Genes without templates: Many genes are completely new inventions and not just modified copies of old genes

Mar 26, 2013

(Phys.org) —It is easier to copy something than to develop something new - a principle that was long believed to also apply to the evolution of genes. According to this, evolution copies existing genes and then adapts the copies to new tasks. However, scientists from the Max Planck Institute for Evolutionary Biology in Plön have now revealed that new genes often form from scratch. Their analyses of genes from mice, humans and fish have shown that new genes are shorter than old ones and simpler in structure. These and other differences between young and old genes indicate that completely new genes can also form from previously unread regions of the genome. Moreover, the new genes often use existing regulatory elements from other genes before they create their own.

When scientists decoded the first , they made a surprising discovery: similar variants of many genes are found even in very different . This finding can be explained by the fact that evolution uses existing genes and adapts them to varying degrees for new tasks. The copying of genes plays an important role here. Copies are made of a gene and incorporated into the genome. Evolution can then experiment with these copies, while the original can continue to fulfil its function in its unaltered form. Completely new genes are very rare events in this model.

Rafik Neme and Diethard Tautz from the Max Planck Institute for Evolutionary Biology have now refuted this idea. Based on initial indications of the existence of completely new individual genes, they analysed over 20,000 mouse genes and traced their origins. According to their findings, genes that arose later in evolution are often shorter than those that have been in existence longer. Moreover, younger genes have fewer exons and fewer . This finding contradicts the accepted view: "If new genes are copies of old ones, a of this kind between length and age would not be expected. However, a young gene needs time to acquire additional exons and introns. Thus, genes become longer with time and consist of numerous exons and introns," explains Rafik Neme from the Max Planck Institute in Plön. Analyses of human, zebrafish and stickleback genes confirm the correlations discovered in the mouse.

The researchers also studied another way in which new genes can arise from existing genes: through a change in the reading frame. The genetic reading frame comprises three consecutive letters of the genetic alphabet. Each of these triplets stands for an amino acid which is translated from the genetic code. If this reading frame is shifted, new triplets arise and the genome is translated into completely different amino acids. "We found several cases, in which genes were overwritten due to such a change in the reading frame," says Neme. An example of this is the Hoxa9 gene – a gene that controls embryonic development. In rodents and primates, this gene uses such an additional alternative reading frame.

According to the findings of the Plön-based researchers, around 60 percent of genes originate from our unicellular ancestors from the early phase of evolution. Large numbers of new genes were added in particular during the advent of fundamental evolutionary innovations: for example, the transition from unicellular to multicellular organisms and the emergence of vertebrates. A particularly high number of new genes also formed after the splitting of the mouse from other rodents. Interestingly, the scientists only found a few locations on the chromosomes in which newly formed genes accumulate. In fact, they are relatively evenly distributed across the entire genome. One of the few exceptions is a cluster of genes on chromosome 14 which control the activity of neurons, among other things.

New genes thus frequently arise from scratch in the course of evolution. They form in the gene-free sections of the genome, between the old genes. This often necessitates only minimal changes. "For example, genes need elements known as promoters which control their activity. It appears that new genes can appropriate promoters belonging to other genes and use them for their own purposes," explains Diethard Tautz, Head of the Department of Evolutionary Genetics at the Max Planck Institute for .

Explore further: Free the seed: OSSI nurtures growing plants without patent barriers

More information: Neme, R. and Tautz, D. Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution,
BMC Genomics 2013, 14:117. doi:10.1186/1471-2164-14-117

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LariAnn
2 / 5 (7) Mar 26, 2013
evolution copies existing genes and then adapts the copies to new tasks


Evolution can then experiment with these copies, while the original can continue to fulfil its function in its unaltered form.


Seems that someone thinks that "evolution" is a sentient being doing things in nature on purpose, rather than a random, accidental assemblage of individually meaningless events that, somehow, resulted in the extreme complexity and intelligence we observe today. "Evolution" doesn't do anything at all; random changes take place in response to other random changes, the ones that result in the survival of organisms continue on to further generations, and the compilation of all those changes is called "evolution". Personally, I feel that there is an "intelligence field" that does direct processes, but not in any religious context. However, wording a science article such that "evolution" comes off as an intelligent designer is facetious at best, pseudo-scientific at worst.
Torbjorn_Larsson_OM
4.5 / 5 (4) Mar 26, 2013
The article is overblown. A simple scrutiny of the abstract shows that the extraordinary claim of the article has no extraordinary evidence in the paper. The paper tests constraints that predict that de novo evolution is a general mechanism, but there is no observation of such.

It would be funny if it is an actual fact though, since creationists thinks the genome is incapable of de novo generation of genes. And of course de novo genes have been observed as such, just not as many as duplication-divergence genes.

@LariAnn: Your's is still creationism, evolution is known to be process based and admits no outside "direction". (Since variation is independent on selection, and selection is purely a result of the environment.)

As for the article, it is deeply flawed in many ways. Usage of teleologic language when describing evolution is an accepted biological praxis since a) it makes the description easier and b) everyone knows how to interpret it in process terms when necessary.
dogbert
1.5 / 5 (8) Mar 27, 2013
Torbjorn_Larsson_OM

It would be funny if it is an actual fact though, since creationists thinks the genome is incapable of de novo generation of genes.


Why say that? You apparently do not believe in creation, but somehow you presume to assert what others believe or don't believe when they have made no such assertions.
nowhere
5 / 5 (2) Mar 27, 2013
Torbjorn_Larsson_OM

It would be funny if it is an actual fact though, since creationists thinks the genome is incapable of de novo generation of genes.


Why say that? You apparently do not believe in creation, but somehow you presume to assert what others believe or don't believe when they have made no such assertions.


There is no presumption. It has often been asserted by creationists on this site that there is extremely limited generic variability in the genome. To say creationists believe the genome is capable of de novo generation of genes is sort of like saying they believe in speciation.
triplehelix
1 / 5 (3) Mar 27, 2013
Very badly written. Makes a mockery of actual evolution science...I don't understand why so many people can't grasp it.
LariAnn
1.8 / 5 (5) Mar 27, 2013
@Torbjorn_Larsson_OM - I don't presume to know what your beliefs or philosophy are so please extend to me the same courtesy. Your statement that "mine" is "still creationism" is a gross assumption that paints me as one with those who reject science and believe the Earth is 6000 years old, none of which I agree with. At some point common sense still must apply, and since even in our "evolving" technological development, intelligence, not random events, is driving it, why is it so refractory to your understanding for me to postulate that there is a field of intelligence that drives evolution over time? It is because there is a desire to make the scientific intellect itself into a "god"?

Also, IMHO, in a science article, teleologic language in reference to something that is not supposed to be teleological is not scientific. Even if it makes the description easier, it also makes it inaccurate. Saying "the sun rises" may make the description easier, but there is no science in it.
Q-Star
1.8 / 5 (5) Mar 27, 2013
At some point common sense still must apply, and since even in our "evolving" technological development, intelligence, not random events, is driving it, why is it so refractory to your understanding for me to postulate that there is a field of intelligence that drives evolution over time?


Could ya add a little more than "field of intelligence" as the driving mechanism of evolution? That doesn't contain much as a postulate.

What is the observational evidence for this "field of intelligence"? What are the parameters that define the "field" and qualify the "intelligence".

Who or what is it that possesses this "intelligence"? What is the source of the "field"?

"field of intelligence" alone could mean one thing, many things, or nothing.
nowhere
5 / 5 (1) Mar 28, 2013
since even in our "evolving" technological development, intelligence, not random events, is driving it, why is it so refractory to your understanding for me to postulate that there is a field of intelligence that drives evolution over time?


Non sequitur. Your postulate has no evidence to support it, and more than that, it would have to invoke magic to support itself. Where exactly does this field exist? How was it formed? Why has no one detected it yet, and how then do you know it exists?
RealScience
3 / 5 (1) Mar 31, 2013
@Q-Star and nowhere - through natural selection our genome has evolved to contain considerable embedded 'intelligence'. It has evolved to tolerate mutations so that it can accumulate them to provide variety. It has evolved to have more mutations and fix them less diligently in areas where past mutations have been beneficial, and to have fewer mutations and fix them more diligently in areas where past mutations have been fatal. It has evolved to tolerate transposons and even use them as a source of variety. It has evolved sex and mate selection as a way to gather variations from the gene pool when they become useful.
One could argue that genomic innovations are based on quasi-random events that lack foresight and are thus not 'intelligence'. But our brains are ultimately based on quasi-random wanderings of sugars and oxygen molecules that lack foresight. We consider our brains intelligent, so considering genomes and gene pools to have a type of 'intelligence' is not unreasonable.

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