New study explains evolution of duplicate genes

April 7, 2014, Georgia Institute of Technology
This image shows the coding region in a segment of eukaryotic DNA. Credit: National Human Genome Research Institute

From time to time, living cells will accidently make an extra copy of a gene during the normal replication process. Throughout the history of life, evolution has molded some of these seemingly superfluous genes into a source of genetic novelty, adaptation and diversity. A new study shows one way that some duplicate genes could have long-ago escaped elimination from the genome, leading to the genetic innovation seen in modern life.

Researchers have shown that a process called DNA methylation can shield from being removed from the genome during . The redundant genes survive and are shaped by evolution over time, giving birth to new cellular functions.

"This is the first study to show explicitly how the processes of DNA methylation and duplicate gene evolution are related," said Soojin Yi, an associate professor in the School of Biology and the Parker H. Petit Institute for Bioengineering and Bioscience at the Georgia Institute of Technology.

The study was sponsored by the National Science Foundation (NSF) and was scheduled to be published the week of April 7 in the Online Early Edition of the journal Proceedings of the National Academy of Sciences (PNAS).

At least half of the genes in the human genome are duplicates. Duplicate genes are not only redundant, but they can be bad for cells. Most duplicate genes accumulate mutations at high rates, which increases the chance that the extra gene copies will become inactive and lost over time due to natural selection.

The new study found that soon after some duplicate genes form, small hydrocarbons called methyl groups attach to a duplicate gene's regulatory region and block the gene from turning on.

When a gene is methylated, it is shielded from natural selection, which allows the gene to hang around in the genome long enough for evolution to find a new use for it. Some young duplicate genes are silenced by methylation almost immediately after being formed, the study found.

"What we have done is the first step in the process to show that young gene duplicates seems to be heavily methylated," Yi said.

The study showed that the average level of DNA methylation on the duplicate gene regulatory region is significantly negatively correlated with evolutionary time. So, younger duplicate genes have high levels of DNA methylation.

For about three-quarters of the duplicate gene pairs studied, the gene in a pair that was more methylated was always more methylated across all 10 human tissues studied, said Thomas Keller, a post-doctoral fellow at Georgia Tech and the study's first author.

"For the tissues that we examined, there was remarkable consistency in methylation when we looked at duplicate gene pairs," Keller said.

The computational study constructed a dataset of all human gene duplicates by comparing each sequence against every other sequence in the human genome. DNA methylation data was then obtained for the 10 different human tissues. The researchers used computer models to analyze the links between DNA methylation and .

The human brain is one example of a tissue for which gene duplication has been particularly important for its evolution. In future studies, the researchers will examine the link between epigenetic evolution and human brain .

Explore further: Permanent changes in brain genes may not be so permanent after all

More information: DNA methylation and evolution of duplicate genes, PNAS,

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1 / 5 (3) Apr 08, 2014
The news release is misleading. Duplicate genes do not automagically 'evolve.' Creation of duplicate genes occurs via conserved molecular mechanisms that link ecological variation to biophysically constrained ecological adaptations in species from microbes to man.

The epigenetic landscape becomes the physical landscape of DNA in organized genomes of species from microbes to man only when energy is available (e.g., in the form of nutrients). The nutrients are metabolized to pheromones, which control the physiology of reproduction.

Species diversity is nutrient-dependent and pheromone-controlled. Genomic diversity does not randomly somehow 'evolve.' Natural selection of food is required and pheromones control the physiology of reproduction. Ecological, social, neurogenic and socio-cognitive niche construction are manifested in species diversity.

See, for examples:
Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
1 / 5 (3) Apr 08, 2014
See also: "...regulatory genes need to be tightly controlled in order to have precise and optimum protein level to properly function." http://www.biomed...abstract

Tight control of regulatory genes is nutrient-dependent and the physiology of reproduction determines whether new genes are fixed in populations that ecologically adapt to ecological variations.
1 / 5 (3) Apr 08, 2014
This following statement and all others like it are ridiculous:

"Random mutations are the substrates on which directional natural selection acts." -- Jay R. Feierman

No experimental evidence of biologically-based cause and effect supports that statement. Population geneticists simply dismissed Darwin's repeated cautions about 'conditions of life.' His 'conditions of life' are nutrient-dependent, which is why nutrient-dependent ecological niche construction must be considered before natural selection for variation in morphological and behavioral phenotypes is considered.
5 / 5 (3) Apr 08, 2014

Oh boy. You're back again with that agenda?
1 / 5 (3) Apr 08, 2014
I wrote: "Creation of duplicate genes occurs via conserved molecular mechanisms that link ecological variation to biophysically constrained ecological adaptations in species from microbes to man." -- and have published a review article that details that fact.

Others are always welcome to provide their opinions about HOW genes are created, so that their opinions can be compared to biological facts -- or to other OPINIONS about cause and effect. For example: "...natural selection is an evolutionary process initiated by mutation. It does not have any creative power in contrast to the statements made by some authors." p 196.

If 'natural selection' does not create genes, what kind of ridiculous agenda is being touted by evolutionary theorists, who won't even try to explain themselves? Are intelligent people really supposed to believe in mutation-driven evolution, as if experimental evidence had been found that supports the idea?
1 / 5 (2) Apr 14, 2014
To be honest, I agree with JVK, other than taking liberties in loading this scripted text with the usual evolutionary jargon, there is no evidence here of evolutionary mechanisms other than invoking such into the literature. This piece above here is a prime example of what Philip Skell wrote in 2005, "Why Do We Invoke Darwin?". In most scientific studies, invoking this man's name or or inserting any number of the usual jargon or euphemisms to explain vague things not clearly understood offers nothing of value in the understanding the mechanical processes at work here. As Skell said, if you were to take out the evolutionary jargon and replace it with God, Christ, Buddha, Allah, etc, it offers no help to the researcher.

I work within the pharmaceutical industry doing research data collection by interviewing numerous Doctors, Specialists, Medical Researchers and other Scientists and nothing about evolution ever comes up. It's totally unnecessary. But religion comes in all forms.
1 / 5 (2) Apr 14, 2014
Thanks Eocene1. I've always wondered why anyone invokes Darwin, when -- as a medical laboratory scientist -- ideas about mutations and evolution are absurd.

Instead, the constant theme has been nutrient-dependent organization of the genome. This has just been detailed again in 'Development of food intake controls: Neuroendocrine and environmental regulation of food intake during early life' http://www.scienc...14000622

Anyone willing to return to our 1996 review, which also was published in Hormones and Behavior, will see that nutrient-dependent organization of the genome is pheromone-controlled via conserved molecular mechanisms in species from microbes to man: "From Fertilization to Adult Sexual Behavior' http://www.hawaii...ion.html

The requirement for de novo Creation of olfactory receptor genes -- not evolution -- in mammals is obvious. But use of the big "C" in creation evokes hate.

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