Jeff Laake

NOAA National Marine Fisheries Service Alaska Fisheries Science Center

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H. Dean Cluff

Government of Northwest Territories

François Messier

Université Laval

Mitchell K. Taylor

Lakehead University

Erik W. Born

Grønlands Naturinstitut

John L. Bengtson

NOAA National Marine Fisheries Service Alaska Fisheries Science Center

Philip D. McLoughlin

University of Saskatchewan

Aqqalu Rosing‐Asvid

Grønlands Naturinstitut

Peter L. Boveng

NOAA National Marine Fisheries Service

Robert L. DeLong

NOAA National Marine Fisheries Service Alaska Fisheries Science Center

M. Bradley Hanson

NOAA National Marine Fisheries Service Northwest Fisheries Science Center

Cooperative Institutions

NOAA National Marine Fisheries Service

Oregon State University

NOAA National Marine Fisheries Service Alaska Fisheries Science Center

United States Geological Survey

University of Washington

Oregon Department of Fish and Wildlife

National Oceanic and Atmospheric Administration

United States Fish and Wildlife Service

Washington Department of Fish and Wildlife

NOAA National Marine Fisheries Service Southwest Fisheries Science Center

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The Use of Surrogate Data in Demographic Population Viability Analysis: A Case Study of California Sea Lions

PLoS ONE (2015)

Claudia J. Hernández‐Camacho Victoria J. Bakker David Aurioles‐Gamboa Jeff Laake Leah R. Gerber

Reliable data necessary to parameterize population models are seldom available for imperiled species. As an alternative, data from populations of the same species or from ecologically similar species have been used to construct models. In this study, we evaluated the use of demographic data collected at one California sea lion colony (Los Islotes) to predict the population dynamics of the same species from two other colonies (San Jorge and Granito) in the Gulf of California, Mexico, for which demographic data are lacking. To do so, we developed a stochastic demographic age-structured matrix model and conducted a population viability analysis for each colony. For the Los Islotes colony we used site-specific pup, juvenile, and adult survival probabilities, as well as birth rates for older females. For the other colonies, we used site-specific pup and juvenile survival probabilities, but used surrogate data from Los Islotes for adult survival probabilities and birth rates. We assessed these models by comparing simulated retrospective population trajectories to observed population trends based on count data. The projected population trajectories approximated the observed trends when surrogate data were used for one colony but failed to match for a second colony. Our results indicate that species-specific and even region-specific surrogate data may lead to erroneous conservation decisions. These results highlight the importance of using population-specific demographic data in assessing extinction risk. When vital rates are not available and immediate management actions must be taken, in particular for imperiled species, we recommend the use of surrogate data only when the populations appear to have similar population trends.

Population viability analysis

Vital rates

Population model

Population decline

10.1371/journal.pone.0139158

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Citations (22)

Linking colonies to fisheries: Spatio-temporal overlap between common murres (Uria aalge) from Tatoosh Island and coastal gillnet fisheries in the Pacific Northwest, USA

Biological Conservation (2008)

Nathalie Hamel Julia K. Parrish Jeff Laake

Uria aalge

Bycatch

10.1016/j.biocon.2008.09.015

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Citations (10)

Multivariate State Hidden Markov Models for Mark-Recapture Data

Statistical Science (2016)

Devin S. Johnson Jeff Laake Sharon R. Melin Robert L. DeLong

State-based Cormack–Jolly–Seber (CJS) models have become an often used method for assessing states or conditions of free-ranging animals through time. Although originally envisioned to account for differences in survival and observation processes when animals are moving though various geographical strata, the model has evolved to model vital rates in different life-history or diseased states. We further extend this useful class of models to the case of multivariate state data. Researchers can record values of several different states of interest, for example, geographic location and reproductive state. Traditionally, these would be aggregated into one state with a single probability of state uncertainty. However, by modeling states as a multivariate vector, one can account for partial knowledge of the vector as well as dependence between the state variables in a parsimonious way. A hidden Markov model (HMM) formulation allows straightforward maximum likelihood inference. The proposed HMM models are demonstrated with a case study using data from a California sea lion vital rates study.

State vector

Mark and recapture

10.1214/15-sts542

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Citations (17)

Cohort effects and spatial variation in age-specific survival of Steller sea lions from southeastern Alaska

Ecosphere (2011)

Kelly K. Hastings Lauri A. Jemison T. S. Gelatt Jeff Laake Grey W. Pendleton

Information concerning mechanistic processes underlying changes in vital rates and ultimately population growth rate is required to monitor impacts of environmental change on wildlife. We estimated age-specific survival and examined factors influencing survival for a threatened population of Steller sea lions (Eumetopias jubatus) in southeastern Alaska. We used mark-recapture models and data from 1,995 individuals marked at approximately one month of age at four of five rookeries in southeastern Alaska, and resighted from Oregon to the Bering Sea. Average annual survival probability for females was 0.64 for pups and 0.77 for yearlings, and increased from 0.91 to 0.96 from age 3–7 yrs. Annual survival probability of males averaged 0.60 for pups and 0.88 by 7 yrs, resulting in probability of survival to age 7, 33% lower for males compared to females. Pups from northern southeastern Alaska (including an area of low summer population size but rapid growth) were twice as likely to survive to age 7 compared to pups from southern rookeries (including a large, historical, stable rookery). Effects of early conditions on future fitness were observed as (1) environmental conditions in the birth year equally affected first- and second-year survival, and (2) effects of body mass at approximately one month of age were still apparent at 7 yrs. Survival from 0–2 yrs varied among five cohorts by a maximum absolute difference of 0.12. We observed survival costs for long-distance dispersal for males, particularly as juveniles. However, survival was higher for non-pups that dispersed to northern southeastern Alaska, suggesting that moving to an area with greater productivity, greater safety, or lower population size may alleviate a poor start and provide a mechanism for spatial structure for sea lion populations.

Rookery

Vital rates

10.1890/es11-00215.1

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Citations (45)

Delineating Canadian and Greenland polar bear (<i>Ursus maritimus</i>) populations by cluster analysis of movements

Canadian Journal of Zoology (2001)

Mitchell K. Taylor Seeglook Akeeagok Dennis Andriashek William Barbour Erik W. Born

Ursus maritimus

10.1139/cjz-79-4-690

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Citations (24)

The Utility of Harvest Recoveries of Marked Individuals to Assess Polar Bear (<i>Ursus maritimus</i>) Survival

ARCTIC (2012)

Elizabeth Peacock Jeff Laake Kristin L. Laidre Erik W. Born Stephen N. Atkinson

Management of polar bear (Ursus maritimus) populations requires the periodic assessment of life history metrics such as survival rate. This information is frequently obtained during short-term capture and marking efforts (e.g., over the course of three years) that result in hundreds of marked bears remaining in the population after active marking is finished. Using 10 additional years of harvest recovery subsequent to a period of active marking, we provide updated estimates of annual survival for polar bears in the Baffin Bay population of Greenland and Canada. Our analysis suggests a decline in survival of polar bears since the period of active marking that ended in 1997; some of the decline in survival can likely be attributed to a decline in springtime ice concentration over the continental shelf of Baffin Island. The variance around the survival estimates is comparatively high because of the declining number of marks available; therefore, results must be interpreted with caution. The variance of the estimates of survival increased most substantially in the sixth year post-marking. When survival estimates calculated with recovery-only and recapture-recovery data sets from the period of active marking were compared, survival rates were indistinguishable. However, for the period when fewer marks were available, survival estimates were lower using the recovery-only data set, which indicates that part of the decline we detected for 2003 – 09 may be due to using only harvest recovery data. Nevertheless, the decline in the estimates of survival is consistent with population projections derived from harvest numbers and earlier vital rates, as well as with an observed decline in the extent of sea ice habitat.

Ursus maritimus

Population decline

Vital rates

Mark and recapture

10.14430/arctic4237

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Citations (18)

Distance sampling with independent observers: Reducing bias from heterogeneity by weakening the conditional independence assumption

CRC Press eBooks (2021)

Jeff Laake

Using replicated surveys of a known population of wooden stakes in a sagebrush habitat, I illustrate the application of surveys which combine sight-resight with line transect sampling. This example demonstrates that the usual assumption of full conditional independence (FCI) for all distances (x ≥ 0) is unnecessarily strict and can be weakened to assuming conditional independence on the traddine (x = 0). I present a likelihood for combined sight-resight and distance sampling based on trackline conditional independence (TCI) and use a likelihood ratio test for comparison of the TCI and FCI models. For the wooden stake surveys, in most cases the TCI model was superior to the FCI model because of heterogeneity in detection probability created by variation in vegetation density for stakes at x > 0. Equivalent factors in marine mammal surveys, such as sea state and cloud cover, will create heterogeneity in detection probability that will bias abundance estimates developed with combined distance and sight-resight surveys under the FCI assumption.

Independence

Conditional independence

10.1201/9781003211167-14

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Citations (9)

SALMOD: A population model for salmonids: user's manual. Version W3

John M. Bartholow John Heasley Jeff Laake Jeff Sandelin Beth A.K. Coughlan

SALMOD is a computer model that simulates the dynamics of freshwater salmonid populations, both anadromous and resident. The conceptual model was developed in a workshop setting (Williamson et al. 1993) using fish experts concerned with Trinity River chinook restoration. The model builds on the foundation laid by similar models (see Cheslak and Jacobson 1990). The model’s premise that that egg and fish mortality are directly related to spatially and temporally variable micro- and macrohabitat limitations, which themselves are related to the timing and amount of streamflow and other meteorological variables. Habitat quality and capacity are characterized by the hydraulic and thermal properties of individual mesohabitats, which we use as spatial “computation units” in the model. The model tracks a population of spatially distinct cohorts that originate as gees and grow from one life stage to another as a function of local water temperature. Individual cohorts either remain in the computational unit in which they emerged or move, in whole or in part, to nearby units (see McCormick et al. 1998). Model processes include spawning (with red superimposition and incubation losses), growth (including egg maturation), mortality, and movement (freshet-induced, habitat-induced, and seasonal). Model processes are implemented such that the user (modeler) has the ability to more-or-less program the model on the fly to create the dynamics thought to animate the population. SALMOD then tabulates the various causes of mortality and the whereabouts of fish.

Chinook wind

Population model

Replicate

10.3133/96234

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Citations (8)

Visibility bias in aerial survey: mark - recapture, line-transect or both?

Wildlife Research (2008)

Jeff Laake Michelle Dawson Jim Hone

Mark–recapture and line-transect sampling procedures both provide estimators for visibility bias in aerial surveys, and have coexisted in the literature for decades. Mark–recapture estimators of abundance tend to be negatively biased in this context as a result of unmodelled heterogeneity. Line-transect sampling can also be negatively biased if detection probability on the line is less than 1.0. Numerous papers have described hybrid approaches using mark–recapture and line transect methods but there have been some subtle but important differences that may not be apparent to the practitioner. We have used wild horse survey data collected in south-eastern Australia and some imaginary data to highlight these subtle differences. We demonstrate the advantage of using the hybrid approach, which uses the strengths of both mark–recapture and line-transect procedures by fitting a detection function (with p(0) = 1) to the line-transect data to estimate the shape of the detection function, and uses a separate detection function for the mark–recapture data to estimate the intercept (p(0)).

Mark and recapture

Visibility

Aerial Survey

Abundance estimation

Distance sampling

Line (geometry)

10.1071/wr07034

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Citations (62)

A salmonid population model with emphasis on habitat limitations

John M. Bartholow Jeff Laake Clair B. Stalnaker S. Williamson

Population model

Source

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Citations (36)