Genomic, chromosomal, and ecological differentiation between the cryptic Eurasian malaria vector-species Anopheles messeae and Anopheles daciae

Abstract

Background A dominant malaria vector, Anopheles messeae, is a highly polymorphic species with wide distribution throughout Eurasia. Five highly polymorphic inversions associated with the geographical distribution of the species have been reported. A sister species, An. daciae, was described and discriminated from An. messeae based on five fixed nucleotide substitutions in the internal transcribed spacer 2 (ITS2) of ribosomal DNA. However, the levels of genomic divergence, chromosomal variation, and ecological differentiation between these two cryptic species remain unexplored. Results In this study, we sequenced ITS2 and analyzed the inversion frequencies of 289 Anopheles larvae specimens collected from three locations in the Moscow region. We identified a high abundance of both An. messeae and An. daciae in all three locations. Five individual genomes for each species of An. messeae and An. daciae from one location were sequenced. Our study confirmed five previously described nucleotide substitutions in the ITS2 of An. messeae. However, we found that the ITS2 sequence in An. daciae was heterogenic in three of the five positions. Fixed nucleotide differences between An. messeae and An. daciae were found only in the last two positions. One mosquito was identified as a hybrid between An. messeae and An. daciae based on heterogeneous substitutions in all five positions. Although, the genomic sequence comparison demonstrated genome-wide divergence between the two species, which is especially pronounced on the X chromosome, an ADMIXTURE cluster analysis demonstrated the presence of two admixed individuals suggesting ongoing hybridization. Cytogenetic analysis demonstrated that An. messeae and An. daciae significantly differ from each other by their frequency of polymorphic inversions. Inversion X1 was fixed in An. messeae but was polymorphic in all An. daciae populations. The frequency of polymorphic autosomal inversions was higher in An. messeae than in An. daciae. The species composition was different among the studied locations suggesting species-specific ecological preferences. Conclusions Our study demonstrated that An. messeae and An. daciae represent closely related cryptic species with incomplete reproductive isolation that are able to maintain genomic differentiation in sympatry despite ongoing genetic introgression. The X chromosome plays an important role in the reproductive isolation between the species.