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Phylogenetic Analyses (Tree Building (Divergence Time Estimation (Could…
Phylogenetic Analyses
Tree Building
Sequence/Character Manipulation
SequenceMatrix
Sequencher
Geneious
TNT
....
Sequence Alignment
MAAFT
...
Tree Inference
Distance Based
NJ
UPGMA
Model Based
Parsimony
Likelihood
Maximum Likelihood
Bayesian
Divergence Time Estimation
Could break this up into broader categories
BEAST
PhyloBayes
MCMCTree
MrBayes
r8S
Diversification Analyses
Constant diversification
No extinction
• Pure-birth (Yule) model
Extinction
• Birth-Death model
Varying diversification
Time-varying
Describing the pattern of lineage accumulation
• Lineages Through Time (LTT) plots
Article:
Nee et al. 1995
Description:
Harmon book
Arbor:
R:
ape::LTT
,
phytools::ltt
Gamma-statistics (rate slows down through time?)
Complete extant taxon sampling?
• Constant Rates (CR) test
Article:
Description:
Arbor:
R:
Incomplete extant taxon sampling?
• Monte Carlo Constant Rates (MCCR) test
Article:
Description:
Arbor:
R:
Rates Through Time (RTT) plots
• TreePar
Article:
Description:
Arbor:
R:
• CoMeT
Article:
Description:
Arbor:
R:
• BAMM
Article:
Description: Bayesian Analyses of Macroevolutionary Mixtures
Arbor:
R:
Other tree statistics
• Laplacian spectral density profile (
RPANDA:::spectR()
)
• Tree imbalance
Factor dependent
• Environmental dependence (
RPANDA:::fit_env()
)
Diversity dependent
• Laser (†)
• Diversity-Dependent Diversification (DDD)
Age dependent
• XXX
Among subclades
Clade-level rates
• Bayesian Analyses of Macroevolutionary Mixtures (BAMM)
• BayesRates
• Method of Moments
Tip-level rates
• Inverse Equal-Splits (tip DR)
• Bayesian Analyses of Macroevolutionary Mixtures (BAMM)
Character dependent diversification
Discrete Traits
Binary
• State-dependent Speciation and Extinction (BiSSE)
• Fast, intuitive State-dependent Speciation and Extinction (FiSSE)
• Hidden State-dependent Speciation and Extinction (HiSSE)
Multiple
• Multiple State-dependent Speciation and Extinction (MuSSE)
Geographic distribution
• Geographic State-dependent Speciation and Extinction (GeoSSE)
• Geographic Hidden State-dependent Speciation and Extinction (GeoHiSSE)
Continuous
• Quantitative State-dependent Speciation and Extinction (QuaSSE)
Character evolution (including Biogeography)
What kind of trait do I have?
Continuous
Inference
(If the response variable is continuous)
non-linear relationships
Mixed-effects models
for complex hierarchical/nested designs or non-Gaussian phenotypic traits
package
MCMCglmm
Bayesian Hierarchical Regression Models
package
brms
Autoregressive method
Delayed-response phylogenetic correlation
Phylogenetic
ANCOVA
package
SLOUCH
Model adequacy issue (packages
Arbutus
,
pmc
, and
sensiPhy
)
Fitting multiple VCV matrices to a phylogeny(phytools::evol.vcv or package
ratematrix
)
Phylogenetic eigenVector Regression
PGLS
equivalent
to
Phylogenetic Independent Contrasts
(PICs) when using BM
Phylogenetic ANOVA
with intraspecific variationin the response trait
Evolutionary models
[
remember to include intraspecific variation
]
Trend
Brownian Motion
geiger::auteur
and Variable Rates model in BayesTraits for automatically detecting rate shifts
package
OUwie
Brownie
Comparing rates of evolution between trees
phytools::evol.rate.mcmc
Detect jumps in evolutionary rates
levolution
Rate shift considering fossil data (
RRphylo
)
Orsntein-Uhlenbeck (OU)
Detection of multiple adaptive peaks and estimation of OU parameters
package
ouch
package
OUwie
Detecting regime shifts automatically
package
SURFACE
package
bayou
shifts in allometric relationships
non-stationarity in the relationship between continuous traits bayou::makeBayouModel
package
l1ou
Package
PhylogeneticEM
for detecting shifts in multivariate traits taking into account correlation between them
Early Burst
FPK model
Models that incorporate
competition
biogeography + competition
between lineages
Pulsed evolution - Lévy Process
Non-Gaussian traits, se
here
Ancestral character estimation
(#6b7dda)
Bayesian (
BayesTraits
and
bayou
)
Maximum-Likelihood
#
Squared-change Parsimony
Weighted
Non-weighted
with missing data -
Rphylopars
Phylogenetic "Signal"
#
Moran's
I
(correlogram)
[Abouheif's
C
]
Decomposition of Rao's Quadratic Entropy along the nodes of a phylogeny
Blomberg's K
without intraspecific variation
with intraspecific variation
Mantel test and correlogram
Pagel's Lambda
R2 of PVR
Why the hell am I using quotes in "signal"? Read
this
Discrete
Inference
(if the response variable is categorical with...)
two levels
Phylogenetic logistic regression
(
MCMCglmm
or
phylolm
::phyloglm)
Correlation of transition rates of binary traits
Pagel's method
Threshold Model
(two discrete, or one discrete and one continuous trait)
correlation using Mk model
with hidden states (
corHMM
)
more than two levels
ordered
MCMCglmm
with family="ordinal" (probit link)
unordered
MCMCglmm with family="categorical" (logit link)
Ancestral character state estimation
Maximum likelihood (using Marvok
k
-state Models)
Stochastic Character Mapping (phytools::make.simmap)
Bayesian (e.g.,
BayesTraits
)
Squared-change parsimony
with hidden states
(corHMM)
Evolutionary models for rate estimation
#
Symmetric
Equal rates
All Rates Differ (ARD)
Custom matrix
Allow heterogeneity in transition rates for MultiState traits among clades (BayesTraits)
Comparing rates of evolution
#
Phylogenetic "signal"
Decomposition of Rao's Quadratic Entropy along the nodes of a phylogeny
Fritz's D
Mantel
Multivariate
(e.g., derived from Geometric morphometrics)
Inference
RRPP
PGLS for multivariate traits
Ordination
Constrained/Canonical
Canonical Phylogenetic Ordination
Phylogenetic Canonical Correlation Analysis
Unconstrained/Factor Analysis
Phylogenetic Principal Component Analysis
Phylogenetic Factor Analysis
Estimation of evolutionary rates
Comparing rates between compartments of a multidimensional trait - modularity
Fitting evolutionary models to multivariate data
Blomberg's K for multiple traits
mvSLOUCH
for models with evolutionary time lag package
mvmorph
Detecting shifts in multivariate correlated traits package
PhylogeneticEM
fitting BM, EB, OU with Penalized LIkelihood
Trait Simulations
[
Molecular Evolution
]
[
Phylogeography / Biogeography
]
[
Phyloclimatic Modeling
]