I propose a research program to address how the genome evolves during speciation. To advance speciation genomics we need to take the field beyond describing genetic differences between species. To this aim I will combine experimental approaches with a study system that enables simultaneously investigating different points along the speciation continuum. Specifically I will address 1) how associations between unlinked loci advantageous to use of a new niche arise, and 2) what the role of regulation of expression is and how it interacts with coding genetic divergence during speciation.
Most genomic studies have focused on characterising the genomic landscape of species differences1,2, while the interpretation of the patterns of divergence is lagging3-5. Ecological divergence is a main driver of speciation6, and one main challenge is to address how associations between traits coding for ecological divergence and reproductive isolation arise when these are genomically unlinked3. These associations are crucial for the completion of speciation7. New research suggests that inversions are important for shielding coadapted complexes from recombination8-10 but such complexes are unlikely to exist at initial ecological niche divergence. Another major challenge lies in disentangling the roles of coding genomic divergence and regulation of gene expression on resulting phenotypes3,11. Malfunctioning regulation cause hybrid inviability in the lab, suggesting a potentially important role for regulation in ecological speciation12.
To address how the genomic architecture evolves during ecological speciation I use different host plant races of specialized monophagous and oligophagous ”generalist” Tephritis conura flies, providing different points along the speciation continuum. Specifically I will:
1. Determine how associations between ecological traits and reproductive isolation arise during niche shifts. I will determine a) whether there are associations between alleles involved in host plant adaptation and RI in specialists; b) whether these associations are stronger in specialists than in generalists; and c) whether such linkage disequilibrium (LD) builds up in experimental F2-crosses between the host races due to differential survival of F2–progeny with different allele combinations.
2. Disentagle effects of coding genetic changes and differences in regulation of gene expression for adaptation to a novel niche. I will perform cross-fostering experiments of host specialists and generalists on different host plants. In the growing larvae, I will assess expression profiles to identify differences linked to host plant use. By comparing the host-induced variation with the coding genetic divergence between specialized host races I will test whether the same genes are involved in plastic responses and coding divergence. The identification of facultatively expressed genes and the tests of their potential to accumulate coding differences will improve our understanding of how the genome can evolve in response to selection and whether initial plastic responses may facilitate speciation.
These studies entail sequencing of a reference genome, a whole genome re-sequencing of ca 100 individuals to describe species differences and another 100 from experiment and RNA-sequencing of 60 individuals.