Questions tagged [molecular-evolution]

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

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127 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 ...
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193 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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587 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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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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79 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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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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157 views

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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3answers
134 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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1answer
4k views

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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2answers
141 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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110 views

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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2answers
200 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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52 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. ...
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234 views

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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109 views

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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63 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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131 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
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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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1answer
145 views

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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43 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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53 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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49 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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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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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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81 views

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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187 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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2answers
166 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?
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181 views

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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1answer
65 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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1answer
26 views

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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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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137 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 ...
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1answer
82 views

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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3k views

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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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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436 views

Are heterozygotes always fitter than homozygotes? Can inbreeding be beneficial?

Inbreeding is mostly not very good because when there is a 'disease' in one allele, the other could/would take over the function. But when you have two of the same genes/alleles, do they, or could ...
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1answer
41 views

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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1answer
145 views

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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1answer
2k views

Hardy-Weinberg applied to three alleles and stimation of allele frequencies

I have this equation: Corresponds to HW in equilibria with three alleles: $(p+q+r)^2=1$ Expanding the square results: $p^2+2pq+r^2+2pr+q^2+2qr = 1$ I need to separate homozygous and ...
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1answer
30 views

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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1answer
36 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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55 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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101 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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1answer
3k 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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90 views

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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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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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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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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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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2answers
473 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 ...