Computational protocol: Weak Genetic Structure in Northern African Dromedary Camels Reflects Their Unique Evolutionary History

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Protocol publication

[…] Classical population genetic parameters (allelic frequencies, number of alleles per locus, observed and expected heterozygosity), Hardy-Weinberg (HW) equilibrium, gametic unbalance, genetic differentiation (FST) were calculated using the Arlequin software package []. Allelic richness and private allelic richness were estimated using HP-RARE [] adopting n = 15 (30 “genes”) as rarefied samples size. The genetic structure of the populations was analysed using the unsupervised Bayesian clustering algorithms implemented in the software STRUCTURE 2.[]. STRUCTURE HARVESTER [] was adopted to visualize STRUCTURE outputs and estimate Evanno’s DeltaK statistics []. To test for consistency among runs, each K value (number of assumed clusters in the population) from 1 to 12 was tested 30 times. Relationships among breeds were also explored by Neighbor network analysis using the distance of Reynolds et al. (1983)[]and Nei (1983) calculated by Power Marker []. Network representations were adopted as they allow accounting for gene flow among breeds (reticulation) and thus providing a more plausible reconstruction than linear tree representations. Neighbor networks were constructed using the Neighbor-Net algorithm [] implemented in the SplitsTree4 package v. 4.13.1 []. To support inference from network topologies, neighbor-joining (NJ) trees were also generated using the distance of Reynolds et al. (1983)[]and Nei (1983), and adopting 1000 bootstrap replications. Finally, to exclude potential population structure due to relatedness, we used COANCESTRY v.1.0.1.5 []. Notably, we adopted the triadic likelihood estimator of pair-wise relatedness (TrioML), which allows for inbreeding and accounts for genotype errors in data. Proportions of pair-wise comparisons falling in different relatedness classes (R ≤ 0.25, Unrelated; 0.25 < R ≤0.5, Half-siblings; R > 0.5, Full-siblings) were calculated. […]

Pipeline specifications

Software tools Arlequin, Structure Harvester, SplitsTree
Applications Phylogenetics, Population genetic analysis
Organisms Camelus dromedarius