Chromosome segregation relies on coordinated activity of a large assembly of proteins, the kinetochore interaction network (KIN). How conserved the underlying mechanisms driving the epigenetic phenomenon of centromere and kinetochore assembly and maintenance are remains unclear, even though various eukaryotic models have been studied. More than 50 different proteins, many...
We constructed a comprehensive phylogeny of the genus Genea, with new molecular data from samples collected in several countries in temperate and Mediterranean Europe, as well as North America. Type specimens and authentic material of most species were examined to support identifications. The molecular identity of the most common species...
Phytophthora species were systematically sampled, isolated, identified and compared for presence in streams, soil and roots of alder (Alnus species) dominated riparian ecosystems in western Oregon. We describe the species assemblage and evaluate Phytophthora diversity associated with alder. We recovered 1250 isolates of 20 Phytophthora species. Only three species were...
Sedecula is a monotypic genus of hypogeous fungi that is rare and endemic to dry conifer forests of the western United States. The only known species, Sedecula pulvinata, was described in 1941 and its taxonomic placement and trophic status have remained uncertain ever since. Here we employ isotopic and molecular...
Kalapuya is described as a new, monotypic truffle genus in the Morchellaceae known only from the Pacific northwestern United States. Its relationship to other hypogeous genera within Morchellaceae is explored by phylogenetic analysis of the ribosomal LSU and EF1α protein coding region. The type species, K. brunnea, occurs in Douglas-fir...
Sedecula is a monotypic genus of hypogeous fungi that is rare and endemic to dry conifer forests of the western United States. The only known species, Sedecula pulvinata, was described in 1941 and its taxonomic placement and trophic status have remained uncertain ever since. Here we employ isotopic and molecular...
Solioccasus polychromus gen. & sp. nov., the most brightly colored hypogeous fungus known, is described from Papua New Guinea and tropical northern Australia south into subtropical forests along the Queensland coast and coastal mountains to near Brisbane. Phylogenetic analysis of molecular data places it as a sister genus to Bothia...
Phylogenetic analyses based on nLSU and ITS sequence data indicate that the sequestrate genus Gigasperma is polyphyletic. Gigasperma cryptica, which is known only from New Zealand, has affinities with the Cortinariaceae whereas G. americanum and two additional undescribed taxa from western North America are derived from Lepiota within the Agaricaceae....
Genome-enabled mycology is a rapidly expanding field that is characterized by the pervasive use of genome-scale data and associated computational tools in all aspects of fungal biology. Genome-enabled mycology is integrative and often requires teams of researchers with diverse skills in organismal mycology, bioinformatics and molecular biology. This issue of...
Using spatial autocorrelation analysis, we
examined the within-population genetic structure of
Rhizopogon vinicolor and R. vesiculosus, two hypogeous
ectomycorrhizal (EM) species that are sympatric
sister taxa known to differ in their clonal structure.
We collected 121 sporocarps and 482 tuberculate EM
of both species from a 20 ha forest stand...
Recent surveys of belowground fungal biodiversity in Mexico and USA have revealed many undescribed truffle species, including many in the genus Tuber. Here we describe seven new species: Tuber beyerlei, T. castilloi, T. guevarai, T. lauryi, T. mexiusanum, T. miquihuanense and T. walkeri. Phylogenetic analyses place these species within the...
Phytophthora borealis and Phytophthora riparia, identified in recent Phytophthora surveys of forest streams in Oregon, California and Alaska, are described as new species in Phytophthora ITS Glade 6. They are similar in growth form and morphology to P. gonapodyides and are predominately sterile. They present unique DNA sequences, however, and...
Molecular phylogenctic analyses indicate that the monophyletic classes Orbiliomycetes and Pezizomycetes are among the earliest diverging branches of Pezizomycotina, the largest subphylum of the Ascomycota. Although Orbiliomycetes is resolved as the most basal lineage in some analyses, molecular support for the node resolving the relationships between the two classes is...
Cenococcum is a genus of ectomycorrhizal Ascomycota that has a broad host range and geographic distribution. It is not known to produce either meiotic or mitotic spores and is known to exist only in the form of hyphae, sclerotia and host-colonized ectomycorrhizal root tips. Due to its lack of sexual...
As we contemplate the future of forest landscapes under changing climate conditions and land-use demands, there is increasing value in studying historic forest conditions and how these landscapes have changed following past disturbances. Historic landscape paintings are a potential source of data on preindustrial forests with highly detailed, full-color depictions...
Pyrosomes are colonial pelagic tunicates that have fascinated marine biologists for over a century. Their name comes from the “fiery” bioluminescence that luminous organs produce at night time. Blooms of pyrosomes, identified as Pyrosoma atlanticum (Peron, 1804), have recently appeared in the North Pacific Ocean, prompting questions about environmental factors...
Managing multiple ecosystem services (ESs) across landscapes presents a central challenge for ecosystem-based management, because services often exhibit spatiotemporal variation and weak associations with co-occurring ESs. Further focus on the mechanistic relationships among ESs and their underlying biophysical processes provides greater insight into the causes of variation and covariation among...
Disease, overharvesting, and pollution have impaired the role of bivalves on coastal ecosystems, some to the point of functional extinction. An underappreciated function of many bivalves in these systems is shell formation. The ecological significance of bivalve shell has been recognized; geochemical effects are now more clearly being understood. A...
Ballast water discharges are a major source of species introductions into marine and estuarine ecosystems. To mitigate the introduction of new invaders into these ecosystems, many agencies are proposing standards that establish upper concentration limits for organisms in ballast discharge. Ideally, ballast discharge standards will be biologically defensible and adequately...
Climate changes in the Pacific Northwest, USA, may cause both retreat of alpine glaciers and increases in the frequency and magnitude of storms delivering rainfall at high elevations absent significant snowpack, and both of these changes may affect the frequency and severity of destructive debris flows initiating on the region's...
Sensor design and mission planning for satellite ocean color measurements requires careful consideration of the signal dynamic range and sensitivity (specifically here signal-to-noise ratio or SNR) so that small changes of ocean properties (e.g., surface chlorophyll-a concentrations or Chl) can be quantified while most measurements are not saturated. Past and...
Vegetation at the aquatic–terrestrial interface can alter landscape features through its growth and interactions with sediment and fluids. Even similar species may impart different effects due to variation in their interactions and feedbacks with the environment. Consequently, replacement of one engineering species by another can cause significant change in the...
Remote-sensing reflectance is easier to interpret for the open ocean than for coastal regions because the optical signals are highly coupled to the phytoplankton (e.g., chlorophyll) concentrations. For estuarine or coastal waters, variable terrigenous colored dissolved organic matter (CDOM), suspended sediments, and bottom reflectance, all factors that do not covary...
We present the results of a study of optical scattering and backscattering of particulates for three coastal sites that represent a wide range of optical properties that are found in U.S. near-shore waters. The 6000 scattering and backscattering spectra collected for this study can be well approximated by a power-law...
Oceanic waves have been found to contribute enhanced back-scattering in the direction of the illumination source in studies that assumed the ocean surface to be a random sum of waves. Here we investigate enhanced back-scattering by coherent capillary-gravity wave trains that co-exist near the crests of short gravity waves in...
Narrow angle light scattering measurements were made for various sizes of spherical particles suspended in water. These were compared to calculated theoretical scattering values as derived from the theory of Mie (1908). Through measurements with different particle concentrations at angles between 0.2° and 0.7° the effect of the unscattered main...
We examine and compare near-forward light scattering that is caused by turbulence and typical particulate assemblages in the ocean. The near-forward scattering by particles was calculated using Mie theory for homogeneous spheres and particle size distributions representative of natural assemblages in the ocean. Direct numerical simulations of a passive scalar...
The relationships between beam attenuation spectra, chlorophyll and pheophytin pigment concentrations, and particle size distributions are examined for a coastal region (Monterey Bay area) believed to have negligible concentrations of terrestrially derived dissolved organic compounds (during May 1977) but large quantities of phytoplankton and resuspended sediments. It was found that...
The backscattering properties of marine phytoplankton, which are assumed to vary widely with differences in size, shape, morphology and internal structure, have been directly measured in the laboratory on a very limited basis. This work presents results from laboratory analysis of the backscattering properties of thirteen phytoplankton species from five...
Fluctuations of the low frequency sound field in the presence of an internal solitary wave packet during the Shallow Water ’06 experiment are analyzed. Acoustic, environmental, and on-board ship radar image data were collected simultaneously before, during, and after a strong internal solitary wave packet passed through the acoustic track....
Preliminary results are presented from an analysis of mid-frequency acoustic transmission data collected at range 550m during the Shallow Water 2006 Experiment. The acoustic data were collected on a vertical array immediately before, during, and after the passage of a nonlinear internal wave on 18 August, 2006. Using oceanographic data...
The Ocean Portable Hyperspectral Imager for Low-Light Spectroscopy (Ocean PHILLS) is a hyperspectral imager specifically designed for imaging the coastal ocean. It uses a thinned, backside-illuminated CCD for high sensitivity and an all-reflective spectrograph with a convex grating in an Offner configuration to produce a nearly distortion-free image. The sensor,...
We analyzed the sedimentological characteristics and magnetic properties of cores from the three basins of Clear Lake, California, USA, to assess the depositional response to a series of land use changes that occurred in the watershed over the 20th century. Results indicate that distinct and abrupt shifts in particle size,...
Climate can affect population dynamics in indirect ways via nonadditive forcing by external variables on internal demographic rates. Current analytical techniques, employed in population ecology, fail to explicitly include nonadditive interactions between internal and external variables, and therefore cannot efficiently address indirect climate effects. Here, we present the results of...
The majority of survival analyses focus on temporal scales. Consequently, there is a limited understanding of how species survival varies over space and, ultimately, how spatial variability in the environment affects the temporal dynamics of species abundance. Using data from the Barents Sea, we study the spatiotemporal variability of the...
Sonar techniques were used to quantitatively observe foraging predators and their prey simultaneously in three dimensions. Spinner dolphins foraged at night in highly coordinated groups of 16–28 individuals using strict four-dimensional patterns to increase prey density by up to 200 times. Herding exploited the prey’s own avoidance behavior to achieve...
The target strength as a function of aspect angle were measured for four species of fish using dolphin-like and porpoise-like echolocation signals. The polar diagram of target strength values measured from an energy flux density perspective showed considerably less fluctuation with azimuth than would a pure tone pulse. Using detection...
The Franciscan Complex accretionary prism was assembled during an similar to 165-m.y.-long period of subduction of Pacific Ocean plates beneath the western margin of the North American plate. In such fossil subduction complexes, it is generally difficult to reconstruct details of the accretion of continent-derived sediments and to evaluate the...
Globally, mangrove forests represents only 0.7% of world's tropical forested area but are highly threatened due to susceptibility to climate change, sea level rise, and increasing pressures from human population growth in coastal regions. Our study was carried out in the Bhitarkanika Conservation Area (BCA), the second-largest mangrove area in...
Here we use SKS shear wave splitting observations from ocean-bottom seismometer data to infer patterns of mantle deformation beneath the Juan de Fuca plate and its adjoining boundaries. Our results indicate that the asthenosphere beneath the Juan de Fuca plate responds largely to absolute plate motion with an anisotropic layer...
In this Letter, we investigate the slow-light effect of subwavelength diffraction gratings via the Rayleigh anomaly using a fully analytical approach without needing to consider specific grating structures. Our results show that the local group velocity of the transmitted light can be significantly reduced due to the optical vortex, which...
PREMISE OF THE STUDY: Mosses, very diverse in modern ecosystems, are currently underrepresented in the fossil record. For the pre-Cenozoic, fossil mosses are known almost exclusively from compression fossils, while anatomical preservation, which is much more taxonomically informative, is rare. The Lower Cretaceous of Vancouver Island (British Columbia, Canada) hosts...
Several approaches to interpreting the Cascadia paleoseismic record are used to derive relationships between fault area, slip, and moment and to compare the results with the scaling relationships determined by Somerville et al. (2015) for recent subduction-zone events. In two models (CA12a and CA12b), taken from Goldfinger et al. (2012),...
Interannual variability in salmon (Oncorhynchus spp.) production in the northeast Pacific is understood to be driven by oceanographic variability and bottom-up processes affecting prey availability to juvenile salmon. Scyphozoan jellyfish have an important role in shaping the pathways of energy flow through pelagic food webs. While jellyfish obtain high production...
Hydrology is the main environmental filter in aquatic ecosystems and may result in shared tolerances and functional traits among species in disparate ecosystems. We analyzed the associations between taxonomic and functional facets of diversity within aquatic ecosystems (ponds vs. streams) across a hydroperiod gradient (1–365 d) to untangle the hydrologic...
Dynamics of dead wood, a key component of forest structure, are not well described for mixed-severity fire regimes with widely varying fire intervals. A prominent form of such variation is when two stand-replacing fires occur in rapid succession, commonly termed an early-seral “reburn.” These events are thought to strongly influence...
Phenology is an integrative science that comprises the study of recurring biological activities or events. In an era of rapidly changing climate, the relationship between the timing of those events and environmental cues such as temperature, snowmelt, water availability, or day length are of particular interest. This article provides an...
The ability to reconstruct past ocean currents is essential for determining ocean circulation’s role in global heat transport and climate change. Our understanding of the relationship between circulation and climate in the past allows us to predict the impact of future climate-driven circulation changes. One proposed tracer of past ocean...
Programmable conductive patterns created by photoexcitation of semiconductor substrates using digital light processing (DLP) provides a versatile approach for spatial and temporal modulation of THz waves. The reconfigurable nature of the technology has great potential in implementing several promising THz applications, such as THz beam steering, THz imaging or THz...