Abstract
Malaria, a tropical disease caused by Plasmodium and transmitted by Anopheles, remains a public health concern in Brazil. While most cases occur in the Amazon, transmission persists in the Atlantic Forest, where Anopheles mosquitoes of the Kerteszia subgenus are the primary vectors of human and simian malaria. Previous studies using cytogenetics, isoenzymes, and molecular markers have suggested cryptic species within Anopheles (Kerteszia) cruzii and Anopheles (Kerteszia) bellator. We sequenced 55 genomes: 35 An. cruzii s.l. (four with Nanopore and 31 with Illumina), 12 An. bellator s.l., and eight An. homunculus, the latter two with Illumina. Phylogenomic analysis revealed at least five cryptic species within An. cruzii s.l., labelled A-E, with evidence of sympatry in some locations. Anopheles bellator s.l. also forms a species complex, comprising at least three distinct lineages. These cryptic species showed high genetic differentiation (FST range: 0.4-0.7), typical of interspecific comparisons. In contrast, An. homunculus populations showed low differentiation (FST ~ 0.2), suggesting a single widespread species. Our analysis confirms cryptic speciation in An. cruzii and An. bellator, but not in An. homunculus. These findings are important for understanding malaria transmission in the Atlantic Forest, given that vector competence may differ among cryptic species.
Data availability
Accession numbers for the samples are available in the NCBI SRA under BioProject PRJNA1269491. Illumina-sequenced samples correspond to accessions SAMN48789258-SAMN48789358, and Nanopore-sequenced samples correspond to accessions SAMN48793262-SAMN48793265. The genes used to generate Fig. 1 and Supplementary Fig. 5 correspond to those annotated by BUSCO v4.1.4 using the Diptera reference set (odb10), downloaded from the BUSCO database (https://busco.ezlab.org/). Details of the phylogenomic analyses are provided in the script “phylogenomic_inferences” available at https://doi.org/10.5281/zenodo.18389048. The data used to generate Figs. 2, 3, and 7, as well as Supplementary Fig. 6, are provided in Supplementary Data 2.
Code availability
The code used for data analysis can be accessed at the following GitHub repository: https://github.com/kamilavoges/Phylogenomics_Kerteszia116.
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Acknowledgements
The authors thank Natália Valério de Souza, Iara Carolini Pinheiro, André Akira Gonzaga Yoshikawa, Sabrina Fernandes Cardoso, João Victor Costa Guesser, Anna Luiza Buainain, Julia Levinstein, Felipe Rocha, and Paulo Paiva for their assistance during fieldwork; Paulo Paiva for critically reading the manuscript; LAMEB—Federal University of Santa Catarina for access to microscopy facilities and technical support; and Dr. Bernard Kim for assistance with Nanopore sequencing. This paper forms part of the Ph.D. thesis of Kamila Voges, undertaken within the Postgraduate Programme in Cell and Developmental Biology (PPGBCD) at the Center for Biological Sciences (CCB), Federal University of Santa Catarina (UFSC), Brazil. This work was supported by CAPES, CNPq-INCT-EM, the Royal Society (grant numbers: AL\191009; AL\201013; AL\211028; AL\221016; AL\24100017) to LR, and the Welcome Trust grant number 207486/Z/17/Z to ABC. FU is supported by CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Finance Code 001.
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K.V., L.D.P.R., A.B.C., C.J.C.P., A.N.P., G.R.D. and H.R.R. collected the mosquitoes. K.V. and C.J.C.P. conducted the morphological identification. K.V., L.D.P.R., A.B.C., J.C., G.R.D., E.G.D., F.U., S.J.F. and T.V. were responsible for data generation, genome assembly, and analysis. K.V. drafted the manuscript, with critical revisions provided by L.D.P.R., A.B.C. and G.R.D. L.D.P.R. and A.B.C. contributed to the design and coordination of the study. All authors read and approved the final manuscript.
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Voges, K., Dias, G.d.R., Dupim, E.G. et al. Anopheles (Kerteszia) cruzii, the main malaria vector in the Brazilian Atlantic Forest, is a complex of at least five cryptic species. Commun Biol (2026). https://doi.org/10.1038/s42003-026-09700-0
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DOI: https://doi.org/10.1038/s42003-026-09700-0
