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

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Evolution of robustness towards mutations [on hold]

Did some proteins evolve to be robust to detrimental mutations, i.e. to not just function well, but to be far away (many steps away) in "mutation space" (sequence space, where the metric is based on ...
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14 views

How to predict a RNA virus generation time?

Generation time could be measured in vivo,but in my case,I want to estimate the generation time from sequences(in silico). Any tool or method to do it?
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10 views

How to choose the best parameters to my BEAST analysis?

I'm trying to perform a bayesian analysis with BEAST. I have an RSV Fusion gene dataset(nucleotide).And I want to estimate the mutation rate per site per year from my sequences.Using Beauti I have to ...
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1answer
26 views

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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70 views

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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1answer
24 views

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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37 views

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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1answer
25 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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0answers
13 views

How do dN/dS and piN/piS differ? Are they both equal to omega?

There appears to be extensive literature on dN/dS, however piN/piS is not as well-documented. What is the difference between dN/dS and piN/piS? Is it true that dN/dS can only be measured if there are ...
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15 views

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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16 views

Evolution Of Organisms outside Earth [duplicate]

Why didn't organisms evolve to live in planets outside the Goldilocks zone where water exists in liquid state? Why is water needed for life to be formed?
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1answer
71 views

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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21 views

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 ...
3
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0answers
35 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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1answer
28 views

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 ...
0
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1answer
48 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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3answers
81 views

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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0answers
21 views

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 ...
2
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2answers
76 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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1answer
64 views

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 ...
2
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1answer
55 views

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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1answer
671 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 ...
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1answer
21 views

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 (...
3
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3answers
112 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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2answers
129 views

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?
5
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1answer
163 views

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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2answers
281 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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1answer
65 views

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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1answer
432 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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0answers
51 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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0answers
42 views

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 ...
2
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2answers
115 views

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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1answer
108 views

Evolution of autophagy and apoptosis

Autophagy and apoptosis are both necessary for survival of a multicellular organism. I have some information on evolution of autophagy and apoptosis. However, the key difference between the pathways ...
3
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1answer
138 views

Text Book Recommendation: Organic Evolution

I was wondering if anyone could point me in the direction of any text books on organic evolution? I have recently become interested in the subject and would like to know more. I think an undergrad ...
5
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1answer
100 views

Polymorphism in number of chromosomes?

The answer to this question, saying that Down Syndrome - a trisomy of human chromosome 21 - is caused by de novo mutation (rather than resulting from standing variation) made me think about ...
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2answers
109 views

Does science have an explanation of how the first “common ancestor” formed in evolution? [closed]

I always have this question on my mind and I need a better explanation on this. Does Charles Darwin's theory explain it or are there any other theories which explain it better than Charles Darwin's ...
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1answer
41 views

Is it possible to have a mechanism to use carbon dioxide as a source of oxygen in human body?

Is it possible to seperate O2 from CO2 and use it for energy In Human? Why Plants and not Humans can do it?
2
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3answers
118 views

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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3answers
609 views

Why do (almost) all energy carriers contain adenine?

Unlike this question which is specific to just ATP, this one includes all energy carriers. When thinking of common energy carrying molecules, I can think of Adenosine triphosphate (ATP), Nicotinamide ...
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42 views

is there any theory about why life evolved to have DNA with 4 different bases and not 6 or other number like in organisms created with artificial DNA? [duplicate]

If organisms can carry DNA with 6 bases which supposedly stores increased genetic information, why living organisms evolved to have DNA made of 4 bases and not 6 or other number? is there any theory ...
5
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1answer
153 views

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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43 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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0answers
41 views

phylogenetics and substitution ratios for positive selection [closed]

So very new to phylogenetics!. I've been scrambling and reading so much to get this done!!. I would like to see if one or more of the sequences I have (from a gene family) are under positive ...
2
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1answer
30 views

Why does V. cholerae produce a human specific choleragen?

V. cholerae secrete choleragen to grow and escape human intestines, however choleragen does not work on other mammals, why so? Why didn't it evolve a general mammal affecting choleragen? This question ...
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0answers
42 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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1answer
30 views

What is the best way to make a phylogeny from a list of genera?

All I have is a list of about 500 eukaryotic genera, and I need a neighbor-joining tree to show their relationship. I want to cast on top of this tree the loss of a particular enzyme. Is the best ...
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1answer
1k views

How to design internal primers?

I have sequences of the Cytochrome c oxidase I (COI) from several populations of Peringia ulvae (Mollusca; Gastropoda; Littorinimorpha; Hydrobiidae). I need additional COI sequences from a specific ...
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1answer
2k views

What causes the variable/conserved structure in the 16S rRNA gene?

See the image below for a visual representation of the 16S rRNA gene. It is composed of conserved and variable regions however I can't see to find a reasoning for why this is the case Thanks
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1answer
46 views

Parthenogenesis Induction

I have read about Parthenogenesis induction in a paper : "Hagimori T, Abe Y, Date S, Miura K (2006) The first finding of a Rickettsia bacterium associated with parthenogenesis induction among insects. ...