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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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: ...
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22 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 ...
6
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310 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 ...
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60 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.
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32 views

Why do tomatoes look so much like pomegranates? [closed]

The pomegranate fruit has been cultivated since ancient times, particularly in the Middle East and the Mediterranean. It has a hard outer rind, and inside are several chambers, each of which contains ...
6
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163 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 ...
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33 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 ...
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41 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 ...
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143 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 ...
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59 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 ...
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2answers
909 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 ...
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160 views

Evolutionary distance between Canidae, Felidae, and Rodentia

Comparing the families Canidae and Felidae, which have the shorter evolutionary distance to the order Rodentia? Less sophisticatedly put, are cats or dogs more related to rodents?
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505 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 ...
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10 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 ...
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60 views

What makes a good phylogenetic tree?

How can one improve a phylogenetic tree? If one was to make the 'golden standard' of phylogenetic trees what features would it have? Would it be highly reliable, well resolved etc? What other features ...
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40 views
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91 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 ...
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29 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 -> ...
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2answers
196 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 ...
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30 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 ...
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187 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 ...
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1answer
59 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 ...
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1answer
143 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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18 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 ...
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1answer
68 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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1answer
86 views

Is there a rule for the annotation of the basepair or gene locus origin in bacterial genomes?

Since all bacteria have one circular chromosome, there is no designated origin to start the systematic gene locus numbering. Therefore, what is the rule to start the numbering at a particular point ...
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1answer
41 views

Testing monophyly from per site log-likelihoods without optimising branch lengths

How can I obtain per site log-likelihoods for a topology against an alignment without optimising branch lengths? (which software can I use to do this) Per site log-likelihoods can be used for various ...
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92 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, ...
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395 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
98 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
222 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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3answers
353 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 ...
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82 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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1answer
158 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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321 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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205 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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40 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
58 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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544 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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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 ...
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1answer
191 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
2k 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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90 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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3answers
46k 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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59 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 ...
4
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1answer
64 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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67 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 ...
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39 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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108 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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234 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 ...