Vol 55, No 5 (2019)

The emergence of genetic diseases and evolutionary processes are associated with the flow of genetic information from one generation to another, in which genetic information carried by gametes can be changed by the appearance of de novo germline mutations. The rate of germline mutations determines the rate of evolution and the incidence of heritable disorders. Despite the great theoretical and practical importance, the problem of establishing mutation rates and their dependence on different factors remains scarcely studied, and the mutation rate values obtained by different methods vary considerably. The review discusses different ways of estimating the rate of these mutations and makes an attempt to explain the reasons for discrepancies in the data obtained. Three levels of the mutation formation are considered: (1) mutations that are formed during the development of a given individual during gametogenesis (basic mutations); (2) mutations transmitted to offspring and determining differences in the genomes of consecutive generations (parents and offspring), which include basic mutations and possible changes resulting from complex processes of sperm transfer to oocyte, fertilization, and subsequent events that lead to only one viable offspring of hundreds of millions spermatozoa and oocytes; (3) mutations which are formed at level 2, fixed in evolution, and determine evolutionary processes and differences between genomes, in particular, of hominoids, hominids, and hominins.

Mycobacterium avium subsp. hominissuis (MAH) are typical inhabitants of the environment, which are known as opportunistic pathogens of animals and humans. The aim of our study was to analyze single-nucleotide polymorphisms (SNPs) in the hsp65 and MACPPE12 genes to characterize the Russian population of MAH in the context of studying phylogenetic relationships and the evolution of geographically distant populations of M. avium subsp. hominissuis. The sequence analysis of the hsp65 and MACPPE12 genes was applied for 40 MAH strains isolated from humans (patients with mycobacteriosis). The nucleotide sequences were aligned to the reference genome of M. avium subsp. hominissuis 104 (accession no. NC_008595.1). The mutational profiles of Russian strains were compared with those isolated in other countries. In total, 40 MAH strains were classified into three different hsp65 sequevars: code 1, code 2, and code 3. The majority of MAH strains (72.5%) belonged to code 1, the same sequevar as for MAH strain 104. The sequence analysis of the MACPPE12 gene revealed 20 SNPs grouped into nine sequevars at the nucleic acid level: NA01, NA02, NA03, NA06, NA10, NA13, NA14, NA19, and NA_Rus01. Eight out of 20 SNPs were nonsynonymous, resulting in seven sequevars at the amino acid level: AA01, AA02, AA04, AA07, AA08, AA13, and AA_Rus01. The sequevar AA02 consisted of three different NA variants with synonymous SNPs profiles: NA02, NA03, and NA06. Half of the MAH strains belonged to the sequevar AA02 (type NA02). The predominant cluster AA02 (type NA02)/code 1 and the unique variant AA_Rus01 (NA_Rus01) were identified among MAH strains from Russia. Thus, we confirmed the relative conservativeness of the nucleotide sequence of the hsp65 gene but the polymorphism of the MACPPE12 gene. At the same time, a comparative analysis of the SNPs profiles of the hsp65 and MACPPE12 genes allowed us to identify differences and similarities between geographically distant populations of MAH, which highlighted the variability of the global population of M. avium species.

The results of morphological and molecular genetic analysis confirming the hybrid nature of Salix × zhataica Efimova, Shurduk et Ahti are presented. In particular, according to the complex of phenotypic features (on the basis of discriminant analysis), the hybrid, which resulted, apparently, from interspecific hybridization of S. brachypoda (Trautv. et C.A. Mey.) Kom. and S. pyrolifolia Ledeb., is closer to S. brachypoda, indirectly indicating that this “parent” can be maternal. The polymorphism of molecular-genetic markers such as nuclear microsatellite loci and nucleotide sequences of the ITS region was analyzed in order to verify the hybrid and its parent species, S. brachypoda (Trautv. et C.A. Mey.) Kom. and S. pyrolifolia Ledeb. For instance, in the ITS region, two single nucleotide transitions were found, which indicate that the hybrid borrowed the corresponding nucleotides from both parent species. The given data indicate that S. × zhataica is indeed a hybrid between S. brachypoda and S. pyrolifolia.

We performed a population genetic analysis of 22 Pacific cod sample sets (n = 986) based on the mtDNA control region (599 bp) polymorphism, which made it possible to specify four distinguished groups of this species: (1) within the seaward parts of the Bering Sea and Sea of Okhotsk and northern part of the Pacific Ocean, affected by the Pacific Ocean gyres; (2) coastal areas of the East/Japan Sea; (3) northern part of the Sea of Okhotsk, more similar to the second group from the East/Japan Sea by haplotype sets than to the seaward groups, despite limited reproductive contacts, special hydrological conditions, and the history of formation of the sea areas; (4) fundamentally different Pacific cod from the Yellow Sea adapted to the conditions of the shallow water area in the subtropical region.

Reconstruction of the mitochondrial genome of a horse from the Ashna-Pando hillfort (the Sura River basin, Middle Volga, Ulyanovsk oblast, Russia) was performed using bone remains. It was established that, according to a fragment of the control region (D-loop), the specimen belongs to the B1 haplotype widespread among modern as well as ancient horses of Europe and Asia. However, in accordance with complete mitochondrial genome analysis, the horse is attributed to the M haplogroup that includes different modern breeds, with the Akhal-Teke breed among them. The obtained data make it possible to postulate the steppe origin of the horse. On the basis of our analysis, penetration of the southern horses deep into the broadleaf forest area likely dates to the second or third quarter of the first millennium BC and is probably connected with interactions of the sedentary population of the Sura River region with Scythian nomads.

Phylogeographic analysis of the variability of whole mitochondrial genomes in the Russian populations of Eastern Europe (n = 557) showed that, in the Russian mitochondrial gene pool, there were subgroups of mtDNA characteristic only of Russians and other Eastern Slavs (11.7%), as well as of Slavs as a whole (12.2%), Slavs and Germans (6.6%), and Slavs and Baltic Finns (5.7%). The results of molecular dating suggest that the mitochondrial subgroups characteristic of Russians and Slavs in general began to arise 2700–3500 years ago. The results of the study of the dynamics of the effective population size based on the Bayesian analysis of data on the variability of mtDNA haplotypes specific to Russians and Slavs showed that a rapid increase in population sizes occurred immediately after its decline 4000–5000 years ago. The data obtained are discussed in comparison with the results of the analysis of Y-chromosome polymorphism in European populations.

A model of weak viability selection at two multiple-allele loci in a haploid population is considered. It is assumed that population is randomly mating, the generations do not overlap, and the genetic structure dynamics is modeled by ordinary differential equations. Weak selection is considered as a perturbation of the model without selection. The quasi-equilibrium estimates for the linkage nonequilibrium coefficient D obtained earlier at diallelic loci are generalized to the case of multiple alleles. Moreover, the interpretation of estimates in terms of average effects in quantitative genetics turned out to be independent of the number of alleles. The first approximation for the quasi-equilibrium of \({{D}_{{{{i}_{1}}{{i}_{2}}}}}\) is \(D_{{{{i}_{{\text{1}}}}{{i}_{{\text{2}}}}}}^{ * }\) = \({{\varepsilon }_{{{{i}_{{\text{1}}}}{{i}_{{\text{2}}}}}}}(\mathbf{p})\frac{\mu }{r}{{x}_{{{{i}_{1}}}}}{{y}_{{{{i}_{2}}}}},\) where μ is the intensity of selection; r is the coefficient of recombination; \({{\varepsilon }_{{{{i}_{{\text{1}}}}{{i}_{{\text{2}}}}}}}(\mathbf{p})\) is the index of epistasis nonadditivity for the viabilities \({{{v}}_{{{{i}_{{\text{1}}}}{{i}_{{\text{2}}}}}}}\) of haploid genotypes i₁i₂; and \({{x}_{{{{i}_{{\text{1}}}}}}},\)\({{y}_{{{{i}_{{\text{2}}}}}}}\) are the frequencies of alleles constituting the genotype with the numbers i₁, i₂ for the first and second locus, respectively. The specificity of the perturbed model is that it distinguishes fast (the coefficient of disequilibrium \({{D}_{{{{i}_{1}}{{i}_{{\text{2}}}}}}}\)) and slow (allele frequencies) variables, which characterizes the model as singularly perturbed. This makes it possible, without solving the equations, to distinguish two dynamic stages. At the first stage, fast variables converge to quasi-equilibrium values, and at the second stage, the evolution of slow variables proceeds under the condition of quasi-equilibrium of the fast ones. The equations obtained by the delta method with respect to the quasi-equilibrium values \({{D}_{{{{i}_{k}}{{i}_{m}}}}}\) give the correct result from the point of view of the expansion in powers of a small parameter of the singularly perturbed equation solutions. The problems of measuring epistasis and decomposition of the coefficient of epistasis into elementary components are discussed, and the two-locus coefficients of epistasis are analyzed as characteristics of a multilocus model. The generalization of the results obtained for the haploid population to the diploid case is briefly indicated.

High concentrations of ethanol and oxidative stress can cause a mutagenic effect on mitochondrial genomes (mtDNAs) of flor yeasts. We performed a comparative analysis of mtDNAs of wine yeast strains and three sequenced flor yeast strains. mtDNAs of flor strains are characterized by high conservation of nucleotide sequences and the structure. The numbers of destabilizing elements of mtDNA (GC clusters, short repeats, active ori sequences) in flor strains are generally lower than that in wine yeasts. The mtDNA conservation of flor strains can be determined by both bottleneck effects in the course of evolution and mechanisms aimed at maintaining the genetic stability. In general, the data obtained do not confirm the hypothesis of increased genetic variability of the mitochondrial genomes of flor yeast strains.