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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How are zooids identified?
Physalia (Portuguese Man O'War) and other siphonophores are called colonial animals because despite their appearance as a complete organism, they are an organized colony of organisms called zooids.
I ...
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Why do many fruit trees have five-petaled flowers?
Peach, pear, apple, cherry, and many other fruit trees seem to have flowers comprised of five petals. Assuming there is no evolutionary advantage to confusing students of trees, is there a plausible ...
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What is the difference between orthologs, paralogs and homologs?
These three terms are often misused in the literature. Many researchers seem to use them as synonymous. So, what is the definition of each of these terms and how do they differ from one another?
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Is there a term to quantify how spread a character is on a phylogenetic tree?
Is there a term which can quantify how 'spread out' a particular character is on a tree? I want to distinguish between a character which is only restricted to a particular clade vs. a character that ...
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Parsimony (cladistics)
I don't understand how to sum the changes in a phylogenetic tree.
Here for example: http://www.med.nyu.edu/rcr/rcr/course/phylo-cladistic.html
How do you end up with 8 for the first and 9 for the ...
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How to get smallest subtree containing a set of nodes from BioPhylo?
I'm testing out various phylogenetic libraries in Python. I want to read in a Newick tree, then, given a list of taxa, generate the smallest tree that contains them all. This task is quite simple and ...
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Finding and Comparing Homologous Genes
I have a gene of of interest that I would like to compare between homologues. How does one go about finding a gene from known coding sequences across phyla? Afterwards I imagine I could do a Clustal ...
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Use of amino-acid sequences versus use of nucleotide sequences in phylogenetic analysis
Reading a paper about gene evolution, I see that they do phylogenetic analysis for bacteria using protein sequences. They take the method from another paper.
I can suspect that amino-acid sequences ...
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How to build S16 rRNAs phylogenetic trees?
Here is what I know so far:
Multiple copies are present in prokaryotes, but according to a paper by Lukjancenko el al.[1] it is enough to select the most similar ones.
There are stem regions in the ...
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phylogenetic analysis of gene enrichment?
Are there any tools to do phylogenetic analysis of gene enrichment? This is, I have a list of genes from an experiment performed in several species, with a z-score that can be described as ...
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How can rooted and unrooted (phylogenetic) trees be distinguished from one another
I understand that both are similar in structure
But how can they be easily identified as one or the other?
Is it simply based on the presence or lack of a named root (the root is identified as a ...
