A sub-discipline of evolutionary biology which involves the study of evolutionary relatedness between different organisms based on their molecular and morphological features.

learn more… | top users | synonyms

2
votes
1answer
52 views

What contributes to the variation of protein sequence across different species?

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 ...
5
votes
0answers
45 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
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
0answers
35 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
votes
0answers
51 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 ...
2
votes
0answers
43 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 ...
1
vote
0answers
35 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 ...
1
vote
0answers
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 ...
1
vote
0answers
46 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 ...
1
vote
0answers
29 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 ...
1
vote
0answers
19 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. (i.e....
1
vote
0answers
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 ...
1
vote
0answers
15 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 ...
1
vote
0answers
73 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 ago....
1
vote
0answers
19 views

What are the main principles of the Bacteriological Code?

Although the Bacteriological Code is an important guideline for taxonomists and microbiologists, describing the criteria for delineating species and higher taxa of the prokaryotes, I, and plenty of ...