Genetic diversity of Anopheles mosquitoes
type: CreativeWork
description: This thesis presents two projects related to the genetic diversity of Anopheles mosquitoes. The first project concerns the development and application of sequence based species assignment methods for any species in the genus. The second project discusses the population structure of the major malaria vector Anopheles funestus, with a specific focus on inversions. The 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 sensitive and specific species assignment than single gene (e.g. COI) barcoding, which is desirable in the light of permeable species boundaries. Here, I present NNoVAE, a method using Nearest Neighbours (NN) and Variational Autoencoders (VAE), which I 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 distinguishes between closely related species, and also has sufficient resolution to reveal population structure within species. In tests on independent samples with over 80% and 16 % amplicon coverage respectively, NNoVAE correctly classifies to species level 98% of samples within the An. gambiae complex and 89% of samples outside the complex. I apply NNoVAE to nearly 10,000 new samples from Burkina Faso, Gabon, Nigeria and Uganda. In Gabon I found four putative An. arabiensis mosquitoes, a species that was not known to occur in the area. I present the ANOSPP Report Cards, the format used to communicate a summary of the ANOSPP results to the partners who contributed the samples. I also show some additional analyses which can be done using the ANOSPP sequence data, e.g. karyotyping of the 2La inversion. The MalariaGEN Vector Observatory Anopheles funestus Genomic …
abstract: This thesis presents two projects related to the genetic diversity of Anopheles mosquitoes. The first project concerns the development and application of sequence based species assignment methods for any species in the genus. The second project discusses the population structure of the major malaria vector Anopheles funestus, with a specific focus on inversions. The 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 sensitive and specific species assignment than single gene (e.g. COI) barcoding, which is desirable in the light of permeable species boundaries. Here, I present NNoVAE, a method using Nearest Neighbours (NN) and Variational Autoencoders (VAE), which I 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 distinguishes between closely related species, and also has sufficient resolution to reveal population structure within species. In tests on independent samples with over 80% and 16 % amplicon coverage respectively, NNoVAE correctly classifies to species level 98% of samples within the An. gambiae complex and 89% of samples outside the complex. I apply NNoVAE to nearly 10,000 new samples from Burkina Faso, Gabon, Nigeria and Uganda. In Gabon I found four putative An. arabiensis mosquitoes, a species that was not known to occur in the area. I present the ANOSPP Report Cards, the format used to communicate a summary of the ANOSPP results to the partners who contributed the samples. I also show some additional analyses which can be done using the ANOSPP sequence data, e.g. karyotyping of the 2La inversion. The MalariaGEN Vector Observatory Anopheles funestus Genomic …
author: Bodde, Marilou
language: eng
keywords: anopheles, genetic diversity, species assignment, inversions
license: https://www.rioxx.net/licenses/all-rights-reserved/
date published: 2022-12-01
date modified: 2026-07-22T22:23:59Z
provider: Cambridge University
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: University of Cambridge

PropertyValue
property ID: DOI
value: 10.17863/CAM.96124