Questions tagged [molecular-evolution]

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

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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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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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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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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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108 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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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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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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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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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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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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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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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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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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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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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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978 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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50 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 ...
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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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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 ...
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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 ...
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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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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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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?
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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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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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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 ...
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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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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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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 ...
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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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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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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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2k 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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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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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. ...
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Does the genome make sense without knowledge of the ovum?

Much of the literature for laypeople seems to consider (and to spread the idea) that an animal (or a plant, I guess) is characterised by its genome. I do not know whether the same goes for more ...
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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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Evolutionary advantage of F plasmid in bacterial conjugation

Hi I would like to ask a question on bacterial DNA exchange, namely conjugation via F plasmid. It seems to me that all the F plasmid codes for is the sex pilus. What is the evolutionary advantage of ...
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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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Can estimating the likelihood of protein sequences adopting functional enzyme folds show life is too complex for evolutionary timescales?

An acquaintance provided me with this article1. I can't understand for sure what it is about. My acquaintance said that it proves that time for generation of even the simplest proteins is on a ...
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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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How did mitochondria make energy long ago?

I've learned that mitochondria is thought to have been eaten by a larger cell, resulting the mitochondria to be part of a bigger cell. Well, here's my Q. If you look at how mitochondria works, you ...
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Learn Bioconductor the hard way!

I came to analyzing population genetics data from the background of a theoretician and a computer biologist but not with the standard tools that a bioinformatician (or empiricist in population ...
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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 ...