Questions tagged [phylogeny]

for questions related to phylogenetic inference or phylogenetic comparative methods

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Can I compare if the outputs of different Generalized least-squares models are distinct in a statistically significant manner?

So I want to compare whether using human scoring or using modelling of avian vision for scoring significantly affects the correlation between rummage brightness and altitude. To do this, I am running ...
Birdman's user avatar
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12 views

What's the minimum number of clades for a valid phylogenetic regression?

I have a dataset with some phenotype measurements of a handful of birds (~ 150 individuals of ~10 species) and I would like to run a mixed effect model on this. Intuitively I would have tried to add a ...
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Incorporating Inverse Probability Weights in phylogenetic imputation

In Cortes et al. “Sample Selection Bias Correction Theory.” In Algorithmic Learning Theory, 5254:38–53. Lecture Notes in Computer Science. 2008., they describe how inverse probability weights can be ...
A. Bollans's user avatar
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22 views

Correct test for categorical response variable and multiple binary independent variables and a phylogenetic relationship

I have a dataset of ~2000 phylogenetically linked strains. These strains encode 2 binary traits and were isolated from 3 different environments (A,B,C). I want to test if encoding the traits makes ...
James's user avatar
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Difference between AICc delta<2 and AICc delta<4 in model.average

I am running a PGLS (Phylogenetic Generalized Least Squares) model selection using the library 'MuMIn' and its functions, see below the code: ...
Natalia31's user avatar
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188 views

Categorical model predictions with MCMCglmm

We are currently using the MCMCglmm package to study the phylogenetic and climatic distribution of deciduousness for a tropical flora. However, we have some difficulties with the prediction of a ...
Anais's user avatar
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1 answer
53 views

Ideas for binomial generalized linear mixed model with both phylogeny and random intercepts?

I've been struggling to find a description of an approach to a situation like mine or any R packages that seem capable of handling my needs. I have a large dataset (~80,000 rows) where my dependent ...
Brad Carlson's user avatar
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18 views

Distribution of genetic distances in a phylogenetic tree

I have a phylogentic tree of samples, and some samples belong to either of two groups. I'm trying to show that the mean pairwise distance of samples in one group is larger than the one from the other ...
raygozag's user avatar
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How does phylogenetic comparative analysis detect phylogenetic signal in the residuals?

A common thing that's stated in the phylogenetic comparative analysis literature is that phylogenetic signal is detected in the residuals of a regression, not in the traits/variables themselves. But ...
Picapica's user avatar
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Is it incorrect to calculate residuals directly from a phylogenetically-controlled linear regression?

I would like to calculate the residuals from a regression of log body mass and log brain mass, controlling for phylogeny. I originally used phylolm in R to run this regression, under a Brownian Motion ...
Picapica's user avatar
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2 answers
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Beta regression (proportions) with phylogenetic comparative analysis?

Is there a package in R that allows phylogenetic comparative analysis of proportion data (i.e. a beta distribution)?
Picapica's user avatar
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Why are prior distributions sometimes conditional probabilities?

I came across the following Bayesian equation in textbook of evolutionary biology: $f(t, r, \theta|X) \propto f(X|t, r, \theta)f(t|\theta)f(r|t,\theta)f(\theta)$ $f(X|t, r, \theta)$ is the likelihood ...
Namenlos's user avatar
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1 answer
469 views

Controlling for phylogeny in linear models

I have run a linear model to test for a relationship between two continuous traits in a sample of 50 taxa. I'm using the packages phylolm and caper in R (just to check they tell me the same thing, ...
Picapica's user avatar
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1 answer
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Build tree to calculate beta diversity

I am trying to calculate beta diversity using the UniFrac distance on my data, each sample having OTUs values. To calculate it, I saw it required building a tree with percentages that represented the ...
odyssey's user avatar
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279 views

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 ...
Carolina Karoullas's user avatar
1 vote
0 answers
55 views

Nested hypothesis vs conditional statement, (likelihood ratio tests)

I am performing likelihood ratio tests (LRTs). The data set is not critical its the purity of the statistics that are important, but this is (phylo)genetics data. I am examining (tree) hypothesis '1' (...
M__'s user avatar
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42 views

Analysing Percentage Data inc. Phylogenetic Bias?

I'm attempting to analyse a percentage / proportional (derived from count) response variable across several species, allowing for consideration of phylogenetic signal. I'd like to model this data ...
coffee_loving_narwhal's user avatar
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205 views

Phylogenetically controlled multivariate analyses with both continuous and categorical predictors

My goal is to test whether native and invasive plants overlap in multivariate trait space while accounting for phylogenetic relatedness, and simultaneously determining which environmental variables ...
Andrea's user avatar
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0 answers
102 views

How to choose between models with very small deltaAIC? (model averaging not an option)

My question is regarding selecting the best fitting model using AIC scores when the deltaAIC is very small between best models. I am running PMM's - Phylogeneticly-informed Mixed Models- using the ...
S.calyptes's user avatar
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151 views

Calculating UniFrac distance

So I am trying to calculate unifrac distance for my OTU table, which has about 3000 taxa, 300 samples. Now my phylogenetic tree only consider the most important 500 taxa. My questions are: Do I ...
Quy Xuan Cao's user avatar
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50 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 ...
SamPassmore's user avatar
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0 answers
209 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 ...
Marco Plebani's user avatar
2 votes
0 answers
57 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 ...
NatWH's user avatar
  • 539
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1 answer
571 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 ...
zozi9126's user avatar
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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 ...
Namenlos's user avatar
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905 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 ...
SlowLoris's user avatar
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0 votes
1 answer
107 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 ...
Jautis's user avatar
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2 votes
0 answers
376 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, ...
jsegrestin's user avatar
1 vote
1 answer
1k 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? ...
Kel's user avatar
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4 votes
1 answer
3k 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. ...
Diogo B Provete's user avatar
1 vote
1 answer
48 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. ...
SamPassmore's user avatar
1 vote
0 answers
59 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 ...
Jautis's user avatar
  • 618
1 vote
1 answer
2k 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 ...
AlexR's user avatar
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2 votes
0 answers
38 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 ...
SlowLoris's user avatar
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1 vote
0 answers
59 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 ...
Diogo B Provete's user avatar
1 vote
0 answers
635 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 ...
user3403745's user avatar
2 votes
1 answer
248 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 ...
AEM's user avatar
  • 151
1 vote
2 answers
2k 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 ...
AlexR's user avatar
  • 67
9 votes
1 answer
2k 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 ...
C_Z_'s user avatar
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2 votes
0 answers
1k 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 ...
user3834916's user avatar
1 vote
1 answer
980 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 ...
Xavier Prudent's user avatar
3 votes
1 answer
344 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 ...
forlooper's user avatar
1 vote
2 answers
168 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 ...
user1871183's user avatar
0 votes
1 answer
364 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-...
Charcha's user avatar
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2 votes
2 answers
416 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). ...
Bryan's user avatar
  • 1,190
5 votes
2 answers
571 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 ...
Nate's user avatar
  • 51
4 votes
0 answers
295 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 ...
Oritteropus's user avatar
2 votes
2 answers
1k 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 ...
user avatar
13 votes
2 answers
811 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'...
user1134516's user avatar