Computational protocol: Evidence for recent gene flow between north-eastern and south-eastern Madagascan poison frogs from a phylogeography of the Mantella cowani group

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Protocol publication

[…] The sequences were checked and aligned using the software Sequence Navigator (Applied Biosystems). Sequences were deposited in GenBank (accession numbers DQ889341–DQ889429). The program Collapse v3.1 [] was used to merge sequences into haplotypes. Modeltest version 3.7 [,] was used in conjunction with PAUP*, version 4.0b10 [] to estimate the best fitting models for our complete dataset and for each partition corresponding to the different codon positions of the cytochrome b gene. Based on the Akaike Information Criterion (AIC), the following models of sequence evolution were determined: (1) for the first codon positions, a TrNef model with a proportion of invariable sites of 0 and equal rates for all sites; (2) for the second codon positions, a F81 model with a proportion of invariable sites of 0 and equal rates for all sites; (3) for the third codon position, a GTR model with a proportion of invariable sites of 0 and equal rates for all sites; (4) for the complete dataset, a GTR model with a proportion of invariable sites of 0 and variable sites distributed according to a gamma distribution shape parameter of 0.3438. Bayesian phylogenetic inference using the program MrBayes 3.1.1. [] was carried out with substitution settings adjusted according to these substitution models, and with four chains with the default heating values, 1,000,000 generations, saving the tree at every tenth generation and discarding the initial 10,000 trees as burn-in. We ran both partitioned and non partitioned analyses, both of which yielded almost identical results. Mantella aurantiaca was used as the outgroup.Haplotype networks were constructed using the TCS software package [], which employs the method of Templeton et al. []. It calculates the number of mutational steps by which pairwise haplotypes differ and computes the probability of parsimony [] for pairwise differences until the probability exceeds 0.95. […]

Pipeline specifications

Software tools ModelTest-NG, MrBayes
Application Phylogenetics
Organisms Makaira nigricans
Diseases Poisoning