October 22, 2005
Genetic Analysis Shows Signs Of Selective Pressure In Human Evolution

Cornell researcher Carlos Bustamante and associates have found signs of Darwinian selective pressure in recent human evolution.

ITHACA, N.Y. -- The most detailed analysis to date of how humans differ from one another at the DNA level shows strong evidence that natural selection has shaped the recent evolution of our species, according to researchers from Cornell University, Celera Genomics and Celera Diagnostics.

In a study published in the Oct. 20 issue of the journal Nature, Cornell scientists analyzed 11,624 genes, comparing how genes vary not only among 39 humans but also between the humans and a chimpanzee, whose DNA is 99 percent identical to humans.

The comparisons within and between species suggest that about 9 percent of genes that show some variability within humans or differences between humans and chimpanzees have evolved too rapidly to be explained simply by chance. The study suggests that positive Darwinian natural selection -- in which some forms of a gene are favored because they increase the probability of survival or reproduction -- is responsible for the increased rate of evolution. Since genes are blueprints for proteins, positive selection causes changes in the amino acid sequence of the protein for which the gene codes.

I wish the press release on this study provided a bit more detail. How recent is "recent" in this context? For any of the genes are there signs of selective pressure just within the last few thousand years? Also, how many of the genes examined have functions specific to the nervous system and what percentage of them show recent signs of selective pressure?

Cheaper DNA sequencing technologies will eventually enable studies with much larger groups of people, larger numbers of genes, and more types of genetic difference. My guess is this study looked mainly at point mutations and not large copy variations (see the second report below about large copy variations). As large copy variations become more easily testable more signs of selective pressure will be found.

Several categories of genes underwent selective pressure to create modern humans.

"Our study suggests that natural selection has played an important role in patterning the human genome," said the paper's lead author, Carlos Bustamante, assistant professor of biological statistics and computational biology at Cornell.

The Cornell/Celera team found that genes involved in immune function, sperm and egg production, sensory perception and transcription factors (proteins that control which genes are turned on or off) have been particularly affected by positive selection and show rapid evolution in the last 5 million years, when humans shared a common ancestor with chimps.

13 percent of the genes examined appear to be under negative selection against variations that are harmful.

Likewise, the researchers found that approximately 13 percent of the genes that may vary show evidence of slightly deleterious or harmful mutations in human populations; these include genes involved in determining the basic structure of cells and muscles as well as genes that control traffic in and out of the cell. These mutations are subject to weak negative selection, according to the study. In general, negative selection eliminates from the population very harmful changes to proteins that kill or stop reproduction. But mutations that have led to slightly deleterious versions of the gene -- mutations that may cause disease or only slightly reduce the average number of children left by those that carried the mutation -- can by chance become quite common in the population.

Mildly harmful mutations take a long time to get selected out. Identification of purely harmful mutations be very useful in offspring genetic engineering to produce human offspring with far fewer purely harmful genetic mutations. Such humans will function better mentally and physically in a large assortment of ways.

All of us now living are already born with lots of harmful mutations. Well, we are not permanently stuck with old flawed genetic software. In a couple of decades we'll be able to get replacement organs grown which will be grown from stem cells genetically engineered to remove harmful mutations. We'll also be able to get stem cell therapies to upgrade our bodies with better genetic software.

Read this excellent article in Nature which surveys recent discoveries of larger amounts of genetic variation in humans than has previously been predicted.

How common, exactly? Last July, Wigler's group reported that it had looked at 20 normal individuals and found 221 places in the genome where those people had different copy numbers of stretches of DNA2. Some of these copy-number changes showed up in more than one person, and so qualify as 'polymorphisms' shorthand for particular spots in the genome that regularly differ between individuals. In the Book of Life analogy, these polymorphisms represent sections of text where certain paragraphs are repeated different numbers of times in different individuals.

About 76 of the variations Wigler's team found were polymorphisms, and each person had about 11 of them in his or her genome2. Soon after, Lee and Scherer reported that in a survey of 55 people they had found 255 copy-number variants, 102 of which were polymorphisms3.

Large copy variations can produce large effects. Picture a gene for making a neuroreceptor. An extra copy of it could increase the concentration of that receptor on the end of a neuron. Or the replication of a gene which makes a protein which stimulates neural stem cells to divide could cause more rapid neural stem cell growth and hence larger brains in those who carry extra copies.

In addition to the large copy variations researchers have since found large scale rearrangements, deletions and insertions. Together all these variations are referred to as structural variations. The number of structural variations being discovered is so large that the claim of 99% shared genetic sequences between different humans may turn out to be too high..

Genome researchers now have a catch-all phrase for the vast array of rearrangements including copy-number polymorphisms, inversions, deletions and duplications that occur normally in the human genome. They call it structural variation, and have described at least 800 individual variants that, in total, account for about 3.5% of the human genome. And the sheer number of variants seems likely to catch up with the number of known single nucleotide polymorphisms the single-letter 'typos' in the Book of Life. That makes structural variation a potentially major source of diversity. It is even possible that we're not all 99.9% similar, as the Human Genome Project predicted.

The increasing discoveries of genetic dissimilarity between humans is evidence of selective pressure to adjust to local environments as humans spread out and colonized the globe.

Also see my previous post "Brain Gene Allele Frequences Show Brain Still Evolving".

Share |      Randall Parker, 2005 October 22 08:45 PM  Trends, Human Evolution

Bulldog said at October 24, 2005 4:59 AM:

Every new human embryo is an experiment in progress. Evolution is not to be denied.
Will human intervention in the genome serve to increase or decrease human genetic diversity? A lot more is going on in gene regulation and expression that hasn't been discovered yet.

scottynx said at October 24, 2005 10:39 AM:

Bulldog writes:
[Will human intervention in the genome serve to increase or decrease human genetic diversity?]

I would say decrease. Look at arabian horses. There was pretty much one function that was selected for: speed. A few superior lines ended up dominating. Also, how genetically diverse is the NBA? High standards of narrowly defined accomplishment lead to less genetic diversity. If humans are engineered for greater intelligence, it is probable that something similiar will happen, at least for genes affecting brain development. For example, an "easy"(comparatively) way to increase intelligence in all humans would be to replace the main chromosomes involved in brain development with those of exceptionaly smart jews. Using jews would be important (as opposed to any smart people) because decendents of those genetically engineered people would regress to the higher mean jewish IQ as opposed to the lower mean IQs of other races. Would humans be less diverse? Yes. Would they be more intelligent? Yes.

Fly said at October 25, 2005 9:23 AM:

Bulldog: A lot more is going on in gene regulation and expression that hasn't been discovered yet.

Yes. Consider the hard-wired structure of the human brain and all the instinctive behaviors. That is complexity with a purpose and it is heritable. So the information needed to create that purposeful complexity has to be in the DNA. I dont believe weve identified where it resides.

3lMATTo said at November 5, 2005 7:38 PM:

go to this web site, http://msnbc.msn.com/id/7348103/

CASpears said at March 19, 2006 6:55 AM:

Oh that is great, so we can also get the heriditary diseases that Askanazi Jews have...no thanks. I'm content with my 126IQ, without the defects.

Andrew Palfreyman said at September 10, 2012 9:24 AM:

I am curious about the highly reduced selection pressures we now enjoy in our modern, comfortable society. With the obvious exception of diseases which prevent reproduction, the sky's the limit these days, it seems.

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