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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35 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 ...
4
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2answers
29 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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44 views

Did the Great Oxygenation Event also cause a mass extinction?

Its usually assumed that the Great Oxidation Event around 2.3 bya caused a great extinction of anaerobic life on earth. But as I was reading Nick Lane's book, ...
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1answer
55 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 ...
29
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2answers
8k 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 ...
4
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1answer
46 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
69 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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31 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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75 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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23 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
111 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?
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1answer
43 views

Why are vertebrae, specifically, so important in classification?

A fundamental level of animal classification is the distinction between vertebrates and invertebrates. The vertebrata are, arguably, often classified as higher life forms than the invertebrata. But ...
3
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2answers
84 views

How to name a case of convergent evolution where the same mutation is involved in both lineages?

Definition of Convergent evolution - from Wikipedia > Convergent Evolution Convergent evolution is the independent evolution of similar features in species of different lineages. Convergent ...
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1answer
30 views

Choice of Molecular markers to carry out molecular phylogenetics

For evolutionary analysis of different individuals within a population, the preferable molecular markers are non-coding regions of mitochondrial DNA. My question is that why they are used what is the ...
4
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1answer
43 views

Best methodology to compare computed phylogeny tree with taxonomy?

I have computed a phylogenetic tree using an alignement of sequences, and I would like to : Compare it to the "known" taxonomy (uniprot/ncbi which I know is not the most up to date one) and extract ...
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1answer
80 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.
2
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1answer
77 views

What are some useful (starter) metrics to use on phylogenetic trees?

Im doing a computational biology project in which I simulate evolution under different inheritance rulesets and I am generating phylogenetic trees (beautifully visualised in python with ete3, which I ...
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0answers
37 views

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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0answers
28 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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0answers
19 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. ...
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0answers
60 views

What genetic link would cause a human to have a extra vertebra? [closed]

Most people have five vertebrae in their lumbar (lower back) region, which are named L1 to L5. However, some people possess an additional lumbar vertebra located below the L5. This extra vertebra, ...
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0answers
11 views

Which should I use the genes of the mitochondrial DNA? [closed]

What should I use for phylogenetic analysis of the genes of the fungus? Which should I use the genes of the mitochondrial DNA?
2
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2answers
42 views

How do I generate a phylometric tree given species names?

I have a list of species. I want to put those names into a tool and get back a visualized tree that includes names of shared order, suborder, family and genus. Is there an existing tool that does this ...
2
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1answer
47 views

What contribute to the variation of protein sequence across different species and how do they influence?

What contribute to the variation of protein sequence across different species (e.g. phenotype, environment, evolutionary pressure) and how do those factors contribute to the variation? I have tried ...
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1answer
46 views

Does the new virus tree of life change their position between living and non-living things?

Viruses still do not fit the criteria of living or it's simplest form (the living cell), why would some say that the new virus tree of life makes it more closer to life? Aren't mitochondria in a point ...
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1answer
89 views

Bootstrap question

I have a question about bootstrapping: The way that I understand it is that each number represents how well a given node is supported. So in the diagram presented, we can see that the ...
5
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2answers
1k views

Living intermediate species?

Hypothetical question regarding three animals 'species' {A, B, C}. Are there any examples in nature where {A and B} cannot regularly produce viable offspring, however {A and C} and {B and C} can ...
2
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0answers
41 views

What program was used to create this visualization of a neighbor-joining tree?

I know there are many programs out there to visualize neighbor-joining trees in phylogenetics. I have a tree in Newick format. Does anyone recognize the features of this image as coming from a ...
2
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1answer
127 views

Is the fixation rate always equal to the mutation rate for neutral alleles?

Background A classical result of population genetic is that the rate of fixation of netreual alleles is the mutation rate $\mu$. The reason is that each generation $PN_e\mu$ mutations enter the ...
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2answers
126 views

Construct Phylogeny form Edgelist

I am working on large scale biodiversity simulations and have collected a lot of data on simulated phylogenies. I have a list of child-parent edgelist species in the form: ...
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0answers
28 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 ...
2
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1answer
256 views

Did modern alligators and caimans come from prehistoric crocodiles?

I know that crocodilians have been here since the time of the dinosaurs. I also know that crocodiles came first. But alligators have been here for a good 37 million years. Did alligators come from ...
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1answer
70 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 ...
5
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2answers
53 views

Is there a name for this phenomenon described in “Phylogenies and the Comparative Method”?

The figures below are from Felsenstein's paper "Phylogenies and the Comparative Method". I was wondering if there was a specific name for this effect where there is an apparant correlation that is ...
3
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1answer
112 views

What does the hominin phylogenetic tree look like?

I'm no biologist, but I'm curious what the rough phylogenetic tree looks like for Hominin. Could you create a rough sketch that includes: Homo rudolfensis Homo ergaster H. georgicus H. antecessor ...
6
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1answer
246 views

Sequence evolution simulation tool

I'm looking for a tool to simulate sequence evolution given a specific mutation model and birth-death model. I'm aware of tools and packages like INDELible, Seq-Gen and PhyloSim, but they simulate ...
5
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2answers
64 views

What ways are there to determine how big genera are?

I want to look at genera as a whole, across the animal kingdom to determine the range of sizes of genera. I have examined species richness and genetic diversity (pairwise distance from sequence data ...
5
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2answers
443 views

Why cannot there be multiple sources for same species origins?

We often associate Africa as the geographical location of the origin of humans. Why cannot there exist multiple geographic locations of origin (given same environmental conditions)? The same ...
6
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1answer
98 views

What are the units of Phylogenetic Independent Contrasts (PICs)

PICs are a popular phylogenetic comparative method and I was wondering what units the actual contrasts are in. I want to say they are unitless but I am not entirely sure.
2
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1answer
387 views

Evolutionary distance between Canidae, Felidae, and Rodentia

Comparing the families Canidae and Felidae, which have the shorter evolutionary distance to the order Rodentia? Less sophisticatedly put, are cats or dogs more related to rodents?
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2answers
1k 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 ...
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0answers
15 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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1answer
153 views

What makes a good phylogenetic tree?

How can one improve a phylogenetic tree? If one was to make the 'golden standard' of phylogenetic trees what features would it have? Would it be highly reliable, well resolved etc? What other features ...
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1answer
253 views

What does saying a phylogenetic tree is 'well resolved' mean? [closed]

I'm not sure what 'resolution' means in the context of phylogenies.
5
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105 views

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 ...
3
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0answers
35 views

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 -> ...
3
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2answers
200 views

What proves that speciation is a pairwise process? [duplicate]

I have been asked this questions by many biology students and even non-biologist without a pretty straightforward answer to give. We are quite accustomed to phylogenetic trees where a common ancestor ...
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0answers
68 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 ...
4
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2answers
249 views

Phylogenetics and the Tree of Life

As far as I understand, evolution is nowadays pretty much analyzed through phylogenetic trees, that is cladograms. These are constructed using the available records and taking some key structures and ...
1
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0answers
19 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 ...