Computational protocol: Systematics, conservation and morphology of the spider genusTayshaneta (Araneae, Leptonetidae) in Central Texas Caves

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Protocol publication

[…] Detailed protocols for the extraction, amplification and sequencing of DNA are reported in . Three gene fragments were selected based on availability, prior use in systematics studies and amplification success. Mitochondrial cytochrome oxidase I (~800bp), nuclear histone 3 (~330bp) and 28s rDNA (~1000bp) were amplified following and the primers and conditions used are reported in . Phylogenetic methods also follow and both independent genes and concatenated data were analyzed under a variety of optimality criteria and conditions (). Sequence alignment was performed using CLUSTAL × v. 2.0 () and additional 28s rDNA alignments were produced using Muscle v. 3.8 (). Models of nucleotide evolution were selected using the Akaike Information Criterion () as implemented in MrModeltest v. 2.2 (). Partitioning strategies for COI and histone 3 were evaluated using Bayes Factors () for fully partitioned, partially partitioned and unpartitioned analyses.Bayesian analysis was performed using MrBayes v. 3.1.2 () using four independent runs until the standard deviation of split frequencies fell below 0.01. Stationarity was evaluated by examining the stability of posterior probabilities for nodes of each MCMC run using the Cumulative and Compare plots in Are We There Yet? (http://ceb.csit.fsu.edu/awty; Nylander et al. 2008) and the first 25% of trees were discarded from the posterior distributions of each analysis. Maximum likelihood analysis was performed using 1000 bootstrap replicates in RAxML v. 7.0.4 () and parsimony analyses were performed in PAUP* () using 1000 iterations of a heuristic search holding 100 trees for each iteration, with random taxon addition and tree bisection-reconnection (TBR) branch-swapping. Branches were collapsed using the default rule in PAUP* v.4.0 b10 (collapse if maximum length is zero). Nonparametric bootstrap support values were calculated using 1000 replicate searches with random taxon addition.Aligned data matrices and trees will be made available online in TreeBASE (http://www.treebase.org/). […]

Pipeline specifications

Software tools Clustal W, MrModelTest, MrBayes, RAxML
Application Phylogenetics