A new species in the Anopheles gambiae complex reveals new evolutionary relationships between vector and non-vector species

Complexes of closely related species provide key insights about the rapid and independent evolution of adaptive traits. Here, we described and studied a presumably new species in the Anopheles gambiae complex, Anopheles fontenillei, recently discovered in the forested areas of Gabon, Central Africa. Our analysis placed the new taxon in the phylogenetic tree of the An. gambiae complex, revealing important introgression events with other members of the complex. In particular, we detected recent introgression with An. gambiae and An. coluzzii of genes directly involved in vectorial capacity. Moreover, genome analysis of the new species also allowed us to resolve the evolutionary history of inversion 3La. Overall, Anopheles fontenillei has implemented our understanding about the relationship of species within the gambiae complex and provides insight into the evolution of vectorial capacity traits, relevant for the successful control of malaria in Africa.Funding was provided by the “Institut de Recherche pour le Developpément”, the “Agence Universitaire de la Francophonie” (grant: OKANDA), the “Centre National de la Recherche Scientifique” (CNRS) and the “Consejo Superior de Investigaciones Cientificas” (CSIC) (grant PICS ANCESTRAL to DA and JG), the “ANR” (grant ANR--18-CE35-0002-01-WILDING to DA), and the “Ministerio de Ciencia, Innovación y Universidades/AEI” (grant BFU2017-82937-P to JG).N

Data from: Natural Wolbachia infections are common in the major malaria vectors in Central Africa

During the last decade, the endosymbiont bacterium Wolbachia has emerged as a biological tool for vector disease control. However, for long time, it was believed that Wolbachia was absent in natural populations of Anopheles. The recent discovery that species within the Anopheles gambiae complex host Wolbachia in natural conditions has opened new opportunities for malaria control research in Africa. Here, we investigated the prevalence and diversity of Wolbachia infection in 25 African Anopheles species in Gabon (Central Africa). Our results revealed the presence of Wolbachia in 16 of these species, including the major malaria vectors in this area. The infection prevalence varied greatly among species, confirming that sample size is a key factor to detect the infection. Moreover, our sequencing and phylogenetic analyses showed the important diversity of Wolbachia strains that infect Anopheles. Co-evolutionary analysis unveiled patterns of Wolbachia transmission within some Anopheles species, suggesting that past independent acquisition events were followed by co-cladogenesis. The large diversity of Wolbachia strains that infect natural populations of Anopheles offers a promising opportunity to select suitable phenotypes for suppressing Plasmodium transmission and/or manipulating Anopheles reproduction, which in turn could be used to reduce the malaria burden in Africa

A new species in the major malaria vector complex sheds light on reticulated species evolution

Complexes of closely related species provide key insights into the rapid and independent evolution of adaptive traits. Here, we described and studied Anopheles fontenillei sp.n., a new species in the Anopheles gambiae complex that we recently discovered in the forested areas of Gabon, Central Africa. Our analysis placed the new taxon in the phylogenetic tree of the An. gambiae complex, revealing important introgression events with other members of the complex. Particularly, we detected recent introgression, with Anopheles gambiae and Anopheles coluzzii, of genes directly involved in vectorial capacity. Moreover, genome analysis of the new species allowed us to clarify the evolutionary history of the 3La inversion. Overall, An. fontenillei sp.n. analysis improved our understanding of the relationship between species within the An. gambiae complex, and provided insight into the evolution of vectorial capacity traits that are relevant for the successful control of malaria in Africa.Funding was provided by the “Institut de Recherche pour le Developpément”, the “Agence Universitaire de la Francophonie” (grant OKANDA), the “Agence Nationale de Recherche” (ANR-18-CE35-0002-01 – WILDING), the “Consejo Superior de Investigaciones Cientificas” and the “Centre National de la Recherche Scientifique” (PICS ANCESTRAL), and the “Ministerio de Ciencia, Innovación y Universidades/AEI/FEDER” (BFU2017-82937-P) and the “Secretaria d’Universitats i Recerca. Departament d’Economia i Coneixement. Generalitat de Catalunya” (GRC 2017 SGR 880)

A new species in the Anopheles gambiae complex reveals new evolutionary relationships between vector and non-vector species

Complexes of closely related species provide key insights about the rapid and independent evolution of adaptive traits. Here, we described and studied a presumably new species in the Anopheles gambiae complex, Anopheles fontenillei, recently discovered in the forested areas of Gabon, Central Africa. Our analysis placed the new taxon in the phylogenetic tree of the An. gambiae complex, revealing important introgression events with other members of the complex. In particular, we detected recent introgression with An. gambiae and An. coluzzii of genes directly involved in vectorial capacity. Moreover, genome analysis of the new species also allowed us to resolve the evolutionary history of inversion 3La. Overall, Anopheles fontenillei has implemented our understanding about the relationship of species within the gambiae complex and provides insight into the evolution of vectorial capacity traits, relevant for the successful control of malaria in Africa.Funding was provided by the “Institut de Recherche pour le Developpément”, the “Agence Universitaire de la Francophonie” (grant: OKANDA), the “Centre National de la Recherche Scientifique” (CNRS) and the “Consejo Superior de Investigaciones Cientificas” (CSIC) (grant PICS ANCESTRAL to DA and JG), the “ANR” (grant ANR--18-CE35-0002-01-WILDING to DA), and the “Ministerio de Ciencia, Innovación y Universidades/AEI” (grant BFU2017-82937-P to JG).N

Assembly of the Anopheles fontenillei genome

Genome assembly of the Anopheles fontenillei genome based on the high coverage sequencing of a single individual of this species. The raw reads for this assembly can be found in SRA under accession number SRX5100439.N

High-resolution species assignment of Anopheles mosquitoes using k-mer distances on targeted sequences.

Peer reviewed: TrueThe ANOSPP amplicon panel is a genus-wide targeted sequencing panel to facilitate large-scale monitoring of Anopheles species diversity. Combining information from the 62 nuclear amplicons present in the ANOSPP panel allows for a more senstive and specific species assignment than single gene (e.g. COI) barcoding, which is desirable in the light of permeable species boundaries. Here, we present NNoVAE, a method using Nearest Neighbours (NN) and Variational Autoencoders (VAE), which we apply to k-mers resulting from the ANOSPP amplicon sequences in order to hierarchically assign species identity. The NN step assigns a sample to a species-group by comparing the k-mers arising from each haplotype's amplicon sequence to a reference database. The VAE step is required to distinguish between closely related species, and also has sufficient resolution to reveal population structure within species. In tests on independent samples with over 80% amplicon coverage, NNoVAE correctly classifies to species level 98% of samples within the An. gambiae complex and 89% of samples outside the complex. We apply NNoVAE to over two thousand new samples from Burkina Faso and Gabon, identifying unexpected species in Gabon. NNoVAE presents an approach that may be of value to other targeted sequencing panels, and is a method that will be used to survey Anopheles species diversity and Plasmodium transmission patterns through space and time on a large scale, with plans to analyse half a million mosquitoes in the next five years