Computational protocol: Genetic variation analysis of the Bali street dog using microsatellites

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Protocol publication

[…] Allelic diversity and observed heterozygosities (HO) were determined by direct counting for each of the 30 subpopulations. Hardy-Weinberg equilibrium (HWE) tests were performed using Genepop version 3.4 []. Pairwise FST estimates and subpopulation expected heterozygosities (HE) for the 30 breeds or dog groups were performed using Genepop version 3.4 []. FIS estimates (inbreeding coefficient of each subpopulation) for each allele following Weir and Cockerham [] were calculated using Genepop version 3.4 and are presented as averages across all loci.Gene diversity or total population heterozygosity (HT) and its associated parameters, HS (average heterozygosity among subpopulations) and GST (coefficient of genetic differentiation), were calculated across all loci using the public domain software, DISPAN []. Two additional measures of variance, FST [] and RST [,] were calculated using Genepop version 3.4. A pairwise genetic distance matrix using Nei's DA distance was also created using DISPAN with bootstrapping. Genotype data for all populations is available in . [...] Allele frequencies were used to compute a matrix of genetic distances [], which were then used to construct a phylogenetic tree of relationships among 5 Asian and 4 non-Asian dog subpopulations. Takezaki's [] POPTREE program was used to create a neighbor joining tree using DA distances with 1000 bootstrap replications. The output of POPTREE was then converted to the New Hampshire format for editing in the stand alone program TREEVIEW version 1.6.6 [] and bootstrap values were added. […]

Pipeline specifications

Software tools Genepop, POPTREEW, TreeViewX
Applications Phylogenetics, Population genetic analysis
Organisms Canis lupus familiaris