Computational protocol: Contrasted levels of genetic diversity in a benthic Mediterranean octocoral: Consequences of different demographic histories?

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Protocol publication

[…] Pairwise F ST were calculated with GENETIX according to Weir and Cockerham (). Their significance was tested with 1000 permutations. The excluding null allele (ENA) method in FreeNA (Chapuis & Estoup, ) was used to calculate pairwise F ST to avoid potential bias induced by null alleles. As a complementary estimate of genetic differentiation, we computed the Jost's D statistic (Jost, ) with the SMOGD software (Crawford, ).The pattern of isolation by distance (IBD) at the Mediterranean scale and within French region only (thanks to the number of samples in this region) was tested through the correlation between F ST/(1‐F ST) and the logarithm of geographical distances (shortest distance by sea) between populations (Rousset, ). The correlation was tested with a Mantel test (n = 10 000 permutations) in IBDWS 3.16 (Jensen, Bohonak, & Kelley, ).An analysis of molecular variance (AMOVA) was performed with F ST and R ST estimators with ARLEQUIN v.3.5 (Excoffier & Lischer, ) and by using the main geographical areas as groups, that is, Turkey, Algeria, continental France, and Menorca and Corsica islands. For these last two islands, we conducted the AMOVA both by separating and by grouping them, as the STRUCTURE analysis grouped them (see results). One thousand permutations were used to test the significance of the different estimates of fixation indices of the AMOVA.The relationships between populations were further investigated using principal coordinate analysis (PCoA) with GenAlEx 6.5 (Peakall & Smouse, , ) using pairwise population matrix of Nei's unbiased genetic distance (Nei, ).A clustering analysis was performed with the Bayesian method implemented in STRUCTURE v.2.2 (Falush, Stephens, & Pritchard, , ; Pritchard, Stephens, & Donnelly, ) launched with admixture model, 500 000 iterations after a burn‐in period of 50 000, and 12 replicates for each configuration. A first round of analyses was launched with the whole data set to assess structure at the Mediterranean scale with K varying from 1 to 16. A second round of analyses was performed on each genetic group depicted by the initial round with the same parameter set of the first round, and K varying from 1 to 12 for France, and 1 to 5 in other cases. The outputs were analyzed through the STRUCTURE HARVERSTER website (Earl, ) to choose the value that captured the major structure in the data. The number of clusters was estimated based on the Delta (K) criterion (Evanno, Regnaut, & Goudet, ).Results for each K value were merged with CLUMPP v.1.1 (Jakobsson & Rosenberg, ), and DISTRUCT v.1.1 (Rosenberg, ) was used to visualize these results.To analyze genetic structure without relying on the model implemented in STRUCTURE, we performed a discriminant analysis of principal components (DAPC; Jombart, Devillard, & Balloux, ) implemented in the adegenet R package (Jombart, ). Data were analyzed in two rounds, one with all samples and a second round with French samples only. The number of clusters was determined based on the Bayesian information criterion (BIC).In all cases, for multiple tests, significance levels were corrected using a 5% false discovery rate (FDR) (Benjamini & Hochberg, ). […]

Pipeline specifications

Software tools IBDWS, Arlequin, GenAlEx, CLUMPP, DISTRUCT, adegenet
Application Population genetic analysis
Organisms Meleagris gallopavo