Management Of Protected Species Research Articles

If these walls could talk: Investigating bottlenose dolphin habitat use in fiord ecosystems

Effective management of protected species requires a comprehensive understanding of their ecology. Within the Te Moana o Atawhenua-FiordlandMarine Area (FMA), Aotearoa-New Zealand, two of the four recognized bottlenose dolphin (Tursiops truncatus) sub-populations are considered to exclusively inhabit discrete fiord systems. Opportunistic sightings outside the Patea-Doubtful and Tamatea-Dusky fiord complexes, however, suggest they occupy a larger space than currently recognized. To investigate the presence of bottlenose dolphins in five neighboring fiord systems, passive acoustic monitoring (PAM) was conducted from February 2022 to November 2023. PAM effort included two instrumentation approaches: F-PODs to continuously detect click trains of odontocetes, and SoundTraps to provide broad spectrum recordings (15 of every 30 min, sampling rate: 96kHz). This study discusses the trade-offs between approaches in terms of cost, recording duration, and data collected. In addition, photo-identification of bottlenose dolphins in these neighboring fiords was used to identify the sub-population of individuals. The results demonstrate that bottlenose dolphins are regularly using fiords that are not formally considered part of their range within the FMA. A greater understanding of the spatial ecology of Fiordland bottlenose dolphin sub-populations necessitates consideration of threats and resources both inside and outside of their namesake fiord complexes.

Reference genome of an iconic lizard in western North America, Blainville's horned lizard Phrynosoma blainvillii.

Genome assemblies are increasingly being used to identify adaptive genetic variation that can help prioritize the population management of protected species. This approach may be particularly relevant to species like Blainville's horned lizard, Phrynosoma blainvillii, due to its specialized diet on noxious harvester ants, numerous adaptative traits for avoiding predation (e.g. cranial horns, dorsoventrally compressed body, cryptic coloration, and blood squirting from the orbital sinuses), and status as Species of Special Concern in California. Rangewide decline since the early 20th century, the basis of its conservation status, has been driven mainly by habitat conversion, over-collecting, and invasion of a non-native ant that displaces its native ant prey base. Here, we report on a scaffold-level genome assembly for P. blainvillii as part of the California Conservation Genomics Project (CCGP), produced using Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology. The de novo assembly has 78 scaffolds, a total length of ~2.21 Gb, a scaffold N50 length of ~352 Mb, and BUSCO score of 97.4%. This is the second species of Phrynosoma for which a reference genome has been assembled and represents a considerable improvement in terms of contiguity and completeness. Combined with the landscape genomics data being compiled by the CCGP, this assembly will help strategize efforts to maintain and/or restore local genetic diversity, where interventions like genetic rescue, translocation, and strategic land preservation may be the only means by which P. blainvillii and other low-vagility species can survive in the fragmented habitats of California.

Implications of past and present genetic connectivity for management of the saltwater crocodile (Crocodylus porosus).

Effective management of protected species requires information on appropriate evolutionary and geographic population boundaries and knowledge of how the physical environment and life-history traits combine to shape the population structure and connectivity. Saltwater crocodiles (Crocodylus porosus) are the largest and most widely distributed of living crocodilians, extending from Sri Lanka to Southeast Asia and down to northern Australia. Given the long-distance movement capabilities reported for C. porosus, management units are hypothesised to be highly connected by migration. However, the magnitude, scale, and consistency of connection across managed populations are not fully understood. Here we used an efficient genotyping method that combines DArTseq and sequence capture to survey 3000 high-quality genome-wide single nucleotide polymorphisms from 1176 C. porosus sampled across nearly the entire range of the species in Queensland, Australia. We investigated historical and present-day connectivity patterns using fixation and diversity indices coupled with clustering methods and the spatial distribution of kin pairs. We inferred kinship using forward simulation coupled with a kinship estimation method that is robust to unspecified population structure. The results demonstrated that the C. porosus population has substantial genetic structure with six broad populations correlated with geographical location. The rate of gene flow was highly correlated with spatial distance, with greater differentiation along the east coast compared to the west. Kinship analyses revealed evidence of reproductive philopatry and limited dispersal, with approximately 90% of reported first and second-degree relatives showing a pairwise distance of <50 km between sampling locations. Given the limited dispersal, lack of suitable habitat, low densities of crocodiles and the high proportion of immature animals in the population, future management and conservation interventions should be considered at regional and state-wide scales.

An assessment of marine, estuarine, and riverine habitat vulnerability to climate change in the Northeast U.S.

Climate change is impacting the function and distribution of habitats used by marine, coastal, and diadromous species. These impacts often exacerbate the anthropogenic stressors that habitats face, particularly in the coastal environment. We conducted a climate vulnerability assessment of 52 marine, estuarine, and riverine habitats in the Northeast U.S. to develop an ecosystem-scale understanding of the impact of climate change on these habitats. The trait-based assessment considers the overall vulnerability of a habitat to climate change to be a function of two main components, sensitivity and exposure, and relies on a process of expert elicitation. The climate vulnerability ranks ranged from low to very high, with living habitats identified as the most vulnerable. Over half of the habitats examined in this study are expected to be impacted negatively by climate change, while four habitats are expected to have positive effects. Coastal habitats were also identified as highly vulnerable, in part due to the influence of non-climate anthropogenic stressors. The results of this assessment provide regional managers and scientists with a tool to inform habitat conservation, restoration, and research priorities, fisheries and protected species management, and coastal and ocean planning.

Ocean Regime Shift is Driving Collapse of the North Atlantic Right Whale Population

Ocean warming linked to anthropogenic climate change is impacting the ecology of marine species around the world. In 2010, the Gulf of Maine and Scotian Shelf regions of the Northwest Atlantic underwent an unprecedented regime shift. Forced by climate-driven changes in the Gulf Stream, warm slope waters entered the region and created a less favorable foraging environment for the endangered North Atlantic right whale population. By mid-decade, right whales had shifted their late spring/summer foraging grounds from the Gulf of Maine and the western Scotian Shelf to the Gulf of St. Lawrence. The population also began exhibiting unusually high mortality in 2017. Here, we report that climate-driven changes in ocean circulation have altered the foraging environment and habitat use of right whales, reducing the population’s calving rate and exposing it to greater mortality risks from ship strikes and fishing gear entanglement. The case of the North Atlantic right whale provides a cautionary tale for the management of protected species in a changing ocean.

Integrating Livestock Grazing and Sympatric Takin to Evaluate the Habitat Suitability of Giant Panda in the Wanglang Nature Reserve.

Simple SummaryGiant pandas are facing the threat of habitat degradation. Both grazing livestock and sympatric animals have certain impacts on the giant panda habitat. This study evaluated the habitat suitability of giant panda in Wanglang Nature Reserve by simultaneously investigating livestock grazing and sympatric takin. Results for the giant panda habitat in Wanglang are not optimistic, and the extensive overlap of suitable habitats for livestock, takin and panda makes the situation worse.Habitat suitability provides essential information for the management of protected species. However, studies that jointly consider the impacts of human disturbance and sympatric animals in habitat suitability assessments of giant panda are limited, which may overestimate the habitat status. To address this issue, we evaluated the habitat suitability of giant panda in Wanglang Nature Reserve by simultaneously investigating livestock grazing and sympatric takin via MAXENT, a new attempt at the assessment of the habitat suitability of giant panda. We focused on describing the habitat suitability of giant panda and determining the habitat overlap between livestock, takin, and panda to evaluate the impacts of livestock grazing and sympatric takin on the suitable giant panda habitat. Results revealed that only 16.33% of the area in Wanglang was suitable giant panda habitat, of which 67.66% was shared by livestock, and 97.99% of the remaining suitable panda habitat not shared by livestock was revealed to be shared by takin. The results indicate an unfavorable habitat status of giant panda in Wanglang, with the potential extensive habitat overlap between livestock, takin and panda exerting further pressure. Thus, to effectively protect giant pandas and their habitats, grazing activity should be controlled. Furthermore, to accurately protect sympatric animals, the monitoring of panda and takin activities in the overlapping areas must be maintained.

Variation in predator diet and prey size affects perceived impacts to salmon species of high conservation concern

Management of protected species is difficult when objectives include the recovery of both predator and its prey. Ideally, identifying trade-offs between competing objectives involves evaluating management alternatives with a quantitative model that integrates information on both species, but data are often limited. We used new predator diet data and simulation modeling to update our understanding of seal predation on juvenile Chinook (Oncorhynchus tshawytscha) and coho salmon (Oncorhynchus kisutch) in the Puget Sound. Under prey size assumptions used by previous studies, estimates suggest predation could be a significant source of mortality for Chinook salmon (mean: 37% of ocean age-0 juveniles), but varied considerably among years (range of median estimates: 22%–49%). However, when we estimated prey size from otoliths recovered from seal scats, the impact (numbers of fish consumed) decreased by 71%. Predation on coho salmon was estimated to be relatively low under both scenarios (6%–8% of ocean age-0 juveniles) with a 21% decrease in consumption using otolith-derived prey size. Our analysis highlights the importance of updating model inputs and re-evaluating assumptions of multi-species models used for ecosystem-based fisheries management.

Enabling pinniped conservation by means of non-invasive genetic population analysis

Conservation and management of protected species, particularly of elusive species such as pinnipeds, is hampered by knowledge gaps. In the case of studies using genetic data these are often attributed to a lack of representative samples. Therefore, there is a pressing need for the development of minimally invasive sampling protocols suitable for genetic analyses of pinnipeds. The present study evaluated the applicability of various protocols for the collection and processing of samples from harbour seals (Phoca vitulina) and grey seals (Halichoerus grypus), encompassing seven source sample types (blood, skin, hair (plucked/moulted), urine, buccal swabs, scat) and three different extraction methods. Protocols were designed for minimally invasive sampling, but also to evaluate differences in their performance based on cost and time of execution in comparison to traditional sampling approaches. The performance of each protocol was measured following successful DNA isolation, molecular sex determination and sequencing of a mitochondrial DNA fragment (control region). Protocols using plucked hair, urine and buccal swab samples proved effective for collection from individuals in captivity, whereas scat was most applicable for non-invasive sampling in the wild. Furthermore, following a pilot study on scat samples, DNA was found to be viable for genetic analysis after exposure to ambient conditions for up to four weeks. This study provides a useful assessment of the suitability of various minimal and non-invasively collected samples for DNA isolation, amplification and mitochondrial sequencing, enabling the effective design of future sampling strategies and a significant increase of samples available for genetic analysis of pinnipeds.

Composition and environmental interpretation of the communities of Sassafras tzumu, a protected species, at Zhejiang province in eastern China

Studying the community composition and environmental characterization is an urgent need for species conservation and forest restoration. Sassafras tzumu (Hemsl.) Hemsl is a protected plant species in southern China. We aimed to assess the relationship between S. tzumu and environmental variables using data from the Noncommercial Forest Ecological Monitoring Plots (NCFEMPs) system in Zhejiang Province. Among the investigated NCFEMPs, we found 96 plots (20 × 20 m) containing S. tzumu species. The species composition and associated environmental data from 96 plots were analyzed using two-way indicator species analysis (TWINSPAN) and canonical correspondence analysis (CCA). The TWINSPAN results showed there were eight types of S. tzumu associations. Each association had its own composition and environmental characteristics. The CCA results showed that the elevation and slope aspect were the major variables that determined the spatial patterns of S. tzumu communities. Our results will be of great theoretical and practical significance for protected species management and conservation.

Regional Variation in Kemp’s Ridley Sea Turtle Diet Composition and Its Potential Relationship With Somatic Growth

Reptile growth is influenced by many ecological processes that can cumulatively give rise to divergent somatic growth rates within spatially structured populations. As somatic growth variation can strongly influence a species’ population dynamics, identifying proximate drivers can be critical to the conservation and management of protected species. Kemp’s ridley sea turtles (Lepidochelys kempii) exhibit spatial variation in both diet composition and growth, but whether components of this variation are linked has not been evaluated. Through an integration of skeletochronological and stable isotope analyses of stranded turtle humerus bones we characterized regional variation in Kemp’s ridley diet composition and potential relationships with somatic growth rates. Turtles were divided among five regions within the U.S. Gulf of Mexico (GoM) and Atlantic Coast based on location of stranding, and humerus bones were sampled for stable carbon (δ13C) and nitrogen (δ15N) isotope ratios. These data were combined with region-specific prey stable isotope data sourced from the primary literature into Bayesian stable isotope mixing models (MixSIAR) to estimate the proportional contribution of five prey groups (crustaceans, bivalves, gastropods, fish, macroalgae/seagrass) to Kemp’s ridley diets. Our analysis revealed strong regional differences in mixing model-derived diet composition estimates that closely tracked published records of Kemp’s ridley diet. Invertebrates generally comprised the largest proportion (43.5–97.7 %) of turtle diets. However, we also observed high proportional contributions of fish (42.6–43.1 %) to western GoM turtle diets and macroalgae/seagrass (42.4–47.8 %), or isotopically similar prey resources (e.g., tunicates), to eastern GoM turtle diets. Growth rates were poorly correlated with δ15N values—a proxy for trophic level—and diet composition estimates, suggesting that diet composition alone may not explain the regional differences in somatic growth observed in this species. This study highlights the value of complementary skeletal and isotopic analyses to understanding regional diet variation in sea turtles as well as the importance of continued collection of isotopic data for both sea turtles and their prey. These results also help fill critical knowledge gaps pertaining to the relationship between sea turtle foraging ecology and somatic growth dynamics, a topic of high importance to sea turtle conservation and management.

Predator recovery, shifting baselines, and the adaptive management challenges they create

AbstractRecent species recoveries following historical depletion have been widely celebrated as conservation success stories. However, the recovery of highly interactive species, particularly predators, generates new management challenges that arise from their potential for wide‐ranging effects on local ecosystems and their poorly understood ecology. In marine systems, many pinniped species share parallel histories of depletion, recovery, and human conflict. Recovering from post‐exploitation populations of small size, these pinnipeds have returned to their present abundance from a largely absent, or severely reduced, recent role in many coastal ecosystems. To address the challenges arising today from real or perceived overabundance of protected pinniped species, we evaluate the prehistorical, historical, and contemporary abundances of six pinniped species that breed in the contiguous United States. This review highlights gaps in current knowledge that limit the implementation of ecologically grounded approaches to adaptive management of protected species in a time of shifting, or lifting, baselines. To address these gaps will require a diverse cadre of natural and social scientists as well as stakeholders to tackle the questions of how we define recovery at a species or ecosystem level, and when we have reached this point, how we move forward in a way that does not repeat a history of depletion, conservation, and recovery. Doing so will require an understanding of what role highly interactive species play in their ecosystems and how this role shifts with changes in ecological context, as well as the sociological and economic impacts of species restoration to humans. This knowledge is integral to the ongoing transition from a focus on preventing species extinction to new, and often unanticipated, challenges arising from the functional implications of species recovery.

Environmental drivers of harbour porpoise fine-scale movements

Quantifying intraspecific variation in movement behaviour of marine predators and the underlying environmental drivers is important to inform conservation management of protected species. Here, we provide the first empirical data on fine-scale movements of free-ranging harbour porpoises (Phocoena phocoena) in their natural habitat. Data were obtained from six individuals, tagged in two areas of the Danish North Sea, that were equipped with Global Positioning System (GPS) and dive recorder units (V-tags). We used multi-model inference and model averaging to evaluate the relative importance of various static and dynamic environmental conditions on the movement characteristics: speed, turning angle, dive duration, dive depth, dive wiggliness (a proxy for prey chasing behaviour), and post-dive duration. Despite substantial individual differences in horizontal and vertical movement patterns, we found that all the tracked porpoises responded similar to variation in environmental conditions and displayed movements that indicate a higher likelihood of foraging behaviour in shallower and more saline waters. Our study contributes to the identification of important feeding areas for porpoises and can be used to improve existing movement-based simulation models that aim to assess the impact of anthropogenic disturbance on harbour porpoise populations.

Hierarchical Phylogeographic Structure of Coho Salmon in California

AbstractEvaluation of population genetic structure and variation is an important part of planning for the recovery and management of protected species. Data from 18 polymorphic microsatellite DNA markers were used to analyze the phylogeographic structure of protected Coho Salmon Oncorhynchus kisutch from populations throughout California. Fish from 30 locations in two evolutionarily significant units (ESUs) representing most of the extant populations in the state were studied. Multiple analyses indicated a hierarchical pattern of population structure: the greatest divergence was found at the broadest geographic scale (ESU), followed by the divergences between basins and populations within basins. The populations of the large Klamath River basin were consistently identified as a distinct phylogenetic group, nearly as divergent from all other populations as the two ESUs were from each other. All populations in different basins were differentiated from each other and a pattern of isolation by distance was found at a California‐wide scale, but not at smaller spatial scales. Similarly, most individuals were accurately assigned to their population of origin, and almost all misassignments were to an adjacent or geographically proximal basin, indicating that there is substantial gene flow within each region but much less between regions. The number of parents contributing to each population was highly variable and reflected larger patterns of genetic variation, which was found to be generally higher in the southerly, low‐elevation coastal populations than in the northern, interior, higher‐elevation populations. The results strongly support the current boundary between the two ESU regions, and the detailed understanding of phylogeographic structure provided here will help to guide the management and recovery of Coho Salmon at the southern end of their geographic range.Received August 25, 2015; accepted May 4, 2016 Published online August 12, 2016

Genetic isolation between coastal and fishery-impacted, offshore bottlenose dolphin (Tursiops spp.) populations.

The identification of species and population boundaries is important in both evolutionary and conservation biology. In recent years, new population genetic and computational methods for estimating population parameters and testing hypotheses in a quantitative manner have emerged. Using a Bayesian framework and a quantitative model-testing approach, we evaluated the species status and genetic connectedness of bottlenose dolphin (Tursiops spp.) populations off remote northwestern Australia, with a focus on pelagic 'offshore' dolphins subject to incidental capture in a trawl fishery. We analysed 71 dolphin samples from three sites beyond the 50 m depth contour (the inshore boundary of the fishery) and up to 170km offshore, including incidentally caught and free-ranging individuals associating with trawl vessels, and 273 dolphins sampled at 12 coastal sites inshore of the 50 m depth contour and within 10km of the coast. Results from 19 nuclear microsatellite markers showed significant population structure between dolphins from within the fishery and coastal sites, but also among dolphins from coastal sites, identifying three coastal populations. Moreover, we found no current or historic gene flow into the offshore population in the region of the fishery, indicating a complete lack of recruitment from coastal sites. Mitochondrial DNA corroborated our findings of genetic isolation between dolphins from the offshore population and coastal sites. Most offshore individuals formed a monophyletic clade with common bottlenose dolphins (T.truncatus), while all 273 individuals sampled coastally formed a well-supported clade of Indo-Pacific bottlenose dolphins (T.aduncus). By including a quantitative modelling approach, our study explicitly took evolutionary processes into account for informing the conservation and management of protected species. As such, it may serve as a template for other, similarly inaccessible study populations.

Large-Scale Trade in Legally Protected Marine Mollusc Shells from Java and Bali, Indonesia.

BackgroundTropical marine molluscs are traded globally. Larger species with slow life histories are under threat from over-exploitation. We report on the trade in protected marine mollusc shells in and from Java and Bali, Indonesia. Since 1987 twelve species of marine molluscs are protected under Indonesian law to shield them from overexploitation. Despite this protection they are traded openly in large volumes.Methodology/Principal FindingsWe collected data on species composition, origins, volumes and prices at two large open markets (2013), collected data from wholesale traders (2013), and compiled seizure data by the Indonesian authorities (2008–2013). All twelve protected species were observed in trade. Smaller species were traded for <USD1.00 whereas prices of larger species were USD15.00–40.00 with clear price-size relationships. Some shells were collected locally in Java and Bali, but the trade involves networks stretching hundreds of kilometres throughout Indonesia. Wholesale traders offer protected marine mollusc shells for the export market by the container or by the metric ton. Data from 20 confiscated shipments show an on-going trade in these molluscs. Over 42,000 shells were seized over a 5-year period, with a retail value of USD700,000 within Indonesia; horned helmet (Cassis cornuta) (>32,000 shells valued at USD500,000), chambered nautilus (Nautilus pompilius) (>3,000 shells, USD60,000) and giant clams (Tridacna spp.) (>2,000 shells, USD45,000) were traded in largest volumes. Two-thirds of this trade was destined for international markets, including in the USA and Asia-Pacific region.Conclusions/SignificanceWe demonstrated that the trade in protected marine mollusc shells in Indonesia is not controlled nor monitored, that it involves large volumes, and that networks of shell collectors, traders, middlemen and exporters span the globe. This impedes protection of these species on the ground and calls into question the effectiveness of protected species management in Indonesia; solutions are unlikely to be found only in Indonesia and must involve the cooperation of importing countries.

Using historical data to assess the biogeography of population recovery

Historical ecology research is valuable for assessing long‐term baselines, and is increasingly applicable to conservation and management. In this study, we describe how historical range data can inform key aspects of protected species management, including evaluating conservation status and recovery, and determining practical management units. We examine contemporary (1973–2012) and historical (1250–1950) data on nesting beach distributions for green sea turtles Chelonia mydas in the Hawaiian Islands. Green turtle populations in Hawai‘i declined until federal and international protections began in the 1970s, but over the past four decades one index population has shown encouraging increases and broader recovery has been inferred. We find that 80% of historically major nesting populations are extirpated, or have heavily reduced nesting abundances in comparison with current estimates. Furthermore, historical nesting areas were not geographically isolated, but distributed across the archipelago. In comparison, today more than 90% of green turtle nesting in Hawai‘i occurs at a single site that is vulnerable to sea level rise. This research suggests that assessing recovery without historical data on spatial patterns may overlook important ecological dynamics at the popu lation or ecosystem level, which can result in improper or inadequate conservation assessments and recovery targets.

Observing incidental harbour porpoise Phocoena phocoena bycatch by remote electronic monitoring

Quantification of marine mammal bycatch is important in the context of conservation and management of protected species. Hitherto, using on-board observers has been the most reli- able and accurate method; however, observer programs can be prohibitively expensive. To inves- tigate the potential of closed-circuit television cameras to document bycatch of marine mammals, 6 Danish commercial gillnetters (10 to15 m in length) operating under the Danish catch quota management system were equipped with remote electronic monitoring (REM) systems. The REM systems provided video footage, time and position of all net hauls and bycatches of marine mam- mals. Comparisons between REM results and fishers' logbooks showed that the REM system gave more reliable results, since fishers, in many cases, did not observe the bycatch while working on the deck because the bycatch had already dropped out of the net before coming on board. Fur- thermore, very high coverage percentages at low cost, compared to on-board observers, could be obtained with REM. Alternative means of conducting the video analysis were tested; they were, however, not found to be very efficient.

Spatial ecology of critically endangered hawksbill turtles Eretmochelys imbricata: implications for management and conservation

Elucidating spatio-temporal movements of animals is an integral component of wildlife conservation and protected species management. Between 2008 and 2010 we satellite tracked 15 adult female hawksbill turtles Eretmochelys imbricata in the eastern Pacific Ocean to evaluate their movement behavior and to guide management and conservation efforts of this highly endangered population. Movements and habitat use were highly neritic, and post-nesting mi g - ration distances (maximum = 283.11 km) were short relative to migrations of other sea turtle species. In foraging areas, the majority of hawksbills established restricted, inshore home ranges within mangrove estuaries. A large proportion (>65%) of turtle location points fell within protected areas, although many of these sites lack enforcement and monitoring. The consistent use of estuar- ine and mangrove habitat for nesting and foraging may explain why hawksbills went virtually un- detected in the eastern Pacific for decades. The spatially restricted and neritic life cycles of adult hawksbills in the eastern Pacific highlight threats (e.g. overlap with coastal fisheries, increased sus- ceptibility to habitat degradation and/or catastrophic events) and opportunities for conservation (e.g. acute conservation target areas, less variant jurisdictional boundaries/regulations) for this spe- cies. Our results underscore the importance of strengthening protected area management, man- grove estuary protection and hawksbill research and conservation in the eastern Pacific.