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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 best free and most up to date phylogenetic tree on the internet?

I found phylogenetic tree in wikipedia is lacks of accuracy. It actually confusing with versions. Some terms was not scientifically accurate with dna analysis anymore So are there anyone know where ...
Thaina's user avatar
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49 votes
3 answers
172k 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?
terdon's user avatar
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11 votes
1 answer
815 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 ...
Eli Korvigo's user avatar
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4 votes
1 answer
355 views

Why is traditional rank based taxomomy considered by some as logically inconsistent with phylogenetic knowledge?

Following is from wikpedia: Under the traditional nomenclature codes, such as the International Code of Zoological Nomenclature and the International Code of Nomenclature for algae, fungi, and ...
Ahmed Abdullah's user avatar
2 votes
1 answer
341 views

Defining "species" (Are species an emergent property or an ensemble of quantitative differences?)

Interbreeding Defining species by the criteria of not being able to breed is problematic: The concept loses its meaning in phylogenetic prospective, since closely related species were able to breed ...
Roger V.'s user avatar
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36 votes
2 answers
24k 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 ...
dwjohnston's user avatar
9 votes
1 answer
3k 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 ...
krismath's user avatar
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7 votes
2 answers
3k views

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 ...
arcyqwerty's user avatar
1 vote
1 answer
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Does a fully-resolved phylogenetic tree have to be dichotomous?

I read that wherever there is polytomy there is an unresolved pattern of divergence. I don't understand why this is so. When divergence takes place, is it necessary that there will be division into ...
biogirl's user avatar
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20 votes
3 answers
72k 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, ...
Irena's user avatar
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12 votes
6 answers
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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 ...
Fer's user avatar
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11 votes
3 answers
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Branch length in phylogenetic trees

I know this is a very basic question, but it is not too clear to me what is the unit of measure of branch length in phylogenetic trees. I have come to understand that it is usually expressed in number ...
Beatrice Baldi's user avatar
11 votes
0 answers
141 views

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 ...
Kevin Kostlan's user avatar
9 votes
2 answers
1k 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, ...
rg255's user avatar
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8 votes
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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?
MySky's user avatar
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7 votes
2 answers
445 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 ...
AliceD's user avatar
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6 votes
2 answers
295 views

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 ...
Remi.b's user avatar
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5 votes
0 answers
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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 ...
Remi.b's user avatar
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4 votes
1 answer
99 views

How can I tell if a certain marker is useful to date a phylogeny?

If I have a phylogenetic tree for a genus, how can I tell if a certain protein would be a good phylogenetic marker to use if one wanted to use a molecular clock to date the age of some speciation ...
Bakhtawar's user avatar
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4 votes
1 answer
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What is the difference between these terms: clade, monophyletic group and taxon?

Wikipedia definitions for these terms are pretty similar: http://en.wikipedia.org/wiki/Clade http://en.wikipedia.org/wiki/Monophyletic_group http://en.wikipedia.org/wiki/Taxon They sound like the ...
lolmaus - Andrey Mikhaylov's user avatar
4 votes
1 answer
388 views

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

I'm 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). My ...
cancerconnector's user avatar
3 votes
1 answer
1k 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 ...
Remi.b's user avatar
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2 votes
2 answers
292 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 ...
zakrapovic's user avatar
0 votes
1 answer
190 views

What could explain discrepancies between dates provided by the fossil record vs. the molecular clock?

I am studying a mud snail genus called Ecrobia. For the Caspian species (Ecrobia grimmi), there is a discrepancy between dates provided by the fossil record and the molecular clock: First appearance ...
jvddorpe's user avatar
  • 245
-2 votes
1 answer
2k 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.
lolmaus - Andrey Mikhaylov's user avatar
-2 votes
3 answers
10k 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 ...
mick's user avatar
  • 153