Computational protocol: Evidence of Habitat Structuring Aedes albopictus Populations in Réunion Island

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Protocol publication

[…] Microsatellite diversity within populations was estimated using observed (Ho) and Nei's 1987 unbiased expected heterozygosity (He) in Genetix 4.03 . All pairs of loci were tested for linkage disequilibrium using the probability test in Genepop . Single and multilocus Fis were estimated using Weir & Cockerham's fixation index (1984). Deviations from the Hardy–Weinberg equilibrium (HWE) were tested using a two-tailed Fisher's exact test based on Markov-chain randomisation (1000 dememorisations, 100 batches and 1000 iterations per batch) in Genepop. [...] Population differentiation was quantified by calculating pairwise Fst values . Significance was verified using the permutational genetic discontinuities among clusters and areas/habitats (east/west and gully/urban) and quantified using the hierarchical analysis of molecular variance (AMOVA). Clusters were grouped according to different combinations: Structure clusters, season, sites (East/West), habitat (gully/urban) and type of larval habitat (natural/artificial) (see ). Differences in the partition of genetic variation (Fct) among and within (Fis) regions were tested using nonparametric permutational procedures (1,023 iterations) of Arlequin 3.5 . Levels of population admixture were quantified using a number of Bayesian clustering procedures as implemented in Structure 2.3.3 . Structure can be used to calculate clustering patterns based on multilocus genotypes and makes it possible to correct for the presence of null alleles . Analyses in Structure were based on the admixture model with no prior information about the population. In order to allow asymmetric patterns of admixture amongst populations, the Dirichlet parameter for degree of admixture (a) was separately determined for each population . The number of population clusters was determined according to Evanno et al. . The ad hoc DK statistic was calculated for K ranging from 1 to 10. Structure was run for 10 million generations (burn-in = 100,000 generations) with 10 iterations for each value of K. To use structure, HWE and linkage equilibrium are assumed for each group. Both hypotheses were tested a posteriori on each cluster. […]

Pipeline specifications

Software tools GENETIX, Genepop, Arlequin
Application Population genetic analysis
Organisms Aedes albopictus
Diseases Dengue