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MSM4PCoD.bib
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@article{authier_power_2020,
title = {Of power and despair in cetacean conservation: estimation and detection of trend in abundance with noisy and short time-series},
volume = {8},
issn = {2167-8359},
shorttitle = {Of power and despair in cetacean conservation},
url = {https://peerj.com/articles/9436},
doi = {10.7717/peerj.9436},
abstract = {Many conservation instruments rely on detecting and estimating a population decline in a target species to take action. Trend estimation is difficult because of small sample size and relatively large uncertainty in abundance/density estimates of many wild populations of animals. Focusing on cetaceans, we performed a prospective analysis to estimate power, type-I, sign (type-S) and magnitude (type-M) error rates of detecting a decline in short time-series of abundance estimates with different signal-to-noise ratio. We contrasted results from both unregularized (classical) and regularized approaches. The latter allows to incorporate prior information when estimating a trend. Power to detect a statistically significant estimates was in general lower than 80\%, except for large declines. The unregularized approach (status quo) had inflated type-I error rates and gave biased (either over- or under-) estimates of a trend. The regularized approach with a weakly-informative prior offered the best trade-off in terms of bias, statistical power, type-I, type-S and type-M error rates and confidence interval coverage. To facilitate timely conservation decisions, we recommend to use the regularized approach with a weakly-informative prior in the detection and estimation of trend with short and noisy time-series of abundance estimates.},
language = {en},
urldate = {2021-09-29},
journal = {PeerJ},
author = {Authier, Matthieu and Galatius, Anders and Gilles, Anita and Spitz, Jérôme},
month = aug,
year = {2020},
note = {Publisher: PeerJ Inc.},
pages = {e9436},
file = {Full Text PDF:/Users/eiren/Zotero/storage/E9CY5C7S/Authier et al. - 2020 - Of power and despair in cetacean conservation est.pdf:application/pdf;Snapshot:/Users/eiren/Zotero/storage/ZHIIKNPZ/9436.html:text/html},
}
@article{boyd_shifting_2021,
title = {Shifting trends: {Detecting} changes in cetacean population dynamics in shifting habitat},
volume = {16},
issn = {1932-6203},
shorttitle = {Shifting trends},
url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0251522},
doi = {10.1371/journal.pone.0251522},
abstract = {The ability to monitor population dynamics and detect major changes in population trend is essential for wildlife conservation and management. However, this is often challenging for cetaceans as surveys typically cover only a portion of a population’s range and conventional stock assessment methods cannot then distinguish whether apparent changes in abundance reflect real changes in population size or shifts in distribution. We developed and tested methods for estimating population size and trend and detecting changes in population trend in the context of shifting habitat by integrating additional data into distance-sampling analysis. Previous research has shown that incorporating habitat information can improve population size estimates for highly mobile species with dynamic spatial distributions. Here, using simulated datasets representative of a large whale population, we demonstrate that incorporating individual mark-recapture data can increase the accuracy and precision of trend estimation and the power to distinguish whether apparent changes in abundance reflect changes in population trend or distribution shifts. We recommend that similar simulation studies are conducted for specific cetacean populations to assess the potential for detecting changes in population dynamics given available data. This approach is especially important wherever population change may be confounded with long-term change in distribution patterns associated with regime shifts or climate change.},
language = {en},
number = {5},
urldate = {2021-09-29},
journal = {PLOS ONE},
author = {Boyd, Charlotte and Punt, André E.},
month = may,
year = {2021},
note = {Publisher: Public Library of Science},
keywords = {Binomials, Blue whales, Boats, Fecundity, Habitats, Population dynamics, Population size, Transect surveys},
pages = {e0251522},
file = {Full Text PDF:/Users/eiren/Zotero/storage/4KM6U3NI/Boyd and Punt - 2021 - Shifting trends Detecting changes in cetacean pop.pdf:application/pdf;Snapshot:/Users/eiren/Zotero/storage/YW8L8DM7/article.html:text/html},
}
@article{curtis_abundance_2021,
title = {Abundance, survival, and annual rate of change of {Cuvier}'s beaked whales ({Ziphius} cavirostris) on a {Navy} sonar range},
volume = {37},
issn = {1748-7692},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mms.12747},
doi = {10.1111/mms.12747},
abstract = {Bayesian mark-recapture estimates of survival, abundance, and trend are reported for Cuvier's beaked whales (Ziphius cavirostris) using a Navy training range off southern California. The deep-diving beaked whale family is exceptionally vulnerable to mid-frequency active sonar (MFAS), which has been implicated in mass strandings and altered foraging behavior. Extremely low sighting probabilities impede studies of population-level impacts of MFAS on beaked whales. The San Nicolas Basin hosts a Navy training range subject to frequent MFAS use and attracts high densities of Z. cavirostris. An 11-year (2007–2018) photo-identification program leveraged automated acoustic detection and location capabilities on the range's 1,800-km2 hydrophone array to enhance capture probability. Estimated population parameters for Z. cavirostris using the range included mean (90\% credibility intervals) apparent annual survival of 0.950 (0.899–0.986), annual number of individuals as 121 (71–219), and annual rate of change of −0.8\% (−5.6\%–4.1\%). Simulations show the probability of detecting abundance changes is currently low, but can be greatly improved through continued monitoring and increased effort. Complementary data collection on habitat use and demographic rates in San Nicolas and surrounding basins is also essential to relating direct effects of MFAS use to changes in vital rates and broader population outcomes.},
language = {en},
number = {2},
urldate = {2021-10-04},
journal = {Marine Mammal Science},
author = {Curtis, K. Alexandra and Falcone, Erin A. and Schorr, Gregory S. and Moore, Jeffrey E. and Moretti, David J. and Barlow, Jay and Keene, Erin},
year = {2021},
note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/mms.12747},
keywords = {sonar, Bayesian mark-recapture, California, Cuvier's beaked whale, inference error, photo-identification, Ziphius cavirostris},
pages = {399--419},
file = {Full Text PDF:/Users/eiren/Zotero/storage/APYFZVJT/Curtis et al. - 2021 - Abundance, survival, and annual rate of change of .pdf:application/pdf;Snapshot:/Users/eiren/Zotero/storage/85GYU2Y7/mms.html:text/html},
}
@article{plard_integrated_2019-1,
title = {Integrated population models: powerful methods to embed individual processes in population dynamics models},
volume = {100},
issn = {1939-9170},
shorttitle = {Integrated population models},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ecy.2715},
doi = {10.1002/ecy.2715},
abstract = {Population dynamics models have long assumed that populations are composed of a restricted number of groups, where individuals in each group have identical demographic rates and where all groups are similarly affected by density-dependent and -independent effects. However, individuals usually vary tremendously in performance and in their sensitivity to environmental conditions or resource limitation, such that individual contributions to population growth will be highly variable. Recent efforts to integrate individual processes in population models open up new opportunities for the study of eco-evolutionary processes, such as the density-dependent influence of environmental conditions on the evolution of morphological, behavioral, and life-history traits. We review recent advances that demonstrate how including individual mechanisms in models of population dynamics contributes to a better understanding of the drivers of population dynamics within the framework of integrated population models (IPMs). IPMs allow for the integration in a single inferential framework of different data types as well as variable population structure including sex, social group, or territory, all of which can be formulated to include individual-level processes. Through a series of examples, we first show how IPMs can be beneficial for getting more accurate estimates of demographic traits than classic matrix population models by including basic population structure and their influence on population dynamics. Second, the integration of individual- and population-level data allows estimating density-dependent effects along with their inherent uncertainty by directly using the population structure and size to feedback on demography. Third, we show how IPMs can be used to study the influence of the dynamics of continuous individual traits and individual quality on population dynamics. We conclude by discussing the benefits and limitations of IPMs for integrating data at different spatial, temporal, and organismal levels to build more mechanistic models of population dynamics.},
language = {en},
number = {6},
urldate = {2021-11-05},
journal = {Ecology},
author = {Plard, Floriane and Fay, Rémi and Kéry, Marc and Cohas, Aurélie and Schaub, Michael},
year = {2019},
note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ecy.2715},
keywords = {population model, data integration for population models special feature, density-dependence, eco-evolutionary feedback, heterogeneity, individual quality, integral projection model, integrated population model, structured population},
pages = {e02715},
file = {Full Text PDF:/Users/eiren/Zotero/storage/JPDAZTZD/Plard et al. - 2019 - Integrated population models powerful methods to .pdf:application/pdf;Snapshot:/Users/eiren/Zotero/storage/QNCA2UPC/ecy.html:text/html},
}
@article{boyd_estimation_2018,
title = {Estimation of population size and trends for highly mobile species with dynamic spatial distributions},
volume = {24},
issn = {1472-4642},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ddi.12663},
doi = {10.1111/ddi.12663},
abstract = {Aim To develop a more ecologically realistic approach for estimating the population size of cetaceans and other highly mobile species with dynamic spatial distributions. Location California Current Ecosystem, USA. Methods Conventional spatial density models assume a constant relationship between densities and habitat covariates over some time period, typically a survey season. The estimated population size must change whenever total habitat availability changes. For highly mobile long-lived species, however, density–habitat relationships likely adjust more rapidly than population size. We developed an integrated population-redistribution model based on a more ecologically plausible alternative hypothesis: (1) population size is effectively constant over each survey season; (2) if habitat availability changes, then the population redistributes itself following an ideal free distribution process. Thus, the estimated relationship between densities and habitat covariates adjusts rather than population size. We constructed Bayesian hierarchical models corresponding to the conventional and alternative hypotheses and applied them to distance sampling data for Dall's porpoise (Phocoenoides dalli), a highly mobile cetacean with distribution patterns closely tied to cool sea-surface temperatures. Results The Dall's porpoise data provided strong support for the hypothesis based on an ideal free redistribution process. Our results indicate that the population size of Dall's porpoise within the survey region was relatively stable over each summer/fall survey season, but the distribution expanded and contracted with the extent of suitable habitat. Over multiple survey seasons, the model partitioned variation in observed densities among three sources: variation in population size, the density–habitat relationship and measurement error, leading to lower and more ecologically plausible estimates of interannual variation in population size. Main conclusions We conclude that the integrated population-redistribution model (IPRM) presented here represents an ecologically plausible model for use in future assessments of the population size and dynamics of cetaceans and other highly mobile long-lived species with variable spatial distributions.},
language = {en},
number = {1},
urldate = {2021-11-08},
journal = {Diversity and Distributions},
author = {Boyd, Charlotte and Barlow, Jay and Becker, Elizabeth A. and Forney, Karin A. and Gerrodette, Tim and Moore, Jeffrey E. and Punt, André E.},
year = {2018},
note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ddi.12663},
keywords = {Bayesian hierarchical model, California Current, Dall's porpoise, distance sampling, habitat model, spatial density model},
pages = {1--12},
file = {Full Text PDF:/Users/eiren/Zotero/storage/I6ASPF5R/Boyd et al. - 2018 - Estimation of population size and trends for highl.pdf:application/pdf;Snapshot:/Users/eiren/Zotero/storage/UD888BJV/ddi.html:text/html},
}
@article{hin_bioenergetic_2019,
title = {Bio‐energetic modeling of medium‐sized cetaceans shows high sensitivity to disturbance in seasons of low resource supply},
volume = {29},
issn = {1051-0761, 1939-5582},
url = {https://onlinelibrary.wiley.com/doi/10.1002/eap.1903},
doi = {10.1002/eap.1903},
language = {en},
number = {5},
urldate = {2021-11-08},
journal = {Ecological Applications},
author = {Hin, Vincent and Harwood, John and Roos, André M.},
month = jul,
year = {2019},
file = {Hin et al. - 2019 - Bio‐energetic modeling of medium‐sized cetaceans s.pdf:/Users/eiren/Zotero/storage/UZJBB8CJ/Hin et al. - 2019 - Bio‐energetic modeling of medium‐sized cetaceans s.pdf:application/pdf},
}
@article{moore_power_nodate,
title = {A power analysis and recommended study design to directly detect population- level consequences of acoustic disturbance},
language = {en},
author = {Moore, Jeffrey and Barlow, Jay and Falcone, Erin and Schorr, Greg and Moretti, David and Curtis, K Alexandra},
pages = {16},
file = {Moore et al. - A power analysis and recommended study design to d.pdf:/Users/eiren/Zotero/storage/FEF478LW/Moore et al. - A power analysis and recommended study design to d.pdf:application/pdf},
}
@article{moore_declining_2013-1,
title = {Declining {Abundance} of {Beaked} {Whales} ({Family} {Ziphiidae}) in the {California} {Current} {Large} {Marine} {Ecosystem}},
volume = {8},
issn = {1932-6203},
url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0052770},
doi = {10.1371/journal.pone.0052770},
abstract = {Beaked whales are among the most diverse yet least understood groups of marine mammals. A diverse set of mostly anthropogenic threats necessitates improvement in our ability to assess population status for this cryptic group. The Southwest Fisheries Science Center (NOAA) conducted six ship line-transect cetacean abundance surveys in the California Current off the contiguous western United States between 1991 and 2008. We used a Bayesian hidden-process modeling approach to estimate abundance and population trends of beaked whales using sightings data from these surveys. We also compiled records of beaked whale stranding events (3 genera, at least 8 species) on adjacent beaches from 1900 to 2012, to help assess population status of beaked whales in the northern part of the California Current. Bayesian posterior summaries for trend parameters provide strong evidence of declining beaked whale abundance in the study area. The probability of negative trend for Cuvier's beaked whale (Ziphius cavirostris) during 1991–2008 was 0.84, with 1991 and 2008 estimates of 10771 (CV = 0.51) and ≈7550 (CV = 0.55), respectively. The probability of decline for Mesoplodon spp. (pooled across species) was 0.96, with 1991 and 2008 estimates of 2206 (CV = 0.46) and 811 (CV = 0.65). The mean posterior estimates for average rate of decline were 2.9\% and 7.0\% per year. There was no evidence of abundance trend for Baird's beaked whale (Berardius bairdii), for which annual abundance estimates in the survey area ranged from ≈900 to 1300 (CV≈1.3). Stranding data were consistent with the survey results. Causes of apparent declines are unknown. Direct impacts of fisheries (bycatch) can be ruled out, but impacts of anthropogenic sound (e.g., naval active sonar) and ecosystem change are plausible hypotheses that merit investigation.},
language = {en},
number = {1},
urldate = {2021-11-08},
journal = {PLOS ONE},
author = {Moore, Jeffrey E. and Barlow, Jay},
month = jan,
year = {2013},
note = {Publisher: Public Library of Science},
keywords = {California, Beaked whales, Death rates, Ecosystems, Fisheries, Marine mammals, Navy, Sonar},
pages = {e52770},
file = {Full Text PDF:/Users/eiren/Zotero/storage/NV3BUSCU/Moore and Barlow - 2013 - Declining Abundance of Beaked Whales (Family Ziphi.pdf:application/pdf;Snapshot:/Users/eiren/Zotero/storage/287EUJ38/article.html:text/html},
}
@article{becker_habitat-based_2020,
title = {Habitat-based density estimates for cetaceans in the {California} {Current} {Ecosystem} based on 1991-2018 survey data},
url = {https://repository.library.noaa.gov/view/noaa/27826},
doi = {10.25923/3ZNQ-YX13},
urldate = {2021-11-08},
author = {Becker, Elizabeth A.},
year = {2020},
note = {Publisher: Southwest Fisheries Science Center (U.S.)},
}
@article{barlow_acoustic-based_2020,
title = {Acoustic-based estimates of {Cuvier}'s beaked whale ({Ziphius} cavirostris) density and abundance along the {U}.{S}. {West} {Coast} from drifting hydrophone recorders},
volume = {n/a},
issn = {1748-7692},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mms.12872},
doi = {10.1111/mms.12872},
abstract = {An acoustic survey of Cuvier's beaked whales (Ziphius cavirostris) was conducted off the U.S. West Coast in August and September 2016 using drifting recorder systems with a vertical array of two hydrophones at a depth of 110 m. Recorders were deployed 22 times to representatively cover a 1,058,000 km2 study area from the shelf break to 556 km offshore. Vertical angles to echolocation pulses were measured using the signal time-difference-of-arrival on the two hydrophones. Echolocation pulses of Cuvier's beaked whales were identified from their arrival angles (always from below the array) and unique acoustic characteristics. The density and abundance of Cuvier's beaked whales were estimated using a group-based point-transect analysis with 2 min time snapshots. The area effectively surveyed was estimated using a maximum simulated likelihood approach to fit the observed distribution of signal arrival angles. The acoustic availability of whales during their dive cycle was estimated from the duration of acoustic encounters using a mark-recapture approach. Overall, Cuvier's beaked whales were present during 0.60\% of snapshots, and their estimated average density is 5.12 animals per 1,000 km2 (CV = 0.27). Their estimated abundance in the study area is 5,454 individuals (95\% credibility intervals: 3,151 to 8,907).},
language = {en},
number = {n/a},
urldate = {2021-11-08},
journal = {Marine Mammal Science},
author = {Barlow, Jay and Moore, Jeffrey E. and McCullough, Jennifer L. K. and Griffiths, Emily T.},
year = {2020},
note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/mms.12872},
keywords = {Cuvier's beaked whale, Ziphius cavirostris, abundance estimation, acoustic survey, drifting buoy recorder, echolocation, point-transect, vertical hydrophone array},
file = {Full Text PDF:/Users/eiren/Zotero/storage/QNZACR3H/Barlow et al. - Acoustic-based estimates of Cuvier's beaked whale .pdf:application/pdf;Snapshot:/Users/eiren/Zotero/storage/BZU7SD9Q/mms.html:text/html},
}
@techreport{baumann-pickering_modeling_2014,
title = {Modeling of {Habitat} and {Foraging} {Behavior} of {Beaked} {Whales} in the {Southern} {California} {Bight}},
url = {https://apps.dtic.mil/sti/citations/ADA618169},
abstract = {The overall goal of this project is to improve our understanding of beaked whale distribution and foraging behavior and to describe inter-specific differences. We are developing habitat models for multiple beaked whale species in the Southern California Bight using passive acoustic encounters. Data from line transect surveys and autonomous recorders are compared with dynamic and static oceanographic habitat variables. We aim to compare habitat models using acoustic line transect data with those generated using autonomous acoustic recorder detections. We intend to model the foraging behavior of beaked whales with respect to spatio-temporal occurrence on a diel or seasonal basis and in correlation to oceanographic or geographic variables.},
language = {en},
urldate = {2021-11-08},
institution = {SCRIPPS INSTITUTION OF OCEANOGRAPHY LA JOLLA CA},
author = {Baumann-Pickering, Simone and Hildebrand, John A. and Yack, Tina and Moore, Jeffrey E.},
month = sep,
year = {2014},
note = {Section: Technical Reports},
file = {Full Text PDF:/Users/eiren/Zotero/storage/4YGXGYQL/Baumann-Pickering et al. - 2014 - Modeling of Habitat and Foraging Behavior of Beake.pdf:application/pdf;Snapshot:/Users/eiren/Zotero/storage/EEMEAQBX/ADA618169.html:text/html},
}
@article{jongejans_dispersal_2008,
series = {Space matters - {Novel} developments in plant ecology through spatial modelling},
title = {Dispersal, demography and spatial population models for conservation and control management},
volume = {9},
issn = {1433-8319},
url = {https://www.sciencedirect.com/science/article/pii/S1433831907000467},
doi = {10.1016/j.ppees.2007.09.005},
abstract = {Spatial population dynamics can seldom be ignored in management aimed at conserving or controlling plant species in a spatial context. Therefore, spatial population models, that bring together knowledge about a species’ local demography and dispersal behavior, are of growing applied importance. Here, we survey increasingly complex analytical and simulation models that are being developed to describe both demography and dispersal in applied studies. Local population dynamics can be modeled in an unstructured way, by specifying age- or stage-structure or by modeling each individual. Dispersal is often summarized in population-spread models with descriptive and simple statistical models. Mechanistic models that incorporate the physical or behavioral dynamics of dispersal vectors, however, provide more insight and can more readily be applied to novel situations. Importantly, mechanistic models provide a tool for linking variation in species traits and environments to dispersal and population spread. Spatial population models span a wide range: from diffusion models, metapopulation models, integrodifference equation models, and Neubert–Caswell models, to spatially explicit individual-based models. The complexity (and biological realism) of such models often trades off with tractability: for instance, individual-based simulation models allow for unlimited incorporation of biological detail, but rarely for analytical exploration of the model dynamics. We discuss the advantages and disadvantages of these various spatial population models; the choice of the most appropriate model will depend on the management objective, the biological complexity, available data and the principle of parsimony. We present five case studies of endangered and invasive species for which spatial population models have been developed to inform management, for instance to decrease the spread rate of invasive species or to improve the regional persistence of endangered species. We also anticipate exciting new developments in both spatial analytical and spatial simulation models with increasing demographic, dispersal and spatial sophistication.},
language = {en},
number = {3},
urldate = {2022-01-18},
journal = {Perspectives in Plant Ecology, Evolution and Systematics},
author = {Jongejans, Eelke and Skarpaas, Olav and Shea, Katriona},
month = mar,
year = {2008},
keywords = {Demography, Seed dispersal, Spatial population models, Species management},
pages = {153--170},
file = {ScienceDirect Snapshot:/Users/eiren/Zotero/storage/MEJR9HXG/S1433831907000467.html:text/html},
}
@article{jongejans_dispersal_2008-1,
title = {Dispersal, demography and spatial population models for conservation and control management},
volume = {9},
issn = {14338319},
url = {https://linkinghub.elsevier.com/retrieve/pii/S1433831907000467},
doi = {10.1016/j.ppees.2007.09.005},
abstract = {Spatial population dynamics can seldom be ignored in management aimed at conserving or controlling plant species in a spatial context. Therefore, spatial population models, that bring together knowledge about a species’ local demography and dispersal behavior, are of growing applied importance. Here, we survey increasingly complex analytical and simulation models that are being developed to describe both demography and dispersal in applied studies. Local population dynamics can be modeled in an unstructured way, by specifying age- or stage-structure or by modeling each individual. Dispersal is often summarized in population-spread models with descriptive and simple statistical models. Mechanistic models that incorporate the physical or behavioral dynamics of dispersal vectors, however, provide more insight and can more readily be applied to novel situations. Importantly, mechanistic models provide a tool for linking variation in species traits and environments to dispersal and population spread.},
language = {en},
number = {3-4},
urldate = {2022-01-18},
journal = {Perspectives in Plant Ecology, Evolution and Systematics},
author = {Jongejans, Eelke and Skarpaas, Olav and Shea, Katriona},
month = mar,
year = {2008},
pages = {153--170},
file = {Jongejans et al. - 2008 - Dispersal, demography and spatial population model.pdf:/Users/eiren/Zotero/storage/2JM3LAXW/Jongejans et al. - 2008 - Dispersal, demography and spatial population model.pdf:application/pdf},
}
@article{bertignac_spatial_1998,
title = {A spatial population dynamics simulation model of tropical tunas using a habitat index based on environmental parameters},
volume = {7},
issn = {1365-2419},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-2419.1998.00065.x},
doi = {10.1046/j.1365-2419.1998.00065.x},
abstract = {We are developing a spatial, multigear, multispecies population dynamics simulation model for tropical tunas in the Pacific Ocean. The model is age-structured to account for growth and gear selectivity. It includes a tuna movement model based on a diffusion–advection equation in which the advective term is proportional to the gradient of a habitat index. The monthly geographical distribution of recruitment is defined by assuming that spawning occurs in areas where sea surface temperature is above 25°C. During the first 3 months of their life, simulated tunas are transported by oceanic currents, after which movement is conditioned by gradients in the habitat index. Independent estimates of natural mortality rates and population size from large-scale tagging experiments carried out by the Secretariat of the Pacific Community are used in the simulations. The habitat index consists of components due to forage density and sea surface temperature, both of which are suspected to play major roles in determining tuna distribution. Because direct observations of forage are not available on a basin scale, we developed a submodel to simulate the surface tuna forage production (Lehodey et al., 1998). At present, only skipjack (Katsuwonus pelamis; a surface tuna species caught by purse seine and by pole-and-line) is considered, at a 1°-square resolution and on a monthly climatological time series. Despite the simplicity of the model and the limitations of the data used, the simulation model is able to predict a distribution of skipjack catch rates, of the different fleets involved in the fishery, that is fairly consistent with observations.},
language = {en},
number = {3-4},
urldate = {2022-01-18},
journal = {Fisheries Oceanography},
author = {Bertignac, M. and Lehodey, P. and Hampton, J.},
year = {1998},
note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-2419.1998.00065.x},
keywords = {habitat, Katsuwonus pelamis, Pacific, population model, skipjack, tuna},
pages = {326--334},
file = {Full Text PDF:/Users/eiren/Zotero/storage/8F6L2GNZ/Bertignac et al. - 1998 - A spatial population dynamics simulation model of .pdf:application/pdf;Snapshot:/Users/eiren/Zotero/storage/32SREP4B/j.1365-2419.1998.00065.html:text/html},
}
@article{fleishman_monitoring_2016-1,
title = {Monitoring population-level responses of marine mammals to human activities},
volume = {32},
issn = {1748-7692},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mms.12310},
doi = {10.1111/mms.12310},
abstract = {We provide guidance for monitoring whether human activities affect the physiology or behavior of marine mammals and, if so, whether those effects may lead to changes in survival and reproduction at the population level. We suggest that four elements be included in designing and implementing such a monitoring program. The first is development of a theory of change: a set of mechanistic hypotheses that outline why a given activity might be expected to have one or more measurable effects on individuals and populations, and ideally the magnitude, timing, and duration of the effects. The second element, definition of biologically meaningful effect sizes, ultimately facilitates the development of a monitoring program that can detect those magnitudes of effect with the desired levels of precision. The third element, selection of response variables for monitoring, allows inference to whether observed changes in the status of individuals or populations are attributable to a given activity. Visual observations, passive acoustic and tagging instruments, and direct physical measurements all can provide data that facilitate quantitative hypothesis testing. The fourth element is specification of the temporal sequence of monitoring. These elements also can be used to inform monitoring of the responses of other taxonomic groups to human activities.},
language = {en},
number = {3},
urldate = {2022-01-18},
journal = {Marine Mammal Science},
author = {Fleishman, Erica and Costa, Daniel P. and Harwood, John and Kraus, Scott and Moretti, David and New, Leslie F. and Schick, Robert S. and Schwarz, Lisa K. and Simmons, Samantha E. and Thomas, Len and Wells, Randall S.},
year = {2016},
note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/mms.12310},
keywords = {acoustics, environmental impact statements, Marine Mammal Protection Act, results chains, take, vital rates},
pages = {1004--1021},
file = {Full Text PDF:/Users/eiren/Zotero/storage/QPT42ZIC/Fleishman et al. - 2016 - Monitoring population-level responses of marine ma.pdf:application/pdf;Snapshot:/Users/eiren/Zotero/storage/8QYBJBX5/mms.html:text/html},
}
@article{moore_population_2017,
title = {Population abundance and trend estimates for beaked whales and sperm whales in the {California} {Current} from ship-based visual line-transect survey data, 1991-2014},
copyright = {Public Domain},
url = {https://repository.library.noaa.gov/view/noaa/15457},
doi = {10.7289/V5/TM-SWFSC-585},
urldate = {2022-01-20},
author = {Moore, Jeffrey E. and Barlow, Jay},
year = {2017},
note = {Publisher: U.S. Department of Commerce, National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Southwest Fisheries Science Center},
}
@article{new_using_2013-1,
title = {Using {Energetic} {Models} to {Investigate} the {Survival} and {Reproduction} of {Beaked} {Whales} (family {Ziphiidae})},
volume = {8},
issn = {1932-6203},
url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0068725},
doi = {10.1371/journal.pone.0068725},
abstract = {Mass stranding of several species of beaked whales (family Ziphiidae) associated with exposure to anthropogenic sounds has raised concern for the conservation of these species. However, little is known about the species’ life histories, prey or habitat requirements. Without this knowledge, it becomes difficult to assess the effects of anthropogenic sound, since there is no way to determine whether the disturbance is impacting the species’ physical or environmental requirements. Here we take a bioenergetics approach to address this gap in our knowledge, as the elusive, deep-diving nature of beaked whales has made it hard to study these effects directly. We develop a model for Ziphiidae linking feeding energetics to the species’ requirements for survival and reproduction, since these life history traits would be the most likely to be impacted by non-lethal disturbances. Our models suggest that beaked whale reproduction requires energy dense prey, and that poor resource availability would lead to an extension of the inter-calving interval. Further, given current information, it seems that some beaked whale species require relatively high quality habitat in order to meet their requirements for survival and reproduction. As a result, even a small non-lethal disturbance that results in displacement of whales from preferred habitats could potentially impact a population if a significant proportion of that population was affected. We explored the impact of varying ecological parameters and model assumptions on survival and reproduction, and find that calf and fetus survival appear more readily affected than the survival of adult females.},
language = {en},
number = {7},
urldate = {2022-01-20},
journal = {PLOS ONE},
author = {New, Leslie F. and Moretti, David J. and Hooker, Sascha K. and Costa, Daniel P. and Simmons, Samantha E.},
month = jul,
year = {2013},
note = {Publisher: Public Library of Science},
keywords = {Animal behavior, Basal metabolic rate measurement, Beaked whales, Bioenergetics, Energy metabolism, Fetuses, Lactation, Predation},
pages = {e68725},
file = {Full Text PDF:/Users/eiren/Zotero/storage/4VM8R5EZ/New et al. - 2013 - Using Energetic Models to Investigate the Survival.pdf:application/pdf;Snapshot:/Users/eiren/Zotero/storage/Y8DJLKMA/article.html:text/html},
}
@article{booth_methods_2020,
title = {Methods for {Monitoring} for the {Population} {Consequences} of {Disturbance} in {Marine} {Mammals}: {A} {Review}},
volume = {7},
issn = {2296-7745},
shorttitle = {Methods for {Monitoring} for the {Population} {Consequences} of {Disturbance} in {Marine} {Mammals}},
url = {https://www.frontiersin.org/article/10.3389/fmars.2020.00115},
abstract = {Assessing the non-lethal effects of disturbance and their population-level consequences is a significant ecological and conservation challenge, because it requires extensive baseline knowledge of behavioral patterns, life-history and demography. However, for many marine mammal populations, this knowledge is currently lacking and it may take decades to fill the gaps. During this time, undetected population declines may occur. In this study we identify methods that can be used to monitor populations subject to disturbance and provide insights into the processes through which disturbance may affect them. To identify and address the knowledge gaps highlighted above, we reviewed the literature to identify suitable response variables and methods for monitoring these variables. We also used existing models of the population consequences of disturbance (PCoD) to identify demographic characteristics (e.g., the proportion of immature animals in the population, or the ratio of calves/pups to mature females) that may be strongly correlated with population status and therefore provide early warnings of future changes in abundance. These demographic characteristics can be monitored using established methods such as visual surveys combined with photogrammetry, and capture-recapture analysis. Individual health and physiological variables can also inform PCoD assessment and can be monitored using photogrammetry, remote tissue sampling, hands-on assessment and individual tracking. We then conducted a workshop to establish the relative utility and feasibility of all these approaches for different groups of marine mammal species. We describe how future marine mammal monitoring programs can be designed to inform population-level analysis.},
urldate = {2022-01-21},
journal = {Frontiers in Marine Science},
author = {Booth, Cormac G. and Sinclair, Rachael R. and Harwood, John},
year = {2020},
file = {Full Text PDF:/Users/eiren/Zotero/storage/WDIICKXH/Booth et al. - 2020 - Methods for Monitoring for the Population Conseque.pdf:application/pdf},
}
@article{king_interim_2015,
title = {An interim framework for assessing the population consequences of disturbance},
volume = {6},
issn = {2041-210X},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.12411},
doi = {10.1111/2041-210X.12411},
abstract = {Changes in natural patterns of animal behaviour and physiology resulting from anthropogenic disturbance may alter the conservation status of a population if they affect the ability of individuals to survive, breed or grow. However, information to forecast population-level consequences of such changes is often lacking. We developed an interim framework to assess the population consequences of disturbance when empirical information is sparse. We show how daily effects of disturbance, which are often straightforward to estimate, can be scaled to the disturbance duration and to multiple sources of disturbance. We used expert elicitation to estimate parameters that define how changes in individual behaviour or physiology affect vital rates and incorporated them into a stochastic population model. Model outputs can be used to evaluate cumulative impacts of disturbance over space and time. As an example, we forecast the potential effects of disturbance from offshore wind farm construction on the North Sea harbour porpoise (Phocoena phocoena) population. Synthesis and applications. The interim framework can be used to forecast the effects of disturbances from human activities on animal populations, to assess the effectiveness of mitigation measures and to identify priority areas for research that reduces uncertainty in population forecasts. The last two applications are likely to be important in situations where there is a risk of unacceptable change in a species' conservation status. The framework should, however, be augmented with empirical data as soon as these are available.},
language = {en},
number = {10},
urldate = {2022-01-21},
journal = {Methods in Ecology and Evolution},
author = {King, Stephanie L. and Schick, Robert S. and Donovan, Carl and Booth, Cormac G. and Burgman, Mark and Thomas, Len and Harwood, John},
year = {2015},
note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.12411},
keywords = {anthropogenic noise, behavioural response, expert elicitation, impact assessment, stochastic population models},
pages = {1150--1158},
file = {Full Text PDF:/Users/eiren/Zotero/storage/INSD449R/King et al. - 2015 - An interim framework for assessing the population .pdf:application/pdf;Snapshot:/Users/eiren/Zotero/storage/SWW6DT3G/2041-210X.html:text/html},
}