Brazilian Anopheles darlingi Root (Diptera: Culicidae) Clusters by Major Biogeographical Region

Abstract

The major drivers of the extensive biodiversity of the Neotropics are proposed to be geological and tectonic events together with Pliocene and Pleistocene environmental and climatic change. Geographical barriers represented by the rivers Amazonas/Solimões, the Andes and the coastal mountain ranges in eastern Brazil have been hypothesized to lead to diversification within the primary malaria vector, Anopheles (Nyssorhynchus) darlingi Root, which primarily inhabits rainforest. To test this biogeographical hypothesis, we analyzed 786 single nucleotide polymorphisms (SNPs) in 12 populations of An. darlingi from across the complex Brazilian landscape. Both model-based (STRUCTURE) and non-model-based (Principal Components and Discriminant Analysis) analysis of population structure detected three major genetic clusters that correspond with newly described Neotropical biogeographical regions: 1) Atlantic Forest province (= southeast population); 2) Parana Forest province (= West Atlantic forest population, with one Chacoan population - SP); and 3) Brazilian dominion population (= Amazonian population with one Chacoan population - TO). Significant levels of pairwise genetic divergences were found among the three clusters, allele sharing among clusters was negligible, and geographical distance did not contribute to differentiation. We infer that the Atlantic forest coastal mountain range limited dispersal between the Atlantic Forest province and the Parana Forest province populations, and that the large, diagonal open vegetation region of the Chacoan dominion dramatically reduced dispersal between the Parana and Brazilian dominion populations. We hypothesize that the three genetic clusters may represent three putative species.

StrAuto: automation and parallelization of STRUCTURE analysis

“…1Speed benchmarking for the analysis of two trial datasets incorporating various numbers of cores on two different computing systems. Single Nucleotide Polymorphisms (SNP) data is from [22] and Simple Sequence Repeat (SSR) data is from [21]. The asymptotic approach to a minimum time represents the time it takes for a single core to compute one complete run of the program STRUCTURE for the given dataset.…”

“…A larger dataset from [22], with 11,533 loci genotyped among 57 individuals, that analyzed 30 replicates for each K ranging from 1 to 6 with MCMC chains as defined above, took just over 9 days to complete on 60 cores using the StrAuto script. Initial exploratory experimentation to determine the MCMC parameters with this dataset was conducted using 500 randomly sampled loci, and took ∼4 h with 30 cores.…”

“…The first data set (SSR) included genotypes at 11 nuclear microsatellite loci from 614 eastern white pine trees ( Pinus strobus ) [21], and the second (SNP) data set included genotypes from 799 nextRAD based SNP loci from 57 individuals of the Neotropical malaria vector Anopheles darlingi [22]. StrAuto was used to set up the STRUCTURE analysis with K varying from 1 to 8 (SSR) and 1 to 5 (SNP) and with MCMC chains of 1.1 million generations with the first 100,000 generations discarded as burnin.…”

Adaptative processes, control measures, genetic background, and resilience of malaria vectors and environmental changes in the Amazon region

“…Recently, two studies obtained samples from populations of A. darlingi collected in North, Southeast, and Central-west Brazil, based on a morphological analysis of the wing (Motoki et al, 2012) and SNP molecular markers (Emerson et al, 2015). No significant differences were found between these populations at the interspecific level.…”

Genetic heterogeneity in Anopheles darlingi related to biting behavior in western Amazon

“…Despite of that, An. darlingi was considered as monophyletic species until Emerson and collaborators [16] proposed the occurrence of three putative species based on well-supported genetic clusters. In that study, Neotropical biogeographical events explained dispersal of An.…”