Computational protocol: Higher speciation and lower extinction rates influence mammal diversity gradients in Asia

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Protocol publication

[…] We also carried out the GeoSSE analysis for the Asia-tree. Within Asia, we classified the tropical and subtropical moist forest biomes (B1), the tropical and subtropical dry forest biomes (B2) and the tropical and sub tropical coniferous forest biomes (B3) as the ‘tropical biomes’ and all the other biomes as ‘non tropical’ biomes. In Asia the tropical and subtropical grasslands, savannas and shrublands (B7) are not very extensively distributed, and hence were not included in the ‘tropical biomes’. We estimated speciation, extinction and dispersal rates across these two regions for all mammals, and for each of the following orders – Rodentia, Soricomorpha, Chiroptera, Artiodactyla and Carnivora. We cross-verified the trends for Carnivora with a complete phylogeny from Nyakatura et al. (Additional file ). Sampling frequencies were correspondingly calculated to incorporate missing species in our phylogenies. Both likelihood and MCMC based methods were employed to estimate the parameters. Since we found temporal variation in diversification rates, time-dependent scenarios were also tested, and a linear rate of change across all parameters through time was allowed.We also tested both global- and Asia-level GeoSSE models with re-dated mammalian phylogeny provided by [] to cross validate our results.All analyses were carried out in the R statistical environment, v 3.0 []. Functions from the package ‘picante’ [] were used to calculate PD and to prune trees. LTT-plots were constructed using the package ‘ape’ [], and abrupt changes in diversification (and their timing) were estimated using functions in package ‘TreePar []. GeoSSE was performed using function from the package ‘diversitree’ []. […]

Pipeline specifications

Software tools Picante, APE, TreePar, Diversitree
Application Phylogenetics
Organisms Homo sapiens