Questions tagged [molecular-evolution]

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

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4answers
558 views

Is a single cell “irreducibly complex”?

(sorry if the title seems like flame-bait - but it's a real question). I'm trying to understand what could have come before the first cell (What are the "minimum requirements" for a single ...
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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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Is evolution a means to an end?

In "The Red Queen", Matt Ridley frequently argues that evolution is a means to an end, without providing much explanation for such a big statement. Is this a fact in biology? Do species mutate their ...
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Why would low complexity regions be linked with relaxed selection?

I'm reading a text (Wagner, 2007) on identifying positive selection. In the paper, the author says that low complexity regions are known to be associated with the relaxed selection. I'm trying to ...
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1answer
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What causes the elongation of Genome down the evolutionary time line [closed]

Theory of natural evolution says that complex life forms arose from simpler ones e.g. starting from Eubacteria to modern day multicellular eukaryotes. {If we try to reduce these changes happening at ...
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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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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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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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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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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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Increase rate of change in coding regions?

If a sequence is under selection will it acquire more changes over time because of faster fixation than if changes were neutral? Is this true or am I missing something?
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Can anyone help me with these Biology evolutionary properties homework questions? [closed]

my teacher assigned these worksheet questions, they are ungraded, but he said something might come up on the test really similar to this so I really want to get all of them right. I am pretty ...
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Why did translation develop a specific codon for initiation?

The translation of mRNA is initiated by a specific methionine-accepting tRNA at a specific initiation codon, usually AUG (complementary to the tRNA anticodon). However translation at suitable (albeit ...
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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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What is the evolutionary relationship between heme, chlorophyll and other tetrapyrroles?

As a non-biologist, I have searched the Internet and found dozens of papers discussing the similarity between the structures of heme and chlorophyll molecules, but I could not find any discussion 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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Does low gravity exposure to early stages of human fetus have potential to unloc unused genetic information from earlier stages of evolution?

The title seems quite self explanatory but let me elaborate. New mutations do take a very long time and many generations to occure in the genetic code. But our genetic code already holds all the ...
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54 views

What created the first ribosome

If a ribosome is made of protein, yet is used in protein sysnthesis, what created the first ribosome? What created the ribosomal RNA?
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Is transition more common than transversion during the evolution of duplicated genes?

Transitions are base mutations of purine to purine (A <-> G) or pyrimidine to pyrimidine (C <-> T). Transversions are purine to pyrimidine or vice versa (A <-> C, A <-> T, G <-> C, G &...
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How did the genetic code evolve?

The genetic code is redundant, there are 20 amino acids for 64 possible nucleotide combinations (triplet codons). Therefore some amino acid are coded by several different codons. While leucine is ...
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How did genome duplication in jawed vertebrates allow gene specialization?

I am currently reading from Chapter 15 in Principles of Life, 2nd Edition: Many gene duplications affect only one or a few genes at a time, but in some cases entire genomes may be duplicated. When ...
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Mutation rate and Evolutionary rate?

What is the difference between then?I have read some jobs that describes analysis about mutations rates and another ones with evolutionary rates.I want to know the diferrence between then.
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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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Can I simulate a previous and next sequence of my fasta files?

I have fasta sequences of a virus protein that had suffered a mutation in 2008 and this mutant had increase it fitness when compared to wild strain (according to literature).I want to simulate if my ...
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Is genetic purging based on random shuffling of the genes of an individual or is it more intentional way of removing deleterious recessive alleles?

Inbreeding depression may be reduced by selection against deleterious alleles, which eliminates, or purges, them from the population. I have two questions: Is genetic purging based on random ...
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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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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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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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Creating ideal conditions for life

Suppose some scientists built a large vat, sterilised it and filled it with distilled water. Then they start dissolving compounds into the water such as amino acids or what ever they deem conducive to ...
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Why has life evolved around oxygen? [closed]

Why has life evolved around oxygen? Many lifeforms require oxygen to breakdown bio-molecules and release energy. I think there are two possibilities: Reactions with oxygen tend to release more energy,...
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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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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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Is there a specific terms to describe variant of existing genes in bacteria?

I have a question regarding a specific term that describes the variant of existing genes. I am analyzing whole-genome sequencing of a bacterial isolate. I found there are a large number of genes that ...
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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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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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How to attain a deep conceptual grasp of key atomic/molecular/genetic/ notions? [closed]

It's a total noob question, I know. I'm a layperson trying to come to grips with basic scientific terminology. I always face a conceptual hurdle in trying to understand micro-talk. The way I'm using ...
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197 views

Are molecular machines encoded in the DNA?

I don't know much, if anything, about molecular biology. I watched the "inner life of the cell" on Youtube which triggered my curiosity about how these molecular machines came to be. My simple ...
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Is there any evidence that supports glycolysis in mitochondria or chloroplasts?

Glycolysis is known to be a part of cellular metabolism undergone by both eukaryotic and prokaryotic cells, whether under aerobic or anaerobic conditions. As the endosymbiotic theory states that ...
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192 views

Have we ever observed fertile offspring with a different number of chromosomes than the parents?

Chimpanzees are supposedly the closest relative of humans from a DNA perspective, they are both diploid, and they both undergo meiosis. However, chimpanzees have 24 chromosome pairs while humans have ...
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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 ...
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Why and how does complexity usually tend to increase through time?

The question of complexity is classic in the very first lectures of evolutionary biology where the teacher usually tries to tell the students that complexity does not necessarily increase and that ...
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Why is ATP the preferred choice for energy carriers?

Why is ATP the most prevalent form of chemical energy storage and utilization in most cells?
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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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Differential Gene Expression

I have a matrix two gene expression datasets, one from 10 normal individuals and ten from diseased individuals, which are normalised log fold change values--, i.e., already processed. My question is:...
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computing relative synonymous codon usage from a coding sequence alignment while accounting for phylogenetic inertia?

I would like to compute the relative synonymous codon usage (RSCU) from coding sequence alignments. But since the coding sequences from an alignment are not independent realization, the statistics (...
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What are some examples of non-homologous sequences having similar functions?

I am trying to find some proteins that are non-homologous but functionally similar. However, I cannot seem to find concrete examples. Can someone please point out any resources or provide examples?
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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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701 views

Pros and cons of amino acid structure vs DNA sequences for evolutionary comparison [closed]

This is an analysis question for a lab on the amino acid differences in beta globin amongst different primates, and using such differences to construct a cladogram and infer evolutionary relationships ...
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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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New evidence about the beginning of life? [closed]

The cover story of the August Scientific American is about new evidence suggesting "volcanic pools" as the location for "first life" as opposed to deep sea smokers like "The Lost City". I was under ...