Computational protocol: Did southern Western Ghats of peninsular India serve as refugia for its endemic biota during the Cretaceous volcanism?

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Protocol publication

[…] Sequences of two mitochondrial DNA (mt) markers, the 16S ribosomal gene (16S) and cytochrome c oxidase I (COI), belonging to seven species from a recently published phylogeny of the genus Digitipes were used for the divergence dating analyses(Joshi and Karanth ). The program BEAST (v1.4.8), which uses a Bayesian approach and Markov chain Monte Carlo (MCMC) method (Drummond and Rambaut ), was implemented on the partitioned mtDNA dataset to estimate node ages. A previous study on the diversification of scolopendrids showed that the genus Digitipes started diversifying ∼86 ± 20 mya in the WG (Joshi and Karanth ). This date was used as a calibration point in this study to date species-level diversification in the phylogeny. A normally distributed prior with mean of 86 my was applied to the most recent common ancestor (tMRCA) for the in-group comprising all Digitipes species. The members of the genus Rhysida were used as out-group (Joshi and Karanth ). The model and priors settings for the analyses were as follows: the GTR + I model of sequence evolution with uniform priors was applied on the partitioned dataset as suggested by Model test (Posada and Crandall ). A relaxed molecular clock model with an uncorrelated lognormal distribution was used (Drummond et al. ). Additionally, the Yule speciation process, which is considered to be appropriate for species-level phylogenies, was used. The program was run for 100 million generations and convergence of the chains to the stationary distribution was determined using the program TRACER (v1.4.1) (Rambaut and Drummond ). The consensus tree was constructed in TreeAnnotator (v1.4.8) and was visualized in the program FigTree (v1.2.2) (Drummond and Rambaut ). [...] We used a Shimodaira–Hasegawa (SH) test to evaluate if the best tree was significantly different from trees based on S2 and S3 (Shimodaira and Hasegawa ). To this end constraint trees that are consistent with these scenarios were obtained using the program Mesquite (v 2.73) (Maddison and Maddison ). In the case of S2, species from south and north of PG were placed in two separate clades, and for S3, species were assigned to four different clades corresponding to the four biogeographic subdivisions. These constraint trees were then used to derive phylogenetic tress that are consistent with S2 and S3 in PAUP* through likelihood heuristic search (Swofford ). To examine the support for the S2 and S3, the likelihood scores of these constrained maximum likelihood (ML) trees were compared with unconstrained ML tree via one-tailed SH log-likelihood ratio test, as implemented in PAUP*, with full optimization resampling and 10,000 bootstrap replications. […]

Pipeline specifications

Software tools BEAST, FigTree, Mesquite, PAUP*
Application Phylogenetics
Organisms cellular organisms
Diseases Encephalomyelitis, Western Equine