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Managing the nonlethal effects of disturbance on wildlife populations has been a long-term goal for decision makers, managers, and ecologists, and assessment of these effects is currently required by European Union and United States legislation. However, robust assessment of these effects is challenging. The management of human activities that have nonlethal effects on wildlife is a specific example of a fundamental ecological problem: how to understand the population-level consequences of changes in the behavior or physiology of individual animals that are caused by external stressors. In this study, we review recent applications of a conceptual framework for assessing and predicting these consequences for marine mammal populations. We explore the range of models that can be used to formalize the approach and we identify critical research gaps. We also provide a decision tree that can be used to select the most appropriate model structure given the available data. Synthesis and applications: The implementation of this framework has moved the focus of discussion of the management of nonlethal disturbances on marine mammal populations away from a rhetorical debate about defining negligible impact and toward a quantitative understanding of long-term population-level effects. Here we demonstrate the framework's general applicability to other marine and terrestrial systems and show how it can support integrated modeling of the proximate and ultimate mechanisms that regulate trait-mediated, indirect interactions in ecological communities, that is, the nonconsumptive effects of a predator or stressor on a species' behavior, physiology, or life history.

I investigated diving behavior, movement, and spatially explicit foraging behavior of the sexually dimorphic male California sea lion and evaluated the extent to which blood and muscle oxygen storage capacity influenced behavioral patterns. Satellite-linked dive recorders were used to investigate the movement and diving patterns of 25 sub-adult and adult male California sea lions during 2003-04 and 2004-05. Male diving behavior was consistent with that of a typical shallow epipelagic to mesopelagic foraging strategy and a strong diurnal pattern. Variation in diving behavior was explained by the presence of three diving strategies among individuals including shallow, mixed depth, and deeper divers. Males dispersed, rather then a previously described migration, traveling north and south while foraging almost exclusively over the continental shelf during short trips in 2003-04. Ocean conditions were highly anomalous in 2004-05 and males altered their foraging effort during previously undocumented offshore excursions up to 450km offshore. Trips during 2004-05 were more than twice the distance and three times the duration of trips during 2003-04. Diving patterns also shifted with increased search time underwater with deeper and longer duration dives, and significant shifts in diet occurred that reflected changes in the diet during the 1997-98 El Niño.I also examined the extent to which blood and muscle oxygen stores varied as a function of age, body size, and sex. Blood oxygen storage capacity was not fully developed by the end of the dependency period and muscle stores were not developed until animals were sub-adult size. Decreased myoglobin in adult males resulted in decreased mass-specific oxygen stores compared to females, which was unexpected given their greater body mass. Delayed development of body oxygen stores coupled with differences between the sexes resulted in different aerobic diving capacity among different size, age, and sex animals. Males dove well within their physiological diving capacity the majority of the time. This apparent excess in physiological dive capacity may provide male sea lions with the plasticity to develop alternative individual foraging strategies, and buffer them against fluctuations in prey distribution and abundance resulting from environmental perturbations such as those observed during 2005 and El Niño events.

Abstract--To assess the impact of California sea lions (Zalophus californianus) on salmon fisheries in the Monterey Bay region of California, the percentages of hooked fish taken by sea lions in [...]

A bioinformatics tool called ODS3 has been created for mapping by sequencing. The tool allows the creation of integrated genomic maps from genetic, physical mapping, and sequencing data and permits an integrated genome map to be stored, retrieved, viewed, and queried in a stand-alone capacity, in a client/server relationship with the Fungal Genome Database (FGDB), and as a web-browsing tool for the FGDB. In that ODS3 is programmed in Java, the tool promotes platform independence and supports export of integrated genome-mapping data in the extensible markup language (XML) for data interchange with other genome information systems. The tool ODS3 is used to create an initial integrated genome map of the AIDS-related fungal pathogen, Pneumocystis carinii. Contig dynamics would indicate that this physical map is ~50% complete with ~200 contigs. A total of 10 putative multigene families were found. Two of these putative families were previously characterized in P. carinii, namely the major surface glycoproteins (MSGs) and HSP70 proteins; three of these putative families (not previously characterized in P. carinii) were found to be similar to families encoding the HSP60 in Schizosaccharomyces pombe, the heat-shock [psi] protein in S. pombe, and the RNA synthetase family (i.e., MES1) in Saccharomyces cerevisiae. Physical mapping data are consistent with the 16S, 5.8S, and 26S rDNA genes being single copy in P. carinii. No other fungus outside this genus is known to have the rDNA genes in single copy.

A Neurospora crassa cosmid library of 12,000 clones (at least nine genome equivalents) has been created using an improved cosmid vector pLorist6Xh, which contains a bacteriophage [Lambda] origin of replication for low-copy-number replication in bacteria and the hygromycin phosphotransferase marker for direct selection in fungi. The electrophoretic karyotype of the seven chromosomes comprising the 42.9-Mb N. crassa genome was resolved using two translocation strains. Using gel-purified chromosomal DNAs as probes against the new cosmid library and the commonly used medium-copy-number pMOcosX N. crassa cosmid library in two independent screenings, the cosmids were assigned to chromosomes. Assignments of cosmids to linkage groups on the basis of the genetic map vs. the electrophoretic karyotype are 93 [+ or -] 3% concordant. The size of each chromosome-specific subcollertion of cosmids was found to be linearly proportional to the size of the particular chromosome. Sequencing of an entire cosmid containing the qa gene cluster indicated a gene density of 1 gene per 4 kbp; by extrapolation, 11,000 genes would be expected to be present in the N. crassa genome. By hybridizing 79 nonoverlapping cosmids with an average insert size of 34 kbp against cDNA arrays, the density of previously characterized expressed sequence tags (ESTs) was found to be slightly [is less than] 1 per cosmid (i.e., 1 per 40 kbp), and most cosmids, on average, contained an identified N. crassa gene sequence as a starting point for gene identification.

A bioinformatics tool called ODS3 has been created for mapping by sequencing. The tool allows the creation of integrated genomic maps from genetic, physical mapping, and sequencing data and permits an integrated genome map to be stored, retrieved, viewed, and queried in a stand-alone capacity, in a client/server relationship with the Fungal Genome Database (FGDB), and as a web-browsing tool for the FGDB. In that ODS3 is programmed in Java, the tool promotes platform independence and supports export of integrated genome-mapping data in the extensible markup language (XML) for data interchange with other genome information systems. The tool ODS3 is used to create an initial integrated genome map of the AIDS-related fungal pathogen, Pneumocystis carinii. Coutig dynamics would indicate that this physical map is ∼50% complete with ∼200 contigs. A total of 10 putative multigene families were found. Two of these putative families were previously characterized in P. carinii, namely the major surface glycoproteins (MSGs) and HSP70 proteins; three of these putative families (not previously characterized in P. caranii) were found to be similar to families encoding the HSP60 in Schizosaccharomyces pombe, the heat-shock ψ protein in S. pombe, and the RNA synthetase family (i.e., MES1) in Saccharomyces cerevisiae. Physical mapping data are consistent with the 16S, 5.8S, and 26S rDNA genes being single copy in P. carinii. No other fnngus outside this genus is known to have the rDNA genes in single copy. [ABSTRACT FROM AUTHOR]