Computational protocol: Testing the Role of Meander Cutoff in Promoting Gene Flow across a Riverine Barrier in Ground Skinks (Scincella lateralis)

Similar protocols

Protocol publication

[…] For all loci and sites we calculated allele number, Nei’s unbiased estimate of gene diversity , and Weir and Cockerham’s FIS index using FSTAT ver2.9.3.2 . We calculated allelic richness using HP-RARE which uses rarefaction to adjust for differences in sample size. Proportions of observed heterozygosity were calculated using Cervus ver3.0.3 (Marshall et al. 1998) and exact tests for Hardy-Weinberg equilibrium (HWE) and linkage disequilibrium among loci were carried out using GENEPOP ver3.4 .We investigated genetic structure among sampling sites to test two predictions of the MLC hypothesis. First, if MLC is responsible for gene flow across the Mississippi River, the number of individuals sampled on the “wrong” side of the river (i.e., with a genetic profile different from those in the pure site on the same side of the river) should be higher on the oxbow side of the river than on the control side. For cytb, we investigated this by assigning all samples to one of two mtDNA clades previously described in the region . This was done using a cytb gene tree which we inferred by carrying out a full maximum likelihood (ML) search with 1000 rapid bootstrap pseudoreplicates using RAxML ver7.2.6 . For the microsatellite loci, we estimated river-based population assignments using the Bayesian clustering algorithm in the program STRUCTURE ver2.2.3 . We ran the program for each of the three latitudes (northern, central, and southern groups of sites) separately (including the two pure sites in each analysis) under the assumption of K = 2 populations. We also estimated the true K for each latitude by comparing log-likelihoods of the data under a series of models assuming different K numbers of populations (from K = 1 to K = 5). We ran the program ten times for each model for at least 1 million generations (with an additional burnin of 500,000).Secondly, if lizards were recently transported across the river due to MLC at the three oxbow sites, then S. lateralis collected from cis sites should have a closer genetic affinity to S. lateralis from across the river (control sites) than from the same side (trans sites). To investigate this prediction using microsatellite loci, we calculated divergence metrics Dest , Wright’s FST, and G’ST for population pairs using AMOVA in Arlequin ver3.1.1 . Although FST can underestimate divergence when rapidly mutating markers such as microsatellites are assayed , , we selected FST over the alternative metric RST (which takes into account a stepwise mutation model; ) due to the observation of superior overall performance of the former in studies which, like ours, involve limited sampling and recent divergence –. Dest and G’ST were calculated using SMOGD ver1.2.5 . These metrics are independent of the degree of genetic diversity within a dataset and are thus particularly suitable for microsatellite loci . […]

Pipeline specifications

Software tools Genepop, RAxML, Arlequin
Application Population genetic analysis