Strong genetic differentiation but limited niche partitioning in a sympatric species pair separated by an allochronic reproductive barrier

Abstract In the absence of differential adaptation to ecological niche and the development of reproductive barriers, boundaries between coexisting species are expected to breakdown. The fruit fly species pair, Bactrocera tryoni and B. neohumeralis , have significant overlap in geographic range and host use, with mating time the only confirmed difference in their mating systems. Using a combination of ecological and genomic data, we tested the roles of competition and reproductive isolation on the maintenance of species boundaries in this pair. Genome‐wide SNP analyses found strong genetic differentiation between the species with no evidence for hybridization. Most outlier SNPs were restricted to narrow regions towards the centromeres and telomeres of chromosomes, while high nucleotide diversity rates were observed in both species. Enrichment of annotation terms indicated an overabundance of genes with the ‘abnormal neuroanatomy’ term, but non‐enrichment of terms associated with sleep and circadian rhythm. Field data found minimal evidence for ecological differentiation based on significant positive temporal, spatial and hostuse correlations between the species. However, B. tryoni appears less sensitive to low humidity than B. neohumeralis and used hosts which were not used by B. neohumeralis suggesting subtle microecological variation between species contributing to reproductive isolation. The simultaneous comparisons of molecular and ecological data in our study have provided a more nuanced understanding of how species boundaries have been maintained in this sibling species pair. Our analyses highlight the importance of genetic divergence for their maintenance in sympatry, but less for a role of competitive displacement or other ecological adaptation.