Genomics of sexual selection and extinction

Bioinformatics
eDNA genetic markers will be developed from our existing drive and wildtype genomes, and tested for consistency against 100 whole genome sequenced individuals. Air, water and surface samples of eDNA will be taken from laboratory cages in which known frequencies of drive and wildtype individuals are kept. These will be used to test the accuracy of eDNA estimates. They will also be verified for accuracy under natural conditions comparing them to existing sampling techniques sequencing individual flies from the wild. The work will act as a proof-of-principle for eDNA in evolutionary genetic field studies.

Field work will be carried out in the Gombak Valley, near Kuala Lumpur, Malaysia, where stalk-eyed flies have already been identified living along small streamlets in the rain forest. We have strong existing relationships with the University of Malaya, and will stay at their field station in the rain forest. Detailed measurements will be made of lek sites occupied by single males that attract variable numbers of females. Male attraction of females and mating rates (most mating occurs on leks) will be monitored. eDNA samples will be collected from a variety of locations to estimate drive frequency. 

Genetics 
Experimental Evolution will involve setting up a well replicated, multiple generation experimental evolution experiment (8-10 generations) in which drive will be introduced into population at either a low or high initial frequency. Replicates will vary in the opportunity for mating thereby altering the mating rate to cause differential competition between individuals both in pre-mating (mate choice) and post-mating (sperm competition) aspects of sexual selection. Population productivity and sex ratio will be monitored, alongside changes in drive frequency (using eDNA and genetic markers); population size will be held low via limited food availability, which increases sexual trait variation and allows the possibility of extinction. 

Variation in protein coding sequence (e.g. non-synonymous and synonymous change, indels, frame shifts, stop codons) as well as structural variants (e.g. duplications, genomic gaps, tandem repeats) will be identified that distinguish the wildtype and drive X chromosomes. Silenced genes will be identified using expression data. A SNP calling pipeline will be applied to both the drive and wildtype genomes and the comprehensively validated Drosophila reference. A number of stringent filters will be applied to remove artifacts and low frequency SNPs. HKA, FWH and MK tests for adaptation will be carried out. ORFs near inversion breakpoints will be identified. The age of inversions will be calculated using divergence distances relative to outgroups. Novel genome assembly will be carried out using our existing approach of PacBio long-read, HiC, expression data and validated with short-read data from multiple individuals.

Simulation/Modelling 
Theoretical investigation of meiotic drive will be carried out as a simulation in our existing modelling set-up using SLiM, extending it to cover meta-populations. This will allow an examination of how mate choice and the mating rate influences the spread of drive. Modelling will track how drive and sexual selection alter population demography, sex ratio and extinction probability in space and time. In addition, the frequency of drive and the accumulation of deleterious alleles located in inversion associated with drive will be modelled. 

Overall, these findings combine fundamental genetic technology development to hypotheses about sexual selection, selfish genetic elements, demography and extinction with wide evolutionary relevance. They also have applied relevance to the development of “gene drive” technology being used to control disease-transmitting insects.