Browsing by Subject "Conservation biology"

A vast range of theoretical and empirical studies now suggests that MPAs can conserve marine biodiversity and, under some circumstances, increase fishery yields. However, despite the importance of pelagic apex predators to ecosystem function, the effectiveness of spatial management for the conservation of pelagic apex predator species is still unknown. I used fishery-dependent logbook and observer datasets to assess fishing effort and both the catch and size of pelagic apex predator species around five different MPAs. The US Hawaii-based deep-set or Atlantic pelagic longline fisheries fish the waters around these MPAs; both of these fisheries have experienced multiple management measures over time to protect species and maximize fishery yield. The MPAs selected for this study range in size, age, level of protection, and reason for establishment. I found that only two MPAs of the five appeared to be benefitting the pelagic apex predator species that I selected: the DeSoto Canyon and East Florida Coast MPAs, both in the Atlantic Ocean. The size of yellowfin tuna around the DeSoto Canyon MPA borders has increased over time, as has fishing effort. In contrast, the size of swordfish has decreased near the boundary of the East Florida Coast MPA, although the catch of swordfish has increased. The increase in catch of smaller swordfish was not a surprise because the East Florida Coast MPA was established around an area that is a nursery habitat for swordfish. These results are promising for the use of static MPAs for the conservation of pelagic apex predators, but three of the MPAs in my study did not show any indication of increased fishing effort, increased catch, or changes in pelagic apex predator size near their boundaries over time. Therefore, the characteristics of the DeSoto Canyon and East Florida Coast MPAs may provide a template for how to best design new MPAs for pelagic apex predators. Both of these MPAs were established with the specific intent of reducing pelagic apex predator bycatch, in areas where there were historically high catch rates. Both areas are relatively large (> 85,000 km2) and are also closed year-round. In combination, these characteristics may provide protection for pelagic apex predators.

Humans universally demonstrate intrinsically motivated prosocial behavior towards kin, non-kin ingroup members, and strangers. However, humans struggle to extend the same prosocial behavior to more abstract concepts like future-others and non-human species. The Adaptive Motivation Hypothesis posits that humans evolved intrinsic motivations to act prosocially towards more tangible social partners like those within an individual’s ingroup, but prosocial behavior towards more distant and abstract partners is constrained by ecological certainty. Prosocial behavior towards these more abstract concepts is more variable and more likely motivated by extrinsic reward. This dissertation aims to examine the development of motivations for prosocial behavior towards these more abstract concepts. My studies rely on common goods games as a proxy for examining behavior towards abstract recipients of prosocial behavior. Common goods are any resource like forests or fisheries that are non-excludable to a population, but rivalrous. In-demand common goods require cooperation of humans to ensure sustainable use in order to avoid depletion. Chapter One examined how children in three populations that differed in ecological certainty behaved in a common goods game where they were asked to contribute portions of their personal endowment to the maintenance of a forest. Participants were either provided a high extrinsic motivation, a low extrinsic motivation, or no extrinsic motivation for contributing to the maintenance of the common good. Results show that overall, children of all ages were more motivated to contribute to abstract recipients when extrinsic motivation is high. However, noticeable variation in behavior between populations was driven by ecological and cultural differences. Chapter Two examined whether aggregated extrinsic rewards increased contributions to common goods in a sample of children aged six to fourteen. Results suggest that both information about personal loss and delay in an acquiring resource together dramatically increase children’s contributions to common goods within both experimental and real-world contexts. Chapter Three explores whether making a typically abstract social partner more tangible increases an individual’s prosocial behavior towards said partner. Results for Chapter Three, conducted with a population in the Democratic Republic of the Congo, find that increasingly the tangibility of an abstract population marginally increases prosocial behavior in children but not in adults. Together, the results of these studies have implications improved understanding of the development of prosocial motivations in school age children, as well as applications to understanding motivations for socially conscious behavior in the face of environmental and conservation dilemmas.

Pinniped species undergo a life history, unique among marine mammals, that includes discrete periods of occupancy on land or ice within a predominantly marine existence. This makes many pinniped species valuable sentinels of marine ecosystem health and models of marine mammal physiology and behavior. Pinniped research has often progressed hand-in-hand with advances at the technological frontiers of wildlife biology, and drones represent a leap forward in the long-established field of aerial photography, heralding opportunities for data collection and integration at new scales of biological importance. The following chapters employ and evaluate recent and emerging methods of wildlife surveillance that are uniquely enabled and facilitated by drone methods, in applied research and management campaigns with near-polar pinniped species. These methods represent advancements in abundance estimation and distribution modeling of pinniped populations that are dynamically shifting amid climate change, fishing pressure, and recovery from historical depletion.Conventional methods of counting animals from aerial imagery—typically visual interpretation by human analysts—can be time-consuming and limits the practical use of this data type. Deep learning methods of computer vision can ease this burden when applied to drone imagery, but are not yet characterized for practical and generalized use. To this end, I used a common implementation of deep learning for object detection in imagery to train and test models on a variety of datasets describing breeding populations of gray seals (Halichoerus grypus) in the northwest Atlantic Ocean (Chapter 2). I compare standardized performance metrics of models trained and tested on different combinations of datasets, demonstrating that model performance varies depending on both training and testing data choices. We find that models require careful validation to estimate error rates, and that they can be effectively deployed to aid, but not replace, conventional human visual interpretation of novel datasets for gray seal detection, location, age-classification and abundance estimation. Spatial analysis and species distribution modeling can use fine-scale drone-derived data to describe local species–habitat relationships at the scale of individual animals. I applied structure-from-motion methods to a survey of three pinniped species, pacific harbor seals (Phoca vitulina richardii), northern fur seals (Callorhinus ursinus), and Steller sea lions (Eumetopias jubatus), in adjacent non-breeding haul-outs to compare occupancy and habitat selection (Chapter 3). I describe and compare fitted occupancy models of pacific harbor seals and northern fur seals, finding that conspecific attraction is a key driver of habitat selection for each species, and that each species exhibits distinct topographic preferences. These findings illustrate both opportunities and limitations of spatial analysis at the scale of individual pinnipeds. Ease of deployment and rapid data collection make drones a powerful tool for monitoring populations of interest over time, while animal locations, revealed in high-resolution imagery, and contextual habitat products can reveal spatial relationships that persist beyond local contexts. I designed and carried out a campaign of drone surveillance over coastal habitats near Palmer Station, Antarctica, in the austral summer of 2020 to assess the seasonal abundance and habitat use of Antarctic fur seals (Arctocephalus gazella) in the Palmer Archipelago and adjacent regions (Chapter 4). I modeled abundance as a function of date, with and without additional terms to capture variance by site, and used these models to estimate peak abundance near Palmer Station in the 2020 summer season. These findings leverage the spatial and temporal advantages of drone methods to estimate species phenology, distribution and abundance. Together, these chapters describe emerging applications of drone technology that can advance pinniped research and management into new scales of analytical efficiency and ecological interpretation. These studies describe methods that have been proven in concept, but not yet standardized for practical deployment, and their findings reveal new ecological insights, opportunities for methodological advancement, and current limitations of drone methods for the study of pinnipeds in high-latitude environments.

Sea turtles, marine mammals and sea birds are vulnerable to higher mortality rates as a direct function of incidental capture (bycatch) in marine fisheries. Their migratory behavior exposes them to multiple fishing gear types and fishing practices and efforts to understand the rates of interaction between these taxa and fishing necessarily entails analysis of data over large spatial areas (ocean-basin) and multiple types of fishing activities. The acquisition the requisite data, however, requires considerable resources and many regions in the world are data-poor with respect to bycatch, including the Wider Caribbean Region (WCR) in the west central Atlantic Ocean basin. This dissertation presents the results of multiple strategies used to assess sea turtle, marine mammal and seabird bycatch in the WCR, with a particular focus on sea turtle bycatch. The research incorporated a synthetic review of the literature, expert consultation, statistical techniques, and geospatial analyses to assess the bycatch seascape for the region. I conclude that sea turtle bycatch in the WRC is significantly linked to turtle rookeries, especially those on the continental land mass and in the southern section of the Caribbean basin, in large part because of the near shore artisanal nature of the fisheries and the importance of these habitats for foraging and reproduction. The limited information on marine mammal bycatch does not permit robust inferences, but it clearly identifies threats to at least one vulnerable marine mammal species, the tucuxi (Sotalia fluviatilis). Information on seabird bycatch was even more limited; the most vulnerable seabird populations occur in the higher latitudes (temperate zones) while the seabird populations in the WCR face significant threats from habitat loss and over-exploitation. This dissertation proposes specific recommendations for improving and advancing the information base for a regional, ecosystem-level management and mitigation of bycatch.

Alien species are considered one of the primary threats to native plant populations and their control is often prominent among proposed management actions. While negative alien effects are well documented, there are also many ways that alien species can have positive effects on native plant populations that may actually contribute to their persistence. Moreover, the effect of alien species on native plants can change in magnitude and direction over varying abiotic conditions. The success of native plant populations is determined by a mix of ecological and genetic factors. Alien (and native) species and abiotic conditions could also drive selection of plant traits. In order to understand the drivers of native plant population success in the face of changing climate and increasing prevalence of alien species, it is vital to understand the relationship between genotype, phenotype, and fitness of native plants. In chapter one, I quantified the effects of neighboring alien and native plants on all demographic rates in a population of the Hawaiian endemic plant Schiedea globosa, performing biannual censuses for 4 years to encompass relatively harsh and as well as benign seasons and years. The effects of alien neighbors were mixed but most often positive across many demographic rates in both harsh and more benign abiotic conditions, suggesting that alien neighbors benefit S. globosa plants through multiple mechanisms, such as nurse plant effects and associational resistance. The effects of heterospecific native neighbors were less often positive, indicating fundamentally different effects of native and alien neighbors on the demography of the focal native. These mixed effects highlight the need to consider potential benefits of alien species in the management of threatened native plants and that those benefits may be altered by changing abiotic conditions. In chapter two, I constructed population models for multiple Schiedea species across populations and years, using demographic rate regressions driven by the effects of alien and native neighbors, integrating the mixed effects of alien and native species on demographic rates of populations to project the net effect on population growth of native populations. The effects of alien and heterospecific native plant neighbors were mixed but most often positive across many demographic rates in both harsh and more benign abiotic conditions, suggesting that alien and native neighbors benefit native plants through multiple mechanisms, such as nurse plant effects and associational resistance. The effect of alien and heterospecific native neighbors on population growth was generally positive-- the mixed, but largely positive, net effects of alien and native neighbors on population growth highlight the need to consider potential benefits of alien, as well as native, species in the management of at-risk native plant populations, and that those benefits may be altered by changing abiotic conditions, as indicated by differing effects across (and within) years and populations. In chapter 3, I used paternal half-sibship pairs to measure the heritability of morphological traits under field conditions of the critically endangered Schiedea adamantis, which were found to be heritable in prior studies in greenhouse conditions, in reintroduced populations. I also performed a selection analysis, regressing fitness components against traits of outplants that I hypothesized might influence response to climate and alien and native neighbors to study the relationship between genotype, phenotype, and fitness of plants in restoration outplantings and assessing potential for evolutionary rescue. I found no significant heritability of any of the morphological traits. I did find evidence of selection, as leaf shape, area, and whole plant morphology had significant effects on fitness components (growth, survival, and reproduction), and significant interaction effects showing traits influenced fitness components differently at different levels of shade. Together, these results suggest that while variation in traits benefit individual plants in differing field conditions, these outplantings may not have the ability to respond to selection through evolution.

The Northern Andes stands as a bastion of unique and narrowly distributed global biodiversity. However, it has also experienced rapid transformation of habitats, posing a serious threat to species in the wild by shrinking their ranges. In this dissertation, I aim to deepen our comprehension of how species react to global changes, pinpointing areas where conservation efforts are lacking and highlighting urgent conservation priorities. Moreover, I demonstrate tangible conservation strategies designed to safeguard vulnerable species, while also prioritizing potential exploration regions to confirm the extent of their ranges.In the first chapter, I assess elevational retreats of nearly 200 range-restricted birds from their lower and upper elevational ranges (Medina et al. 2023). Using abundant crowd-sourced data from the Cornell Lab of Ornithology database, eBird, and the Global Biodiversity Information Facility, I examine whether species shifted their elevational ranges over time by comparing observed versus expected occurrences below a low elevational threshold and above a high elevational threshold for two periods: before and after 2005. I also test for deforestation effects at lower elevations within each species’ distribution ranges. Species’ retreats from lower elevations are ubiquitous and involve a 23–40% decline in prevalence at the lowest elevations. Increases at higher elevations are not consistent. The retreats occur across a broad spectrum of species, from predominantly lowland to predominantly highland. Because deforestation show no relationship with species retreats, I contend that a warming climate is the most parsimonious explanation for such shifts. In the second chapter, I identify priority range-restricted bird species and their conservation hotspots in the Northern Andes (Medina et al. 2024). I employ updated maps of Area of Habitat (AOH), following a protocol I contributed along a set of experts from the Cornell Lab, Birdlife International, and American Bird Conservancy (Huang et al. 2021). In this protocol, I was tasked to build R and Python scripts capable to handle crowd-sourced data and batch-generate habitat maps for a thousand birds across the Americas. With the updated maps of species distribution, I estimate protection within each species’ AOH and for the cumulative distribution of birds. For the latter, I also calculate protection across the elevational gradient. I estimate how much additional protection community lands (Indigenous and Afro-Latin American lands) would contribute if they were conservation-focused. AOHs ranged from 8 to 141,000 km2. I identify four conservation priorities based on cumulative species richness. These priorities are high-resolution mapped representations of Endemic Bird Areas for the Tropical Andes that should be considered critically important. Protected areas cover only 31% of the cumulative AOH, but community lands could add 19% more protection. Sixty-two per cent of the 335 species have ranges smaller than their published estimates, yet IUCN designates only 23% of these as Threatened. Top 50 priority species concentrate in areas of low protection near community lands and at middle elevations where, on average, only 34% of the land is protected. I highlight the importance of collaborative efforts among stakeholders: governments should support private and community-based conservation practices to protect the region with the most range-restricted birds worldwide. Private reserves hold promise for the restoration of degraded landscapes and the protection of fragmented animal populations. In the third chapter, I advocate for the creation and implementation of private reserves as concluded in the previous chapter, drawing upon a case study from the Eastern Andes of Colombia to illustrate their potential. This study examines the rehabilitation efforts spanning four decades within Rogitama, aiming to assess their impact on mammal diversity and composition (Medina et al. 2021). Findings reveal the presence of 22 species, predominantly bats and rodents. These results mirror biodiversity levels akin to those observed in less disturbed areas of the Eastern Cordillera, indicating promising advances in ecosystem recovery within the reserve. I posit Rogitama, as a noteworthy case of successful plant rejuvenation, highlighting its significance in the broader context of biological conservation efforts. I firmly advocate for stakeholders to take heed of this case study as a blueprint for development in Northern Andean regions, where I have previously identified critical conservation gaps and priorities. In the last chapter, I identify species and areas that urgently need exploration to increase knowledge on distribution limits (Medina et al. in prep). I consider the AOH where there is less probability of finding a target species given its closeness to non-detection areas. These non-detection areas have checklists where a target species has yet to be reported. The proportion of species absent from an area over the species present will result in relatively uncertain areas. To define potential exploration sites, I mapped these areas along cumulative AOH for 281 species. I found priority exploration areas (high richness and high relative uncertainty) are relatively small compared to non-priority areas. Since 2000, human impact has penetrated 8% of priority areas and allowed 8% of the areas to be studied. Deforestation has progressively reduced, but some countries are still dealing with it. Protection along the priority regions is low. It is essential that governments devote more efforts to exploring biodiversity to better understand patterns in species distribution and thus develop accurate conservation and management plans.

Sea turtles are long lived marine species that are currently endangered because their life history and population dynamics hinder them from withstanding modern anthropogenic threats. Worldwide, fisheries bycatch in on the major threats to the survival of sea turtles and that is also the case in the Eastern Pacific. To establish regional conservation priorities for the mitigation of bycatch, it is essential to first obtain a comprehensive picture of the regional sea turtle bycatch situation. This comprehensive analysis was lacking for the Eastern Pacific; therefore one component of this dissertation (the first chapter) is focused on delivering a regional bycatch analysis for the Eastern Pacific. A literature review was conducted to obtain numbers of turtles captured, frequencies, bycatch and mortality rates per species and country in trawl, longline, and gillnet fisheries, and to compile results of mitigation measures. Moreover, estimates for current annual capture rates in trawl fisheries were obtained and compared with population numbers.

This regional bycatch used all the information compiled and synthesized to give conservation priorities at the regional level. The review underlines the high bycatch rates in trawls for Costa Rica, Guatemala, and El Salvador and the detrimental impact that these captures could have specially for hawksbill Eretmochelys imbricata due to its reduced population numbers and for green turtle Chelonia mydas due to its highest mortality rate. It also emphasizes the continuous lack of use of TEDs as a bycatch mitigation measure. In longline fisheries, the review identifies the high bycatch rates in pelagic longline fisheries of Costa Rica, Ecuador, and Nicaragua in a global context but given that olive ridley Lepidochelys olivacea is the most common species captured in these countries, it highlights the capture of loggerhead Caretta caretta and leatherback Dermochelys coriacea off Peru and Chile due to their small population numbers. Bottom longlines have high mortality rates compared with pelagic longlines in the region and the review identifies a need for further research in this area due to the scarce information but high mortality rates. The review also noted that some mitigation measures for pelagic longlines like circle hooks and hooks with appendages could bring improvements in the mitigation of bycatch in longline fisheries in the region, there is still considerable work to be done in technology transfer, sea turtle handling, and estimates of post-release mortality rates.

For gillnet fisheries, the most important highlight is how little information exists for the region given the high rates of bycatch for sea turtles in this gear. However, the difficulties of studying bycatch in highly dynamic and artisanal fisheries are recognized as the major impediment for this situation. Nevertheless, the high bycatch rates in areas where sea turtles congregate in high numbers like in foraging grounds for loggerhead in Baja California, Mexico and for greens in Paracas and Sechura, Peru, calls for either gear modifications (which has not been that successful), change of gear, or areas closed for gillnets.

The second half of the dissertation is focused on foraging ecology of oceanic sea turtles in the Southeast Pacific Ocean. Sea turtles in the oceanic stage are the least known stage due to the difficulty of accessing these individuals. However, it is a very important stage in the life cycle and can be critical for the population dynamics of sea turtles as some population models have shown. Therefore, this dissertation is filling a gap in the life cycle of sea turtle populations in the Eastern Pacific.

To study foraging ecology, we used Stable Isotope Analysis (SIA) of turtle tissues as well as potential prey items from the oceanic realm. SIA is a great tool because it gives an integrated view, from days to weeks, of prey from a consumer tissue. SIA also can be used to link consumers to habitats when elements that have spatial trends are used. In chapter two, we investigate the foraging ecology of three species of sea turtles to compare trophic status and to observe if spatial patterns were shown in the SIA signatures of sea turtles. To our knowledge this is the first study employing SIA to research the ecology of three species of sea turtles from the same time and space. Our results show that spatial patterns in delta15N and delta13C were observed in sea turtle's tissues as correlations with latitude. We also found that loggerhead's signatures differed significantly from green and olive ridleys, especially in terms of delta15N. Loggerheads had higher values of delta15N and also a wider nitrogen trophic niche. Greens and olive ridleys were similar in isotopic nitrogen values but they were significantly different in carbon. When analyzing a smaller group of animals captured in a more restricted area, nitrogen differences were not found which suggests that latitudinal spatial patterns play an important role in the nitrogen signature. On the contrary, carbon signatures still differed among turtles in the restricted area which suggest that the inshore-offshore trend is strong and made us conclude that loggerheads are restricted to oceanic areas but that greens and olive ridleys could be using both coastal and oceanic areas.

In chapter three, we conduct a mixing model analysis using the Bayesian program SIAR to identify the most important prey items for green, olive ridley, and loggerhead off Peru. Also, we wanted to identify the contribution of longline baits in the diet of oceanic turtles. The analysis was restricted to the central zone of our study area to avoid spatial trends in nitrogen. To use as sources in the model, we collected potential prey items offshore Peru during trips on longline fishing vessels and obtained their stable isotope signatures. Results from our mixing models show that for greens and olive ridleys, crustaceans, mollusks, and coastal Ulva (indicator of coastal prey) were the only important food items. In the case of greens, crustaceans had a very high proportional contribution and due to the fact that nitrogen values of crustaceans were the lowest ones among the sources it seems that greens would be eating in a lower trophic level. The importance of coastal Ulva for greens and olive ridleys is a confirmation of our findings from chapter two where we suggest that these two species could be using oceanic as well as coastal areas.

Results for loggerheads showed cnidarians, mollusks, mackerel and squid bait as foraging items and highlights the differences among this species and the other two. The lack of importance of coastal Ulva again suggests that loggerheads remain only in oceanic areas off Peru. Moreover, the importance of mackerel and squid, the most common longline baits, suggests this species is the one interacting the most with longline fisheries and that cumulative effect of multiple interactions could have a detrimental effect in this population.

China is one of the most biodiverse countries in the world, harboring more than 10% of the species in the world. Among them, 11% of the vertebrate genera and 7% plant genera are endemic to China. During its rapid social and economic development, increasing habitat loss and fragmentation have occurred. However, it wakes up to the threats of biodiversity in recent years. Protected areas, as an essential conservation tool to reduce habitat loss and species extinction have expanded dramatically in China. Protected areas with various other concepts such as umbrella species and payment for ecosystem services have been promoted to conserve the biodiversity. However, questions remain that whether they work, how they work and how we could do better. It is crucial to answer these questions with the data and technology that are more available to us now.

Thus, my dissertation divides into four chapters and tackles the following four questions. 1) Where do the most of the endemic species concentrate in China? Do umbrellas species such as giant pandas effectively protect other species? 2) With the increasing of tree plantation and available remote sensing data, how does it change the available habitat for forest species, their threat levels and priority setting? 3) Within the conservation priority areas, new threats that are hardly detected by traditional evaluation index such as forest cover emerge. How does a prevalent human disturbance - livestock grazing impact the conservation of giant pandas? What are the socio-economic drivers and solutions to this issue? 4) To better monitor the population and evaluate conservation efforts, new techniques need to be added. Can we use footprints from wild pandas to identify individuals and provide a cost-effective alternative to the current methods?

In Chapter 1, I first used detailed data on geographical ranges for endemic forest species to identify patterns of species richness. After refining each species' range by its known elevational range and remaining forest habitats as determined from remote sensing, I identified the top 5% richest areas as the centers of endemism. Over 96% of the panda habitat overlapped the endemic centers. Thus, investing in almost any panda habitats will benefit many other endemics. Existing panda national nature reserves cover all but one of the endemic species that overlap with the panda’s distribution. For whole China, of particular interest are 14 mammal, 20 bird, and 82 amphibian species that are inadequately protected. Most of these the IUCN currently deems threatened. But 7 mammal, 3 bird, and 20 amphibian species are currently non-threatened, yet their geographical ranges are <20,000 km2 which is the threshold for IUCN to consider it as threatened. There is a high concentration of these species in the east Daxiang and Xiaoxiang Mountains of Sichuan where pandas are absent and where there are no national nature reserves. The others concentrate in Yunnan, Nan Mountains and Hainan. Here, ten prefectures might establish new protected areas or upgrade local nature reserves to national status.

In Chapter 2, I used remote sensing data to differentiate oil palm and rubber plantation from natural forests in Southeast Asia and reevaluated the threat level of endemic forest species identified by IUCN. Tropical, mainland Southeast Asia is under exceptional threat, yet relatively poorly known. This region contains over 122, 183, and 214 endemic mammals, birds, and amphibians, respectively, of which the IUCN considers 37, 21, and 37 threatened. When corrected for the amount of remaining natural habitats, the average sizes of species ranges shrink to <40% of their published ranges and more than 42 percent of species face a much higher risk of extinction from habitat loss than previously thought. Moreover, these species are not better protected by the existing network of protected areas than are species that IUCN accepts as threatened. Furthermore, incorporating remote sensing data showing where habitat loss is prevalent changes the locations of conservation priorities.

Chapter three focuses on a specific threat - livestock grazing in the endemic center that I identified in the first chapter. With the Natural Forest Conservation Program and Grain to Green programs, the deforestation that was once the biggest threat to pandas has been halted. However, a previously unrecognized threat is emerging. Livestock grazing has become the most prevalent human disturbance throughout panda habitats. I applied field sign survey, vegetation survey, GPS collar tracking, and species distribution modeling to study how the livestock grazing impacts the habitat use of giant pandas. This study shows that livestock grazing especially from horses has caused a dramatic decline in bamboos and reduced its regeneration. In the past 15 years, pandas have changed its habitat use and are driven out of areas that are heavily used by livestock. 49% of panda habitat has been lost especially in the lower elevation areas from 2004 till now due to impacts of livestock. Loss of income because of the policies Natural Forest Conservation Project and Grain for Green projects, reduced tourists because of dam construction and earthquake, encouraged horse riding practice during the development of ICDP have contributed to the increasing dependence on livestock sector. Livestock ban with payment for ecosystem services or feedlot operation could be possible solutions for this issue.

Chapter four explores the innovative technique to identify giant panda individuals to facilitate better conservation. Two methods have been used previously to identify individuals and population for giant pandas, fecal bamboo bite size combined with home range analysis and microsatellite analysis of fecal DNA. However, the first one suffers from the lack of accuracy and the latter one is limited by the freshness of the fecal sample and high cost. I developed the footprint identification technique in JMP based on two multivariate methods: discriminant analysis and the canonical centroid plot method using the anatomy measurements of footprints. I used 30 captive pandas to develop the algorithm and 11 individuals for validation. The overall accuracy of FIT for individual identification is 90% and sex discrimination is 85%. This technique is embedded in FIT as an add-in and free for conservation practitioners now.

In summary, this dissertation includes the following four papers.

Chapter 1, Li and Pimm. 2016. China's endemic vertebrates sheltering under the protective umbrella of the giant panda. Conservation Biology 30:329-339.

Chapter 2, Li et al., 2016. Remotely sensed data informs Red List evaluations and conservation priorities in Southeast Asia. PloS one, 11(8), e0160566.

Chapter 3, Li et al., Emerging threat from livestock on giant panda conservation

Chapter 4, Li et al., Identifying individual and sex of giant pandas through Footprint Identification Technique.

With supporting information from the following publication during my Ph.D.:

Li, B. et al. 2014. Effects of feral cats on the evolution of anti-predator behaviours in island reptiles: insights from an ancient introduction. Proc. R. Soc. B 281: 20140339.

Ocampo-Peñuela, N., Jenkins, C. N, Vijay, V., Li, B.V., & Pimm., S.L. 2016. Incorporating explicit geospatial data shows more species at risk of extinction than the current Red List. Science Advances, 2(11), e1601367.

Pimm, S.L., Harris, G., Jenkins, C.N., Ocampo-Peñuela, N. & Li, B.V. 2016 Unfulfilled promise of data-driven approaches: response to Peterson et al. Conservation Biology, In press.

Few areas of the planet are untouched by human actions, be they marine or terrestrial. Marine habitats face disturbance from overexploitation of fisheries and pollution while terrestrial habitats face significant threat from land cover conversion and degradation. To address these threats, conservationists utilize a variety of population viability analyses to both assess and manage species’ health. The results of these analyses often play a key role in determining when intervention is necessary and which actions will be the most successful. Within this dissertation, I used several population modeling approaches to advance our understanding of changes in the landscape on the persistence of populations and by extension, species.

This dissertation may be broadly divided into two halves, the first assessing a single, local population and the second evaluating metapopulations. In Chapter 2, I combined telemetry data on sooty terns (Onychoprion fuscatus) with a long-term capture-mark-recapture dataset from the Dry Tortugas National Park to map the movements at sea for this species, calculate estimates of mortality, and investigate the impact of hurricanes on a migratory seabird. Included in the latter analysis is information on the locations of recovered bands from deceased individuals wrecked by tropical storms. I present the first known map of sooty tern migration in the Atlantic Ocean. The results indicate that the birds had minor overlaps with areas affected by the major 2010 oil spill and a major shrimp fishery. Indices of hurricane strength and occurrence are positively correlated with annual mortality and indices of numbers of wrecked birds. As climate change may lead to an increase in severity and frequency of major hurricanes, this may pose a long-term problem for this colony.

In the latter half of this dissertation, I utilized a variety of metapopulation analyses for conservation at multiple scales. As a landscape becomes increasingly fragmented through habitat loss, the individual patches become smaller and more isolated and thus less likely to sustain a local population. Metapopulation theory is appropriate for analyzing fragmented landscapes because it combines empirical landscapes features with species-specific information to produce direct information on population extinction risks. Combining a spatially explicit metapopulation model with empirical data on endemic species’ ranges and maps of habitat cover, I could calculate the metapopulation capacity— a measure of a landscape’s ability to sustain a metapopulation.

Mangroves provide an ideal, model landscape for my analysis in Chapter 3. Of conservation concern, one can easily delineate their patch boundaries. I calculated metapopulation capacity for 99 metapopulations from 32 different mangrove-endemic bird species globally in the years 2000 and 2015. Northern Australia and South East Asia have the highest richness of mangrove-endemic birds, with some hotspots also occurring in Guyana and French Guiana. The areas with the highest metapopulation loss are the Caribbean, the Pacific coast of Central America, Madagascar, Borneo, and isolated patches in Southeast Asia in Burma and Malaysia. Regions with the highest loss of habitat area are not necessarily those with the highest loss of metapopulation capacity. Often it is not a matter of how much, but how the habitat is lost since fragmentation of patches has a complicated relationship with extinction risk.

After analyzing the effects of habitat loss and fragmentation on a species’ risk of extinction, it is natural to examine the reverse, the restoration of habitat. In Chapter 4, I used metapopulation models to prioritize locations for potential habitat corridors. I compared these results to standard connectivity models that have grown in popularity to illustrate how together they provide a more complete set of recommendations for the recovery of species. For this chapter, I use the golden lion tamarin (Leontopithecus rosalia) as the focal species. Endemic to the highly fragmented Atlantic coastal forest of Brazil, the golden lion tamarins are a highly studied species of top conservation concern. I identified the best locations for habitat restoration to increase metapopulation capacity and how they compare with movement of individuals in the current landscape. I also evaluated how a previous corridor restoration ranked according to these methods and how it effects future conservation planning. While large, occupied patches are significant for both sets of models, metapopulation models also indicate the importance of nearby, medium-sized empty patches that if connected by a corridor would facilitate the growth and recovery of tamarin populations.

In summary, I applied a suite of population modeling techniques to an assortment of landscapes and species for conserving biodiversity. Despite the variety of models used, I illustrate the flexibility and utility of population ecology to conservation management.

Human use of the oceans is increasingly in conflict with conservation of endangered species. Methods for managing the spatial and temporal placement of industries such as military, fishing, transportation and offshore energy, have historically been post hoc; i.e. the time and place of human activity is often already determined before assessment of environmental impacts. In this dissertation, I build robust species distribution models in two case study areas, US Atlantic (Best et al. 2012) and British Columbia (Best et al. 2015), predicting presence and abundance respectively, from scientific surveys. These models are then applied to novel decision frameworks for preemptively suggesting optimal placement of human activities in space and time to minimize ecological impacts: siting for offshore wind energy development, and routing ships to minimize risk of striking whales. Both decision frameworks relate the tradeoff between conservation risk and industry profit with synchronized variable and map views as online spatial decision support systems.

For siting offshore wind energy development (OWED) in the U.S. Atlantic (chapter 4), bird density maps are combined across species with weights of OWED sensitivity to collision and displacement and 10 km2 sites are compared against OWED profitability based on average annual wind speed at 90m hub heights and distance to transmission grid. A spatial decision support system enables toggling between the map and tradeoff plot views by site. A selected site can be inspected for sensitivity to a cetaceans throughout the year, so as to capture months of the year which minimize episodic impacts of pre-operational activities such as seismic airgun surveying and pile driving.

Routing ships to avoid whale strikes (chapter 5) can be similarly viewed as a tradeoff, but is a different problem spatially. A cumulative cost surface is generated from density surface maps and conservation status of cetaceans, before applying as a resistance surface to calculate least-cost routes between start and end locations, i.e. ports and entrance locations to study areas. Varying a multiplier to the cost surface enables calculation of multiple routes with different costs to conservation of cetaceans versus cost to transportation industry, measured as distance. Similar to the siting chapter, a spatial decisions support system enables toggling between the map and tradeoff plot view of proposed routes. The user can also input arbitrary start and end locations to calculate the tradeoff on the fly.

Essential to the input of these decision frameworks are distributions of the species. The two preceding chapters comprise species distribution models from two case study areas, U.S. Atlantic (chapter 2) and British Columbia (chapter 3), predicting presence and density, respectively. Although density is preferred to estimate potential biological removal, per Marine Mammal Protection Act requirements in the U.S., all the necessary parameters, especially distance and angle of observation, are less readily available across publicly mined datasets.

In the case of predicting cetacean presence in the U.S. Atlantic (chapter 2), I extracted datasets from the online OBIS-SEAMAP geo-database, and integrated scientific surveys conducted by ship (n=36) and aircraft (n=16), weighting a Generalized Additive Model by minutes surveyed within space-time grid cells to harmonize effort between the two survey platforms. For each of 16 cetacean species guilds, I predicted the probability of occurrence from static environmental variables (water depth, distance to shore, distance to continental shelf break) and time-varying conditions (monthly sea-surface temperature). To generate maps of presence vs. absence, Receiver Operator Characteristic (ROC) curves were used to define the optimal threshold that minimizes false positive and false negative error rates. I integrated model outputs, including tables (species in guilds, input surveys) and plots (fit of environmental variables, ROC curve), into an online spatial decision support system, allowing for easy navigation of models by taxon, region, season, and data provider.

For predicting cetacean density within the inner waters of British Columbia (chapter 3), I calculated density from systematic, line-transect marine mammal surveys over multiple years and seasons (summer 2004, 2005, 2008, and spring/autumn 2007) conducted by Raincoast Conservation Foundation. Abundance estimates were calculated using two different methods: Conventional Distance Sampling (CDS) and Density Surface Modelling (DSM). CDS generates a single density estimate for each stratum, whereas DSM explicitly models spatial variation and offers potential for greater precision by incorporating environmental predictors. Although DSM yields a more relevant product for the purposes of marine spatial planning, CDS has proven to be useful in cases where there are fewer observations available for seasonal and inter-annual comparison, particularly for the scarcely observed elephant seal. Abundance estimates are provided on a stratum-specific basis. Steller sea lions and harbour seals are further differentiated by ‘hauled out’ and ‘in water’. This analysis updates previous estimates (Williams & Thomas 2007) by including additional years of effort, providing greater spatial precision with the DSM method over CDS, novel reporting for spring and autumn seasons (rather than summer alone), and providing new abundance estimates for Steller sea lion and northern elephant seal. In addition to providing a baseline of marine mammal abundance and distribution, against which future changes can be compared, this information offers the opportunity to assess the risks posed to marine mammals by existing and emerging threats, such as fisheries bycatch, ship strikes, and increased oil spill and ocean noise issues associated with increases of container ship and oil tanker traffic in British Columbia’s continental shelf waters.

Starting with marine animal observations at specific coordinates and times, I combine these data with environmental data, often satellite derived, to produce seascape predictions generalizable in space and time. These habitat-based models enable prediction of encounter rates and, in the case of density surface models, abundance that can then be applied to management scenarios. Specific human activities, OWED and shipping, are then compared within a tradeoff decision support framework, enabling interchangeable map and tradeoff plot views. These products make complex processes transparent for gaming conservation, industry and stakeholders towards optimal marine spatial management, fundamental to the tenets of marine spatial planning, ecosystem-based management and dynamic ocean management.

Antillean manatees (Trichechus manatus manatus) were heavily hunted in the past throughout the Wider Caribbean Region (WCR), and are currently listed as endangered on the IUCN Red List of Threatened Species. In most WCR countries, including Haiti and the Dominican Republic, remaining manatee populations are believed to be small and declining, but current information is needed on their status, distribution, and local threats to the species.

To assess the past and current distribution and conservation status of the Antillean manatee in Hispaniola, I conducted a systematic review of documentary archives dating from the pre-Columbian era to 2013. I then surveyed more than 670 artisanal fishers from Haiti and the Dominican Republic in 2013-2014 using a standardized questionnaire. Finally, to identify important areas for manatees in the Dominican Republic, I developed a country-wide ensemble model of manatee distribution, and compared modeled hotspots with those identified by fishers.

Manatees were historically abundant in Hispaniola, but were hunted for their meat and became relatively rare by the end of the 19th century. The use of manatee body parts diversified with time to include their oil, skin, and bones. Traditional uses for folk medicine and handcrafts persist today in coastal communities in the Dominican Republic. Most threats to Antillean manatees in Hispaniola are anthropogenic in nature, and most mortality is caused by fisheries. I estimated a minimum island-wide annual mortality of approximately 20 animals. To understand the impact of this level of mortality, and to provide a baseline for measuring the success of future conservation actions, the Dominican Republic and Haiti should work together to obtain a reliable estimate of the current population size of manatees in Hispaniola.

In Haiti, the survey of fishers showed a wider distribution range of the species than suggested by the documentary archive review: fishers reported recent manatee sightings in seven of nine coastal departments, and three manatee hotspot areas were identified in the north, central, and south coasts. Thus, the contracted manatee distribution range suggested by the documentary archive review likely reflects a lack of research in Haiti. Both the review and the interviews agreed that manatees no longer occupy freshwater habitats in the country. In general, more dedicated manatee studies are needed in Haiti, employing aerial, land, or boat surveys.

In the Dominican Republic, the documentary archive review and the survey of fishers showed that manatees still occur throughout the country, and occasionally occupy freshwater habitats. Monte Cristi province in the north coast, and Barahona province in the south coast, were identified as focal areas. Sighting reports of manatees decreased from Monte Cristi eastwards to the adjacent province in the Dominican Republic, and westwards into Haiti. Along the north coast of Haiti, the number of manatee sighting and capture reports decreased with increasing distance to Monte Cristi province. There was good agreement among the modeled manatee hotspots, hotspots identified by fishers, and hotspots identified during previous dedicated manatee studies. The concordance of these results suggests that the distribution and patterns of habitat use of manatees in the Dominican Republic have not changed dramatically in over 30 years, and that the remaining manatees exhibit some degree of site fidelity. The ensemble modeling approach used in the present study produced accurate and detailed maps of manatee distribution with minimum data requirements. This modeling strategy is replicable and readily transferable to other countries in the Caribbean or elsewhere with limited data on a species of interest.

The intrinsic value of manatees was stronger for artisanal fishers in the Dominican Republic than in Haiti, and most Dominican fishers showed a positive attitude towards manatee conservation. The Dominican Republic is an upper middle income country with a high Human Development Index. It possesses a legal framework that specifically protects manatees, and has a greater number of marine protected areas, more dedicated manatee studies, and more manatee education and awareness campaigns than Haiti. The constant presence of manatees in specific coastal segments of the Dominican Republic, the perceived decline in the number of manatee captures, and a more conservation-minded public, offer hope for manatee conservation, as non-consumptive uses of manatees become more popular. I recommend a series of conservation actions in the Dominican Republic, including: reducing risks to manatees from harmful fishing gear and watercraft at confirmed manatee hotspots; providing alternative economic alternatives for displaced fishers, and developing responsible ecotourism ventures for manatee watching; improving law enforcement to reduce fisheries-related manatee deaths, stop the illegal trade in manatee body parts, and better protect manatee habitat; and continuing education and awareness campaigns for coastal communities near manatee hotspots.

In contrast, most fishers in Haiti continue to value manatees as a source of food and income, and showed a generally negative attitude towards manatee conservation. Haiti is a low income country with a low Human Development Index. Only a single dedicated manatee study has been conducted in Haiti, and manatees are not officially protected. Positive initiatives for manatees in Haiti include: protected areas declared in 2013 and 2014 that enclose two of the manatee hotspots identified in the present study; and local organizations that are currently working on coastal and marine environmental issues, including research and education on marine mammals. Future conservation efforts for manatees in Haiti should focus on addressing poverty and providing viable economic alternatives for coastal communities. I recommend a community partnership approach for manatee conservation, paired with education and awareness campaigns to inform coastal communities about the conservation situation of manatees in Haiti, and to help change their perceived value. Haiti should also provide legal protection for manatees and their habitat.

Global climate change can cause shifts in species distributions, and increases in some of their competitors, predators, and diseases that might even cause their extinction. Species may respond to a warming climate by moving to higher latitudes or elevations. Shifts in geographic ranges are common responses in temperate regions. For the tropics, latitudinal temperature gradients are shallow: the only escape for species may be to move to higher elevations. There are few data to suggest that they do, and our understanding of the process is still very limited. Yet, the greatest loss of species from climate disruption may be for tropical montane species. To better understand the potential process of elevational range shifts in the tropics and their implications we have to: 1) Build theoretical models for the process of range shifting, 2) Evaluate potential constraints that species could face while moving to higher elevations, 3) Obtain empirical evidence confirming the uphill shift of species ranges, 4) Determine the number of extinctions that could arise from elevational range shifts (mountain top extinctions) and 5) Identify vulnerable species and areas, and determine their representation by the Protected Areas Network. The purpose of this dissertation is to address these issues, by applying novel methods and collecting empirical evidence.

In the second chapter I incorporated temperature gradients and land-cover data from the current ranges of species in a model of range shifts in response to climate change. I tested 4 possible scenarios of amphibian movement on a tropical mountain and estimated the constraints to range shifts imposed by each scenario. Confirming the occurrence of elevational range shifts with empirical data is also essential, but requires historical data as a baseline for comparison. I repeated a historical transect in Peru, sampling birds at the same locations they were sampled 40 years ago, and compared their elevational ranges between sampling occasions to evaluate if they were moving uphill as a response to warming temperatures. Finally, based on the results from this comparison, I estimated the potential extinctions derived from elevational range shifts, using information on the species distribution, the topography and land cover within the ranges and surrounding areas. I evaluated the extent of mountain top extinctions for 172 bird species with restricted ranges in the northern Andes. I also considered how Colombia's protected Area Network represents species and sites that are vulnerable in the face of climate change.

More than 30% of the range of 21 of 46 amphibian species in the tropical Sierra Nevada de Santa Marta is likely to become isolated as climate changes. More than 30% of the range of 13 amphibian species would shift to areas that currently are unlikely to sustain survival and reproduction. Combined, over 70% of the current range of 7 species would become thermally isolated or shift to areas that currently are unlikely to support survival and reproduction. The constraints on species' movements to higher elevations in response to climate change can increase considerably the number of species threatened by climate change in tropical mountains.

In the comparison of bird distributions in the Cerrros del Sira, in Peru, I found an average upward shift of 49 m for 55 bird species over a 41 year interval. This shift is significantly upward, but also significantly smaller than the 152 m one expects from warming in the region. The range shifts in elevation were similar across different trophic guilds. Endothermy may provide birds with some flexibility to temperature changes and allow them to move less than expected. Instead of being directly dependent on temperature, birds may be responding to gradual changes in the nature of the habitat or availability of food resources, and presence of competitors. If so, this has important implications for estimates of mountaintop extinctions from climate change.

The estimated number of mountain top extinctions from climate disruption in the northern Andes is low, both the absolute number (5 species) and the relative number (less than 0.5% of Colombian land birds). According to future climate predictions these extinctions will not likely occur in this century. The extent of species loss in the Andes is not predicted by absolute mountaintop extinctions modeled by the kind of processes most other studies use. Rather, it is highly contingent -- the species will survive or not depending on how well we protect their much reduced ranges from the variety of other threats.

Estimates of the energetic costs of locomotion (COL) are necessary to understand one of the potential impacts of anthropogenic disturbance on marine mammals. A new generation of biologging devices has enabled the measurement of fine-scale behavioral responses to disturbance, but calibration experiments are required to convert these measured changes in activity level into energy expenditure. Such calibrations have been conducted in many terrestrial and avian taxa but, due to logistical constraints, have been performed with only a few marine mammals. Very few studies have tested these calibrations against independent estimates of energy expenditure, such as measurements of caloric intake and the doubly labeled water (DLW) method. Calibration studies will help us to better understand how best to estimate energy expenditure from activity measurements. In my dissertation, I ask whether short-term increases in activity caused by disturbance may impact marine mammal energy budgets. I address this question with the long-term resident community of common bottlenose dolphins (Tursiops truncatus) living in Sarasota Bay, Florida, which experiences very high levels of traffic from small vessels. I first correlated overall dynamic body acceleration (ODBA) and energy expenditure with bottlenose dolphins in human care. I combined measurements of ODBA derived from accelerometry tags with respirometry during submerged swim trials. I then subtracted measured resting metabolic rate (RMR) from the energy expenditure of each trial to estimate COL. I found a linear relationship between ODBA and COL. Next, I deployed tags on the same dolphins for longer periods (24 hours) and combined COL, RMR, and specific dynamic action (SDA; energy expenditure associated with digestion) to estimate total daily energy expenditure. I compared this estimate of total daily expenditure with estimates derived from measurements of caloric intake records and DLW. The COL+RMR+SDA values largely agreed with the calories ingested, but the smaller DLW sample was considerably more variable. I then used the correlation between ODBA and COL to estimate the cumulative energetic costs associated with responses to vessels by wild dolphins in Sarasota. I analyzed 12 digital acoustic tag (DTAG) records for the presence or absence of vessels. I used periods without vessels as controls to calculate baseline estimates of COL for each animal. I then subtracted this baseline from total COL to derive the cumulative COL attributable to vessels. The overall increase in COL attributable to the response to vessels was less than 0.3% of estimated daily energy expenditure, suggesting that avoidance, while necessary to prevent injury or death, does not contribute significantly to the daily energy budgets of these dolphins. The methods I developed can be applied to a variety of other marine mammals to study the fitness consequences of anthropogenic disturbance. Future studies should focus on sensitive species that are likely to exhibit significant avoidance responses to acoustic stimuli.

High-resolution bio-logging tools were used to examine the fine-scale foraging behaviors of humpback whales (Megaptera novaeangliae) in the coastal waters of the Western Antarctic Peninsula during the austral autumn of 2009 and 2010. Discrete feeding events (i.e., lunges) were inferred from the biologging records of thirteen whales, including a mother and her calf. In general, humpback whales exhibited efficient foraging behaviors that allowed them to maximize energetic gains and minimize energetic costs as predicted by optimal foraging theory. They fed at a continuous and high rate in the upper portion of the water column (< 100 m) from approximately dusk to dawn when their prey (Antarctic krill, Euphausia superba) were most vulnerable and less costly to acquire (i.e., near the surface). When forced to dive to greater depths, they adjusted their behaviors (e.g., descent and ascent rates) so that they could maximize their foraging durations and increase their lunging rates. In addition, humpbacks appeared to accept short term (i.e., dive by dive) costs associated with depleted oxygen stores in favor of maximizing long term (i.e., daily) energetic gains. Such efficient behaviors are particularly beneficial for mother-calf pairs who have additional energetic costs associated with foraging, such as lactation (mother), growth (calf), and maintaining proximity. In addition, because the physiology of humpback whales is poorly understood yet critically important for predicting their behaviors in response to fluctuations in their environmental conditions, foraging behaviors inferred from the bio-logging records were used to estimate their metabolic rates, oxygen storage capacities, and oxygen replenishment rates under the framework of optimal foraging theory. This research suggests that the current techniques used to estimate humpback whale oxygen stores is appropriate but that the estimation of metabolic rates of humpbacks while foraging and while traveling need to be addressed further. This work aims to increase the current understanding of humpback whale foraging behaviors along the Western Antarctic Peninsula so that appropriate measures can be taken to aid in their recovery and in the sustainability of the Antarctic marine ecosystem.

Forest elephants (Loxodonta cyclotis), the smallest and least studied of the three extant elephant species, predominately inhabit the Guinean and Congolian tropical forests from Guinea to the Democratic Republic of Congo. Known as ecosystem engineers, forest elephants create and maintain forest habitat, shape faunal communities, transport nutrients, and disperse seeds to distant areas. Despite their essential ecological role, very little is known about forest elephant social behavior. Living in social groups provides individuals with many benefits, including information about resources, protection from predators, and access to mates. For highly social species, like elephants, understanding social behavior is crucial to implementing sustainable conservation practices and mitigating the negative impacts of human development. To date, what is known about forest elephant social behavior originates from observations in baïs – mineral rich forest clearings. As a result, our understanding is limited by the short periods of time forest elephants spend in baïs, less than 2% of their time, and the small area relative to the rest of their home range and lifespan that we are able to observe. In this dissertation, I present research from the first project to attempt to understand elephant social interactions from throughout the range of habitats that forest elephants exploit on a daily basis, including dense, closed-canopy forest. I combine genetic and satellite technologies (GPS tracking and remote sensing) using novel computational methods to address: (1) factors that influence fluctuations in forest elephant group size; (2) forest elephant group age-sex composition and the factors influencing the probability of interactions between two elephants; and (3) improvements to forest elephant monitoring via line transect surveys for dung by creating an adaptive dung decay model. I conclude that: (1) group size is variable with forest elephants displaying a fission-fusion social system – a flexible social system in which individuals or sub-groups intermittently join other groups – across habitats in response to fruit availability and human disturbance; (2) interaction between individuals is influenced by social, but not environmental, factors and forest elephants spend more time in mixed sex groups than Asian or savanna elephants; and (3) estimating dung degradation via remotely sensed imagery is a feasible, cost-efficient alternative or supplement to in-situ dung degradation studies for non-invasive population surveys. This dissertation highlights the value of untangling the complex interplay between environmental, social, and anthropogenic drivers of species group composition and social behavior to inform conservation action., the results herein will be informative for monitoring forest elephant populations and promoting human-elephant coexistence through improved management of potential conflict areas.

The eastern North Pacific right whale (NPRW; Eubalaena japonica) is one of the world’s rarest large whales, with fewer than 35 animals remaining. Foundational data on the distribution and biology of this species is lacking, hampering effective monitoring and conservation. In this dissertation, I used disparate ecological approaches – food web modeling and stable isotope analysis– to broaden our understanding of the distribution and trophic ecology of this rare whale. The right whale’s primary forging ground on the highly productive Southeastern Bering Sea shelf is experiencing a rapid decline in seasonal sea ice extent. Annual fall surveys of zooplankton in this region provides a data-rich resource to explore relationships between shifting environmental and right whale prey – the zooplankton genera Calanus, Neocalanus, and Thysanoessa. The results of these surveys have been used extensively in prior research to study zooplankton dynamics, but few studies have incorporated species interactions. I created a discrete-time Bayesian biophysical food web model of the Bering shelf zooplankton community to jointly model relationships between environmental covariates and individual zooplankton species during a warming period on the shelf (1996-2016). This model framework allowed me to quantify the contribution of density independence and density dependence to zooplankton community dynamics. Similar to the results of prior research, I found that sea ice dynamics drove density-independent growth across zooplankton species, but species interactions contributed only minimally to community dynamics. My results suggest that the presumed preferred prey of right whales, Calanus glacialis, will shift north with the decreasing sea ice cover to stay in cold bottom water conditions. Next, I used carbon and nitrogen stable isotope values in NPRW skin and baleen to study the distribution and foraging ecology of North Pacific right whales. Whale skin provides a seasonal snapshot of the whale's ecology (weeks to months prior to sampling), whereas right whale baleen can be used to reconstruct years of ecology history. I first analyzed carbon and nitrogen isotope values in right whale skin collected on the feeding grounds in recent decades (1997-2021) and modeled these data jointly to look for trends that correlated with sea ice cover and region. As part of this, I estimated the trophic level of NPRWs and constructed a map of baseline stable isotope values in the North Pacific using zooplankton. I used these regional source values in a mixing model of NPRW skin tissue to estimate the primary regional sources in NPRW skin samples. I found that skin biopsies collected on the feeding ground primarily reflected summer feeding, but analysis of the outer skin layer hints at possible spring distribution. I also found I found evidence of shifting distribution and individual foraging strategies with oceanographic conditions. Further I found evidence of shifts in baseline nitrogen isotope values and phytoplankton bloom composition with oceanographic conditions. I used similar methods to study migratory patterns of historical North Pacific right whales using samples of baleen obtained from the commercial whaling era. I analyzed carbon and nitrogen isotope values in six baleen plates collected from 1871 to 1961 to reconstruct the migratory patterns of these specimens. My results include the first documentation of migratory patterns, overwintering areas, year-round foraging ecology, and possible life history using stable isotope ratios. Overall, my dissertation illustrates the power of bringing disparate analytical approaches to the study of an extremely rare and data-limited species of baleen whale. My dissertation provides important new baseline information on the eastern population of North Pacific right whales, which managers can use to implement targeted monitoring programs.

Hawaiian monk seal abundance is currently declining by about 4% per year with current population estimates around 1,100 individuals. Although the overall population continues to decline, a small sub-population in the main Hawaiian Islands (MHI) appears to be increasing by roughly 6% per year. Monk seal conservation and recovery efforts in the MHI have been hindered by the perception that seals do not belong there, and that they compete with fisheries and damage coral reefs. Education and outreach efforts describing the actual impact of monk seals in the MHI are currently underway, but we actually know very little about their at-sea behavior, especially in the MHI, even though Hawaiian monk seals have been studied extensively since the 1980s. The central objective of my dissertation was to describe monk seal behavior and develop a baseline for monk seal foraging ecology and habitat use in the MHI. To accomplish this I combined three-axis accelerometers, National Geographic Crittercams, and GPS tags to study monk seal foraging behavior. I instrumented 16 seals between 2010 and 2014 on the islands of Molokai, Kauai, and Oahu and deployed an additional 24 GPS tags without the accelerometer and Crittercam. I recovered each Crittercam/accelerometer package 3-6 days after deployment, resulting in an average of 6.14 hours of video footage per seal. The GPS tags continued to record data for 3-6 months providing long-term summaries of dive and haul-out behavior. Using a Bayesian framework I modeled monk seal behavior and habitat use, and developed a method to identify feeding events from accelerometer data. There was a high level of individual variation in the movements of monk seals, but general descriptions of their behavior were accurate at the population level. On average, foraging trips lasted 0.81 ± 1.38 days and seals traveled 28.45 ± 82.03 km per trip. Most seals began benthic dives shortly after entering the water, with most dives occurring between 20-40 m. I used kernel density estimation to define the 50% (core area) and 95% (home range) utilization distribution for each seal. The median home range and core area size for seals in the MHI was 265.62 km2 and 1,564.56 km2, respectively. The pitch axis of the accelerometer was a reliable metric, with over 70% accuracy, for identifying foraging events for monk seals. Body motion over the course of a dive, and how close the seal was to the seafloor during a dive (dive ratio) were the best predictors of these foraging events. Consequently, dive ratio was used to infer foraging in long-term telemetry records that lacked concurrent accelerometer data. Analysis of these data relative to habitat preferences revealed two distinct movement modes for monk seals in the MHI: near shore and offshore/inter-island. My research developed the first thorough understanding of monk seal movements and habitat use in the MHI and provided insight into the mechanisms contributing to the behavioral variability observed for this species. I hope that a detailed understanding of the foraging behavior of monk seals will provide insight into their true role in the ecosystem and help foster the recovery of this critically endangered species.

Mismatches in the spatiotemporal variability of resource, resource users and management actions breeds inefficiency in the management of marine resources. To date, the spatiotemporal resolution and extent of fisheries management has been largely dictated by logistical and political constraints, and secondarily by the geographic range of the species or meta-population dynamics. Management units are rarely smaller than 1000 km2 in developed coastal fisheries, and management measures generally occur at resolutions larger than 100 km2. From a temporal perspective, the finest resolution of management measures is at best a month but more generally a year. As such, attempts to manage processes and patterns at sub-10 km, sub-1 month resolution often involve some level of spatiotemporal mismatch. To address the obvious spatiotemporal mismatch between a dynamic ocean and static management, to allow for a comprehensive implementation of ecosystem-based fisheries management, and to minimize inefficiency in our management of marine resources, we must seek to develop more dynamic management measures that allow managers to address scales, processes and patterns occurring under ten kilometers.

In this dissertation I apply point pattern processes, cumulative distribution functions, receiver operator characteristic curves, simulated annealing tools, regression models and clustering techniques to develop examples of two dynamic management measures and to compare the efficiency of static versus dynamic management measures. I show that autocorrelation analysis can inform the distances and times used in real-time closures based on move-on rules. Further, I identify optimum bottom temperature threshold values to separate individual species within the Northeast Multispecies Fishery from Atlantic cod. Results demonstrate that dynamic spatiotemporal management measures are widely applicable, and more effective and more efficient than static time-area closures. Unexpected trends in some results due to a changing climate indicate possible increasing thermal overlap between Atlantic cod and many other species in the fishery. Implications of scale in fisheries management and the importance of coarse scale (1 - 10km) ecological patterns to fisheries are discussed.

The biotic forces that shape plant communities across ontogenetic stages drive patterns in survival, vegetation structure, and species diversity. In tropical forests, many of these forces are facilitated by interactions with animals, which can either promote or inhibit plant reproduction. Disruptions to these interactions – such as defaunation resulting from hunting and logging – can generate broad changes in tree recruitment, forest structure, and carbon storage, with demographic filtering at the seed and seedling stages responsible for many of the effects. Research to date has largely focused on a subset of prominent interactions (especially seed dispersal), while concurrent disruptions to other less-studied ecological processes may drive changes of opposite directionality for individual species or entire communities. With a limited understanding of seed predation, seedling establishment, and seedling physical damage and survival – particularly in Central African forests – it remains difficult to predict the outcomes of defaunation for tropical forest plant communities. In this dissertation, I use a combination of literature reviews, field-based experimental methods (including telemetric seed tags, seed and seedling exclosures, and artificial seedlings) and statistical analyses to assess 1) the role of plant-animal interactions and the influence of hunting on the regeneration of timber trees across tropical forests; 2) patterns of secondary dispersal and seed fate for two tree species in northeastern Gabon; 3) the role of seed traits and both seed density and distance from the parent tree in driving patterns of seed mortality and seedling establishment for ten tree species in northeastern Gabon; 4) the impacts of hunting on seed predation and seedling establishment for eight commercially important tree species across a defaunation gradient in northeastern Gabon; and 5) the role of physical damage by vertebrate trampling, rooting, and digging to artificial seedlings in intact and hunted and/or logged forests in Peru, Gabon, and Malaysian Borneo. I conclude that 1) hunting is likely to disrupt plant-animal interactions and tropical forest timber regeneration, but that these effects can be ameliorated given appropriate management; 2) seed fate is dependent on seed size and the identity of the seed predator, with evidence of scatterhoarding and secondary dispersal in northeastern Gabon; 3) seed traits, not density or distance from the parent tree, drive patterns in seed mortality and seedling establishment in northeastern Gabon, with vertebrate seed predation a stronger force than other mortality factors; 4) hunting-induced defaunation drives increased rodent seed predation and decreased seedling establishment of commercially-important tree species; and 5) vertebrate physical damage to seedlings is a consistent force in forests across the tropics, and hunting significantly reduces its strength. This dissertation highlights the important roles of wildlife in tropical forest ecological processes as well as the degree to which these interactions can be disrupted through hunting-induced defaunation, and emphasizes the value of appropriate management and continued comparative research across tropical forest regions.