Geology and evolution

Geology (more precisely, paleontology) has always been widely used in studies on molecular evolution for calibrating evolutionary trees. The fact is that modern methods of reconstruction of the history of species in most cases can quite reliably restore the topology of the evolutionary tree and even the length of its branches, there would be enough data. However, the temporary scale on such a tree is measured by the number of replacements for a position in the protein, and in order to translate it into ordinary astronomical time, it is necessary to date intermediate nodes - set the time when the ancestors of modern taxa appeared. And for this they use data on when representatives of these taxa appear in the paleontological annals. However, in recent years, work began to appear in which geology and evolutionary biology interact in a new, unexpected way.

Coal

Lignin is a complex polymer that gives the stiffness and strength of the wood and protect the cell walls, consisting of cellulose, from microbial attacks. In addition, lignin is one of the main predecessors of stone coal. Lignin is decomposed by mushrooms that cause white rot - unlike mushrooms that cause brown rot that modify lignin, but cannot decompose it completely. In order to establish a molecular genetic nature and the evolutionary history of white rot, researchers from the combined genome institute (Joint Genome Institute, a scream, California, USA) determined the genomic sequences of six mushrooms causing white rot, and five brown, and analyzed them, as well as the sequences of another twenty mushrooms Abaricomycotina.

It turned out that the repertoire of proteins involved in the metabolism of polysaccharides in the mushrooms of white rot on average is twice as extensive than in mushrooms with brown rot - both in terms of quantity and in representation of various families. In particular, two families of glycoside-gydrolase, including proteins that decompose cellulose, were present in all mushrooms of white rot and in no one-brown. The same thing was noticed for two more families of proteins involved in the destruction of cellulose molecules.

But in order to get to cellulose, the mushroom must be destroyed by lignin. These are engaged in type II peroxidases. Such proteins are divided into four groups, of which three contain proteins that can destroy lignin, and the fourth - no. Three “destroyers” contain special amino acids in strictly defined positions, and therefore, by the protein, you can find out if it is a destroyer.

As in the case of cellulose hydrolazes, genes encoding peroxidase of the first three groups were found only in the genome of white rot mushrooms. The construction of the evolutionary tree peroxidase showed that the ancestor protein could not destroy Lignin - he did not have critical amino acids. Such a set of amino acids for the first time arose for the common ancestor of the AgaricomyCetes class (including, for example, well -known plate mushrooms, such as russula and fly agaric, and tubular mushrooms, say, princes), and representatives of three groups arose during the evolution several times, regardless of different orders of this class: this evolution.

Further, the authors calibrated the evolutionary trees using available paleontological data about mushrooms, and dated both the time of the appearance of the first liginum-destructive peroxidase, and the time of the appearance of the Agaricomycetes (for which there were no paleontological data). This time almost coincided - 290 million years ago. And shortly after, at the end of Karbon and Perm, the formation of large volumes of stone coal stopped: mushrooms began to eat lignin.

Note that this study could not be performed on the basis of only the paleontological chronicle (because the groups determined by morphological signs may include both mushrooms of white rot and mushrooms with brown rot), nor on the basis of only molecular constructions (because they are not tied to time).

Metals

A similar approach, but on a much wider scale, was used by Lorens David and Eric Alma from the Massachusetts Institute of Technology to the analysis of Prokaryotes (bacteria and archaea). For each family of enzymes, the analysis of the taxonomic tree showed when this family appeared - a special method was developed for this that analyzes the distribution of genes in modern genomes, and the possibility of horizontal transfers is taken into account.

It turned out that most of the families (of those that the latter did not have a common ancestor of all existing organisms) arose in the Archean era, about 3.3 billion years ago. Further, the authors analyzed the cofactors and substrates of these enzymes and found out that among the proteins encoded by the Archaean genes, the proportion of those that bind iron, iron-gray clusters and molecular oxygen, as well as other groups involved in oxidative and restoration reactions. This can reflect the expansion of the repertoire of respiratory processes and the transfer of electrons, and the genes involved in oxygen breathing appear massively only by the end of the Archaean explosion. This is consistent with geological models of increasing oxygen content in the atmosphere.

The frequent use of copper and molybdenum as cofactors of the Archaean genes is also consistent with geochemical information about the appearance of manganese in nestions and increased solubility of these metals with increasing oxygen content in sea water: only dissolved metals are available for living organisms. The situation with Nickel is also generally consistent with geochemical data. But the situation with the iron turned out to be contradictory: the number of enzymes whose cofactor is iron grow, despite the fact that the solubility of iron drops with an increase in oxygen in water, and in oxygen -sized deep waters the iron is precipitated as a result of reactions with sulfide. One of the explanations of this may be evolutionary inertia, due to which it was easier for prokaryots to develop iron production systems, such as siderophores, instead of abandoning iron-dependent enzymes.

Temperature

Another approach is the reconstruction of ancient proteins and the study of their properties. The fact is that modern methods of building evolutionary trees not only restore history, but also (with some probability) - ancestral sequences in each node. Further, the methods of genetic engineering allow you to recreate this sequence in the form of a DNA molecule, insert it into a living bacterium and develop the corresponding protein. And then you can study its properties, for example, the temperature optimum - the temperature at which the enzyme is most active.

Simple evolutionary considerations (confirmed by numerous observations) show that the temperature optimum coincides with the temperature at which (mainly) the body lives. So, having reconstructed ancient proteins and measuring their temperature optimum, we can establish at what temperature the ancestors of modern organisms lived. It was this approach that was used in the work made in the laboratory of Eric Gosher. Since the ambitions of the authors extended very far, they investigated a very conservative protein, the EF-Tu broadcast factor. The authors reconstructed proteins in several internal nodes, measured the temperature optimums and compared them with the temperature of the oceans. It turned out that two graphs were almost completely coincided - with the accuracy of the imperfection of the evolutionary dating of internal nodes and measuring temperature according to indirect geochemical data.

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The narrow place of the second and third of the work under discussion is the dating of internal nodes. In the first case - for mushrooms - everything is clear: the dating is carried out according to paleontological data, which, even taking into account the incompleteness of the paleontological annals, give reasonable assessments (it should be borne in mind that the appearance of a taxon in the form of famous paleontological objects can happen noticeably later than its occurrence during evolution). But how to calibrate the evolutionary tree prokaryot? Firstly, there are also paleontological and geological considerations, say, an increase in the concentration of oxygen in the atmosphere (which can be observed) naturally associated with the occurrence of photosynthesis-and, therefore, the corresponding proteins (at the molecular level) and cyanobacteria (at the taxonomy level). The second way is to tie the evolution of bacteria to the evolution of other organisms (say, owners for pathogens or endosimbiones), for which you can recalculate molecular watches in astronomical time and thus pump the molecular hours of prokaryotes.

It is clear that so far such works are more likely bright curves. However, it is also clear that with an increase in the volume of excessive genomic data, the flow of such results will increase, and, as always in science, gradually a colorful, but generally consistent picture of what (apparently) actually happened. And the moral, arising from these first attempts, consists in the fact that interesting observations are made when attracting very diverse considerations. And this morality is not new.

1. D. Flouds et al., The Paleozoic Origin of Enzymatic Lignin Deconsition Reconsted from 31 Fungal Genomes. Science 336: 1715 (2012).
2. La David, EJ Alm. Rapid Evolutionary Innovation During An Archaean Genetic Expansion. Nature 469: 93 (2011).
3. EA Gaucher et al. Palaeotemperature Trend for Precambrian Life Inferred from Resurrected Proteins. Nature 451: 704 (2008).