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

In the absence of differential adaptation to ecological niche and the
development of reproductive barriers, boundaries between co-existing
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
host-use 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 micro-ecological 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.