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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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 ...
24
votes
3answers
66k views

What is the difference between orthologs, paralogs and homologs?

These three terms are often misused in the literature. Many researchers seem to treat them as synonyms. So, what is the definition of each of these terms and how do they differ from one another?
14
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3answers
2k views

Why are turtles classified as reptiles and not amphibians?

I understand that turtles are reptiles because like all reptiles, they have scales on their body. But turtles (specifically sea turtles) live on both land and water, very much like amphibians. Also, ...
11
votes
1answer
996 views

Darwin's first sketch of a phylogenetic tree

Coming from Darwin's notebook this first sketch of a phylogenetic tree became one of the most emblematic image from Darwin's work. I have a hard time to read what is written on it. What is written ...
9
votes
5answers
879 views

Finding and Comparing Homologous Genes

I have a gene of of interest that I would like to compare between homologues. How does one go about finding a gene from known coding sequences across phyla? Afterwards I imagine I could do a Clustal ...
9
votes
3answers
827 views

Why do many fruit trees have five-petaled flowers?

Peach, pear, apple, cherry, and many other fruit trees seem to have flowers comprised of five petals. Assuming there is no evolutionary advantage to confusing students of trees, is there a plausible ...
8
votes
2answers
4k views

Use of amino-acid sequences versus use of nucleotide sequences in phylogenetic analysis

Reading a paper about gene evolution, I see that they do phylogenetic analysis for bacteria using protein sequences. They take the method from another paper. I can suspect that amino-acid sequences ...
8
votes
1answer
386 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 ...
8
votes
2answers
1k views

How can rooted and unrooted (phylogenetic) trees be distinguished from one another

I understand that both 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 root (the root is identified as a ...
7
votes
2answers
582 views

Goats are so fearless but sheep are not. Is there any genetic difference responsible?

As you see in the picture goats (not only wild goats) are so fearless, but I never saw any sheep do this. What is the source of this difference in behavior?
7
votes
3answers
396 views

How should I put a large phylogeny into a scientific paper?

I've been trying to put a phylogeny tree into a scientific paper. This tree includes ~220 species, which is too too large for one page for journal articles (Letter or A4 size). But in my paper it is ...
7
votes
2answers
618 views

Which phylum appeared most recently

I'm aware that our earliest records of many major animal and plant phyla come from the Cambrian or Precambrian periods, and I'm also vaguely aware of some of the objections raised with general concept ...
7
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1answer
124 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?
7
votes
2answers
152 views

Evidence & discussions of hard polytomy

Phylogenetic trees with >2 branches on a node are polytomic, and polytomy can appear on trees for two reasons. Firstly a lack of information in the data prevents proper resolution within a clade, ...
6
votes
1answer
251 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 ...
6
votes
2answers
125 views

phylogenetic analysis of gene enrichment?

Are there any tools to do phylogenetic analysis of gene enrichment? This is, I have a list of genes from an experiment performed in several species, with a z-score that can be described as "enrichment"...
6
votes
1answer
99 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.
6
votes
1answer
96 views

Visualisation of phylogeography

I am working on phylogeography on one model species and I am a beginner. You can imagine one species that came on locality more than 5 mya (million years ago). It was a good environment, so the ...
6
votes
1answer
225 views

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 ...
5
votes
2answers
2k 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 ...
5
votes
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 ...
5
votes
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
votes
2answers
449 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 ...
5
votes
2answers
376 views

How to get smallest subtree containing a set of nodes from BioPhylo?

I'm testing out various phylogenetic libraries in Python. I want to read in a Newick tree, then, given a list of taxa, generate the smallest tree that contains them all. This task is quite simple and ...
5
votes
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 ...
5
votes
0answers
44 views

The Perplexing Trilobite: What is the Evidence Supporting The Hypothesis That They are Not Crustaceans?

In the field of paleontology, one question that's really bugged me (er, no pun intended) of late is why the subphylum/class Trilobitomorpha/Trilobita is off on its own branch of the Arthropoda phylum, ...
5
votes
0answers
108 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 ...
4
votes
3answers
664 views

Does anyone know a 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 a software in which to do this with, and I have tried using Dendroscope and TreeMap,...
4
votes
2answers
252 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 ...
4
votes
2answers
319 views

How do taenia form a species?

I know that there are many hermaphrodite animals and plants. But many of them seem to still exchange genes by mating with another member of their species. I now happened to read the Wikipedia ...
4
votes
1answer
940 views

Are wild cats the same species as house cats?

I thought that the definition of species is "can interbreed" From Wikipedia: The wildcat (Felis silvestris) is a small cat found throughout most of Africa, Europe, and southwest and central ...
4
votes
1answer
34 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
votes
2answers
33 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 ...
4
votes
1answer
564 views

Null distribution of Blomberg's K

I've noticed different functions in different R libraries have different ways of assessing significance for Blomberg's K. For instance, picante's phylosignal looks at a distribution of PIC variance ...
4
votes
1answer
92 views

relative-rate of evolution

I am supposed to calculate the relative rate of evolution of two sequences (human and sheep) with a chicken serving as the outgroup. The sequences are pretty long, so I will just create a short ...
4
votes
1answer
80 views

Parsimony (cladistics)

I don't understand how to sum the changes in a phylogenetic tree. Here for example: http://www.med.nyu.edu/rcr/rcr/course/phylo-cladistic.html How do you end up with 8 for the first and 9 for the ...
4
votes
1answer
48 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: ...
4
votes
1answer
47 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 ...
4
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0answers
45 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, ...
3
votes
1answer
610 views

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 ...
3
votes
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 ...
3
votes
2answers
91 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 ...
3
votes
2answers
132 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: ...
3
votes
1answer
122 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 H....
3
votes
1answer
48 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
votes
4answers
321 views

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 ...
3
votes
1answer
69 views

Is there a term to quantify how spread a character is on a phylogenetic tree?

Is there a term which can quantify how 'spread out' a particular character is on a tree? I want to distinguish between a character which is only restricted to a particular clade vs. a character that ...
3
votes
1answer
72 views

phylogenetic Independent contrasts with unresolved tree

I have a dataset containing morphological and performance measures of species from various groups, including insects, lizards, frogs, spiders etc, and want to analyse the relationship between these ...
3
votes
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 ...
3
votes
1answer
76 views

Common Ancestry of ETCs and ATP Synthase complexes

Rickettsiales are widely regarded as the ancestor of eukaryotic mitochondria through endosymbiosis. Cyanobacteria are widely regarded as the ancestor of eukaryotic chloroplasts through endosymbiosis. ...