Questions tagged [molecular-evolution]

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

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Is there selection against long proteins and long genes?

Background thought Titin and TTN Titin is the largest protein in the human genome with 33423 amino acids. Titin is coded by the gene TTN that must be at least $3 \cdot 33423 \approx 100kb$ long. ...
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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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How do I know whether or not a nuclear gene is single copy?

As a part of a phylogenetic study, I need to find a nuclear gene that meets the following requirements: Single copy gene; Highly variable gene; Gene longer than 400 bps; Gene that gives information ...
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Random Mutagenesis vs Directed Evolution as Strategies to boost expression

Do people use random mutagenesis (say using UV) to generate host variants that have high expression of a metabolite / enzyme? I've seen it mentioned as a strategy but it confuses me as to why. How ...
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Identity By Descent vs Identity By State

Background The concepts of Identity By Descent (IBD) vs Identity By State (IBS) are central in population genetics, yet I fail to fully wrap my head around the definitions. You can find examples ...
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Approaches towards a theory of innovation in evolution

Evolutionary biologist Andreas Wagner writes in his book "The Origins of Evolutionary Innovations: A Theory of Transformative Change in Living Systems" (Oxford University Press, 2011): We are ...
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What came first? The DNA or the DNA polymerases?

I know this sounds a lot like chicken and egg question and while the latter has an answer, I am intrigued about the former. A modified form of the question would be, in the course of abiogenesis, ...
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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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Why do nerve cells convert electric signals to chemical signals?

One would assume that a faster response time in the nervous system would be beneficial. However, nerve cells have to convert electrical impulses to chemical signals and cross a synapse. Why didn't ...
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Using evolution of bacteria against themselves

We know that mutations happen regularly in bacteria and also that one bacteria might get the mutation and become stronger than the others and thus survive, causing antibiotic resistance as well. Can ...
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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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Have there been any macro-evolution experiements?

I'd like to start first by saying that I don't believe in creationism at all, nor any non-Darwinian-evolution explanation of the diversity of life on Earth. The theory, the fossil record, and the ...
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Two 20 million yr old fossils of Hummingbirds found "The amazing thing about the fossil is that it's essentially a modern hummingbird [closed]

does this only mean that the Hummingbird is perfect in creation and needs no change to survive? http://news.bbc.co.uk/2/hi/science/nature/3691169.stm
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Evolution of blood types [duplicate]

What are the popular theories regarding how our blood divided into 4 groups. Particularly I'm interested in whether this was originally linked to disease. Thanks for your answers, useful articles and ...
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Junk DNA and "random" mutations [closed]

I'm somewhat irritated by "mutation" generally being described as a fully random factor in evolution: pure randomness does not seem like something that can survive in a long evolutionary process. And ...
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Evolution of the Redundancy of the Genetic Code

In short Looking at the genetic code, it appears that most redundancy is on the third letter rather than on the first or the second letter of the codon. Why has it evolved this way? Longer version ...
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What is the point at which abiogenesis is complete and evolution begins? [closed]

Is the minimum criterion for life a single cell? It seems that self-replicating RNA is not enough, but I don't know. What would be the most basic cell that could fit this criterion and what cells ...
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How do minute changes in an organism, as a result of evolution, get carried over to next generation

The theory of evolution states that random variations in organisms occur to better suit their surroundings. We take for example a bacteria's flagella. There's a bacteria who has a tube kind of ...
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Non Coding DNA and its effect on evolution

I had a discussion with a friend of mine; from his understanding, bacteria and other small organisms have higher amounts of "coding" DNA and, as such, are able to evolve much faster than organisms ...
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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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What factors, other than its homochirality, make our "brand" of biology unique? [closed]

If humans were to discover organisms on another planet, it is supposed that (unless both we and they were seeded by the same source) we would have nothing to fear from alien pathogens, as they would ...
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What is the relationship between radiation and evolution?

There is always a certain amount of background radiation present, for example due to ionizing radiation from the sun and other stars. Also certain materials like granite may emit relatively large ...
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How can (or did) Deinococcus radiodurans continue to evolve after developing resistance to mutation?

Deinococcus radiodurans has a remarkable ability to resist damage to its DNA due to radiation, dehydration or (to my knowledge) any other source. It keeps multiple copies of its genome and has a ...
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1answer
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What is the minimum functional biological light sensor? [closed]

As a follow up to this question regarding the evolution of the eye, it was suggested that primitive eyes only needed to evolve a light sensor and could perhaps use the existing biochemical cascade ...
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Do animals other than humans have different blood types?

Humans have the ABO and Rhesus blood typing systems. I have two questions about it: Why have we evolved these blood types? Do other animals have different blood types as well?
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Why are there both stop and start codons?

Based on my understanding from wikipedia, there is the (RNA) start codon AUG and the stop codons UAA, UGA, UAG. AUG can also encode Methionine, I'm assuming if it appears in the middle of a mRNA ...
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Formation of Life

Originally, life evolved from non-living matter. Why is life only generated from other life nowadays, and why doesn't it evolve from inanimate matter, like it did originally billions of years ago, ...
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Why is mRNA needed in the Protein translation?

The original question was to predict the basic requirements for information storage. Then the discussion moved to why is it necessary to include mRNA in the protein translation process. Why can't ...
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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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The origin of molecular machines

DNA holds genetic information and holds the key to the evolution of living organisms. Transcription and translation mechanisms enable living cells to process information encoded in DNA. To that end, ...
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Mechanisms of genotype*sex interactions [closed]

I'm looking for suggestions of the mechanistic level at which genotype*sex interactions can occur. These give different phenotypes from the same genotype dependent on the sex they are expressed in. ...
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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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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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When did CRISPR/Cas9 evolve and what is the likelihood that a superior system for live cell genome editing has already evolved on earth since then?

I've read that CRISPR/Cas9 is currently being implemented and tested for its ability to edit genomes in live cells, and that it is supplanting other genome editing tools in labs, such as TALENs and ...
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Is the heterotroph hypothesis universally accepted?

I was wondering whether there are hypotheses that take a different approach that is contrary to the heterotroph hypothesis. The heterotroph hypothesis states that autotrophs evolved from heterotrophs ...
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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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Heterochromatin production limitations

Currently playing with some ideas for a project and needed some guidance. I am wondering, both in Drosophila melanogaster and in general, is the amount of heterochromatin a cell/nucleus can produce ...
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A question about the intersection of evolution and thermodynamics

From this 2014 article in Quanta magazine by Natalie Wolchover there is a quote from a physicist with an intriguing idea about evolution: “You start with a random clump of atoms, and if you shine ...
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Converting Ensembl Compara gene tree DNA alignment to corresponding amino acid alignment

I have Ensembl compara gene tree alignments (Compara.gene_trees.57.fasta.gz downloaded from ftp://ftp.ensembl.org/pub/release-57/emf/ensembl-compara/homologies/) in nucleotide format. According to ...
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Inbreeding depression and dominance

From this article, second paragraph of the second page A classic theoretical result is that the mean of a character controlled by a single locus i with two alleles Ai1 and Ai2 is only affected by ...
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Coefficient of relationship and path of coefficient

A path of coefficient of relationship is defined as $$\rho_{AO} = \left( \frac{1}{2}\right)^n \sqrt { \frac{1+f_A}{1+f_O}}$$ This SE post discusses this definition From this, the coefficient of ...
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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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Book Recommendation: Complex Traits and Complex Genetic Architecture

I am looking for a book (or any good source of information) that offers an in-depth discussion and models about the evolution and analysis of complex traits and complex genetic architecture. Do you ...
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Is there a name for this principle in biological contexts?

This is mostly a question about usage. There is a probability-related idea that has been used in at least two biological contexts. The idea is that if something happened, it was probably likely to ...
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Book recommendations for evolutionary models

I was recently working on getting a statistical model of a DNA sequence. To do this I found that understanding evolution quantitatively seems to be quite important. I would really appreciate any book ...
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Book suggestion on computational molecular evolution

I'm currently reading Computational Molecular Evolution by Yang. Can you recommend alternative books? I am finding it to be lacking on conceptual discussion (it's more focussed on the mathematics and ...
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Selection on linked loci in a diploid population

Let’s consider two linked loci $A$ and $B$ that are both bi-allelic. In consequence, we have four different possible haplotypes $A_1B_1$, $A_1B_2$, $A_2B_1$, $A_2B_2$, which frequencies are $X_1$, $...
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Mutation rate in viruses

Mutation rate is a phenotypic trait that evolves. The process of evolution of such kind of traits are often referred to as evolvability. I am wondering about the evolution of the mutation rates in ...
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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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Evolutionary conservativeness

List the following proteins in the order of decreasing evolutionary conservativeness of their primary structure: Somatotropin. Catalytic subunit of a DNA – polymerase. Histone H1. ...