Introduction to eco-phylogenetics and comparative analyses using R (ECPH01)
https://www.prstatistics.com/course/introduction-to-eco-phylogenetics-and-comparative-analyses-using-r-ecph01/ Please feel free to share! 7th - 11th February 2022 Course overview: In this five day course, we provide an introduction to eco-phylogenetics and comparative analyses using R. We begin by providing an overview on the use of phylogenies as a tool for evolutionary biologists and modern techniques to deal with large phylogenies and to incorporate phylogenetic uncertainty in the analyses (day 1). We then cover some of the most relevant eco-phylogenetic analyses and provide examples from the community to the macro-ecological scale (day 2-3). Finally, we introduce a diversity of classic and modern phylogenetic comparative methods to consider the historical relationship of lineages in eco-evolutionary research, including models of trait evolution, analysis of clade diversification and the use of phylogenies in spatial distribution models among others (day 4-5). email oliverhoo...@prstatistics.com with any questions Course program Monday 7th – Classes from 08:00 to 16:30 • Introduction and a brief phylogenetic primer. Basic terminology for non- phylogeneticists, phylogenetic inference (quick overview), phylogenies aevolutionary hypotheses. • Working with phylogenies. Newick format and structure of the R phylo object. Elementary operations on phylogenies (pruning, resolving polytomies, sticking species). Visualizing large phylogenies. • Building purpose-specific mega-trees from extant trees and incorporating phylogenetic uncertainty. Software phylocom, V.PhyloMaker, SUNPLIN and randtip R package. Tuesday 8th – Classes from 08:00 to 16:30 • Introduction to the eco-phylogenetic framework, classical conception and posterior modifications. • Phylogenetic alpha diversity (how much? how different? how regular?). Community data matrices, null models, applications to biodiversity conservation. • Phylogenetic beta diversity. The turnover and nestedness component of beta diversity. Wednesday 9th – Classes from 08:00 to 16:30 • Incorporating the exact branching pattern of phylogenies into eco-phylogenetic analyses. • Spatial phylogenetics. RPD, RPE and CANEPE analysis. • Overview of functional trait ecology. Functional richness, evenness and divergence.Community weighted means. • Phylogenetic imputation of trait datasets. Bounding prediction uncertainty using evolutionary models. Phylogenies as a null model in ecology. Thursday 10th from 08:00 to 16:30 · The phylogenetic comparative method, from independent contrasts to sophisticated modelling. · Analyses of phylogenetic signal and models of evolution: rationale, common- practice, and new trends. · Correlated evolution and ancestral trait reconstruction. · Analyses of diversification, speciation and extinction rates in a geographic context. Friday 11th – Classes from 08:00 to 16:30 · The need to account for phylogenetic relationships in models. · Most common phylogenetic modelling approaches: PGLS, PGLMM, BayesianPMM. · Putting phylogenies in the geography: how to combine phylogenies with species distribution models. -- Oliver Hooker PhD. PR statistics [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
