paper.bib

@article{wade_calculating_1998,
	title = {Calculating {Limits} to the {Allowable} {Human}-{Caused} {Mortality} of {Cetaceans} and {Pinnipeds}},
	volume = {14},
	issn = {1748-7692},
	url = {https://onlinelibrary-wiley-com.offcampus.lib.washington.edu/doi/abs/10.1111/j.1748-7692.1998.tb00688.x},
	doi = {10.1111/j.1748-7692.1998.tb00688.x},
	abstract = {A simulation method was developed for identifying populations with levels of human-caused mortality that could lead to depletion, taking into account the uncertainty of available information. A mortality limit (termed the Potential Biological Removal, PBR, under the U. S. Marine Mammal Protection Act) was calculated as the product of a minimum population estimate (NMIN), one-half of the maximum net productivity rate (RMAX), and a recovery factor (FR). Mortality limits were evaluated based on whether at least 95\% of the simulated populations met two criteria: (1) that populations starting at the maximum net productivity level (MNPL) stayed there or above after 20 yr, and (2) that populations starting at 30\% of carrying-capacity (K) recovered to at least MNPL after 100 yr. Simulations of populations that experienced mortality equal to the PBR indicated that using approximately the 20th percentile (the lower 60\% log-normal confidence limit) of the abundance estimate for NMIN met the criteria for both cetaceans (assuming RMAX= 0.04) and pinnipeds (assuming RMAX= 0.12). Additional simulations that included plausible levels of bias in the available information indicated that using a value of 0.5 for FR would meet both criteria during these “bias trials.” It is concluded that any marine mammal population with an estimate of human-caused mortality that is greater than its PBR has a level of mortality that could lead to the depletion of the population. The simulation methods were also used to show how mortality limits could be calculated to meet conservation goals other than the U. S. goal of maintaining populations above MNPL.},
	language = {en},
	number = {1},
	journal = {Marine Mammal Science},
	author = {Wade, Paul R.},
	year = {1998},
	keywords = {Bycatch, cetacean, conservation, incidental fisheries mortality, management, mortality limit, PBR, pinniped, population modeling, U. S. MMPA},
	pages = {1--37},
	file = {Full Text PDF:/Users/mcsiple/Zotero/storage/V38KKQQH/Wade - Calculating Limits to the Allowable Human-Caused M.pdf:application/pdf;Snapshot:/Users/mcsiple/Zotero/storage/D93W7RQU/j.1748-7692.1998.tb00688.html:text/html},
}

@techreport{punt_a._e._annex_1999,
	address = {Hobart, Australia},
	title = {Annex {R}: {A} full description of the standard {Baleen} {II} model and some variants thereof},
	url = {https://duwamish.lib.washington.edu/uwnetid/illiad.dll?Action=10&Form=75&Value=1651729},
	urldate = {2018-08-07},
	institution = {Division of Marine Research, CSIRO Marine Laboratories},
	author = {Punt, A. E.},
	year = {1999},
	file = {Punt et al. 1999:/Users/mcsiple/Zotero/storage/REFWACK2/illiad.pdf:application/pdf},
}

@article{delong_age-_2017,
	title = {Age- and sex-specific survival of {California} sea lions ({Zalophus} californianus) at {San} {Miguel} {Island}, {California}},
	volume = {33},
	issn = {1748-7692},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mms.12427},
	doi = {10.1111/mms.12427},
	abstract = {We conducted a mark-recapture study of California sea lions (Zalophus californianus) using pups branded on San Miguel Island, California, from 1987 to 2014, and annual resightings from 1990 to 2015. We used the Burnham model (Burnham 1993), an extension of the Cormack-Jolly-Seber mark-recapture model, which includes recoveries of dead animals, to analyze age, sex, and annual patterns in survival. Generally, females had higher survival than males. For female pups, the average annual survival was 0.600 and for male pups it was 0.574. Yearling survival was 0.758 and 0.757 for females and males, respectively. Peak annual survival was at age 5 and was 0.952 for females and 0.931 for males. Pups with larger mass at branding had higher survival as pups and yearlings, but the effect was relative within each cohort because of large between-cohort variability in survival. Annual variability in sea surface temperature (SST) affected survival. For each 1°C increase in SST, the odds of survival decreased by nearly 50\% for pups and yearlings; negative SST anomalies yielded higher survival. Annual variation in male survival was partly explained by leptospirosis outbreaks. Our study provides a unique view of one demographic parameter that contributed to the successful recovery of the California sea lion population.},
	language = {en},
	number = {4},
	urldate = {2018-07-30},
	journal = {Marine Mammal Science},
	author = {DeLong, Robert L. and Melin, Sharon R. and Laake, Jeffrey L. and Morris, Patricia and Orr, Anthony J. and Harris, Jeffrey D.},
	year = {2017},
	keywords = {survival, El Niño, California sea lion, leptospirosis, mark-recapture, Zalophus},
	pages = {1097--1125},
	file = {Full Text PDF:/Users/mcsiple/Zotero/storage/VE8R4IA6/DeLong et al. - Age- and sex-specific survival of California sea l.pdf:application/pdf;Snapshot:/Users/mcsiple/Zotero/storage/QH2ZWB4G/mms.html:text/html},
}

@article{hastings_sex-_2012,
	title = {Sex- and age-specific survival of harbor seals ({Phoca} vitulina) from {Tugidak} {Island}, {Alaska}},
	volume = {93},
	issn = {0022-2372},
	url = {https://academic.oup.com/jmammal/article/93/5/1368/860838},
	doi = {10.1644/11-MAMM-A-291.1},
	abstract = {Abstract.  We estimated sex- and age-specific apparent survival of harbor seals (Phoca vitulina richardii) born at Tugidak Island, Alaska, from 2000 to 2007 usi},
	language = {en},
	number = {5},
	urldate = {2018-07-27},
	journal = {Journal of Mammalogy},
	author = {Hastings, Kelly K. and Small, Robert J. and Pendleton, Grey W.},
	month = oct,
	year = {2012},
	pages = {1368--1379},
	file = {Full Text PDF:/Users/mcsiple/Zotero/storage/MPGMYDTZ/Hastings et al. - 2012 - Sex- and age-specific survival of harbor seals (Ph.pdf:application/pdf;Hastings et al 2012.pdf:/Users/mcsiple/Zotero/storage/AASDM2JY/Hastings et al 2012.pdf:application/pdf;Hastings et al 2012.pdf:/Users/mcsiple/Zotero/storage/ZUMWAYHJ/Hastings et al 2012.pdf:application/pdf;Snapshot:/Users/mcsiple/Zotero/storage/PK7E3CB4/860838.html:text/html},
}

@article{punt_conserving_2018,
	title = {Conserving and recovering vulnerable marine species: a comprehensive evaluation of the {US} approach for marine mammals},
	volume = {75},
	issn = {1054-3139},
	shorttitle = {Conserving and recovering vulnerable marine species},
	url = {https://academic.oup.com/icesjms/advance-article/doi/10.1093/icesjms/fsy049/5035891},
	doi = {10.1093/icesjms/fsy049},
	language = {en},
	number = {5},
	urldate = {2018-09-24},
	journal = {ICES Journal of Marine Science},
	author = {Punt, A. E. and Moreno, Paula and Brandon, John R and Mathews, Michael A},
	month = jun,
	year = {2018},
	pages = {1813--1831},
}

@article{breiwick_population_1984,
	title = {Population {Dynamics} of {Western} {Arctic} {Bowhead} {Whales} ( \textit{{Balaena} mysticetus} )},
	volume = {41},
	issn = {0706-652X},
	url = {http://www.nrcresearchpress.com/doi/10.1139/f84-058},
	doi = {10.1139/f84-058},
	language = {en},
	number = {3},
	urldate = {2018-11-06},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	author = {Breiwick, Jeffrey M. and Eberhardt, L. Lee and Braham, Howard W.},
	month = mar,
	year = {1984},
	pages = {484--496},
	file = {Breiwsck et al. - 1984 - Population Dynamics of Western Arctic Bowhead Whal.pdf:/Users/mcsiple/Zotero/storage/UA4GQ6RD/Breiwsck et al. - 1984 - Population Dynamics of Western Arctic Bowhead Whal.pdf:application/pdf},
}

@article{butterworth_effects_1995,
	title = {The effects of future consumption by the {Cape} fur seal on catches and catch rates of the {Cape} hakes. 3. {Modelling} the dynamics of the {Cape} fur seal {Arctocephalus} pusillus pusillus},
	volume = {16},
	issn = {0257-7615},
	url = {https://doi.org/10.2989/025776195784156511},
	doi = {10.2989/025776195784156511},
	abstract = {The current status of and future trends for the Cape fur seal Arctocephalus pusillus pusillus population are assessed using information from aerial counts of pup abundance. The model used in the analyses is age- and sex-structured, and assumes density-dependence in the survival rate of pups. Uncertainty is assessed by conducting sensitivity tests and estimating 90\% confidence intervals by the percentile method. The results confirm the increase of the seal population since the introduction of legal controls at the end of the 19th century, and the estimate of 1,7 million animals of Age 1 and older at the start of 1993 is relatively robust to model assumptions and values for biological parameters. The food consumption by the seal population is estimated to have almost doubled between 1973 and 1993, and to be roughly 2 million tons annually at present. Future trajectories of seal numbers and annual consumption of food cannot be determined with great precision and are sensitive to the values assumed for the post-first-year survival rate and the degree of compensation in density-dependence. Depending on such assumptions, the seal population could already have reached its pre-exploitation equilibrium level or still be well below this level. Data from the 1993 aerial survey have considerable influence on the model results, and particularly on inferences concerning whether the population is now approaching its pre-exploitation level. This suggests that further surveys should be conducted to ascertain the reliability of the changed trend in pup abundance indicated by that 1993 count.},
	number = {1},
	urldate = {2018-12-27},
	journal = {South African Journal of Marine Science},
	author = {Butterworth, D. S. and Punt, A. E. and Oosthuizen, W. H. and Wickens, P. A.},
	month = dec,
	year = {1995},
	pages = {161--183},
	file = {Full Text PDF:/Users/mcsiple/Zotero/storage/HW5IK8MD/Butterworth et al. - 1995 - The effects of future consumption by the Cape fur .pdf:application/pdf;Snapshot:/Users/mcsiple/Zotero/storage/UMK4SILR/025776195784156511.html:text/html},
}

@article{dillingham_improved_2016,
	title = {Improved estimation of intrinsic growth rmax for long-lived species: integrating matrix models and allometry},
	volume = {26},
	copyright = {© 2016 by the Ecological Society of America},
	issn = {1939-5582},
	shorttitle = {Improved estimation of intrinsic growth rmax for long-lived species},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/14-1990},
	doi = {10.1890/14-1990},
	abstract = {Intrinsic population growth rate (rmax) is an important parameter for many ecological applications, such as population risk assessment and harvest management. However, rmax can be a difficult parameter to estimate, particularly for long-lived species, for which appropriate life table data or abundance time series are typically not obtainable. We describe a method for improving estimates of rmax for long-lived species by integrating life-history theory (allometric models) and population-specific demographic data (life table models). Broad allometric relationships, such as those between life history traits and body size, have long been recognized by ecologists. These relationships are useful for deriving theoretical expectations for rmax, but rmax for real populations may vary from simple allometric estimators for “archetypical” species of a given taxa or body mass. Meanwhile, life table approaches can provide population-specific estimates of rmax from empirical data, but these may have poor precision from imprecise and missing vital rate parameter estimates. Our method borrows strength from both approaches to provide estimates that are consistent with both life-history theory and population-specific empirical data, and are likely to be more robust than estimates provided by either method alone. Our method uses an allometric constant: the product of rmax and the associated generation time for a stable-age population growing at this rate. We conducted a meta-analysis to estimate the mean and variance of this allometric constant across well-studied populations from three vertebrate taxa (birds, mammals, and elasmobranchs) and found that the mean was approximately 1.0 for each taxon. We used these as informative Bayesian priors that determine how much to “shrink” imprecise vital rate estimates for a data-limited population toward the allometric expectation. The approach ultimately provides estimates of rmax (and other vital rates) that reflect a balance of information from the individual studied population, theoretical expectation, and meta-analysis of other populations. We applied the method specifically to an archetypical petrel (representing the genus Procellaria) and to white sharks (Carcharodon carcharias) in the context of estimating sustainable fishery bycatch limits.},
	language = {en},
	number = {1},
	urldate = {2019-04-08},
	journal = {Ecological Applications},
	author = {Dillingham, Peter W. and Moore, Jeffrey E. and Fletcher, David and Cortés, Enric and Curtis, K. Alexandra and James, Kelsey C. and Lewison, Rebecca L.},
	year = {2016},
	keywords = {population dynamics, demography, Bayesian analysis, allometric (rT) models, Carcharodon carcharias, integrated population models, intrinsic growth rate, life-table models, long-lived species, Procellaria, white shark},
	pages = {322--333},
	file = {Snapshot:/Users/mcsiple/Zotero/storage/3R2ZMPC2/14-1990.html:text/html},
}

@article{arso_civil_variations_2019,
	title = {Variations in age- and sex-specific survival rates help explain population trend in a discrete marine mammal population},
	volume = {9},
	issn = {20457758},
	url = {http://doi.wiley.com/10.1002/ece3.4772},
	doi = {10.1002/ece3.4772},
	abstract = {Understanding the drivers underlying fluctuations in the size of animal populations is central to ecology, conservation biology, and wildlife management. Reliable estimates of survival probabilities are key to population viability assessments, and patterns of variation in survival can help inferring the causal factors behind detected changes in population size. We investigated whether variation in age‐ and sex‐specific survival probabilities could help explain the increasing trend in population size detected in a small, discrete population of bottlenose dolphins Tursiops truncatus off the east coast of Scotland. To estimate annual survival probabilities, we applied capture–recapture models to photoidentification data collected from 1989 to 2015. We used robust design models accounting for temporary emigration to estimate juvenile and adult survival, multistate models to estimate sex‐specific survival, and age models to estimate calf survival. We found strong support for an increase in juvenile/ adult annual survival from 93.1\% to 96.0\% over the study period, most likely caused by a change in juvenile survival. Examination of sex‐specific variation showed weaker support for this trend being a result of increasing female survival, which was overall higher than for males and animals of unknown sex. Calf survival was lower in the first than second year; a bias in estimating third‐year survival will likely exist in similar studies. There was some support first‐born calf survival being lower than for calves born subsequently. Coastal marine mammal populations are subject to the impacts of environmental change, increasing anthropogenic disturbance and the effects of management measures. Survival estimates are essential to improve our understanding of population dynamics and help predict how future pressures may impact populations, but obtaining robust information on the life history of long‐lived species is challenging. Our study illustrates how knowledge of survival can be increased by applying a robust analytical framework to photoidentification data.},
	language = {en},
	number = {1},
	urldate = {2019-06-28},
	journal = {Ecology and Evolution},
	author = {Arso Civil, Mònica and Cheney, Barbara and Quick, Nicola J. and Islas-Villanueva, Valentina and Graves, Jeff A. and Janik, Vincent M. and Thompson, Paul M. and Hammond, Philip S.},
	month = jan,
	year = {2019},
	pages = {533--544},
	file = {Arso Civil et al. - 2019 - Variations in age- and sex-specific survival rates.PDF:/Users/mcsiple/Zotero/storage/RIGB6D9Q/Arso Civil et al. - 2019 - Variations in age- and sex-specific survival rates.PDF:application/pdf},
}

@article{olafsdottir_growth_2003,
	title = {Growth and reproduction in harbour porpoises (\textit{{Phocoena} phocoena}) in {Icelandic} waters},
	volume = {5},
	copyright = {Copyright (c) 2003 Droplaug Ólafsdóttir, Gísli A Víkingsson, Sverrir Daníel Halldórsson, Jóhann Sigurjónsson},
	issn = {2309-2491},
	url = {https://septentrio.uit.no/index.php/NAMMCOSP/article/view/2747},
	doi = {10.7557/3.2747},
	language = {en},
	urldate = {2019-07-13},
	journal = {NAMMCO Scientific Publications},
	author = {Ólafsdóttir, Droplaug and Víkingsson, Gísli A. and Halldórsson, Sverrir Daníel and Sigurjónsson, Jóhann},
	month = jul,
	year = {2003},
	keywords = {growth, reproduction, by-catch, harbour porpoises},
	pages = {195--210},
	file = {Full Text PDF:/Users/mcsiple/Zotero/storage/XW6Q9AKT/Ólafsdóttir et al. - 2003 - Growth and reproduction in harbour porpoises (iP.pdf:application/pdf;Snapshot:/Users/mcsiple/Zotero/storage/SYZ32AB3/2747.html:text/html},
}

@article{speakman_mark-recapture_2010,
	title = {Mark-recapture estimates of seasonal abundance and survivorship for bottlenose dolphins ({Tursiops} truncatus) near {Charleston}, {South} {Carolina}, {USA}},
	abstract = {The stock structure of western North Atlantic bottlenose dolphins (Tursiops truncatus) is complex, with seasonally migratory stocks often overlapping with year-round resident stocks. High rates of exchange between northernmost sites have been documented but movement and seasonal fluctuation in abundance among sites along the southern portion of the US Atlantic coast is not well understood. To better understand seasonal abundance, a three-year mark-recapture study of bottlenose dolphins in coastal and estuarine waters near Charleston, South Carolina, USA was conducted. A robust design was employed in order to minimise bias and more precisely determine seasonal estimates of abundance and concurrently examine temporary immigration/emigration and survivorship. Systematic boat-based surveys were carried out (n = 192) from January 2004 to December 2006. The entire study area was surveyed one week per month; an additional survey was conducted in the months in which seasonal abundance was estimated: January (winter), April (spring), July (summer) and October (autumn). Standard photo-identification techniques were used to accumulate sightings of 521 distinctively marked dolphins, 65\% of which were sighted more than once. Pollock’s robust design was applied using MARK and the ensuing abundance estimates were adjusted for the seasonal proportion of unmarked dolphins (ranging from 0.27 to 0.40) in the population. Estimates ranged from 364 (95\% CI = 305–442) in January 2004 to 910 (95\% CI = 819–1018) in October 2006. Summer abundance estimates were consistently greater than those from winter months, although estimates varied considerably among years. The same model was used to calculate an annual survival rate estimate of 0.951 (95\% CI = 0.882–1.00) for marked individuals within the population. A high degree of transience, demonstrated by seasonal influxes of single-sighted individuals, made it difficult to differentiate between mortality and permanent emigration. The results support the occurrence of three distinct dolphin groups found in Charleston waters: year-round residents; seasonal residents; and transients. Reporting abundance and survivorship estimates together is useful in explaining and validating results for populations in which transient individuals occur. These results provide important information for stock and viability assessment of coastal bottlenose dolphins in the western North Atlantic.},
	language = {en},
	author = {Speakman, Todd R and Lane, Suzanne M and Schwacke, Lori H and Fair, Patricia A and Zolman, Eric S},
	year = {2010},
	pages = {11},
	file = {Speakman et al. - 2010 - Mark-recapture estimates of seasonal abundance and.pdf:/Users/mcsiple/Zotero/storage/SSIBI4I2/Speakman et al. - 2010 - Mark-recapture estimates of seasonal abundance and.pdf:application/pdf},
}

@techreport{moore_unpublished_2019,
	title = {Unpublished estimates following the methods of {Dillingham} et al. 2016.},
	author = {Moore, J. E.},
	year = {2019},
}

@article{wade_best_2021,
	title = {Best {Practices} for {Assessing} and {Managing} {Bycatch} of {Marine} {Mammals}},
	volume = {8},
	issn = {2296-7745},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2021.757330},
	doi = {10.3389/fmars.2021.757330},
	abstract = {Bycatch in marine fisheries is the leading source of human-caused mortality for marine mammals, has contributed to substantial declines of many marine mammal populations and species, and the extinction of at least one. Schemes for evaluating marine mammal bycatch largely rely on estimates of abundance and bycatch, which are needed for calculating biological reference points and for determining conservation status. However, obtaining these estimates is resource intensive and takes careful long-term planning. The need for assessments of marine mammal bycatch in fisheries is expected to increase worldwide due to the recently implemented Import Provisions of the United States Marine Mammal Protection Act. Managers and other stakeholders need reliable, standardized methods for collecting data to estimate abundance and bycatch rates. In some cases, managers will be starting with little or no data and no system in place to collect data. We outline a comprehensive framework for managing bycatch of marine mammals. We describe and provide guidance on (1) planning for an assessment of bycatch, (2) collecting appropriate data (e.g., abundance and bycatch estimates), (3) assessing bycatch and calculating reference points, and (4) using the results of the assessment to guide marine mammal bycatch reduction. We also provide a brief overview of available mitigation techniques to reduce marine mammal bycatch in various fisheries. This paper provides information for scientists and resource managers in the hope that it will lead to new or improved programs for assessing marine mammal bycatch, establishing best practices, and enhancing marine mammal conservation globally.},
	urldate = {2022-01-07},
	journal = {Frontiers in Marine Science},
	author = {Wade, Paul R. and Long, Kristy J. and Francis, Tessa B. and Punt, André E. and Hammond, Philip S. and Heinemann, Dennis and Moore, Jeffrey E. and Reeves, Randall R. and Sepúlveda, Maritza and Sullaway, Genoa and Sigurðsson, Guðjón Már and Siple, Margaret C. and Víkingsson, Gísli A. and Williams, Rob and Zerbini, Alexandre N.},
	year = {2021},
	pages = {1566},
	file = {Full Text PDF:/Users/mcsiple/Zotero/storage/SWSCDJ4Q/Wade et al. - 2021 - Best Practices for Assessing and Managing Bycatch .pdf:application/pdf},
}

@article{moore_estimating_2021,
	title = {Estimating {Bycatch} {Mortality} for {Marine} {Mammals}: {Concepts} and {Best} {Practices}},
	volume = {8},
	issn = {2296-7745},
	shorttitle = {Estimating {Bycatch} {Mortality} for {Marine} {Mammals}},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2021.752356},
	doi = {10.3389/fmars.2021.752356},
	abstract = {Fisheries bycatch is the greatest current source of human-caused deaths of marine mammals worldwide, with severe impacts on the health and viability of many populations. Recent regulations enacted in the United States under the Fish and Fish Product Import Provisions of its Marine Mammal Protection Act require nations with fisheries exporting fish and fish products to the United States (hereafter, “export fisheries”) to have or establish marine mammal protection standards that are comparable in effectiveness to the standards for United States commercial fisheries. In many cases, this will require estimating marine mammal bycatch in those fisheries. Bycatch estimation is conceptually straightforward but can be difficult in practice, especially if resources (funding) are limiting or for fisheries consisting of many, small vessels with geographically-dispersed landing sites. This paper describes best practices for estimating bycatch mortality, which is an important ingredient of bycatch assessment and mitigation. We discuss a general bycatch estimator and how to obtain its requisite bycatch-rate and fisheries-effort data. Scientific observer programs provide the most robust bycatch estimates and consequently are discussed at length, including characteristics such as study design, data collection, statistical analysis, and common sources of estimation bias. We also discuss alternative approaches and data types, such as those based on self-reporting and electronic vessel-monitoring systems. This guide is intended to be useful to managers and scientists in countries having or establishing programs aimed at managing marine mammal bycatch, especially those conducting first-time assessments of fisheries impacts on marine mammal populations.},
	urldate = {2022-01-07},
	journal = {Frontiers in Marine Science},
	author = {Moore, Jeffrey E. and Heinemann, Dennis and Francis, Tessa B. and Hammond, Philip S. and Long, Kristy J. and Punt, André E. and Reeves, Randall R. and Sepúlveda, Maritza and Sigurðsson, Guðjón Már and Siple, Margaret C. and Víkingsson, Gísli A. and Wade, Paul R. and Williams, Rob and Zerbini, Alexandre N.},
	year = {2021},
	pages = {1793},
	file = {Full Text PDF:/Users/mcsiple/Zotero/storage/FA3URVTV/Moore et al. - 2021 - Estimating Bycatch Mortality for Marine Mammals C.pdf:application/pdf},
}

@article{hammond_estimating_2021,
	title = {Estimating the {Abundance} of {Marine} {Mammal} {Populations}},
	volume = {8},
	issn = {2296-7745},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2021.735770},
	doi = {10.3389/fmars.2021.735770},
	abstract = {Motivated by the need to estimate the abundance of marine mammal populations to inform conservation assessments, especially relating to fishery bycatch, this paper provides background on abundance estimation and reviews the various methods available for pinnipeds, cetaceans and sirenians. We first give an “entry-level” introduction to abundance estimation, including fundamental concepts and the importance of recognizing sources of bias and obtaining a measure of precision. Each of the primary methods available to estimate abundance of marine mammals is then described, including data collection and analysis, common challenges in implementation, and the assumptions made, violation of which can lead to bias. The main method for estimating pinniped abundance is extrapolation of counts of animals (pups or all-ages) on land or ice to the whole population. Cetacean and sirenian abundance is primarily estimated from transect surveys conducted from ships, small boats or aircraft. If individuals of a species can be recognized from natural markings, mark-recapture analysis of photo-identification data can be used to estimate the number of animals using the study area. Throughout, we cite example studies that illustrate the methods described. To estimate the abundance of a marine mammal population, key issues include: defining the population to be estimated, considering candidate methods based on strengths and weaknesses in relation to a range of logistical and practical issues, being aware of the resources required to collect and analyze the data, and understanding the assumptions made. We conclude with a discussion of some practical issues, given the various challenges that arise during implementation.},
	urldate = {2021-11-01},
	journal = {Frontiers in Marine Science},
	author = {Hammond, Philip S. and Francis, Tessa B. and Heinemann, Dennis and Long, Kristy J. and Moore, Jeffrey E. and Punt, André E. and Reeves, Randall R. and Sepúlveda, Maritza and Sigurðsson, Guðjón Már and Siple, Margaret C. and Víkingsson, Gísli and Wade, Paul R. and Williams, Rob and Zerbini, Alexandre N.},
	year = {2021},
	pages = {1316},
	file = {Full Text PDF:/Users/mcsiple/Zotero/storage/CGXWUKSW/Hammond et al. - 2021 - Estimating the Abundance of Marine Mammal Populati.pdf:application/pdf},
}

@Manual{r2021,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2021},
    url = {https://www.R-project.org/},
}

@Manual{shiny2021,
    title = {shiny: Web Application Framework for {R}},
    author = {Winston Chang and Joe Cheng and JJ Allaire and Carson Sievert and Barret Schloerke and Yihui Xie and Jeff Allen and Jonathan McPherson and Alan Dipert and Barbara Borges},
    year = {2021},
    note = {R package version 1.7.1},
    url = {https://CRAN.R-project.org/package=shiny},
}