Computational protocol: Variation and Genetic Structure in Platanus mexicana (Platanaceae) along Riparian Altitudinal Gradient

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Protocol publication

[…] All the amplified bands were treated as dominant genetic markers. ISSR bands were scored as 1 (present) or 0 (absent) and this binary data was used to assemble a rectangular matrix. Allele frequencies p and q were inferred using the Lynch and Milligan adjustment for dominant markers, were recessive allele is determined by q=(N0N0+N1) and dominant allele by p=1−q []. The percentage of polymorphic loci (% p), number of alleles per locus (A), effective number of alleles per locus (Ne), Nei’s gene diversity (He) and Shannon index (I) were calculated using the TFPGA v1.3 software []. To detect any differences in heterozygosity among elevations, Wilcoxon paired tests were run in STATISTICA, v8 [].To estimate the genetic differences among sites along the altitudinal gradient, an analysis of molecular variance (AMOVA) was run in GenAlEx, v. 6.41 software [], this analysis produces variance components estimates that are similar to the F statistics of Wright, called ΦST. In addition, paired AMOVAs were computed between sites to pairwise differentiation indices. To test the results of this analysis, genetic distances were inferred with the method of Nei and Lee [], and similarity estimates were analyzed using Unweighted Pair Group Method with Arithmetic Averages (UPGMA) with TFPGA, v 1.3 software [].A further classification was made using STRUCTURE v. 2.3 software []. The RECESSIVEALLELE = 1 algorithm for dominant markers was used, where 0 = recessive allele for each locus. The number of inferred groups was evaluated at values of K ranging from 2 to 10, a burn-in length of 50,000 followed by 10 runs at each value of K. Estimates were obtained under the admixture model using the correlated allele frequencies and the LocPrior algorithm, which incorporates sampling location information and is appropriate for detecting weak population structure []. The most likely number of clusters (K) was determined using the ΔK method, as well as by examining the plateau of the Ln Pr(X/K) [].To test whether the genetic structure is a result of isolation because of distance, pairwise ΦST versus geographic distances were tested for correlation using Mantel’s test [] run in TFPGA, v. 1.3. As another measure related to allele fixation from genetic drift, the quantity of fixed loci or those with allele frequencies lower than 0.05 between sites were tested using Wilcoxon’s test in STATISTICA, v. 8 []. […]

Pipeline specifications

Software tools TFPGA, Statistica, GenAlEx
Applications Miscellaneous, Population genetic analysis
Organisms Poecilia mexicana