Genome complexity: orphan genes have functions (Introduction)

by David Turell , Thursday, April 09, 2020, 22:16 (1688 days ago) @ David Turell
edited by David Turell, Thursday, April 09, 2020, 22:22

New thoughts on how they arise:

https://www.quantamagazine.org/where-do-new-genes-come-from-20200409/

"De novo genes “represent a really unprecedented or unrivaled kind of genetic novelty,” said Caroline Weisman, a doctoral student in biophysics at Harvard University who is conducting research into the origin of genes. “That’s a really exciting possibility for evolutionary biologists who are thinking about how things like novelty evolve.”

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"During the past decade, researchers have vigorously argued about the relative importance of de novo gene creation and divergence beyond recognition. But there was still no easy way to look at orphan genes and determine how they arose. “The field was hamstrung by that, in a sense, because if you can’t really know how many are real [de novo genes], and what’s the significance of this phenomenon, then you’re a bit stuck,” McLysaght said.

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"The researchers made a conservative assumption that if a gene’s neighbors appear in the same order in another species, then the gene is likely to correspond to whatever is sandwiched between them in the other species as well — even if the sequences don’t match.

"Using the synteny method, the researchers estimated that at most a third of orphan genes in flies, yeast and humans could be explained by divergence beyond recognition. “The rest must be explained by other ways, and the de novo origin is the best way to explain those,” McLysaght said.

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"Weisman estimated that somewhere between 55% and 73% percent of the orphan genes in these yeasts — a majority — were explained by divergence; that figure is higher than McLysaght’s synteny approach suggested.

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"How Function Emerges:
Long and his colleagues identified about 175 genes that originated de novo within the last 3.4 million years; they could tell that these genes were de novo because corresponding nongenic sequences were still recognizable in closely related species. These de novo genes appeared to be biologically active — that is, they were transcribed into RNA and translated into peptide chains, and most of them showed signs of being shaped by natural selection.

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"Although their study demonstrated the adaptive potential of emerging de novo genes, the actual contribution of de novo genes to adaptation might always “remain somewhat cloaked in mystery,” McLysaght said. As mutations accumulate in de novo genes, it gets harder to identify the nongenic sequences from which they came. Past some uncertain deadline, it may always be impossible to prove that an old gene arose de novo. Pinning down the true number of de novo genes and their contribution to novel adaptations in most complex organisms may therefore be an intractable problem.

"Still, Long emphasized that orphan genes have biology worth investigating regardless of their origin. Weisman thinks that may be particularly true of genes whose divergence seems to have suddenly accelerated at some recent point in their evolution: They might be able to tell us about how novel biological functions evolve.

"For the creation of orphan genes, “we know there’s a diversity of mechanisms,” Begun said. But “the guiding principles for why certain biological processes might have more de novo gene evolution, while others might have more duplication and divergence — that, we don’t really have a grip on yet.'”

Comment: as we knew its not Darwin's theory as ID has pointed out, and the field has not fully explained it. If it is not within the Darwin theory, where does it comes from? The dsigner?