Computational protocol: Rapid expansion of the invasive oyster Crassostrea gigas at its northern distribution limit in Europe: Naturally dispersed or introduced?

Similar protocols

Protocol publication

[…] Genotyping results were analyzed with Micro-Checker v2.3.3 [] to identify potential inconsistencies and errors (e.g., null alleles and large allele drop-out). All incidences identified by Micro-Checker were chromatographically inspected before proceeding with further analyses. GenAlEx software v6.5 [] was used to report overall observed (HO) and expected (HE) heterozygosity. Genepop v4.2 [, ] was used to report observed (HO) and expected (HE) heterozygosity for each locus within each sampling location. The number of observed alleles (NA) and calculated allelic richness (AR), compensating for less individuals in NB (Rarefaction option), at each locus within each location was assessed using HP-RARE []. Independence among loci was tested by linkage disequilibrium (LD) and Hardy-Weinberg equilibrium (HWE) was calculated to identify loci and populations departing from theoretical equilibrium of allele frequencies, using the Arlequin software v3.5.1.3 []. Calculations of statistical significance were corrected for multiple tests according to the B-Y FDR method []. A multivariate Discriminant Analysis of Principal Components (DAPC) was used to resolve genetic connectivity between populations through sequential clustering and model selection. The DAPC was performed in R v3.3.2 [] using the adegenet package [] and the sampling locations as prior groups. The genetic relationship between samples, at the population level, was evaluated according to Chords distances (DCE) [], calculated and bootstrapped 2000 times with MSA v4.05 [], and presented in a neighbour joining (NJ) tree [] using the PHYLIP v3.68 software package [] and SPLITSTREE v4.0 []. The significance of splits in the NJ tree were evaluated according to Hillis & Bull [], i.e., all splits > 70% are considered statistically significant. Calculated pairwise DCE’s were also used to generate a Principal Coordinates Analysis (PCoA) in GenAlEx v6.5 []. Pairwise genetic differentiation was estimated by calculating the fixation index, FST [], and the statistical significance of the differences between populations was tested by 10,000 permutations of individuals between samples using MSA v4.05. […]

Pipeline specifications

Software tools GenAlEx, Genepop, Arlequin, adegenet, PHYLIP, SplitsTree
Applications Phylogenetics, Population genetic analysis
Organisms Crassostrea gigas, Caenorhabditis elegans