Meeting Abstract
There are many cases of parallel gene expression underlying the evolution of convergent niche specialization, but parallel expression could also underlie divergent specialization. We combined transcriptome sequencing with genome-wide divergence scans to study the molecular evolution of two specialist Cyprinodon pupfish species – a ‘scale-eater’ and a ‘snail-eater’ – that rapidly diverged from a sympatric generalist ancestor within the last 10,000 years. These specialist species are adapted to highly divergent niches that are unique within atherinomorphs. We identified 16 million single nucleotide polymorphisms, 11 million indels, and 7,394 differentially expressed genes by whole-genome resequencing of 42 individuals and transcriptome sequencing of 29 individuals. 82% of genes that were differentially expressed between snail-eaters and generalists were up or downregulated in the same direction between scale-eaters and generalists, indicating significant parallel gene expression between divergent specialists. Surprisingly, there were no shared fixed variants underlying this parallel expression. Genes showing parallel expression were enriched for effects on metabolic processes, whereas genes showing divergent expression were enriched for effects on cranial skeleton development and pigment biosynthesis, reflecting the most divergent phenotypes observed between specialist species. Together, our findings show that convergent adaptation to higher trophic levels in divergent specialists is driven by unique genetic variants regulating the same gene networks.
