Human evolution: not stopping, but accelerating
GENETICS OF THE EIGHTH DAY
E.Kleshchenko, "Chemistry and Life" No. 3-2009
(published on the Izvestia Nauki website)
Maybe now, after hundreds of millions of years, NATURE has begun natural selection on the basis of mind, intellect, spirit.
Maybe NATURE is entering a new era. Fools will degenerate, wise ones will develop and grow stronger.
Thornton Wilder. Day Eight
The theory of evolution is a young science. In less than two centuries, it is not easy to gather the facts necessary to study processes that have lasted millions of years. Of course, there is a paleontological chronicle, but judging by the fossil remains, the Cro-Magnon, who lived on Earth 150-200 thousand years ago, morphologically differed little from modern Homo sapiens. Does this mean that the evolution of our species has stopped? Some think so, others disagree with them.
Discussions on this topic remained mostly speculative until an even younger science, molecular genetics, gained strength. It turned out that it is not necessary to go on long-distance expeditions for material evidence of evolution: you can look for them in the genomes of modern people. Variability, heredity, natural selection are the necessary conditions of evolution, according to Darwin, and two of them are provided at the DNA level, so every step of evolution is reflected in it.
In December 2007, there were reports of a study that showed that in the last 10 thousand years, human evolution has not stopped or slowed down, but accelerated. A group of scientists led by anthropology professor Henry Harpending from the University of Utah backed up their bold statement with the results of a mathematical analysis of the genomes of modern humans.
One letter misreading
The most accessible material for research is our DNA. Recently, the isolation and analysis of human DNA has moved from the cutting edge of science to ordinary laboratories and clinics. Comparative analysis of the DNA of many people has also given rise to a new science – human genomics.
The international project "1000 Genomes", launched in January 2008, as the name implies, aims to sequence a thousand genomes of anonymous volunteers from different parts of the world. Both doctors and scientists are looking forward to the results of the project, but reading three billion nucleotides a thousand times is not an easy and expensive task. So far, we have to use the results of another international project – “NarMar". Latin letters – from haplotype map, "haplotype map". Recall that the haplotype is called the "half", haploid genotype – the decoding of only one of the two strands of DNA. In a narrower sense, a haplotype is a set of variants of SNP (single nucleotid polymorphism, pronounced "snip"), that is, single nucleotide polymorphisms characteristic of a given DNA strand.
Although the genomes of any two randomly taken people coincide by at least 99.5%, there are differences between them. A significant part of them are SNP differences in one nucleotide, as in the words "bump" and "barrel". (And just like with words, a one-letter substitution can radically change the "meaning" of a gene, distort it or make it unreadable.) It is not quite correct to call SNP the term "point mutations" familiar from school: we usually call mutations a one-time event that occurred for the first time in this individual. A specific variant of the SNP can occur in a significant number of people – even if it is only 0.5–1%, in terms of the whole of humanity (6.76 billion according to the latest data) does not pull at a single event in any way.
This is where the fun begins. To put it simply, if it is known that nine out of ten people have the letter G in this place of the genome, and one out of ten has a T (in this case, they are talking about G and T alleles), perhaps this means that carriers of a rarer variant have a common ancestor, who had the mutation. And then the whole set of SNPs is information about all the mutations that took place in our ancestors. But how to process and comprehend it? How to find out, for example, whether guanine was replaced by thymine for the first time in this person, or whether this replacement was inherited from mom or dad, who, in turn, could inherit it from grandparents?
We do not have information about the entire set of SNPs yet, but there is, as already mentioned, “NarMar” – a freely available collection of alleles of millions of SNPs in representatives of four populations. Their genomes were provided by 30 triples of "mother – father – adult son or daughter" from the Nigerian Yorumba tribe, 30 of the same triples of US residents, mostly Mormons from Utah, whose ancestors came from Northern and Western Europe, 45 Tokyites who are not related to each other, and 45 Han Chinese from Beijing. Thus, the collection has data on three main races, they can be compared with each other or within groups. (By the way, the genomes of these very people will be completely sequenced as part of the "1000 Genomes" project.)
The reader has already realized that when we talk about "normal and mutant genes", we often mean "different SNP alleles" if the properties of a gene are determined by a single nucleotide substitution. Thus, information about differences in human genomes for many practical tasks successfully replaces the full sequence. “NarMar” has already brought a lot of benefits to medical genetics: by examining SNP, it is possible to identify genes of predisposition to diseases, and genes associated with an atypical reaction to drugs or vaccines, and much more.
But what about evolution? Is it possible to reconstruct evolutionary processes from this scattering of point replacements?
Fossils in DNA
Attempts to restore the course of human evolution, based on theoretical considerations, give opposite results. The intensity of the appearance of new mutations in an individual is logically considered constant (if we do not take into account exotic hypotheses about the yields of radioactive ores as centers of speciation). But firstly, the number of mankind has been growing continuously. And where there are more individuals, there are more adaptive mutations. Insecticide developers are well aware of this: in the laboratory, the experimental group of insects obediently dies out, and in vast natural populations there is a high probability of a resistant pest. Similar experiments on bacteria also confirm that population size matters. Secondly, the increase in the number was accompanied by the development of new territories, which means that they got into new conditions in which, obviously, completely different signs became adaptive. If this is true, then the evolution of man from the Neolithic to the present day should accelerate.
Opponents object: the increase in the number of species indicates that the species is at the peak of adaptation and to change something is only to spoil, but adaptation to new conditions can be carried out, and is carried out, in a non-genetic way – due to high intelligence. Maybe a person has long since got rid of the selection press – increased the survival rate of offspring, provided comfortable conditions even for not too powerful and healthy individuals and thereby slowed down his own evolution? It sounds no less logical. How to find out who is right?
Mutations are the raw materials with which natural selection works. An untrained person will assume that the faster the diversity of the genome grows – the more new SNPs appear that are passed on to descendants – the higher the rate of evolution. This is not quite true. When a gene becomes an object of positive selection, that is, its carrier gains an advantage and the gene is passed on to a larger number of descendants, the probability of transmission for neighboring genome sites also increases. As a result, not a single mutation is widely distributed, but a "pattern" of certain SNP variants. The length of the "pattern" is tens or hundreds of thousands of nucleotides, depending on the age of the site and the intensity of recombination – the exchange of DNA sections between paired chromosomes. Over time, recombination, of course, will destroy these groups. So, by the degree of destruction of the widespread SNP pattern, one can judge how long ago the "central" gene became the target of selection. The better the pattern has been preserved, the closer its first appearance is to us in time.
The task is akin to paleontological – first to find the "fossil remains" of useful mutations in the genome (that is, stable groups of SNP alleles), then to estimate the age by the degree of destruction... It is clear that it can be solved only with the help of a specially developed mathematical apparatus. It's hard work, it's not like you're shoveling in an excavation. However, seriously, modern paleontologists cannot do without mathematics.
Acceleration of restructuring
In this way, Henry Harpending and co-authors found about 1800 genes in the human genome (7% of the total number) that were selected relatively recently. Recently, by paleontological standards: "The rate of change has increased markedly in the last forty thousand years, especially at the end of the ice age – about ten thousand years ago." If we remember that the age of our species is 150-200 thousand years, it is probably not worth talking about stopping evolution. In addition, as the authors write in an article published in the Proceedings of the National Academy of Science of the USA (December 26, 2007, vol. 104, No. 52), there is reason to believe that most of the mutational events over the past 80 thousand years have been caught: improving the method does not increase their number. It is noteworthy that few of these genes can be called common to all groups represented in the database: most are specific to populations, and this also indicates their recent occurrence.
The distribution of elementary acts of evolution over time is shown in Fig. 1 (only for the European and African groups, but for the Japanese and Chinese the picture was similar). The time intervals in which especially many useful mutations were selected are clearly visible: it started about 8000 years ago in Africa and only 5250 in Europe. The pace of evolution has increased a hundred times!
When planning the study, the authors wanted to test the hypothesis that the rate of occurrence of adaptive mutations in humans has been constant throughout the history of the species. But if it had always been the same as in the last stages, then the percentage of genes affected by the changes would have been higher and, for example, the genetic difference between humans and chimpanzees would have been 160 times greater than what is actually observed. Do we have to admit that human evolution has made a breakthrough?
(The fact that a sharp rise is followed by a fall on the graph does not mean that the rate of evolution has decreased by now. If we do not delve into mathematical difficulties, it is not easy to find adaptive mutations among recent ones, that is, those that will be supported by selection, due to the lack of data from the future.)
Thirty-three centuries BC... the end of the Neolithic revolution, the appearance of the first civilizations – the Uruk culture in Mesopotamia, the birth of cuneiform writing, mathematics, the invention of the potter's wheel. In Europe, the now famous monuments of the Neolithic era are being built, from the Scottish Skara Bray to the megaliths in Malta. By the way, at the same time, around 3300 BC, a man froze in the Tyrolean Alps – either a priest or a shepherd, intricately dressed and tattooed, whose mummy, discovered in 1991, was nicknamed Etzi.
It is tempting to recall that the biblical dating of the creation of the world mainly falls on the sixth millennium BC, that is, just to accelerate the pace of evolution in the African population. Creationists need not worry: the fact that man as a species appeared much earlier is clearly established and cannot be revised. And yet it was at that time that something important happened to our ancestors. What exactly?
Cultural evolution
Harpending and co-authors could not help but note how the changes in the rate of evolution correlate with our population dynamics (Fig. 2). Remembering the dependence of the number of beneficial mutations on the total population, the authors collected data on how the number of people changed and what they were doing at that time.
Smooth population growth began in the Upper Paleolithic, and perhaps a little earlier, from 50 thousand years ago. It remained relatively slow until the Holocene (8-10 thousand years ago), when people settled the future centers of domestication of animals and plants – the Middle East, Egypt, China – and in the next six millennia spread to Europe, North, South and Southeast Asia, as well as to Australia. The inflection on the European and Asian charts is clearly visible here (note that the scale is logarithmic!). The African population was initially larger, but grew more slowly, and agriculture south of the Sahara arose no earlier than 4,000 years ago. About 2500 years ago (that is, half a century before our era), according to some estimates, less than 7 million people lived there, while the populations of Europe, Western, Eastern and South Asia numbered 30 million each.
It is easy to see that the acceleration of evolution correlates well with this settlement of peoples, and most importantly, with population growth. (It seems that the assumption that the number of beneficial mutations is proportional to the total number of individuals turned out to be true?) It is also clear why the speed increased earlier in Africa, but in Europe it rose a little higher. But still, the observed picture, according to the authors, is difficult to explain without involving the interaction of genes with the environment.
Indeed, migrations changed the climatic conditions in which man lived, and the Neolithic agricultural revolution, that is, the emergence of agriculture and animal husbandry, radically changed his diet. In addition, epidemic diseases such as chickenpox, malaria, yellow fever, typhus and cholera became a serious cause of death around the same time: it is believed that their impact on small nomadic tribes was negligible. This means that the selection of disease resistance genes began right then.
"For the Neolithic and later periods, the pace of adaptive evolution should be characteristic, more than a hundred times higher than those that took place in other periods of human evolution," the authors of the article write in conclusion. – Cultural changes have reduced mortality, but reproduction variations still fuel genetic changes. In our opinion, the rapid evolution of culture in the late Pleistocene, with all the new perspectives that communication, social interactions and creativity gave, provided more opportunities for future genetic changes, rather than reducing their likelihood."
Mutant Battles
In the mass media, the authors of the work expressed themselves both less scientifically and more boldly. They reminded us that over the 10 thousand years separating us from the Cro-Magnons, changes in the skeleton and dental system were still noted, and, probably, they correspond to genetic changes that ensure adaptation to new conditions. "If you take a hunter who is used to eating meat and put him on a grain diet, he will develop diabetes. And adaptation to such a diet is still ongoing," says Henry Harpending. "Some new genes, the spread of which in the population we see, contribute to prosperity on high–carbon food." In addition, the settlement of Europe was accompanied by an inherited decrease in skin pigmentation: this contributed to the absorption of sunlight and better absorption of vitamin D. There were probably other changes that helped people adapt to a temperate climate and an unusual diet.
According to Harpending (his words are quoted in a press release from the University of Utah), we are no longer what our ancestors were even a thousand or two thousand years ago, and this may explain the difference between bloodthirsty Vikings and modern peace-loving Scandinavians. "According to the prevailing dogma, these are just cultural differences, but almost any feature of temperament is actually largely due to genetics."
He further recalled that human races developed independently and genes in African, European, and Asian populations change, although equally rapidly, but not identically. According to him, we are becoming less similar, rather than forming a single humanity, and gene flows between remote populations are not so strong as to smooth out these differences.
Another participant in the work, Gregory Cochran, spoke even more figuratively: "The history of mankind increasingly resembles a fantasy novel, where mutants appear over and over again and replace normal people – sometimes slowly, due to better survival in conditions of disease and hunger, sometimes gathering in militant hordes. We are these mutants." Cochran is a doctor from New Mexico, self–educated in evolutionary biology, assistant professor at the University of Utah. The other authors of the work, in addition to those mentioned, are anthropologist John Hawkes, geneticist Eric Wong and biochemist Robert Moisis. Admittedly, such a team composition strengthens confidence in the results.
About Ashkenazi hereditary intelligence
A remarkable fact: in 2005 and 2006, Harpending and Cochran (together and in collaboration with other researchers) published several papers that caused heated debate. They argued that the high intelligence of Ashkenazi Jews is the result of a kind of natural selection. The increased intelligence of Jews from the northern part of Europe is confirmed by statistical data, as well as their certain genetic isolation. A textbook example is the high incidence of hereditary diseases of Tay-Sachs and Gaucher. But researchers from Utah made a spectacular assumption: in their opinion, the high intelligence of this group is explained by the fact that in medieval Europe, the advantage in the "struggle for existence" was given to Jews engaged in trade, financial transactions, tax collection – and the stupid in these areas do not succeed. Wealthier families could have more, and in addition, children immediately received opportunities that were not available in poor families engaged in unskilled labor. Harpending and Cochran even suggested that gene clusters responsible for hereditary diseases typical of Ashkenazi in a heterozygous state can contribute to the development of intelligence!
It sounds impressive, but who can prove that the main reason was not non-genetic factors, in particular cultural differences? Of course, candidate genes that increase IQ are already being investigated and, in all likelihood, play a role. On the other hand, it is well known that Jewish parents – in any century, in any country and regardless of religious beliefs – are somewhat more concerned than parents of other nationalities about the success of their children and that they receive the best education...
By the way, nothing like what happened to James Watson after his infamous statements about the intelligence of people from Africa, did not happen to Harpending and Cochran. Maybe because they were talking about someone's hereditary superiority, and not about lagging behind.
Before we return to the main topic of the article, one more interesting fact: Henry Harpending has published several articles co–authored with Russian colleagues from the Institute of General Genetics of the Russian Academy of Sciences and they are devoted to the genetic characteristics of the inhabitants of Dagestan - both plain and mountainous (largely isolated) areas. This, of course, is a completely different story, but if you remember that the Caucasus has been a nodal point of human migrations since ancient times, the topics may be related to each other.
Lactase and its role in world history
In Thornton Wilder's novel The Eighth Day, the kind and intelligent Dr. Gillies believed that the evolution of modern man works to increase the intelligence of humanity as a whole. Doctors Harpending and Cochran and co–authors do not make such rosy predictions - probably because they live a century later. Although there are interesting data on the early stages of human evolution – for example, positive selection by the microcephalin gene (MCRN1), which regulates the size of the brain. But in the end, besides the evolution of the mind, there are a lot of interesting things in the history of our species.
It was known about many genes before that their alleles were subjected to intensive selection: CCR5 (the protein of this gene is famous for being used as a coreceptor by the AIDS virus), the FY blood protein gene (people who lack this protein have immunity against malaria), as well as the lactase enzyme gene, which is well known to our readers responsible for the breakdown of milk sugar – lactose. In China and in most regions of Africa, adults cannot drink milk. However, in Sweden and Denmark there are practically no adults in whom lactase would be inactive. Hence it is clear why dairy cattle breeding developed mainly in Europe, and not in the Mediterranean and Africa – here is an example of the influence of genetics on history and culture.
According to Harpending, it would be interesting to check how the mutation that ensured lactose tolerance spurred the migration of peoples – for example, when speakers of Indo-European languages inhabited the entire space from Northwestern India and Central Asia to Persia and Europe 4000-5000 years ago. He even suggested that it was nutritious dairy products that gave the Indo-Europeans enough energy. It is not for nothing that cows are sacred animals in India; unfortunately, the lactase enzyme molecule is too small to pay homage to it.
Prior to the study by Harpending and co-authors, it was believed that there were relatively few such genes. Now it turns out that there are almost two thousand of them, and it is possible that each of them hides the same interesting story as with lactase.
Probably, in the next decade we should expect new successes in paleogenomics (or maybe also "historical genomics"?). When this issue was being prepared for publication, a research group from the Max Planck Institute for Evolutionary Anthropology and 454 Life Science announced the receipt of the first, "draft" version of the complete genome of a Neanderthal. (An earlier stage of the same project was devoted to an article in Chemistry and Life, 2007, No. 1.) But about this – in one of the following issues.
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10.04.2009