Identifying key threats and conservation requirements for the Critically Endangered Yangtze finless porpoise

Evidence-based conservation is the most effective way to preserve biodiversity. However, for many species robust long-term data sets are not available and so the process of selecting effective interventions is poorly-informed and at risk of being ineffective. The Critically Endangered Yangtze finless porpoise (Neophocaena asiaeorientalis), a unique freshwater cetacean endemic to the Yangtze River, China, is subject to numerous anthropogenic threats that have led to significant population decline in recent decades. Conservation of this species has been severely limited by a poor understanding of the causes of population decline. By using four novel lines of analysis on already existing data sets, this study firstly assessed whether there is currently a sufficient evidence base to inform conservation of this species. This process established conservation-relevant conclusions and identified key remaining knowledge gaps without having to use valuable resources and time to gather further data. Subsequently, boat-based mapping studies have revealed conservation-relevant spatial and temporal patterns relating to potential threat presence and YFP habitat use on multiple spatial scales, whilst extensive interview-based surveys with fishers have been used to gather detailed information on patterns in illegal fishing gear use and YFP bycatch, as well as conservation-relevant socio-economic data. In addition, longitudinal interview data has provided an invaluable insight into changes in human-wildlife interactions and high-risk human behaviours over time. Lastly, an interview survey with key stakeholders involved in Yangtze finless porpoise conservation has demonstrated that evidence-based conservation is not being applied to this species, meaning that interventions are not targeted to key causes of decline and there is a risk of conservation complacency and extinction of a second Yangtze River cetacean. The multi-disciplinary research presented here has demonstrated how the conservation process for data-poor endangered species can be improved by increasing the knowledge base surrounding potential threats and causes of direct and indirect mortality, which has wider application for other at-risk species

Loss of Genetic Diversity Means Loss of Geological Information: The Endangered Japanese Crayfish Exhibits Remarkable Historical Footprints

Intra-specific genetic diversity is important not only because it influences population persistence and evolutionary potential, but also because it contains past geological, climatic and environmental information. In this paper, we show unusually clear genetic structure of the endangered Japanese crayfish that, as a sedentary species, provides many insights into lesser-known past environments in northern Japan. Over the native range, most populations consisted of unique 16S mtDNA haplotypes, resulting in significant genetic divergence (overall FST = 0.96). Owing to the simple and clear structure, a new graphic approach unraveled a detailed evolutionary history; regional crayfish populations were comprised of two distinct lineages that had experienced contrasting demographic processes (i.e. rapid expansion vs. slow stepwise range expansion) following differential drainage topologies and past climate events. Nuclear DNA sequences also showed deep separation between the lineages. Current ocean barriers to dispersal did not significantly affect the genetic structure of the freshwater crayfish, indicating the formation of relatively recent land bridges. This study provides one of the best examples of how phylogeographic analysis can unravel a detailed evolutionary history of a species and how this history contributes to the understanding of the past environment in the region. Ongoing local extinctions of the crayfish lead not only to loss of biodiversity but also to the loss of a significant information regarding past geological and climatic events

Applications of environmental DNA (eDNA) to detect subterranean and aquatic invasive species: A critical review on the challenges and limitations of eDNA metabarcoding

The world is struggling to solve a devastating biodiversity loss that not only affects the extinction of treasured species and irreplaceable genetic variation, but also jeopardizes the food production, health, and safety of people. All initiatives aimed to conserve biodiversity rely heavily on the monitoring of both species and populations to get accurate spatial patterns and overall population assessments. Conventional monitoring techniques, such as visual surveys and counting individuals, are problematic due to challenges in identifying cryptic species or immature life stages. Environmental DNA (eDNA) is a relatively new technology that has the potential to be a faster, non-invasive, and cost-effective tool for monitoring biodiversity, conservation, and management practices. eDNA has been extracted from materials that are both ancient and present, and its applications range from the identification of individual species to the study of entire ecosystems. In the past few years, there has been a substantial increase in the usage of eDNA in research pertaining to ecological preservation and conservation. However, several technological problems still need to be solved. To reduce the number of false positives and/or false negatives produced by current eDNA technologies, it is necessary to improve and optimize calibration and validation at every stage of the procedure. There is a significant need for greater information about the physical and ecological constraints on eDNA use, as well as its synthesis, current state, expected lifespan, and potential modes of movement. Due to the widespread use of eDNA research, it is also essential to assess the extent and breadth of these studies. In this article, we critically reviewed the primary applications of eDNA in subterranean and aquatic invasive species. Through this review, readers can better understand the challenges and limitations of eDNA metabarcoding

Global Extinction Risk for Seahorses, Pipefishes and Their Near Relatives (Syngnathiformes)

Few marine taxa have been comprehensively assessed for their conservation status, despite heavy pressures from fishing, habitat degradation and climate change. Here we report on the first global assessment of extinction risk for 300 species of syngnathiform fishes known as of 2017, using the IUCN Red List criteria. This order of bony teleosts is dominated by seahorses, pipefishes and seadragons (family Syngnathidae). It also includes trumpetfishes (Aulostomidae), shrimpfishes (Centriscidae), cornetfishes (Fistulariidae) and ghost pipefishes (Solenostomidae). At least 6% are threatened, but data suggest a mid-point estimate of 7.9% and an upper bound of 38%. Most of the threatened species are seahorses (Hippocampus spp.: 14/42 species, with an additional 17 that are Data Deficient) or freshwater pipefishes of the genus Microphis (2/18 species, with seven additional that are Data Deficient). Two species are Near Threatened. Nearly one-third of syngnathiformes (97 species) are Data Deficient and could potentially be threatened, requiring further field research and evaluation. Most species (61%) were, however, evaluated as Least Concern. Primary threats to syngnathids are (1) overexploitation, primarily by non-selective fisheries, for which most assessments were determined by criterion A (Hippocampus) and/or (2) habitat loss and degradation, for which assessments were determined by criterion B (Microphis and some Hippocampus). Threatened species occurred in most regions but more are found in East and South-east Asia and in South African estuaries. Vital conservation action for syngnathids, including constraining fisheries, particularly non-selective extraction, and habitat protection and rehabilitation, will benefit many other aquatic species

2017 Texas Bays and Estuaries Meeting

Program for the 2017 Texas Bays and Estuaries Meeting held in Port Aransas, Texas, April 12-13, 2017.Coastal Bend Bays & Estuaries Program, Coastal Bend Bays Foundation, The University of Texas Marine Science Institute, Sea Grant Texas at Texas A&M University, Harte Research Institute for Gulf of Mexico Studies, and Mission Aransas National Estuarine Research Reserve.Marine Scienc

Closing the gap between science and management of cold-water refuges in rivers and streams

Human activities and climate change threaten coldwater organisms in freshwater eco-systems by causing rivers and streams to warm, increasing the intensity and frequency of warm temperature events, and reducing thermal heterogeneity. Cold-water refuges are discrete patches of relatively cool water that are used by coldwater organisms for thermal relief and short-term survival. Globally, cohesive management approaches are needed that consider interlinked physical, biological, and social factors of cold-water refuges. We review current understanding of cold-water refuges, identify gaps between science and management, and evaluate policies aimed at protecting thermally sensitive species. Existing policies include designating cold-water habitats, restricting fishing during warm periods, and implementing threshold temperature standards or guidelines. However, these policies are rare and uncoordinated across spatial scales and often do not consider input from Indigenous peoples. We propose that cold-water refuges be managed as dis-tinct operational landscape units, which provide a social and ecological context that is relevant at the watershed scale. These operational landscape units provide the founda-tion for an integrated framework that links science and management by (1) mapping and characterizing cold-water refuges to prioritize management and conservation actions, (2) leveraging existing and new policies, (3) improving coordination across jurisdictions, and (4) implementing adaptive management practices across scales. Our findings show that while there are many opportunities for scientific advancement, the current state of the sciences is sufficient to inform policy and management. Our proposed framework pro-vides a path forward for managing and protecting cold-water refuges using existing and new policies to protect coldwater organisms in the face of global change. behavioral thermoregulation, climate change adaptation, lotic ecosystem management, refugia, salmonids, temperature, thermal heterogeneity, thermal refugespublishedVersio

Prospects and challenges of environmental DNA (eDNA) metabarcoding in mangrove restoration in Southeast Asia

Species detection using environmental DNA (eDNA) is a biomonitoring tool that can be widely applied to mangrove restoration and management. Compared to traditional surveys that are taxa-specific and time-consuming, eDNA metabarcoding offers a rapid, non-invasive and cost-efficient method for monitoring mangrove biodiversity and characterising the spatio-temporal distribution of multiple taxa simultaneously. General guidelines for eDNA metabarcoding are well-established for aquatic systems, but habitat-specific guidelines are still lacking. Mangrove habitats, as priority ecosystems for restoration in Southeast Asia, present unique prospects and challenges in these regards. Environmental DNA metabarcoding can be used to (1) track functional recovery in ecological restoration, (2) prioritise conservation areas, (3) provide early warning for threats, (4) monitor threatened taxa, (5) monitor response to climate change, and (6) support community-based restoration. However, these potential applications have yet been realized in Southeast Asia due to (1) technical challenges, (2) lack of standardised methods, (3) spatio-temporal difficulties in defining community, (4) data limitations, and (5) lack of funding, infrastructure and technical capacity. Successful implementation of eDNA metabarcoding in mangrove restoration activities would encourage the development of data-driven coastal management and equitable conservation programs. Eventually, this would promote Southeast Asia’s shared regional interests in food security, coastal defence and biodiversity conservation

Environmental DNA analysis as an emerging non-destructive method for plant biodiversity monitoring: a review

Environmental DNA (eDNA) analysis has recently transformed and modernized biodiversity monitoring. The accurate detection, and to some extent quantification, of organisms (individuals/populations/communities) in environmental samples is galvanizing eDNA as a successful cost and time-efficient biomonitoring technique. Currently, eDNA’s application to plants remains more limited in implementation and scope compared to animals and microorganisms. Thus, this review evaluates the development of eDNA-based methods for (vascular) plants, comparing its performance and power of detection with that of traditional methods, to critically evaluate and advise best practices needed for innovating plant biomonitoring. Recent advancements, standardization, and field applications of eDNA-based methods have provided enough scope to utilize it in conservation biology for numerous organisms. eDNA also has considerable potential for plants, where successful detection of invasive, endangered and rare species, and community-level interpretations have provided proof-of-concept. Monitoring methods using eDNA were found to be equal or more effective than traditional methods, however species detection increased when both the methods were coupled. Additionally, eDNA methods were found to be effective in studying species interactions, community dynamics, and even effects of anthropogenic pressure. Currently, elimination of potential obstacles (e.g., lack of relevant DNA reference libraries for plants) and the development of user-friendly protocols would greatly contribute to comprehensive eDNA-based plant monitoring programs. This is particularly needed in the data-depauperate tropics and for some less-concern plant groups. We further advocate it may be valuable to couple traditional methods with eDNA approaches, as the former is often cheaper and methodologically more straightforward, while the latter offers a non-destructive approach with the ability to identify plants in situations where morphological identification is difficult or impossible. Furthermore, in order to make a global platform for eDNA, governmental and academic-industrial collaborations are essential to make eDNA surveys a broadly adopted and implemented, rapid, cost-effective, and non-invasive plant monitoring approach

A Critical Assessment of the Congruency between Environmental DNA and Palaeoecology for the Biodiversity Monitoring and Palaeoenvironmental Reconstruction

The present study suggests that standardized methodology, careful site selection, and stratigraphy are essential for investigating ancient ecosystems in order to evaluate biodiversity and DNA-based time series. Based on specific keywords, this investigation reviewed 146 publications using the SCOPUS, Web of Science (WoS), PUBMED, and Google Scholar databases. Results indicate that environmental deoxyribose nucleic acid (eDNA) can be pivotal for assessing and conserving ecosystems. Our review revealed that in the last 12 years (January 2008–July 2021), 63% of the studies based on eDNA have been reported from aquatic ecosystems, 25% from marine habitats, and 12% from terrestrial environments. Out of studies conducted in aquatic systems using the environmental DNA (eDNA) technique, 63% of the investigations have been reported from freshwater ecosystems, with an utmost focus on fish diversity (40%). Further analysis of the literature reveals that during the same period, 24% of the investigations using the environmental DNA technique were carried out on invertebrates, 8% on mammals, 7% on plants, 6% on reptiles, and 5% on birds. The results obtained clearly indicate that the environmental DNA technique has a clear-cut edge over other biodiversity monitoring methods. Furthermore, we also found that eDNA, in conjunction with different dating techniques, can provide better insight into deciphering eco-evolutionary feedback. Therefore, an attempt has been made to offer extensive information on the application of dating methods for different taxa present in diverse ecosystems. Last, we provide suggestions and elucidations on how to overcome the caveats and delineate some of the research avenues that will likely shape this field in the near future. This paper aims to identify the gaps in environmental DNA (eDNA) investigations to help researchers, ecologists, and decision-makers to develop a holistic understanding of environmental DNA (eDNA) and its utility as a palaeoenvironmental contrivance

A Critical Assessment of the Congruency between Environmental DNA and Palaeoecology for the Biodiversity Monitoring and Palaeoenvironmental Reconstruction

The present study suggests that standardized methodology, careful site selection, and stratigraphy are essential for investigating ancient ecosystems in order to evaluate biodiversity and DNA-based time series. Based on specific keywords, this investigation reviewed 146 publications using the SCOPUS, Web of Science (WoS), PUBMED, and Google Scholar databases. Results indicate that environmental deoxyribose nucleic acid (eDNA) can be pivotal for assessing and conserving ecosystems. Our review revealed that in the last 12 years (January 2008–July 2021), 63% of the studies based on eDNA have been reported from aquatic ecosystems, 25% from marine habitats, and 12% from terrestrial environments. Out of studies conducted in aquatic systems using the environmental DNA (eDNA) technique, 63% of the investigations have been reported from freshwater ecosystems, with an utmost focus on fish diversity (40%). Further analysis of the literature reveals that during the same period, 24% of the investigations using the environmental DNA technique were carried out on invertebrates, 8% on mammals, 7% on plants, 6% on reptiles, and 5% on birds. The results obtained clearly indicate that the environmental DNA technique has a clear-cut edge over other biodiversity monitoring methods. Furthermore, we also found that eDNA, in conjunction with different dating techniques, can provide better insight into deciphering eco-evolutionary feedback. Therefore, an attempt has been made to offer extensive information on the application of dating methods for different taxa present in diverse ecosystems. Last, we provide suggestions and elucidations on how to overcome the caveats and delineate some of the research avenues that will likely shape this field in the near future. This paper aims to identify the gaps in environmental DNA (eDNA) investigations to help researchers, ecologists, and decision-makers to develop a holistic understanding of environmental DNA (eDNA) and its utility as a palaeoenvironmental contrivance