Vol 53, No 11 (2017)

This paper presents a brief history of two different methods for studying the species population structure. The first method employs ecological markers that characterize population-specific environmental conditions, as well as biological features of populations. The second one involves genetic markers: DNA and RNA fragments, allozymes, etc. The problem of combining these two methods is discussed. A two-step approach is suggested for studying the species population structure using both the ecological and genetic markers. Firstly, the studied part of the species range is subdivided into so-called ecogeographic units (EGUs) according to environmental gradients, life strategies, and other characteristics that presumably associate with adaptation gradients and interpopulation gene flows. Secondly, the EGUs are tested genetically by using the data on multiple population samples that represent population segments within each of the ecogeographic units. The notion of representative samples with respect to the population structure, hierarchy of EGUs–populations, strategies of population management, and selection of the management units for optimizing exploitation, reproduction, and conservation of species fragments are discussed on the basis of this approach.

Epigenetic mechanisms of speciation are considered, including heterochromatic modifications and changes in spatial chromosome organization in the generative cell systems. The value of lamina, topoisomerase II, and a DNA polypurine tract in the attachment of chromosomes to the nuclear envelope is discussed. It is postulated that the main event leading to species-specific fixation of gene mutations, chromosomal mutations, and heterochromatin modifications in speciation is the rearrangement of spatial chromosome organization in the nucleus. The change in interchromosomal relationships associated with the reorganization of the system of chromosomal contacts with the nuclear envelope and the rearrangement of the chromocenter apparatus of the interphase nucleus is estimated as a systemic mutation directly related to speciation.

This special issue of the journal is devoted to the outstanding population geneticist Yuri Petrovich Altukhov, who paid much attention in his research to the development of molecular genetic markers for population studies. Over the past time markers and methods of their development have undergone significant change. Thanks to modern methods of whole genome sequencing, it has become possible to develop markers of very different types—selectively neutral, as well as functional. Among them, microsatellite markers remain the most informative, convenient, reproducible, relatively inexpensive, and polymorphic. Whole genome sequencing greatly facilitates their discovery and development. This paper is devoted to the development of new microsatellite markers for a very important species of boreal forest—Siberian larch (Larix sibirica Ledeb.). Using a draft assembly of the larch genome, several thousand contigs containing microsatellite loci with di-, tri, tetra-, and pentanucleotide motifs were selected. A total of 59 pairs of PCR primers were tested for loci with dinucleotide motifs as the most variable. From them, 11 pairs were finally selected for 11 loci with dinucleotide repeats, which showed a high level of polymorphism and can be used in various population genetic studies and to identify the origin of wood and plant material. This study was done at the Laboratory of Forest Genomics of the Genome Research and Education Center of the Siberian Federal University with the support of the Department of Forest Genetics and Forest Tree Breeding of the Georg-August University of Göttingen, the Department for Monitoring of Forest Genetic Resources of the Forest Protection Center of the Krasnoyarsk Territory, and the Laboratory of Forest Genetics and Selection of the Sukachev Institute of Forest of the Siberian Branch of the Russian Academy of Sciences within the framework of the project “Genomics of the Key Boreal Forest Conifer Species and Their Major Phytopathogens in the Russian Federation” funded by the Government of the Russian Federation (grant no. 14.Y26.31.0004).

Panax ginseng Meyer is one of the important medicinal plants in the world, particularly in Asian countries. Ginseng encounters many stress exposure during its long cultivation period. However, the molecular mechanism of stress resistance is still poorly understood in spite of its importance. In this study, pathogenesis-related protein 6 (PR6), also called proteinase inhibitor (PI), was isolated from ginseng embryogenic callus, named PgPR6. The small size of PR6, containing an open reading frame of 219 bp encoding 72 amino acids, the typical characteristic of PR6 protein, shares the highest sequence similarity to PR6 of Theobroma cacao (69% identity). Sequence and structural analysis indicated that PgPR6 belongs to class Kunitz-type PI family. This is the first report pertaining to the identification of PR6 gene from the P. ginseng genome. The high-level expression of PgPR6 was observed in root as revealed by quantitative real-time PCR. The temporal expression analysis demonstrated that PgPR6 expression was highly up-regulated by signaling molecules, heavy metals, mechanical wounding, chilling, salt, sucrose, and mannitol stress, indicating that PgPR6 may play an important role in the molecular defense response of ginseng to a various range of environmental stresses.

The present-day contact zone between the Beringian and Arctic phylogenetic lineages of charrs of the genus Salvelinus in the Northwest Pacific is documented. A comparative analysis of the genetic differentiation and divergence indices for allopatric and sympatric populations of charrs and phylogenetic and genealogical analyses of the mtDNA haplotypes indicate that Lake Achchen and the Lake Pekulineiskoe are the zones of secondary contact between S. m. malma and S. taranetzi; Lake Nachikinskoe, between S. m. malma and Salvelinus sp. 4; and Lake Dal’nee, between S. m. malma and S. krogiusae. The level of divergence between phylogenetic groups of haplotypes considerably exceeds the range of intraspecific variability of S. m. malma and could not have been achieved after colonization of the lakes in conditions of sympathy. The obtained data suggest that the territory of Kamchatka was colonized by the common ancestor of the Arctic phylogroup of Taranetz charr.

Recent research in the field of genomics and epigenetics has provided evidence that alterations in the system of epigenetic regulation are highly involved in the molecular etiology of neurodegenerative and neuropathic disorders. However, there is a gap in knowledge on the epigenetic perturbations that may accompany the CNS impairments during the development in the prenatal period and their manifestation as a congenital encephalopathy in the early postnatal period of child development. The present study is one of the first attempts aimed at addressing this gap. Here, we present data on genome-wide profiles of DNA methylation obtained using the Illumina HumanMethylation450 microarray in peripheral blood cells in a sample of young children (up to four years of age) diagnosed with congenital encephalopathy. We provide evidence on systematic alterations in the epigenome—predominant hypermethylation of gene promoter associated CpG islands—related to the CNS impairment in children. Specifically, we found significant DNA methylation changes in genes involved in DNA-dependent transcription regulation and transcription factor binding, with a key role of the transcription factor JUN; in genes controlling cellular response to hypoxia; and in genes involved in the control of neuronal development, functioning, and death.

Genetic-demographic parameters of natural reproduction in the most numerous ethnic groups of Moscow and St. Petersburg were assessed on the basis of the 2002 All-Russia Population Census data and other sources. The intensity of intragroup selection due to individual differences in fertility in the cohorts of women born in the 1930s–1950s decreased in all ethnic groups studied. It was concluded that, in both megacities, the relaxation of the selection component due to differential fertility almost stopped: the values of the Crow’s index I_f stabilized at 0.3 < I_f < 0.4, which was associated with relative stabilization of the interfamily variance of fertility. The temporal dynamics of the intensity of intergroup selection due to interethnic differences in fertility rates was more complex. It was only recently that this type of selection came into action, since even at the beginning of the 20th century fertility rates in various ethno-territorial and ethno-confessional groups of the population of the Russian Empire were similar (5–6 offspring per marriage). In the subsequent decades, interethnic differentiation in progeny size increased because the reproductive behavior of different population groups underwent “modernization” with uneven speed. In Moscow and St. Petersburg, the intensity of intergroup selection decreased in women birth cohorts of the 1930s–1950s, while it was an order of magnitude lower than the intragroup selection. Currently, the average number of offspring varies among ethnic groups in a narrow range from 1.3 to 1.6. It can be expected that interethnic differences in fertility rates in these megacities will increase again owing to growing numbers of migrants from regions with traditionally high birth rates, resulting in differential natural growth of ethnic groups and the corresponding dynamics of the gene pool of the population.