Steven T. Lindley

Hidden Process Models For Animal Population Dynamics

Hidden process models are a conceptually useful and practical way to simultaneously account for process variation in animal population dynamics and measurement errors in observations and estimates made on the population. Process variation, which can be both demographic and environmental, is modeled by linking a series of stochastic and deterministic subprocesses that characterize processes such as birth, survival, maturation, and movement. Observations of the population can be modeled as functions of true abundance with realistic probability distributions to describe observation or estimation error. Computer-intensive procedures, such as sequential Monte Carlo methods or Markov chain Monte Carlo, condition on the observed data to yield estimates of both the underlying true population abundances and the unknown population dynamics parameters. Formulation and fitting of a hidden process model are demonstrated for Sacramento River winter-run chinook salmon (Oncorhynchus tshawytsha).

ESTIMATION OF POPULATION GROWTH AND EXTINCTION PARAMETERS FROM NOISY DATA

The random-walk-with-drift model of population dynamics is an important tool in conservation biology, partly because its parameters are easily estimated from periodic observations of population size. Estimating the model with noisy data is problematic, however, because the commonly used estimators of process variation are biased if population abundance measurements are imprecise, and a recently developed method that attempts to remove this bias is not robust. In this paper, I show how the random-walk-with-drift model can be applied to noisy time series of population estimates by converting the random-walk- with-drift model to state-space form and applying the Kalman filter to yield the likelihood of the data. The likelihood function allows the variances of the process error and mea- surement error and the growth rate of the population to be estimated in a way that is robust and fully supported by statistical theory. Comparative analysis using simulated data indi- cates that the Kalman-filter method reduces the bias in estimates of process variance without yielding negative variance estimates. I apply the method to California sea otter and Yel- lowstone grizzly bear data to illustrate how the method (and simple extensions) can be used to assess the status of real populations. California sea otters appear to have little risk of extinction over the next 100 years although the population may not be secure over the long term if a recent apparent cessation of population growth persists. The grizzly bear population appears to have responded positively to the 1988 Yellowstone fires, and if the population continues to grow at the average rate observed over the study period, it is extremely unlikely to go extinct.

Marine Migration of North American Green Sturgeon

Abstract An understanding of the distribution of North American green sturgeon Acipenser medirostris in coastal waters is crucial to minimize impacts on this vulnerable species from various fisheries. To determine migratory patterns, we tagged 213 subadult and adult green sturgeon in spawning rivers and summer aggregation areas with uniquely coded ultrasonic pingers and observed their coastal movements with arrays of automated hydrophones deployed along the West Coast of North America from southeast Alaska to Monterey Bay, California. Green sturgeon exhibited an annual migration along the continental shelf from U.S. to Canadian waters in the fall and an apparent return migration in the spring. Peak migration rates exceeded 50 km/d during the springtime southward migration. Large numbers of green sturgeon were detected near Brooks Peninsula on northwest Vancouver Island, British Columbia, during May-June and October-November. A single fish was detected in southeast Alaska in December. This pattern of detec...

Population Status of North American Green Sturgeon, Acipenser medirostris

North American green sturgeon, Acipenser medirostris, was petitioned for listing under the Endangered Species Act (ESA). The two questions that need to be answered when considering an ESA listing are; (1) Is the entity a species under the ESA and if so (2) is the “species” in danger of extinction or likely to become an endangered species in the foreseeable future throughout all or a significant portion of its range? Green sturgeon genetic analyses showed strong differentiation between northern and southern populations, and therefore, the species was divided into Northern and Southern Distinct Population Segments (DPSs). The Northern DPS includes populations in the Rogue, Klamath-Trinity, and Eel rivers, while the Southern DPS only includes a single population in the Sacramento River. The principal risk factors for green sturgeon include loss of spawning habitat, harvest, and entrainment. The Northern DPS is not considered to be in danger of extinction or likely to become an endangered species in the foreseeable future. The loss of spawning habitat is not large enough to threaten this DPS, although the Eel River has been severely impacted by sedimentation due to poor land use practices and floods. The two main spawning populations in the Rogue and Klamath-Trinity rivers occupy separate basins reducing the potential for loss of the DPS through catastrophic events. Harvest has been substantially reduced and green sturgeon in this DPS do not face substantial entrainment loss. However there are significant concerns due to lack of information, flow and temperature issues, and habitat degradation. The Southern DPS is considered likely to become an endangered species in the foreseeable future. Green sturgeon in this DPS are concentrated into one spawning area outside of their natural habitat in the Sacramento River, making them vulnerable to catastrophic extinction. Green sturgeon spawning areas have been lost from the area above Shasta Dam on the Sacramento River and Oroville Dam on the Feather River. Entrainment of individuals into water diversion projects is an additional source of risk, and the large decline in numbers of green sturgeon entrained since 1986 causes additional concern.

Migration of green sturgeon, Acipenser medirostris, in the Sacramento River

Adult green sturgeon, Acipenser medirostris, were collected in San Pablo Bay, California, and surgically implanted with ultrasonic acoustic tags from 2004 to 2006. An array of automated acoustic monitors was maintained in the Sacramento River to record movements of these fish. We presumed movements to known spawning areas (based on previous green sturgeon egg collections) or areas with potential spawning habitat (characterized by substrate, flow, and temperature criteria) represented a “spawning migration.” Three separate annual “spawning migrations” were recorded involving 15 individuals. The majority of the Sacramento River migrants entered the system in the months of March and April. Two different patterns of “spawning migration” and out-migration were observed. Six individuals potentially spawned, over-summered and moved out of the river with the first fall flow event. This is believed to be the common behavior of the green sturgeon. Alternatively, nine individuals promptly moved out of the Sacramento River before 1 September, and any known flow or temperature cue. Some green sturgeon appeared to be impeded on their upstream movement by the 15 May closure of the Red Bluff Diversion Dam, and at least five passed under the dam gates during downstream migration. A delay in the closure of the Red Bluff Diversion Dam would likely allow upstream passage of spawning green sturgeon, further, the potential mortality affects of downstream passage beneath the Red Bluff Diversion Dam should be assessed. Specific protection should be also given to the large aggregation of green sturgeon located in the reach of the Sacramento River adjacent to the Glen Colusa Irrigation District pumping facility.

Diel movements of out-migrating Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (Oncorhynchus mykiss) smolts in the Sacramento/San Joaquin watershed

We used ultrasonic telemetry to describe the movement patterns of late-fall run Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (O. mykiss) smolts during their entire emigration down California’s Sacramento River, through the San Francisco Bay Estuary and into the Pacific Ocean. Yearling hatchery smolts were tagged via intracoelomic surgical implantation with coded ultrasonic tags. They were then released at four upriver locations in the Sacramento River during the winters of 2007 through 2010. Late-fall run Chinook salmon smolts exhibited a nocturnal pattern of migration after release in the upper river. This is likely because individuals remain within a confined area during the day, while they become active at night and migrate downstream. The ratio between night and day detections of Chinook salmon smolts decreased with distance traveled downriver. There was a significant preference for nocturnal migration in every reach of the river except the Estuary. In contrast, steelhead smolts, which reside upriver longer following release, exhibited a less pronounced diel pattern during their entire migration. In the middle river, Delta, and Estuary, steelhead exhibited a significant preference for daytime travel. In the ocean Chinook salmon preferred to travel at night, yet steelhead were detected on the monitors equally during the night and day. These data show that closely related Oncorhynchus species, with the same ontogenetic pattern of out-migrating as yearlings, vary in migration tactic.

Accounting for demographic and environmental stochasticity, observation error, and parameter uncertainty in fish population dynamics models

Abstract Bayesian hierarchical state-space models are a means of modeling fish population dynamics while accounting for both demographic and environmental stochasticity, observation noise, and parameter uncertainty. Sequential importance sampling can be used to generate posterior distributions for parameters, unobserved states, and random effects for population models with realistic dynamics and error distributions. Such a state-space model was fit to the Sacramento River winter-run Chinook salmon Oncorhynchus tshawytscha population, where a key objective was to develop a tool for predicting juvenile out-migration based on multiple sources of data. One-year-ahead 90% prediction intervals based on 1992−2003 data, while relatively wide, did include the estimated values for 2004. Parameter estimates for the juvenile production function based on the state-space model formulation differed appreciably from Bayesian estimates that ignored autocorrelation and observation noise.

Performance of salmon fishery portfolios across western North America

Summary Quantifying the variability in the delivery of ecosystem services across the landscape can be used to set appropriate management targets, evaluate resilience and target conservation efforts. Ecosystem functions and services may exhibit portfolio‐type dynamics, whereby diversity within lower levels promotes stability at more aggregated levels. Portfolio theory provides a framework to characterize the relative performance among ecosystems and the processes that drive differences in performance. We assessed Pacific salmon Oncorhynchus spp. portfolio performance across their native latitudinal range focusing on the reliability of salmon returns as a metric with which to assess the function of salmon ecosystems and their services to humans. We used the Sharpe ratio (e.g. the size of the total salmon return to the portfolio relative to its variability (risk)) to evaluate the performance of Chinook and sockeye salmon portfolios across the west coast of North America. We evaluated the effects on portfolio performance from the variance of and covariance among salmon returns within each portfolio, and the association between portfolio performance and watershed attributes. We found a positive latitudinal trend in the risk‐adjusted performance of Chinook and sockeye salmon portfolios that also correlated negatively with anthropogenic impact on watersheds (e.g. dams and land‐use change). High‐latitude Chinook salmon portfolios were on average 2·5 times more reliable, and their portfolio risk was mainly due to low variance in the individual assets. Sockeye salmon portfolios were also more reliable at higher latitudes, but sources of risk varied among the highest performing portfolios. Synthesis and applications. Portfolio theory provides a straightforward method for characterizing the resilience of salmon ecosystems and their services. Natural variability in portfolio performance among undeveloped watersheds provides a benchmark for restoration efforts. Locally and regionally, assessing the sources of portfolio risk can guide actions to maintain existing resilience (protect habitat and disturbance regimes that maintain response diversity; employ harvest strategies sensitive to different portfolio components) or improve restoration activities. Improving our understanding of portfolio reliability may allow for management of natural resources that is robust to ongoing environmental change.

Incorporating Climate Science in Applications of the U.S. Endangered Species Act for Aquatic Species

Aquatic species are threatened by climate change but have received comparatively less attention than terrestrial species. We gleaned key strategies for scientists and managers seeking to address climate change in aquatic conservation planning from the literature and existing knowledge. We address 3 categories of conservation effort that rely on scientific analysis and have particular application under the U.S. Endangered Species Act (ESA): assessment of overall risk to a species; long-term recovery planning; and evaluation of effects of specific actions or perturbations. Fewer data are available for aquatic species to support these analyses, and climate effects on aquatic systems are poorly characterized. Thus, we recommend scientists conducting analyses supporting ESA decisions develop a conceptual model that links climate, habitat, ecosystem, and species response to changing conditions and use this model to organize analyses and future research. We recommend that current climate conditions are not appropriate for projections used in ESA analyses and that long-term projections of climate-change effects provide temporal context as a species-wide assessment provides spatial context. In these projections, climate change should not be discounted solely because the magnitude of projected change at a particular time is uncertain when directionality of climate change is clear. Identifying likely future habitat at the species scale will indicate key refuges and potential range shifts. However, the risks and benefits associated with errors in modeling future habitat are not equivalent. The ESA offers mechanisms for increasing the overall resilience and resistance of species to climate changes, including establishing recovery goals requiring increased genetic and phenotypic diversity, specifying critical habitat in areas not currently occupied but likely to become important, and using adaptive management. Incorporación de las Ciencias Climáticas en las Aplicaciones del Acta Estadunidense de Especies en Peligro para Especies Acuáticas.

Seasonal Patterns of Terrestrial and Aquatic Prey Abundance and Use by Oncorhynchus mykiss in a California Coastal Basin with a Mediterranean Climate

Abstract Terrestrial invertebrates are a major source of prey for salmonids in many streams. Their importance as prey appears to be related to (1) the seasonal timing of terrestrial inputs relative to the abundance of aquatic prey and (2) water temperature, which affects food demand by fish. Most studies of seasonal patterns of terrestrial inputs have come from temperate systems, and patterns in most other systems are unknown. We measured monthly biomass of aquatic invertebrates, input of terrestrial invertebrates, and diets of Oncorhynchus mykiss (non-anadromous and juvenile anadromous life history forms) for 15 months in two streams in a basin with a Mediterranean-type climate on the Big Sur coast of California. Biomass of aquatic invertebrates and terrestrial inputs followed a similar seasonal pattern; highest levels occurred in summer and early autumn and were highly correlated with water temperature. Total annual input of terrestrial invertebrates was 8.7 g·m−2·year−1, and terrestrial inputs provided...