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Current Trends in Phylogenetics
No description
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)
?Full transcript
by
TweetJens Ringelberg
on 27 November 2013Transcript of 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)
?
