Jeffrey E. Moore

National Oceanic and Atmospheric Administration | NOAA · Southwest Fisheries Science Center

In the northeastern Pacific, sightings of small numbers of killer whales (Orcinus orca) of unknown ecotype have been sporadically reported during open ocean marine mammal surveys, pelagic birding expeditions, and high seas fishing operations (Pitman et al., 2001; Pitman & Dutton, 2004; Forney & Wade, 2006; Dahlheim et al., 2008; McInnes et al., 202...

This publication, in conjunction with our 2021 published technical memorandum, Transient Killer Whales of Central and Northern California and Oregon: a Catalog of Photo-identified Individuals, provides additional user friendly natural history information on the ecology of transient killer whales in Monterey Bay and surrounding California waters. In...

A twelve-year hiatus in fishery-independent marine mammal surveys in the eastern tropical Pacific Ocean (ETP), combined with a mandate to monitor dolphin stock status under international agreements and the need for reliable stock status information to set dolphin bycatch limits in the tuna purse-seine fishery, has renewed debate about how best to a...

This tool provides a way for managers and other stakeholders to explore bycatch scenarios, based on simple information about marine mammal life history and rough estimates of abundance and bycatch. The tool consists of an R package (R Core Team, 2021) and a Shiny application (Chang et al., 2021). The primary machinery in the package is an age-struc...

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...

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 b...

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 est...

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 off...

Acoustic point-transect distance-sampling surveys have recently been used to estimate the density of beaked whales. Typically, the fraction of short time “snapshots” with detected beaked whales is used in this calculation. Beaked whale echolocation pulses are only intermittently available, which may affect the best choice of snapshot length. The ef...

The effects of human-caused mortality, such as fisheries bycatch, of endangered, threatened and protected (ETP) species of marine mammals can be evaluated using population model-based stock assessments. The information available to conduct such assessments is often very limited. Available data might include fragmented time-series of abundance estim...

The Indo-Pacific finless porpoise (Neophocaena phocaenoides) occurs year-round in waters of southern and eastern Hong Kong. The population biology of the population was studied in the late 1990s and early 2000s, but has not been examined recently. There are several threats facing the animals, and there has been recent concern about this species’ st...

The west coast (WC) transient killer whale (Orcinus orca) sub-population range throughout the inland waterways of Washington, British Columbia, and Southeast Alaska; as a result these whales have been extensively studied. Transient killer whales encountered off the Central Coast of California were once considered part of the WC sub-population, but...

Pacific leatherback turtles (Dermochelys coriacea) are critically endangered, and declines have been documented at multiple nesting sites throughout the Pacific. The western Pacific leatherback forages in temperate and tropical waters of the Indo-Pacific region, and about 38–57% of summer-nesting females from the largest remaining nesting populatio...

Harbor porpoises, Phocoena phocoena, off California, comprise four recognized population stocks: Morro Bay (MOR), Monterey Bay (MRY), San Francisco‐Russian River (SFRR), and Northern California‐Southern Oregon (NCSO). The three southernmost stocks experienced substantial bycatch in gill net fisheries during the 1970s and 1980s. While the SFRR stock...

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...

The potential biological removal (PBR) formula used to determine a reference point for human-caused mortality of marine mammals in the United States has been shown to be robust to several sources of uncertainty. This study investigates the consequences of the quality of monitoring on PBR performance. It also explores stochastic and demographic unce...

The potential biological removal (PBR) formula used to determine a reference point for human-caused mortality of marine mammals in the United States has been shown to be robust to several sources of uncertainty. This study investigates the consequences of the quality of monitoring on PBR performance. It also explores stochastic and demographic unce...

Beaked whales (family Ziphiidae), sperm whales (Physter macrocephalus), and dwarf and pygmy sperm whales (genus Kogia) are difficult to survey visually due to their long dives. In order to improve density estimates and habitat models for these species, acoustic recordings were collected from drifting buoys during a dedicated cetacean survey off the...

In the California Current off the United States West Coast, there are three offshore cetacean species that produce narrow-band high frequency (NBHF) echolocation pulses: Dall's porpoise (Phocoenoides dalli) and two species of Kogia. NBHF pulses exist in a highly specialized acoustic niche thought to be outside the hearing range of killer whales and...

A management strategy evaluation (MSE) is used to estimate success at achieving conservation goals for marine mammals while also aiming to minimize impacts on commercial fisheries. It is intended to improve understanding of US import rules that require countries exporting fish and fish products to the USA to adhere to marine mammal bycatch standard...

The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis), has experienced rapid declines in recent decades. We estimate its abundance based on surveys conducted between November and December 2017 in the main-stem of the Yangtze River and adjacent Poyang and Dongting Lakes. We compare these to published abundance estimates from 200...

The vaquita (Phocoena sinus) is a small porpoise endemic to Mexico. It is listed by IUCN as Critically Endangered because of unsustainable levels of bycatch in gillnets. The population has been monitored with passive acoustic detectors every summer from 2011 to 2018; here we report results for 2017 and 2018. We combine the acoustic trends with an i...

The vaquita is a critically endangered species of porpoise. It produces echolocation clicks, making it a good candidate for passive acoustic monitoring. A systematic grid of sensors has been deployed for 3 months annually since 2011; results from 2016 are reported here. Statistical models (to compensate for non-uniform data loss) show an overall de...

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 pe...

Small cetaceans (dolphins and porpoises) face serious anthropogenic threats in coastal habitats. These include bycatch in fisheries; exposure to noise, plastic and chemical pollution; disturbance from boaters; and climate change. Generating reliable abundance estimates is essential to assess sustainability of bycatch in fishing gear or any other fo...

The number of Mexico's endemic porpoise, the vaquita (Phocoena sinus), is collapsing primarily due to bycatch in illegal gillnets set for totoaba (Totoaba macdonaldi), an endangered fish whose swim bladders are exported to China. Previous research estimated that vaquitas declined from about 567 to 245 individuals between 1997 and 2008. Acoustic mon...

The vaquita (Phocoena sinus) is the world's most endangered marine mammal with ≈245 individuals remaining in 2008. This species of porpoise is endemic to the northern Gulf of California, Mexico, and has historically suffered population declines from unsustainable bycatch in gillnets. An illegal gillnet fishery for an endangered fish, the totoaba (T...

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 de...

Biological limit reference points (LRPs) for fisheries catch represent upper bounds that avoid undesirable population states. LRPs can support consistent management evaluation among species and regions, and can advance ecosystem-based fisheries management. For transboundary species, LRPs prorated by local abundance can inform local management decis...

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 d...

To address growing concern over the effects of fisheries non-target catch on elasmobranchs worldwide, the accurate reporting of elasmobranch catch is essential. This requires data on a combination of measures, including reported landings, retained and discarded non-target catch, and post-discard survival. Identification of the factors influencing d...

To address growing concern over the effects of fisheries non-target catch on elasmobranchs worldwide, the accurate reporting of elasmobranch catch is essential. This requires data on a combination of measures, including reported landings, retained and discarded non-target catch, and post-discard survival. Identification of the factors influencing d...

Population abundance and trends are informative metrics for assessing population status and basing management decisions, but it can be challenging to estimate these metrics for species that are difficult to detect. We used a Bayesian hierarchical approach to improve estimates of abundance and trends for sperm whales Physeter macrocephalus in the Ca...

Fisheries bycatch is a global threat to marine megafauna. Environmental laws require bycatch assessment for protected species, but this is difficult when bycatch is rare. Low bycatch rates, combined with low observer coverage, may lead to biased, imprecise estimates when using standard ratio estimators. Bayesian model-based approaches incorporate u...

Significance Loss of megafauna, termed trophic downgrading, has been found to affect biotic interactions, disturbance regimes, species invasions, and nutrient cycling. One recognized cause in air-breathing marine megafauna is incidental capture or bycatch by fisheries. Characterizing megafauna bycatch patterns across large ocean regions is limited...

Fisheries bycatch threatens populations of marine megafauna such as marine mammals, turtles, seabirds, sharks and rays, but fisheries impacts on non-target populations are often difficult to assess due to factors such as data limitation, poorly defined management objectives and lack of quantitative bycatch reduction targets. Limit reference points...

Reference points can help implement an ecosystem approach to fisheries management (EAF), by establishing precautionary removal limits for nontarget species and target species of ecological importance. PBR (Potential Biological Removal), developed under the U.S. Marine Mammal Protection Act (MMPA), is a limit for direct mortality for marine mammals,...

Human‐caused mortality threatens many marine turtle populations worldwide, with fisheries interactions being a primary cause for population declines. National and international management of fisheries interactions with marine turtles are rarely tied to turtle population biology. Quantitative tools tied to population‐based objectives can provide ins...

Local ecological knowledge constitutes a potentially useful source of information for conservation, but the quality, limitations and biases of this body of knowledge remain largely untested. The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) is a highly threatened freshwater cetacean found in one of the world’s most densely...

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...

Data sources for beaked whale stranding records from Alaska, British Columbia, Washington, Oregon, and California. Records in table indicate number of individual animals. These were reduced to the number of unique events (i.e., a group of animals = 1 event) for analysis in main paper (DOC)

Final abundance estimates (Bayesian posterior summaries) for Cuvier's beaked whale (Ziphius cavirostris) in the California Current study area. Estimates include pro-rated allocation of unidentified beaked whales to this species. (DOC)

Final abundance estimates (Bayesian posterior summaries) for Mesoplodon beaked whales in the California Current study area. Estimates include pro-rated allocation of unidentified beaked whales to this species group. (DOC)

Final abundance estimates (Bayesian posterior summaries) for Baird's beaked whales ( Berardius bairdii ) in the California Current study area. (DOC)

1. Estimating temporal trends in animal abundance is central to ecology and conservation, but obtaining useful trend estimates is challenging when animal detection rates vary across surveys (e.g. because of differences in observers or conditions). Methods exist for obtaining abundance estimates using capture–recapture and distance sampling protocol...

a b s t r a c t Sea turtles interact with a variety of fishing gears across their broad geographic distributions and onto-genetic habitat shifts. Cumulative assessments of multi-gear bycatch impacts on sea turtle populations are critical for coherent fisheries bycatch management, but such estimates are difficult to achieve, due to low fisheries obs...

Minimizing fisheries bycatch, the incidental capture of non-target species, is a global environmental challenge. In many regions, bycatch of imperiled species is one of a number of issues that threatens species viability and impedes the development of sustainable fisheries. effectively addressing bycatch of species of conservation concern and impro...

Fisheries bycatch is a recognized threat to marine megafauna. Addressing bycatch of pelagic species however is challenging owing to the dynamic nature of marine environments and vagility of these organisms. In order to assess the potential for species to overlap with fisheries, we propose applying dynamic habitat models to determine relative probab...

Recent case studies have highlighted high bycatch mortality of sea turtles and marine mammals in arti-sanal fisheries, but in most countries there are few data on artisanal fishing effort, catch, or bycatch. With artisanal fisheries comprising >95% of the world's fishermen, this knowledge gap presents a major chal-lenge to threatened species conser...

The Union of the Comoros is host to internationally-significant populations of sea turtles, dugongs and cetaceans, all of which are potentially threatened by incidental catch in artisanal fishing gears. This work presented here was part of a larger initiative, known as Project GloBAL (Global Bycatch Assessment of Long-lived species), to evaluate ar...

Widespread conversion of deciduous forests to agriculture in the midwestern United States has resulted in landscapes whose remaining native habitats are highly fragmented, with well-documented consequences for wildlife community structure. We analyzed trap data for 5 forest rodent species from 525 sites in 35 study landscapes throughout the upper W...

We analyzed capture-mark-recapture (CMR) data from 1,061 Black Brant (Branta bernicla nigricans) using Humboldt Bay, California, during northward migration (Jan–May), 2000–2001. We estimated immigration and emigration rates, and calculated stopover duration (length of stay), volume (total number of birds using the Bay), and chronology (time frame o...

This paper reviews the available information (observer programs, estimates, statutes, regulations) for bycatch of marine mammals, sea turtles, and seabirds in fisheries of the United States. Goals of the review were to evaluate the state of knowledge of bycatch and the role of existing protective legislation in shaping bycatch management for differ...

Fire has been the dominant disturbance in boreal America since the Pleistocene, resulting in a spatial mosaic in which the most fire occurs in the continental northwest. Spatial variation in snowshoe hare (Lepus americanus) density reflects the fire mosaic. Because fire initiates secondary forest succession, a fire mosaic creates variation in the a...

For point-count data to reliably index bird abundance or density, estimates must be corrected for variation in detection probabilities across species, observers, and environmental conditions. Removal and double-observer modeling are two recently developed statistical techniques for estimating detection probabilities and bird abundance. We collected...

We assessed dietary preference of 14 captive Blue Jays (Cyanocitta cristata) for different food types under different conditions of availability. In four separate feeding trials, we provisioned jays with the following: Trial 1, two nuts each of white oak (Quercus alba), pin oak (Q. palustris), black oak (Q. velutina), northern red oak (Q. rubra), a...

Arctic-nesting geese depend on nutrients acquired during spring migration for reproduction, and thus should attempt to maximize nutrient intake while on staging areas. We investigated site use of Black Brant (Branta bernicla nigricans) at an important staging location—Humboldt Bay, California—to determine whether birds selected the most profitable...

Wildlife ecologists and managers are challenged to make the most of sparse information for understanding demography of many species, especially those that are long lived and difficult to observe. For many odontocete (dolphin, porpoise, toothed whale) populations, only fertility and age-at-death data are feasibly obtainable. We describe a Bayesian a...

S.B. Vander Wall et al. (Ecology, 86:801806 (2005)) criticized seed dispersal studies that use seed removal as a proxy for seed predation, because secondary dispersal processes following removal are important to seed fates for many plants. We compared seed removal rates with direct estimates of seed mortality and another mortality index, based on a...

Adapting state-space models (SSMs) to telemetry data has been helpful for dealing with location error and for modeling animal movements. We used a combination of two hierarchical Bayesian SSMs to estimate movement pathways from Argos satellite-tag data for 15 juvenile loggerhead turtles (Caretta caretta) in the western Mediterranean Sea, and to pro...

In fragmented landscapes, the likelihood that a species occupies a particular habitat patch is thought to be a function of both patch area and patch isolation. Ecologically scaled landscape indices (ESLIs) combine a species’ ecological profile, i.e., area requirements and dispersal ability, with indices of patch area and connectivity. Since their i...