Lineage maintenance due to assortative mating but not ecological divergence in a sympatric sibling species pair

Abstract Background Lineage theory suggests that the development of traits associated with reproductive isolation coupled with traits associated with ecological differentiation are essential for the maintenance of sympatric lineages. However, the relative importance of these factors have rarely been tested simultaneously. Bactrocera tryoni and B. neohumeralis are a tephritid fruit fly species pair that have significant overlap in geographic range and host use, with time of male mating the only known difference in their mating systems. Using this system, we tested the relative importance of ecological differentiation versus assortative mating in sympatric lineage maintenance. Results Genome-wide SNP analyses found strong genetic differentiation between the species with no evidence for hybridization in the field. Most outlier SNPs were restricted to narrow regions towards the centromeres and telomeres of chromosomes. Enrichment of annotation terms indicated an overabundance of genes with the ‘abnormal neuroanatomy’ term. Terms of interest associated with sleep and circadian rhythm, potentially important to the allochronic reproductive barrier, were non-enriched. Ecological data found no evidence for ecological divergence or competitive displacement between the two species based on significant positive correlations between species numbers trapped at different times of the year, trapped in different habitats within a region, or when reared from fruit. Conclusions Our study highlights the significance of assortative mating over ecological differentiation for sympatric lineage maintenance of the B. tryoni / B. neohumeralis sibling pair. The paper represents one of the most well-characterized examples of the importance of genomic divergence in the coexistence of two closely related species.