[R-sig-genetics] Introduction to eco-phylogenetics and comparative analyses using R (ECPH01)

[Oliver Hooker]

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/

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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 oliverhooker using 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.
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