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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Cats, Dogs and Bears - how are they related?
What is the ancestral relationship between cats, dogs and bears?
I presume they are more closely related to one another than other paraphyletic clades of mammal.
Which came first?
What did their ...
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How to get conservation of vaccine candidates between hundreds of bacterial strains?
We have identified vaccine candidates via an ex-vivo RNA-seq approach. Next step would be to perform conservation of these candidates (about 20) between multiple bacterial strains (about 200). I would ...
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Are wild cats the same species as house cats?
I thought that the definition of species is "can interbreed"
From Wikipedia:
The wildcat (Felis silvestris) is a small cat found throughout most of
Africa, Europe, and southwest and central Asia ...
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Common Ancestry of ETCs and ATP Synthase complexes
Rickettsiales are widely regarded as the ancestor of eukaryotic mitochondria through endosymbiosis.
Cyanobacteria are widely regarded as the ancestor of eukaryotic chloroplasts through endosymbiosis.
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Family tree for edible plants?
I am looking for a family tree for plants, particularly veg / herbs / fruit.
Something similar to:
If it could be slightly less technical than all the Latin ...
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What are the statistical tools for distinguishing molecular analogy from homology?
Scientists have developed statistical tools that distinguish "distant" homologies from coincidental molecular homoplasy in extremely divergent sequences.
What are these tools?How are they used ?
I ...
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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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Goats are so fearless but sheep are not. Is there any genetic difference responsible?
As you see in the picture goats (not only wild goats) are so fearless, but I never saw any sheep do this. What is the source of this difference in behavior?
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Why is a slow worm not considered a snake?
Slow worms are considered lizards as opposed to snakes, both are reptiles. Now I get that there are traits that distinguish them (eye lids, ears ...). But snake species themselves vary already quite a ...
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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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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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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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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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What is the difference between orthologs, paralogs and homologs?
These three terms are often misused in the literature. Many researchers seem to treat them as synonyms. So, what is the definition of each of these terms and how do they differ from one another?
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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 "enrichment"...
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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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How can rooted and unrooted (phylogenetic) trees be distinguished from one another
I understand that rooted and unrooted phylogenetic trees 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 ...
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