Questions tagged [molecular-evolution]

The study of evolutionary mechanisms in operation at the molecular scale, primarily DNA, RNA, and proteins.

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Do ring species exist?

In trying to understand evolution better, I have been looking at examples of speciation, and have thus come across the topic of ring species. I have tried to find concrete examples of how these work, ...
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At what rate do chromosomal rearrangements occur?

How often do chromosomal rearrangements occur? I am interested about these kind of chromosomal rearrangements that are passed on to the descendants, i.e. germ line chromosomal rearrangements. The ...
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54 views

Is there recent info about the hypothetical ancient two-codon genetic code?

Here is the latest I have found. link This is the basic idea: Evolution does not look ahead and make plans. It would not create a system of mRNA with giant ribosomes to create proteins, until ...
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79 views

How to choose the most appropriate measure of genetic distance

I am conducting a phylogeography study of a fish species and am trying to construct a phylogenetic tree to describe population structure and ancestry. I have constructed trees using various measures ...
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157 views

Inbreeding Coefficient and Coefficient of Relationship

Wikipedia gives the following formula to calculate a "path of coefficient of relationship" between an ancestor $A$ and an offspring $O$: $$\rho_{AO} = 2^{-n} \left( \frac{1+f_A}{1+f_O} \right)^{1/2} =...
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How would inserting a nonfunctional protein impact fitness of an organism?

Producing proteins costs energy, and producing longer proteins costs more energy than shorter proteins. Producing proteins which have no function, would therefore presumably negatively impact the ...
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53 views

Source for an upper bound in the number of genes based on mutation rates

So I've found myself referring in an answer once again to the idea that complexity (insofar as it's a quantity for which "number of genes" is a proxy) has an upper bound, limited by Muller's ratchet-...
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49 views

psbA-trnH intergeneteic spacer inversion

What kind of software tool would you recommend as best suited to detect psbA-trnH inverisons? I have 1x coverage Sanger .fasta files and >2000 sequences, with 1 sequence per species. Most tools I have ...
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18 views

Intron sequences in course of evolution

In course of evolution did some exons become intronic sequences or will introns in some species acts as exons in other species.
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55 views

Do The Traces Genetic Diseases Remain in families?

I know that there are certain diseases that are predominant on genes. But, is there any sort of surety that if parents are suffering from a disorder then their offspring has to suffer from the same. ...
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80 views

Odds of Fusion of Chromosome #2

There is strong evidence that chromosome 2 in humans is a fusion of two chimp chromosomes (i.e. common ancestor of chimps and humans) as explained at wikipedia here The question is what are the odds ...
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How valid is Schwartz's criticism of molecular phylogenetics?

A proponent of the human-orangutan clade, Jeffrey Schwartz argues, in this paper [1], that molecular phylogenetics is largely based on a baseless assumption. To sum up, according to him: this type of ...
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When we talk of functional macromolecules (e.g. proteins as enzymes, hormones, receptors, antibodies etc), towards what are they evolving?�

Actually this is a question which is given in a book and to be honest,it has baffled me.I'm not so much well versed with molecular evolution so my guess would be,say some sort of enzyme which could ...
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Are there any open phylogenetic projects that don't require coding to make a contribution

I am stay at home learner, not pursuing education formal education and currently doing a part time job. I've however completed masters in biotechnology and I'm studying to pursue PhD in molecular ...
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What is the point of inter-species specific quorum-sensing?

So apparently, according to this TED video, there is a kind of quorum sensing involving a universal, inter-species specific molecule that all bacteria secrete. Is there any evidence of bacteria being ...
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2answers
468 views

How to interpret McDonald-Kreitman test results?

It is easy to get the numbers right and calculate neutrality index. It is easy to memorize "equals", "greater", "lesser", etc. At least on the exams, when certain level of simplicity is assumed. But ...
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187 views

What theories exist as to how self-replicating molecules organised into the first cells?

When I was a biology student in the early 90's, what I learned and read seemed to indicate a gap in theories around the origins of life. There was, of course, no real evidence about how the first self-...
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15 views

Are ITS1 and ITS2 good for divergence time estimation?

I had a discussion with a colleague who told me internal transcribed spacers (ITSs) are not good for divergence time estimation: Because they are non protein coding genes; Because they belong to a ...
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57 views

How does epigenetics affect the birth conditions via alcohol?

Recent study has shown that epigenetics can play role in male-caused infertility and it cites for example studies which showed an enhancing of silent genes when drinking alcohol. Since the study ...
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60 views

How is “fine mapping of pelvic regulatory region” done in the stickleback PitX1 paper?

I'm working through this paper for a class. I'm a bit confused by the methods they used in one experiment. So the researchers are studying spine development in stickleback fish. They noticed some ...
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271 views

What genetic distance model should be used when calculating genetic differences in Arelquin?

I'm using Arelquin to look at the genetic structure between a number of different populations. I want to compare the populations by producing pairwise FST values, however I don't know what model for ...
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83 views

How far in evolutionary distance is the P-distance estimator “accurate”?

I'm reading Yang's computational molecular evolution and in the very first chapter it says the P distance is a "simplistic distance measure" between two sequences. It is the number of different sites /...
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20 views

Effect on gene loss because of compartmentalisation of plastids/mitochondria/endosymbiont?

Considering the transfer of genes during endosymbiosis a gene transfer event (at least fundamentally, even if it's a special case), how does the fact that in this case the genes are inside a ...
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46 views

What are the methods for detecting anagenetic versus cladogenetic change?

I'm new to the study of phylogenetics and am wondering if there are ways of identifying evolutionary changes that associate with cladogenetic events versus those that arise via anagenesis.
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Is there a software simulator for monomeric formation, a la Miller-Urey?

At the moment, does any widely-available software exist for small-scale, programmable simulation of monomeric formation in specific conditions? Could one, for instance, recreate the Miller-Urey ...
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1answer
46 views

Can I make an population genetic analysis from incomplete protein?

I have an dataset of fasta sequences. This proteins are not complete (My sequences have 700 nucleotides,while complete sequences have 1725 nucleotides)I would like to know if i can make an population ...
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Coacervater were more like Viruses or Cells?

The answer considers them as first formed living cells as they were precursor of life. But they had no lipid bilayer nor any cellular organization, shouldnt they be more like Viruses ,or like Prions ...
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72 views

What causes the complementary copy of an RNA molecule to separate?

I have recently read an article which explains that, in the RNA World hypothesis, an RNA molecule gets 'scanned' by nucleic acid, catalysed by a different specifically-folded RNA molecule, to arrange ...
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1k views

Proteins in different organisms

I know that DNA is universal meaning that all organisms have the same 4 base pairs and also that the same codons code for the same amino acid in all organisms. What I am wondering is that say humans ...