Species and population specific gene expression in blood transcriptomes of marine turtles.

BACKGROUND: Transcriptomic data has demonstrated utility to advance the study of physiological diversity and organisms' responses to environmental stressors. However, a lack of genomic resources and challenges associated with collecting high-quality RNA can limit its application for many wild populations. Minimally invasive blood sampling combined with de novo transcriptomic approaches has great potential to alleviate these barriers. Here, we advance these goals for marine turtles by generating high quality de novo blood transcriptome assemblies to characterize functional diversity and compare global transcriptional profiles between tissues, species, and foraging aggregations. RESULTS: We generated high quality blood transcriptome assemblies for hawksbill (Eretmochelys imbricata), loggerhead (Caretta caretta), green (Chelonia mydas), and leatherback (Dermochelys coriacea) turtles. The functional diversity in assembled blood transcriptomes was comparable to those from more traditionally sampled tissues. A total of 31.3% of orthogroups identified were present in all four species, representing a core set of conserved genes expressed in blood and shared across marine turtle species. We observed strong species-specific expression of these genes, as well as distinct transcriptomic profiles between green turtle foraging aggregations that inhabit areas of greater or lesser anthropogenic disturbance. CONCLUSIONS: Obtaining global gene expression data through non-lethal, minimally invasive sampling can greatly expand the applications of RNA-sequencing in protected long-lived species such as marine turtles. The distinct differences in gene expression signatures between species and foraging aggregations provide insight into the functional genomics underlying the diversity in this ancient vertebrate lineage. The transcriptomic resources generated here can be used in further studies examining the evolutionary ecology and anthropogenic impacts on marine turtles.

Assessing Ecological and Social Dimensions of Success in a Community-based Sustainable Harvest Program.

Community-based conservation and resource management (CBCRM) programs often incorporate the dual goals of poverty alleviation and conservation. However, robust assessments of CBCRM program outcomes are relatively scarce. This study uses a multidisciplinary, systems approach to assess the ecological and social dimensions of success of an internationally acclaimed CBCRM program. This program, located in one of the largest protected areas in the Peruvian Amazon (Pacaya-Samiria National Reserve), strives for the sustainable harvest and trade of a turtle species (Podocnemis unifilis). We used mixed methods analysis, including interviews and population viability modeling, to understand three elements: how local perceptions of changes in the managed population compare to changes inferred by ecological analyses, the indicators stakeholders use to measure success, and the barriers to long-term program success and social-ecological system sustainability. We find that stakeholders perceive a growth trend in the managed turtle population, but this perception may diverge from our ecological understanding of the system under current management. Population viability analyses with a 1:1 sex ratio suggested population size will decline under two of three management scenarios (different degrees of harvest). Yet this and similar studies are plagued by a lack of species- and site-specific population parameters that could improve understanding of the system. Significant vulnerabilities exist for system sustainability, notably the recent decrease in foreign demand for the traded resource. Identifying a sustainable species-specific harvest rate, developing locally-grounded ecological and social indicators, and focusing on data-driven adaptive management will facilitate the identification of key leverage points for future management interventions.

Ecological niche modeling for a cultivated plant species: a case study on taro (Colocasia esculenta) in Hawaii.

Under the threat of ongoing and projected climate change, communities in the Pacific Islands face challenges of adapting culture and lifestyle to accommodate a changing landscape. Few models can effectively predict how biocultural livelihoods might be impacted. Here, we examine how environmental and anthropogenic factors influence an ecological niche model (ENM) for the realized niche of cultivated taro (Colocasia esculenta) in Hawaii. We created and tuned two sets of ENMs: one using only environmental variables, and one using both environmental and cultural characteristics of Hawaii. These models were projected under two different Intergovernmental Panel on Climate Change (IPCC) Representative Concentration Pathways (RCPs) for 2070. Models were selected and evaluated using average omission rate and area under the receiver operating characteristic curve (AUC). We compared optimal model predictions by comparing the percentage of taro plots predicted present and measured ENM overlap using Schoener's D statistic. The model including only environmental variables consisted of 19 Worldclim bioclimatic variables, in addition to slope, altitude, distance to perennial streams, soil evaporation, and soil moisture. The optimal model with environmental variables plus anthropogenic features also included a road density variable (which we assumed as a proxy for urbanization) and a variable indicating agricultural lands of importance to the state of Hawaii. The model including anthropogenic features performed better than the environment-only model based on omission rate, AUC, and review of spatial projections. The two models also differed in spatial projections for taro under anticipated future climate change. Our results demonstrate how ENMs including anthropogenic features can predict which areas might be best suited to plant cultivated species in the future, and how these areas could change under various climate projections. These predictions might inform biocultural conservation priorities and initiatives. In addition, we discuss the incongruences that arise when traditional ENM theory is applied to species whose distribution has been significantly impacted by human intervention, particularly at a fine scale relevant to biocultural conservation initiatives.

Purpose, processes, partnerships, and products: four Ps to advance participatory socio-environmental modeling.

Including stakeholders in environmental model building and analysis is an increasingly popular approach to understanding ecological change. This is because stakeholders often hold valuable knowledge about socio-environmental dynamics and collaborative forms of modeling produce important boundary objects used to collectively reason about environmental problems. Although the number of participatory modeling (PM) case studies and the number of researchers adopting these approaches has grown in recent years, the lack of standardized reporting and limited reproducibility have prevented PM's establishment and advancement as a cohesive field of study. We suggest a four-dimensional framework (4P) that includes reporting on dimensions of (1) the Purpose for selecting a PM approach (the why); (2) the Process by which the public was involved in model building or evaluation (the how); (3) the Partnerships formed (the who); and (4) the Products that resulted from these efforts (the what). We highlight four case studies that use common PM software-based approaches (fuzzy cognitive mapping, agent-based modeling, system dynamics, and participatory geospatial modeling) to understand human-environment interactions and the consequences of ecological changes, including bushmeat hunting in Tanzania and Cameroon, agricultural production and deforestation in Zambia, and groundwater management in India. We demonstrate how standardizing communication about PM case studies can lead to innovation and new insights about model-based reasoning in support of ecological policy development. We suggest that our 4P framework and reporting approach provides a way for new hypotheses to be identified and tested in the growing field of PM.

Slow Loris Trade in Vietnam: Exploring Diverse Knowledge and Values.

Wildlife trade can present a major threat to primate populations. In Vietnam, slow lorises (genus Nycticebus) are subject to local, regional and international demand for diverse uses including as medicine, as meat and for pets. Ethnographic approaches explore the nuances of human-primate interactions in complex sociocultural contexts. We combined ethnographic interviews of key informants with information from questionnaires, focus groups and a movie broadcast on Vietnamese television to explore diverse knowledge and values related to slow lorises and their use in trade in Vietnam. We infer prices, uses and networks for expanding targeted regional and international markets as compared to the opportunistic local one. We highlight key findings related to gendered knowledge about slow lorises and more-than-human ontologies of slow lorises as active participants in human-slow loris interactions. We suggest that conservation efforts should pay attention to the clarification of vernacular names, and use names that highlight ecological or behavioural qualities of slow lorises, rather than other names that could be confused with medicinal remedies. Our results confirm the dynamic complexity of trade in Vietnam, highlighting the importance of ethnographic methods to explore diverse knowledge and values for place-based or site-appropriate conservation management of primates and other highly traded taxa.

Multidisciplinary studies of wildlife trade in primates: Challenges and priorities.

Wildlife trade is increasingly recognized as an unsustainable threat to primate populations and informing its management is a growing focus and application of primatological research. However, management policies based on ecological research alone cannot address complex socioeconomic or cultural contexts as drivers of wildlife trade. Multidisciplinary research is required to understand trade complexity and identify sustainable management strategies. Here, we define multidisciplinary research as research that combines more than one academic discipline, and highlight how the articles in this issue combine methods and approaches to fill key gaps and offer a more comprehensive understanding of underlying drivers of wildlife trade including consumer demand, enforcement patterns, source population status, and accessibility of targeted species. These articles also focus on how these drivers interact at different scales, how trade patterns relate to ethics, and the potential effectiveness of different policy interventions in reducing wildlife trade. We propose priorities for future research on primate trade including expanding from multidisciplinary to interdisciplinary research questions and approaches co-created by research teams that integrate across different disciplines such as cultural anthropology, ecology, economics, and public policy. We also discuss challenges that limit the integration of information across disciplines to meet these priorities.

Applying systems thinking to inform studies of wildlife trade in primates.

Wildlife trade presents a major threat to primate populations, which are in demand from local to international scales for a variety of uses from food and traditional medicine to the exotic pet trade. We argue that an interdisciplinary framework to facilitate integration of socioeconomic, anthropological, and biological data across multiple spatial and temporal scales is essential to guide the study of wildlife trade dynamics and its impacts on primate populations. Here, we present a new way to design research on wildlife trade in primates using a systems thinking framework. We discuss how we constructed our framework, which follows a social-ecological system framework, to design an ongoing study of local, regional, and international slow loris (Nycticebus spp.) trade in Vietnam. We outline the process of iterative variable exploration and selection via this framework to inform study design. Our framework, guided by systems thinking, enables recognition of complexity in study design, from which the results can inform more holistic, site-appropriate, and effective trade management practices. We place our framework in the context of other approaches to studying wildlife trade and discuss options to address foreseeable challenges to implementing this new framework.

Building capacity for protected area management in Lao PDR.

Declining biodiversity in protected areas in Laos is attributed to unsustainable exploitation of natural resources. At a basic level, an important need is to develop capacity in academic and professional training institutions to provide relevant training to conservation professionals. The paper (a) describes the capacity building approach undertaken to achieve this goal, (b) evaluates the effectiveness of the approach in building capacity for implementing conservation and (c) reviews implementation outcomes. Strong linkages between organizations implementing field conservation, professional training institutions, and relevant Government agencies are central to enhancing effectiveness of capacity building initiatives aimed at improving the practice of conservation. Protected area management technical capacity needs will need to directly influence curriculum design to insure both relevance and effectiveness of training in improving protected area management. Sustainability of capacity building initiatives is largely dependent on the level of interest and commitment by host-country institutions within a supportive Government policy framework in addition to engagement of organizations implementing conservation.

Correction: Blair et al. Molecular Phylogenetic Relationships and Unveiling Novel Genetic Diversity among Slow and Pygmy Lorises, including Resurrection of Xanthonycticebus intermedius. Genes 2023, 14, 643.

In the original publication [...].

Molecular Phylogenetic Relationships and Unveiling Novel Genetic Diversity among Slow and Pygmy Lorises, including Resurrection of Xanthonycticebus intermedius.

Genetic analysis of historical museum collections presents an opportunity to clarify the evolutionary history of understudied primate groups, improve taxonomic inferences, and inform conservation efforts. Among the most understudied primate groups, slow and pygmy lorises (genera Nycticebus and Xanthonycticebus) are nocturnal strepsirrhines found in South and Southeast Asia. Previous molecular studies have supported five species, but studies using morphological data suggest the existence of at least nine species. We sequenced four mitochondrial loci, CO1, cytb, d-loop, and ND4, for a total of 3324 aligned characters per sample from 41 historical museum specimens for the most comprehensive geographic coverage to date for these genera. We then combined these sequences with a larger dataset composed of samples collected in Vietnam as well as previously published sequences (total sample size N = 62). We inferred phylogenetic relationships using Bayesian inference and maximum likelihood methods based on data from each locus and on concatenated sequences. We also inferred divergence dates for the most recent common ancestors of major lineages using a BEAST analysis. Consistent with previous studies, we found support for Xanthonycticebus pygmaeus as a basal taxon to the others in the group. We also confirmed the separation between lineages of X. pygmaeus from northern Vietnam/Laos/China and southern Vietnam/Cambodia and included a taxonomic revision recognizing a second taxon of pygmy loris, X. intermedius. Our results found support for multiple reciprocally monophyletic taxa within Borneo and possibly Java. The study will help inform conservation management of these trade-targeted animals as part of a genetic reference database for determining the taxonomic unit and provenance of slow and pygmy lorises confiscated from illegal wildlife trade activities.

Assessing evidence on the impacts of nature-based interventions for climate change mitigation: a systematic map of primary and secondary research from subtropical and tropical terrestrial regions.

BACKGROUND: Nature-based interventions (NbIs) for climate change mitigation include a diverse set of interventions aimed at conserving, restoring, and/or managing natural and modified ecosystems to improve their ability to store and sequester carbon and avoid greenhouse gas (GHG) emissions. Recent projections estimate that terrestrial NbIs can lead to more than one-third of the climate change mitigation necessary to meet the Paris Climate Agreement by 2030. Further, these interventions can provide co-benefits in the form of social and ecological outcomes. Despite growing recognition of the potential benefits, a clear characterization of the distribution and occurrence of evidence which supports linkages between different types of NbIs and outcomes for climate change mitigation, ecosystems, and people remains poorly understood. METHODS: This systematic map assesses the evidence base on the links between NbIs and climate change mitigation, social, and ecological outcomes in tropical and subtropical terrestrial regions. We searched three bibliographic databases, 65 organization websites, and conducted backward citation chasing within 39 existing evidence syntheses to identify relevant articles. Additionally, we reached out to key informants for additional sources of evidence. We then used machine learning to rank returned results by relevance at the title and abstract stage and manually screened for inclusion using predefined criteria at the title, abstract, and full text stages. We extracted relevant meta-data from included articles using an a priori coding scheme. Lastly, we conducted a targeted, complementary search to identify relevant review and synthesis articles to provide broader context for the findings of the systematic map. REVIEW FINDINGS: We included 948 articles in this systematic map. Most of the evidence base (56%) examined links between protection, natural resource management, and restoration interventions with changes to 'proxy' outcomes for climate change mitigation (changes to land condition, land cover, and/or land use). Other areas with high occurrence of articles included linkages between interventions within natural resource management and trees in croplands categories and changes to aboveground carbon storage and/or sequestration (17% of articles). A key knowledge gap was on measured changes in GHG emissions across all intervention types (6% of articles). Overall, articles in the evidence base did not often assess changes in co-benefits alongside direct or indirect changes for climate change mitigation (32%). In most cases, the evidence base contained studies which did not explicitly test for causal linkages using appropriate experimental or quasi-experimental designs. CONCLUSIONS: The evidence base for NbIs is significant and growing; however, key gaps in knowledge hamper the ability to inform ongoing and future investment and implementation at scale. More comprehensive evidence is needed to support causal inference between NbIs and direct outcomes for climate change mitigation to better determine additionality, permanence, leakage, and other unintended consequences. Similarly, priorities emerging from this map include the need for coordinated and harmonized efforts to collect diverse data types to better understand whether and how other outcomes (e.g. social, ecological) of NbIs can be achieved synergistically with mitigation objectives. Understanding potential benefits and trade-offs of NbIs is particularly urgent to inform rapidly expanding carbon markets for nature.

A systemic view of biodiversity and its conservation: processes, interrelationships, and human culture: presentation of a systemic view of biodiversity and its conservation that emphasizes complex interrelationships among subsystems and includes human culture.

Historically, views and measurements of biodiversity have had a narrow focus, for instance, characterizing the attributes of observable patterns but affording less attention to processes. Here, we explore the question: how does a systems thinking view - one where the world is seen as elements and processes that connect and interact in dynamic ways to form a whole - affect the way we understand biodiversity and practice conservation? We answer this question by illustrating the systemic properties of biodiversity at multiple levels, and show that biodiversity is a collection of dynamic systems linking seemingly disparate biological and cultural components and requiring an understanding of the system as a whole. We conclude that systems thinking calls traditional views of species, ecosystem function, and human relationships with the rest of biodiversity into question. Finally, we suggest some of the ways in which this view can impact the science and practice of conservation, particularly through affecting our conservation targets and strategies.

What evidence exists on the links between natural climate solutions and climate change mitigation outcomes in subtropical and tropical terrestrial regions? A systematic map protocol.

Background: Natural climate solutions (NCS)-actions to conserve, restore, and modify natural and modified ecosystems to increase carbon storage or avoid greenhouse gas (GHG) emissions-are increasingly regarded as important pathways for climate change mitigation, while contributing to our global conservation efforts, overall planetary resilience, and sustainable development goals. Recently, projections posit that terrestrial-based NCS can potentially capture or avoid the emission of at least 11 Gt (gigatons) of carbon dioxide equivalent a year, or roughly encompassing one third of the emissions reductions needed to meet the Paris Climate Agreement goals by 2030. NCS interventions also purport to provide co-benefits such as improved productivity and livelihoods from sustainable natural resource management, protection of locally and culturally important natural areas, and downstream climate adaptation benefits. Attention on implementing NCS to address climate change across global and national agendas has grown-however, clear understanding of which types of NCS interventions have undergone substantial study versus those that require additional evidence is still lacking. This study aims to conduct a systematic map to collate and describe the current state, distribution, and methods used for evidence on the links between NCS interventions and climate change mitigation outcomes within tropical and sub-tropical terrestrial ecosystems. Results of this study can be used to inform program and policy design and highlight critical knowledge gaps where future evaluation, research, and syntheses are needed. Methods: To develop this systematic map, we will search two bibliographic databases (including 11 indices) and 67 organization websites, backward citation chase from 39 existing evidence syntheses, and solicit information from key informants. All searches will be conducted in English and encompass subtropical and tropical terrestrial ecosystems (forests, grasslands, mangroves, agricultural areas). Search results will be screened at title and abstract, and full text levels, recording both the number of excluded articles and reasons for exclusion. Key meta-data from included articles will be coded and reported in a narrative review that will summarize trends in the evidence base, assess gaps in knowledge, and provide insights for policy, practice, and research. The data from this systematic map will be made open access. Supplementary Information: The online version contains supplementary material available at 10.1186/s13750-022-00268-w.

What evidence exists on the links between natural climate solutions and climate change mitigation outcomes in subtropical and tropical terrestrial regions? A systematic map protocol.

BACKGROUND: Natural climate solutions (NCS)-actions to conserve, restore, and modify natural and modified ecosystems to increase carbon storage or avoid greenhouse gas (GHG) emissions-are increasingly regarded as important pathways for climate change mitigation, while contributing to our global conservation efforts, overall planetary resilience, and sustainable development goals. Recently, projections posit that terrestrial-based NCS can potentially capture or avoid the emission of at least 11 Gt (gigatons) of carbon dioxide equivalent a year, or roughly encompassing one third of the emissions reductions needed to meet the Paris Climate Agreement goals by 2030. NCS interventions also purport to provide co-benefits such as improved productivity and livelihoods from sustainable natural resource management, protection of locally and culturally important natural areas, and downstream climate adaptation benefits. Attention on implementing NCS to address climate change across global and national agendas has grown-however, clear understanding of which types of NCS interventions have undergone substantial study versus those that require additional evidence is still lacking. This study aims to conduct a systematic map to collate and describe the current state, distribution, and methods used for evidence on the links between NCS interventions and climate change mitigation outcomes within tropical and sub-tropical terrestrial ecosystems. Results of this study can be used to inform program and policy design and highlight critical knowledge gaps where future evaluation, research, and syntheses are needed. METHODS: To develop this systematic map, we will search two bibliographic databases (including 11 indices) and 67 organization websites, backward citation chase from 39 existing evidence syntheses, and solicit information from key informants. All searches will be conducted in English and encompass subtropical and tropical terrestrial ecosystems (forests, grasslands, mangroves, agricultural areas). Search results will be screened at title and abstract, and full text levels, recording both the number of excluded articles and reasons for exclusion. Key meta-data from included articles will be coded and reported in a narrative review that will summarize trends in the evidence base, assess gaps in knowledge, and provide insights for policy, practice, and research. The data from this systematic map will be made open access.

Standards of conduct and reporting in evidence syntheses that could inform environmental policy and management decisions.

Accurate, unbiased and concise synthesis of available evidence following clear methodology and transparent reporting is necessary to support effective environmental policy and management decisions. Without this, less reliable and/or less objective reviews of evidence could inform decision making, leading to ineffective, resource wasteful interventions with potential for unintended consequences. We evaluated the reliability of over 1000 evidence syntheses (reviews and overviews) published between 2018 and 2020 that provide evidence on the impacts of human activities or effectiveness of interventions relevant to environmental management. The syntheses are drawn from the Collaboration for Environmental Evidence Database of Evidence Reviews (CEEDER), an online, freely available evidence service for evidence users that assesses the reliability of evidence syntheses using a series of published criteria. We found that the majority of syntheses have problems with transparency, replicability and potential for bias. Overall, our results suggest that most recently published evidence syntheses are of low reliability to inform decision making. Reviews that followed guidance and reporting standards for evidence synthesis had improved assessment ratings, but there remains substantial variation in the standard of reviews amongst even these. Furthermore, the term 'systematic review', which implies conformity with a methodological standard, was frequently misused. A major objective of the CEEDER project is to improve the reliability of the global body of environmental evidence reviews. To this end we outline freely available online resources to help improve review conduct and reporting. We call on authors, editors and peer reviewers to use these resources to ensure more reliable syntheses in the future.

Taxonomy and conservation of Vietnam's primates: a review.

Vietnam has the highest number of primate taxa overall (24-27) and the highest number of globally threatened primate taxa (minimum 20) in Mainland Southeast Asia. Conservation management of these species depends in part on resolving taxonomic uncertainties, which remain numerous among the Asian primates. Recent research on genetic, morphological, and acoustic diversity in Vietnam's primates has clarified some of these uncertainties, although a number of significant classification issues still remain. Herein, we summarize and compare the major current taxonomic classifications of Vietnam's primates, discuss recent advances in the context of these taxonomies, and suggest key areas for additional research to best inform conservation efforts in a region crucial to global primate diversity. Among the most important next steps for the conservation of Vietnam's primates is a new consensus list of Asian primates that resolves current differences between major taxonomies, incorporates recent research advances, and recognizes units of diversity at scales below the species-level, whether termed populations, morphs, or subspecies. Priority should be placed on recognizing distinct populations, regardless of the species concept in use, in order to foster the evolutionary processes necessary for primate populations to cope with inevitable environmental changes. The long-term conservation of Vietnam's primates depends not only on an accepted and accurate taxonomy but also on funding for on-the-ground conservation activities, including training, and the continued dedication and leadership of Vietnamese researchers and managers.

Sea turtles across the North Pacific are exposed to perfluoroalkyl substances.

Perfluorinated alkyl substances (PFASs) are global, persistent, and toxic contaminants. We assessed PFAS concentrations in green (Chelonia mydas) and hawksbill (Eretmochelys imbricata) turtles from the North Pacific. Fifteen compounds were quantified via liquid chromatography tandem mass spectrometry from 62 green turtle and 6 hawksbill plasma samples from Hawai'i, Palmyra Atoll, and the Northern Marianas Islands. Plasma from 14 green turtles severely afflicted with fibropapillomatosis, and eggs from 12 Hawaiian hawksbill nests from 7 females were analyzed. Perfluorooctane sulfonate (PFOS) predominated in green turtle plasma; perfluorononanoic acid (PFNA) predominated in hawksbill tissues. Concentrations were greater in hawksbill than green turtle plasma (p < 0.05), related to trophic differences. Green turtle plasma PFOS concentrations were related to human populations from highest to lowest: Hawai'i, Marianas, Palmyra. Influence on fibropapillomatosis was not evident. PFASs were maternally transferred to hawksbill eggs, with decreasing concentrations with distance from airports and with clutch order from one female. A risk assessment of PFOS showed concern for immunosuppression in Kailua green turtles and alarming concern for hawksbill developmental toxicity. Perfluoroundecanoic (PFUnA) and perfluorotridecanoic (PFTriA) acid levels were correlated with reduced emergence success (p < 0.05). Studies to further examine PFAS effects on sea turtle development would be beneficial.

Stakeholder participation in IPBES: connecting local environmental work with global decision making.

The Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services(IPBES) strengthens the science-policy interface by producing scientific assessments on biodiversity and ecosystem services to inform policy. IPBES fosters knowledge exchange across disciplines, between researchers and other knowledge holders, practitioners, societal actors and decision makers working at different geographic scales. A number of avenues for participation of stakeholders across the four functions if IPBES exist. Stakeholders come from diverse backgrounds, including Indigenous Peoples and local communities, businesses, and non-governmental organization. They represent multiple sources of information, data, knowledge, and perspectives on biodiversity. Stakeholder engagement in IPBES seeks to 1. communicate, disseminate, and implement the findings of IPBES products; 2. Develop guidelines for biodiversity conservation within member countries; and 3. create linkages between global policy and local actors - all key to the implementation of global agreements on biodiversity. This paper reflects on the role of stakeholders in the first work programme of IPBES (2014-2018). It provides an overview of IPBES processes and products relevant to stakeholders, examines the motivation of stakeholders to engage with IPBES, and explores reflections by the authors (all active participants on the platform) for improved stakeholder engagement and contributions to future work of the platform.