Computational protocol: Genetic Isolation among the Northwestern, Southwestern and Central-Eastern Indian Ocean Populations of the Pronghorn Spiny Lobster Panulirus penicillatus

Similar protocols

Protocol publication

[…] Sequence data were aligned using ClustalX [], with default alignment parameters and were checked manually for misalignments. The nucleotide compositions and numbers of variable sites were assessed with MEGA6 []. Haplotype and nucleotide diversity for each location were estimated using Arlequin (ver. 3.5) software []. AMOVA were performed to test the geographic divisions among population experimented with various groupings. This approach is a hierarchical approach that computes the proportion of variations among groups (ΦCT), the proportion of variation among population within groups (ΦSc), and the proportion of variation within populations (ΦST). We ran preliminary analysis of pairwise ΦST comparisons on each data sheet. The statistical significance of ΦST value was tested by 1000 permutations in Arlequin (ver. 3.5) software []. The Bonferroni test [] was used to correct for multiple tests of the hypothesis that pairwise ΦST statistics did not differ from zero. An UPGMA tree based on ΦST values was constructed using Neighbor in Phylip (ver. 3.6) [,]. The median-joining network [], for the haplotypes was estimated using Network (ver. 4.611) []. Past demographic patterns were inferred by Tajima’s D [], and Fu’s F [], estimated using Arlequin (ver. 3.5). Both tests are commonly used to test neutrality; however, they can also be used to examine population growth because population expansion may result in rejection of the null hypothesis of neutrality (significant negative value). […]

Pipeline specifications

Software tools Clustal W, MEGA, Arlequin, PHYLIP
Application Population genetic analysis
Organisms Antilocapra americana
Diseases Neoplasms