Computational protocol: Genetic diversity and population differentiation of small giant clam Tridacna maxima in Comoros islands assessed by microsatellite markers

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Protocol publication

[…] For each marker, allele number (Na), allele frequency, observed heterozygosity (H O), expected heterozygosity (H E), Nei’s unbiased genetic distance and genetic similarity between populations were calculated using POPGENE 1.32 (Yeh et al. ). Allele richness (A R) was carried out using FSTAT 2.9.3 (Goudet ). Hardy–Weinberg equilibrium (HWE) and linkage disequilibrium were conducted using or GENEPOP 4.2 program (Rousset ). Sequential Bonferroni correction was conducted to adjust the significant level (Holm ; Rice ). The presence of null allele was detected using MICOR-CHECKER 2.2.3 (Van Oosterhout et al. ). F-statistics (F IS, F ST and F IT) and gene flow (Nm) were calculated using GENETIX 4.05. Hierarchical Analysis of Molecular Variance (AMOVA) was conducted with ARLEQUIN 3.5 (Excoffier and Lischer ) to investigate regional population differentiation. Cluster analysis was performed to construct dendrogram using the unweighted pair group method average (UPGMA) by MEGA 6.06. […]

Pipeline specifications

Software tools POPGENE, Genepop, Arlequin
Application Population genetic analysis
Organisms Thysanolaena latifolia, Drosophila melanogaster
Diseases Pulmonary Fibrosis