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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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43 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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63 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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155 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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136 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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459 views

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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27 views

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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61 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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71 views

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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225 views

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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24 views

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
109 views

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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2answers
34 views

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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1answer
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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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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
176 views

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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1answer
45 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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2answers
110 views

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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1answer
162 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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1answer
35 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
25 views

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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1answer
31 views

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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173 views

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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1answer
102 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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2answers
45 views

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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1answer
106 views

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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38 views

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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25 views

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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How to add taxa to a published tre file. What program to use? How to do it in Mesquite?

I need to add taxa to an already published tre file. (the Prum 2015 avian phylogeny). *For example if I wanted to add Western Gull to the tree (Larus occidentalis) knowing that Larus & Sterna are ...
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1answer
29 views

How to define ammonites?

I miss the definition of ammonite. In my opinion, many authors confuse the term "Ammonite" and "Ammonoid". Ammonoids (Ammonoidea) are large group of cephalopods including for example goniatites (...
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How many times have Ecdysozoans made the transition to land? [duplicate]

In my evolutionary course we were taught that land plants are a monophyletic group, the transistion to land happened only once. The same goes for the tetrapods within the vertabrates. However this ...
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19 views

Contructing phylogeny from an asymmetric distance matrix?

Is there any method for constructing a phylogenetic tree from a distance matrix which is not symmetric (i.e. the distance from A to be is not the same as the distance from B to A)? The distances I ...
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1answer
101 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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105 views

How would homologous recombination and mutations affect speciation?

I'm wondering how homologous recombination and mutations can affect how speciation can occur from one species (so that 2 will be created). I'm doing research and I found that different mutations and ...
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1answer
317 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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2answers
142 views

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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1answer
492 views

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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1answer
51 views

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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3answers
5k views

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 ...