Genetic variation and differentiation in striped field mouse Apodemus agrarius inferred from RAPD-PCR analysis

Genetic variation and differentiation of the trans-Palearctic species Apodemus agrarius (striped field mouse), whose range consists of two large isolates-European-Siberian and Far Eastern-Chinese, were examined using RAPD-PCR analysis. The material from the both parts of the range was examined (41 individual of A. agrarius from 18 localities of Russia, Ukraine, Moldova, and Kazakhstan); the Far-Eastern part was represented by samples from the Amur region, Khabarovsk krai, and Primorye (Russia). Differences in frequencies of polymorphic RAPD loci were found between the European-Siberian and the Far Eastern population groups of striped field mouse. No "fixed" differences between them in RAPD spectra were found, and none of the used statistical methods permitted to distinguish with absolute certainty animals from the two range parts. Thus, genetic isolation of the European-Siberian and the Far Eastern population groups of A. agrarius is not strict. These results support the hypothesis on recent dispersal of striped field mouse from East to West Palearctics (during the Holocene climatic optimum, 7000 to 4500 years ago) and subsequent disjunction of the species range (not earlier than 4000-4500 years ago). The Far Eastern population group is more polymorphic than the European-Siberian one, while genetic heterogeneity is more uniformly distributed within it. This is probably explained by both historical events that happened during the species dispersal in the past, and different environmental conditions for the species in different parts of its range. The Far Eastern population group inhabits the area close to the distribution center of A. agrarius. It is likely that this group preserved genetic variation of the formerly integral ancestral form, while some amount of genetic polymorphism could be lost during the species colonization of the Siberian and European areas. To date, the settlement density and population number in general are higher than within the European-Siberian isolate, which seems to account for closer interpopulation associations, intense genetic exchange, and "smoothing" of polymorphism within the Far Eastern population group of A. agrarius.     

Morphological and genetic variability in small island populations of the striped field mouse <Emphasis Type="Italic">Apodemus agrarius</Emphasis> Pallas, 1771

Morphological (craniometrical characteristics and variations of cusp t3 on the second upper molar (M²)) and genetic (polymorphism of chromosomes and blood proteins) variability was analyzed in small island populations of the striped field mouse Apodemus agrarius Pallas, 1771 from the Peter the Great Bay (Sea of Japan). It was found that the absence of t3 on M² is not a specific trait for A. agrarius. It was demonstrated that the population of field mice on the Bolshoy Pelis Island significantly differs from the populations from other islands and from the mainland according to the craniometrical parameters, teeth phenes, and variants of blood transferrin. The possible age of establishment of the island populations of the striped field mouse is discussed.     

Environmental factors affecting population level genetic divergence of the striped field mouse (<Emphasis Type="Italic">Apodemus agrarius</Emphasis>) in South Korea

The cognizing of connectivity among small mammal populations across heterogeneous landscapes is complicated due to complex influences of landscape and anthropogenic factors on gene flow. A landscape genetics approach offers inferences on how landscape features drive population structure. Through a landscape genetics approach, we investigated influences of geographical, environmental, and anthropogenic features on populations of Apodemus agrarius, the striped field mouse, the prime vector of hemorrhagic fever by a landscape genetic approach. We identified landscape features that might affect the population structure of striped field mice by analyzing microsatellite markers of 197 striped field mice from 21 populations throughout South Korea. We developed Maximum-likelihood population effects models based on landscape distances and resistance matrices and pairwise F_ST values for meta-populations of striped field mouse. We also conducted Mantel and partial Mantel tests to investigate geographic patterns of genetic similarities. In Mantel and partial Mantel tests, the F_ST was significantly correlated with all three models of movement; movement cost, Euclidian distance and least-cost distance, although the magnitudes of correlations varied. The 4 top-ranked models included three variables; temperature, precipitation and one human disturbance factor (population). We did not attain a significant effect for anthropogenic factors on genetic similarities among populations in the Korean striped field mouse, but we confirmed a significant association for genetic similarity with climatic features (temperature and precipitation).     

Genetic markers of adaptive processes in the Far Eastern pink salmon <Emphasis Type="Italic">Oncorhynchus gorbuscha</Emphasis>: Allelic diversity at the locus of major histocompatibility complex MHC I-<Emphasis Type="Italic">A1</Emphasis>

To clarify allelic diversity at the locus of major histocompatibility complex MHC class I-A1 in the Far Eastern pink salmon Oncorhynchus gorbuscha, sequencing of the electrophoretic alleles isolated from the gel (DGGE alleles) was performed. In 47 individuals, the genotypes of which consisted of ten DGGE alleles, 18 MHC I-A1 nucleotide sequences were revealed, and thus, eight cryptic alleles not detected by electrophoresis were identified. Eleven of these alleles were identified earlier in pink salmon from Hokkaido, Alaska, and British Columbia, and seven, possibly, were unique to the populations from some Far Eastern regions. Six of the previously determined DGGE alleles corresponded to more than one nucleotide sequence. However, the sequences attributed to the same DGGE allele differed on average by less than 1 nucleotide. These findings point to sufficient sensitivity of the DGGE method, although the genetic diversity and differentiation estimates obtained with it will obviously be somewhat underestimated. Considerable predominance of nonsynonymous substitutions over the synonymous ones in the codons of the MHC I-A1 antigen-binding site confirms the presence of positive selection aimed at providing the population resistance to local spectrum of pathogens. Refinement of the allelic composition of the adaptively important MHC genetic marker will contribute to more complete understanding of the adaptive genetic structure of pink salmon as an important element of the overall population structure of the species.     

Comparative phylogeography of diadromous and freshwater daces of the genus <Emphasis Type="Italic">Tribolodon</Emphasis> (Cyprinidae)

Far Eastern daces, genus Tribolodon (Cyprinidae), are thought to have diversified and developed unique diadromous life histories under changing conditions in the Sea of Japan and the surrounding environment. To examine the relationships between life history traits, distribution, and genetic population structures, we conducted a comparative phylogeographic analysis using partial mtDNA sequence data from samples collected over almost the full ranges of all four Tribolodon species. Phylogenetic analyses revealed several intraspecific haplotype groups that differentiated in the early Pleistocene to the Pliocene with or without geographic overlaps. A time-calibrated phylogeny suggested that the relatively smaller geographic ranges of the strictly freshwater species, T. sachalinensis and T. nakamurai, were explained not by the recent origins of these species, but by their limited dispersal abilities and smaller historical population sizes. The wider-ranging diadromous species, T. brandtii and T. hakonensis, exhibited similar major phylogeographic structures in their distributions, but the chronological order and timing of formation of this structure largely differed between the two species. In addition to those differences, the overlapping patterns of the differentiated intraspecific lineages in these species suggest dynamic, but somewhat restricted dispersal during the Plio-Pleistocene. Tribolodon hakonensis, one of the most widespread species of East Asian freshwater fishes, included both common and unique phylogeographic patterns compared to other fish species; the unique patterns (i.e., its wide range across freshwater biogeographic boundaries like the sea and mountains) would reflect its ecological features as a remarkable generalist inhabiting lakes, upper and lower reaches of rivers, and even coastal areas.     

Morphological and genetic differentiation among four pigment producing Indian species of <Emphasis Type="Italic">Phoma</Emphasis> (Saccardo, 1899)

A PCR-based technique, involving the random amplification of polymorphic DNA (RAPD), was used for assessing genetic relatedness among isolates of the genus Phoma. Randomly Amplified Polymorphic DNA (RAPD) revealed the presence of interspecific genetic variation among the pigment producing isolates of Phoma and has shown distinct phylogenetic cluster. The major objective of the study was to study the genetic variation, if any. Study was aimed to differentiate four pigment producing species of Phoma based on morphological studies and molecular markers in general and RAPD in particular. We found that the test species of Phoma can be very well differentiated using molecular markers. Phoma sorghina was differentiated from P. exigua, P. fimeti and P. herbarum. RAPD profiles of P. herbarum and P. fimeti has shown the maximum similarity, which indicates the genetic relatedness among these two species which were considered earlier as distinct species based on morphological observation.     

Unspecific histological and hematological alterations in anadromous and resident <Emphasis Type="Italic">Salvelinus malma</Emphasis> induced by volcanogenic pollution

Knowledge of larval dispersal and connectivity in coral reef species is crucial for understanding population dynamics, resilience, and evolution of species. Here, we use ten microsatellites and one mitochondrial marker (cytochrome b) to investigate the genetic population structure, genetic diversity, and historical demography of the powder-blue tang Acanthurus leucosternon across more than 1000 km of the scarcely studied Eastern African region. The global AMOVA results based on microsatellites reveal a low but significant F _ST value (F _ST = 0.00252 P < 0.001; D _EST = 0.025 P = 0.0018) for the 336 specimens sampled at ten sample sites, while no significant differentiation could be found in the mitochondrial cytochrome b dataset. On the other hand, pairwise F _ST, PCOA, and hierarchical analysis failed to identify any genetic breaks among the Eastern African populations, supporting the hypothesis of genetic homogeneity. The observed genetic homogeneity among Eastern African sample sites can be explained by the lengthy post-larval stage of A. leucosternon, which can potentiate long-distance dispersal. Tests of neutrality and mismatch distribution signal a population expansion during the mid-Pleistocene period.     

Small mammals as sentinels of antimicrobial-resistant staphylococci

A total of 39 coagulase-negative staphylococci and seven Staphylococcus aureus strains were isolated from small mammal feces, i.e., the striped field mouse (Apodemus agrarius) and the yellow-necked mouse (A. flavicollis) in two sampling areas, deciduous forest and karst plains. MALDI-TOF analysis revealed five species of coagulase-negative staphylococci: S. sciuri, S. hominis, S. warneri, S. haemolyticus, and S. xylosus. All strains were susceptible to tetracycline, linezolid, vancomycin, and teicoplanin. Three MRSA strains with the mecA gene were detected. The beta-lactamase gene blaZ was detected in ampicillin-resistant staphylococci and in the high-level resistant strains (oxacillin over 2 mg/L) mecA gene. The mecC gene was not detected by PCR. Erythromycin-resistant staphylococci harbored the ermC gene and/or the efflux gene msrA. There were no detectable dfr genes in trimethoprim-resistant staphylococci and the rifampicin-resistant strains were without mutation in the rpoB gene. In summary, wild small mammals may serve as sentinels of mecA-positive S. aureus with erythromycin resistance genes ermC and efflux msrA. Small mammals appear to be useful indicators of antibiotic resistance.     

Historical range contraction,and not taxonomy,explains the contemporary genetic structure of the Australian tree <Emphasis Type="Italic">Acacia dealbata</Emphasis> Link

Irrespective of its causes, strong population genetic structure indicates a lack of gene flow. Understanding the processes that underlie such structure, and the spatial patterns it causes, is valuable for conservation efforts such as restoration. On the other hand, when a species is invasive outside its native range, such information can aid management in the non-native range. Here we explored the genetic characteristics of the Australian tree Acacia dealbata in its native range. Two subspecies of A. dealbata have previously been described based on morphology and environmental requirements, but recent phylogeographic data raised questions regarding the validity of this taxonomic subdivision. The species has been widely planted within and outside its native Australian range and is also a highly successful invasive species in many parts of the world. We employed microsatellite markers to investigate the population genetic diversity and structure among 42 A. dealbata populations from across the species’ native range. We also tested whether environmental variables purportedly relevant for the putative separation of subspecies are linked with population genetic differentiation. We found no relationship between population genetic structure of A. dealbata in Australia and these environmental features. Rather, we identified two geographically distinct genetic clusters that corresponded with populations in the northeastern part of mainland Australia, and the southern mainland and Tasmanian range of the species. Our results do not support the taxonomic subdivision of the species into two distinct subspecies based on environmental features. We therefore assume that the observed morphological differences between the putative subspecies are plastic phenotypic responses. This study provides population genetic information that will be useful for the conservation of the species within Australia as well as to better understand the invasion dynamics of A. dealbata.     

Flies (Diptera) Associated with <Emphasis Type="Italic">Polygraphus proximus</Emphasis> Blandford, 1894 (Coleoptera,Curculionidae) in Siberia and the Russian Far East

The faunal composition of Diptera (Insecta) inhabiting the galleries of Polygraphus proximus over the territory of Siberia and the Russian Far East was studied. As a result, 14 species of Diptera were discovered representing 8 families. Within its secondary range, the invasive beetle P. proximus Blandford, 1894 is affected not only by the well-known introduced species Medetera penicillata Negrobov, 1970 but also by numerous other widespread predatory flies, such as Medetera excellens Frey, 1909, M. pinicola Kowarz, 1877, Xylophagus cinctus (De Geer, 1776), and Toxoneura ephippium (Zettersted, 1860). Four predatory fly species, M. penicillata, M. signaticornis Loew, 1857, Lonchaea bukowskii Czerny, 1934, and Xylophagus sachalinensis (Pleske, 1925), affect P. proximus within its native range in the Russian Far East. Data on the predation of each species of Diptera on several species of bark beetles testify to their polyphagy. Saprophagous larvae of Dicranomyia modesta (Meigen, 1818), Chalcosyrphus piger (Fabricius, 1794), Xylosciara lignicola (Winnertz, 1867), and Pseudolycoriella unispina (Mohrig et Krivosheina, 1983) were discovered in bark beetle galleries for the first time.     

The genus <Emphasis Type="Italic">Copris</Emphasis> (Coleoptera,Scarabaeidae) in the Far East of Russia

The species of the genus Copris of the Russian Far East are reviewed. Copris tripartitus Waterhouse, 1875 is recorded for the fauna of Russia for the first time. The distribution of the Eastern Asian species of this genus in Russia is analyzed in detail. The data on their phenology, trophic associations, and habitat preferences are considered.     

AFLP,RAPD, and ISSR analysis of intraspecific polymorphism and interspecific differences of allotetraploid species <Emphasis Type="Italic">Aegilops kotschyi</Emphasis> Boiss. and <Emphasis Type="Italic">Aegilops variabilis</Emphasis> Eig

To evaluate genetic variation, 27 accessions of allotetraploid species Aegilops kotschyi and Ae. variabilis with the US genome were analyzed using the AFLP, RAPD, and ISSR methods. A total of 316 polymorphic RAPD fragments, 750 polymorphic AFLP fragments, and 234 polymorphic ISSR fragments were obtained. It was demonstrated that the analyzed species were characterized by a considerable level of nuclear genome variation. According to the data of ISSR and RAPD analysis, the average value of the Jaccard similarity coefficient for the accessions of Ae. variabilis from different geographical regions was slightly lower than that for the accessions of Ae. kotschyi. At the same time, AFLP analysis showed no considerable differences in the levels of intraspecific variation of the studied species. Analysis of the summarized RAPD, ISSR, and AFLP marking data in the Structure software program showed that most of the analyzed accessions with high degree of probability could be assigned to one of two groups, the first of which corresponded to Ae. kotschyi and the second corresponded to Ae. variabilis, thereby confirming the species independence of Ae. kotschyi and Ae. variabilis. Accessions k900, k907, k908, and v90 could not with a sufficiently high degree of probability be assigned to one of the species, which possibly was the result of interspecific hybridization. Analysis of the species diversity using different molecular markers made it possible to identify the accessions that were notably different from other accessions of its species.     

Population genetic structure of <Emphasis Type="Italic">Helix pomatia</Emphasis> L. (Mollusca,Pulmonata) from the southeastern and eastern parts of the range

On the basis of the analysis of genetic variation detectable by ISSR-PCR, the state of the gene pools of 14 populations of Roman snail Helix pomatia L. in the conditions of urbanized landscapes of the southeastern and eastern parts of the current range was examined. According to the data obtained, the majority of the studied populations of this mollusk are in satisfactory condition. This is evidenced by the increased level of genetic diversity (H _e = 0.199 ± 0.025, I _sh = 0.306 ± 0.035) and the high values of effective population size, calculated, on the basis of the straight-line regression equation, between the pairwise genetic and geographic distances (Ne = 2.0–4.9) that are comparable with indigenous common species of terrestrial mollusks. Despite the high level of differentiation (G_st = 0.255, Φ_st = 0.233, N _m = 0.822), the population distribution was not random (R _m =–0.591, p = 0.0004) and corresponded to the model of isolation by distance. It is hypothesized that, in the adventitious colonies of this mollusk, effective formation of a balanced genetic structure takes place that, in the context of biological and ecological features, facilitates its adaptation to the conditions of an urban environment and the population of the new territories of Eastern Europe.     

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.     

Merging of <Emphasis Type="Italic">Pedicularis exaltata</Emphasis> and <Emphasis Type="Italic">P. hacquetii</Emphasis> in the Carpathians: from local history to regional phylogeography based on complex evidence

The disjunct occurrence of Pedicularis exaltata in the White Carpathians (Czech Republic), isolated by more than 500 km from the nearest populations in the Eastern Carpathians, has been considered one of the mysteries of the Western Carpathian flora. We used molecular methods (AFLP, ITS and cpDNA sequencing) to reconstruct a possible scenario of the evolution of P. exaltata and its closely related congener P. hacquetii and to evaluate their differentiation. We paid particular attention to the origin of the isolated population in the White Carpathians. We also analysed the vegetation composition at the sampling sites to characterize the habitat preferences of the Pedicularis species and compare different sites. The pattern of molecular variability does not support a species boundary between P. exaltata and P. hacquetii. These assumed species should be merged into one bearing the name Pedicularis hacquetii following the priority rule, as also proposed by several early morphology-based taxonomic studies. The cpDNA variability pattern supports an evolutionary scenario involving a distribution centre (refugium) in the Eastern Carpathians from which the species expanded to the more westerly parts of its extant geographical range. Low population differentiation in AFLPs, high gene diversity and high DW index in isolated populations indicate that this expansion was contiguous rather than based on long-distance dispersal. Under such a scenario, the White Carpathian population is considered one of isolated relict populations scattered throughout the Carpathians and the East European Plain. A complete phylogeographic reconstruction of P. hacquetii s.l., however, requires ancient DNA analysis of herbarium specimens of nowadays extinct populations of the East European Plain. Extant habitats of P. hacquetii s.l. consist of species-rich dry-mesic to mesic (sub)montane grasslands and subalpine tall-herb growths, which may be relics of vegetation widespread in the late Glacial/early Holocene, when the contiguous expansion of the species possibly proceeded. The analysis of species with high fidelity to P. hacquetii s.l. throughout its range indicated that middle altitudes of south-western White Carpathians belong to the regions most suitable for the taxon within the Czech Republic and Slovakia. We found no support for the late introduction/long-distance dispersal scenarios and consider the relic survival scenario most parsimonious for the White Carpathians.     

Different dispersal histories of lineages of the earthworm <Emphasis Type="Italic">Aporrectodea caliginosa</Emphasis> (Lumbricidae,Annelida) in the Palearctic

Earthworms are among the most abundant and ecologically important invasive species, and are therefore a good object for studying genetic processes in invasive populations. Aporrectodea caliginosa is one of the most widespread invasive earthworms in the temperate zone. It is believed to have dispersed from Europe to all continents except Antarctica. It is known that A. caliginosa consists of three genetic lineages, and genetic diversity is high both among and between them. We attempted to use that high genetic diversity to study A. caliginosa dispersal in the Palearctic based on a sample of 40 localities ranging from eastern Europe to the Russian Far East, and to compare our data to other studies on this species in western Europe and North America. Two genetic lineages were found in the studied sample. Only negligible decrease in genetic diversity was observed for the lineage 2 of A. caliginosa from West Europe to the Far East, suggesting multiple human-mediated introductions. In contrast, lineage 3 is abundant in West Europe and Belarus, but is absent from the East European Plain, the Urals, and the Far East. However, it is present in West Siberia, where it has greatly reduced genetic diversity, indicating long-distance dispersal accompanied by a bottleneck event. Thus, although these two lineages of A. caliginosa are morphologically indistinguishable, they have dramatic differences in their distributions and dispersal histories.     

On the Gene Pool of Roe Deer (<Emphasis Type="Italic">Capreolus</Emphasis>) of Eastern Europe: Analysis of the Cyt <Emphasis Type="Italic">b</Emphasis> Gene Sequence Variability

Sequence analysis of the mtDNA cytochrome b gene (974 bp) was performed using 139 roe deer specimens from different regions of the European part of Russia and Ukraine. The data obtained showed that, at present, both European and Siberian roe deer inhabit this part of the range with predominance of the later: about 60% of individuals carry various Siberian haplotypes, most of which are similar to those in the populations of Capreolus pygargus from the Urals, Siberia, and the Far East. A great variety of mtDNA haplotypes of Siberian roe deer in Eastern Europe is undoubtedly caused by the heterogeneity of founder individuals (immigrants) that were imported from different parts of Asia. Some problems of coexistence of closely related species are discussed.     

New data on the distribution and host plants of weevils (Coleoptera,Curculionoidea: Apionidae,Curculionidae) in the south of Baikal Siberia and in Mongolia

Two weevil species, Rhinoncus autumnalis Korotyaev, 1980 and Orchestes medvedevi (Korotyaev, 1995), comb. n. (from Rhynchaenus), both described from Mongolia, are recorded from Russia (Buryatia) for the first time. A key to five Orchestes species associated with elms in Eastern Siberia, the Russian Far East, and Mongolia is provided. Aizobius sedi (Germar, 1818) is recorded for the first time from Eastern Siberia based on the recent findings in Buryatia and on older collections from Tuva where it is associated with Orostachys spinosa (L.) C.A. Mey. (Crassulaceae); it is also recorded for the first time from Kyrgyzstan and Mongolia. Magdalis (Aika) margaritae Barrios, 1984, native of Mongolia, Northern China and the south of the Russian Far East, is recorded from Buryatia. Lixus (Broconius) korotyaevi Ter-Minassian, 1989, formerly known in Russia only from southern Tuva, is recorded from Buryatia where it was collected on Suaeda ?prostrata Pallas, which is the first known host of this species. Rhamphus ?oxyacanthae (Marsham, 1802) is reported from Buryatia where it was collected from Cotoneaster melanocarpa, and from Mongolia.     

Reconstruction of molecular phylogeny of closely related <Emphasis Type="Italic">Amorphophallus</Emphasis> species of India using plastid DNA marker and fingerprinting approaches

Plastid DNA markers sequencing and DNA fingerprinting approaches were used and compared for resolving molecular phylogeny of closely related, previously unexplored Amorphophallus species of India. The utility of individual plastid markers namely rbcL, matK, trnH–psbA, trnLC–trnLD, their combined dataset and two fingerprinting techniques viz. RAPD and ISSR were tested for their efficacy to resolves Amorphophallus species into three sections specific clades namely Rhaphiophallus, Conophallus and Amorphophallus. In the present study, sequences of these four plastid DNA regions as well as RAPD and ISSR profiles of 16 Amorphophallus species together with six varieties of two species were generated and analyzed. Maximum likelihood and Bayesian Inference based construction of phylogenetic trees indicated that among the four plastid DNA regions tested individually and their combined dataset, rbcL was found best suited for resolving closely related Amorphophallus species into section specific clades. When analyzed individually, rbcL exhibited better discrimination ability than matK, trnH–psbA, trnLC–trnLD and combination of all four tested plastid markers. Among two fingerprinting techniques used, the resolution of Amorphophallus species using RAPD was better than ISSR and combination of RAPD +ISSR and in congruence with resolution based on rbcL.