Computational protocol: Combining genetic and demographic data for prioritizing conservation actions: insights from a threatened fish species

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Protocol publication

[…] The presence/absence of large allele dropouts and null alleles was determined using the software MICRO-CHECKER 2.3 (Van Oosterhout et al. ). Departures from Hardy–Weinberg (HW) equilibrium were estimated using the program GENEPOP v4.0 (Rousset ). Levels of significance for HW were adjusted using the false discovery rate (FDR) procedure (Benjamini and Hochberg ). Linkage disequilibrium among loci within sites was tested with the program FSTAT (Goudet ).The mean number of alleles per site, the average observed (Ho) and expected (He) heterozygosity over loci, as well as Ho and He per loci per site were estimated using ARLEQUIN 3.5 (Excoffier and Lischer ). We used a rarefaction procedure, as implemented in the software ADZE 1.0 (Szpiech et al. ), to estimate allelic richness (Petit et al. ) for each site, considering minimum sample sizes of N = 8 and N = 18 individuals. […]

Pipeline specifications

Software tools Genepop, Arlequin
Application Population genetic analysis