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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 \u223c73,000 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 (r2max\/2) between 1359 and 2429 bp. The overall LD estimated for the species reaches r2max\/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.<\/jats:p>","DOI":"10.1534\/g3.116.027235","type":"journal-article","created":{"date-parts":[[2016,6,17]],"date-time":"2016-06-17T22:16:10Z","timestamp":1466201770000},"page":"1573-1584","source":"Crossref","is-referenced-by-count":13,"title":["Patterns of Genome-Wide Variation in<i>Glossina fuscipes fuscipes<\/i>Tsetse Flies from Uganda"],"prefix":"10.1093","volume":"6","author":[{"given":"Andrea","family":"Gloria-Soria","sequence":"first","affiliation":[{"name":"Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511"},{"name":"Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"W Augustine","family":"Dunn","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Erich L","family":"Telleria","sequence":"additional","affiliation":[{"name":"Laboratorio de Fisiologia e Controle de Artropodes Vetores, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, 21040-360 RJ, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Benjamin R","family":"Evans","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Loyce","family":"Okedi","sequence":"additional","affiliation":[{"name":"Department of Biology, Faculty of Science, Gulu University, Loroo Division, 256 Gulu, Uganda"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard","family":"Echodu","sequence":"additional","affiliation":[{"name":"Department of Biology, Faculty of Science, Gulu University, Loroo Division, 256 Gulu, Uganda"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wesley C","family":"Warren","sequence":"additional","affiliation":[{"name":"The Genome Institute, McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri 63108"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael J","family":"Montague","sequence":"additional","affiliation":[{"name":"The Genome Institute, McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri 63108"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Serap","family":"Aksoy","sequence":"additional","affiliation":[{"name":"School of Public Health, Yale University, New Haven, Connecticut 06510"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adalgisa","family":"Caccone","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,6,1]]},"reference":[{"issue":"13","key":"2021062506024782500_bib1","doi-asserted-by":"crossref","first-page":"4627","DOI":"10.1128\/AEM.00806-12","article-title":"Implications of microfauna-host interactions for trypanosome transmission dynamics in Glossina fuscipes fuscipes in Uganda.","volume":"78","author":"Alam","year":"2012","journal-title":"Appl. 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