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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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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48 views

Distance matrix with different length sequences

In a project we're doing (in python), we want to create a distance matrix for a phylogenetic tree with multiple, different length sequences. However, what we've seen so far (AlignIO in biopython, ...
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1answer
73 views

How closely related are two parasites Giardia intestinalis and Trichomonas vaginalis?

How closely related (from the evolutional point of view) are parasites Giardia intestinalis and Trichomonas vaginalis? Giardia genome is about 12 Mb and its major cellular proceses are rather simple. ...
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1answer
43 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 ...
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1answer
108 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 ...
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59 views

How to track and describe the evolution of a gene?

So I have a project student (undergraduate) who has been assigned a project to study the evolution of a gene (and possibly related genes) through species. I am not an evolutionary biologist, and hence ...
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2answers
127 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 ...
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31 views

DNA barcoding, querry regarding tree based (cluster) methods for species identification

I am working on success rate of DNA barcoding in identification of species using distance and tree based methods. Regarding distance based method, I have used Adhoc and species identifier and ...
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2answers
45 views

What is the formal terminology for two species that are “close” to each other in a phylogenetic tree?

Take for example the human and the chimpanzee, they are "closely related" species since they are "close" to each other in a phylogenetic tree. However, this terminology seems pretty informal, what ...
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498 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 ...
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1answer
71 views

Plant's phylogeny tree to identify which of them are closer (genetically) with another plant

I'am trying to create a phylogeny tree from some plants, as the post's title says, to help me conclude which of those plants are closer genetically with another one plant. So let's say that this is ...
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1answer
192 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 ...
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2answers
140 views

Draw simplified phylogenetic tree for kids

I need to draw simple, phylogenetic tree for kids lecture. I am looking for an online tool where I can enter organisms (e.g., human, wasp, fungus) and get figure of a phylogenetic tree. Tree should ...
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3answers
90 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 ...
2
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1answer
41 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 ...
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1answer
32 views

Usage of the taxonomic classification “Pinnipedia”

According to ITIS the classification Pinnipedia is invalid, and it is proposed to rather use Caniformia. The later group however includes a range of terrestrial animals as opposed to the pinnipeds ...
3
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1answer
53 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 ...
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2answers
33 views

Could alpha-numeric taxonomy of fungi make things simpler?

Please feel free to construe this question broadly--I don't see why the question would not apply to branches of biology other than mycology. If the goal of taxonomy is to create classification of ...
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1answer
68 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 ...
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35 views

comparing conventional phylogenetic tree to phylogenetic trees which are based on enzymes

I built trees (for 4 organisms: mouse, human, drosophila and C-elegans) for different enzymes family, compared them to the conventional tree, and try to explain them. how would you explain these ...
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3answers
85 views

Phylogenetic tree

I want to find the conventional phylogenetic tree of human, mouse, C elegans and drosophila, without all the other organisms. Do you know where can I get it? thanks, Noga
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0answers
42 views

Speciation and Phylogeny of Lactobacillus

The lactobacillus, also called Döderlein's bacillus is a genus of facultative aerobic bacteria. There are several species such as Lactobacillus acidophillus and Lactobacillus reuteri. I have several ...
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3answers
154 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 ...
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3answers
75 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 ...
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3answers
79 views

Definition of species - location of gene

I know that species have been classified on basis of reproduction , DNA similarity , niche, etc. Has there been a classification based on locus of genes ? What are the drawbacks/shortcomings of ...
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1answer
197 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 ...
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1answer
21 views

How to get conservation of vaccine candidates between hundreds of bacterial strains?

We have identified vaccine candidates via an ex-vivo RNA-seq approach. Next step would be to perform conservation of these candidates (about 20) between multiple bacterial strains (about 200). I would ...
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1answer
210 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 ...
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1answer
49 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. ...
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1answer
363 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 ...
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2answers
88 views

What are the statistical tools for distinguishing molecular analogy from homology?

Scientists have developed statistical tools that distinguish "distant" homologies from coincidental molecular homoplasy in extremely divergent sequences. What are these tools?How are they used ? I ...
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1answer
199 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 ...
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1answer
63 views

How do I figure out which of the valleys I came from?

I had my DNA tested by 23andme.com. They give me a very long string for my DNA. How do I determine which of the three Ethiopian valleys I descended from? I'm of European descent. ...
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2answers
498 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?
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315 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 ...
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1answer
62 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 ...
3
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1answer
56 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 ...
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2answers
166 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 ...
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3answers
33k 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?
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2answers
2k 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 ...
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1answer
81 views

How to build S16 rRNAs phylogenetic trees?

Here is what I know so far: Multiple copies are present in prokaryotes, but according to a paper by Lukjancenko el al.[1] it is enough to select the most similar ones. There are stem regions in the ...
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2answers
110 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 ...
9
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5answers
640 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 ...
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2answers
991 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 ...