Lineage divergence detected in the malaria vector Anopheles marajoara (Diptera: Culicidae) in Amazonian Brazil

Background: Cryptic species complexes are common among anophelines. Previous phylogenetic analysis based on the complete mtDNA COI gene sequences detected paraphyly in the Neotropical malaria vector Anopheles marajoara. The ""Folmer region"" detects a single taxon using a 3% divergence threshold. Methods: To test the paraphyletic hypothesis and examine the utility of the Folmer region, genealogical trees based on a concatenated (white + 3' COI sequences) dataset and pairwise differentiation of COI fragments were examined. The population structure and demographic history were based on partial COI sequences for 294 individuals from 14 localities in Amazonian Brazil. 109 individuals from 12 localities were sequenced for the nDNA white gene, and 57 individuals from 11 localities were sequenced for the ribosomal DNA (rDNA) internal transcribed spacer 2 (ITS2). Results: Distinct A. marajoara lineages were detected by combined genealogical analysis and were also supported among COI haplotypes using a median joining network and AMOVA, with time since divergence during the Pleistocene (< 100,000 ya). COI sequences at the 3' end were more variable, demonstrating significant pairwise differentiation (3.82%) compared to the more moderate 2.92% detected by the Folmer region. Lineage 1 was present in all localities, whereas lineage 2 was restricted mainly to the west. Mismatch distributions for both lineages were bimodal, likely due to multiple colonization events and spatial expansion (similar to 798 - 81,045 ya). There appears to be gene flow within, not between lineages, and a partial barrier was detected near Rio Jari in Amapa state, separating western and eastern populations. In contrast, both nDNA data sets (white gene sequences with or without the retention of the 4th intron, and ITS2 sequences and length) detected a single A. marajoara lineage. Conclusions: Strong support for combined data with significant differentiation detected in the COI and absent in the nDNA suggest that the divergence is recent, and detectable only by the faster evolving mtDNA. A within subgenus threshold of >2% may be more appropriate among sister taxa in cryptic anopheline complexes than the standard 3%. Differences in demographic history and climatic changes may have contributed to mtDNA lineage divergence in A. marajoara.We thank M Povoa’s research group at Instituto Evandro Chagas/SVS/MS in\ud Ananindeua, Pará, Brazil as well as Rosa and Roger Hutchings, Instituto\ud Nacional de Pesquisas da Amazônia, Manaus, Brazil, for assistance in\ud mosquito collection and logistics. We also appreciate the help of W.\ud Kilpatrick, UVM, with analysis and interpretation of the eastern Amazon data\ud early on. Funding for this study was provided by Instituto Evandro Chagas,\ud Ananindeua, Pará, Brazil and NIH grants 1T32AI05532901A1, “Training in\ud Biodefense and Emerging Infectious Disease” and NIH 2R01 A154139 to JEC.\ud Permission to collect in the Amazon basin was provided by the Conselho\ud Nacional de Desenvolvimento Científico e Tecnológico (CNPq) processo:\ud CMC 028/04 - Expedição Científica and IBAMA RMX 021/04 (Projeto: ?\ud Biologia e sistemática de vetores de malária no Brasil: genética e ecologia?)