species known to have extensive sexual conflict. The student will participate in a large scale sampling programme coordinated across multiple European fly laboratories. The student will obtain new data on differences in population genomic parameters between males and females from these wild populations. They will identify sex-specific differences in gene frequencies at loci across the genome and relate these to patterns of sex-biased gene expression compared to measures of stabilising selection.

The prediction from theory and other empirical studies is that genes evolving under antagonistic sexual selection will show sex-biased differences in gene frequencies (Fst), differences in sex-biased gene expression, and signatures of balancing selection. In particular, a “Twin Peaks” pattern of association between sex-biased expression and sex-biased Fst has been predicted. This has proven controversial as it is confounded by effects of genetic drift in small populations, genetic load and sampling error. Our project will provide new insight to this unresolved and important question about evolution.

Wild fruit flies (Drosophila melanogaster) are the ideal species to test this contrasting theory. Sexually antagonistic and sexual selection are known to be important in this species. Estimates of population size are very large, and the coordinated collection effort ensures good sampling. Many samples are in hand already. Especially important is that genes which show signatures of potential sexual selection can be investigated for sex-specific effects on behaviour and fitness through the ready availability of mutant genes for this species, which can be backcrossed into wild type flies. The project can be take in numerous directions, including examining gene flow for these genes in natural populations and between species.

The project will be based in the laboratory of Michael G Ritchie at St Andrews and co-supervised by Iapetus partner Kathryn Elmer, who works on ecological and reproductive system evolution in a variety of species. Fabian Staubach at Frieberg, Germany, is involved in obtaining the genomic data provided from the “DrosEU” consortium. MGR is a participant in DrosEU and the student will contribute to this pan-European collaborative network.

Methodology

The student will obtain genome sequences from MGR collections and the DrosEU consortium project. Bioinformatics procedures will be used to process samples, align sequences and identify appropriate population genomic parameters. Laboratory techniques for handling and experimenting with Drosophila will also be used, including experimental design and analyses of mating success and sex-specific fitness measurements with mutant stocks. The student will receive training in contemporary techniques of bioinformatics, population genetics, experimental biology, functional genetics and quantitative biology.

Project Timeline

Year 1

Learning basic Bioinformatics, analysing existing DNA sequences and fly husbandry and preliminary experiments. Participation in local and other Bioinformatics courses.

Year 2

Obtaining new samples of flies from the wild, visiting collaborators, completion of first pass of “Twin Peaks” analysis. Contribution to Network sampling. Study visits to partners, including potential CASE placing.

Year 3

Follow on work to first analyses; laboratory studies of flies expressing mutants in candidate genes identified, sequencing additional species and samples. Contribution to Network sampling.

Year 3.5

Completing experimental work and extension of work to other species. Studies of gene flow between locally adapted populations.

Training
& Skills

The student will become trained in Bioinformatics, including courses provided by the St Andrews Bioinformatics Unit and other collaborating laboratories. They will also participate in a broad Network project collecting and analysing samples of wild Drosophila from throughout Europe, which involves techniques in entomology, field sampling, phenotyping and quantitative biology. They will learn laboratory procedures associated with behavioural and functional genetic analyses of Drosophila in the laboratory, including studies of mutant strains.

The student will also gain important transferrable skills such as excellent scientific communication, outreach and synthesis, and have the opportunity to engage in the scientific community through conferences and participation in our related networks.

References & further reading

Mank, J.E. 2017. Population genetics of sexual conflict in the genomic era. Nature Reviews Genetics 18: 721-730.
Cheng, C.D. & Kirkpatrick, M. 2016. Sex-Specific Selection and Sex-Biased Gene Expression in Humans and Flies. Plos Genetics 12: e1006170.
Mank, J.E., Shu, J.J. & Wright, A.E. 2020. Signature of sexual conflict is actually conflict resolved. Molecular Ecology 29: 215-217.
Cheng, C.D. & Kirkpatrick, M. 2020. The signal of sex-specific selection in humans is not an artefact: Reply to Mank et al. Molecular Ecology 29: 1406-1407.
Kasimatis, K.R., Ralph, P.L. & Phillips, P.C. 2019. Limits to genomic divergence under sexually antagonistic selection. G3-Genes Genomes Genetics 9: 3813-3824.
DrosEU:
http://droseu.net/
Kapun, M., et al. 2020. Genomic analysis of European Drosophila melanogaster populations reveals longitudinal structure, continent-wide selection, and previously unknown DNA viruses. Molecular Biology and Evolution. 37: 2661-2678.

Further Information

Contact Michael Ritchie; mgr@st-andrews.ac.uk

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