Phylogeography of the Siberian newt Salamandrella keyserlingii by mitochondrial DNA sequence analysis

Differentiation of geographical populations of the Siberian newt Salamandrella keyserlingii throughout the species range was analyzed using a fragment of the cytochrome b gene. The population of the Primorye region (Russian Far East) is separated to the greatest extent; the Japanese and South Kuril populations are the next most separate. These populations are possibly subspecies. Geographical differentiation of populations in the Siberian part of the species range is lower, lacks a clinal variation, and is irregular. The molecular variation of S. keyserlingii supports the hypothesis that several primary vicarious refugia of pre-Pleistocene differentiation of a common ancestor of Salamandrella occurred in the southeastern part of its current distribution range and that northern and western regions were gradually colonized via repeated steps of expansion and retreat in the Siberian part of the modern species range.     

Development of microsatellite genetic markers in Siberian stone pine (<Emphasis Type="Italic">Pinus sibirica</Emphasis> Du Tour) based on the <Emphasis Type="Italic">de novo</Emphasis> whole genome sequencing

Siberian stone pine, Pinus sibirica Du Tour is one of the most economically and environmentally important forest-forming species of conifers in Russia. To study these forests a large number of highly polymorphic molecular genetic markers, such as microsatellite loci, are required. Prior to the new high-throughput next generation sequencing (NGS) methods, discovery of microsatellite loci and development of micro-satellite markers were very time consuming and laborious. The recently developed draft assembly of the Siberian stone pine genome, sequenced using the NGS methods, allowed us to identify a large number of microsatellite loci in the Siberian stone pine genome and to develop species-specific PCR primers for amplification and genotyping of 70 microsatellite loci. The primers were designed using contigs containing short simple sequence tandem repeats from the Siberian stone pine whole genome draft assembly. Based on the testing of primers for 70 microsatellite loci with tri-, tetra- or pentanucleotide repeats, 18 most promising, reliable and polymorphic loci were selected that can be used further as molecular genetic markers in population genetic studies of Siberian stone pine.     

Comments on the morphology of Nicsmirnovius eximius (Kiser, 1948) (Aloninae,Anomopoda, Cladocera) in Thailand,with description of its male

The density, diet and habitat use of brown trout (Salmo trutta) and Siberian sculpin (Cottus poecilopus) were studied in the subalpine River Atna in southeastern Norway in the autumn during a six year period (1986–1991). There was an inverse relationship between the density of brown trout and Siberian sculpin. Diet overlap, as indicated by the Schoener index, was high between the two species, ranging between 0.48 and 0.86. Chironomid larvae and other aquatic insects were the most common food items for both species. Brown trout also consumed substantive amounts of surface insects. Siberian sculpin typically occupied sites with finer substrates and greater water depths than brown trout, even though there was considerable overlap in habitat use between the two species. Because the two species shared similar habitats, we suggest that the potential for species interactions exists, particularly at sites where density of sculpin is high.     

Hydrological Modelling for Siberian Crane Grus Leucogeranus Stopover Sites in Northeast China

Habitat loss is one of the key factors underlying the decline of many waterbird species, including Siberian Crane (Grus leucogeranus), a threatened species worldwide. Wetlands are the primary stopover for many waterbirds and restoration of these wetlands involves both hydrological restoration and water resource management. To protect the stopover sites of Siberian Cranes, we collected Siberian Crane stopover numbers, meteorological and hydrological data, and remote sensing data from 2008 to 2011 in Momoge National Nature Reserve, one of the largest wetlands in northeastern China. A model was developed to estimate the suitability of Siberian Crane stopover sites. According to our results, the most suitable daily water level for Siberian Cranes between 2008 and 2012 occurred in the spring of 2008 and in the Scirpus planiculmis growing season and autumn of 2010. We suggest a season-dependent water management strategy in order to provide suitable conditions at Siberian Crane stopover sites.     

Genetic passportization and identification of Siberian cranes (Grus leucogeranus Pallas) in captivity

The genetic diversity of the founders of an artificial population of the Siberian crane Grus leucogeranus Pallas (rare species of cranes) was characterized using 10 microsatellite loci. It was established that the allelic diversity (on average, 5.9 alleles per locus) and genic (H _O = 0.739) diversity of the Siberian crane is rather high and comparable with the estimations for natural populations of different crane species. Genetic passportization of the birds (119 individuals) from the register of the Siberian crane International Studbook was carried out at the initial stage. The efficiency of genetic passportization for individual identification, identification of the origin, paternity analysis, and exclusion of inbreeding was demonstrated in Siberian cranes under natural mating and artificial insemination. Cases of natural reproduction in pairs of Siberian cranes imprinted to the human and continuous storage of spermatozoa in the female reproductive ducts were registered.     

Genotyping of Capreolus pygargus fossil DNA from Denisova cave reveals phylogenetic relationships between ancient and modern populations

Background

The extant roe deer (Capreolus Gray, 1821) includes two species: the European roe deer (C. capreolus) and the Siberian roe deer (C. pygargus) that are distinguished by morphological and karyotypical differences. The Siberian roe deer occupies a vast area of Asia and is considerably less studied than the European roe deer. Modern systematics of the Siberian roe deer remain controversial with 4 morphological subspecies. Roe deer fossilized bones are quite abundant in Denisova cave (Altai Mountains, South Siberia), where dozens of both extant and extinct mammalian species from modern Holocene to Middle Pleistocene have been retrieved.

Methodology/Principal Findings

We analyzed a 629 bp fragment of the mitochondrial control region from ancient bones of 10 Holocene and four Pleistocene Siberian roe deer from Denisova cave as well as 37 modern specimen belonging to populations from Altai, Tian Shan (Kyrgyzstan), Yakutia, Novosibirsk region and the Russian Far East. Genealogical reconstructions indicated that most Holocene haplotypes were probably ancestral for modern roe deer populations of Western Siberia and Tian Shan. One of the Pleistocene haplotypes was possibly ancestral for modern Yakutian populations, and two extinct Pleistocene haplotypes were close to modern roe deer from Tian Shan and Yakutia. Most modern geographical populations (except for West Siberian Plains) are heterogeneous and there is some tentative evidence for structure. However, we did not find any distinct phylogenetic signal characterizing particular subspecies in either modern or ancient samples.

Conclusion/Significance

Analysis of mitochondrial DNA from both ancient and modern samples of Siberian roe deer shed new light on understanding the evolutionary history of roe deer. Our data indicate that during the last 50,000 years multiple replacements of populations of the Siberian roe deer took place in the Altai Mountains correlating with climatic changes. The Siberian roe deer represent a complex and heterogeneous species with high migration rates and without evident subspecies structure. Low genetic diversity of the West Siberian Plain population indicates a recent bottleneck or founder effect.     

Classification of meadows of the South Siberian uplands and mountains

The classification of South Siberian meadows using the Braun-Blanquet approach was carried out on the basis of a geographically wide-ranging data set from the West Siberian Plain and the Altai-Sayanian mountain systems. Two main phytosociological types of meadows were distinguished within the classMolinio-Arrhenatheretea. The natural Siberian forest meadows were included in the orderCarici macrourae-Crepidetalia sibiricae comprising two alliances (Crepidion sibiricae, Aconito barbati-Vicion unijugae) and 7 associations. The anthropogenic types of dry meadows were included in the European-West Siberian orderArrhenatheretalia, comprising one alliance (Festucion pratensis) and 5 associations. DCA ordination revealed clear differences in the floristic composition of the higher units and in the diagnostic importance of the main ecological and phytosociological species groups.     

Revision of the superfamily Acrotheloidea (Brachiopoda,class Linguliformea,order Lingulida) from the Lower and Middle Cambrian of the Siberian Platform

This paper continues our revision of Yu.L. Pelman’s collection of the superfamily Acrotheloidea (phosphatic brachiopods) and of our own material from the Early–Middle Cambrian of the Siberian Platform. The following representatives of the superfamily Acrotheloidea (order Lingulida, class Linguliformea) are restudied and revised based on new techniques: the genus Botsfordia (family Botsfordiidae Schindewolf, 1955) and the genera Acrothele, Eothele, and Orbithele (family Acrothelidae), which are widespread on the Siberian Platform. Only one out of the three Acrothele species described by Pelman is recognized as a valid species, and one new species of this genus that comprises some part of the brachiopods that Pelman figured and placed in another taxon is described. All these species are described using data on shell microsculpture and microstructure. In addition, the genera Eothele and Orbithele are described for the first time from the Siberian Platform.     

Trilobites Plicatolina lucida Lazarenko from the Upper Cambrian of the Kharaulakh Mountains (Northeastern Siberian Platform)

A collection of trilobites of the genus Plicatolina Shaw, 1951 from the upper Ogon’or Formation, Cambrian Section, Chekurovka Anticline (northeastern Siberian Platform, Kharaulakh Mountains), is studied. It is shown that all specimens of this collection belong to the same species, Plicatolina lucida Lazarenko, 1966, but represent different age stages. It is also shown that species of the genus Plicatolina (P. quadrata Pokrovskaya, 1966 and P. yakutica Pokrovskaya, 1966) described from the Upper Cambrian of the Siberian Platform are probably synonyms of P. lucida.     

Induction of conifer immune responses by phytopathogenic fungus metabolites

The elicitor activity of compounds extracted from the mycelia of six species of phytopathogenic fungi was assessed from the sizes of necrotic lesions on the external surface of the living trunk phloem of five coniferous species inhabiting Siberia: Siberian larch (Larix sibirica L.), Scotch pine (Pinus sylvestris L.), Siberian spruce (Picea obovata Ledeb.), Siberian fir (Abies sibirica L.), and cedar pine (Pinus sibirica (Rupr.) Mayr.). The compounds for inoculation were extracted from the mycelium of ascomycetes imperfect, and basidium fungi; the living mycelia of these fungi were also used. The fungal extract or mycelium was placed into the hollows 7 mm in diameter in the trunk bark. Infection triggered the formation of hypersensitivity necrotic lesions in the inner bark exceeding in size those appeared after control wounding of four tree species (larch, pine, spruce, and cedar); fir was an exclusion. In experiments with tree trunks and conifer calluses, a dependence of immune response parameters (the sizes of necrotic lesions and the content of lignin and bound proanthocyanidins) on the quantity of the fungal preparation was elucidated. The largest necrotic lesions appeared after injection of 500μg of the fungal preparation into the hollow in the trunk, and its higher quantities did not increase the indices measured. The size of the necrotic lesion on the trunk bark is supposed to be used as a promising index characterizing the level of tree immunity and tolerance under various ecological conditions.     

Genetic diversity and differentiation of Siberian spruce populations at nuclear microsatellite loci

The results of the study of 21 populations of Siberian spruce (Picea obovata Ledeb.) from different parts of the species natural range by microsatellite (SSR) analysis of nuclear DNA are presented. Using nine loci developed for Picea abies (L.) Karst. and Picea glauca (Moench) Voss and detecting variation in Picea obovata, the parameters of intra- and interpopulation genetic diversity, as well as the degree of population differentiation, were determined. It was demonstrated that the population of Siberian spruce in the study was characterized by a relatively high average level of intrapopulation variability (H_o = 0.408; H_e = 0.423) and low interpopulation differentiation (F_st = 0.048, P = 0.001) at this class of DNA markers. The genetic distance between populations ranged from 0.009 to 0.167, averaging 0.039. The isolated Magadan population, located in the extreme Northeast of Russia at a considerable distance from the main species range and characterized by the lowest genetic diversity among the studied populations, was maximally differentiated from the rest of the spruce populations. In addition, the steppe Ubukun population from Buryatia and the population from the Bogd Khan Uul Biosphere Reserve, Mongolia, were considerably different in the genetic structure from most populations of Siberian spruce, although to a lesser extent than the Magadan population. These findings are consistent with the results of previous studies of this species carried out using allozyme and microsatellite loci of chloroplast DNA and point to the prospects of using nuclear microsatellites as DNA markers to analyze the population genetic structure of Siberian spruce.     

Molecular and Immunological Characterization of the First Allergenic Lipocalin in Hamster: THE MAJOR ALLERGEN FROM SIBERIAN HAMSTER (PHODOPUS SUNGORUS)*

The most frequent pet allergy is to cat and dog, but in recent years, it has become increasingly popular to have other pets, and the risk of exposure to new allergens is more prevalent. The list of new pets includes hamsters, and one of the most popular hamsters is the Siberian hamster (Phodopus sungorus). The aim of this study was the characterization and cloning of the major allergen from this hamster. The study of its allergenicity and cross-reactivity could improve the specific diagnosis and treatment for hamster-allergic patients. Thirteen Siberian hamster-allergic patients were recruited at the outpatient clinic. Protein extracts were prepared from the hair, urine, and salivary glands of four hamster species (European, golden, Siberian, and Roborovski). IgE-binding proteins were detected by immunoblotting and identified by mass spectrometry. The recombinant protein was produced in Escherichia coli and then purified by metal chelate affinity chromatography. The allergenic properties of the recombinant protein were tested by ELISA and immunoblotting, and biological activity was tested according to capacity for basophil activation. Three IgE-binding proteins were identified in extracts obtained from Siberian hamster hair, urine, and salivary glands. All proteins corresponded to the same protein, which was identified as a lipocalin. This lipocalin had no cross-reactivity with common and golden hamsters. The recombinant allergen was cloned and purified, showing similar IgE reactivity in vitro to Siberian hamster protein extracts. Also, the recombinant allergen was capable of producing biological activation in vivo. The major Siberian hamster allergen was cloned, and allergenic properties were characterized, providing a new tool for specific diagnosis of allergy to Siberian hamster.     

Comparative protein profiles: Potential molecular markers from spermatozoa of Acipenseriformes (Chondrostei,Pisces)

Sturgeon and paddlefish (Acipenseriformes), the source of roe consumed as caviar, are a unique and commercially valuable group of ancient fishes. In this study, comparative proteomics was used to analyze protein profiles of spermatozoa from five sturgeon species and one paddlefish: Siberian sturgeon (Acipenser baerii), sterlet (A. ruthenus), Russian sturgeon (A. gueldenstaedtii), starry sturgeon (A. stellatus), beluga (Huso huso), and Mississippi paddlefish (Polyodon spathula). Protein profiles of spermatozoa were determined by isoelectric focusing and two-dimensional electrophoresis (2-DE) high-resolution gels. The peptides, previously selected by 2-DE analysis as potentially species-specific, were obtained by “in-gel” tryptic digestion, followed by matrix-associated laser desorption/ionization time-of-flight/mass spectrometry (MALDI-TOF/MS). Among the 23 protein spots selected, 14 were identified as isoforms of enolase B present in all species, but with different isoelectric points or molecular mass. Exceptions were A. ruthenus and H. huso, species with a close phylogenetic relationship. Glycerol-3-phosphate dehydrogenase was detected exclusively in P. spathula. Phosphoglycerate kinase was detected only in A. ruthenus and H. huso, and 3 additional proteins (fructose bisphosphate aldolase A-2, glycogen phosphorylase type IV and glyceraldehyde-3-phosphate dehydrogenase) were found exclusively in A. gueldenstaedtii and H. huso. This study points to the application of proteomics for differential characterization and comparative studies of acipenseriform species at the molecular level.     

Local-scale disturbance by Siberian marmots has little influence on regional plant richness in a Mongolian grassland

Our objective was to examine the relative importance of local-scale disturbance by Siberian marmots in increasing regional (landscape-wide) plant richness. We used an additive diversity partitioning framework and quantified species richness patterns of grassland plant communities affected by marmot disturbance across different spatial scales: within and among on- and off-marmot-mound subsites, among sites, and among landscape units (corresponding to α and three levels of β richness). Values of β richness among subsites and β richness among landscape units were similar to those expected by chance. This suggests that plant species are randomly distributed among subsites and among landscape units, despite the prediction based on previous studies that local-scale disturbance by Siberian marmots and its interactive effects with landscape contexts disproportionately influence spatial patterns of plant species. Of the spatial components of regional richness, only the β richness among sites was significantly different from the expected value, probably reflecting the differential spatial pattern of disturbance by marmots at a site scale. The β richness among landscape units contributed the most to regional richness, whereas β richness among subsites and among sites contributed less. Thus, our results suggest that local-scale disturbance by Siberian marmots has little influence on regional plant richness in a Mongolian grassland.     

Non-invasive method of sex identification of crane chicks by the DNA from capillary vessels of allantois

The non-invasive method of determining the sex of chicks after hatching based on the DNA isolated from capillary vessels of allantois of the egg-shell membranes was demonstrated on four crane species (Gruinae, Aves), which were bred in the Crane Breeding Centre of the Oka Nature Reserve in 2009–2012. Using the EE0.6 molecular marker of sex, the gender of 26 Siberian (Grus leucogeranus), 15 Red-crowned (G. japonensis), 4 Common (G. grus) and 1 Demoiselle (Anthropoides virgo) crane chicks was identified. This method can be recommended for determining the sex of chicks and the ratio of sexes in cranes that reproduce both in captivity and natural populations.     

Ground beetles (coleoptera,carabidae) of the Ola Plateau highlands,Kolyma Uplands

The ground beetle fauna was studied in 12 biotopes of the tundra belt on Ola Plateau, 130 km NW of Magadan. In all, 16 species were found above timber line (900–1220 m), which is comparable with the diversity in the mountain tundras of the upper reaches of the Kolyma (Berman et al., 1984; Bukhkalo, 1997), but the faunistic similarity of these regions is low (Jaccard’s coefficient 22–29%). Besides the widespread species, a group of ground beetles with limited ranges is present; it includes Carabus kolymensis Lafer, 1989 occurring in the East Siberian mountain tundras, the Siberian-Nearctic, mainly arctic Pterostichus agonus G. Horn, 1880, and the East Siberian Pterostichus eximius A. Mor., 1862. The use of the term “arctic species” in arealogical and ecological studies is discussed.     

Revision of the Early-Middle Cambrian Lingulida (Brachiopoda) from the Siberian Platform

Based on Yu.L. Pelman’s lingulid collection and our own material, the Early-Middle Cambrian genus Eoobolus, which was widespread on the Siberian Platform, is revised. The Siberian members of this genus have previously been assigned to Lingulella. Two out of these six members are recognized as valid species: Eoobolus siniellus (Pelman) and E. variabilis (Pelman). Lingulella acuta Pelman and L. linguata Pelman are considered here to be junior synonyms of E. priscus (Poulsen, 1932). The valid species are redescribed and their stratigraphic and geographic ranges are given. A new species, E. pelmani sp. nov., is described. New data on the Eoobolus microornamentation and shell structure are provided.     

High Fidelity – No Evidence for Extra-Pair Paternity in Siberian Jays (Perisoreus infaustus)

Extra-pair paternity (EPP) in birds is related to a number of ecological and social factors. For example, it has been found to be positively related with breeding density, negatively with the amount of paternal care and especially high rates have been observed in group-living species. Siberian jays (Perisoreous infaustus) breed at low densities and have extended parental care, which leads to the expectation of low rates of EPP. On the other hand, Siberian jays live in groups which can include also unrelated individuals, and provide opportunities for extra-pair matings. To assess the potential occurrence of EPP in Siberian jays, we analysed a large data pool (n = 1029 offspring) covering ca. 30 years of samples from a Finnish Siberian jay population. Paternities were assigned based on up to 21 polymorphic microsatellite markers with the additional information from field observations. We were unable to find any evidence for occurrence of EPP in this species. Our findings are in line with earlier studies and confirm the generally low rates of EPP in related Corvid species. These results suggest that ecological factors may be more important than social factors (group living) in determining costs and benefits of extra-pair paternity.     

Mitochondrial DNA genetic differentiation of the muksun <Emphasis Type="Italic">Coregonus muksun</Emphasis> (Pallas) and related Siberian species of <Emphasis Type="Italic">Coregonus</Emphasis> (Coredonidae,Salmoniformes)

Restriction enzyme analysis of the mitochondrial DNA (mtDNA) fragment encoding subunit 1 of the NADH dehydrogenase complex (ND-1) amplified via polymerase chain reaction (PCR) has been used to obtain data on genetic differentiation of muksun Coregonus muksun (Pallas) populations. Population polymorphism with respect to the restriction sites of 18 endonucleases has been described. It has been demonstrated that the muksun is genetically related to the pidschian C. pidschian (Gmelin), its sympatric species in Siberian waters. Analysis of the median network of mtDNA haplotypes has shown that haplotypes of muksun from various Siberian basins form a common group with haplotypes of pidschian of the Arctic Ocean basin, some frequent haplotypes been found in both forms. This raises the question as to the validity of the muksun as a species. Differences within this group of haplotypes are much smaller than those typical of species of the genus Coregonus. The possibility of a hybrid origin of the muksun from a pidschian-like ancestor and species of the cisco-peled (C. sardinella-C. peled) complex is discussed.     

气候变化对鄱阳湖白鹤越冬种群数量变化的影响

分析了1983—2011年鄱阳湖国家级自然保护区越冬白鹤种群数量的年际变化趋势,检验了白鹤种群动态与繁殖地和越冬地气候变化的相关性,气候变量包括月平均气温、月平均最高气温、月平均最低气温和月降水量。研究结果表明,鄱阳湖国家级自然保护区内的白鹤年最大数量平均为(2 130±153)只,呈显著地线性增长趋势(R2=0.454,F=22.441,df=28,P=0.000),但年际波动较大。在越冬地,越冬当年10月、11月、12月的气候变量与白鹤种群数量没有显著的相关性,但越冬初期10月份和越冬后期翌年3月份的气温变量与第4年、第5年、第6年及第7年的白鹤种群数量存在显著的正相关,表明越冬地气候对白鹤种群大小的影响存在时滞效应。越冬初期和末期可能是白鹤补充能量的关键阶段,而且越冬初期的气候可能也与冬季食物的数量或质量相关,因此这两个阶段的适宜气温可能有利于个体尤其是幼鹤的存活,使更多的个体参加繁殖,由于白鹤的性成熟年龄在3—5a,因此其对白鹤种群增长的有利影响会在3a以后表现出来。白鹤种群数量变化与繁殖地繁殖期的降水量没有显著的相关性,而与7月份的气温变量存在显著的正相关。多元线性回归分析结果表明,6a前的10月份平均最低温度、2a前的10月最高温度及5a前的10月平均气温是白鹤种群数量变化的显著预测因子,共同解释了鄱阳湖国家级自然保护区白鹤种群数量变化的74.8%(F=23.807,df=27,P=0.000)。