Learning from the rapidly growing body of scientific articles is constrained by human bandwidth. ... more Learning from the rapidly growing body of scientific articles is constrained by human bandwidth. Existing methods in machine learning have been developed to extract knowledge from human language and may automate this process. Here, we apply sentiment analysis, a type of natural language processing, to facilitate a literature review in reintroduction biology. We analyzed 1,030,558 words from 4,313 scientific abstracts published over four decades using four previously trained lexicon-based models and one recursive neural tensor network model. We find frequently used terms share both a general and a domain-specific value, with either positive (success, protect, growth) or negative (threaten, loss, risk) sentiment. Sentiment trends suggest that reintroduction studies have become less variable and increasingly successful over time and seem to capture known successes and challenges for conservation biology. This approach offers promise for rapidly extracting explicit and latent information from a large corpus of scientific texts.
Over the past 4 decades there has been a growing concern for the conservation status of elasmobra... more Over the past 4 decades there has been a growing concern for the conservation status of elasmobranchs (sharks and rays). In 2002, the first elasmobranch species were added to Appendix II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Less than 20 yr later, there were 39 species on Appendix II and 5 on Appendix I. Despite growing concern, effective conservation and management remain challenged by a lack of data on population status for many species, human−wildlife interactions, threats to population viability, and the efficacy of conservation approaches. We surveyed 100 of the most frequently published and cited experts on elasmobranchs and, based on ranked responses, prioritized 20 research questions on elasmobranch conservation. To address these questions, we then convened a group of 47 experts from 35 institutions and 12 countries. The 20 questions were organized into the following broad categories: (1) status and threats, (2) population and ecology, and (3) conservation and management. For each section, we sought to synthesize existing knowledge, describe consensus or diverging views, identify gaps, and suggest promising future directions and research priorities. The resulting synthesis aggregates an array of perspectives on emergent research and priority directions for elasmobranch conservation.
Recovery of wildlife and their ecosystems may require enhancement of vulnerable populations throu... more Recovery of wildlife and their ecosystems may require enhancement of vulnerable populations through human intervention. As a southern sea otter (Enhydra lutris nereis) enhancement strategy, surrogate rearing and releasing of stranded orphans provides these individuals with another opportunity of life in the wild, promotes species-specific development of behaviors necessary for survival and reproduction after release, and may bolster targeted populations and resiliency of nearshore ecosystems. To further advance surrogacy as a viable recovery strategy for this threatened subspecies, we comprehensively describe our methods and use a machine learning algorithm to monitor and evaluate program success. Specifically, we model 20 years (2002 2021) of rehabilitation outcomes for 64 pups (i.e., success or failure reacclimating to the wild) based on 34 parameters representing three release sites and five treatment stages: stranding, stabilization, surrogacy, pre-release, and release. We find that surrogacy is a successful rehabilitation method (75%), robust to all measured factors through release preparation, including idiosyncrasies in pup origin, age, early development, and pairings with female sea otters. Instead, key performance indicators of successful outcomes in the wild are environmental conditions experienced during release, such as favorable sea conditions and weather, localized dispersal, and minimal competition from local populations. Most importantly, success requires optimal values among all environmental conditions at chosen release sites because a decline in any one factor may result in failure. Our findings highlight the importance of continuously evaluating rehabilitation methods to enhance species recovery and may have broader application to restoring other threatened species and their ecosystems.
of ~5-15 °C. Additionally, results from this study suggest that the waters near the Aleutian Isla... more of ~5-15 °C. Additionally, results from this study suggest that the waters near the Aleutian Islands are important feeding grounds for steelhead kelts from the Situk River, and thus may play a critical role in the successful reconditioning of repeat spawners in this population. These results provide the first detailed insights into the ocean ecology of steelhead and may be used for a variety of applications (e.g., niche construction, and forecasting future range dynamics under climate scenarios).
Climate change exposes marine ecosystems to extreme conditions with increasing frequency. Capital... more Climate change exposes marine ecosystems to extreme conditions with increasing frequency. Capitalizing on the global reconstruction of sea surface temperature (SST) records from 1870-present, we present a centennial-scale index of extreme marine heat within a coherent and comparable statistical framework. A spatially (1˚× 1˚) and temporally (monthly) resolved index of the normalized historical extreme marine heat events was expressed as a fraction of a year that exceeds a locally determined, monthly varying 98 th percentile of SST gradients derived from the first 50 years of climatological records (1870-1919). For the year 2019, our index reports that 57% of the global ocean surface recorded extreme heat, which was comparatively rare (approximately 2%) during the period of the second industrial revolution. Significant increases in the extent of extreme marine events over the past century resulted in many local climates to have shifted out of their historical SST bounds across many economically and ecologically important marine regions. For the global ocean, 2014 was the first year to exceed the 50% threshold of extreme heat thereby becoming "normal", with the South Atlantic (1998) and Indian (2007) basins crossing this barrier earlier. By focusing on heat extremes, we provide an alternative framework that may help better contextualize the dramatic changes currently occurring in marine systems.
Progress in global shark conservation has been limited by constraints to understanding the specie... more Progress in global shark conservation has been limited by constraints to understanding the species composition and geographic origins of the shark fin trade. Previous assessments that relied on earlier genetic techniques and official trade records focused on abundant pelagic species traded between Europe and Asia. Here, we combine recent advances in DNA barcoding and species distribution modelling to identify the species and source the geographic origin of fins sold at market. Derived models of species environmental niches indicated that shark fishing effort is concentrated within Exclusive Economic Zones, mostly in coastal Australia, Indonesia, the United States, Brazil, Mexico and Japan. By coupling two distinct tools, barcoding and niche modelling, our results provide new insights for monitoring and enforcement. They suggest stronger local controls of coastal fishing may help regulate the unsustainable global trade in shark fins.
Pelagic ecosystems are dynamic ocean regions whose immense natural capital is affected by climate... more Pelagic ecosystems are dynamic ocean regions whose immense natural capital is affected by climate change, pollution, and commercial fisheries. Trophic level-based indicators derived from fishery catch data may reveal the food web status of these systems, but the utility of these metrics has been debated because of targeting bias in fisheries catch. We analyze a unique, fishery-independent data set of North Pacific seabird tissues to inform ecosystem trends over 13 decades (1890s to 2010s). Trophic position declined broadly in five of eight species sampled, indicating a long-term shift from higher-trophic level to lower-trophic level prey. No species increased their trophic position. Given species prey preferences, Bayesian diet reconstructions suggest a shift from fishes to squids, a result consistent with both catch reports and ecosystem models. Machine learning models further reveal that trophic position trends have a complex set of drivers including climate, commercial fisheries,...
The use of limbs for foraging is documented in both marine and terrestrial tetrapods. These behav... more The use of limbs for foraging is documented in both marine and terrestrial tetrapods. These behaviors were once believed to be less likely in marine tetrapods due to the physical constraints of body plans adapted to locomotion in a fluid environment. Despite these obstacles, ten distinct types of limb-use while foraging have been previously reported in nine marine tetrapod families. Here, we expand the types of limb-use documented in marine turtles and put it in context with the diversity of marine tetrapods currently known to use limbs for foraging. Additionally, we suggest that such behaviors could have occurred in ancestral turtles, and thus, possibly extend the evolutionary timeline of limb-use behavior in marine tetrapods back approximately 70 million years. Through direct observation and crowd-sourcing, we document the range of behaviors across habitats and prey types, suggesting its widespread occurrence. We argue the presence of these behaviors among marine tetrapods may be ...
Page 1. Local extinctions in flocking birds in Amazonian forest fragments Kyle S. Van Houtan,1 St... more Page 1. Local extinctions in flocking birds in Amazonian forest fragments Kyle S. Van Houtan,1 Stuart L. Pimm,1* Richard O. Bierregaard Jr.,2,3 Thomas E. Lovejoy2,4 and Philip C. Stouffer2,5 1Nicholas School of the Environment ...
Given the threats of climate change, understanding the relationship of climate to long-term popul... more Given the threats of climate change, understanding the relationship of climate to long-term population dynamics is critical for wildlife conservation. Previous studies have linked decadal climate oscillations to indices of juvenile recruitment in loggerhead sea turtles (Caretta caretta), but without a clear understanding of mechanisms. Here we explore the underlying processes that may explain these relationships. Using the eddy-resolving Ocean General Circulation Model for the Earth Simulator (OFES) we generate hatch-year trajectories for loggerhead turtles emanating from Japan over six decades (1950-2010). We find the proximity of the high-velocity Kuroshio Current (KC) to the primary nesting areas in southern Japan is remarkably stable, and that hatchling dispersal to oceanic habitats itself does not vary on decadal timescales. However, we observe a shift in latitudes of trajectories, consistent with the Pacific Decadal Oscillation (PDO). In a negative PDO phase, the Kuroshio Exte...
Proceedings. Biological sciences / The Royal Society, Jan 13, 2016
Some of the most basic questions of sea turtle life history are also the most elusive. Many uncer... more Some of the most basic questions of sea turtle life history are also the most elusive. Many uncertainties surround lifespan, growth rates, maturity and spatial structure, yet these are critical factors in assessing population status. Here we examine the keratinized hard tissues of the hawksbill (Eretmochelys imbricata) carapace and use bomb radiocarbon dating to estimate growth and maturity. Scutes have an established dietary record, yet the large keratin deposits of hawksbills evoke a reliable chronology. We sectioned, polished and imaged posterior marginal scutes from 36 individual hawksbills representing all life stages, several Pacific populations and spanning eight decades. We counted the apparent growth lines, microsampled along growth contours and calibrated Δ(14)C values to reference coral series. We fit von Bertalanffy growth function (VBGF) models to the results, producing a range of age estimates for each turtle. We find Hawaii hawksbills deposit eight growth lines annual...
Learning from the rapidly growing body of scientific articles is constrained by human bandwidth. ... more Learning from the rapidly growing body of scientific articles is constrained by human bandwidth. Existing methods in machine learning have been developed to extract knowledge from human language and may automate this process. Here, we apply sentiment analysis, a type of natural language processing, to facilitate a literature review in reintroduction biology. We analyzed 1,030,558 words from 4,313 scientific abstracts published over four decades using four previously trained lexicon-based models and one recursive neural tensor network model. We find frequently used terms share both a general and a domain-specific value, with either positive (success, protect, growth) or negative (threaten, loss, risk) sentiment. Sentiment trends suggest that reintroduction studies have become less variable and increasingly successful over time and seem to capture known successes and challenges for conservation biology. This approach offers promise for rapidly extracting explicit and latent information from a large corpus of scientific texts.
Over the past 4 decades there has been a growing concern for the conservation status of elasmobra... more Over the past 4 decades there has been a growing concern for the conservation status of elasmobranchs (sharks and rays). In 2002, the first elasmobranch species were added to Appendix II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Less than 20 yr later, there were 39 species on Appendix II and 5 on Appendix I. Despite growing concern, effective conservation and management remain challenged by a lack of data on population status for many species, human−wildlife interactions, threats to population viability, and the efficacy of conservation approaches. We surveyed 100 of the most frequently published and cited experts on elasmobranchs and, based on ranked responses, prioritized 20 research questions on elasmobranch conservation. To address these questions, we then convened a group of 47 experts from 35 institutions and 12 countries. The 20 questions were organized into the following broad categories: (1) status and threats, (2) population and ecology, and (3) conservation and management. For each section, we sought to synthesize existing knowledge, describe consensus or diverging views, identify gaps, and suggest promising future directions and research priorities. The resulting synthesis aggregates an array of perspectives on emergent research and priority directions for elasmobranch conservation.
Recovery of wildlife and their ecosystems may require enhancement of vulnerable populations throu... more Recovery of wildlife and their ecosystems may require enhancement of vulnerable populations through human intervention. As a southern sea otter (Enhydra lutris nereis) enhancement strategy, surrogate rearing and releasing of stranded orphans provides these individuals with another opportunity of life in the wild, promotes species-specific development of behaviors necessary for survival and reproduction after release, and may bolster targeted populations and resiliency of nearshore ecosystems. To further advance surrogacy as a viable recovery strategy for this threatened subspecies, we comprehensively describe our methods and use a machine learning algorithm to monitor and evaluate program success. Specifically, we model 20 years (2002 2021) of rehabilitation outcomes for 64 pups (i.e., success or failure reacclimating to the wild) based on 34 parameters representing three release sites and five treatment stages: stranding, stabilization, surrogacy, pre-release, and release. We find that surrogacy is a successful rehabilitation method (75%), robust to all measured factors through release preparation, including idiosyncrasies in pup origin, age, early development, and pairings with female sea otters. Instead, key performance indicators of successful outcomes in the wild are environmental conditions experienced during release, such as favorable sea conditions and weather, localized dispersal, and minimal competition from local populations. Most importantly, success requires optimal values among all environmental conditions at chosen release sites because a decline in any one factor may result in failure. Our findings highlight the importance of continuously evaluating rehabilitation methods to enhance species recovery and may have broader application to restoring other threatened species and their ecosystems.
of ~5-15 °C. Additionally, results from this study suggest that the waters near the Aleutian Isla... more of ~5-15 °C. Additionally, results from this study suggest that the waters near the Aleutian Islands are important feeding grounds for steelhead kelts from the Situk River, and thus may play a critical role in the successful reconditioning of repeat spawners in this population. These results provide the first detailed insights into the ocean ecology of steelhead and may be used for a variety of applications (e.g., niche construction, and forecasting future range dynamics under climate scenarios).
Climate change exposes marine ecosystems to extreme conditions with increasing frequency. Capital... more Climate change exposes marine ecosystems to extreme conditions with increasing frequency. Capitalizing on the global reconstruction of sea surface temperature (SST) records from 1870-present, we present a centennial-scale index of extreme marine heat within a coherent and comparable statistical framework. A spatially (1˚× 1˚) and temporally (monthly) resolved index of the normalized historical extreme marine heat events was expressed as a fraction of a year that exceeds a locally determined, monthly varying 98 th percentile of SST gradients derived from the first 50 years of climatological records (1870-1919). For the year 2019, our index reports that 57% of the global ocean surface recorded extreme heat, which was comparatively rare (approximately 2%) during the period of the second industrial revolution. Significant increases in the extent of extreme marine events over the past century resulted in many local climates to have shifted out of their historical SST bounds across many economically and ecologically important marine regions. For the global ocean, 2014 was the first year to exceed the 50% threshold of extreme heat thereby becoming "normal", with the South Atlantic (1998) and Indian (2007) basins crossing this barrier earlier. By focusing on heat extremes, we provide an alternative framework that may help better contextualize the dramatic changes currently occurring in marine systems.
Progress in global shark conservation has been limited by constraints to understanding the specie... more Progress in global shark conservation has been limited by constraints to understanding the species composition and geographic origins of the shark fin trade. Previous assessments that relied on earlier genetic techniques and official trade records focused on abundant pelagic species traded between Europe and Asia. Here, we combine recent advances in DNA barcoding and species distribution modelling to identify the species and source the geographic origin of fins sold at market. Derived models of species environmental niches indicated that shark fishing effort is concentrated within Exclusive Economic Zones, mostly in coastal Australia, Indonesia, the United States, Brazil, Mexico and Japan. By coupling two distinct tools, barcoding and niche modelling, our results provide new insights for monitoring and enforcement. They suggest stronger local controls of coastal fishing may help regulate the unsustainable global trade in shark fins.
Pelagic ecosystems are dynamic ocean regions whose immense natural capital is affected by climate... more Pelagic ecosystems are dynamic ocean regions whose immense natural capital is affected by climate change, pollution, and commercial fisheries. Trophic level-based indicators derived from fishery catch data may reveal the food web status of these systems, but the utility of these metrics has been debated because of targeting bias in fisheries catch. We analyze a unique, fishery-independent data set of North Pacific seabird tissues to inform ecosystem trends over 13 decades (1890s to 2010s). Trophic position declined broadly in five of eight species sampled, indicating a long-term shift from higher-trophic level to lower-trophic level prey. No species increased their trophic position. Given species prey preferences, Bayesian diet reconstructions suggest a shift from fishes to squids, a result consistent with both catch reports and ecosystem models. Machine learning models further reveal that trophic position trends have a complex set of drivers including climate, commercial fisheries,...
The use of limbs for foraging is documented in both marine and terrestrial tetrapods. These behav... more The use of limbs for foraging is documented in both marine and terrestrial tetrapods. These behaviors were once believed to be less likely in marine tetrapods due to the physical constraints of body plans adapted to locomotion in a fluid environment. Despite these obstacles, ten distinct types of limb-use while foraging have been previously reported in nine marine tetrapod families. Here, we expand the types of limb-use documented in marine turtles and put it in context with the diversity of marine tetrapods currently known to use limbs for foraging. Additionally, we suggest that such behaviors could have occurred in ancestral turtles, and thus, possibly extend the evolutionary timeline of limb-use behavior in marine tetrapods back approximately 70 million years. Through direct observation and crowd-sourcing, we document the range of behaviors across habitats and prey types, suggesting its widespread occurrence. We argue the presence of these behaviors among marine tetrapods may be ...
Page 1. Local extinctions in flocking birds in Amazonian forest fragments Kyle S. Van Houtan,1 St... more Page 1. Local extinctions in flocking birds in Amazonian forest fragments Kyle S. Van Houtan,1 Stuart L. Pimm,1* Richard O. Bierregaard Jr.,2,3 Thomas E. Lovejoy2,4 and Philip C. Stouffer2,5 1Nicholas School of the Environment ...
Given the threats of climate change, understanding the relationship of climate to long-term popul... more Given the threats of climate change, understanding the relationship of climate to long-term population dynamics is critical for wildlife conservation. Previous studies have linked decadal climate oscillations to indices of juvenile recruitment in loggerhead sea turtles (Caretta caretta), but without a clear understanding of mechanisms. Here we explore the underlying processes that may explain these relationships. Using the eddy-resolving Ocean General Circulation Model for the Earth Simulator (OFES) we generate hatch-year trajectories for loggerhead turtles emanating from Japan over six decades (1950-2010). We find the proximity of the high-velocity Kuroshio Current (KC) to the primary nesting areas in southern Japan is remarkably stable, and that hatchling dispersal to oceanic habitats itself does not vary on decadal timescales. However, we observe a shift in latitudes of trajectories, consistent with the Pacific Decadal Oscillation (PDO). In a negative PDO phase, the Kuroshio Exte...
Proceedings. Biological sciences / The Royal Society, Jan 13, 2016
Some of the most basic questions of sea turtle life history are also the most elusive. Many uncer... more Some of the most basic questions of sea turtle life history are also the most elusive. Many uncertainties surround lifespan, growth rates, maturity and spatial structure, yet these are critical factors in assessing population status. Here we examine the keratinized hard tissues of the hawksbill (Eretmochelys imbricata) carapace and use bomb radiocarbon dating to estimate growth and maturity. Scutes have an established dietary record, yet the large keratin deposits of hawksbills evoke a reliable chronology. We sectioned, polished and imaged posterior marginal scutes from 36 individual hawksbills representing all life stages, several Pacific populations and spanning eight decades. We counted the apparent growth lines, microsampled along growth contours and calibrated Δ(14)C values to reference coral series. We fit von Bertalanffy growth function (VBGF) models to the results, producing a range of age estimates for each turtle. We find Hawaii hawksbills deposit eight growth lines annual...
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Papers by Kyle Van Houtan
intervention. As a southern sea otter (Enhydra lutris nereis) enhancement strategy, surrogate rearing and releasing of stranded orphans provides these individuals with another opportunity of life in the wild, promotes species-specific development of behaviors necessary for survival and reproduction after release, and may bolster targeted populations and resiliency of nearshore ecosystems. To further advance surrogacy as a viable recovery strategy for this threatened subspecies, we comprehensively describe our methods and use a machine learning algorithm to monitor and evaluate program success. Specifically, we model 20 years (2002 2021) of rehabilitation outcomes for 64 pups (i.e., success or failure reacclimating to the wild) based on 34 parameters representing three release sites and five treatment stages: stranding, stabilization, surrogacy, pre-release, and release. We find that surrogacy is a successful rehabilitation method (75%), robust to all measured factors through release preparation, including idiosyncrasies in pup origin, age, early development, and pairings with female sea otters. Instead, key performance indicators of successful outcomes in the wild are environmental conditions experienced during release, such as favorable sea conditions and weather, localized dispersal, and minimal competition from local populations. Most importantly, success requires optimal values among all environmental conditions at chosen release sites because a decline in any one factor may result in failure. Our findings highlight the importance of continuously evaluating rehabilitation methods to enhance species recovery and may have broader application to restoring other threatened species and their ecosystems.
intervention. As a southern sea otter (Enhydra lutris nereis) enhancement strategy, surrogate rearing and releasing of stranded orphans provides these individuals with another opportunity of life in the wild, promotes species-specific development of behaviors necessary for survival and reproduction after release, and may bolster targeted populations and resiliency of nearshore ecosystems. To further advance surrogacy as a viable recovery strategy for this threatened subspecies, we comprehensively describe our methods and use a machine learning algorithm to monitor and evaluate program success. Specifically, we model 20 years (2002 2021) of rehabilitation outcomes for 64 pups (i.e., success or failure reacclimating to the wild) based on 34 parameters representing three release sites and five treatment stages: stranding, stabilization, surrogacy, pre-release, and release. We find that surrogacy is a successful rehabilitation method (75%), robust to all measured factors through release preparation, including idiosyncrasies in pup origin, age, early development, and pairings with female sea otters. Instead, key performance indicators of successful outcomes in the wild are environmental conditions experienced during release, such as favorable sea conditions and weather, localized dispersal, and minimal competition from local populations. Most importantly, success requires optimal values among all environmental conditions at chosen release sites because a decline in any one factor may result in failure. Our findings highlight the importance of continuously evaluating rehabilitation methods to enhance species recovery and may have broader application to restoring other threatened species and their ecosystems.