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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61 views

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

Im 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, which I ...
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18 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 ...
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19 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 ...
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16 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. ...
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27 views

What genetic link would cause a human to have a extra vertebra?

Most people have five vertebrae in their lumbar (lower back) region, which are named L1 to L5. However, some people possess an additional lumbar vertebra located below the L5. This extra vertebra, ...
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11 views

Which should I use the genes of the mitochondrial DNA? [closed]

What should I use for phylogenetic analysis of the genes of the fungus? Which should I use the genes of the mitochondrial DNA?
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2answers
35 views

How do I generate a phylometric tree given species names?

I have a list of species. I want to put those names into a tool and get back a visualized tree that includes names of shared order, suborder, family and genus. Is there an existing tool that does this ...
2
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1answer
36 views

What contribute to the variation of protein sequence across different species and how do they influence?

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 ...
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1answer
40 views

Does the new virus tree of life change their position between living and non-living things?

Viruses still do not fit the criteria of living or it's simplest form (the living cell), why would some say that the new virus tree of life makes it more closer to life? Aren't mitochondria in a point ...
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1answer
79 views

Bootstrap question

I have a question about bootstrapping: The way that I understand it is that each number represents how well a given node is supported. So in the diagram presented, we can see that the ...
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2answers
1k views

Living intermediate species?

Hypothetical question regarding three animals 'species' {A, B, C}. Are there any examples in nature where {A and B} cannot regularly produce viable offspring, however {A and C} and {B and C} can ...
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35 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 ...
2
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1answer
92 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 ...
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89 views

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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25 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 ...
2
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1answer
117 views

Did modern alligators and caimans come from prehistoric crocodiles?

I know that crocodilians have been here since the time of the dinosaurs. I also know that crocodiles came first. But alligators have been here for a good 37 million years. Did alligators come from ...
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56 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 ...
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2answers
39 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 ...
3
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1answer
73 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 ...
5
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208 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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2answers
61 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 ...
5
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416 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 ...
6
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1answer
79 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.
2
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1answer
291 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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803 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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13 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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101 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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1answer
157 views

What does saying a phylogenetic tree is 'well resolved' mean? [closed]

I'm not sure what 'resolution' means in the context of phylogenies.
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98 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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33 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
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2answers
199 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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52 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 ...
4
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2answers
232 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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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 ...
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1answer
91 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
50 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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2answers
119 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, ...
3
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1answer
62 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 ...
7
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1answer
281 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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1answer
198 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, ...
2
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1answer
106 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. ...
4
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1answer
402 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 ...
6
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1answer
201 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 ...
4
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2answers
251 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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48 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
75 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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571 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 ...
2
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1answer
275 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 ...
2
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1answer
4k 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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558 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 ...