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 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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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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Controlling for phylogenetic signal - what is statistically appropriate?

I am currently collaborating with a fellow PhD student. We are both in the same Biology department, but my collaborator is more of a natural historian, so I am handling the statistical side of things. ...
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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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An online tree of life with extinct species present?

There are awesome online phylogenetic trees such as OneZoom. But they all only list living species. I want to see dinosaurs between birds and crocodiles. I wanna see that humans are reptiliomorphs ...
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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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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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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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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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What is the minimum number of clades necessary to partition Vertebrates while maintaining the classical groups of Birds, Mammals, and Amphibians?

At school I was taught the Linnaean view of vertebrate life - that vertebrate animals consisted of 5 distinct groups: mammals, birds, reptiles, amphibians, fish. I learned later however that this was ...
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What does it mean for there to be no correlation between phylogenetic independent contrast?

I am testing the correlation between two physiological parameters in plants using the pic function in R. I am a bit stuck on the interpretation of the phylogenetic independent contrast (PIC). Without ...
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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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What is the technical term for when a clade on a phylogenetic tree does not have an extended branch? (see image)

As we see with ZCA2, ECA2 & XCA2 these branches are compressed and do not extend as TCA does. Is there a technical term for this and what usually causes it?
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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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Why is marginal reconstruction “more correct” than joint reconstruction in some cases?

When reconstructing the ancestral states on a phylogenetic tree given the states at the tips, there are a number of methods for performing the reconstruction. This question is about marginal and joint ...
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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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How to determine the number of parameters in a phylogenetic model?

I want to calculate the AIC for a phylogeny that I inferred via maximum likelihood. To calculate the AIC I need to know the number of parameters in the model. But how do I determine this?
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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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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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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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Does the minimum spanning tree tell us anything useful about evolutionary ancestry?

Question migrated from bioinformatics stackexchange due to lack of interest. I'm new to bioinformatics and have been reading through a bioinformatics book, and it seems calculating a phylogenetic ...
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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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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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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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How evolutionarily conserved are UTRs?

Coding sequences of genes have a certain degree of evolutionary conservation, so that comparisons based on sequences (BLAST, HMMER etc) can be informative. Generally speaking, the more two species are ...
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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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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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The phylogenetic definition of the clade Dinosauria

Up until two years ago the clade of Dinosauria was defined as all the descendants of the most recent common ancestor of Triceratops and birds. From Wikipedia: Under phylogenetic nomenclature, ...
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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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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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Are phylogenetic tree construction algorithms any different than general clustering algorithms?

I suspect the answer is no. But I don't know enough to be sure that that is the case. Of course phylogenetic tree construction uses biological knowledge, e.g special distance metrics, but does it ...
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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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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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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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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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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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Draw simplified phylogenetic tree for kids

I need to draw simple, phylogenetic tree for kids lecture. I am looking for an online tool where I can enter organisms (e.g., human, wasp, fungus) and get figure of a phylogenetic tree. Tree should ...
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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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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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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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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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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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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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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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The protostome/deuterostome distinction and why it is important

As I unerstand it, at some point an embryo develops a hole; this hole continues to punch through, and eventually makes an opening at the other side of the embryo. If the original hole becomes the ...
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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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The parts of the phylogenetic nomenclature that need to be “unique”

I am not quite sure I have sorted through the diversity of approaches to nomenclature, but I had a specific question to help clarify what is going on. Basically I am just wondering what needs to be ...