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State Of The Arctic October 2006, J. Richter-Menge, J. Overland, A. Proshutinsky, V. Romanovsky, L. Bengtsson, L. Brigham, M. Dyurgerov, J.C. Gascard, S. Gerland, R. Graversen, C. Hahaas, M. Karcher, P. Kuhry, J. Maslanik, H. Melling, W. Maslowski, J. Morison, D. Perovich, R. Przybylak, V. Rachold, I. Rigor, A. Shiklomanov, J. Stroeve, D. Walker, J. Walsh

United States Department of Commerce: Staff Publications

This State of the Arctic Report presents a review of recent data by an international group of scientists who developed a consensus on the information content and reliability. The report highlights data primarily from 2000 to 2005 with a first look at winter 2006, providing an update to some of the records of physical processes discussed in the Arctic Climate Impact Assessment (ACIA, 2004, 2005). Of particular note:

• Atmospheric climate patterns are shifting (Fig. 1). The late winter/spring pattern for 2000–2005 had new hot spots in northeast Canada and the East Siberian Sea relative to 1980–1999. Late winter 2006, …

The Phylogenetic Relationships And Biogeography Of True Porpoises (Mammalia: Phocoenidae) Based On Morphological Data, Liliana Fajardo-Mellor, Annalisa Berta, Robert L. Brownell Jr., Claudia Boy, R. Natalie Goodall

United States Department of Commerce: Staff Publications

Prior studies of phylogenetic relationships among phocoenids based on morphology and molecular sequence data conflict and yield unresolved relationships among species. This study evaluates a comprehensive set of cranial, postcranial, and soft anatomical characters to infer interrelationships among extant species and several well-known fossil phocoenids, using two different methods to analyze polymorphic data: polymorphic coding and frequency step matrix. Our phylogenetic results confirmed phocoenid monophyly. The division of Phocoenidae into two subfamilies previously proposed was rejected, as well as the alliance of the two extinct genera Salumiphocaena and Piscolithax with Phocoena dioptrica and Phocoenoides dalli. Extinct phocoenids are basal …

Genetic Monitoring As A Promising Tool For Conservation And Management, Michael K. Schwartz, Gordon Luikart, Robin Waples

United States Department of Commerce: Staff Publications

In response to ever-increasing anthropogenic changes to natural ecosystems, regional, national and international organizations have established guidelines for monitoring biological diversity. Most monitoring programs, however, do not take full advantage of the potential afforded by molecular genetic markers, which can provide information relevant to both ecological and evolutionary time frames, while costing less and being more sensitive and reliable than traditional monitoring approaches. As several molecular and computational approaches are relatively new, many technical and theoretical issues remain to be resolved. Here, we illustrate how DNA and population genetic data can provide valuable information, often unattainable via other approaches, for …

Preliminary Report On The Photo-Identification Of Blue Whales Off Isla De Chiloé, Chile From 2004 To 2006, Elsa Cabrera, Carole A. Carlson, Bárbara Galletti Vernazzani, Robert L. Brownell Jr.

United States Department of Commerce: Staff Publications

Photo identification of individual blue whales during summer and autumn off the northwestern Isla de Chiloé, southern Chile, were collected from marine surveys conducted from 2004 to 2006. Re-sightings of individual whales both within and between years may provide evidence of residency and site fidelity by blue whales in the area. These records further document the importance of the northwestern Isla de Chiloé as a feeding area for blue whales. These records also highlight the necessity of further comparisons with photographic catalogues from other areas in southern Chile, off the northwestern coast of South America and the Pacific coast of …

Population Assessment Of Western Gray Whales In 2006, Justin G. Cooke, David W. Weller, Amanda L. Bradford, Alexander M. Burdin, Robert L. Brownell Jr.

United States Department of Commerce: Staff Publications

A population assessment of the western gray whale (Eschrichtius robustus) was conducted using the Photo-identification data collected off Sakhalin Island under the joint Russia-U.S. program from 1994 to 2005. This is an update of the assessment by Reeves et al (2005) which used data up to 2003, fitted to the same, individually-based population model. New median estimates of key population parameters (with 90% Bayesian confidence intervals) are 0.986 (0.975 - 0.995) for the adult survival rate; 0.72 (0.60 - 0.83) for the survival rate from calf to yearling; 3.0% per annum (2.1% – 4.2%) for the average annual …

Evaluation Of The National Weather Service Operational Hydrologic Model And Forecasts For The American River Basin, Eylon Shamir, Theresa M. Carpenter, Peter Fickenscher, Konstantine P. Georgakakos

United States Department of Commerce: Staff Publications

This paper evaluates the National Weather Service operational hydrologic model and operational flow forecasts for several subbasins of the American River. The evaluation includes: (1) the quality of the 6-h operational flow forecasts with up to 5 days lead time; (2) the hydrologic model ability to reproduce observed mean daily flows; and (3) the reliability of the ensemble streamflow predictions of the hydrologic model to reproduce extremes of the monthly volume of full natural flow to Folsom Lake. The results indicate that the model represents the observed flow record well for sites and/or flow ranges unaffected by upstream regulation. Real …

Effect Of Deposition Conditions On Mechanical Properties Of Low-Temperature Pecvd Silicon Nitride Films, H. Huang, K. J. Winchester, A. Suvorova, B. R. Lawn, Y. Liu, X. Z. Hu, J. M. Dell, L. Faraone

United States Department of Commerce: Staff Publications

The effect of deposition conditions on characteristic mechanical properties – elastic modulus and hardness – of low-temperature PECVD silicon nitrides is investigated using nanoindentation. It is found that increase in substrate temperature, increase in plasma power and decrease in chamber gas pressure all result in increases in elastic modulus and hardness. Strong correlations between the mechanical properties and film density are demonstrated. The silicon nitride density in turn is shown to be related to the chemical composition of the films, particularly the silicon/nitrogen ratio.

Blue Whale (Balaenoptera Musculus) Sightings And Recordings South Of The Aleutian Islands, Shannon Rankin, Jay Barlow, Kathleen M. Stafford

United States Department of Commerce: Staff Publications

Blue whales have been sighted throughout the North Pacific Ocean (Mizroch et al. 1984), and were harvested around the Pacific Rim from Mexico to Japan (Fig. 1). The International Whaling Commission (IWC) currently recognizes only one stock of blue whales in the North Pacific (Donovan 1991); however, there may be up to five (reviewed in Stafford 2003). While past shipboard and aerial surveys in the Aleutian Island chain found no blue whales (Rice and Wolman 1982, Stewart et al. 1987), their contemporary presence in this area has been well documented by acoustic monitoring (Watkins et al. 2000, Stafford et al. …

Survival Estimates Of Western Gray Whales Eschrichtius Robustus Incorporating Individual Heterogeneity And Temporary Emigration, Amanda Bradford, Paul R. Wade, David Weller, Alexander M. Burdin, Yulia V. Ivashchenko, Grigory A. Tsidulko, Glenn R. Vanblaricom, Robert L. Brownell Jr.

United States Department of Commerce: Staff Publications

Gray whales Eschrichtius robustus exist as a 2 geographically and genetically distinct populations in the eastern and western North Pacific. Subjected to intensive commercial whaling during the 19th and 20th centuries, the western population presently numbers approximately 100 individuals and is regarded as one of the most endangered baleen whale populations in the world.

Studies Of Beaked Whale Diving Behavior And Odontocete Stock Structure In Hawai‘I In March/April 2006, Robin W. Baird, Gregory S. Schorr, Daniel L. Webster, Daniel J. Mcsweeney, Sabre D. Mahaffy

United States Department of Commerce: Staff Publications

Small-boat surveys were undertaken in March/April 2006 off the west side of the island of Hawai‘i for the purposes of obtaining dive data from Blainville’s (Mesoplodon densirostris) and Cuvier’s (Ziphius cavirostris) beaked whales, as well as collecting biopsy samples and photo-identification of these and other species of odontocetes for studies of stock structure and residency patterns. There were 157 sightings of 13 species of odontocetes in 4,264 km of effort, with 120 genetic samples from seven species and over 29,000 photographs from 13 species obtained. Photographic matching to existing catalogs is currently underway for eight species. …

Cetacean Abundance In Hawaiian Waters Estimated From A Summer/Fall Survey In 2002, Jay Barlow

United States Department of Commerce: Staff Publications

Cetacean abundance is estimated for the U.S. Exclusive Economic Zone (EEZ) around the Hawaiian Islands based on a ship line-transect survey from August to November, 2002. Sighting detection functions are estimated from this and other NOAA research surveys from 1986 to 2002 using a new, multiple-covariate approach. Twenty-four species were seen on this survey, including two species (Fraser’s dolphin [Lagenodelphis hosei] and sei whale [Balaenoptera borealis]) that had not been previously documented to occur in Hawaiian waters. The most abundant large whales are sperm whales (Physeter macrocephalus) and Bryde’s whales (Balaenoptera edeni). The most …

Scientific Reports Of Soviet Whaling Expeditions In The North Pacific, 1955-1978, Yulia V. Ivashchenko, Phillip J. Clapham, Robert L. Brownell Jr.

United States Department of Commerce: Staff Publications

The translated and annotated materials in this volume constitute a collection of 18 formerly secret internal reports written by Soviet scientists working aboard whaling factory ships in the North Pacific. The reports cover the period from 1955 to 1978. During most of this time, the USSR was engaged in a massive campaign of illegal whaling worldwide; these illegal catches continued until introduction of the International Whaling Commission’s International Observer Scheme in 1972. The reports were copied from the archives of the Pacific Research and Fisheries Center (TINRO) in Vladivostok by Alfred A. Berzin, the former director of TINRO’s marine mammal …

Lessons From Monitoring Trends In Abundance Of Marine Mammals, Barbara L. Taylor, Melissa Martinez, Tim Gerrodette, Jay Barlow, Yvana N. Hrovat

United States Department of Commerce: Staff Publications

We assessed scientists’ ability to detect declines of marine mammal stocks based on recent levels of survey effort, when the actual decline is precipitous. We defined a precipitous decline as a 50% decrease in abundance in 15 yr, at which point a stock could be legally classified as “depleted” under the U.S. Marine Mammal Protection Act.We assessed stocks for three categories of cetaceans: large whales (n = 23, most of which are listed as endangered), beaked whales (n = 11, potentially vulnerable to anthropogenic noise), and small whales/dolphins/porpoises (n = 69, bycatch in fisheries and important abundant …

Continued Disappearance Of The Benthic Amphipod Diporeia Spp. In Lake Michigan: Is There Evidence For Food Limitation?, Thomas F. Nalepa, David L. Fanslow, Andrew J. Foley Iii, Gregory A. Lang, Brian J. Eadie, Michael A. Quigley

United States Department of Commerce: Staff Publications

Benthic surveys were conducted in the southern basin of Lake Michigan and throughout the lake to assess trends in benthic populations, emphasizing recent changes in densities of the benthic amphipod Diporeia spp. and dreissenid mussels. In the southern basin, Diporeia populations declined 89%, 91%, and 45% between 1993 and 2002 at sites <30, 31–50, and 51–90 m, respectively. Lakewide, the population declined 65% between 1994–1995 and 2000. Over the same time period, dreissenid densities, particularly Dreissena bugensis, increased. Intensive studies at 45 m sites in the southeastern region examined changes in lipid content, age structure, and benthic food inputs relative to the hypothesis that food limitation was a factor in Diporeia’s disappearance. As Diporeia densities declined to zero, length–weight remained unchanged, …

A Bias Correction For Estimates Of Effective Population Size Based On Linkage Disequilibrium At Unlinked Gene Loci, Robin Waples

United States Department of Commerce: Staff Publications

Analysis of linkage disequilibrium (ȓ²=mean squared correlation of allele frequencies at different gene loci) provides a means of estimating effective population size (N_e) from a single sample, but this method has seen much less use than the temporal method (which requires at least two samples). It is shown that for realistic numbers of loci and alleles, the linkage disequilibrium method can provide precision comparable to that of the temporal method. However, computer simulations show that estimates of N_e based on ȓ² for unlinked, diallelic gene loci are sharply biased downwards ( N^ …

What Is A Population? An Empirical Evaluation Of Some Genetic Methods For Identifying The Number Of Gene Pools And Their Degree Of Connectivity, Robin Waples, Oscar Gaggiotti

United States Department of Commerce: Staff Publications

We review commonly used population definitions under both the ecological paradigm (which emphasizes demographic cohesion) and the evolutionary paradigm (which emphasizes reproductive cohesion) and find that none are truly operational. We suggest several quantitative criteria that might be used to determine when groups of individuals are different enough to be considered ‘populations’. Units for these criteria are migration rate (m) for the ecological paradigm and migrants per generation (Nm) for the evolutionary paradigm. These criteria are then evaluated by applying analytical methods to simulated genetic data for a finite island model. Under the standard parameter set …

Marine Species, Paul R. Armsworth, Carrie V. Kappel, Fiorenza Micheli, Eric P. Bjorkstedt

United States Department of Commerce: Staff Publications

The 4.1 million square miles of ocean inside the 200-mile exclusive economic zone around the United States surpasses the 3.6 million square miles total land area within federal jurisdiction (Lindholm and Barr 2001). The coastal oceans contain a great diversity of habitat types and ecosystems. These habitats are associated with particular substrate features such as coral reefs, sea grass beds, rocky shores and soft-bottom habitats, and also with persistent oceanographic features such as frontal convergence zones and upwelling regions.

Our marine ecosystems contain unique and rich biotas. At higher taxonomie levels, biodiversity is much richer in the marine environment than …

Working Seascapes, Paul R. Armsworth, Carrie V. Kappel, Fiorenza Micheli, Eric P. Bjorkstedt

United States Department of Commerce: Staff Publications

Marine species are being listed under the Endangered Species Act with increasing frequency and this trend can be expected to continue (Armsworth et al. 2006). The taxonomie focus of marine listings is also diversifying (Armsworth et al. 2006). Despite long-held assumptions that life his tory characteristics of so me marine species render them less vulnerable to extinction, anthropogenie impacts to marine ecosystems have imperiled a growing number of species. In this chapter, we review both the threats endangering marine species and some of the strategies being employed to mitigate those threats.

Listing decisions reveal the relative importance of different threats …

Preserving Nature, Shahid Naeem, Robin S. Waples, Craig Moritz

United States Department of Commerce: Staff Publications

To consider the broader environmental significance of protecting species at risk of extinction, we must first consider the roles or functions that species fulfill in nature. Although "nature" has many definitions, here we define it to mean the end product of ecological and evolutionary processes. That is, within ahabitat, region, or biosphere, the condition of the soil, water, air, and biota reßects the outcome of physical, chemical, ecological, and evolutionary processes. We refer to this combination of abiotic and biotic conditions as "nature" and to the ecological and evolutionary processes that create it as "natural processes."

Using these definitions, we …

Science And Implementation, Mary Ruckelshaus, Donna Darm

United States Department of Commerce: Staff Publications

The U.S. Endangered Species Act (ESA) relies heavily on science, and not surprisingly science has become a major battleground in the controversy surrounding its implementation (Doremus, this volume). Apparently, Congress hoped that ESA decisions could be made based on science alone and thereby insulated from politics (U.S. Congress 1982, 19). This hope was unrealistic for at least two reasons. First, science cannot answer with certainty many of the questions that must be answered in ESA decision making, especially in the time frames demanded by the statute. Second, while science has a central role in informing natural resource decisions, scientific information …

Distinct Population Segments, Robin S. Waples

United States Department of Commerce: Staff Publications

In reflecting on how the U.S. Endangered Species Act (ESA) has dealt with biodiversity issues over the past thirty years, it is instructive to review the collection of fifty-seven papers in the 1988 volume by Wilson entitled Biodiversity (1988b). Anchored in time midway between enactment of the ESA in 1973 and the present (2006 and counting), Wilson's volume provides a snapshot of the issues related to biodiversity that occupied conservation biologists during the first half of these three decades. The vast majority (over 80 percent) dealt with higher levels of biological organization (species or ecosystems), while only two (less than …

Shepherd's Beaked Whale (Tasmacetus Shepherdi): Information On Appearance And Biology Based On Strandings And At-Sea Observations, Robert L. Pitman, Anton L. Van Helden, Peter B. Best, A. Pym

United States Department of Commerce: Staff Publications

Shepherd’s beaked whale (Tasmacetus shepherdi), one of the least known cetaceans in the world (Mead 1989, 2002), is currently represented by approximately 42 stranding records and 5 unconfirmed live sightings. Most of the strandings have been from New Zealand (including the Chatham Islands—24 records), but also the Juan Fernandez Islands (2), Argentina (7), Tristan da Cunha (6), and Australia (3) (Fig. 1). A stranding reported from the South Sandwich Islands (Mead 2002) was actually a “probable” at-sea sighting near Shag Rocks (position of sighting: 53°45'S, 42°30' W) reported by Laughlin (1996, see below), and purported strandings from South Africa (e.g., …

Tornado And Severe Weather Climatology And Predictability By Enso Phase In The North Central U.S.: A Compositing Study, Barbara E. Mayes, Craig Cogil, Glenn R. Lussky, Jeffrey S. Boyne, Richard S. Ryrholm

United States Department of Commerce: Staff Publications

Climatological factors, including the phase of the El Niño-Southern Oscillation (ENSO), are known predictors for parameters such as seasonal temperature and precipitation and tropical cyclone activity. ENSO phase also has a relationship to severe weather activity and may have utility in predicting anomalies in severe weather climatology, including the number of significant tornadoes and the number of tornado days. While not useful in daily severe weather operations and forecasting, determining the relationship between ENSO phase and severe weather climatology anomalies can aid preparedness for potentially active seasons among operational meteorologists, emergency managers, the media, and others with a role in …

Spatial Statistical Models That Use Flow And Stream Distance, Jay M. Ver Hoef, Erin Peterson, David Theobald

United States Department of Commerce: Staff Publications

We develop spatial statistical models for stream networks that can estimate relationships between a response variable and other covariates, make predictions at unsampled locations, and predict an average or total for a stream or a stream segment. There have been very few attempts to develop valid spatial covariance models that incorporate flow, stream distance, or both. The application of typical spatial autocovariance functions based on Euclidean distance, such as the spherical covariance model, are not valid when using stream distance. In this paper we develop a large class of valid models that incorporate flow and stream distance by using spatial …

Differential Expression Of Immune Response Genes In Steller Sea Lions (Eumetopias Jubatus): An Indicator Of Ecosystem Health?, Lizabeth Bowen, Brian Aldridge, Kimberlee Beckmen, Tom Gelatt, Lorrie Rea, Kathy Burek, Ken Pitcher, Jeffrey L. Stott

United States Department of Commerce: Staff Publications

Characterization of the polygenic and polymorphic features of the Steller sea lion major histocompatibility complex (MHC) provides an ideal window for evaluating immunologic vigor of the population and identifying emergence of new genotypes that reflect ecosystem pressures. MHC genotyping can be used to measure the potential immunologic vigor of a population. However, since ecosystem-induced changes to MHC genotype can be slow to emerge, measurement of differential expression of these genes can potentially provide real-time evidence of immunologic perturbations. MHC DRB genes were cloned and sequenced using peripheral blood mononuclear leukocytes derived from 10 Steller sea lions from southeast Alaska, Prince …

Relating Chronic Toxicity Responses To Population-Level Effects: A Comparison Of Population-Level Parameters For Three Salmon Species As A Function Of Low-Level Toxicity, Julann A. Spromberg, James P. Meador

United States Department of Commerce: Staff Publications

Standard laboratory toxicity tests assess the physiological responses of individual organisms to exposure to toxic substances under controlled conditions. Time and space restrictions often prevent the assessment of population-level responses to a toxic substance. Contaminants can affect various biological functions (e.g. growth, fecundity or behavior), which may alter different demographic traits, leading to population-level impacts. In this study,immune suppression, reproductive dysfunction and somatic growth impairment were examined using life history matrix models for coho salmon (Oncorhynchus kisutch), sockeye salmon (Oncorhynchus nerka) and chinook salmon (Oncorhynchus tshawytscha). Our intent was to gauge the relative magnitude …

A Survey For Odontocete Cetaceans Off Kaua‘I And Ni‘Ihau, Hawai‘I, During October And November 2005: Evidence For Population Structure And Site Fidelity, Robin W. Baird, Gregory S. Schorr, Daniel L. Webster, Sabre D. Mahaffy, Anne B. Douglas, Antoinette M. Gorgone, Daniel J. Mcsweeney

United States Department of Commerce: Staff Publications

Considerable uncertainty exists regarding population structure and population sizes of most species of odontocetes in the Hawaiian Islands. A small-boat based survey for odontocetes was undertaken off the islands of Kaua‘i and Ni‘ihau in October and November 2005 to photoidentify individuals and collect genetic samples for examining stock structure. Field effort on 24 days covered 2,194 km of trackline. Survey coverage was from shallow coastal waters out to over 3,000 m depth, though almost half (47%) was in waters less than 500 m in depth. There were 56 sightings of five species of odontocetes: spinner dolphins (30 sightings); bottlenose dolphins …

Genetic Implications Of Reduced Survival Of Male Red Deer Cervus Elaphus Under Harvest, Jeffrey J. Hard, L. Scott Mills, James M. Peek

United States Department of Commerce: Staff Publications

We use simple, multivariate evolutionary models to evaluate the short-term potential for size-selective harvest to reduce genetic variability and alter life history in cervids. These genetic effects limit sustainable levels of harvest of the animals because they determine how changes in sex ratio, generation length and traits contributing to fitness influence population growth rate and local adaptation. Our analysis of harvest-mediated adaptive evolution employs a genetic approach that parameterizes models with empirical data obtained from European red deer Cervus elaphus. The analysis indicates that harvest, if sufficiently high to reduce the breeding ratio of males to females to below …

Seed Banks, Salmon, And Sleeping Genes: Effective Population Size In Semelparous, Age-Structured Species With Fluctuating Abundance, Robin Waples

United States Department of Commerce: Staff Publications

Previous studies reached contrasting conclusions regarding how fluctuations in abundance affect N_e in semelparous species with variable age at maturity: that N_e is determined by the arithmetic mean N among the T years within a generation (N_e ≈ T͞͞N̅͞_t; monocarpic plants with seed banks) or the harmonic mean t (N ≈ TÑ ; Pacific salmon). I show that these conclusions arise from different model assumptions rather than inherent differences between the species. Sequentially applying standard, discrete-generation formulas for inbreeding N_e to a series of nominal generations accurately predicts the multigenerational rate of …