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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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 ...
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1answer
43 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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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 ...
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1answer
40 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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0answers
53 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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1answer
234 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 ...
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2answers
66 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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28 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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107 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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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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22 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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2answers
78 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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41 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 ...
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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
39 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
79 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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2answers
115 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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32 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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1answer
73 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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2answers
41 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 ...
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24 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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17 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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1answer
7k views

Cats, Dogs and Bears - how are they related?

What is the ancestral relationship between cats, dogs and bears? I presume they are more closely related to one another than other paraphyletic clades of mammal. Which came first? What did their ...
2
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1answer
226 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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2answers
439 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 ...
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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?
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1answer
45 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
87 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 ...
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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 ...
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39 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 ...
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1answer
121 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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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 ...
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1answer
96 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.
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1answer
66 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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1answer
343 views

Regarding the kingdom Animalia, which phylogenic tree is more common: Molecular Comparisons or Body-Plan Grades

In the picture below, which I obviously do not own: it depicts two different phylogenic trees, one which is based on molecular comparisons and another one which is based on body-plan grades. My ...
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52 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 ...
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1answer
107 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 ...
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63 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 ...
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2answers
1k views

Why is a slow worm not considered a snake?

Slow worms are considered lizards as opposed to snakes, both are reptiles. Now I get that there are traits that distinguish them (eye lids, ears ...). But snake species themselves vary already quite a ...
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1answer
369 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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983 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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14 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
137 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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235 views
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104 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 ...
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34 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
199 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
63 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 ...
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2answers
248 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 ...
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1answer
69 views

What is the most recent well-attested common ancestor of chimpanzees and humans?

Humans and chimpanzees are related and thus have a most recent common ancestor. Of course pinning down this precise point is essentially impossible, so I'm interested in close ancestors of this most ...