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 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 ...
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2answers
123 views

Could homoplasy occur within a clade?

Consider the below phylogeny. taxon1 and 2 are sister taxa but: - share a brown color coat - differ from their closest common ancestor (light color coat) Is this a case of homoplasy (Analogous trait)?...
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72 views

How to choose the most appropriate measure of genetic distance

I am conducting a phylogeography study of a fish species and am trying to construct a phylogenetic tree to describe population structure and ancestry. I have constructed trees using various measures ...
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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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346 views

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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1answer
145 views

Phylogenetic Independent Contrasts with discrete traits

I understand that PICs are normally only used for continuous traits. However, on this how-to site (https://www.r-phylo.org/wiki/HowTo/Phylogenetic_Independent_Contrasts) there is mention of "Discrete ...
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3answers
13k views

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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1answer
102 views

What is the difference between phylogenetic tree “construction” and “reconstruction”?

When I look through papers, there are two terms Phylogenetic tree construction Phylogenetic tree "Re"construction What is the difference between phylogenetic tree "construction" and "reconstruction" ...
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1answer
92 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
439 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
52 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
715 views

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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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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2answers
54 views

How to get the file of a published phylogeny of a taxon

If an article has a published phylogeny, is it common to get the newick file with branch lengths from the authors? In order to do further research with the tree.
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46 views

phylogenetics and substitution ratios for positive selection [closed]

So very new to phylogenetics!. I've been scrambling and reading so much to get this done!!. I would like to see if one or more of the sequences I have (from a gene family) are under positive ...
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1answer
275 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
33 views

What is the best way to make a phylogeny from a list of genera?

All I have is a list of about 500 eukaryotic genera, and I need a neighbor-joining tree to show their relationship. I want to cast on top of this tree the loss of a particular enzyme. Is the best ...
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1answer
230 views

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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1answer
58 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

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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1answer
195 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
505 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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1answer
7k views

What is the difference between a species tree, a gene tree and a phylogenetic tree?

I have found websites and text books disagreeing over this. For example, Phylogenies are also known as “species trees”... http://biologos.org/blogs/dennis-venema-letters-to-the-duchess/evolution-...
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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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2answers
341 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
68 views

How can I tell if a certain marker is useful to date a phylogeny?

If I have a phylogenetic tree for a genus, how can I tell if a certain protein would be a good phylogenetic marker to use if one wanted to use a molecular clock to date the age of some speciation ...
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1k views

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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1answer
156 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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40 views

Merge NCBI and Ensembl data

Apologies if this is a really naive question, but I cannot figure out how to do this easily. Here is a related post regarding the best method to find orthologous genes of a species. Let's say I have ...
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2answers
1k views

Creating a Phylogenetic tree using DNA sequences [closed]

I was wondering given DNA samples, how can we create a phylogenetic tree? I mean I don't even want to have actual DNA sequence. Can I generate small samples, like reads of a length 100 or 1000 of ...
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59 views

Lampreys and the origin of certain brain structures

I'm not sure why, but I'd been under the impression that things like the optic tectum and basal ganglia developed post-2R (the double duplication of the genome ~1/2 Ga). Lampreys (as far as I'm aware)...
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50 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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1answer
62 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
1k views

Is brachydactyly due to mutation?

I have this so called "clubbed thumbs"also known as brachydactyly. It is of D-type. I searched for it on internet and found that it is a dominant inherited disease. But to my surprise,none of my ...
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1answer
97 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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1answer
113 views

Humans genetic/phylogenetic “next relative” in central Europe? [closed]

What species in central Europe in the phylogenetic tree shows the closest difference in time to the most recent common ancestor with Homo sapiens?
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3answers
59k views

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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1answer
669 views

The Perplexing Trilobite: What is the Evidence Supporting The Hypothesis That They are Not Crustaceans?

In the field of paleontology, one question that's really bugged me (er, no pun intended) of late is why the subphylum/class Trilobitomorpha/Trilobita is off on its own branch of the Arthropoda phylum, ...
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2k views

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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2answers
503 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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2answers
327 views

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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1answer
825 views

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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1answer
5k views

How to read cladograms/phylograms?

I understand the difference between cladograms and phylograms; the latter can show the evolutionary linkage over time. However, I am having trouble finding out which two organisms are most closely ...
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2answers
17k views

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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1answer
329 views

How to get taxonomic specific ids for kingdom, phylum, class, order, family, genus and species from taxid?

I have a list of taxids that looks like this: 1204725 2162 1300163 420247 I am looking to get a file with taxonomic ids in order from the taxids above: ...
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2answers
247 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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151 views

How to construct tumor phylogenetic tree?

I would like to know if anyone has tried any software that constructs tumor evolution trees where the trunks represent the common mutations and the private alterations are noted on each branch. I can ...
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0answers
131 views

What were the Neanderthal innovations?

At some point the neanderthal and modern human lineages diverged. I'm not sure what exactly their most common recent ancestor was (I see some sources suggesting homo heidelbergensis), but in any case ...
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85 views

Describing trait evolution across a very small phylogenetic tree [closed]

I am very new to phylogenetic comparative methods but I want to explore the evolutionary patterns of a number of quantitative traits I have across a small sample (5) of closely related species (...
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1answer
987 views

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?