Determination of Genetic Sex in Chinook Salmon (<Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>) Using the Male-Linked Growth Hormone Pseudogene by Real-Time PCR

This study used a real-time quantitative polymerase chain reaction (qPCR) method based on the growth hormone pseudogene (GHp) in chinook salmon (Oncorhynchus tshawytscha) to determine genetic sex. The GHp is present as a single copy in the genome of the male chinook salmon but is absent in the female, providing a means of using this real-time qPCR method to discriminate genetic sex. Comparisons between genomic DNA samples from 2 geographically distinct populations of chinook salmon (Columbia River, Washington, and Yukon River, Alaska) showed, within each population examined, that the males were clearly differentiated from the females. There were no interpopulation differences between males or females. The advantages of this real-time qPCR method are that it is rapid, is amenable to high sample throughput, and provides an accurate numerical value that allows comparisons between samples by statistical methods.     

Taxonomic novelties in <Emphasis Type="Italic">Rhynchospora</Emphasis> (<Emphasis Type="Italic">Cyperaceae</Emphasis>) from South America

Summary  Two new species of Rhynchospora, R. acanthoma and R. rupestris, are described and illustrated. Their geographical distributions are discussed. The status of R. exilis and its synonymy is clarified.     

Experimental evidence of population-specific marine spatial distributions of Chinook salmon, <Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>

Migratory behavior can be affected by attributes of the animals themselves such as size and growth rate, external factors such as biotic and abiotic features of the environment, and also genetic tendencies. To better understand the role of genetics in the migratory behavior of Chinook salmon, Oncorhynchus tshawytscha, we report the results of an experiment in which two populations (University of Washington (UW) hatchery and Elwha River) and their hybrid offspring were reared at, tagged, and released from a single site, the UW hatchery, at a common size and date. The patterns of recoveries in fisheries differed markedly with respect to spatial distribution and also age of the fish. A larger proportion of the Elwha River fish were recovered in Puget Sound in their first year of marine life than the other groups (40.7% vs. 11.2% for UW and 7.0% for the hybrids). The Elwha River fish also showed a higher proportion of northerly recoveries (21.9%) than UW fish (1.7%), and hybrids showed an intermediate value (8.1%). In contrast, no Elwha River fish were recovered south along the Washington coast compared to 1.3% of the hybrids and 7.7% of the UW fish. The specific mechanisms controlling the migration patterns of the populations remain unclear but the results strongly indicated a genetic influence on distribution patterns.     

New combinations amongst Bolivian <Emphasis Type="Italic">Compositae</Emphasis>

Summary  New combinations are provided for nine taxa in the Bolivian Compositae — four in Dendrophorbium (Senecioneae), four in Vernonia (Vernonieae) and one in Viguiera (Heliantheae) — in advance of an on-line publication of a ‘Preliminary checklist of the Compositae of Bolivia’.     

Microsatellite variation reveals weak genetic structure and retention of genetic variability in threatened Chinook salmon (<Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>) within a Snake River watershed

Pacific salmon (Oncorhynchus spp.) have been central to the development of management concepts associated with evolutionarily significant units (ESUs), yet there are still relatively few studies of genetic diversity within threatened and endangered ESUs for salmon or other species. We analyzed genetic variation at 10 microsatellite loci to evaluate spatial population structure and genetic variability in indigenous Chinook salmon (Oncorhynchus tshawytscha) across a large wilderness basin within a Snake River ESU. Despite dramatic 20th century declines in abundance, these populations retained robust levels of genetic variability. No significant genetic bottlenecks were found, although the bottleneck metric (M ratio) was significantly correlated with average population size and variability. Weak but significant genetic structure existed among tributaries despite evidence of high levels of gene flow, with the strongest genetic differentiation mirroring the physical segregation of fish from two sub-basins. Despite the more recent colonization of one sub-basin and differences between sub-basins in the natural level of fragmentation, gene diversity and genetic differentiation were similar between sub-basins. Various factors, such as the (unknown) genetic contribution of precocial males, genetic compensation, lack of hatchery influence, and high levels of current gene flow may have contributed to the persistence of genetic variability in this system in spite of historical declines. This unique study of indigenous Chinook salmon underscores the importance of maintaining natural populations in interconnected and complex habitats to minimize losses of genetic diversity within ESUs.     

Distribution of Masu Salmon <Emphasis Type="Italic">Oncorhynchus masou</Emphasis> (Salmonidae) in Amur River Basin

The presented data on the distribution of the masu salmon Oncorhynchus masou in the Amur River Basin are collected in 1976–2015. In the analyzed region the species’ spawning range includes the lower part of the Amur River basin from the rivers flowing into the Amur estuary to the basins of the Anyui and Amgun’ Rivers in their middle courses. The information on the catch of a masu salmon specimen in the Khor River Basin (approximately 1300 km from the Amur River mouth) in 2015 is presented. It is assumed that the total Amur population does not exceed several thousand of adult anadromous fish.     

Characterization of Na,K-ATPase genes in Atlantic salmon (<Emphasis Type="Italic">Salmo salar</Emphasis>) and comparative genomic organization with rainbow trout (<Emphasis Type="Italic">Oncorhynchus mykiss</Emphasis>)

A combination of molecular and in silico approaches was employed to assemble a survey of Na, K-ATPase genes contained in the ancestrally tetraploid genome of the Atlantic salmon (Salmo salar). Molecular characterization of genomic clones coding for the subunit revealed two single genes (1a and 2) and two pairs of presumably homeologous genes (1b/i-ii and 1c/i-ii). Each of the six genes showed high sequence similarity to isoforms previously isolated from rainbow trout and extensive structural differences relative to putative orthologs in the human genome. In silico analysis of expressed sequence tag (EST) collections indicated that at least five (1a, 1b, 1c, 2, and 3) and four (1a, 1b, 2, and 3b) subunit isoforms are expressed in Atlantic salmon. Meiotic linkage analysis further showed that Na, K-ATPase genes are dispersed throughout the salmon genome, with the exception of two multigene clusters on linkage groups AS-22 and AS-28. Duplicate gene copies for the isoform 1b were assigned to linkage groups with multiple homeologous anchors (AS-22 and AS-23), while 2 duplicates suggested a new homeologous affinity between AS-05 and AS-28. In addition, the comparison of linkage arrangements with rainbow trout also showed that the genomic organization of Na, K-ATPase genes is consistent with the evolutionary conservation of syntenic chromosome regions between these species.Electronic Supplementary Material Supplementary material is available for this article at .     

Defining marine habitat of juvenile Chinook salmon, <Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>, and coho salmon, <Emphasis Type="Italic">O. kisutch</Emphasis>, in the northern California Current System

We investigated habitat use by juvenile Chinook salmon (Oncorhynchus tshawytscha) and coho salmon (O. kisutch) to identify environmental characteristics that may define their optimal marine habitat. We utilized physical and biological data from four cruises in the northern California Current system from Newport, Oregon, to Crescent City, California, in June and August 2000 and 2002. A non-parametric statistical method was used to analyze and select environmental parameters that best defined ocean habitat for each species. Regression trees were generated for all cruises combined to select the most important habitat variables. Chlorophyll a concentration best defined habitat of yearling Chinook salmon, while decapod larvae, salinity, and neuston biovolume defined habitat of yearling coho salmon. Using criteria from the regression tree analysis, GIS maps were produced to show that the habitat of yearling Chinook salmon was widespread over the continental shelf and the habitat of yearling coho salmon was variable and mainly north of Cape Blanco.     

<Emphasis Type="Italic">Ty</Emphasis>1<Emphasis Type="Italic">/copia</Emphasis>- and <Emphasis Type="Italic">Ty</Emphasis>3<Emphasis Type="Italic">/gypsy</Emphasis>-like DNA sequences in <Emphasis Type="Italic">Helianthus </Emphasis>species

Two repeated DNA sequences isolated from a partial genomic DNA library of Helianthus annuus, p HaS13 and p HaS211, were shown to represent portions of the int gene of a Ty3 /gypsy retroelement and of the RNase-Hgene of a Ty1 /copia retroelement, respectively. Southern blotting patterns obtained by hybridizing the two probes to BglII- or DraI-digested genomic DNA from different Helianthus species showed p HaS13 and p HaS211 were parts of dispersed repeats at least 8 and 7 kb in length, respectively, that were conserved in all species studied. Comparable hybridization patterns were obtained in all species with p HaS13. By contrast, the patterns obtained by hybridizing p HaS211 clearly differentiated annual species from perennials. The frequencies of p HaS13- and p HaS211-related sequences in different species were 4.3x10(4)-1.3x10(5) copies and 9.9x10(2)-8.1x10(3) copies per picogram of DNA, respectively. The frequency of p HaS13-related sequences varied widely within annual species, while no significant difference was observed among perennial species. Conversely, the frequency variation of p HaS211-related sequences was as large within annual species as within perennials. Sequences of both families were found to be dispersed along the length of all chromosomes in all species studied. However, Ty3 /gypsy-like sequences were localized preferentially at the centromeric regions, whereas Ty1/ copia-like sequences were less represented or absent around the centromeres and plentiful at the chromosome ends. These findings suggest that the two sequence families played a role in Helianthusgenome evolution and species divergence, evolved independently in the same genomic backgrounds and in annual or perennial species, and acquired different possible functions in the host genomes.     

Velocity and dominance affect prey capture and microhabitat selection in juvenile Chinook (<Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>)

Habitat selection is an important phenomenon that may greatly affect individual fitness. Using an artificial stream, we examined the relationship between the percentage of prey captured, reactive distance, dominance, and water velocity for juvenile Chinook Salmon (Oncorhynchus tshawytscha) from the Chena River, Alaska, and tested the fitness-based microhabitat selection model of Grossman et al. (Ecol Freshw Fish 11:2–10, 2002). Recent declines in the abundance of Chinook accentuate our need for habitat selection studies on this species. We conducted three experiments: two with single fish (1st N?=?27, fish SL 58–84 mm, 2nd N?=?14, fish SL 49–56 mm) and one with pairs of dominant and subordinate fish (N?=?10 pairs, 64–96 mm, mean difference in SL?=?7 mm). We placed individual or pairs of fish in an artificial flume and recorded reactive distance and the percent prey capture with individual dead brine shrimp (Artemia spp.) as prey. Prey were presented at 10 cm/s velocity intervals ranging from 10 to 60 cm/s; velocities found in the natural habitat. Mean reactive distance in single fish experiments (henceforth SFE) averaged 33 and 29 cm respectively, and was not related to velocity. We detected a negative, curvilinear relationship between velocity and percent prey capture. Holding velocities for juvenile Chinook were significantly lower than prey capture velocities. The Grossman et al. (Ecol Freshw Fish 11:2–10, 2002) model yielded an optimal focal-point velocity prediction of 35 cm/s for juvenile Chinook, however focal-point velocities occupied by juveniles in the Chena River averaged 12 cm/s. Predicted optimal velocities were present in the Chena River; hence, this discrepancy suggests that other factors such as distraction from drifting debris or predation risk influenced habitat selection. There were no differences in reactive distances or holding velocity/capture velocity relationships for dominant and subordinate fish; however, dominants captured significantly more prey than subordinates. Being subordinate resulted in a decrease of 61% in mean percent prey capture (the difference between what was captured by the fish alone versus the difference with a dominant), whereas the mean cost to fish with dominant rank was a 21% decline between the percentage captured alone versus that with a subordinate.     

Rearing and migration of juvenile Chinook salmon (<Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>) in a large river floodplain

Off-channel habitat has become increasingly recognized as key for migratory fishes such as juvenile Chinook salmon (Oncorhynchus tshawytscha). Hence, floodplain habitat has been identified as critical for the continued persistence of California’s Central Valley salmon, particularly the Yolo Bypass, the primary floodplain of the Sacramento River. To provide insight into factors supporting juvenile salmon use of this 240 km², partially leveed floodplain, we examined inter- and intra-annual relationships between environmental correlates and residency time, apparent growth, emigration, migratory phenotype, and survival over more than a decade for natural-origin (“wild”) fish and experimentally-released hatchery fish. Flood duration was positively associated with hatchery juveniles residing longer and achieving larger size. Wild juveniles grew larger and emigrated later with cumulative temperature experience (accumulated thermal units) and warmer average annual temperatures during flood years. Within years, both wild and hatchery salmon departed the floodplain as flood waters receded. Parr-sized juveniles dominated outmigrant composition, though fry and smolt-sized juveniles were also consistently observed. Survival to the ocean fishery was not significantly different between hatchery fish that reared in the Yolo Bypass versus those that reared in the main stem Sacramento River. Our study indicates improved frequency and duration of connectivity between the Sacramento River and the Yolo Bypass could increase off-channel rearing opportunities that expand the life history diversity portfolio for Central Valley Chinook salmon.     

<Emphasis Type="Italic">Erysiphe patagoniaca</Emphasis>: a new species of <Emphasis Type="Italic">Erysiphe </Emphasis>sect. <Emphasis Type="Italic">Uncinula </Emphasis>from Patagonia,Argentina

 A new species of Erysiphe sect. Uncinula is described and illustrated from Patagonia, Argentina. Erysiphe patagoniaca sp. nov., found on leaves of Nothofagus × antarctica, is similar to E. nothofagi and E. kenjiana, but differs in its appendages being twisted throughout their length and the number of appendages, asci, and ascospores. The two endemic species of Erysiphe sect. Uncinula, E. magellanica and E. nothofagi, coexisted on the same leaves together with Erysiphe patagoniaca. Received: September 19, 2002 / Accepted: November 28, 2002 Acknowledgments The authors are grateful to Ms. Seiko Niinomi for providing the micrographs of ascomata of Erysiphe spp. on Nothofagus. Correspondence to:S. Takamatsu     

<Emphasis Type="Italic">In vitro</Emphasis> minimum growth for conservation of <Emphasis Type="Italic">Drosophyllum lusitanicum</Emphasis>

The present paper reports a protocol for minimum growth conservation of Drosophyllum lusitanicum (L.) Link. in vitro. Double-node cuttings were maintained for 4, 8 and 12 months at 5 or 25 °C in the dark. The effects of sucrose either alone at 5, 20, 30, 40 and 60 g dm⁻³ or at 20, 40 and 60 g dm⁻³ in combination with 20 g dm⁻³ mannitol, on survival and post-storage shoot multiplication efficiency were investigated. The cultures could effectively be conserved under minimum growth at 5 °C for 8 months on Murashige and Skoog’s medium supplemented with 60 g dm⁻³ sucrose, 20 g dm⁻³ mannitol and 0.91 μM zeatin. Following extended conservation, the cultures could be successfully regenerated into new shoots, and they were morphologically similar to those of non-stored controls.     

<Emphasis Type="Italic">Agrobacterium</Emphasis><Emphasis Type="Italic">tumefaciens</Emphasis>-mediated transformation of callus cells of <Emphasis Type="Italic">Crataegus</Emphasis><Emphasis Type="Italic">aronia</Emphasis>

A genetic transformation system has been developed for callus cells of Crataegus aronia using Agrobacterium tumefaciens. Callus culture was established from internodal stem segments incubated on Murashige and Skoog (MS) medium supplemented with 5 mg l⁻¹ Indole-3-butyric acid (IBA) and 0.5 mg l⁻¹ 6-benzyladenine (BA). In order to optimize the callus culture system with respect to callus growth and coloration, different types and concentrations of plant growth regulators were tested. Results indicated that the best average fresh weight of red colored callus was obtained on MS medium supplemented with 2 mg l⁻¹ 2,4-dichlorophenoxyacetic acid (2,4-D) and 1.5 mg l⁻¹ kinetin (Kin) (callus maintenance medium). Callus cells were co-cultivated with Agrobacterium harboring the binary plasmid pCAMBIA1302 carrying the mgfp5 and hygromycin phosphotransferase (hptII) genes conferring green fluorescent protein (GFP) activity and hygromycin resistance, respectively. Putative transgenic calli were obtained 4 weeks after incubation of the co-cultivated explants onto maintenance medium supplemented with 50 mg l⁻¹ hygromycin. Molecular analysis confirmed the integration of the transgenes in transformed callus. To our knowledge, this is the first time to report an Agrobacterium-mediated transformation system in Crataegus aronia.     

Revision of the <Emphasis Type="Italic">Serrulati</Emphasis> species of <Emphasis Type="Italic">Penstemon</Emphasis> section <Emphasis Type="Italic">Saccanthera</Emphasis> subsection <Emphasis Type="Italic">Serrulati</Emphasis>

A revision of Penstemon sect. Saccanthera subsect. Serrulati includes a new species (P. salmonensis), a new variety (P. triphyllus var. infernalis), and the elevation of a subspecies to species (P. curtiflorus), bringing the total number of species to eight, which are keyed and described, complete with nomenclature and type citations.     

<Emphasis Type="Italic">Galleria</Emphasis><Emphasis Type="Italic">mellonella</Emphasis> are Resistant to <Emphasis Type="Italic">Pneumocystis</Emphasis><Emphasis Type="Italic">murina</Emphasis> Infection

Studying Pneumocystis has proven to be a challenge from the perspective of propagating a significant amount of the pathogen in a facile manner. The study of several fungal pathogens has been aided by the use of invertebrate model hosts. Our efforts to infect the invertebrate larvae Galleria mellonella with Pneumocystis proved futile since P. murina neither caused disease nor was able to proliferate within G. mellonella. It did, however, show that the pathogen could be rapidly cleared from the host.     

<Emphasis Type="Italic">Nepenthes</Emphasis> group <Emphasis Type="Italic">Montanae</Emphasis> (Nepenthaceae) in Indo-China,with <Emphasis Type="Italic">N. thai</Emphasis> and <Emphasis Type="Italic">N. bokor</Emphasis> described as new

Summary  A key is presented to the Nepenthes group Montanae in Peninsular Malaysia, Thailand and Cambodia. Nepenthes bokor Cheek is described from Cambodia and Nepenthes thai Cheek from peninsular Thailand. The affinities of both taxa are discussed and their conservation status assessed.     

<Emphasis Type="Italic">Caragana aliensis</Emphasis>, a new species of <Emphasis Type="Italic">Caragana</Emphasis> (<Emphasis Type="Italic">Leguminosae</Emphasis>) from Tibet,China

Summary   Caragana aliensis a new species from Tibet, China, is described and illustrated.     

The tyrosine <Emphasis Type="Italic">O</Emphasis>-prenyltransferase SirD catalyzes <Emphasis Type="Italic">O</Emphasis>-, <Emphasis Type="Italic">N</Emphasis>-, and <Emphasis Type="Italic">C</Emphasis>-prenylations

Recently, the prenyltransferase SirD was found to be responsible for the O-prenylation of tyrosine in the biosynthesis of sirodesmin PL in Leptosphaeria maculans. In this study, the behavior of SirD towards phenylalanine/tyrosine and tryptophan derivatives was investigated. Product formation has been observed with 12 of 19 phenylalanine/tyrosine derivatives. It was shown that the alanine structure attached to the benzene ring and an electron donor, e.g., OH or NH₂, at its para-position are essential for the enzyme activity. Modifications were possible both at the side chain and the benzene ring. Enzyme products from seven phenylalanine/tyrosine derivatives were isolated and characterized by MS and NMR analyses including HSQC and HMBC and proven to be O- or N-prenylated derivatives at position C4 of the benzene rings. K _M values of six selected derivatives were found in the range of 0.10–0.68 mM. Catalytic efficiencies (K _cat/K _M ) were determined in the range of 430–1,110 s⁻¹·M⁻¹ with l-tyrosine as the best substrate. In addition, 7 of 14 tested tryptophan analogs were also accepted by SirD and converted to C7-prenylated derivatives, which was confirmed by comparison with products obtained from enzyme assays using a 7-dimethylallyltryptophan synthase 7-DMATS from Aspergillus fumigatus.