Sympatric speciation with gene flow of Drosophila hydei from Evolution Canyon

Mounting theoretical and empirical studies prove that sympatric speciation is possible in nature, however, it’s commonality is still debated. Here we show genomic evidence for incipient sympatric speciation in Drosophila hydei from Evolution Canyon I in Mount Carmel Israel. First, we provide a reference genome with contig N50 of 4.72 Mb. Population genomes were clearly separated between the hot-dry savannoid African slope (AS) and cool-humid temperate European slope (ES). Genetic diversity and recombination rate was significantly higher in ES new sympatric species than that in AS. Tajima’s D is significantly higher in AS than that in ES suggesting they were under different non-random selection patterns, rejecting neutrality. We identified 137 islands and the genetic parameters were significantly different with that of the backgrounds. Putatively selected genes (GO enrichment) from ES population were enriched in higher aggression, photoreception, autophagy, temperature, neurogenetics and reproduction, and defense responses against bacteria and fungi. By contrast, in the AS, the selected genes were enriched in aging, autophagy, visual system and response to nutrient level.