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Questions tagged [phylogeny]

for questions related to phylogenetic inference or phylogenetic comparative methods

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Graphical model of phylogenetic linear regression

I have been trying to give the graphical model of the PGLS (phylogenetic generalized least squares) but can't seem to fully understand something. PGLS is a generalization of the general linear ...
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18 views

Stratify phylogeny based on variables - e.g. which ST are represented by high % males

So I have tree file and metadata. Metadata includes sequence type ST (clusters that correspond in most part to the phylogeny), but also some patient data, age, sex etc. I am trying to identify which ...
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15 views

Multiple comparisons in Bayesian phylogenetic models

I am writing a paper that tests multiple hypotheses under a Bayesian framework. The hypotheses are ~15 previously established hypotheses which I am retesting under a phylogenetic framework (to ...
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0answers
18 views

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 ...
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9 views

Substitution model for maximum likelihood in linguistic phylogenetics?

When using maximum likelihood to estimate a phylogenetic tree on the basis of linguistic data, is there a standard substitution model that one should use?
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26 views

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 ...
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1answer
181 views

How to conduct Phylogenetic Principal Component Analysis (pPCA) using tree with no branch lengths in R?

I'd like to carry out a phylogenetic comparative modeling, for which I have to use predictors that are substantially correlated with one another. I'd like to apply phylogenetic principal component ...
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1answer
40 views

Is there a way to identify the characters/variables that have the greatest impact on the inference of a phylogenetic tree?

I have a dataset of molecular sequences from which I have inferred a phylogenetic tree (a.k.a a dendrogram) with various algorithms (maximum parsimony, neighbor-joining, and maximum likelihood). What ...
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470 views

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 ...
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1answer
32 views

Within phytools, what distribution does the pbtree function use to simulate a phylogeny?

I have seen the function pbtree (within R package phytools) be used to simulate phylogeny. How does this actually work? I'm particularly interested in the model distributions used to pick the time ...
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102 views

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, ...
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1answer
199 views

R- Using PGLS with discrete and continuous data

The model output coefficients list only two out of the three discrete values. What am I doing wrong? I'm relatively new to R so I hope this is not a stupid question. ...
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1answer
638 views

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. ...
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1answer
39 views

Combining parameter errors with phylogenetic errors

Say I am running a phylogenetic generalised least squares (PGLS) regression with one predictor. A model will return me a coefficient with a standard error - corrected for phylogenetic relatedness. ...
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42 views

Estimating ML under brownian motion

I have data for 5 individuals of 15 lineages (normalized gene expression, 75 total samples), a phylogeny, and would like to calculate the maximum likelihood under brownian motion, then compare the ...
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1answer
656 views

Model selection in PGLS?

I am using Phylogenetic General Least Squares in the R package 'caper'. I have 4 predictor variables and I would like to know which are correlated with my response variable, while taking the ...
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21 views

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 ...
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0answers
45 views

How to incorporate intraspecific variation in discrete characters in comparative analysis?

I'd like to run a multivariate analysis (Pavoine et al. 2011) that aims to disentagle the effect of environmental gradients on traits, considering its autocorrelation with phylogeny and space. It uses ...
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0answers
231 views

Phylogeny edge lengths are 0 error with MCMCglmm

I'm trying to run an MCMCglmm using a pedigree to control for phylogeny. I downloaded the tree from birdtree.org and imported it into R using read.nexus. When I run the MCMCglmm it gives me the ...
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1answer
124 views

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 ...
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2answers
680 views

When the dependent variable and random effects 'overlap' in mixed effects models

I have added a new example here for clarity, see original question below Eg. I have 10 schools in 5 countries, ten students from each school is sampled. Prediction variables: student test marks for ...
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1answer
446 views

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 ...
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0answers
965 views

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 ...
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1answer
642 views

R: difference between Generalized Least Square and the Standard Least Squares with Cholesky

According to Wikipedia (source of all truth and knowledge...), http://en.wikipedia.org/wiki/Generalized_least_squares#Properties a weighted least square regression is equivalent to a standard least ...
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1answer
205 views

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 ...
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2answers
134 views

Phylogenetic tree with known historical sequences?

I have a multiple sequence alignment that I'm using to construct a phylogenetic tree. Usually, phylogenetic trees are constructed under the assumption that the input sequences are all from the present ...
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1answer
271 views

Significance of adjacency in correlation matrix with ordered variables

I am using the Discrete module in BayesTraits. I have a set of 1-9 serially homologous traits. For each pair of traits, I am comparing the 4-parameter model of independent evolution and the 8-...
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2answers
247 views

Three-dimensional phylogenetic tree “anchored” in a scatter plot

I have a phylogenetic tree and data on two traits, x and y. To present them, I would like to show the phylogenetic relationships while preserving the xy positions in trait space (i.e., convex hulls). ...
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2answers
379 views

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 ...
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0answers
195 views

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 ...
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2answers
964 views

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 ...
13
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2answers
541 views

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'...