Questions tagged [phylogenetics]

A sub-discipline of evolutionary biology which involves the study of evolutionary relatedness between different organisms based on their molecular and morphological features.

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26 views

How does one go from a couple of DNA sequences to a distance-matrix?

For a project we need to explain the subject of UPGMA. We think we understand thee method itself but I fail to see how you go from a number of DNA-sequences to the distance matrix. I understand ...
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598 views

How to interpret weighted Robinson-Foulds distance between phylogenies?

The Robinson-Foulds (RF) metric provides symmetric distance between two phylogenies as a sum of monophyletic groups present in one tree but not in the other. The normalised RF distance is given as $\...
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How detailed a construction of the family tree of known human fossils do we have?

For the sake of this question, by "human" I mean Hominina. The best I could find is this, which isn't very detailed. Of the dozens of paleospecies we'd seek to link up, do we have a more detailed tree ...
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Phylogenetic tree with tagging

I'm working for a software company. For one of our projects, we need software to cluster nodes in a phylogenetic tree by a certain kind of similarity and give them a user-defined tag. Preferably, the ...
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51 views

Metazoan branching: Placozoa or Porifera?

Of Placozoa and Porifera, which branched off first? (Conversely: which are closer cousins to us?) I've heard both suggested as our most distant cousins with bodies, so was wondering which ordering is ...
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255 views

Infer gene frequency within a species over time

I was reading Karlsson et al. (2014) and I came into this: A selected variant that increases rapidly in frequency in the past ~250,000 years can be detected as an unusual reduction in genetic ...
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383 views

Why is marginal reconstruction “more correct” than joint reconstruction in some cases?

When reconstructing the ancestral states on a phylogenetic tree given the states at the tips, there are a number of methods for performing the reconstruction. This question is about marginal and joint ...
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63 views

What program was used to create this visualization of a neighbor-joining tree? [closed]

I know there are many programs out there to visualize neighbor-joining trees in phylogenetics. I have a tree in Newick format. Does anyone recognize the features of this image as coming from a ...
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3answers
182 views

Definition of species - location of gene

I know that species have been classified on basis of reproduction , DNA similarity , niche, etc. Has there been a classification based on locus of genes ? What are the drawbacks/shortcomings of ...
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3k views

Classification and differences between homologous, homoplastic, analogous, derived and ancestral traits?

My question is contextualised for basic phylogeny knowledge. Here is my understanding: similar or identical traits between any two species, at the basic level, can be either homologous, meaning the ...
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1answer
223 views

Are “constraint trees” in phylogenetic analysis cheating? How can I correctly use them?

How do phylogenetic experts evaluate results which use constraint trees? Are there examples in the literature where phylogenetic experts detail how they use constraint trees? Here is my problem. I ...
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1answer
1k views

What makes a good phylogenetic tree?

How can one improve a phylogenetic tree? If one was to make the 'golden standard' of phylogenetic trees, what features would it have? Would it be highly reliable, well resolved etc? What other ...
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Finding different Proteins with same function [closed]

Could you help me about finding two different proteins that coming from different ancestors, perform same function? Thank you
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23 views

computing relative synonymous codon usage from a coding sequence alignment while accounting for phylogenetic inertia?

I would like to compute the relative synonymous codon usage (RSCU) from coding sequence alignments. But since the coding sequences from an alignment are not independent realization, the statistics (...
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1answer
1k views

Bootstrap values

What do the bootstrap values indicate about the relationship between the species? I'm working on Mega program but I don;t understand what bootstrap value means in simple terms and also what does it ...
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1answer
429 views

Bootstrap question

I have a question about bootstrapping: The way that I understand it is that each number represents how well a given node is supported. So in the diagram presented, we can see that the "Seal-Bear-Cat" ...
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2answers
81 views

Could alpha-numeric taxonomy of fungi make things simpler?

Please feel free to construe this question broadly--I don't see why the question would not apply to branches of biology other than mycology. If the goal of taxonomy is to create classification of ...
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1answer
2k views

Does a fully-resolved phylogenetic tree have to be dichotomous?

I read that wherever there is polytomy there is an unresolved pattern of divergence. I don't understand why this is so. When divergence takes place, is it necessary that there will be division into ...
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1answer
54 views

How to determine the number of parameters in a phylogenetic model?

I want to calculate the AIC for a phylogeny that I inferred via maximum likelihood. To calculate the AIC I need to know the number of parameters in the model. But how do I determine this?
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The parts of the phylogenetic nomenclature that need to be “unique”

I am not quite sure I have sorted through the diversity of approaches to nomenclature, but I had a specific question to help clarify what is going on. Basically I am just wondering what needs to be ...
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53 views

MLE estimation with Mk model in ape or phangorn?

When doing MLE with the R package ape or phangorn, is it possible to set the substitution model to Mk? If so, how does one do this?
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1answer
107 views

More informative phylogenetic trees

In the presentation of phylogenetic trees, the geometric shape of the trees often seems somehow arbitrary and is more driven by aesthetics than by informative reasons. But wouldn't it make sense to ...
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1answer
486 views

Which nucleotide as start point for maximum parsimony?

Background Maximum parsimony is used to build an evolutionary tree by choosing the "simplest" one. I see a lot of examples about how this should be done. For example: Question However it's not clear ...
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1answer
53 views

Infer distance since duplication from tree?

Question I have a really simple question, but I'm not able to figure it out. I made a tree (using BLOSUM62). Here is a part of the tree: How can I calculate the distance till the duplication ...
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1answer
298 views

Calculating ultrametric distance matrix

I am fairly new to phylogenetic analysis, so I'm guessing this is a basic question. If I have a bunch of aligned sequences, and I ultimately only care about pairwise distance (e.g. for calculating ...
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1answer
59 views

Which algorithm to find the evolutionary relation of 5 sequences?

After Multiple Sequence Alignment (MSA), data sets are produced on which models of evolution are used. I've seen in books that if there is strong similarity between the sequences then Maximum ...
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1answer
109 views

Does the minimum spanning tree tell us anything useful about evolutionary ancestry?

Question migrated from bioinformatics stackexchange due to lack of interest. I'm new to bioinformatics and have been reading through a bioinformatics book, and it seems calculating a phylogenetic ...
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Are phylogenetic tree construction algorithms any different than general clustering algorithms?

I suspect the answer is no. But I don't know enough to be sure that that is the case. Of course phylogenetic tree construction uses biological knowledge, e.g special distance metrics, but does it ...
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1answer
107 views

How would I represent this on a cladogram?

So, right now I am making a cladogram (More of a dendrogram) for a kingdom of fictional species, and I'm not exactly sure how to represent a certain relationship. Let's say that the oldest class in ...
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1answer
73 views

Minimum number of clades needed to partition Vertebrates while maintaining Birds, Mammals, and Amphibians as distinct clades?

At school I was taught the Linnaean view of vertebrate life - that vertebrate animals consisted of 5 distinct groups: mammals, birds, reptiles, amphibians, fish. I learned later however that this was ...
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95 views

How to use a published phylogenetic tree?

I would like to know how should I use a phylogenetic tree from an already published article, to put it on my own article so I can analyze the evolution of a trait. Is there any software I can use, or ...
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1answer
116 views

Tools that take a kinship matrix for phylogenetic decorrelation

I have plant genotypes that have been classified as Invasive, Wild or Domestic. I am trying ...
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537 views

How to build a phylogenetic tree without an outgroup? [duplicate]

I have whole genome aligned sequences of four beetle populations of same species. I wish to construct a phylogenetic tree with the four. However, I am unable to find a suitable outgroup of the species,...
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2answers
371 views

User friendly phylogenetic tree editing software

Background: I have Hackett 2009 (from birdtree.org) phylogenetic tree and I need to reorder it according to Prum 2015. I also work only with some species relevant to my project, not the entire tree. ...
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1answer
161 views

Phylogenetic algorithms: How to interpret multiple ML trees from the same dataset?

There's still something that confuses me about how many of these algorithms work, and how results are presented in the literature. Let's consider a Maximum Likelihood based algorithm like MrBayes or ...
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1answer
63 views

How do you call the species that gives its name to a upper-level clade?

Just a silly question: I don't remember how the species giving its name to an upper-level clade is called. e.g. the name of family Canidae derives from Canis lupus You could say it is the "name-...
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1answer
98 views

clades on a tree - biopython

Suppose we have an alignment. When a phylogeny tool (PhyML in this case) is used on this alignment, a tree consisting of 5 clades is returned. The thing is: suppose we have this alignment on a web ...
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2answers
526 views

Simple computational biology project for AP Biology class. Ideas? [closed]

Our teacher assigned us a project to do with an extremely open-ended prompt and it should be completed within a month. I was planning on doing something related to computation and evolution in terms ...
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1answer
84 views

Does the new virus tree of life change their position between living and non-living things?

Viruses still do not fit the criteria of living or it's simplest form (the living cell), why would some say that the new virus tree of life makes it more closer to life? Aren't mitochondria in a point ...
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What does saying a phylogenetic tree is 'well resolved' mean? [closed]

I'm not sure what 'resolution' means in the context of phylogenies.
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166 views

Is there a rule for the annotation of the basepair or gene locus origin in bacterial genomes?

Since all bacteria have one circular chromosome, there is no designated origin to start the systematic gene locus numbering. Therefore, what is the rule to start the numbering at a particular point (i....
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Phylogenical differences with nuclear and mitochondrial DNA

This is a textbook question, I would like to verify my answers. According to the textbook it is possible to construct a phylogeny using nuclear and mitochondrial DNA and these trees to be different, I ...
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How valid is Schwartz's criticism of molecular phylogenetics?

A proponent of the human-orangutan clade, Jeffrey Schwartz argues, in this paper [1], that molecular phylogenetics is largely based on a baseless assumption. To sum up, according to him: this type of ...
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Is there a measure for degree of reticulation in a phylogenetic network?

When working with phylogenetic networks, how does one talk about reticulate (i.e., web-like) the branches are? Is there a standard measure of this?
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Have traditional categories such as phylum, class, genus, been dispensed with in modern taxonomy?

Looking through the one zoom and EOL projects I see no reference to such categories.
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Example Clade Names in PhyloCode

After looking through the PhyloCode, the only thing I found that looked like an example was in Article 9, Chapter 4: A node-based definition may be abbreviated "<A&B" or "<A&B&C&...
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Are there any open phylogenetic projects that don't require coding to make a contribution

I am stay at home learner, not pursuing education formal education and currently doing a part time job. I've however completed masters in biotechnology and I'm studying to pursue PhD in molecular ...
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how origin of koi carp is different from goldfish

where did koi-carp originate? how are they different from goldfish? Wikipedia say that goldfish originated by genetic mutation but what about koi-carps?
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Is it possible for parsimony to estimate more state changes than stochastic character mapping

I'm mapping states (geographic regions) onto a phylogeny to estimate the number of transmissions between countries. I'm using two methods, stochastic character mapping implemented in Phytools and ...
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What is the difference between phylogroup and subclade? [closed]

Looking for clarification in terminology, examples would be greatly appreciated! Not sure how this is off-topic. It is a general question about the difference between biological concepts defined in ...