title: Patterns of Genome-Wide Variation in Glossina fuscipes fuscipes Tsetse Flies from Uganda.
abstract: The tsetse fly Glossina fuscipes fuscipes (Gff) is the insect vector of the two forms of Human African Trypanosomiasis (HAT) that exist in Uganda. Understanding Gff population dynamics, and the underlying genetics of epidemiologically relevant phenotypes is key to reducing disease transmission. Using ddRAD sequence technology, complemented with whole-genome sequencing, we developed a panel of ∼73,000 single-nucleotide polymorphisms (SNPs) distributed across the Gff genome that can be used for population genomics and to perform genome-wide-association studies. We used these markers to estimate genomic patterns of linkage disequilibrium (LD) in Gff, and used the information, in combination with outlier-locus detection tests, to identify candidate regions of the genome under selection. LD in individual populations decays to half of its maximum value (r(2) max/2) between 1359 and 2429 bp. The overall LD estimated for the species reaches r(2) max/2 at 708 bp, an order of magnitude slower than in Drosophila Using 53 infected (Trypanosoma spp.) and uninfected flies from four genetically distinct Ugandan populations adapted to different environmental conditions, we were able to identify SNPs associated with the infection status of the fly and local environmental adaptation. The extent of LD in Gff likely facilitated the detection of loci under selection, despite the small sample size. Furthermore, it is probable that LD in the regions identified is much higher than the average genomic LD due to strong selection. Our results show that even modest sample sizes can reveal significant genetic associations in this species, which has implications for future studies given the difficulties of collecting field specimens with contrasting phenotypes for association analysis.
authors.affiliation: Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511 andrea.gloria-soria@yale.edu.
authors.forename: Andrea
authors.initials: A
authors.lastname: Gloria-Soria
authors.affiliation: Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511.
authors.forename: W Augustine
authors.initials: WA
authors.lastname: Dunn
authors.affiliation: Laboratorio de Fisiologia e Controle de Artropodes Vetores, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, 21040-360 RJ, Brazil.
authors.forename: Erich L
authors.initials: EL
authors.lastname: Telleria
authors.affiliation: Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511.
authors.forename: Benjamin R
authors.initials: BR
authors.lastname: Evans
authors.affiliation: Department of Biology, Faculty of Science, Gulu University, Loroo Division, 256 Gulu, Uganda.
authors.forename: Loyce
authors.initials: L
authors.lastname: Okedi
authors.affiliation: Department of Biology, Faculty of Science, Gulu University, Loroo Division, 256 Gulu, Uganda.
authors.forename: Richard
authors.initials: R
authors.lastname: Echodu
authors.affiliation: The Genome Institute, McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri 63108.
authors.forename: Wesley C
authors.initials: WC
authors.lastname: Warren
authors.affiliation: The Genome Institute, McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri 63108.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Montague
authors.affiliation: School of Public Health, Yale University, New Haven, Connecticut 06510.
authors.forename: Serap
authors.initials: S
authors.lastname: Aksoy
authors.affiliation: Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511.
authors.forename: Adalgisa
authors.initials: A
authors.lastname: Caccone
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D004272:DNA, Mitochondrial; D059647:Gene-Environment Interaction; D017344:Genes, Insect; D008040:Genetic Linkage; D014644:Genetic Variation; D005828:Genetics, Population; D049750:Genome, Insect; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods; D005838:Genotype; D005843:Geography; D059014:High-Throughput Nucleotide Sequencing; D015810:Linkage Disequilibrium; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D014370:Tsetse Flies / Q000235:genetics*; D014454:Uganda
chemical_list: D004272:DNA, Mitochondrial
keywords: association studies; ddRAD; linkage disequilibrium; population genomics; tsetse flies