Comparative analysis of STR and SNP polymorphism in the populations of sockeye salmon (Oncorhynchus nerka) from Eastern and Western Kamchatka

Sockeye salmon samples from five largest lacustrine-riverine systems of Kamchatka Peninsula were tested for polymorphism at six microsatellite (STR) and five single nucleotide polymorphism (SNP) loci. Statistically significant genetic differentiation among local populations from this part of the species range examined was demonstrated. The data presented point to pronounced genetic divergence of the populations from two geographical regions, Eastern and Western Kamchatka. For sockeye salmon, the individual identification test accuracy was higher for microsatellites compared to similar number of SNP markers. Pooling of the STR and SNP allele frequency data sets provided the highest accuracy of the individual fish population assignment.     

Variability of size-age indices and genetic variability of sockeye salmon <Emphasis Type=Italic>Oncorhynchus nerka</Emphasis> from the Western Coast of Kamchatka: Comparative analysis of methods of differentiation of local populations

Study of variability of size-age indices and polymorphism of 6 microsatellite loci, 5 loci of SNP, and accidentally amplified polymorphic DNA (RAPD) of sockeye salmon Oncorhynchus nerka of three largest populations from the western coast of Kamchatka Peninsula was performed. The efficiency of using different types of markers for the differentiation of populations and determination of the population belonging of sockeye salmon from lake-river systems of western Kamchatka was analyzed. Significant interpopulation differences were revealed from the frequencies of alleles of genetic markers and from a set of biological indices. It was established that genetic markers are characterized by a better differentiating capacity, as compared to biological characteristics. The most satisfactory results during determination of population belonging of sockeye salmon were obtained using an integrated data base of allele frequencies of microsatellite and SNP loci.     

Morphological diversity of sockeye salmon (<Emphasis Type="Italic">Oncorhynchus nerka</Emphasis> (Walbaum)) of the Kamchatka River

A method based on morphological characters is proposed to evaluate biological diversity of a sockeye salmon population. In all samples, morphological diversity of males is greater than that of females. In addition, the inter-annual dynamics determined on the basis of separate morphological characters differs in individuals of different sex. The necessity of studying biological diversity for preserving population homeostasis is also considered.     

The effect of the infectious hematopoietic necrosis virus on the population of sockeye salmon <Emphasis Type=Italic>Oncorhynchus nerka</Emphasis> (Salmoniformes,Salmonidae) from Lake Nachikinskoe

The results of virological examination of adult sockeye salmon Oncorhynchus nerka in Lake Nachikinskoe from 2003 to 2008 demonstrated high values of prevalence of the infectious hematopoietic necrosis virus (IHNV) in the fish population (up to 100%). In the studied water reservoir there are optimal conditions for the development and revealing of the epizootic of infectious hematopoietic necrosis (IHN). In Lake Nachikinskoe, two natural epizootics of IHN in juvenile sockeye salmon were recorded in 2003 and 2006. The tendencies for change of prevalence of IHNV by years were analyzed, and their relation to the numbers of adult sockeye salmon at the spawning grounds of Lake Nachikinskoe was determined. The correlation of IHNV prevalence with the numbers of adult sockeye salmon in the studied water reservoir is direct but insignificant (r _s = 0.695, p < 0.05). It was shown that the epizootic of 2003 could affect the fact that fish return in 2007 and 2008 was minimum for the considered time interval while the numbers of their parents were, on the other hand, very high.     

Seasonal and interannual variations of sockeye salmon (<Emphasis Type="Italic">Oncorhynchus nerka</Emphasis>) microsatellite DNA in two Kamchatka lake-river systems

Seasonal and interannual variations in the sockeye salmon populations from two lake-river systems of the East and West Kamchatka were studied. Stability of allele and genotypic frequencies of six microsatellite DNA loci in the adjacent generations and spawning populations of the sockeye salmon of the Bol’shaya River was confirmed experimentally. The pairwise intersample differentiation (F _st) of the local sockeye salmon populations from the southwestern Kamchatka coast (Ozernaya and Bol’shaya Rivers) was almost 7 times higher than the corresponding values for the spawning populations of the Bol’shaya River sockeye salmon of the adjacent years; 15 times, for the adjacent Bol’shaya River sockeye salmon generations; and four times, for the seasonal races within the Kamchatka River.     

Migration patterns and phenotypic diversity of underyearlings of sockeye salmon <Emphasis Type="Italic">Oncorhynchus nerka</Emphasis> in the Ozernaya River basin (Kamchatka)

Migratory behavior, size composition, and feeding patterns of the underyearlings of sockeye salmon Oncorhynchus nerka from different intraspecific phenotypic groups in the Ozernaya River basin are studied. Complex organization of main phenotypic groups is demonstrated: several labile spatial-temporal groups are defined within them. The discovered phenotypic polymorphism is temporal and manifested by the sockeye salmon underyearlings only during the period in which they reach the main rearing grounds.     

Single-nucleotide polymorphism in populations of sockeye salmon Oncorhynchus nerka from Kamchatka Peninsula

The genetic variability of 45 single-nucleotide polymorphism loci was examined in the four largest wild populations of sockeye salmon Oncorhynchus nerka from drainages of the Asian coast of the Pacific Ocean (Eastern and Western Kamchatka). It was demonstrated that sockeye salmon from the Palana River were considerably different from all other populations examined. The most probable explanation of the observed differences is the suggestion on possible demographic events in the history of this population associated with the decrease in its effective number. To study the origin, colonization patterns, and evolution of Asian sockeye salmon, as well as to resolve some of the applied tasks, like population assignment and genetic identification, a differential approach to SNP-marker selection was suggested. Adaptively important loci that evolve under the pressure of balancing (stabilizing) selection were identified, owing to this fact the number of loci that provide the baseline classification error rates in the population assignment tests was reduced to 30. It was demonstrated that SNPs located in the MHC2 and GPH genes were affected by diversifying selection. Procedures for selecting single-nucleotide polymorphisms for phylogenetic studies of Asian sockeye salmon were suggested. Using principal-component analysis, 17 loci that adequately reproduce genetic differentiation within and among the regions of the origin of Kamchatka sockeye salmon were selected.     

Efficient separation and purification of allophycocyanin from <Emphasis Type=Italic>Spirulina</Emphasis> (<Emphasis Type=Italic>Arthrospira</Emphasis>) <Emphasis Type=Italic>platensis</Emphasis>

Allophycocyanin (APC) is a minor component of phycobiliproteins in cyanobacteria and red algae. This paper describes a simple and inexpensive extracting method for isolating APC from Spirulina (Arthrospira) platensis with high efficiency. The crude phycobiliprotein extract was pretreated by ammonium sulfate fractionation. Then, by adding hydroxylapatite into crude phycobiliprotein extract dissolved in 20 mM phosphate buffer (pH 7.0), APC was selectively adsorbed by hydroxylapatite but C-phycocyanin (C-PC) was not. The hydroxylapatite was collected and APC was extracted from the crude phycobiliprotein extract. Then, the enriched APC was washed off from the hydroxylapatite using 100 mM phosphate buffer (pH 7.0). In this simple extracting method it was easy to remove C-PC and isolate APC in large amounts. The absorbance ratio A ₆₅₀/A ₂₈₀ of extracted APC reached 2.0. The recovery yield was 70%, representing 4.61 mg · g⁻¹ wet weight. The extracted APC could be further purified by a simple anion-exchange chromatography with a pH gradient from 5.6 to 4.0. The absorbance ratio A ₆₅₀/A ₂₈₀ of the purified APC reached 5.0, and the overall recovery yield was 43%, representing 2.83 mg · g⁻¹ wet weight. Its purity was confirmed by native polyacrylamide gel electrophoresis (PAGE) and sodium dodecyl sulfate-PAGE.     

The state of gonads of resident sockeye salmon <Emphasis Type="Italic">Oncorhynchus nerka</Emphasis> from the Tolmachev Reservoir

Morphology of gonads and structure of sex cells in females and males of the resident sockeye salmon Oncorhynchus nerka—kokanee—from Tolmachevskoe Reservoir are investigated. Anomalies in structure of sex cells and structure of oocytes are found. Partial or mass resorpbion of cells in the ovaries of males and testes of males is found, leading to sterility of gonads. The relationship between anomalies found in structure of the sex system of kokanee, changes in biological parameters of fish and the increase of the population abundance is discussed.     

Comparative analysis of <Emphasis Type=Italic>iol</Emphasis> clusters in <Emphasis Type=Italic>Lactobacillus casei</Emphasis> strains

The present study was designed to expand genetic knowledge of myo -inositol (MI) metabolism in Lactobacillus casei. Twenty-four L. casei isolates of dairy origin were tested for the presence of iol cluster. PCR screening revealed eight strains encoded functions involved in MI utilization, of which one strain was able to use MI as carbon source. To gain a deeper understanding of the function of iol genes, four of the eight observed iol clusters were subjected to the full sequencing procedure. The results showed that the iol cluster was not a common feature among dairy L. casei strains. In addition, the four iol clusters were highly similar to one another in terms of sequence similarity and operon architecture. However, abundant polymorphisms that comprised a majority of synonymous mutations were detected throughout the full sequences. Three of them distributed among iolB, iolC, and iolT genes were found in linkage to MI-negative phenotype. Compared with other bacterial iol clusters, the iol cluster of L. casei showed a high similarity with that of Bacillus subtilis.     

Structure of the school of sock-eyed salmon <Emphasis Type="Italic">Oncorhynchus nerka</Emphasis> from the Apuka River (the Northeastern Kamchatka)

Results of study of sock-eyed salmon Oncorhynchus nerka from the Apuka River—the largest river of the northeast of Kamchatka—inflowing Olyutorskii Bay of the Bering Sea are presented. It is established that the school of the Apuka River is represented by the early-run sock-eyed salmon that spawns in Lake Vatyg-Gytkhyn located in the lower part of the basin and by individuals of the later run that spawn in the upper reaches of the river. Early-run sock-eyed salmon appears in the river with signs of spawning changes and a high value of gonadosomatic index (GSI). Late-run sock-eyed salmon migrates to the river without signs of spawning changes and with a relatively low GSI. The age composition of spawners of the early- and late-run sock-eyed salmon is different.     

Swimming performance and morphology of juvenile sockeye salmon, <Emphasis Type="Italic">Oncorhynchus nerka</Emphasis>: comparison of inlet and outlet fry populations

We raised two populations of sockeye salmon fry from fertilized eggs in the laboratory and tested the hypothesis that outlet fry populations, fish which must migrate upstream to reach rearing lakes after yolk-sac absorption, have better swimming ability and morphological characteristics conducive to enhanced swimming performance than inlet fry populations, fish which migrate downstream to rearing lakes. Despite being of identical age, fry from the outlet population were larger (approx. 6.7% longer, ~5 mm on average) and more laterally compressed than inlet fry at the time of our initial experiments. Using an open-top box flume, we found that the burst-swimming performance (in cm s⁻¹) of the outlet population was 31% better. We found no differences between populations in prolonged-swimming performance. We were unable to find any direct relationships between measures of swimming performance and size or shape variables, suggesting that the larger, more robust morphology of outlet fry was not responsible for the superior burst ability. Recent biochemical studies indicate outlet fry may be metabolically better provisioned for burst swimming than inlet fry. It is possible that the morphological differences between the populations of fry reflect adaptations needed by adults during their migration and spawning.     

New species of <Emphasis Type=Italic>Dypsis</Emphasis> and <Emphasis Type=Italic>Ravenea</Emphasis> (Arecaceae) from Madagascar

Fourteen new species of palms (Arecaceae) from Madagascar are described and named, based on material collected over the last 15 years. Twelve species belong to the genus Dypsis, namely D. andilamenensis Rakotoarin. & J. Dransf., D. anjae Rakotoarin. & J. Dransf., D. betsimisarakae Rakotoarin. & J. Dransf., D. culminis Rakotoarin. & J. Dransf., D. dracaenoides Rakotoarin. & J. Dransf., D. gautieri Rakotoarin. & J. Dransf., D. gronophyllum Rakotoarin. & J. Dransf., D. jeremiei Rakotoarin. & J. Dransf., D. metallica Rakotoarin. & J. Dransf., D. reflexa Rakotoarin. & J. Dransf., D. sancta Rakotoarin. & J. Dransf. and D. vonitrandambo Rakotoarin. & J. Dransf. and two species belong to the genus Ravenea: R. beentjei Rakotoarin. & J. Dransf. and R. hypoleuca Rakotoarin. & J. Dransf. Despite the fact that most of these species have been recorded from protected areas that are difficult to access in the eastern region of Madagasacar, they are all threatened. Based on IUCN categories and criteria, seven are Critically Endangered and seven are Vulnerable.     

Genetic diversity of sockeye salmon <Emphasis Type="Italic">Oncorhynchus nerka</Emphasis> Walbaum of Kamchatka and the Commander Islands based on analysis of the variability of microsatellite DNA

The genetic diversity of the resident and migratory forms of sockeye salmon is investigated in 14 populations from various water bodies of Kamchatka and the Commander Islands by ten loci of microsatellite DNA. There are considerable differences in the frequencies of alleles among the populations of kokanee from Lake Kronotskoe, the residual form of sockeye salmon from Lake Kopylie, and other populations analyzed. Clustering of samples corresponds to their geographic position. No differences in the frequencies of alleles of the investigated loci are found between two forms of resident sockeye salmon from Kronotskoe Lake. In the sockeye salmon from the Commander Islands, a relatively low genetic diversity is found, as well as the greatest remoteness from the other Kamchatka group.     

Characteristics of <Emphasis Type=Italic>Phomopsis sclareae</Emphasis> obtained from sage (<Emphasis Type=Italic>Salvia officinalis</Emphasis>)

In the years 2004–2006 the species P. sclareae was isolated from sage stems showing the symptoms in the form of bark peeling off and breaking. On the basis of 5 isolates randomly chosen from the fungus population, morphology and the conditions of temperatures favourable for the most intensive growth and creation of the fungus infectious material were studied. The temperature of −6°C was viewed as unfavourable for the fungus growth, and that of 32°C was considered to prevent the formation of picnidia and conidia. The dynamic growth of the colonies and the formation of numerous picnidia and conidia were observed at the temperatures ranging from 20°C to 28°C.     

<Emphasis Type=Italic>Barleria compacta</Emphasis>: a new species in <Emphasis Type=Italic>Barleria</Emphasis> sect. <Emphasis Type=Italic>Prionitis</Emphasis> (Acanthaceae) from Somalia

Following a re-examination of the material treated under Barleria brevispina (Fiori) Hedrén in the recent Flora of Somalia account of the Acanthaceae, it is concluded that two distinct species are involved and Barleria compacta Malombe & I. Darbysh. is described here from north-eastern Somalia. Its affinities and conservation status are discussed.     

Analysis of microsatellite DNA of rainbow trout (<Emphasis Type=Italic>Parasalmo</Emphasis> (<Emphasis Type=Italic>Oncorhynchus</Emphasis>) <Emphasis Type=Italic>mykiss</Emphasis>) of Kamchatka: Selection of loci and optimization of the method

The variation of a sample of rainbow trout (Parasalmo (Oncorhynchus) mykiss) from natural populations of several rivers of the Kamchatka Peninsula with respect to 43 microsatellite DNA loci has been studied. These loci were earlier used for analysis of Asian populations of closely related salmonids. Ten of them may be regarded as markers and seen promising for further studies on intraspecific relationships of rainbow trout of Kamchatka. Their use in studies on more numerous samples from different localities and populations of Parasalmo (O.) mykiss in the Asian part of the species range will ensure efficient population genetic analysis of the Kamchatka population group of this species.