Rise and fall of species occupancy in Cenozoic fossil mollusks

In the time between speciation and extinction, a species' ecological and biogeographic footprint-its occupancy-will vary in response to macroecological drivers and historical contingencies. Despite their importance for understanding macroecological processes, general patterns of long-term species occupancy remain largely unknown. We documented the occupancy histories of Cenozoic marine mollusks from New Zealand. For both genera and species, these show a distinct pattern of increase to relatively short-lived peak occupancy at mid-duration, followed by a decline toward extinction. Thus, species at greatest risk for extinction are those that have already been in decline for a substantial period of time. This pattern of protracted rise and fall stands in contrast to that of incumbency, insofar as species show no general tendency to stay near maximal occupancy once established.     

Resource-use,body condition and parasite load metrics indicate contrasting health of stocked and native game fishes in Canadian prairie lakes

This study evaluated the status of native and stocked fish species in 13 prairie lakes in central Canada over eight years (2007–14) using three metrics: resource-use (benthic versus pelagic carbon via stable isotopes); body condition (relative weight index W_r); and parasite load (cestode gut enumerations). Analyses included game and non-game fishes, like naturally occurring northern pike, Esox lucius L., and yellow perch, Perca flavescens Mitchill, but focused on stocked walleye, Sander vitreus (Mitchill) because it supports a robust recreational fishery. Walleye and northern pike were significantly more reliant on benthic carbon than yellow perch or forage fishes (p < 0.05), but this reliance was not associated with any measured environmental variables for any species. In lakes with game fishes, forage fishes exhibited higher reliance on benthic energy, possibly due to predator avoidance strategy, particularly yellow perch. Walleye body condition index was consistently lower (<95–105) than values exhibited by the other two game fishes (81–139), and parasites were only common in walleye and associated with lake-water salinity (r² = 0.93, p < 0.05) and sex (p < 0.05). Based on the results, the most desirable game fish, walleye, appears less resilient to environmental variability than northern pike and yellow perch, making this species more susceptible to impacts of future climate change.     

Assessing and managing data‐limited ornamental fisheries in coral reefs

Coral reefs support numerous ornamental fisheries, but there are concerns about stock sustainability due to the volume of animals caught. Such impacts are difficult to quantify and manage because fishery data are often lacking. Here, we suggest a framework that integrates several data‐poor assessment and management methods in order to provide management guidance for fisheries that differ widely in the kinds and amounts of data available. First, a resource manager could assess the status of the ecosystem (using quantitative metrics where data are available and semi‐quantitative risk assessment where they are not) and determine whether overall fishing mortality should be reduced. Next, productivity susceptibility analysis can be used to estimate vulnerability to fishing using basic information on life history and the nature of the fishery. Information on the relative degree of exploitation (e.g. export data or ratios of fish density inside and outside no‐take marine reserves) is then combined with the vulnerability ranks to prioritize species for precautionary management and further analysis. For example, species that are both highly exploited and vulnerable are good candidates for precautionary reductions in allowable capture. Species that appear to be less vulnerable could be managed on a stock‐specific basis to prevent over‐exploitation of some species resulting from the use of aggregate catch limits. The framework could be applied to coral reef ornamental fisheries which typically lack landings, catch‐per‐unit‐effort and age‐size data to generate management guidance to reduce overfishing risk. We illustrate the application of this framework to an ornamental fishery in Indonesia.     

Eurasian perch Perca fluviatilis growth and fish community structure,inside and outside a marine‐protected area in the Baltic Sea

Growth of Eurasian perch Perca fluviatilis L. and fish community structure between sites within a marine‐protected area (MPA) and unprotected sites in the Baltic Sea were examined. Von Bertalanffy, logistic and Gompertz growth models were fitted to P. fluviatilis length at age data, and the logistic model was the most parsimonious for growth between locations. A larger mean maximum size (L_∞) and a smaller instantaneous growth rate (g) were found within the MPA. All three models also predicted that after age seven, fish inside the MPA would be larger. Community structure differed with more P. fluviatilis collected outside of the MPA, and more roach Rutilus rutilus (L.) and bleak Alburnus alburnus (L.) collected inside the MPA. These growth differences may be indicative of recreational fishing effects on P. fluviatilis outside of the MPA, a result of complex interspecific and intraspecific species interactions, or other undetected environmental variation between locations.     

The potential environmental impact of pesticides removed from sprayers during cleaning

BACKGROUND: There is concern that pesticide residues on the external surfaces of sprayers could have an adverse impact on the environment if they are washed off, yet there is a need to remove these residues for health reasons. The aim of this study was to quantify pesticide residues contained in washings from cleaning discrete parts of a sprayer and to assess their likely environmental impact. RESULTS: The boom/rear of the sprayer and the spray tank accounted for 80% of the total pesticide load in the washings. Predicted environmental pesticide concentrations from sprayer washings were lower than predictions from the FOCUS surface water model for pesticides used under normal agricultural conditions, although for tebuconazole this difference was smaller than for the other compounds investigated. The field area over which the residues may need to be uniformly deposited to avoid overdosing during infield cleaning was typically less than 0.5 m(2), with a maximum value of 4 m(2). CONCLUSIONS: It is unlikely that infield cleaning will lead to overdosing. External residues are not insignificant, so any adverse impact on the environment must be mitigated. Appropriate measures include cleaning in the field away from surface waters and other sensitive areas, and cleaning machines over bunded areas or similar.     

Molecular defect in a gamma-2 heavy chain

The first gamma-2 (gamma2) heavy chain disease protein Gif has pyrroli-dinecarboxylic acid as its amino terminal residue, much of the Fd variable region, and an internal deletion of the heavy chain of about 100 residues corresponding to most of the Fd constant region. Normal sequence resumes with a glutamic acid residue at position 216 in the hinge region. This is the third gamma heavy chain disease protein where normal sequence resumes at the same position after the deletion.     

Conservation of the jackass penguin (Spheniscus demersus (L.))

The jackass penguin Spheniscus demersus (L.) is confined to the coastal waters of southern Africa, and breeds on 18 islands predominantly within the region of the cold, nutrient rich Benguella current. Since the early 1900s the species' population has declined in numbers of unknown magnitude. The decline appears to be continuing, although the absence of reliable census data precludes an accurate measurement of the rate of change. The initial fall in numbers was undoubtedly due to severe disturbance of nesting birds and excessive commercial exploitation of eggs. The average annual egg crop for the period 1900-30 exceeded 450,000 eggs from Dassen Island alone. Egg collection has been suspended temporarily, but the species now appears to be threatened by oil pollution, and by competition with a pelagic shoal fish industry. Threats to breeding colonies are posed by harbour developments. These factors are discussed and evaluated. South African marine organisms are considered officially to be an economic resource and are heavily exploited. Legislation governing the control of this resource is the concern of the Ministry for Economic Affairs. There is no provision for any government body to investigate the status and biology of economically insignificant, but yet integral, components of the marine ecosystem. The major priority of conservations is to safeguard the jackass penguin population at its present level. This includes proclamation of several offshore islands and their surroundings as national nature reserves. We consider current efforts to rescue, clean and rehabilitate oiled seabirds as contributing little to conservation in real terms, even though the activity has an important humanitarian and educational function. Research priorities include a comprehensive census of the jackass penguin and other seabird populations in southern Africa; a study of mortality and recruitment, with particular attention to factors affecting the rates of these processes; a study of the dynamics of the penguin/prey interaction, with special reference to the possible effects of competition with the pelagic fishing industry; an evaluation of the degree of disturbance that nesting penguins can tolerate; an investigation into the temporal and spatial patterns of oil pollution incidents, oil slick occurrence and movement, and the development of methods of keeping birds away from oil slicks; and, lastly, an evaluation of the efficacy of rehabilitating oiled penguins as a contribution to maintaining or increasing the current jackass penguin population. The responsibility for these projects rests with the South African government.     

Cellular transforming genes

Cellular genes potentially capable of inducing oncogenic transformation have been identified by homology to the transforming genes of retroviruses and by the biological activity of cellular DNA's in transfection assays. DNA's of various tumors induce transformation with high efficiencies, indicating that oncogenesis can involve dominant genetic alterations resulting in activation of cellular transforming genes. The identification and characterization of cellular transforming genes and their possible involvement in naturally occurring cancers, is discussed.     

Diverse plant and animal genetic records from Holocene and Pleistocene sediments

Genetic analyses of permafrost and temperate sediments reveal that plant and animal DNA may be preserved for long periods, even in the absence of obvious macrofossils. In Siberia, five permafrost cores ranging from 400,000 to 10,000 years old contained at least 19 different plant taxa, including the oldest authenticated ancient DNA sequences known, and megafaunal sequences including mammoth, bison, and horse. The genetic data record a number of dramatic changes in the taxonomic diversity and composition of Beringian vegetation and fauna. Temperate cave sediments in New Zealand also yielded DNA sequences of extinct biota, including two species of ratite moa, and 29 plant taxa characteristic of the prehuman environment. Therefore, many sedimentary deposits may contain unique, and widespread, genetic records of paleoenvironments.     

A systematic survey of loss-of-function variants in human protein-coding genes

Genome-sequencing studies indicate that all humans carry many genetic variants predicted to cause loss of function (LoF) of protein-coding genes, suggesting unexpected redundancy in the human genome. Here we apply stringent filters to 2951 putative LoF variants obtained from 185 human genomes to determine their true prevalence and properties. We estimate that human genomes typically contain ~100 genuine LoF variants with ~20 genes completely inactivated. We identify rare and likely deleterious LoF alleles, including 26 known and 21 predicted severe disease-causing variants, as well as common LoF variants in nonessential genes. We describe functional and evolutionary differences between LoF-tolerant and recessive disease genes and a method for using these differences to prioritize candidate genes found in clinical sequencing studies.