Computational protocol: DNA barcodes reveal microevolutionary signals in fire response trait in two legume genera

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[…] All the samples were sent to the Canadian Centre for DNA Barcoding (CCDB) in Canada, where total DNA was extracted and the two core DNA barcodes (matK and rbcLa) were sequenced according to standard CCDB protocols (). Sequence alignment was performed using Multiple Sequence Comparison by Log Expectation (MUSCLE v. 3.8.31, ) plugin in Geneious v.8.0.4 () and manually adjusted using MESQUITE v.2.5 (). The two regions were aligned separately and then combined. [...] We explored the potential of the DNA barcode data to reveal microevolutionary patterns by testing for phylogenetic signal in the affinity of lineages to fire-survival and regeneration strategies. We used a phylogeny of the southern African Psoraleoid species and a binary matrix of reseeders versus resprouters. The phylogeny was reconstructed using a combination of matK and rbcLa data sets, based on a maximum-likelihood (ML) approach (), enforcing topological constraints from a consensus tree of the Bayesian analysis of the data set. We used the GTR + G + I substitution model based on the result of Akaike information criterion from Modeltest v.2.3 (), and ran 1000 ML searches. Phylogenetic signal was tested on the ML best tree and binary matrix of reseeders versus resprouters using the D statistics of in the R package Caper (). The D statistics calculates the sum of changes of a binary trait along the branches of a phylogeny, and compares it with a random model and clumping expected under a Brownian evolution. Significance was assessed by shuffling the trait values 999 times at the tips of the phylogeny. D = 1 corresponds to a random distribution of traits at the tip of the phylogeny; D = 0 corresponds to a Brownian motion model (). […]

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