Questions tagged [molecular-evolution]

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

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141 views

Why isn't speciation a negative feedback loop?

To rephrase my question more articulately: Speciation begins when two groups within a species starts to become reproductively isolated, and is complete when the two groups can't interbreed (for the ...
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Why does mitochondrial DNA have a high mutation rate, even though the mitochondrial function is highly conserved?

My understanding is that genes that are functionally important are more highly conserved. The DNA coding for ribosomal RNA is one example of that. I was surprised to find out that mitochondrial DNA ...
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What is the mathematical relationship between selection coefficient and dN/dS

dN/dS is often used as a measure of the intensity of selective pressure on a mutation or gene, but I'm curious about how it can be written as a function of the selection coefficient. I'm specifically ...
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Why are Chromosome Territories important?

Chromosomes occupy discrete regions of the nucleus, referred to as 'Chromosome Territories'. This spatial organization is emerging as a crucial aspect of gene regulation and genome stability in health ...
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can a cell evolve into a different species in the lab?

A friend of mine does not believe in evolution. He claimed that we can not as humans observe a single cell evolving into a different cell. Is that possible to be observed in the lab? Thanks in advance....
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35 views

Do TADs derive from operons?

TADs (Topologically associated domains) are DNA sequences in the eukaryotes genome (except plants) that are between two sequences named "Insulator". The genes in TAD just are affected by ...
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Which genes/proteins constitute the core components of the circadian clock?

What the title says. For instance in Drosophila melanogaster and Mus musculus (see Patke et al. 2020) the CLOCK, CYCLE/BMAL, CRYPTOCHROME, PERIOD setup seems to be conserved. But other components also ...
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62 views

Do mutations that cause the loss of a complex trait occur more often than mutations causing gain of a complex traits?

The Wiki entry on the evolution of biological complexity states that "[m]utations causing loss of a complex trait occur more often than mutations causing gain of a complex trait". There is ...
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275 views

Defining "species" (Are species an emergent property or an ensemble of quantitative differences?)

Interbreeding Defining species by the criteria of not being able to breed is problematic: The concept loses its meaning in phylogenetic prospective, since closely related species were able to breed ...
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1answer
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Is there an published method for removing the effect of isolation by distance from genetic distances?

Isolation by distance is the phenomena that (even partial) reproductive isolation due to geographical distance between reproductive populations will result in greater genetic distance between those ...
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Reasons for the existence of symporters and antiporters

I'm wondering what is an evolutionary adaptation to the evolution of symporters and antiporters instead of just uniporters. Antiporters might help preserve electrical neutrality by pumping in/out an ...
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Caloric Mimicry

Was thinking about natural "zero calorie" sweetness and how these compounds could come to be via evolution. I was specifically thinking about monk fruit. While artificial selection likely ...
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373 views

Does the Miller-Urey experiment explain the origin of life?

According to the Miller-Urey experiment, the early earth atmosphere could have supported the formation of amino acids - and the experiment is hailed as being important in the explanation for the ...
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55 views

What are the relative roles of coding DNA versus regulatory DNA thought to be in evolution?

Intuitively, once you have the idea that some DNA is responsible for turning on and off the DNA that codes for proteins, it's possible to imagine that the regulatory DNA is actually the most important ...
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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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Population Genetics Using WGS: How do I know when I have enough individuals?

I am having a difficult time finding information about a minimum threshold for number of individuals to use in wgs pop gen analyses. Are there software or formulas/theory available to determine what ...
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49 views

Common ancestry of our cells to the first unicellular cell

If we start the chapter of life with low fidelity self replicating RNAs forming exactly identical copies of themselves, which then later evolved to form the first primordial basic cells which further ...
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710 views

Why is DNA replication so much faster in prokaryotes than eukaryotes?

There are many statements to be found on the internet of the sort: “DNA replication occurs at elongation rates of about 500 nucleotides per second in bacteria and about 50 nucleotides per second in ...
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Population genetics of pan-genome

I am beginning to work in the field of human gut microbiome, and wondering how (and if) the concepts of population genetics could be applied there. Considering the competition between the species ...
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66 views

gene mutation occurs on two strands of DNA or just one strand?

Suppose we have one strand with 3'-AAA-5' and the other strand is 5'-TTT-3'. So when point mutation occurs, does it happen to two strands at the same time? e.g. 3'-AAA-5' becomes 3'-AGA-5' and 5'-TTT-...
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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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154 views

What is neutral theory of evolution?

The question is not about the very basics, but more about where the line separating the neutral theory from the rest of population genetics lies. One often reads/hears claims that "the findings ...
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687 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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What is the impact of selection on orthologous and paralogous genes? How would this impact differ in different regions of protein coding genes?

Since paralogs increase the size of the genome and provide more opportunity for the evolution of novel characteristics, would they be more prone to selection?
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1answer
62 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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CRISPR/Cas9: What are the main differences between sgRNA and the Cr:TracrRNA ?

So from what I understand, in gene editing, the CRISPR vector expresses a small RNA sequence comprised of a small guide-RNA that is complementary to your target sequence. The sgRNA comprises a 20 Bp ...
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1answer
73 views

How do we formulate the mutational load for "junk DNA"?

Question(s) Based on Joe Felsenstein's textbook, I was trying to formulate the mutational load for the majority of eukaryotic genomes that are junk DNA ($L_{most\_of\_genome}$). (See background ...
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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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Why is selection less effective in small populations than in larger?

I can understand that the genetic drift has a higher impact on smaller populations, but what does it mean for the selection to be less effective in small populations than higher?
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Questions regarding serial passage of virus through animals arising from the paper The proximal origin of SARS-CoV-2

In this answer on bioinformatics.stackexchange.com to the question inquiring about the validity of the paper Kristian G. Andersen et al, The proximal origin of SARS-CoV-2, the author asserts the ...
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Definition of "genomic adaptation"

I have encountered the term genomic adaptation in some literature (for example Sikkink et al. 2017). I am struggling to parse the term, and I have not been able to ...
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1answer
39 views

Are the alleles that code for the same phenotype all the same exact sequence?

The idea that you can be homozygous for a gene means that there are limited options or alleles , correct ? My question is, if the mom has the allele b which codes for a blue eye, and the dad has an ...
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433 views

Why is glycerol the backbone of fat?

Fats are fatty acids joined onto the backbone of a glyercol (propane-1,2,3-triol). Why was glycerol seemingly chosen by nature to be the backbone of fats? Why can't it have been a butane -1,2,3,4- ...
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67 views

Why is the GULO pseudo gene expressed in humans?

The GULO pseudo gene is being expressed in humans according to Genecards. Why is this still taking place after tens of millions of years since then gene lost the capacity to encode for a functional ...
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1answer
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Relationship of RNA-binding proteins to peptidyl-prolyl cis-trans isomerase [closed]

I am studying a Plasmodium gene, known to encode an RNA-binding protein. However a BLAST search brings up mainly peptidyl-prolyl cis-trans isomerases from other species. Why would this be so?
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How many times has SARS-CoV-2 mutated?

According to Coronavirus has mutated at least once The novel coronavirus that has infected thousands of people across the world may have mutated at least once — meaning there may be two ...
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Why are probionts not considered cellular life? [duplicate]

I am currently studying Prescott's Microbiology, 10th edition, by Willey, Sherwood, and Woolverton. Chapter 1.2 Microbes Have Evolved and Diversified for Billions of Years presents the following ...
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Evolution of the common honey bee's stinger

Has the common Honey Bee evolved a stinger designed for penetrating human skin so it will cause as much damage possible even if it means death? A honey bee can sting other insects and mammals more ...
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4answers
202 views

Why doesn't evolution converge on perfection? [duplicate]

I got to know about an organism called "Tardigrade(water bear)" which is an extremely hardy organism and can survive in most conditions. My question is that if the aim of life in general is to ...
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1answer
80 views

What are the implications/predictions of the selfish gene theory?

Are there any testable predictions or implications of the selfish gene theory? Or it is just interesting interpretation of the observations/experimental data? If this theory is not falsifiable and ...
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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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What is known about major events of pre-LUCA evolution?

All organisms share many common biochemical features (including 20 amino acid genetic code) and are believed to have a common ancestor (so-called LUCA). According to wikipedia article, this common ...
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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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207 views

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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48 views

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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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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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 ...