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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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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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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Were there any terrestrial species in the ancestry of all crustaceans?
To the exception of woodlice, Crustaceans live in aquatic (marine or freshwater) environments. Crustaceans are arthropods which is an immensely diverse taxon. Many arthropods live in terrestrial ...
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DNA barcoding, querry regarding tree based (cluster) methods for species identification
I am working on success rate of DNA barcoding in identification of species using distance and tree based methods.
Regarding distance based method, I have used Adhoc and species identifier and ...
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Database of unique attributes of biological model systems
I am interested in deviations from standard eukaryotic biological mechanisms:
Sperm chromatin lacks nucleosomes, and are instead highly condensed by protamines. (most eukaryotic chromatin has ...
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Is there a single protostomate common ancestor that has pseudocoelomate structure?
I think about 15 years ago I saw a new classification system that placed Plathyhelminthes worms with Annelids and Mollusks into a superphylum (or other systematic clade) Lophotrochozoa, while ...
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How to interpret weighted Robinson-Foulds distance between phylogenies?
The Robinson-Foulds (RF) metric provides symmetric distance between two phylogenies as a sum of monophyletic groups present in one tree but not in the other. The normalised RF distance is given as $\...
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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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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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How to quantify the Abundance of a particular gene in Bacteria and Archaea?
For 16s rDNA metagenomic analysis, do I need to do the following steps?
DNA extraction-> Purification-> PCR amplification-> Clone -> Pick every single
colony-> PCR amplify -> Sequence -> ...
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Is the General Cirrate Octopus Form the Basalmost Octopoda Morphology?
The reason I ask this is due to the distinctive internal mantle shells of cirrina, of which the incerrata have stylets that are a remnant of the cirrate shell. Along with this, both cirrate octopuses ...
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How valid is Schwartz's criticism of molecular phylogenetics?
A proponent of the human-orangutan clade, Jeffrey Schwartz argues, in this paper [1], that molecular phylogenetics is largely based on a baseless assumption.
To sum up, according to him:
this type of ...
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Where can I find datasets containing large phylogenetic networks?
There are many datasets out there for phylogenetic trees, one can example can be found here.
However, I couldn't find something for phylogenetic networks. According to Wikipedia:
A phylogenetic ...
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What is the closest relative to odd-toed ungulate?
I have seen about 3 variation of phylogenetic tree about odd-toed ungulate and I don't know which one is really updated or outdated or which one have more backed up theory
First is odd-toed ungulate ...
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Estimating population divergence time with a single mitochondrial marker
Is it possible to estimate population divergence time with a single mitochondrial marker?
Here is additional information for my specific case:
Mitochondrial marker: Cytochrome Oxidase Subunit 1 (...
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How does one go from a couple of DNA sequences to a distance-matrix?
For a project we need to explain the subject of UPGMA.
We think we understand thee method itself but I fail to see how you go from a number of DNA-sequences to the distance matrix.
I understand ...
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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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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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Is Zayed et al.’s revision of Orthornavirae robust?
Zayed et al. (April 7, 2022) in Science “Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome” report several major hitherto-unknown Ribovirial phyla:
The two most ...
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Creating a phylogenetic tree from my selected publicly-available sequences (WGS) in NCBI
I'm currently writing a paper on the comparison of virulence genes for a group of bacteria. I got my data from publicly-available whole genome sequences in NCBI. Now, I want to create a phylogenetic ...
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Phylogenical differences with nuclear and mitochondrial DNA
This is a textbook question, I would like to verify my answers. According to the textbook it is possible to construct a phylogeny using nuclear and mitochondrial DNA and these trees to be different, I ...
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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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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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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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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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Recommendations for Books on Systematic Phylogenetics
I am a physics major and need to study systematic phylogenetics for a research project. Can someone please recommend at least one introductory and one advanced book, please?
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How do we logically infer large time scales using Molecular Clocks?
If molecular clocks are uses in genetics to determine the mutation rate of genes to estimate times speciation occurred between two or more life forms, are there genes that have mutation rates that we ...
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Converting branch length (durations) to absolute time in phylogenetic tree
I have a phylogenetic tree in Newick format with branch lengths in (millions of) years. Now I want to convert this into a chronogram with absolute time points (millions of years before present). Is ...
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Where is the position of PV92 locus?
The PV92 locus may contain an ALU- SINE that is used for phylogenetic reconstruction.
The literature mentions that PV92 is located at chr16 and is part of an intron.
However I can’t find anything on ...
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Advice on type of database and software for research on genetic diversity of crops
for a research project I am evaluating the potential of Robusta coffee genetic resources in the tropic region of Africa. Different ex-situ genetic lines will be mapped as well as chemical, ...
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Which is the best model organism to implement an evolutionary study for P.falciparum?
I have to study and implement some evolutionary statistics for P.falciparum. In your opinion and by your experience, which organism should I consider in order to take the orthologs to implement this ...
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how to estimate phylogeny without using DNA sequences?
I am new to bioinformatics, I am reading ‘Analysis of Phylogenetics Second Edition and Evolution with R’ from Emmanuel Paradis.
I can create phylogeny from DNA sequences, by first calculating the ...
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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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