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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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 ...
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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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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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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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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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Protostomia classification and characteristics

While working through a practice test for my final exam in an introductory organism biology course, I came across this question: Protostome characteristics include which of the following? a) a ...
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Machine-readable APG III trees?

Does anyone know where I can find a machine-readable version of the phylogenetic trees from APG III? I'm looking for something that contains the full tree structure, including unnamed branches. (i.e....
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63 views

What is the distribution of the expected number of lineages in a birth-death tree after time T?

I've been looking at The reconstructed evolutionary process by Nee et al. 1994 and they provide a number of equations dealing with the birth-death process, specifically the "reconstructed" birth-death ...
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What are phenetic analyses used for?

Phenetics (grouping of organisms based on similarity) used to be claimed to be an alternative to cladistics, but now it is widely accepted that phenetic analyses cannot be used to infer evolutionary ...
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How do I use BEAST for divergence time estimation in this case?

I am interested in using BEAST to find the divergence time estimates of species separations within a genus of frogs. The genus separated from a outgroup taxon I have chosen around 80 million years ago....
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What are the main principles of the Bacteriological Code?

Although the Bacteriological Code is an important guideline for taxonomists and microbiologists, describing the criteria for delineating species and higher taxa of the prokaryotes, I, and plenty of ...
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1answer
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Testing monophyly from per site log-likelihoods without optimising branch lengths

How can I obtain per site log-likelihoods for a topology against an alignment without optimising branch lengths? (which software can I use to do this) Per site log-likelihoods can be used for various ...
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Is “Monophyly” context dependent?

I am thinking about this thought experiment: Suppose we have three taxa which are grouped into the following tree: {{A,B},C}, clearly {B,C} is a paraphyletic group. But if A go extinct in the near ...
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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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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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Phylogenetic tree

I want to find the conventional phylogenetic tree of human, mouse, C elegans and drosophila, without all the other organisms. Do you know where can I get it? thanks, Noga
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Is there any program or website that allows me to create phylogenetic trees without having to insert an already created dataset?

I asked a similar question on Quora before, but did not get any useful answers as the program the one answerer suggested turned out to have the exact same problems as all others I have found so far. ...
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54 views

Question regarding when it's a homoplasy in a phylogenetic tree

If you have 2 organisms that both come directly from the same common ancestor on a phylogenetic tree, and that common ancestor does not have trait "x", is it possible for both of its direct ...
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115 views

What could explain discrepancies between dates provided by the fossil record vs. the molecular clock?

I am studying a mud snail genus called Ecrobia. For the Caspian species (Ecrobia grimmi), there is a discrepancy between dates provided by the fossil record and the molecular clock: First appearance ...
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Manipulating phylogenetic trees

I am looking to manipulate manually constructed phylogenetic trees (adding bootstrap values, markers to indicate trate loss/gain etc.) I came across a paper that used Macclade, however, this no longer ...
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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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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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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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How to create a phylogenetic tree (using Maximum Likelihood method) in newick format for a Multiple Sequence Alignment file in FASTA format?

The file size is really big (26.7 MB). So, I am unable to use the online web tools, as they cannot handle such large input data.
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Basic question about phylogenetic trees

The following is an illustration rom my book of the phylogenetic tree of 6 animal phyla (the red stuff is mine): I think what's causing some confusion is that there are no names/years at the circled ...
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126 views

In what does Genetic clustering and Cline sharpness differ?

They are both ways to measure divergence in species but I'm not understanding in what exactly the differ if both use hybrid zones and gene frequencies in the study.
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Question about phylogenies and DNA sequencing

I'm reading this web page which talks about phylogenies and DNA sequencing: https://bioinf.comav.upv.es/courses/biotech3/theory/phylogeny.html A certain sentence says, "If we consider dolphins and ...
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Finding phylogenetic distance between sequences?

I'm working on a piece of software that does comparative genomic analysis; and I found out in homology methods for functional annotation, it's preferable to pick the high scoring homolog from a ...
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Is there a way for POPart to accept indels in chloroplastidial genes?

I need to construct a network concerning chloroplastidial genes using POPart. My problem is that POPart does not know how to deal with indels. I have already coded them using SeqState (simple indel ...
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Metrics to analyze branch lengths in phylogenetic trees

I'm interested know about some basic metrics that could be used to discriminate trees based on their branch lengths. I know of branch length unaware topological/tree shape-based methods such as ...
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Is the Alpaca-CoV still the closest known relative of HCoV-229E?

From a 2017 paper that suggests the more distant (and common) origin of both HCoV-229E and HCoV-NL63 is in African bat coronaviruses, I see that the closest virus most similar to HCoV-229E is Aplaca-...
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Lineage inference based on N randomly partitioned copies of a gene

I am interested in reconstructing cell lineages based on the sequences of randomly partitioning plasmids. I can find lots of models to build lineages based on a single sequence (e.g. bacterial gene) ...
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Protein content in chemical composition of different phyla?

The protein content in the human body is roughly 15%, what are the percentages for other organisms? Bacteria, plants, fungi, protozoa, etc.
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What are the methods for detecting anagenetic versus cladogenetic change?

I'm new to the study of phylogenetics and am wondering if there are ways of identifying evolutionary changes that associate with cladogenetic events versus those that arise via anagenesis.
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How to reduce the number of sequences in a Multiple Sequence Alignment?

I have a Multiple Sequence Alignment, where there are around 5000 sequences. There also exists many sequences where, there are so much of non-sequenced regions (for instance, AU----CGGGCA--NNNNNNNNNN)....
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380 views

Why do tomatoes look so much like pomegranates? [closed]

The pomegranate fruit has been cultivated since ancient times, particularly in the Middle East and the Mediterranean. It has a hard outer rind, and inside are several chambers, each of which contains ...
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Why the SNPs from the earliest human haplogroups are missing in people outside of Africa if they are infact the descendants of it?

The SNPs M91, P97, M31, P82, M23, M114, P262, M32, M59, P289, P291, P102, M13, M171, M118 from haplogroup A and SNPs M60, M181, P90 from haplogroup B are missing in people without recent African ...
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Did cats evolve from monkeys ? or vice versa?

Did cats evolve from monkeys? or vice versa? How similar are the genes of cats and monkeys? What is the proof that they are related or that they are not related? Most monkeys climb in trees and ...
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Am I a lobe-finned fish? [closed]

I really wish this question only contained the title and tags, but the website forces me to write some text.
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Can anyone help me with these Biology evolutionary properties homework questions? [closed]

my teacher assigned these worksheet questions, they are ungraded, but he said something might come up on the test really similar to this so I really want to get all of them right. I am pretty ...

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