Computational protocol: Genetic diversity of high-elevation populations of an endangered medicinal plant

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Protocol publication

[…] Calculations for genetic distance, pairwise population matrix of Nei's genetic identity, allele frequency by population, Mantel test for correlation of genetic and geographic distance and principal coordinate analysis (PCoA) were conducted using GenAlEx 6.501 (, ). STRUCTURE version 2.3.4 () was used to infer the genetic structure so as to obtain an estimate of the likely number of population genetic clusters (K). The numbers of clusters of the populations (K) were identified by performing six iterations and setting the value of K from 1 to 25 with a burn-in period of 100 000 and 100 000 number of the Markov Chain Monte Carlo (MCMC) repeats after burn-in. The maximal value of LnP(D), the posterior probability of data as per , was obtained using STRUCTURE HARVESTER (). To further confirm the number of genetic clusters, the value of K was estimated through analysis of molecular variance (AMOVA)-based clustering using kMeans software (). To infer the partitioning of the diversity, Gst & G′st software package GenoType/GenoDive () was used. In the first step GenoType detects the genotyping errors and prepares an input file for GenoDive. In the second step GenoDive calculates the parameters of diversity and diversity partitioning. AFLPSURV (), which follows a Bayesian method with non-uniform prior distribution (), was used to infer the genetic relationships among populations by calculating Nei's unbiased genetic distance () among all possible pairs of populations from allele frequencies. Hierarchical AMOVA and Fst was conducted using ARLEQUIN 3.5.1.2 (). The input file for ARLEQUIN was prepared using the program CONVERT (). The dendrogram was computed by using the neighbour joining (NJ) clustering with DARwin5 version 5.0.158 (). […]

Pipeline specifications

Software tools GenAlEx, Structure Harvester, Genodive, Arlequin
Application Population genetic analysis
Organisms Sinopodophyllum hexandrum