Open Access Publication
Gloria-Soria, Andrea; Dunn, W. Augustine; Telleria, Erich L.; Evans, Benjamin R.; Okedi, Loyce; Echodu, Richard; Warren, Wesley C.; Montague, Michael J.; Aksoy, Serap; and Caccone, Adalgisa, ,"Patterns of genome-wide variation in Glossina fuscipes fuscipes tsetse flies from Uganda." G3.6,6. 1573-1584. (2016).
Manhattan plot of Tajimasï¿½D values computed from 73, 297 SNPs in 1000 bp windows across the Glossina fuscipes fuscipes reference supercontigs
FigureS2.pdf (72 kB)
Genetic membership bar plot based on 73, 297 SNPs SNPs obtained using fastStructure (Raj et al. 2014).
FigureS3.pdf (196 kB)
Decay of linkage disequilibrium with physical distance in Glossina fuscipes fuscipes.
FigureS4.pdf (66 kB)
Bayescan Fst posterior probabilty plot on populations of four Glossina fuscipes fuscipes from Uganda (infected and uninfected flies) to identify SNPs associated with susceptibility to infection by Trypanosome.
FigureS5.pdf (80 kB)
Results from the PCadapt analysis (Duforet-Frebourg 2014) on the MS, KG and OT populations.
FigureS6.pdf (189 kB)
Hapflk was run with default parameters and K=3.
FileS1.pdf (160 kB)
Bioclimatic information for the four Gff populations from Uganda used in this study (Hijmans et al. 2005).
FileS2.pdf (217 kB)
FileS3.xls (126 kB)
Genes located within 1000 bp of SNPs identified as 1) outliers by BayeScan in pairwise population comparisons for local adaptation; 2) SNPs ranked within the BayeScan top 10% alpha values and common to all individual population comparisons for trypanosome infection status; and 3) SNPs ranked within the BayeScan top 10% alpha values, for trypanosome infection status when all populations were grouped together, filtered by LD.
FileS4.xls (17 kB)
SNPs identified as outliers in BayeScan during the pairwise population comparison to detect environmental local adaptation candidates.
TableS1.txt (1 kB)
Detailed individual sample information (KG: Kalangala; MS: Masindi; OT: Otuboi; NB: Namutumba; Infection = Trypanosomes detected in sample; WGS= whole genome sequencing).
TableS2.xls (4044 kB)
Tajima's D values measured across the Gff genome using the 73, 297 SNPs and a window size of 1000bp. Only windows with at least one SNP are listed.
TableS3.xls (509 kB)
List of SNPs ranked within the top 10% BayeScan alpha values in the infection status analysis performed on all populations simultaneously (infected vs uninfected flies), and list of SNPs common to the 10% ranked alpha values across all individual population analyses for infection status.
TableS4.pdf (38 kB)
Tentative candidates for local adaptation as determined by PCadapta (Duforet-Frebourg 2014).