Increase in the number of the B-chromosomes and variants of their system in mouse <Emphasis Type="Italic">Apodemus peninsulae</Emphasis> in Mountain Altai population over 26 years

A new evolutionary genetic phenomenon—increase in the number of B-chromosomes (almost threefold) accompanied by change in B chromosome morphotypes—was discovered in the Artybash population of East Asian mouse Apodemus peninsulae (Mountain Altai) over a historically short period (22 years), comparable with a small number of mouse generations (ten generations). The process of increase in the number of A. peninsulae B-chromosomes in Mountain Altai has been monitored over 26 years (1980, 1986, 1988, 1990, 2002, and 2006). A concept of a new type of genomic mutations—mutations in the number of B-chromosomes—has been substantiated. The phenomenon of genomic mutations in pro-B-chromosomes has been discovered only in the Mountain Altai populations. This region differs from the remaining A. peninsulae dwelling localities by pollution with unspent liquid propellant (UDMH, heptyl). It is assumed that the variants of mouse B chromosome system in the studied A. peninsulae populations in the overall habitation area over long-term periods are likely to remain relatively stable and that their variation is controlled by homeostatic processes. Disturbance of these processes, in particular, due to anthropogenic load, can disrupt the cyclic pattern of increase and decrease in the number of A. peninsulae B-chromosomes in individual years.     

The mechanisms of formation and evolution of B chromosomes in Korean field mice <Emphasis Type="Italic">Apodemus peninsulae</Emphasis> (Mammalia,Rodentia)

Several hypotheses concerning variations in the frequency of some elementary events determining the formation and reorganization of mammalian B chromosomes are proposed on the basis of the data on their number, morphology, and DNA composition in Korean field mice Apodemus peninsulae (Mammalia, Rodentia) from natural populations of Altai, Buryatia, Irkutsk oblast, and Primorye. The mechanisms and causes responsible for the formation of B chromosomes and differences in their organization in populations of mice from geographically separated regions are discussed.     

Low-pass single-chromosome sequencing of human small supernumerary marker chromosomes (sSMCs) and <Emphasis Type="Italic">Apodemus</Emphasis> B chromosomes

Supernumerary chromosomes sporadically arise in many eukaryotic species as a result of genomic rearrangements. If present in a substantial part of species population, those are called B chromosomes, or Bs. This is the case for 70 mammalian species, most of which are rodents. In humans, the most common types of extra chromosomes, sSMCs (small supernumerary marker chromosomes), are diagnosed in approximately 1 of 2000 postnatal cases. Due to low frequency in population, human sSMCs are not considered B chromosomes. Genetic content of both B-chromosomes and sSMCs in most cases remains understudied. Here, we apply microdissection of single chromosomes with subsequent low-pass sequencing on Ion Torrent PGM and Illumina MiSeq to identify unique and repetitive DNA sequences present in a single human sSMC and several B chromosomes in mice Apodemus flavicollis and Apodemus peninsulae. The pipeline for sequencing data analysis was made available in Galaxy interface as an addition to previously published command-line version. Human sSMC was attributed to the proximal part of chromosome 15 long arm, and breakpoints leading to its formation were located into satellite DNA arrays. Genetic content of Apodemus B chromosomes was species-specific, and minor alterations were observed in both species. Common features of Bs in these Apodemus species were satellite DNA and ERV enrichment, as well as the presence of the vaccinia-related kinase gene Vrk1. Understanding of the non-essential genome elements content provides important insights into genome evolution in general.     

Genetic diversity of local spring bread wheats (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.) of West and East Siberia in gliadin genes

A considerable polymorphism in gliadin genes was detected in the wheat landraces of West Siberia (Altai krai, Omsk oblast, and Kurgan oblast) and the local cultivars characteristic of several East Siberian regions (Krasnoyarsk krai, Irkutsk oblast, Tuva, and Yakutia), and the genetic formulas were determined. The common alleles characteristic of the wheats of both regions were detected, namely, Gli-A1f, Gli-A1j, Gli-A1i, Gli-A1m, Gli-B1e, Gli-B1m, Gli-D1a, Gli-A2q, Gli-A2k, Gli-A2u, Gli-D2a, and Gli-D2q, as well as 14 novel alleles unknown earlier. It was demonstrated that several genotypes had formed in Siberia. Of them, the genotypes Gli-A1f_Gli-B1e_Gli-D1a and Gli-A1j_Gli-B1e_Gli-D1a occur both in West and East Siberia, whereas the genotypes Gli-A1i_Gli-B1m_Gli-D1a_Gli-A2new10, Gli-A1m_Gli-B1b_Gli-D1a_Gli-A2f, and Gli-A1m_Gli-B1m_Gli-D1a_Gli-A2u are found only in East Siberia.     

On the northernmost distribution of leaf beetles of the genus <Emphasis Type="Italic">Oreomela</Emphasis> (Coleoptera,Chrysomelidae): New species from mountains of southern Siberia

Three new species of leaf beetles are described: Oreomela dudkorum sp. n. (Terektinskii Ridge, Central Altai Mountains), O. tuvensis sp. n. (mountains of southeastern Republic of Tuva), and O. romantsovi sp. n. (Western Sayan Mountains). The representatives of this genus, and especially of the nominotypical subgenus, were found in Russia and in the territories mentioned for the first time. Thus, the distribution boundary of this genus is shifted 3–4° northwards. The representatives of Oreomela have most probably migrated from Tien Shan to the mountains of southern Siberia via the Mongolian Altai Mountains.     

The endosymbiont <Emphasis Type="Italic">Wolbachia</Emphasis> in Eurasian populations of <Emphasis Type="Italic">Drosophila melanogaster</Emphasis>

The endosymbiotic α-proteobacteria Wolbachia is widely spread among arthropods and Filariidae nematodes. This bacterium is transmitted vertically via a transovarian route. Wolbachia is a cause of several reproductive abnormalities in the host species. We analyzed the isofemale lines created using flies collected from Drosophila melanogaster natural populations for infection with the endosymbiont Wolbachia. Wolbachia were genotyped according to five variable markers: the presence of insertion sequence IS5 in two loci, the copy number of two minisatellite repeats, and an inversion. Overall, 665 isofemale lines isolated from the populations of D. melanogaster from Ukraine, Belarus, Moldova, Caucasus, Central Asia, Ural, Udmurtia, Altai, West and East Siberia, and Far East in 1974 through 2005 were used in the work. The samples from Ukrainian, Altaian, and Middle Asian populations were largest. The infection rate of D. melanogaster populations from Middle Asia, Altaian, and Eastern Europe (Ukraine, Moldavia, and Belarus) with Wolbachia amounted to 64, 56, and 39%, respectively. The D. melanogaster population from the Caucasus displayed heterogeneity in the genotypes of this cytoplasmic infection. The Wolbachia genotype wMel, detected in all the populations studied, was the most abundant. The genotype wMelCS2 was always present in the populations from Middle Asia and Altai and was among the rare variants in the D. melanogaster populations from the Eastern Europe. Single instances of the Wolbachia genotype wMelCS occurred in a few flies from the Central Asian and Altai populations, but was not found this genotype in the other regions.     

Butterflies (Lepidoptera,Rhopalocera) of West Altai

A total of 176 species of butterflies have been found in West Altai. Their distribution ranges, phenology, biological preferences, and taxonomic structure are analyzed. Numerous Siberian butterfly species from the genera Erebia, Oeneis, Clossiana, Boeberia, and Colias have been found in West Altai which may be accounted for its westernmost position in the mountain system of southern Siberia and very humid climate. At the same time, many western Palaearctic as well as few Middle Asian butterflies have been discovered in West Altai for the first time. West Altai is the region where pairs of sister species which diverged in the Western and Eastern Palaearctic can be found in secondary contact. In this study, a zone of stable secondary sympatry of Melitaea didyma (western element) and M. latonigena (eastern element) as well as that of Maculinea arion (western element) and M. cyanecula (eastern element) has been found. These findings provide the first strong evidence for the distinctness of the species in these sister pairs.     

Salicaceae-Feeding Leaf-Mining Insects in Siberia: Distribution,Trophic Specialization,and Pest Status

This paper provides an overview of the leaf-mining insect community feeding on willows (Salix spp.) and poplars (Populus spp.) in Siberia. According to published data and our own observations, 50 leaf-mining insect species (i.e., 24 species of Lepidoptera, 15 Coleoptera, 6 Diptera, and 5 Hymenoptera) feed on those two plant genera in Siberia. Using an integrative approach combining field work, morphological and DNA barcoding analyses, we identified 32 leaf-mining insect species from 14 regions across Siberia (i.e. 64% of all leaf-mining species known on Salicaceae in this part of Russia). Among them, 26 species most often found in parks and botanical gardens, represented new faunistic records for several poorly explored regions of Siberia. We have more than doubled the list of Salicaceae-feeding leaf-mining insects in Tomsk oblast, Altai krai, and the Republic of Tuva, and for the first time provided data on leaf-miners for the Khanty–Mansi Autonomous Okrug. The micromoth Phyllocnistis gracilistylella (Gracillariidae), recently described from Japan, was found on a new host plant (Salix caprea) in the south of Krasnoyarsk krai, is new for Russia. Eight leafmining insect species (i.e., five gracillariids: Phyllocnistis labyrinthella, Ph. unipunctella, Phyllonorycter apparella, Ph. sagitella, and Ph. populifoliella; two beetles: Zeugophora scutellaris and Isochnus sequensi; and one sawfly: Heterarthrus ochropoda) can outbreak on poplars, most often in urban plantations, botanical gardens, and plant nurseries in Siberia, and can also affect natural stands. Forty-five species of 50 leaf-mining insects known to feed on willow and poplar in Siberia also occur in Central and Eastern Europe. The remaining five species (Phyllocnistis gracilistylella, Phyllonorycter sibirica, Heterarthrus fasciatus, Tachyerges dauricus, and Isochnus arcticus) are recorded in Asia only. Species richness of the family Gracillariidae, the most diverse on Salicaceae in Siberia, displays 80% similarity to that in the European part of Russia and 71% to the Russian Far East. We discuss the faunal similarity of these regions and highlight the importance of applying an integrative approach combining ecological, morphological analyses, and DNA barcoding to explore and characterize the insect fauna of poorly studied regions of Asian part of Russia.     

Dynamics of the range of <Emphasis Type="Italic">Artemisia</Emphasis> genus over the territory of Western Siberia and adjacent regions in holocene in connection with climate change on the basis of pollen data

Reconstruction of the dynamics of the range of Artemisia genus was carried out with the help of palynoareological method on the basis of the data of 97 pollen diagrams from the territory of Western Siberia and the Altai-Sayan mountainous region over the millennial time sections since the Late Glacial time till the present time. It was revealed that the maximal spread of the Artemisia steppe communities (probably of the cryoarid pattern) occurred at the territory under examination at 13–10 ka yr BP. After the time point of 9 ka yr BP a fundamental change in landscapes of Western Siberia occurred which resulted in the disintegration of previously continuous Artemisia steppe cover into separate blocks. Since 8 ka yr BP the Artemisia steppe communities of modern appearance occupied the zones of modern steppe and forest-steppe of Western Siberia and Northern Kazakhstan while over the taiga zone the Artemisia plant communities were spread occasionally under the extra zonal conditions and as the pioneering plant groupings on naturally disturbed soils. Since the time point of 4 ka yr BP till the present time the northern boundary of the steppe zone under-went pulsing shifts to the north and back and also broadening and narrowing of isolated insular steppes in Altai-Sayan mountain region took place. At present time we observe an increase in the role of plants of Artemisia genus in the tundra zone of Western Siberia and in the Altai mountains.     

Diversity and distribution of leaf mining insects on birches (<Emphasis Type="Italic">Betula</Emphasis> spp.) in Siberia

The diversity and distribution of leaf mining insects developing on birches (Betula spp.) in Siberia were reviewed based on published records and our observations. Analysis of the literature revealed 52 species of leaf miners recorded as feeding on different Betula species in Siberia. Among them, three species were listed under different names and six species were erroneously recorded as birch consumers. Thus, the revised list of birch leaf miners contains 44 species. Five moth and four sawfly species are mentioned in the literature as pests of Betula. Four sawflies are known to be invasive in North America. Our collections comprised 25 species, including the micro-moth Stigmella continuella (Lepidoptera, Nepticulidae), a new species for Siberia found in Novosibirsk. Immature stages of 15 species were identified using DNA barcoding. Twenty species were recorded from several regions of Siberia for the first time. The dominant group is Lepidoptera (31 species), followed by Coleoptera (7), Hymenoptera (5), and Diptera (1). Two-thirds of all the known leaf miners develop exclusively on birches; the remaining species also colonize alders (Alnus, Betulaceae), some Rosaceae, Salicaceae, and Ulmaceae. In our observations, the majority of insects (96%) developed on B. pendula. About half of them were also observed on the East Asian birches B. dahurica, B. divaricata, B. costata, B. ermanii, and B. gmelinii; five species were found on the North American birches B. occidentalis and B. papyrifera. All the leaf mining species listed in our paper for Siberia also occur in Europe. The similarity between the miner faunas of these regions is discussed and it is warned about possible errors in diagnostics of the Siberian species using the keys and catalogues for the European fauna. The importance of DNA barcoding in the study of the local insect faunas of poorly explored regions is also emphasized.     

Ecological and molecular genetic features of <Emphasis Type="Italic">Ixodes persulcatus</Emphasis> and <Emphasis Type="Italic">I. pavlovskyi</Emphasis> ticks in Southern West Siberia

Ixodiae ticks have been counted and sampled in six distant locations within the Altai-Sayan Mountain Area and northern forest steppe in 2012. In total, 1829 individuals of I. persulcatus and 719 of I. pavlovskyi ticks were collected by flagging. I. persulcatus is found in all six examined locations and I. pavlovskyi is found in Western Altai, Northeastern Altai, and Northern Altai, as well as in forest parks near Akademgorodok of Novosibirsk. In total, 16S rRNA and COI sequences have been determined in 144 and 164 I. persulcatus individuals, as well as in 60 and 55 I. pavlovskyi. Selectively equivalent mutant forms are present in I. pavlovskyi populations of Northeastern Altai and Northern Altai. The hydrothermal regime in the forest parks near Novosibirsk is optimal for the I. pavlovskyi ticks. These ticks have recently colonized the forest parks near Novosibirsk and therefore are genetically close to I. pavloskyi from the Altai–Sayan Mountain Area populations.     

A review of sciarids of the genus <Emphasis Type="Italic">Leptosciarella</Emphasis> Tuomikoski 1960 (Diptera,Sciaridae) in the Altai fauna,with description of three new species

The taxonomy of the genus Leptosciarella Tuomikoski, 1960 in the Altai Area within Altai Territory and the Altai Republic was studied. Eleven species were recognized, including three new species which are described and illustrated here: Leptosciarella (L.) ulagana Komarova sp. n., L. (L.) angustistylus Komarova sp. n., L. (L.) senex Komarova sp. n. Additionally, L. (L.) fuscipalpa (Mohrig et Mamaev 1979) and L. (L.) truncata (Tuomikoski 1960) are recorded from Altai for the first time. A key to the Altai species is provided.     

Karyotyping of <Emphasis Type="Italic">Amoeba proteus</Emphasis>

In this paper, we have developed a method to prepare spreads of mitotic chromosomes of Amoeba proteus and described the process of Amoeba proteus karyotyping. This protocol allows obtaining spread chromosomes with a characteristic pattern of chromomeres on individual chromosomes. It is shown that, in the metaphase of mitosis, amoebas of strain B (one of the type strains of A. proteus in the Amoebae Cultures Collection of the Institute of Cytology, Russian Academy of Sciences) contain 27 pairs of chromosomes. It is established that the pattern of chromomeres is a chromosome-specific feature. A typical karyogram and image bank of DAPI- and YoYo1-banded individual chromosomes of A. proteus, strain B composed of five different spreads of mitotic cells are presented.     

Behavior of sex chromosomes at early meiosis stages in three wood mice species of the genus <Emphasis Type="Italic">Apodemus</Emphasis> (Rodentia,Muridae)

The prophase of the first meiotic division was studied in field mice of the species Apodemus (Sylvaemus) flavicollis, A. (S.) ponticus, and A. (S.) uralensis by light and electron microscopy. The karyotypes of three species were described on the base of electron microscopy of synaptonemal complexes in spermatocytes I. The axial elements of the sex chromosomes at early-middle pachytene synapse along the major portion of the Y axis; at late pachytene-early diplotene, the synapsis region shrinks; and at diakinesis-metaphase I, X and Y chromosomes associate end-to-end in all species studied. The behavior of sex chromosomes in the synapsis in the species studied was quite uniform. The results are discussed in the context of earlier data on the behavior of sex chromosomes in various rodent species in meiosis prophase I and their banding.     

Cold hardiness and range of the earthworm <Emphasis Type="Italic">Eisenia sibirica</Emphasis> (Oligochaeta,Lumbricidae)

A hypothesis of range formation of the earthworm Eisenia sibirica Perel et Graphodatsky 1984, which is an endemic species of the Altai–Sayan mountain system and is also found on the adjacent plains of Siberia across the valleys of the rivers, is suggested. The limited distribution of the species can be connected with the insufficient cold hardiness of the worm stage (–10 to–12°C). The plains of Western Siberia lie in an area of minimum soil temperature isotherms at a depth of 3 cm:–12 to–14°C, i.e., on average 2–4°C below the tolerable limits for this species. Foothill and mountain soils are warmer, since they obtain much more solid precipitation. Low soil temperatures of the plains apparently “lock up” this species within the Altai–Sayan system. At the same time, there are reasons to consider the northernmost locations of E. sibirica to be relict.     

Hidden diversity in the <Emphasis Type="Italic">Antrodia malicola</Emphasis> group (Polyporales,Basidiomycota)

Taxonomy of the Antrodia malicola group is revised based on DNA, morphological, ecological, and geographic data. This species complex is not related to Antrodia s. str. but constitutes its own lineage within the large Fomitopsis – Daedalea clade. The A. malicola group includes five species. Antrodia malicola s. str. is distributed in North America and East Asia, and a few records of this species are reported from Azores and Africa. Its European counterpart is A. kuzyana, comb. nova, with wider pores. Infraspecific variability of A. malicola and possible gene flow between it and A. kuzyana in East Asia are detected based on tef1 sequence data. Antrodia cyclopis, sp. nova, is described as a large-spored relative of A. malicola from New Guinea. Antrodia minuta is reported here from several European countries and Siberia, and its morphological characters and host preferences are discussed. Its close relative is A. tuvensis, sp. nova, from Central Siberia, an unusual member of the group with sparse, flexuous skeletal hyphae.     

A new species of the genus <Emphasis Type="Italic">Boreophylloceras</Emphasis> Alekseev et Repin, 1998 (Ammonitida) from the Berriasian <Emphasis Type="Italic">kochi</Emphasis> zone of north-central Siberia

Study of the shells of phylloceratids from the kochi Zone (Berriasian) of north-central Siberia (Boyarka River, basin of the Kheta River) allowed their assignment to the genus Boreophylloceras Alekseev et Repin, 1998. A new species B. densicostatum is described.     

A SNP-based genetic linkage map of <Emphasis Type="Italic">Capsicum baccatum</Emphasis> and its comparison to the <Emphasis Type="Italic">Capsicum annuum</Emphasis> reference physical map

Capsicum baccatum L., one of five domesticated species of Capsicum, is a valuable species in chili pepper breeding. In particular, it is a source of disease resistance against anthracnose and powdery mildew. Genetic maps and molecular markers are important to improve the efficiency of crop breeding programs. Recently, using genetic maps several researchers have identified quantitative trait loci (QTLs) for important horticultural traits and have cloned genes of interest. In this study, we constructed a genetic map of C. baccatum in an intraspecific population from a cross between ‘Golden-aji’ and ‘PI594137.’ A total of 395 high-resolution melting markers were developed based on single-nucleotide polymorphisms identified by comparing genome sequences generated through next-generation resequencing of the parents, ‘Golden-aji’ and ‘PI594137.’ The genetic linkage map contained 12 linkage groups, covered a total distance of 1056.2 cM, and had an average distance of 2.67 cM between markers. In addition, the final map was compared to the reference physical map of C. annuum ‘CM334.’ Interestingly, two major reciprocal translocations between chromosomes 3 and 5 and between chromosomes 3 and 9 were found, suggesting that these translocations might act as a genetic barrier between C. annuum and C. baccatum. Translocations between chromosomes 1 and 8 were also observed, as were previously reported in C. chinense, C. frutescens, and wild C. annuum. The synteny of other chromosomes was maintained, on the whole, except for several small inversions. The information on this genetic map will be helpful to analyze QTLs for important traits such as anthracnose resistance in C. baccatum and to study the causes of genetic barriers between C. annuum and C. baccatum.     

Quinacrine Fluorescence Patterns and Terminal DNA Labelling of Human <Emphasis Type="Italic">C</Emphasis> Group Chromosomes

THE human C group chromosomes have been difficult to study because they have rather similar morphology. Application of the quinacrine fluorescent staining technique developed by Caspersson et al.¹ now allows the identification of individual chromosomes and of the chromosome segments involved in translocations because the fluorescent patterns are not altered by the translocation^2–4. We have reported the value of this technique in analysing abnormalities of the D⁴ and G³ groups. We report here a variety of structural changes of C group chromosomes which have been characterized in this way, as well as the terminal DNA replication pattern of the C group chromosomes.     

Karyotyp und DNS-Gehalt von Bufo bufo,B. viridis,B. bufo × B. viridis und B. calamita (Amphibia,Anura)

The karyotypes in spermatogonial and leukocyte metaphases of the toads Bufo bufo, B. viridis and B. calamita (all 2n=22) were analysed and the DNA content of colchicine treated and Feulgen stained spermatogonial metaphase chromosomes measured microspectrophotometrically. The toad species possess similar karyotypes, but the chromosomes of B. bufo are somewhat longer than the chromosomes of B. viridis and B. calamita. All chromosomes of B. bufo contain significantly more than, but in no case twice as much DNA as their homologues in the other two species. Eight chromosomes of B. bufo contain 30–40%, three about 50% more DNA than their homologues in B. viridis. Exactly the same DNA-differences between both sets of chromosomes were found in B. bufo × B. viridis hybrids. Significant differences in the DNA amount of B. viridis and B. calamita exist only between the large chromosomes of these species. The ratio of the total DNA amount of the genomes in the three species is 1.49∶1.07∶1. These DNA-differences between the three toad species are confirmed by microspectrophotometric DNA measurements of their erythrocyte nuclei. It is supposed that these interspecific differences in DNA content of the toads are not a consequence of differential polyteny but are caused during the evolution process by local increase in DNA in all chromosomes of B. bufo and in the large chromosomes of B. viridis.