Current Trends in Phylogenetics

Analyse the effect of a character on speciation/extinction rates

Discrete (BiSSE, MuSSE) or continuous (QuaSSE) characters

Different model shapes may be used

Can be combined with MEDUSA output

Possible to test for evolutionary trends towards greater/smaller character values
Character-driven diversification

Bodega Phylogenetics Wiki (http://treethinkers.org/)

AnthroTree Workshop (http://www.anthrotreeworkshop.info/)

10kTrees (http://10ktrees.fas.harvard.edu/)

Liam Revell's Blog (http://phytools.blogspot.com/)

R-sig-phylo mailing list (https://stat.ethz.ch/mailman/listinfo/r-sig-phylo) (search in the archives using http://markmail.org/)

R-phylo Wiki (http://www.r-phylo.org/wiki/Main_Page)

Phylogenetics Task View (http://cran.r-project.org/web/views/Phylogenetics.html)
Useful tools

Make sure your trees are fully resolved, rooted, and (preferably) ultrametric

Make sure that taxa names in phylogeny and data are identical

Think about clade coverage and sampling bias

Take into account phylogenetic uncertainty

Use several measures for one character

Always Google your problems
General tips

Tree and character simulation

Correlation between two (or more) characters

Phylogenetic ANOVA or PCA

Other methods to analyse (character) diversification

And much more
Other possibilities
Discrete or continuous characters

Different models (disc.) or Brownian Motion (cont.)

ML, REML, pic, GLS, parsimony

Nodes, rates of evolution, 95% CI intervals
ace {APE}
Ancestral Character Estimation

Modeling Evolutionary Diversification
Using Stepwise AIC

Fits different birth-death models to data

Only based on phylogeny (characters not taken into account)
Diversification rate shifts
Models:
All of Pagel's Transformations
Brownian Motion
Early Burst
Ornstein-Uhlenbeck
White model
fitContinuous {Geiger}
Model fitting

APE

Geiger

Diversitree

Phytools

...and many more
R - Useful libraries


Phylogenetic signal:
Lambda
Directional evolution:
Beta
Tempo of evolution:
Delta
Mode of evolution:
Kappa
Continuous character evolution
Lineage through time plots
Phylogenetic analyses in R
Jens Ringelberg

Current Trends
in Phylogenetics

17-10-2013
make.simmap {Phytools}
Stochastic character mapping
Brownian Motion (random walk)

Standard model for evolution of continuous characters

Severe shortcomings
Pagel's Transformations
Transformation of tree based on character
Four transformations:
Results QuaSSE
Character evolution rate shifts
Differences in rate of character evolution

Bayesian method

Similar function in Phytools
(evol.rate.mcmc)
(Eastman et al. 2011)
Use R!
To find this presentation, look for my name (Jens Ringelberg) on www.prezi.com
Ancestral character states
(http://blog.phytools.org/)
(http://mesquiteproject.org)
Only discrete characters

Bayesian approach

Similar function in Diversitree(?)
seconds

Mesquite
?

SIMMAP
minute(s)

BayesTraits
(http://treethinkers.org/tutorials/lineage-diversification-in-r/)
ltt.plot {APE}
Similar functions
in Laser and Treesim
seconds

?
Check whether your new model provides a significant improvement over Brownian Motion!

medusa {Geiger}
minutes

?
make.quasse {Diversitree}
days

?
QuaSSE output
rjmcmc.bm {auteur}
day(s)

?