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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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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Who are humans' closest relatives, after primates?
This question here addresses the controversy of whether humans are more closely related to bonobos or chimps.
My question is - which group of animals are are closest relatives, beyond primates? Or ...
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Did the Great Oxygenation Event also cause a mass extinction?
It's usually assumed that the Great Oxidation Event around 2.3 billion years ago caused a great extinction of anaerobic life on earth. However, I was reading Nick Lane's book, The Vital Question, and ...
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Why are turtles classified as reptiles and not amphibians?
I understand that turtles are reptiles because like all reptiles, they have scales on their body. But turtles (specifically sea turtles) live on both land and water, very much like amphibians. Also, ...
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Why would a 2019-nCoV protein sequence in the NCBI database match a protein submitted in 2018?
There seems to be a bit of a conspiracy theory brewing over some data in the NCBI database, and I don't have the necessary knowledge to make sense of it.
It basically goes like this:
Go to NCBI ...
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Is there a downloadable list of all species along with their traditional classification?
I'm looking for a downloadable list of all known (or better said, online documented) species in this straightforward format, as an example the European Frog:
Kingdom: Animalia
Division: Chordata
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Branch length in phylogenetic trees
I know this is a very basic question, but it is not too clear to me what is the unit of measure of branch length in phylogenetic trees.
I have come to understand that it is usually expressed in number ...
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Sequence evolution simulation tool
I'm looking for a tool to simulate sequence evolution given a specific mutation model and birth-death model. I'm aware of tools and packages like INDELible, Seq-Gen and PhyloSim, but they simulate ...
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The almost extinct dinosaurs
Dinosaurs split into "lizard-hipped" and "bird-hipped" dinosaurs. Of these two groups, only the "lizard-hipped" (Saurischia) survived (these names are backwards).
Of ...
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Darwin's first sketch of a phylogenetic tree
Coming from Darwin's notebook this first sketch of a phylogenetic tree became one of the most emblematic image from Darwin's work.
I have a hard time to read what is written on it.
What is written ...
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Regarding the kingdom Animalia, which phylogenic tree is more common: Molecular Comparisons or Body-Plan Grades
In the picture below, which I obviously do not own:
it depicts two different phylogenic trees, one which is based on molecular comparisons and another one which is based on body-plan grades. My ...
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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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If we sequenced the genome of every species, would all phylogenies agree?
The Tree of Life is still up for debate. Most of this debate seems to be due to a lack of genomic information, but that deficiency is decreasing rapidly with advances in technology and sequencing ...
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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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The best free and most up to date phylogenetic tree on the internet?
I found phylogenetic tree in wikipedia is lacks of accuracy. It actually confusing with versions. Some terms was not scientifically accurate with dna analysis anymore
So are there anyone know where ...
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Evidence & discussions of hard polytomy
Phylogenetic trees with >2 branches on a node are polytomic, and polytomy can appear on trees for two reasons. Firstly a lack of information in the data prevents proper resolution within a clade, ...
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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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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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What is the function of multiple nuclei in syncytial cells?
What is the function of multiple nuclei in syncytial cells specially in protists with cilia? Is multiple nuclei a special characteristics of only ciliated cells?
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Does anyone know good software for producing tanglegrams?
I'm trying to look at relationships between parasite and host phylogenetic trees. I have done a bit of searching for software with which to do this, and I have tried using Dendroscope and TreeMap, but ...
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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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How should I put a large phylogeny into a scientific paper?
I've been trying to put a phylogeny tree into a scientific paper. This tree includes ~220 species, which is too too large for one page for journal articles (Letter or A4 size). But in my paper it is ...
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Phylogenetics and the Tree of Life
As far as I understand, evolution is nowadays pretty much analyzed through phylogenetic trees, that is cladograms. These are constructed using the available records and taking some key structures and ...
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Why cannot there be multiple sources for same species origins?
We often associate Africa as the geographical location of the origin of humans. Why cannot there exist multiple geographic locations of origin (given same environmental conditions)?
The same ...
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Which phylum appeared most recently
I'm aware that our earliest records of many major animal and plant phyla come from the Cambrian or Precambrian periods, and I'm also vaguely aware of some of the objections raised with general concept ...
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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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Why do fetuses have membranes between fingers and toes?
Are the membranes present between the fetal fingers and toes a remainder of the phylogenetic evolution, or just a way organs do grow most easily?
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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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Did Carl Linnaeus ever name a species he never saw?
According to this post Carl Linnaeus named more than 13,000 species which is definitely quite impressive. If we consider a 50 years career it makes about 5 species per week! It would feel impressive ...
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Is there a name for this phenomenon described in "Phylogenies and the Comparative Method"?
The figures below are from Felsenstein's paper "Phylogenies and the Comparative Method". I was wondering if there was a specific name for this effect where there is an apparant correlation that is ...
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Has the most recent common ancestor of all living birds lived after dinosaur mass extinction?
I wonder if one or more phylogenetic threads of dinosaurs survived the mass extinction.
In other words, are all living birds equally related to any given ancient dinosaur, or do some birds relate ...
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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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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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What are the units of Phylogenetic Independent Contrasts (PICs)
PICs are a popular phylogenetic comparative method and I was wondering what units the actual contrasts are in. I want to say they are unitless but I am not entirely sure.
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Visualisation of phylogeography
I am working on phylogeography on one model species and I am a beginner. You can imagine one species that came on locality more than 5 mya (million years ago). It was a good environment, so the ...
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Living intermediate species?
Hypothetical question regarding three animals 'species' {A, B, C}.
Are there any examples in nature where {A and B} cannot regularly produce viable offspring, however {A and C} and {B and C} can ...
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In the NCBI Taxonomy tree what does "no rank" mean?
NCBI publish their taxonomy browser at https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi
While many taxa have a well defined rank (Order, Family, Genus etc..), some of them have "no rank".
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What ways are there to determine how big genera are?
I want to look at genera as a whole, across the animal kingdom to determine the range of sizes of genera. I have examined species richness and genetic diversity (pairwise distance from sequence data ...
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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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Best methodology to compare computed phylogeny tree with taxonomy?
I have computed a phylogenetic tree using an alignement of sequences, and I would like to :
Compare it to the "known" taxonomy (uniprot/ncbi which I know is not
the most up to date one) and extract a ...
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If evolution is a gradual and continuous process, how can we say humans came about 200k years ago? What is so special about that point in time?
It just seems arbitrary to me to say "ok, now THIS is officially a human" when you could look at its parents and find no noticeable differences. At no point in the line of my ancestral history is ...
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How do I know whether or not a nuclear gene is single copy?
As a part of a phylogenetic study, I need to find a nuclear gene that meets the following requirements:
Single copy gene;
Highly variable gene;
Gene longer than 400 bps;
Gene that gives information ...
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What is the most recent well-attested common ancestor of chimpanzees and humans?
Humans and chimpanzees are related and thus have a most recent common ancestor. Of course pinning down this precise point is essentially impossible, so I'm interested in close ancestors of this most ...
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Null distribution of Blomberg's K
I've noticed different functions in different R libraries have different ways of assessing significance for Blomberg's K. For instance, picante's phylosignal looks at a distribution of PIC variance ...
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Phylogenetic method to detect shift in mean of continuous variable
I am currently working on a project where I study the change of a continuous morphological variable with body size (measured as body weight) across diverse taxa (insects, spiders, lizards, frogs). In ...
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What is the best argument for maximum parsimony method in phylogenetic tree construction?
Beside the fact that maximum parsimony is computationally cheap, what other good arguments are there for it? Is there any model behind this principle? Why would one expect this principle to provide ...
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Construct Phylogeny form Edgelist
I am working on large scale biodiversity simulations and have collected a lot of data on simulated phylogenies. I have a list of child-parent edgelist species in the form:
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Why is traditional rank based taxomomy considered by some as logically inconsistent with phylogenetic knowledge?
Following is from wikpedia:
Under the traditional nomenclature codes, such as the International
Code of Zoological Nomenclature and the International Code of
Nomenclature for algae, fungi, and ...
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What is the difference between these terms: clade, monophyletic group and taxon?
Wikipedia definitions for these terms are pretty similar:
http://en.wikipedia.org/wiki/Clade
http://en.wikipedia.org/wiki/Monophyletic_group
http://en.wikipedia.org/wiki/Taxon
They sound like the ...
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Why is the null hypothesis of trait evolution Brownian motion?
Many models of continuous trait evolution assume that traits evolve according to Brownian motion. What is the biological or physical basis for this choice?
I realize there are models that do not ...
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