We tested if distantly related pea aphid host races have additional prezygotic isolation barriers compared to more closely related ones. We observed mating behaviour and egg fertilization rates for three types of crosses: among individuals of the same host race, between closely related host races, and between distantly related host races. We did not find significant differences in mating behaviour among three types of crosses, but we observed drastic reduction in the number of fertilized eggs for the crosses between distantly related host races. From this we infer the presence of post-mating pre-zygotic barrier in the more distantly related host races.
We generated and analysed whole-genome sequencing data (61 genomes at 20x coverage) to infer patterns associated with different reproductive isolation barriers. Results of genome-wide sliding window analysis show that for the closely related host races – separated by habitat choice and post-zygotic isolation – genomic divergence is variable, but overall relatively weak. For the distantly related host races – in addition isolated by the pre-zygotic post-mating barrier – genomic divergence is variable but overall stronger. We also find that sex chromosome divergence for the distantly related host races is higher and less variable than autosomal. Using cytogenetic approaches, we confirmed that higher sex chromosome divergence is not related to unstable karyotypes (i.e. different chromosome number) in distantly related host races.
We estimated gene flow for distantly and closely related host races, based on neutral sites across the genome, using a diffusion approximation. Our results show that gene flow is very limited between distantly related host-races compared with closely related ones (about 5 times smaller). This suggests an important role of the intrinsic pre-zygotic isolation barrier at impeding gene flow.
We also investigated accumulation of genomic divergence in a model of ecological speciation with gene flow. Our results show that at early stages of speciation, divergence is limited to the loci under selection. At a later stage of speciation, neutral loci also become differentiated. In the parameter space we examined, we did not find homogeneous widespread divergence across the genome. This may be explained by episodes of gene flow diminishing divergence at neutral loci. However, it turned out that the model of speciation with gene flow is not suitable for the pea aphid system. During implementation of this project, we re-examined the age of the pea aphid radiation by estimating genome-wide divergence (using sequencing data from this project) and by estimating spontaneous mutation rate for pea aphids. Our results show that pea aphids diversified about 500 thousand years ago (contrary to previous estimates of about 10 thousand years ago). This ancient pea aphid radiation suggests host race formation may have been influenced by geographic isolation during Pleistocene climatic oscillations.
Overall, our results suggest that completion of speciation in the pea aphid complex is largely affected by intrinsic post-mating pre-zygotic reproductive isolation. It is accompanied by strong genomic divergence, especially on the sex chromosome. Genomic patterns of divergence cannot be interpreted under scenario of speciation with gene flow due to the age and possible contribution of allopatric isolation to diversification of the pea aphids.
Results of this project were reported at five international research conferences and three research papers (1 published, 2 in preparation). Knowledge transfer has also occurred at daily interactions, group meetings and journal clubs. Results of the project were (and the remaining results will also be) published with open access via the green route. Two public dissemination events were carried out.
The researcher enhanced career perspectives by receiving training in the fields of population genomics and experimental biology, by developing own network of collaborations, and by obtaining project management experience.
