ECOLOGY: Enhanced: North Atlantic Right Whales in Crisis

Unseen overlap between fishing vessels and top predators in the northeast Pacific

Accurate assessments of human-wildlife risk associated with industrial fishing are critical for the conservation of marine top predators. Automatic Identification System (AIS) data provide a means of mapping fishing and estimating human-wildlife risk; however, risk can be obscured by gaps in the AIS record due to technical issues and intentional disabling. We assessed the extent to which unseen fishing vessel activity due to AIS gaps obscured estimates of overlap between fishing vessel activity and 14 marine predators including sharks, tunas, mammals, seabirds, and critically endangered leatherback turtles. Among vessels equipped with AIS in the northeast Pacific, up to 24% of total predator overlap with fishing vessel activity was unseen, and up to 36% was unseen for some individual species. Waters near 10°N had high unseen overlap with sharks yet low reported shark catch, revealing potential discrepancies in self-reported datasets. Accounting for unseen fishing vessel activity illuminates hidden human-wildlife risk, demonstrating challenges and solutions for transparent and sustainable marine fisheries.

Mitochondrial Genomes Assembled from Non-Invasive eDNA Metagenomic Scat Samples in Critically Endangered Mammals

The abundance of many large-bodied vertebrates, both in marine and terrestrial environments, has declined substantially due to global and regional climate stressors that define the Anthropocene. The development of genetic tools that can serve to monitor population’s health non-intrusively and inform strategies for the recovery of these species is crucial. In this study, we formally evaluate whether whole mitochondrial genomes can be assembled from environmental DNA (eDNA) metagenomics scat samples. Mitogenomes of four different large vertebrates, the panda bear (Ailuropoda melanoleuca), the moon bear (Ursus thibetanus), the Java pangolin (Manis javanica), and the the North Atlantic right whale (Eubalaena glacialis) were assembled and circularized using the pipeline GetOrganelle with a coverage ranging from 12x to 480x in 14 out of 18 different eDNA samples. Partial mitochondrial genomes were retrieved from three other eDNA samples. The complete mitochondrial genomes of the studied species were AT-rich and comprised 13 protein coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a putative D-loop/control region. Synteny observed in all assembled mitogenomes was identical to that reported for specimens of the same and other closely related species. This study demonstrates that it is possible to assemble accurate whole mitochondrial chromosomes from eDNA samples (scats) using forthright bench and bioinformatics workflows. The retrieval of mitochondrial genomes from eDNA samples represents a tool to support bioprospecting, bio-monitoring, and other non-intrusive conservation strategies in species considered ‘vulnerable’, ‘endangered’, and/or ‘critically endangered’ by the IUCN Red List of Threatened Species.

Global collision-risk hotspots of marine traffic and the world's largest fish, the whale shark

Marine traffic is increasing globally yet collisions with endangered megafauna such as whales, sea turtles, and planktivorous sharks go largely undetected or unreported. Collisions leading to mortality can have population-level consequences for endangered species. Hence, identifying simultaneous space use of megafauna and shipping throughout ranges may reveal as-yet-unknown spatial targets requiring conservation. However, global studies tracking megafauna and shipping occurrences are lacking. Here we combine satellite-tracked movements of the whale shark, Rhincodon typus, and vessel activity to show that 92% of sharks’ horizontal space use and nearly 50% of vertical space use overlap with persistent large vessel (>300 gross tons) traffic. Collision-risk estimates correlated with reported whale shark mortality from ship strikes, indicating higher mortality in areas with greatest overlap. Hotspots of potential collision risk were evident in all major oceans, predominantly from overlap with cargo and tanker vessels, and were concentrated in gulf regions, where dense traffic co-occurred with seasonal shark movements. Nearly a third of whale shark hotspots overlapped with the highest collision-risk areas, with the last known locations of tracked sharks coinciding with busier shipping routes more often than expected. Depth-recording tags provided evidence for sinking, likely dead, whale sharks, suggesting substantial “cryptic” lethal ship strikes are possible, which could explain why whale shark population declines continue despite international protection and low fishing-induced mortality. Mitigation measures to reduce ship-strike risk should be considered to conserve this species and other ocean giants that are likely experiencing similar impacts from growing global vessel traffic.

Genomic impact of whaling in North Atlantic fin whales

It is generally recognized that large-scale whaling in the 19th and 20th century led to a substantial reduction of the size of many cetacean populations, particularly those of the baleen whales (Mysticeti). The impact of these operations on genomic diversity of one of the most hunted whales, the fin whale (Balaenoptera physalus), has remained largely unaddressed because of the paucity of adequate samples and the limitation of applicable techniques. Here, we have examined the effect of whaling on the North Atlantic fin whale based on genomes of 51 individuals from Icelandic waters, representing three temporally separated intervals, 1989, 2009 and 2018 and provide a reference genome for the species. Demographic models suggest a noticeable drop of the effective population size of the North Atlantic fin whale around a century ago. The present results suggest that the genome-wide heterozygosity is not markedly reduced and has remained comparable with other baleen whale species. Similarly, there are no signs of apparent inbreeding, as measured by the proportion of long runs of homozygosity, or of a distinctively increased mutational load, as measured by the amount of putative deleterious mutations. Compared with other baleen whales, the North Atlantic fin whale appears to be less affected by anthropogenic influences than other whales such as the North Atlantic right whale, consistent with the presence of long runs of homozygosity and higher levels of mutational load in an otherwise more heterozygous genome. Thus, genome-wide assessments of other species and populations are essential for future, more specific, conservation efforts.

Dive behavior of North Atlantic right whales on the calving ground in the Southeast USA: implications for conservation

The North Atlantic right whale Eubalaena glacialis is a Critically Endangered whale whose habitat overlaps with areas of high human use. On feeding grounds, aspects of its behavior increase the vulnerability of this species to anthropogenic threats such as entanglement in fishing gear and vessel strikes. On the calving ground, natural dive behavior and the implications for conservation efforts in this species remain to be evaluated. In this study, we used 102.17 h of tag data collected over 15 deployments of archival tags on 14 individuals to describe the dive behavior of right whales in the Southeast USA. Lactating females spent up to 80% of the time at depths ≤3.5 m, leading to increased risk of vessel strike compared to other whale groups that spent a maximum of 30% of the time at those depths in this habitat. Non-lactating whales had significantly deeper maximum dive depths (12.1 m) than lactating females (7.3 m) and spent more time in the bottom phase of dives, closer to the sea floor (45 vs. 37% of the dive duration, respectively). Time spent closer to the sea floor increases the probability of interaction with fishing gear. Therefore, these dive data are useful to justify seasonal closures of fishing activity on the calving ground to protect both lactating and non-lactating whales. Opportunistic comparisons revealed that diel period, calf presence and calf age affect dive behavior of female right whales. In the face of the impacts of anthropogenic mortality on right whale populations, these results will aid vessel strike and entanglement risk assessment on the Southeast USA calving ground.

Natural Entrapments of Killer Whales (Orcinus orca): A Review of Cases and Assessment of Intervention Techniques

Identifying mortality sources and mitigation solutions is crucial in species management and conservation. In killer whales (Orcinus orca), mortality events may pose a serious concern for the conservation of small discrete populations, especially if they involve entire groups. This study investigated 19 incidents involving 116 killer whales from a minimum of five populations becoming naturally entrapped in inshore areas of the North Pacific (n = 12) and North Atlantic (n = 7) oceans between 1949 and 2019. Here, we aim to provide an assessment of possible causal factors, lethality and human responses to these events. Site characteristics and group size identified three categories of entrapments. In Category 1, nine cases involved small groups of killer whales (median = 5, range: 1–9) at sites characterized by severe geographic and food constraints. Four cases in Category 2 included larger groups (median= 14, range: 6–19) and entrapment sites with no obvious geographic constraints but at which man-made structures could have acted as deterrents. Five cases assigned to Category 3 involved lone, often young individuals settling in a restricted home range and engaging in interactions with people and boats. Overall, all or some of the killer whales swam out on their own after a mean of 36 d of entrapment (range: 1–172, SD = 51, n = 9 cases), died of nutritional/physiological stress after 58 d (range: 42–90, SD = 21, n = 3 cases) or of injury after ~5 years of daily interactions with boat traffic (n = 1 case). Indication of the killer whales' declining condition or being at risk of injury, and of poor habitat quality, led to the decision to intervene in seven cases where a variety of methods were used to guide or relocate remaining individuals back to open waters after 39 d (SD = 51, range = 8–150). Monitoring protocols, which aided in identifying entrapment situations, and intervention methods which enhanced the health and survival of entrapped killer whales, are discussed.

Trends in Propeller Strike-Induced Mortality in Harbor Seals (Phoca vitulina) of the Salish Sea

Documenting human impacts on marine mammals is critical for understanding and mitigating harm. Although propeller strike injuries in small marine mammals are often debilitating and fatal, little is known about the occurrence or demographics of these types of injuries in pinniped populations. Using data of stranded harbor seals (Phoca vitulina) in the Salish Sea from 2002-19, we identified 27 cases of fatal propeller strikes. Weaned pups were the most frequently affected (64% of cases) with a much higher rate of propeller strikes than expected for the age class. Although they do represent animal welfare concerns, harbor seals in the Salish Sea probably are not threatened by these types of injuries at the population level; nevertheless, propeller strike cases increased significantly over the time of this study period, indicating increased interactions between boats and seals in the region. Continued monitoring and increased efforts to consistently quantify vessel traffic in the area are recommended to create and monitor long-term effectiveness of mitigation measures.

Co-occurrence of gray whales and vessel traffic in the North Pacific Ocean

All species of large whales are susceptible to vessel strikes, but the true scale and geographical extent of such strikes is not known. This paper provides a qualitative assessment of the range-wide risks posed to gray whales Eschrichtius robustus by vessels, by comparing patterns of whale distribution with the density of vessel traffic seasonally throughout the North Pacific in 2019. Areas of very high vessel density were evident year-round near many coastlines, along inter-continental trade routes, and at hubs of commercial shipping near port entrances. Gray whales were exposed to vessel strikes throughout their range and in their feeding, southbound migration, wintering, and northbound migration periods. Areas of apparently high risk were in the Russian Far East (Kamchatka peninsula and Okhotsk Sea), Bering Sea (including the Aleutian Islands), Gulf of Alaska, and along the entire west coast of North America. Risk appeared greatest during south- and northbound migration when much of the gray whale population is moving through waters near shore. Tanker, container, and bulk-carrier ships represent considerable risk to whales in the North Pacific Ocean, but the large geographical extent of commercial fishing activities suggests that fisheries are also a substantial source of risk. Vessel-strike risk maps indicate the relative extent of exposure of gray (and other) whales to underwater vessel noise. The number of gray whales killed by ship strikes each year may be in the tens, or perhaps the low hundreds. Additional analyses, including quantitative assessments, are warranted to further clarify the risk of vessel strikes to gray whales.

Up in the air: drone images reveal underestimation of entanglement rates in large rorqual whales

Entanglement in fishing gear is a significant threat to many cetaceans. For the 2 largest species, the blue whale Balaenoptera musculus and the fin whale B. physalus, reports of entangled individuals are rare, leading to the assumption that entanglements are not common. Studies of interaction with fisheries in other species often rely on the presence of scars from previous entanglements. Here, scar detection rates were first examined in humpback Megaptera novaeangliae, fin and blue whales using standard vessel-based photo-identification photographs collected between 2009 and 2016 in the Gulf of St. Lawrence, Canada. We then examined aerial images of fin whales collected with a drone in 2018 and 2019 and compared both methods. Entanglement rates were 6.5% for fin and 13.1% for blue whales using photo-identification images of individuals. Prominent scarring was observed around the tail and caudal peduncle, visible only when animals lifted those body sections above water when diving. For the small subset of pictures which captured the entire caudal peduncle, entanglement rates ranged between 60% for blue and 80% for fin whales. This result was similar to the 85% entanglement rate estimated in humpback whales. The assessment of aerial-based photography yielded an entanglement rate of 44.1 to 54.7% in fin whales. Scars were always around the peduncle, often the tail, rarely the dorsal fin and never around the pectoral fins, while the mouth cannot be examined from above. Thus, in species that do not regularly expose their tail or peduncle, aerial imagery is the preferred method to quantify entanglement rates by assessment of scars.

Fluctuations in Hawaii’s humpback whale Megaptera novaeangliae population inferred from male song chorusing off Maui

Approximately half of the North Pacific humpback whale Megaptera novaeangliae stock visits the shallow waters of the main Hawaiian Islands seasonally. Within this breeding area, mature males produce an elaborate acoustic display known as song, which becomes the dominant source of ambient underwater sound between December and April. Following reports of unusually low whale numbers that began in 2015/16, we examined song chorusing recorded through long-term passive acoustic monitoring at 6 sites off Maui as a proxy for relative whale abundance between 2014 and 2019. Daily root-mean-square sound pressure levels (RMS SPLs) were calculated to compare variations in low-frequency acoustic energy (0-1.5 kHz). After 2014/15, the overall RMS SPLs decreased between 5.6 and 9.7 dB re 1 µPa2 during the peak of whale season (February and March), reducing ambient acoustic energy from chorusing by over 50%. This change in song levels co-occurred with a broad-scale oceanic heat wave in the northeast Pacific termed the ‘Blob,’ a major El Niño event in the North Pacific, and a warming period in the Pacific Decadal Oscillation cycle. Although it remains unclear whether our observations reflect a decrease in population size, a change in migration patterns, a shift in distribution to other areas, a change in the behavior of males, or some combination of these, our results indicate that continued monitoring and further studies of humpback whales throughout the North Pacific are warranted to better understand the fluctuations occurring in this recently recovered population and other populations that continue to be endangered or threatened.

A mini ROV-based method for recovering marine instruments at depth

Instruments are often deployed at depth for weeks to years for a variety of marine applications. In many cases, divers can be deployed to retrieve instruments, but divers are constrained by depth limitations and safety concerns. Acoustic release technology can also be employed but can add considerable expense and acoustic releases will at times fail. Here, we report a simple method that utilizes a commercially available mooring hook integrated with a mini remotely operated vehicle to attach lines to instruments deployed on the sea floor, which can then be winched to the surface. The mooring hook apparatus was tested in a pool setting and then used to retrieve acoustic telemetry receiver bases (50 kg) or fish traps (30-50 kg) from the northern Gulf of Mexico continental shelf at depths between 28 and 80 m. During 2013-2019, 539 retrievals (100% success rate) were made of receiver bases (n = 239) and traps (n = 300) on 30 sea days using this approach. This method could easily be applied to other types of instruments, or recovery and salvage of objects that are too deep for standard diving operations.

Phenological changes in North Atlantic right whale habitat use in Massachusetts Bay

The North Atlantic right whale (Eubalaena glacialis) is one of the world's most highly endangered baleen whales, with approximately 400-450 individuals remaining. Massachusetts Bay (MB) and Cape Cod Bay (CCB) together comprise one of seven areas in the Gulf of Maine where right whales seasonally congregate. Here, we report on acoustically detected presence of right whales in MB over a nearly 6 year period, July 2007-April 2013, a time of both rapid ocean warming throughout the Gulf of Maine and apparent changes in right whale migratory dynamics. We applied an automated detection algorithm to assess hourly presence of right whale "up-calls" in recordings from a 19-channel acoustic array covering approximately 4,000 km² in MB. Over the survey, up-calls were detected in 95% of 8 day periods. In each year, as expected, we observed a "peak season" of elevated up-call detections in late winter and early spring corresponding to the season when right whales congregate to feed in CCB. However, we also saw an increase in right whale occurrence during time periods thought to be part of the "off-season." With the exception of 2009-2010, when acoustic presence was unusually low, the mean percent of hours in which up-calls were detected increased every year, both during the peak season (from 38% in 2008 to 70% in 2012), and during the summer-fall season (from 2% in 2007 to 13% in 2012). Over the entire study, the peak season start date varied between 17 January and 26 February. Changes in right whale phenology in MB likely reflect broadscale changes in habitat use in other areas within the species range. This study demonstrates the value of continuous long-term survey datasets to detect and quantify shifts in cetacean habitat use as environmental conditions change and the long-term continued survival of right whales remains uncertain.

Deep neural networks for automated detection of marine mammal species

Deep neural networks have advanced the field of detection and classification and allowed for effective identification of signals in challenging data sets. Numerous time-critical conservation needs may benefit from these methods. We developed and empirically studied a variety of deep neural networks to detect the vocalizations of endangered North Atlantic right whales (Eubalaena glacialis). We compared the performance of these deep architectures to that of traditional detection algorithms for the primary vocalization produced by this species, the upcall. We show that deep-learning architectures are capable of producing false-positive rates that are orders of magnitude lower than alternative algorithms while substantially increasing the ability to detect calls. We demonstrate that a deep neural network trained with recordings from a single geographic region recorded over a span of days is capable of generalizing well to data from multiple years and across the species’ range, and that the low false positives make the output of the algorithm amenable to quality control for verification. The deep neural networks we developed are relatively easy to implement with existing software, and may provide new insights applicable to the conservation of endangered species.

A review on the environmental impacts of shipping on aquatic and nearshore ecosystems

There are several environmental and ecological effects of shipping. However, these are rarely assessed in total in the scientific literature. Thus, the aim of this study was to summarize the different impacts of water-based transport on aquatic and nearshore ecosystems and to identify knowledge gaps and areas for future research. The review identified several environmental and ecological consequences within the main impact categories of water discharges, physical impacts, and air emissions. However, although quantitative data on these consequences are generally scarce the shipping contribution to acidification by SO_x- and NO_x-emissions has been quantified to some extent. There are several knowledge gaps regarding the ecological consequences of, for example, the increasing amount of chemicals transported on water, the spread of non-indigenous species coupled with climate change, and physical impacts such as shipping noise and artificial light. The whole plethora of environmental consequences, as well as potential synergistic effects, should be seriously considered in transport planning.

Long-term isolation at a low effective population size greatly reduced genetic diversity in Gulf of California fin whales

The Gulf of California, Mexico is home to many cetacean species, including a presumed resident population of fin whales, Balaenoptera physalus. Past studies reported very low levels of genetic diversity among Gulf of California fin whales and a significant level of genetic differentiation from con-specifics in the eastern North Pacific. The aim of the present study was to assess the degree and timing of the isolation of Gulf of California fin whales in a population genetic analysis of 18 nuclear microsatellite genotypes from 402 samples and 565 mitochondrial control region DNA sequences (including mitochondrial sequences retrieved from NCBI). The analyses revealed that the Gulf of California fin whale population was founded ~2.3 thousand years ago and has since remained at a low effective population size (~360) and isolated from the eastern North Pacific (N_em between 0.89-1.4). The low effective population size and high degree of isolation implied that Gulf of California fin whales are vulnerable to the negative effects of genetic drift, human-caused mortality and habitat change.

Gross and histopathologic diagnoses from North Atlantic right whale Eubalaena glacialis mortalities between 2003 and 2018

Seventy mortalities of North Atlantic right whales Eubalaena glacialis (NARW) were documented between 2003 and 2018 from Florida, USA, to the Gulf of St. Lawrence, Canada. These included 29 adults, 14 juveniles, 10 calves, and 17 of unknown age class. Females represented 65.5% (19/29) of known-sex adults. Fourteen cases had photos only; 56 carcasses received external examinations, 44 of which were also necropsied. Cause of death was determined in 43 cases, of which 38 (88.4%) were due to anthropogenic trauma: 22 (57.9%) from entanglement, and 16 (42.1%) from vessel strike. Gross and histopathologic lesions associated with entanglement were often severe and included deep lacerations caused by constricting line wraps around the flippers, flukes, and head/mouth; baleen plate mutilation; chronic extensive bone lesions from impinging line, and traumatic scoliosis resulting in compromised mobility in a calf. Chronically entangled whales were often in poor body condition and had increased cyamid burden, reflecting compromised health. Vessel strike blunt force injuries included skull and vertebral fractures, blubber and muscle contusions, and large blood clots. Propeller-induced wounds often caused extensive damage to blubber, muscle, viscera, and bone. Overall prevalence of NARW entanglement mortalities increased from 21% (1970-2002) to 51% during this study period. This demonstrates that despite mitigation efforts, entanglements and vessel strikes continue to inflict profound physical trauma and suffering on individual NARWs. These cumulative mortalities are also unsustainable at the population level, so urgent and aggressive intervention is needed to end anthropogenic mortality in this critically endangered species.

Oil adsorption does not structurally or functionally alter whale baleen

Mysticete whales filter small prey from seawater using baleen, a unique keratinous oral tissue that grows from the palate, from which it hangs in hundreds of serial plates. Laboratory experiments testing effects of oils on material strength and flexibility, particle capture and tissue architecture of baleen from four mysticete species (bowhead, Balaena mysticetus; North Atlantic right, Eubalaena glacialis; fin, Balaenoptera physalus; humpback, Megaptera novaeangliae) indicate that baleen is hydrophilic and oleophobic, shedding rather than adsorbing oil. Oils of different weights and viscosities were tested, including six petroleum-based oils and two fish or plankton oils of common whale prey. No notable differences were found by oil type or whale species. Baleen did not adsorb oil; oil was readily rinsed from baleen by flowing water, especially from moving fringes. Microscopic examination shows minimal wrinkling or peeling of baleen's cortical keratin layers, probably due to oil repelling infiltrated water. Combined results cast doubt on fears of baleen fouling by oil; filter porosity is not appreciably affected, but oil ingestion risks remain. Particle capture studies suggest potentially greater danger to mysticetes from plastic pollution than oil.

Low energy expenditure and resting behaviour of humpback whale mother-calf pairs highlights conservation importance of sheltered breeding areas

Understanding the behaviour of humpback whale mother-calf pairs and the acoustic environment on their breeding grounds is fundamental to assessing the biological and ecological requirements needed to ensure a successful migration and survival of calves. Therefore, on a breeding/resting ground, Exmouth Gulf, Western Australia, we used animal-borne DTAGs to quantify the fine-scale behaviour and energetic expenditure of humpback whale mothers and calves, while sound recorders measured the acoustic environment. We show that: (i) lactating humpback whales keep their energy expenditure low by devoting a significant amount of time to rest, and their use of energy, inferred from respiration rates, is ~half than that of adults on their foraging grounds; (ii) lactating females mainly rest while stationary at shallow depths within reach of the hull of commercial ships, thus increasing the potential for ship strike collisions; (iii) the soundscape is dominated by biological sources; and (iv) even moderate increases of noise from vessels will decrease the communication range of humpback whales. Planned commercial infrastructure in Exmouth Gulf will cause a substantial increase in shipping traffic with the risk of ship strikes and acoustic disturbance potentially compromising energy reserves for the southern migration of humpback whales.

Variations in age- and sex-specific survival rates help explain population trend in a discrete marine mammal population

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.

Implications of survey effort on estimating demographic parameters of a long-lived marine top predator

Effective management of wildlife populations rely on knowledge of their abundance, survival, and reproductive rates. Maintaining long‐term studies capable of estimating demographic parameters for long‐lived, slow‐reproducing species is challenging. Insights into the effects of research intensity on the statistical power to estimate demographic parameters are limited. Here, we investigate implications of survey effort on estimating abundance, home range sizes, and reproductive output of Indo‐Pacific bottlenose dolphins (Tursiops aduncus), using a 3‐year subsample of a long‐term, capture–recapture study off Bunbury, Western Australia. Photo‐identification on individual dolphins was collected following Pollock's Robust Design, where seasons were defined as “primary periods”, each consisting of multiple “secondary periods.” The full dataset consisted of 12 primary periods and 72 secondary periods, resulting in the study area being surveyed 24 times/year. We simulated reduced survey effort by randomly removing one, two, or three secondary periods per primary period. Capture–recapture models were used to assess the effect of survey intensity on the power to detect trends in population abundance, while individual dolphin sighting histories were used to assess the ability to conduct home range analyses. We used sighting records of adult females and their calving histories to assess survey effort on quantifying reproductive output. A 50% reduction in survey effort resulted in (a) up to a 36% decline in population abundance at the time of detection; (b) a reduced ability to estimate home range sizes, by increasing the time for individuals to be sighted on ≥30 occasions (an often‐used metric for home range analyses) from 7.74 to 14.32 years; and (c) 33%, 24%, and 33% of annual calving events across three years going undocumented, respectively. Results clearly illustrate the importance of survey effort on the ability to assess demographic parameters with clear implications for population viability analyses, population forecasting, and conservation efforts to manage human–wildlife interactions.

A voluntary conservation agreement reduces the risks of lethal collisions between ships and whales in the St. Lawrence Estuary (Québec, Canada): From co-construction to monitoring compliance and assessing effectiveness

Lethal collisions with ships are limiting the recovery of several at-risk whale species worldwide. In the St. Lawrence Estuary (Quebec, Canada), the endangered blue whale and of special concern fin whale are among the migratory species subject to collisions with large ships. In 2011, a working group composed of representatives from the maritime industry, the government, non-governmental organizations, and academia was created to explore solutions to mitigate ship-whale collisions in the St. Lawrence Estuary. Adopting an adaptive risk management framework, the working group took advantage of the best available scientific data and tools to co-construct realistic collision mitigation options and evaluate their likely benefits for whale conservation and costs for the industry. In 2013, the working group recommended the implementation of voluntary measures to mitigate collision risks, consisting of a slow-down area, a no-go area, and a caution area; a recommended route was added in 2014. Along with the voluntary framework, the working group agreed to continuously monitor compliance with and assess effectiveness of these mitigation measures. After the fourth year of implementation, voluntary measures showed encouraging results, with a reduction of up to 40% of lethal collision risks with fin whales in the highest density area. This reduction in risk is mainly related to ship speed reduction in the slow-down area from 14.1 ± 2.6 knots in 2012 to 11.3 ± 1.7 knots since 2014. The presence of a mandatory pilotage area overlapping with the slow-down area was instrumental to facilitate communication about the mitigation measures, with the pilotage corporation sitting as a regular member of the working group. This resulted in significantly slower speeds in the slow-down area for ships with a pilot from the pilotage corporation onboard compared to those without (-0.8 knots, p-value < 0.001). It is also likely to explain the weaker compliance of the maritime industry with the no-go area located outside of the mandatory pilotage area. Other factors of success include: the continuous dedication of the government to a voluntary and transparent participatory process; the use of available data, tools and institutions; the presence of an environmental certification program representative in the working group; and the adoption by consensus of an adaptive risk management approach. The traditional regulatory approach to conservation is often blamed for its focus on deterring negative behaviors, doing nothing to encourage and reward positive ones. In agreement with other case studies, the benefits of the voluntary measures implemented in the St. Lawrence Estuary include the pro-active commitment from the industry (which is likely to reduce conflicts with regulators), the greater flexibility and freedom that allowed to come up with cost-effective and tailored-made mitigation measures, and the fast achievement of conservation gains. More importantly perhaps, the human and working capital built throughout the concertation process have the potential to be a fundamental cornerstone in dealing with more complex issues such as the chronically increasing level of underwater noise in whale habitats.

Extensive Core Microbiome in Drone-Captured Whale Blow Supports a Framework for Health Monitoring

The pulmonary system is a common site for bacterial infections in cetaceans, but very little is known about their respiratory microbiome. We used a small, unmanned hexacopter to collect exhaled breath condensate (blow) from two geographically distinct populations of apparently healthy humpback whales (Megaptera novaeangliae), sampled in the Massachusetts coastal waters off Cape Cod (n = 17) and coastal waters around Vancouver Island (n = 9). Bacterial and archaeal small-subunit rRNA genes were amplified and sequenced from blow samples, including many of sparse volume, as well as seawater and other controls, to characterize the associated microbial community. The blow microbiomes were distinct from the seawater microbiomes and included 25 phylogenetically diverse bacteria common to all sampled whales. This core assemblage comprised on average 36% of the microbiome, making it one of the more consistent animal microbiomes studied to date. The closest phylogenetic relatives of 20 of these core microbes were previously detected in marine mammals, suggesting that this core microbiome assemblage is specialized for marine mammals and may indicate a healthy, noninfected pulmonary system. Pathogen screening was conducted on the microbiomes at the genus level, which showed that all blow and few seawater microbiomes contained relatives of bacterial pathogens; no known cetacean respiratory pathogens were detected in the blow. Overall, the discovery of a shared large core microbiome in humpback whales is an important advancement for health and disease monitoring of this species and of other large whales. IMPORTANCE The conservation and management of large whales rely in part upon health monitoring of individuals and populations, and methods generally necessitate invasive sampling. Here, we used a small, unmanned hexacopter drone to noninvasively fly above humpback whales from two populations, capture their exhaled breath (blow), and examine the associated microbiome. In the first extensive examination of the large-whale blow microbiome, we present surprising results about the discovery of a large core microbiome that was shared across individual whales from geographically separated populations in two ocean basins. We suggest that this core microbiome, in addition to other microbiome characteristics, could be a useful feature for health monitoring of large whales worldwide.

High mortality of blue, humpback and fin whales from modeling of vessel collisions on the U.S. West Coast suggests population impacts and insufficient protection

Mortality from collisions with vessels is one of the main human causes of death for large whales. Ship strikes are rarely witnessed and the distribution of strike risk and estimates of mortality remain uncertain at best. We estimated ship strike mortality for blue humpback and fin whales in U.S. West Coast waters using a novel application of a naval encounter model. Mortality estimates from the model were far higher than current minimum estimates derived from stranding records and are closer to extrapolations adjusted for detection probabilities of dead whales. Our most conservative model estimated mortality to be 7.8x, 2.0x and 2.7x the U.S. recommended limit for blue, humpback and fin whales, respectively, suggesting that death from vessel collisions may be a significant impediment to population growth and recovery. Comparing across the study area, the majority of strike mortality occurs in waters off California, from Bodega Bay south and tends to be concentrated in a band approximately 24 Nm (44.5 km) offshore and in designated shipping lanes leading to and from major ports. While some mortality risk exists across nearly all West Coast waters, 74%, 82% and 65% of blue, humpback and fin whale mortality, respectively, occurs in just 10% of the study area, suggesting conservation efforts can be very effective if focused in these waters. Risk is highest in the shipping lanes off San Francisco and Long Beach, but only a fraction of total estimated mortality occurs in these proportionally small areas, making any conservation efforts exclusively within these areas insufficient to address overall strike mortality. We recommend combining shipping lane modifications and re-locations, ship speed reductions and creation of ‘Areas to be Avoided’ by vessels in ecologically important locations to address this significant source of whale mortality.

The Ecology of Human Mobility

Mobile phones and other geolocated devices have produced unprecedented volumes of data on human movement. Analysis of pooled individual human trajectories using big data approaches has revealed a wealth of emergent features that have ecological parallels in animals across a diverse array of phenomena including commuting, epidemics, the spread of innovations and culture, and collective behaviour. Movement ecology, which explores how animals cope with and optimize variability in resources, has the potential to provide a theoretical framework to aid an understanding of human mobility and its impacts on ecosystems. In turn, big data on human movement can be explored in the context of animal movement ecology to provide solutions for urgent conservation problems and management challenges.

Seasonal survival estimation for a long-distance migratory bird and the influence of winter precipitation

Conservation of migratory animals requires information about seasonal survival rates. Identifying factors that limit populations, and the portions of the annual cycle in which they occur, are critical for recognizing and reducing potential threats. However, such data are lacking for virtually all migratory taxa. We investigated patterns and environmental correlates of annual, oversummer, overwinter, and migratory survival for adult male Kirtland's warblers (Setophaga kirtlandii), an endangered, long-distance migratory songbird. We used Cormack-Jolly-Seber models to analyze two mark-recapture datasets: 2006-2011 on Michigan breeding grounds, and 2003-2010 on Bahamian wintering grounds. The mean annual survival probability was 0.58 ± 0.12 SE. Monthly survival probabilities during the summer and winter stationary periods were relatively high (0.963 ± 0.005 SE and 0.977 ± 0.002 SE, respectively). Monthly survival probability during migratory periods was substantially lower (0.879 ± 0.05 SE), accounting for ~44% of all annual mortality. March rainfall in the Bahamas was the best-supported predictor of annual survival probability and was positively correlated with apparent annual survival in the subsequent year, suggesting that the effects of winter precipitation carried over to influence survival probability of individuals in later seasons. Projection modeling revealed that a decrease in Bahamas March rainfall >12.4% from its current mean could result in negative population growth in this species. Collectively, our results suggest that increased drought during the non-breeding season, which is predicted to occur under multiple climate change scenarios, could have important consequences on the annual survival and population growth rate of Kirtland's warbler and other Neotropical-Nearctic migratory bird species.

Critical Decline of the Eastern Caribbean Sperm Whale Population

Sperm whale (Physeter macrocephalus) populations were expected to rebuild following the end of commercial whaling. We document the decline of the population in the eastern Caribbean by tracing demographic changes of well-studied social units. We address hypotheses that, over a ten-year period of dedicated effort (2005–2015), unit size, numbers of calves and/or calving rates have each declined. Across 16 units, the number of adults decreased in 12 units, increased in two, and showed no change in two. The number of adults per unit decreased at -0.195 individuals/yr (95% CI: -0.080 to -0.310; P = 0.001). The number of calves also declined, but the decline was not significant. This negative trend of -4.5% per year in unit size started in about 2010, with numbers being fairly stable until then. There are several natural and anthropogenic threats, but no well-substantiated cause for the decline.

Effects of Model Formulation on Estimates of Health in Individual Right Whales (Eubalaena glacialis)

Right whales are vulnerable to many sources of anthropogenic disturbance including ship strikes, entanglement with fishing gear, and anthropogenic noise. The effect of these factors on individual health is unclear. A statistical model using photographic evidence of health was recently built to infer the true or hidden health of individual right whales. However, two important prior assumptions about the role of missing data and unexplained variance on the estimates were not previously assessed. Here we tested these factors by varying prior assumptions and model formulation. We found sensitivity to each assumption and used the output to make guidelines on future model formulation.

Endangered Right Whales Enhance Primary Productivity in the Bay of Fundy

Marine mammals have recently been documented as important facilitators of rapid and efficient nutrient recycling in coastal and offshore waters. Whales enhance phytoplankton nutrition by releasing fecal plumes near the surface after feeding and by migrating from highly productive, high-latitude feeding areas to low-latitude nutrient-poor calving areas. In this study, we measured NH₄⁺ and PO₄^3- release rates from the feces of North Atlantic right whales (Eubalaena glacialis), a highly endangered baleen whale. Samples for this species were primarily collected by locating aggregations of whales in surface-active groups (SAGs), which typically consist of a central female surrounded by males competing for sexual activity. When freshly collected feces were incubated in seawater, high initial rates of N release were generally observed, which decreased to near zero within 24 hours of sampling, a pattern that is consistent with the active role of gut microflora on fecal particles. We estimate that at least 10% of particulate N in whale feces becomes available as NH₄⁺ within 24 hours of defecation. Phosphorous was also abundant in fecal samples: initial release rates of PO₄^3- were higher than for NH₄⁺, yielding low N/P nutrient ratios over the course of our experiments. The rate of PO₄^3- release was thus more than sufficient to preclude the possibility that nitrogenous nutrients supplied by whales would lead to phytoplankton production limited by P availability. Phytoplankton growth experiments indicated that NH₄⁺ released from whale feces enhance productivity, as would be expected, with no evidence that fecal metabolites suppress growth. Although North Atlantic right whales are currently rare (approximately 450 individuals), they once numbered about 14,000 and likely played a substantial role in recycling nutrients in areas where they gathered to feed and mate. Even though the NH₄⁺ released from fresh whale fecal material is a small fraction of total whale fecal nitrogen, and recognizing the fact that the additional nitrogen released in whale urine would be difficult to measure in a field study, the results of this study support the idea that the distinctive isotopic signature of the released NH₄⁺ could be used to provide a conservative estimate of the contribution of the whale pump to primary productivity in coastal regions where whales congregate.

Abundance and Distribution of Sperm Whales in the Canary Islands: Can Sperm Whales in the Archipelago Sustain the Current Level of Ship-Strike Mortalities?

Sperm whales are present in the Canary Islands year-round, suggesting that the archipelago is an important area for this species in the North Atlantic. However, the area experiences one of the highest reported rates of sperm whale ship-strike in the world. Here we investigate if the number of sperm whales found in the archipelago can sustain the current rate of ship-strike mortality. The results of this study may also have implications for offshore areas where concentrations of sperm whales may coincide with high densities of ship traffic, but where ship-strikes may be undocumented. The absolute abundance of sperm whales in an area of 52933 km², covering the territorial waters of the Canary Islands, was estimated from 2668 km of acoustic line-transect survey using Distance sampling analysis. Data on sperm whale diving and acoustic behaviour, obtained from bio-logging, were used to calculate g(0) = 0.92, this is less than one because of occasional extended periods when whales do not echolocate. This resulted in an absolute abundance estimate of 224 sperm whales (95% log-normal CI 120–418) within the survey area. The recruitment capability of this number of whales, some 2.5 whales per year, is likely to be exceeded by the current ship-strike mortality rate. Furthermore, we found areas of higher whale density within the archipelago, many coincident with those previously described, suggesting that these are important habitats for females and immature animals inhabiting the archipelago. Some of these areas are crossed by active shipping lanes increasing the risk of ship-strikes. Given the philopatry in female sperm whales, replacement of impacted whales might be limited. Therefore, the application of mitigation measures to reduce the ship-strike mortality rate seems essential for the conservation of sperm whales in the Canary Islands.

Endo- and ectoparasites of large whales (Cetartiodactyla: Balaenopteridae, Physeteridae): Overcoming difficulties in obtaining appropriate samples by non- and minimally-invasive methods

Baleen and sperm whales, belonging to the Order Cetartiodactyla, are the largest and heaviest existent mammals in the world, collectively known as large whales. Large whales have been subjected to a variety of conservation means, which could be better monitored and managed if physiological and pathophysiological information, such as pathogen infections, could already be gathered from free-swimming animals instead of carcasses. Parasitic diseases are increasingly recognized for their profound influences on individual, population, and even ecosystem health. Furthermore, a number of parasite species have gained importance as opportunistic neozoan infections in the marine environment. Nonetheless, traditional approaches to study parasitic diseases have been impractical for large whales, since there is no current routine method for the capture and handling of these large animals and there is presently no practical method to obtain blood samples remotely from free-ranging whales. Therefore, we here not only intend to review the endo- and ectoparasite fauna of large whales but also to provide new insights in current available methods for gathering parasitological data by using non- or minimally invasive sampling techniques. We focus on methods, which will allow detailed parasitological studies to gain a broader knowledge on parasitoses affecting wild, free-swimming large whale populations.

Sperm whales ability to avoid approaching vessels is affected by sound reception in stratified waters

Collision with vessels is a major cause of whale mortality in the Mediterranean Sea. The effect of non-spherical sound propagation effects on received levels (RL) was investigated for the sperm whale (Physeter macrocephalus). Relevant dive patterns were considered in each case and the RL were compared for two periods using a ray tracing software, the winter conditions and the summer stratified situation. RL were plotted as a function of time in a simulated collision case for two vessel speeds representative of a conventional merchant ship (15knots) and a fast-ferry (37knots). In almost all simulated cases, RL featured a brutal 23-31dB re 1μPa rise from below 100dB while the vessel approached the whale at close range. Summer situations were worse because this transition occurred at closer ranges, resulting in acoustic warning times of less than 30s in the fast ferry case. These results suggested that sperm whales could not be able to achieve an escape manoeuvre in a critical situation such as a fast vessel approaching under stratified waters conditions.