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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6
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2answers
1k views

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 ...
35
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3answers
130k 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?
11
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1answer
737 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 ...
33
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2answers
18k 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 ...
9
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1answer
2k 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 ...
1
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1answer
2k views

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 ...
8
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2answers
2k 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 ...
8
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4answers
5k 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
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3answers
5k 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 ...
9
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2answers
805 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?
9
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2answers
969 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, ...
5
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2answers
195 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 ...
3
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1answer
18k views

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 ...
3
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0answers
41 views

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 ...
2
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2answers
255 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 ...
2
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1answer
69 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 ...