Composition and abundance of periphyton and aquatic insects in Sierra Nevada, California, stream

The species composition of periphyton and benthic insect communities and abundances of common taxa (&;gt;0.1&;#37; of individuals) were examined during snow-free months in Convict Creek, a permanent snowmelt- and spring-fed stream in the Sierra Nevada of California. The communities were highly diverse. The most abundant taxa in the periphyton were diatoms ( Achnanthes minutissima, Cocconeis placentula lineata, Cymbella microcephala, C. sinuata, Fragilaria construens, F. crotonensis , Navicula spp., Synedra acus , and S. rumpens ), except in late spring and summer when several seasonal blue-green algae ( Chamaesiphon incrustans, Lyngbya spp. and Oscillatoria spp.) are at their maximum densities. Most common periphyton taxa vary systematically in abundance with season, but relative abundances of taxa also appear to be influenced by streambed scouring and by concentrations of ambient nutrients. Data on population densities and length frequencies of larval and nymphal stages of common benthic insects and occurrences of pupal and adult stages were examined to determine life history patterns. Taxa hatching in winter and spring and abundant as immatures in late spring include ephemeropterans ( Epeorus longimanus, Drunella flavilinea , and Caudatella heterocaudata ), plecopterans ( Calineuria californica, Doroneuria baumanni, and Pteronarcys princeps ) and dipterans ( Cryptolabis sp.). Common taxa hatching in late spring or summer are the plecopteran Malenka ( californica? ) and the trichopterans Arctopsyche grandis and Rhyacophila acropedes . Several bivoltine and multivoltine ephemeropterans ( Baetis devinctus and B. tricaudatus ) and dipterans ( Simulium spp. and Chironomidae) have summer cohorts. Taxa hatching in late summer or autumn and most abundant in autumn include ephemeropterans ( Baetis spp., Ephemerella infrequens, Epeorus dulciana, Ironodes lepidus , and Paraleptophlebia pallipes ), trichopterans ( Hydropsyche oslari, Lepidostoma spp., Glossosoma califica, Micrasema sp., Brachycentrus americanus, Neophylax sp., and Rhyacophila vaccua ) and dipterans ( Antocha monticola, Pericoma sp., and Chironomidae). Major recurring events that may influence life history patterns and structure of the benthic insect community are (1) near-freezing, nighttime winter water temperatures and occasional anchor ice, (2) a prolonged period of high discharge in late spring and early summer (3) a brief summer, and (4) a prolonged period of moderate stream discharge in autumn when the substratum is stable and food is abundant.     

Zoogeographic patterns and faunal change of South Dakota fishes

We summarized historic and recent fish distributions in South Dakota and analyzed fish faunal similarity at 2 spatial scales (geomorphic province and river drainage) for both historic (native) and recent (post-1990) faunas. We quantified zoogeographic patterns between geomorphic provinces and among neighboring river drainages for historic and recent faunas. We also quantified faunal change (species losses and additions) between provinces and among drainages. Ninety-seven fishes were native to South Dakota, but 111 fishes were present in recent collections because 8 native species were missing, and 22 nonnatives were present. There was high β diversity among historic and recent river drainage fish faunas, but there was between 22% and 56% faunal change between periods. Recent faunas were homogenized compared to historic faunas at both provincial and river drainage spatial scales. Patterns of nonnative species establishment were geographically distinct from patterns of native species loss. Most nonnative species additions were in cold-water or human-made habitats of the Great Plains. Most native species declines stemmed from warm water streams of the Central Lowlands and Missouri River valley. Conservation of rare and declining native species and containment of nonnatives are both necessary to preserve historical patterns of fish biodiversity in South Dakota.     

Looking for structure in all the wrong places: Ramsey sentences, multiple realisability, and structure

‘Epistemic structural realism’ (ESR) insists that all that we know of the world is its structure, and that the ‘nature’ of the underlying elements remains hidden. With structure represented via Ramsey sentences, the question arises as to how ‘hidden natures’ might also be represented. If the Ramsey sentence describes a class of realisers for the relevant theory, one way of answering this question is through the notion of multiple realisability. We explore this answer in the context of the work of Carnap, Hintikka and Lewis. Both Carnap and Hintikka offer clear structuralist perspectives which, crucially, accommodate the openness inherent in theory change. Unfortunately there is little purchase for a viable form of realism in either case. Lewis’s approach, on the other hand, offers more scope for realism but, as we shall see, concerns arise as to whether a relevant form of structuralism can be maintained. In particular his thesis of Ramseyan humility undermines certain conceptions of scientific laws that the structural realist might naturally cleave to. Our overall conclusion is that the representational device of Ramsey sentence plus multiple realisability can accommodate either the structuralist or realist aspects of ESR but has difficulties capturing both.     

Resurrecting ancestral alcohol dehydrogenases from yeast

Modern yeast living in fleshy fruits rapidly convert sugars into bulk ethanol through pyruvate. Pyruvate loses carbon dioxide to produce acetaldehyde, which is reduced by alcohol dehydrogenase 1 (Adh1) to ethanol, which accumulates. Yeast later consumes the accumulated ethanol, exploiting Adh2, an Adh1 homolog differing by 24 (of 348) amino acids. As many microorganisms cannot grow in ethanol, accumulated ethanol may help yeast defend resources in the fruit. We report here the resurrection of the last common ancestor of Adh1 and Adh2, called Adh(A). The kinetic behavior of Adh(A) suggests that the ancestor was optimized to make (not consume) ethanol. This is consistent with the hypothesis that before the Adh1-Adh2 duplication, yeast did not accumulate ethanol for later consumption but rather used Adh(A) to recycle NADH generated in the glycolytic pathway. Silent nucleotide dating suggests that the Adh1-Adh2 duplication occurred near the time of duplication of several other proteins involved in the accumulation of ethanol, possibly in the Cretaceous age when fleshy fruits arose. These results help to connect the chemical behavior of these enzymes through systems analysis to a time of global ecosystem change, a small but useful step towards a planetary systems biology.     

Electronic tagging and population structure of Atlantic bluefin tuna

Electronic tags that archive or transmit stored data to satellites have advanced the mapping of habitats used by highly migratory fish in pelagic ecosystems. Here we report on the electronic tagging of 772 Atlantic bluefin tuna in the western Atlantic Ocean in an effort to identify population structure. Reporting electronic tags provided accurate location data that show the extensive migrations of individual fish (n = 330). Geoposition data delineate two populations, one using spawning grounds in the Gulf of Mexico and another from the Mediterranean Sea. Transatlantic movements of western-tagged bluefin tuna reveal site fidelity to known spawning areas in the Mediterranean Sea. Bluefin tuna that occupy western spawning grounds move to central and eastern Atlantic foraging grounds. Our results are consistent with two populations of bluefin tuna with distinct spawning areas that overlap on North Atlantic foraging grounds. Electronic tagging locations, when combined with US pelagic longline observer and logbook catch data, identify hot spots for spawning bluefin tuna in the northern slope waters of the Gulf of Mexico. Restrictions on the time and area where longlining occurs would reduce incidental catch mortalities on western spawning grounds.     

Wolbachia variability and host effects on crossing type in Culex mosquitoes

Wolbachia is a common maternally inherited bacterial symbiont able to induce crossing sterilities known as cytoplasmic incompatibility (CI) in insects. Wolbachia-modified sperm are unable to complete fertilization of uninfected ova, but a rescue function allows infected eggs to develop normally. By providing a reproductive advantage to infected females, Wolbachia can rapidly invade uninfected populations, and this could provide a mechanism for driving transgenes through pest populations. CI can also occur between Wolbachia-infected populations and is usually associated with the presence of different Wolbachia strains. In the Culex pipiens mosquito group (including the filariasis vector C. quinquefasciatus) a very unusual degree of complexity of Wolbachia-induced crossing-types has been reported, with partial or complete CI that can be unidirectional or bidirectional, yet no Wolbachia strain variation was found. Here we show variation between incompatible Culex strains in two Wolbachia ankyrin repeat-encoding genes associated with a prophage region, one of which is sex-specifically expressed in some strains, and also a direct effect of the host nuclear genome on CI rescue.     

Evolution of helium isotopes in the Earth's mantle

Degassing of the Earth's mantle through magmatism results in the irreversible loss of helium to space, and high (3)He/(4)He ratios observed in oceanic basalts have been considered the main evidence for a 'primordial' undegassed deep mantle reservoir. Here we present a new global data compilation of ocean island basalts, representing upwelling 'plumes' from the deep mantle, and show that island groups with the highest primordial signal (high (3)He/(4)He ratios) have striking chemical and isotopic similarities to mid-ocean-ridge basalts. We interpret this as indicating a common history of mantle trace element depletion through magmatism. The high (3)He/(4)He in plumes may thus reflect incomplete degassing of the deep Earth during continent and ocean crust formation. We infer that differences between plumes and the upper-mantle source of ocean-ridge basalts reflect isolation of plume sources from the convecting mantle for approximately 1-2 Gyr. An undegassed, primordial reservoir in the mantle would therefore not be required, thus reconciling a long-standing contradiction in mantle dynamics.     

Isolation of a gene from Drosophila by complementation in yeast

Transformation of mutant yeast cells by cloned genomic DNA from a higher eukaryote has made it possible to isolate a Drosophila DNA sequence that complements a yeast adenine-8-mutation. A 0.8-kilobase poly(A)-containing RNA is transcribed from the cloned Drosophila segment in transformed yeast cells and can account for functional expression of the gene.     

The Amazon basin in transition

Agricultural expansion and climate variability have become important agents of disturbance in the Amazon basin. Recent studies have demonstrated considerable resilience of Amazonian forests to moderate annual drought, but they also show that interactions between deforestation, fire and drought potentially lead to losses of carbon storage and changes in regional precipitation patterns and river discharge. Although the basin-wide impacts of land use and drought may not yet surpass the magnitude of natural variability of hydrologic and biogeochemical cycles, there are some signs of a transition to a disturbance-dominated regime. These signs include changing energy and water cycles in the southern and eastern portions of the Amazon basin.     

Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment

Two decades of scientific ocean drilling have demonstrated widespread microbial life in deep sub-seafloor sediment, and surprisingly high microbial-cell numbers. Despite the ubiquity of life in the deep biosphere, the large community sizes and the low energy fluxes in this vast buried ecosystem are not yet understood. It is not known whether organisms of the deep biosphere are specifically adapted to extremely low energy fluxes or whether most of the observed cells are in a dormant, spore-like state. Here we apply a new approach--the D:L-amino-acid model--to quantify the distributions and turnover times of living microbial biomass, endospores and microbial necromass, as well as to determine their role in the sub-seafloor carbon budget. The approach combines sensitive analyses of unique bacterial markers (muramic acid and D-amino acids) and the bacterial endospore marker, dipicolinic acid, with racemization dynamics of stereo-isomeric amino acids. Endospores are as abundant as vegetative cells and microbial activity is extremely low, leading to microbial biomass turnover times of hundreds to thousands of years. We infer from model calculations that biomass production is sustained by organic carbon deposited from the surface photosynthetic world millions of years ago and that microbial necromass is recycled over timescales of hundreds of thousands of years.