Every now and then, in various sources, a myth pops up that “a pig is genetically closer to humans than a chimpanzee,” and this misconception is very persistent.
Partly because pig internal organs are very suitable for transplantation into humans. And Bernard Werber added fuel to the fire with his rubbish “Father of Our Fathers” (but, you have to understand, it’s pure fantasy).
But what do geneticists think about this? How close are pigs and humans genetically?
Vladimir Aleksandrovich Trifonov: Genome homology numbers are of rather low value; it all depends heavily on what we are comparing with what: whether we take into account structural changes in the genome, whether we take into account repeated sequences, or whether we are talking only about substitutions in coding regions.
As a comparative cytogeneticist, I can say that the evolution of pig karyotypes was accompanied by a large number of rearrangements - even 11 breaks and 9 inversions separate pigs from the common ancestor with ruminants and cetaceans, plus 7 mergers and three inversions occurred in the line of pigs after the separation of peccaries. When we build molecular phylogenies based on sequencing data, pigs are never related to humans; there is a lot of such data that can be cited and they are much more accurate and reliable than general estimates of molecular differences. There are hundreds of thousands of differences between the pig and human genomes, so special programs are used to evaluate them, which build phylogenetic trees based on the similarities and differences of many characters. Position on the phylogenetic tree precisely reflects the degree of similarity or difference between species.
Phylogeneticists have their difficulties and their controversies, but few today doubt some basic ideas. Here, for example, are three recent papers where phylogenies were constructed by different groups (who are generally recognized experts in the field) based on a variety of characters taken from DNA sequences:
Conrad A. Matthee et al. Indel evolution of mammalian introns and the utility of non-coding nuclear markers in eutherian phylogenetics. Molecular Phylogenetics and Evolution 42 (2007) 827–837.
Olaf R. P. Bininda-Emonds et al. The delayed rise of present-day mammals. Nature, Vol 446|29 March 2007.
William J. Murphy et al. Using genomic data to unravel the root of the placental mammal phylogeny. Genome Res. 2007 17: 413-421.
In all published phylogenies (see figure below), the pig firmly takes its place among the artiodactyls, and humans “do not jump out” from the order of primates, i.e. data obtained from the analysis of different DNA sequences equally answer this question, confirming in this matter the phylogenies built on morphological characteristics back in the 19th century.
From the figure it can be seen that the pig is further from the person than the mouse, rabbit and porcupine. Source: William J. Murphy et al. Using genomic data to unravel the root of the placental mammal phylogeny. Genome Res. 2007 17:418.
Mikhail Sergeevich Gelfand: To be honest, I won’t say right away about the exact % of DNA matches, and it’s not very clear what that would mean: in genes? in intergenic spaces? Most of the pig genome simply does not align with humans (unlike chimpanzees), so it makes no sense to talk about the percentage of matches. In any case, a pig is further from a person than a mouse. But those who are close to pigs are whales (though they are even closer to hippos).
Question. Konstantin Zadorozhny, editor-in-chief of the magazine for teachers "Biology" (Ukraine): In the e-book of the respected S.V. Drobyshevsky "The Missing Link" it is indicated that the second human chromosome was formed as a result of the fusion of two chromosomes of the ancestral species, which in chimpanzees remained unfused (this I personally came across the information before, but it was practically not covered in popular publications). Accordingly, a question for one of the experts. At what stage of human evolution (early hominids, australopithecus, early homo, etc.) did this chromosomal aberration occur? Is it possible to determine this?
Answer. Vladimir Aleksandrovich Trifonov: I will be happy to answer your question, since the fusion of the chromosomes of the ancestor of chimpanzees and humans (corresponding to chimpanzee chromosomes PTR12 and PTR13) is indeed the last significant event that changed the human karyotype.
Let's start with the ancestor of great apes - comparative genomics data indicate that these two karyotype elements were acrocentric, and it was in this unchanged form that they were preserved in the orangutan.
Next, in the common ancestor of humans, gorillas and chimpanzees, a pericentric inversion occurs, turning one of these elements into a submetacentric (this element corresponds to the chimpanzee chromosome PTR13 and the gorilla chromosome GGO11). Then, in the common ancestor of humans and chimpanzees, another pericentric inversion occurs (in the homologue of the chimpanzee PTR12 chromosome), turning it into a submetacentric.
And finally, the last event in the Homo lineage is the fusion of two submetacentrics with the formation of the human chromosome HSA2. This is not a Robertsonian fusion (centric), but a tandem one, with the PTR12 centromere retaining its function, the PTR13 centromere inactivated, and at the point of tandem fusion ancestral telomeric sites are found (Ijdo et al., 1991).
Based on the time of formation of the human chromosome HSA2, we can only say that the fixation of this rearrangement occurred after the divergence of the human-chimpanzee lines, i.e. no earlier than 6.3 million years ago.
I don't think there is an increased incidence of Robertsonian translocations in apes. They have very conservative karyotypes, changing little over millions of years; during this time, dozens of significant transformations have occurred in the karyotypes of species of other taxa. There is evidence from clinical cytogenetics indicating a frequency of 0.1% in human meiosis (Hamerton et al., 1975). However, genome analysis shows that such rearrangements have not been recorded in the human lineage.
Question. Alexey (letter to the Editor): Questions arise during the lectures on genomics for the Phystech. The gene has not been defined...
Answer. Svetlana Aleksandrovna Borinskaya: It was easy to define a gene when not much was known about it. For example, “a gene is a unit of recombination”, or “a gene is a section of DNA that encodes a protein”, “One gene - one enzyme (or protein)”, “One gene - one trait”.
It is now clear that the situation is more complicated with both recombination and coding. Genes have different structures, sometimes quite complex. One gene can encode many different proteins. One protein can be encoded by different DNA fragments located at a large distance in the genome, the products of which (RNA or polypeptide chains) are combined into one polypeptide as they mature.
In addition, the gene contains regulatory regions. And there are also genes that do not encode proteins, but encode only RNA molecules (in addition to the well-known ribosomal RNAs, these are RNA molecules that are part of other molecular machines, recently discovered microRNAs and others
types of RNA). Therefore, now there are many definitions of what a gene is. The gene is a concept that is difficult to condense into one short, all-encompassing definition.
Answer S.B.: The genome is DNA. Or a complete set of DNA molecules of an organism (in a separate cell) = genome.
By this we do not mean cells in which DNA rearrangements occur during development (such as cells of the immune system in mammals or animal cells in which “chromatin diminution” occurs - the loss of a significant part of DNA during development).
Answer S.B.: E. coli is the most studied bacterium, but even for it, the functions of all genes are still not known. Although the nucleotide sequence of a gene can be used to “deduce” the amino acid sequence of a protein. For well-studied bacteria, approximately half of the genes have known functions of the proteins they encode. For some genes, experimental confirmation of functions has been obtained; for others, predictions are made based on the similarity of the protein structure with other proteins with known functions.
Question. Alexey: Do I understand correctly that the number of nucleotides included in a gene is different for each gene? There is no pattern here.
Answer S.B.: Absolutely right.
Question. Alexey: Can different genes have an absolutely similar nucleotide sequence, but differ only in location?
Answer S.B.: There are probably no absolutely identical genes. But there are genes located in different parts of the genome with very similar nucleotide sequences. Only they are called not “analogous”, but “homologous”. These genes are the result of duplication of an ancestral gene. Over time, they accumulate nucleotide substitutions. And the closer to us the time of duplication is, the more similar the genes are. Gene duplications occur in all organisms, from bacteria to humans.
Moreover, different genes in different people can be contained in different numbers of copies. Copy number can influence the activity of the corresponding gene products. For example, different numbers of genes for certain cytochromes affect the rate of metabolism and excretion of drugs from the body and, accordingly, different doses are recommended.
Question. Alexey: I would also like to hear the opinion of experts regarding the materials provided by Garyaev (meaning the so-called “wave genome” theory). He claims that his experiments are confirmed experimentally in laboratories. Is that so? What can you say to this?
Answer S.B.: You, too, can say whatever you want. But the scientific world will pay attention to your statements only if they are published in peer-reviewed scientific journals, and even presented with a description of the details of the experiment, allowing it to be repeated.
Mr. Garyaev does not publish his “discoveries” in scientific journals, he only tells them to journalists. There is no data about the “experiments” he conducted, only his words. Let them at least show a laboratory journal with a detailed record of the conditions and results of the experiments.
People love looking at photographs of animals. Cats, dogs, horses, llamas - all of them, especially babies, seem very cute to us. However, few people call monkeys, especially great apes, cute or cute. These animals look like a parody of humans. Obvious similarities mixed with distinctly animal characteristics evoke mixed feelings.
Man and monkey are really similar. At the DNA level, the similarities between Homo sapiens And Pan troglodytes- chimpanzees - exceeds 98 percent. In numbers, this difference does not seem so small: of the three billion “letters” of the human genome, as many as 60 million are unique to H. sapiens. In this case, the numbers create a false impression of the gap separating man from ape. Almost all the genes of these two groups of organisms differ only by minor variations in DNA sequence.
Scientists still cannot explain how these small genetic differences were able to provide a colossal evolutionary leap from apes to humans. The first answer that comes to mind is the sequences characteristic of H. sapiens, were compiled into special “humanity genes” in his genome. However, in practice this theory is not confirmed: researchers have not found unique genes in humans. All genes H. sapiens evolved from the genes of a common ancestor with chimpanzees. For the first time, the authors of the new study found three exceptions to this rule.
Evolution at the gene level
Before describing the new discovery, it is worth telling in a little more detail how exactly the evolution of genetic sequences occurs. The genomes of the very first living organisms to appear on our planet contained only a few hundred genes. To reproduce, the first inhabitants of the Earth divided their body, consisting of a single cell, in two. Each of the offspring received one copy of the parental genome. Copying of the DNA of the “father” (or “mother”) occurred with errors - some genes were lost, while others, on the contrary, appeared in a double version. In some cases, the “extra” genes did not lead to the death of the host. They were preserved in a chain of generations and gradually mutated. After several tens of hundreds of copies, the sequence of such genes changed beyond recognition. Accordingly, the sequence of proteins encoded by the genes also changed. Gradually, the structure of living beings became more complex, but the mechanisms for the formation of new genes remained unchanged.
In some cases, new genes appeared without doubling old ones - mutations also appeared in genes presented in a single copy. If the changes did not worsen the viability of the organism, they could persist through a series of generations. Eventually, a critical number of such neutral or positive mutations accumulated in the gene, and new functions appeared in the encoded protein.
Another way new genes are formed is through the loss of part of the sequence. A shortened gene sometimes continued to work no worse than a full copy, in addition, the place of the lost “letters” could be taken by neighboring DNA sequences. Another option for the birth of new genes is the “merging” of old genes with each other or their splitting.
In all the described cases, genes are not created de novo: the basis for them is always the variants already existing in the body. Biologists were confident in this fact until 2006, when the journal Proceedings of the National Academy of Sciences a group of researchers working with fruit flies appeared Drosophila melanogaster.
The authors discovered as many as five genes in the Drosophila genome that are not found in its closest relatives. All of them were formed from so-called “junk” DNA. Scientists use this unflattering epithet to describe non-protein-coding DNA sequences whose function is unknown. The term was proposed in 1972 by Japanese-American geneticist Susumu Ohno and has since stuck. In advanced organisms, junk DNA makes up more than 95 percent of the genome.
After the publication of the fly's work, biologists rushed to look for unique genes in other organisms. However, to date they have only been found in yeast. However, the authors of the new study, led by Aoife McLysaght from Trinity College Dublin, set out to find new genes in humans.
Keys to Humanity
MacLysath and her colleagues compared the genomes H. sapiens And P. troglodytes. Using special programs, they compared the sequences of currently known human and chimpanzee genes. The authors discovered 644 genes in the human genome that have no analogues in chimpanzees.
The order of genes in chimpanzees and humans is practically the same. The researchers closely examined areas of the monkey genome where suspicious sequences could be located. In existing DNA databases P. troglodytes Some of these places were missing large chunks of code, so the researchers had to exclude 425 of the 644 genes they found.
In the next stage of the work, the scientists re-searched the remaining 219 sequences in the chimpanzee genome, using a slightly different algorithm. 150 supposedly unique human genes in the genome P. troglodytes analogues have been discovered. Thus, the “circle of suspects” was narrowed to 69 genes. Scientists removed from this list sequences that were found in the genomes of species other than chimpanzees. Finally, MacLysath and her co-authors discarded genes that were only present in one human DNA database and might have gotten there by mistake.
Only three genes passed through all stages of selection - CLLU1, C22orf45 And DNAH10OS. To further verify their uniqueness to humans, the researchers checked the genomes of macaques, gibbons and gorilla. Sequences reminiscent CLLU1, C22orf45 And DNAH10OS, were found in all primates studied, but they could not be full-fledged genes and were present in “junk” DNA.
To be considered a genome, a sequence must contain certain combinations of “letters,” specifically those marking the end and beginning of the gene. Such characteristic “letter combinations” are recognized by enzymes responsible for protein synthesis from this gene. The macaque, chimpanzee, gibbon and gorilla did not have distinctive genetic characteristics. Moreover, they had areas that interfered with the full functioning of the enzymes. Moreover, in all primates (except humans) these areas were the same.
The researchers suggested that during human evolution, some regions of "junk" DNA present in primates accumulated the necessary changes that allowed them to become real genes. It was the work of these genes that led to the emergence of the genus Homo.
Because of gaps in genetic databases and very strict selection criteria, scientists were only able to fully study 20 percent of the genes initially selected. Accordingly, in the future, when the holes are filled, the authors expect to discover at least 15 more unique genes. In the meantime, the authors have focused on searching for proteins encoded by “human” genes. Work by other research groups has shown that proteins from these sequences are synthesized, but what their function may be is not entirely clear at the moment. If MacLysath and his colleagues manage to find out this, then humanity may be a little closer to answering the question of how humans differ from apes.
About garbage and RNA
In fact, scientists know a partial answer to this question. The results of many studies looking for differences between humans and monkeys indicate that the secret lies not in the sequence of proteins, but in the regulation of their work. Moreover, not only regulatory proteins, but also special RNA molecules can control the functioning of the human genome and proteins. The genes encoding these molecules are also located in “junk” DNA. So sometimes trash can be useful.
