Statistical Analysis Stack Exchange
Statistical Analysis Stack Exchange

Questions tagged [phylogeny]

for questions related to phylogenetic inference or phylogenetic comparative methods

A phylogeny is a birfucating tree representing the evolutionary relationships among taxa. Phylogenies are estimated using phylogenetic inference methods, which estimate evolutionary relationships based on genetic or phenotypic similarity.

Once a phylogeny is estimated, its structure can be analyzed to study macroevolutionary patterns such as shifts in diversification rates. When combined with continuous or discrete trait data for the organisms at the tips of the phylogeny, phylogenetic comparative methods can be used to model trait evolution.

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Phylogenetic dependent variables: ANOVA?

I understand deriving a covariance matrix from phylogenetic data to make $cov(X,Y) = 0$ for two variables you're making a regression on. But what happens if you have one continuous variable, that you've previously shown to be dependent on phylogeny,…
user1134516
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Is a Bayesian estimate with a "flat prior" the same as a maximum likelihood estimate?

In phylogenetics, phylogenetic trees are often constructed using MLE or Bayesian analysis. Oftentimes, a flat prior is used in the Bayesian estimate. As I understand it, a Bayesian estimate is a likelihood estimate that incorporates a prior. My…
C_Z_
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Testing significant differences between regressions in R

I am running several phylogenetic least squares analyses in R, where I'm taking an existing data set for several species, and adding two new species for which I have data. I want to do is test whether the new all-species regression is significantly…
Nate
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Consequences of heteroskedasticity for regression with correlated errors

What are the statistical consequences of heteroskedasticity for regression models where the errors are correlated, e.g., due to spatial or phylogenetic autocorrelation? For example, consider a phylogenetic regression model of skull length vs. body…
Slow loris
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Using taxonomic levels as factors in random forests: does it make sense? Is it needed?

I want to test the effect of a set of predictors (ecological and morphological factors) on a categorical response variable (an animal behaviour). As far as I've read, random forests do not make assumptions about data independence. Therefore, can I…
Oritteropus
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Random effect specification in MCMCglmm to account for intraspecific variation

I'm trying to fit a mixed-effects model to a problem that includes: a continuous response variable (mean jumped distance by 17 species of frogs) in 3 different arenas and under 2 types of stimuli. A glimpse of the data: …
Diogo B Provete
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Partial correlations among three distance matrices

I am trying to test the hypothesis that related species should deviate more in niche space the more they overlap in geographic space. In other words, related species either forage similarly and don't show a lot of geographic overlap, or if they…
forlooper
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Log likelihood, aic and aicc values suggest different models should be selected

I am trying to determine which evolutionary model is best for my discrete data using the function fitDiscrete() from the geiger package. These are the values that I get for the number of parameters (k), maximum log likelihood (lnL), AIC and AICc for…
Carolina Karoullas
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How to perform a phylogenetically informed regression on individuals rather than species?

Let's imagine a scenario in which I have 100 individuals from five different species of the same genus. Their phylogenetic relationship is known (a tree is available). I want to look at the overall correlation between two of their traits at the…
Marco Plebani
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Analyzing data expressed as a percentage allowing for phylogenetic signal

I am analyzing a dataset which consists of measurements for several different metabolites over a number of species. In each cell, the data are expressed as the percentage of the metabolite j in the total volume measured, for species i. I would like…
NatWH
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Phylogenetic Pearson r using phyl.vcv function in “phytools”

The phyl.vcv function in 'phytools' R package computes a phylogenetic trait variance-covariance matrix between two variables. Can I use this matrix to compute a phylogenetic Pearson r value? If so, can this r-value be used in a t test (with n-2 df)…
jsegrestin
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Proposal for transition matrix for Metropolis-Hastings phylogenetic inference

I am using the Metropolis-Hastings algorithm for phylogenetic inference. To do so I would like to draw the substitution matrix Q from the generalized time-reversible model. To do so I need proposal distributions for the stationary distribution and…
peri4n
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Why does the likelihood of ML ancestral states change when tree is scaled?

I realize this might not be the best place to have this question answered, but I figured I'd try anyway. My question concerns the calculation of log likelihoods for ancestral state estimates using the maximum likelihood Brownian motion model from…
Slow loris
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Intraspecific variation in MCMCglmm

I want to use MCMCglmm to account for phylogenetic autocorrelation on my GLMM. However I have more than one trait measurement for certain species. Is there a way to account for intraspecific variation using MCMCglmm such as it can be done in…
AEM
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Phylogenetic General Least Squares, multivariate regression

I'm working on a biological question, with species data derived from an external database, which has multiple response and predictor variables. As a result, I want to do multivariate regression across a phylogeny to empirically test if my response…
user3834916
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