Computational protocol: Landscape variability explains spatial pattern of population structure of northern pike (Esox lucius) in a large fluvial system

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Protocol publication

[…] Fis values and exact tests for deviations from Hardy–Weinberg proportions and linkage equilibrium were computed using GENEPOP (Raymond and Rousset ) with Bonferroni corrections (α = 0.05; Rice ). We evaluated expected (HE) and observed (HO) heterozygosity with GENETIX v.4.05.2 (Belkhir et al. ), allelic richness (Ar) and private allelic richness (Apr) over all loci standardized for smallest sample size (N = 20) with HP-RARE (Kalinowski ). Temporal stability of genetic structure between 2009 and 2010 samples was assessed with an analysis of molecular variance (AMOVA; ARLEQUIN v.3.1, Excoffier et al. ) performed on sites with N > 20 each year (2007 excluded because it had only one sample). We also assessed the stability of genetic structure as a function of sampling period (prior and during spawning period). Given the results of both AMOVAs (see Results section), temporal samples were pooled for further analyses. […]

Pipeline specifications

Software tools Genepop, Arlequin
Application Population genetic analysis
Organisms Esox lucius, Hemisus marmoratus, Homo sapiens