Linking extinction risk to the economic and nutritional value of sharks in small-scale fisheries.

To achieve sustainable shark fisheries, it is key to understand not only the biological drivers and environmental consequences of overfishing, but also the social and economic drivers of fisher behavior. The extinction risk of sharks is highest in coastal tropical waters, where small-scale fisheries are most prevalent. Small-scale fisheries provide a critical source of economic and nutritional security to coastal communities, and these fishers are among the most vulnerable social and economic groups. We used Kenya's and Zanzibar's small-scale shark fisheries, which are illustrative of the many data-poor, small-scale shark fisheries worldwide, as case studies to explore the relationship between extinction risk and the economic and nutritional value of sharks. To achieve this, we combined existing data on shark landings, extinction risk, and nutritional value with sales data at 16 key landing sites and information from interviews with 476 fishers. Shark fisheries were an important source of economic and nutritional security, valued at >US$4 million annually and providing enough nutrition for tens of thousands of people. Economically and nutritionally, catches were dominated by threatened species (72.7% and 64.6-89.7%, respectively). The most economically valuable species were large and slow to reproduce (e.g. mobulid rays, wedgefish, and bull, silky, and mako sharks) and therefore more likely to be threatened with extinction. Given the financial incentive and intensive fishing pressure, small-scale fisheries are undoubtedly major contributors to the decline of threatened coastal shark species. In the absence of effective fisheries management and enforcement, we argue that within small-scale fisheries the conditions exist for an economically incentivized feedback loop in which vulnerable fishers are driven to persistently overfish vulnerable and declining shark species. To protect these species from extinction, this feedback loop must be broken.

Conexión entre el riesgo de extinción y el valor nutricional de los tiburones en las pesquerías a pequeña escala Resumen Para lograr la sustentabilidad de las pesquerías de tiburones se deben entender los factores ecológicos y las consecuencias ambientales de la sobrepesca, así como los factores sociales y económicos del comportamiento del pescador. El riesgo de extinción de los tiburones es mucho mayor en las aguas tropicales costeras, en donde son más frecuentes las pesquerías a pequeña escala. Las pesquerías a pequeña escala, que además se encuentran entre los grupos con mayor vulnerabilidad social y económica, proporcionan una fuente importante de seguridad económica y nutricional para las comunidades costeras. Usamos las pesquerías de Kenia y Zanzíbar, las cuales representan muy bien a muchas de las pequeñas pesquerías de tiburones con deficiencia de datos, como estudios de caso para explorar la relación entre el riesgo de extinción y el valor económico y nutricional de los tiburones. Para lograr esto, combinamos los datos ya existentes de desembarques de tiburones, riesgo de extinción y valor nutricional con la información de ventas en 16 sitios clave de desembarque e información de las entrevistas a 476 pescadores. Las pesquerías de tiburones son una fuente importante de seguridad alimentaria y económica, valorada en más de US$4 millones anuales y que proporciona suficiente alimentación para miles de personas. En cuanto a la economía y la alimentación, las capturas estuvieron dominadas por especies amenazadas (72.7% y 64.6­89.7%, respectivamente). Las especies con mayor valor económico eran aquellas de gran tamaño y lenta reproducción, y, por lo tanto, con mayor probabilidad de estar en peligro de extinción. A causa del incentivo económico y la presión intensa de pesca, las pesquerías pequeñas sin duda son uno de los principales contribuyentes a la declinación de especies amenazadas de tiburones en las costas. Ya que no hay una aplicación ni un manejo efectivos de las pesquerías, argumentamos que en las pequeñas pesquerías existen las condiciones para un bucle de retroalimentación con incentivación económica en el que los pescadores vulnerables con frecuencia necesitan sobre pescar las especies de tiburones vulnerables y en declinación. Para proteger a estas especies de la extinción, este bucle de retroalimentación debe romperse.

The high cost of movement in an arid working landscape for an endangered amphibian.

Connectivity is essential for the maintenance of genetic diversity and stability of wildlife populations. Drought and changing precipitation regimes have caused natural aquatic amphibian breeding habitats to disappear or become isolated and have led to the replacement of natural surface water with artificial livestock water tanks. Terrestrial movement is the only means of responding to aquatic threats in arid landscapes and to allow population connectivity. Aridity may present an impenetrable barrier in hydrologically fragmented environments. We used a facultatively paedomorphic and federally endangered salamander to assess the challenges of movement across arid working lands. Sonoran tiger salamanders (Ambystoma mavortium stebbinsi) are endemic to the San Rafael Valley of southeastern Arizona, United States of America, where they depend on livestock water tanks as breeding habitat. The ecology of this species' metamorphs outside of stock tanks is virtually unknown. To assess survival on the landscape during terrestrial movement we used radio-transmitters to track 78 adult metamorphosed salamanders over 2 years. Sonoran tiger salamanders moved up to 1 km from the tank edge, and average distances moved of over 400 m were higher than most Ambystoma species. However, during the study period, none reached neighboring stock tanks. We found high mortality due to predation and desiccation. Individuals that dispersed to terrestrial habitat in summer survived longer than individuals that dispersed in spring. High mortality suggests terrestrial movement is exceptionally risky and may contribute to isolated subpopulations and elevated levels of inbreeding. Conservation actions that improve and maintain artificial aquatic habitats as well as increase connectivity may improve long-term management for pond-breeding amphibians in arid regions.

Diurnal activity time budget of Grevy's zebra (Equus grevyi, Oustalet 1882) in a protected savannah area.

Understanding natural history such as diurnal activity of wildlife species is important for their conservation intervention. The aim of the current study was to examine Grevy's zebra diurnal activity time budget in Hallaydeghe Asebot Proposed National Park (HAPNP) considering both wet and dry seasons. Scan sampling method was used. Activities of the species were recorded based on age and sex. Species were observed for 15 min (10 min activities recording followed 5 min rest). Analysis of Variance (ANOVA) was used to analysis data. Grazing (31.26%) was the highest followed by resting (30.24%) during the wet season and grazing (37.13%) was the highest followed by moving (27.25%) during dry season. The peak grazing time of species was morning 6:00-9:00 a.m. and late afternoon 16:00-18:00 p.m. while resting was observed during midday. The time the species spent over grazing (df = 1, F = 27.15, p = 0.000132), Grooming (df = 1, F = 24.082, p = 0.000231), mating (df = 1, F = 24.850, p = 0.0002) and moving (df = 1, F = 5.550, p = 0.0336) activity during both seasons were significantly different. There is statistical difference for grazing (df = 2, F = 9.336, p = 0.002653), mating (df = 2, F = 6.216, p = 0.0117), moving (df = 2, F = 5.604, p = 0.0163) and other (df = 2, F = 5.006, p = 0.0229) activities based on sex of species. The current study examined only diurnal activity time budget of the species. As a result, future research shall be conducted by taking into account the impact of different factors (temperature and livestock) that can influence the activity time budget of Grevy's zebra in HAPNP. Lastly, we recommend thorough species management plan in HAPNP for sustainable conservation of Grevy's zebra.

Genetic diversity assessment of Helichrysum arenarium (Asteraceae) for the genetic restoration of declining populations.

Helichrysum arenarium (L.) Moench (Asteraceae) is a self-compatible, insect-pollinated herb occurring in sand grasslands, and is declining and endangered in many parts of its European distribution range. A recovery plan of H. arenarium has been conducted in southern Belgium, involving plant translocations. We developed multiplex genotyping protocol for nine microsatellite markers previously published for Helichrysum italicum and two newly developed microsatellite markers for H. arenarium. Eleven polymorphic loci were associated (pooled) in two multiplex panels, to assess the genetic status of the only small remaining population in Belgium and of three large German populations used as seed source for propagating transplants. The small Belgian population was characterized by high clonality, with only two, however heterozygous, genets detected. The three large German populations showed high genetic diversity (H e ranging from 0.635 to 0.670) and no significant inbreeding coefficient values, despite expectations of geitonogamous selfing. Management practices (grazing livestock) increasing seed dispersal distances, inbreeding depression at early stages of development, and mechanisms preventing or delaying selfing might be hypothesized to explain the observed patterns. The two Belgian genotypes remained within genetic variation range of German populations so that the high genetic differentiation between Belgian and German populations (F ST values ranging from 0.186 to 0.206) likely resulted from genetic drift effects and small sample size. Transplants obtained from seeds sampled from the three large source populations from Germany constitute a highly diverse, noninbred gene pool, and are thus of high genetic quality for plant translocations.

Project-specific bumble bee habitat quality assessment.

The listing of Bombus affinis Cresson 1863 (Rusty Patched Bumble Bee; RPBB) in 2017 under the Endangered Species Act (ESA) created a regulatory need for assessment methods, in order to limit take of this species by construction and development. As the first social insect listed under the ESA, the listing of RPBB has required new methods for biological assessment. This species has a complex life cycle requiring a mosaic of different habitat types, with each life cycle stage facing unique challenges and threats. I have established a method for separately assessing habitats critical to each vulnerable life history stage, using a combination of aerial photography, GIS maps and target-specific ground survey efforts. This method identifies factors that may potentially limit bumble bee colony success in each stage and provides project planners with facts about physical structures or plant communities that may have elevated importance to bumble bees during certain seasonal windows. Previous efforts to assess bumble bee habitat considered landscape features thought to be linked to bumble bee colony success. This effort extends these methods to estimate project specific impacts of construction and development projects, necessary for Section 7 Consultation with the United States Fish and Wildlife Service (USFWS) under the ESA. •Systematic spatial assessment of landscape features linked to critical periods in the life history trajectory of a bumble bee colony across a season•Construction and development project proponents can approach USFWS consultation with quantitative estimates of the area of a project area classified by habitat types and qualities•Factors limiting bumble bee recovery may be inferred from the distribution and abundance of the constituent elements of quality bumble bee habitat.

Identifying opportunities for high resolution pesticide usage data to improve the efficiency of endangered species pesticide risk assessment.

The US pesticide registration and review process requires regular re-assessment of the risk of pesticide use to species listed under the Endangered Species Act (ESA), yet current assessment methods are inefficient when applied to hundreds of pesticides potentially impacting multiple species across a continent. Thus, many pesticides remain on the market without complete review. We assessed the value of using high resolution pesticide usage data in the risk assessment process to rapidly improve process efficiency. By using data available only in California, we found that high resolution data increased the number of species deemed not likely to be adversely affected by pesticides from <5 % to nearly 50 %. Across the contiguous US, we predicted that 48 % of species would be deemed not likely to be adversely affected using high resolution data, compared to 20 % without. However, if such data were available in just 11 states, 68 % of the available gains in efficiency could be obtained. Overall, using existing high-resolution data in California and a focused collection of such information from 11 other states could reduce risk assessment burden across the contiguous U.S. by one-quarter.

Assessment of chlorinated pesticide exposure to white-rumped vulture Gyps bengalensis in India.

Populations of the critically endangered white-rumped vulture (WRV) Gyps bengalensis have declined drastically due to the use of diclofenac for veterinary purposes in Indian subcontinent. Thirty-two dead WRVs collected from three states, namely Gujarat, Assam and Tamil Nadu in India between 2011 and 2014 were investigated to understand the role of diclofenac in the death, and the results were published. Furthermore, since organochlorine pesticides have been linked to long-term impact on populations in many species of birds across the globe, available tissues of 21 WRVs were tested also for six organochlorine pesticides (DDT, HCH, endosulfan, heptachlor, dieldrin and dicofol) and chlorpyrifos. All vultures were found to have had one or more detectable levels of pesticides in their tissues except one. Similarly, all the pesticides included in the study were detected in at least one of the vultures analysed. DDT (95.2%) was the most frequently detected pesticide followed by HCH (90.5%), and DDT (73.6%) contributed the most to the total pesticide load. Total pesticide load ranged between below detection limit (BDL) and 8753.4 ng/g. High levels of total pesticide load recorded in gut contents showed recent exposure to these legacy pesticides even long after their ban. However, it is perceived that studied pesticides' exposure to birds and their presence in the environment is in decreasing trend in India. Although, varying levels of pesticides were detected, all of which were below the levels reported to be toxic, and also reported earlier in the same species in India. Recorded levels may not create a problem to vultures unlike diclofenac; nevertheless, as continued exposure to the pesticides studied may lead to sub lethal effects in birds, it is prudent to monitor these pesticides along with new generation pesticides and NSAIDs in the critically endangered white-rumped vulture in India, towards its conservation.

Adaptive plasticity and fitness costs of endangered, nonendangered, and invasive plants in response to variation in nitrogen and phosphorus availabilities.

Global change drivers such as eutrophication and plant invasions will create novel environments for many plant species. Through adaptive trait plasticity plants may maintain their performance under these novel conditions and may outcompete those showing low-adaptive trait plasticity. In a greenhouse study, we determined if plasticity in traits is adaptive or maladaptive in endangered, nonendangered, and invasive plant species in response to variation of nitrogen (N) and phosphorus (P) availability (N:P ratios 1.7, 15, and 135) and whether plastic trait responses are adaptive and/or costly for fitness (i.e., biomass). Species choice comprised 17 species from three functional groups (legumes, nonlegume forbs, and grasses), either classified as endangered, nonendangered, or invasive. After 2 months, plants were harvested and nine traits related to carbon assimilation and nutrient uptake were measured (leaf area, SLA, LDMC, SPAD, RMR, root length, SRL, root surface area, and PME activity). We found more traits responding plastically to variation in P than in N. Plasticity only created costs when P was varied. Plasticity in traits was mostly adaptively neutral toward fitness, with plasticity in three traits being similarly adaptive across all species groups: SPAD (as a measure of chlorophyll content, adaptive to N and P limitation), leaf area, and root surface area (adaptive to P limitation). We found little differences in trait plasticity between endangered, nonendangered, and invasive species. Synthesis. Along a gradient from N limitation, balanced N:P supply, and P limitation, we found that the type of fluctuating nutrient (i.e., if N or P is varied) is decisive for the adaptive value of a trait. Variation in P availability (from balanced supply to P limitation) created both a stronger reduction in fitness as well as created plasticity costs in more traits than variation in N availability (from balanced supply to N limitation). However, the patterns observed in our study may change if nutrient availability is altered, either by nutrient inputs or by a shift in nutrient availabilities, for example, by decreasing N input as foreseen by European Legislation, but without simultaneously decreasing P input.

Assessment of the impact of climate change on endangered conifer tree species by considering climate and soil dual suitability and interspecific competition.

Climate change results in the habitat loss of many conifer tree species and jeopardizes species biodiversity and forest ecological functions. Delineating suitable habitats for tree species via climate niche model (CNM) is widely used to predict the impact of climate change and develop conservation and management strategies. However, the robustness of CNM is broadly debated as it usually does not consider soil and competition factors. Here we developed a new approach to combine soil variables with CNM and evaluate interspecific competition potential in the niche overlapping areas. We used an endangered conifer species - Chamaecyparis formosensis (red cypress) - as a case study to predict the impact of climate change. We developed a novel approach to integrate the climate niche model and soil niche model predictions and considered interspecific competition to predict the impacts of climate change on tree species. Our results show that the suitable habitat for red cypress would decrease significantly in the future with an additional threat from the competition of an oak tree species. Our approach and results may represent significant implications in making conservation strategies and evaluating the impacts of climate change, and providing the direction of the refinement of the ecological niche model.

Integrating invasive species risk assessment into environmental DNA metabarcoding reference libraries.

Environmental DNA (eDNA) metabarcoding has shown promise as a tool for estimating biodiversity and early detection of invasive species. In aquatic systems, advantages of this method include the ability to concurrently monitor biodiversity and detect incipient invasions simply through the collection and analysis of water samples. However, depending on the molecular markers chosen for a given study, reference libraries containing target sequences from present species may limit the usefulness of eDNA metabarcoding. To explore the extent of this issue and how it may be resolved to aid biodiversity and invasive species early detection goals, we focus on fishes in the well-studied Laurentian Great Lakes region. First, we provide a synthesis of species currently known from the region and of non-indigenous species identified as threats by international, national, regional, and introduction pathway-specific fish risk assessments. With these species lists, we then evaluate 23 primer pairs commonly used in fish eDNA metabarcoding with available databases of sequence coverage and species specificity. Finally, we identify established and potentially invasive non-indigenous fish that should be prioritized for genetic sequencing to ensure robust eDNA metabarcoding for the region. Our results should increase confidence in using eDNA metabarcoding for fisheries conservation and management in the Great Lakes region and help prioritize reference sequencing efforts. The ultimate utility of eDNA metabarcoding approaches will come when conservation management of existing fish communities is integrated with early detection efforts for invasive species surveillance to assess total fish biodiversity.

Probabilistic co-occurrence assessment for suites of listed species.

Section 7 of the Endangered Species Act requires the US Environmental Protection Agency (US EPA) to consult with the Services (US Fish and Wildlife Service and National Marine Fisheries Service) over potential pesticide impacts on federally listed species. Consultation is complicated by the large number of pesticide products and listed species, as well as by lack of consensus on best practices for conducting co-occurrence analyses. Previous work demonstrates that probabilistic estimates of species' ranges and pesticide use patterns improve these analyses. Here we demonstrate that such estimates can be made for suites of sympatric listed species. Focusing on two watersheds, one in Iowa and the other in Mississippi, we obtained distribution records for 13 species of terrestrial and aquatic listed plants and animals occurring therein. We used maximum entropy modeling and bioclimatic, topographic, hydrographic, and land cover variables to predict species' ranges at high spatial resolution. We constructed probabilistic spatial models of use areas for two pesticides based on the US Department of Agriculture Cropland Data Layer and reduced classification errors by incorporating information on the relationships between individual pixels and their neighbors using object-based images analysis. We then combined species distribution and crop footprint models to derive overall probability of co-occurrence of listed species and pesticide use. For aquatic species, we also integrated an estimate of downstream residue transport. We report each separate species-by-use-area co-occurrence estimate and also combine these modeled co-occurrence probabilities across species within watersheds to produce an overall metric of potential pesticide exposure risk for these listed species at the watershed level. We propose that the consultation process between US EPA and the Services be based on such batched estimation of probabilistic co-occurrence for multiple listed species at a regional scale. Integr Environ Assess Manag 2022;18:1088-1100. © 2021 SETAC.

Population assessment and habitat associations of the Visayan Hornbill (Penelopides panini) in Northwest Panay, Philippines.

BACKGROUND: Seven out of ten hornbill species in the Philippines are threatened with extinction. Among these is the endangered Visayan Hornbill (Penelopides panini), found on the islands of Panay and Negros. Threatened by habitat loss and hunting, its population size is thought to have declined from 1800 individuals 20 years ago to less than 1000. However, a recent study on Negros estimated 3564 individuals across three core forest blocks. This study aims to quantify the Visayan Hornbill population size in and around the Northwest Panay Peninsula Natural Park (NWPPNP) on Panay, the largest contiguous low-elevation forest landscape remaining across its range, and its broad habitat associations across a gradient of environmental degradation. METHODS: Hornbills were surveyed using 10-min distance sampling point counts (n = 367) along transects (average length 1.1 km). Environmental variables were recorded along transects, while habitat was classified into primary forest, secondary forest, plantation, or open habitat. Distance software was used to estimate population densities stratified by habitat, with the overall population estimate taken as a mean of habitat density estimates weighted by habitat area. Using generalized linear mixed models, hornbill occurrence was modelled using combinations of nine environmental variables as main and two-way fixed effects. RESULTS: Surveys covered 204.4 km2 of the 374.8 km2 Northwest Panay Peninsula. Hornbills were not recorded in plantations or open habitats. Hornbill density was significantly higher in primary forest (17.8 individuals/km2 ± 26.9% CV) than in secondary forest (3.7 individuals/km2 ± 33.2% CV; z = 15.212, P < 0.001). The overall population estimate for the NWPPNP and environs is 2109 individuals, and 2673 individuals for the entire Northwest Panay Peninsula. Hornbill presence was best explained by a model including distance from the Park boundary alongside five interaction effects and transect as a random effect. Distance, and the interaction between distance and medium-sized trees were significant predictors of hornbill presence. CONCLUSIONS: Our study evidences the habitat preference of the Visayan Hornbill, highlights the importance of the NWPPNP for the species' conservation, and provides strong evidence for re-assessing the global population size. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40657-021-00303-3.

The genome of the endangered Macadamia jansenii displays little diversity but represents an important genetic resource for plant breeding.

Macadamia, a recently domesticated expanding nut crop in the tropical and subtropical regions of the world, is one of the most economically important genera in the diverse and widely adapted Proteaceae family. All four species of Macadamia are rare in the wild with the most recently discovered, M. jansenii, being endangered. The M. jansenii genome has been used as a model for testing sequencing methods using a wide range of long read sequencing techniques. Here, we report a chromosome level genome assembly, generated using a combination of Pacific Biosciences sequencing and Hi-C, comprising 14 pseudo-molecules, with a N50 of 52 Mb and a total genome assembly size of 758 Mb of which 56% is repetitive. Completeness assessment revealed that the assembly covered -97.1% of the conserved single copy genes. Annotation predicted 31,591 protein coding genes and allowed the characterization of genes encoding biosynthesis of cyanogenic glycosides, fatty acid metabolism, and anti-microbial proteins. Re-sequencing of seven other genotypes confirmed low diversity and low heterozygosity within this endangered species. Important morphological characteristics of this species such as small tree size and high kernel recovery suggest that M. jansenii is an important source of these commercial traits for breeding. As a member of a small group of families that are sister to the core eudicots, this high-quality genome also provides a key resource for evolutionary and comparative genomics studies.

Assessment of risks to listed species from the use of atrazine in the USA: a perspective.

Atrazine is a triazine herbicide used predominantly on corn, sorghum, and sugarcane in the US. Its use potentially overlaps with the ranges of listed (threatened and endangered) species. In response to registration review in the context of the Endangered Species Act, we evaluated potential direct and indirect impacts of atrazine on listed species and designated critical habitats. Atrazine has been widely studied, extensive environmental monitoring and toxicity data sets are available, and the spatial and temporal uses on major crops are well characterized. Ranges of listed species are less well-defined, resulting in overly conservative designations of "May Effect". Preferences for habitat and food sources serve to limit exposure among many listed animal species and animals are relatively insensitive. Atrazine does not bioaccumulate, further diminishing exposures among consumers and predators. Because of incomplete exposure pathways, many species can be eliminated from consideration for direct effects. It is toxic to plants, but even sensitive plants tolerate episodic exposures, such as those occurring in flowing waters. Empirical data from long-term monitoring programs and realistic field data on off-target deposition of drift indicate that many other listed species can be removed from consideration because exposures are below conservative toxicity thresholds for direct and indirect effects. Combined with recent mitigation actions by the registrant, this review serves to refine and focus forthcoming listed species assessment efforts for atrazine.Abbreviations: a.i. = Active ingredient (of a pesticide product). AEMP = Atrazine Ecological Monitoring Program. AIMS = Avian Incident Monitoring SystemArach. = Arachnid (spiders and mites). AUC = Area Under the Curve. BE = Biological Evaluation (of potential effects on listed species). BO = Biological Opinion (conclusion of the consultation between USEPA and the Services with respect to potential effects in listed species). CASM = Comprehensive Aquatic System Model. CDL = Crop Data LayerCN = field Curve Number. CRP = Conservation Reserve Program (lands). CTA = Conditioned Taste Avoidance. DAC = Diaminochlorotriazine (a metabolite of atrazine, also known by the acronym DACT). DER = Data Evaluation Record. EC25 = Concentration causing a specified effect in 25% of the tested organisms. EC50 = Concentration causing a specified effect in 50% of the tested organisms. EC50RGR = Concentration causing a 50% reduction in relative growth rate. ECOS = Environmental Conservation Online System. EDD = Estimated Daily Dose. EEC = Expected Environmental Concentration. EFED = Environmental Fate and Effects Division (of the USEPA). EFSA = European Food Safety Agency. EIIS = Ecological Incident Information System. ERA = Environmental Risk Assessment. ESA = Endangered Species Act. ESU = Evolutionarily Significant UnitsFAR = Field Application RateFIFRA = Federal Insecticide, Fungicide, and Rodenticide Act. FOIA = Freedom of Information Act (request). GSD = Genus Sensitivity Distribution. HC5 = Hazardous Concentration for ≤ 5% of species. HUC = Hydrologic Unit Code. IBM = Individual-Based Model. IDS = Incident Data System. KOC = Partition coefficient between water and organic matter in soil or sediment. KOW = Octanol-Water partition coefficient. LC50 = Concentration lethal to 50% of the tested organisms. LC-MS-MS = Liquid Chromatograph with Tandem Mass Spectrometry. LD50 = Dose lethal to 50% of the tested organisms. LAA = Likely to Adversely Affect. LOAEC = Lowest-Observed-Adverse-Effect Concentration. LOC = Level of Concern. MA = May Affect. MATC = Maximum Acceptable Toxicant Concentration. NAS = National Academy of Sciences. NCWQR = National Center of Water Quality Research. NE = No Effect. NLAA = Not Likely to Adversely Affect. NMFS = National Marine Fisheries Service. NOAA = National Oceanic and Atmospheric Administration. NOAEC = No-Observed-Adverse-Effect Concentration. NOAEL = No-Observed-Adverse-Effect Dose-Level. OECD = Organization of Economic Cooperation and Development. PNSP = Pesticide National Synthesis Project. PQ = Plastoquinone. PRZM = Pesticide Root Zone Model. PWC = Pesticide in Water Calculator. QWoE = Quantitative Weight of Evidence. RGR = Relative growth rate (of plants). RQ = Risk Quotient. RUD = Residue Unit Doses. SAP = Science Advisory Panel (of the USEPA). SGR = Specific Growth Rate. SI = Supplemental Information. SSD = Species Sensitivity Distribution. SURLAG = Surface Runoff Lag Coefficient. SWAT = Soil & Water Assessment Tool. SWCC = Surface Water Concentration Calculator. UDL = Use Data Layer (for pesticides). USDA = United States Department of Agriculture. USEPA = United States Environmental Protection Agency. USFWS = United States Fish and Wildlife Service. USGS = United States Geological Survey. WARP = Watershed Regressions for Pesticides.

Global warming assessment suggests the endemic Brazilian kelp beds to be an endangered ecosystem.

Kelps are canopy-forming brown seaweed sustaining critical ecosystem services in coastal habitats, including shelter, nursery grounds, and providing food resources to a myriad of associated species. This study modeled the fundamental niche of Laminaria abyssalis along the Brazilian continental margin, an endemic species of the South Atlantic, to anticipate potential distributional range shifts under two contrasting scenarios of future environmental changes (RCP2.6 and RCP8.5). The model for fundamental niche predictions considering the "present scenario" has shown a wider potential area than the realized niche (i.e., the area where the species actually occurs) along the Brazilian coast. In both future scenarios, the models have shown niche erosion on the northern portion of the Brazilian coast and niche gains towards the south. In both scenarios, L. abyssalis populations tend to shift to deeper regions of the reef. The restricted range of occurrence (33,000 km2), intense anthropic activities along these beds (e.g., trawling fisheries, oil/gas mining, or removal for agricultural purposes) acting synergically with global warming, may drive this ecosystem to collapse faster than kelp species' ability to adapt. We propose to classify L. abyssalis as Endangered - (EN) under IUCN criteria, and highlight that long-term monitoring of kelp beds is an urgent need to develop effective conservation initiatives to protect such rare and invaluable ecosystem.

Genetic assessment of captive red pandas (Ailurus fulgens) in American zoos to address management separation by putative subspecies.

Red pandas (Ailurus fulgens) are small charismatic mammals native across montane southern Asia, now endangered by human impacts. They are considered "living fossils" as the sole member of a distinct family, warranting higher conservation priority. Therefore, ex situ breeding programs were initiated to prevent extinction and act as genetic reservoirs for reintroduction, although complicated by apparent taxonomic subdivision. This study investigated whether the separation of captive red pandas in the North American Species Survival Plan® by putative subspecies was justified. A 383-bp segment of mitochondrial DNA control region was therefore sequenced from 67 members representing matriarchal lineages of both groups. A network analysis placed the 11 haplotypes found into separate but closely connected clusters, with one group more strongly related than the other. Statistical analyses and diversity indices corroborated differentiation between the two management units. Phylogenetic analyses employing multiple outgroups confirmed, although not robustly, reciprocal monophyly of the four- and seven-haplotype clades representing putative subspecies Ailurus fulgens fulgens and Ailurus fulgens styani, respectively. These empirical results are adequate to justify continued independent management of these zoo subpopulations, but cannot be definitive for taxonomic classification due to limited sampling from their native range. They will, however, be useful in evaluating long-term genetic diversity changes, focusing management efforts on newly revealed evolutionary limitations, and comparing with an assessment of wild red pandas to determine how representative zoo populations are for reintroduction purposes. Maintaining genetic diversity and population structure of endangered species is essential to protect evolutionary potential and adaptations for long-term sustainability.

Sequencing and annotation of the endangered wild buffalo (Bubalus arnee) mitogenome for taxonomic assessment.

The wild water buffalo (Bubalus arnee) is one of the most endangered and least studied large bovid in the Indian subcontinent. India retains 90% of the estimated global population of >4000 individuals as two fragmented populations in Assam and Chhattisgarh, both threatened by habitat loss and degradation, hunting, disease from livestock, and hybridization with the domestic buffalos. Small, fragmented population size and potential hybridisation pressures from co-occurring domestic buffalos are the major conservation challenges. For the first time, we sequenced the 16,357 bp long mitogenome of three opportunistically collected wild water buffalo samples from Assam (n = 1) and Chhattishgarh (n = 2). The annotated sequence has a base composition of 26.4% T, 26.6% C, 33.1% A and 13.9% G depicting an AT-rich mitogenome composition, including 13 protein-coding genes (11,361 bp), 22 transfer RNA (tRNA) (1514 bp), two ribosomal genes (2525 bp), and a non-coding control region (928 bp). The gene order is conserved with other bovid species. Comparative mitogenome analyses showed both populations are genetically similar but significantly different from domestic buffalo. We also identified structural differences in seven tRNA secondary structures between both species. The genetic distance between wild buffalo and other bovids varied between 0.103 and 0.122. Multiple Bayesian phylogenetic trees showed that both wild and domestic water buffalo formed sister clades which were paraphyletic to other potentially sympatric species of genus Bos. This study provides baseline information on wild buffalo mitogenome for further research on phylogeny, phylogeography and hybrid assessment and help conserving this endangered species.

Genetic diversity assessment for the vulnerable migratory cownose ray Rhinoptera bonasus (Myliobatiformes: Rhinopteridae) from the southwestern Atlantic Ocean

ABSTRACT Rhinoptera bonasus is a bento-pelagic and highly migratory species occurring from southern United States to northern Argentina. Due to overfishing effects, R. bonasus is currently at risk, classified by the IUCN Red List as vulnerable. Considering the lack of molecular data available for R. bonasus, this study aimed to describe the genetic variability and population structure of specimens sampled from three Brazilian coast ecoregions (Amazon ecoregion, Pará; Northeastern ecoregion, Pernambuco and Southeastern ecoregion, Rio de Janeiro, São Paulo and Santa Catarina), through five polymorphic microsatellite markers. Here testing the panmixia hypothesis for Brazilian ecoregions and test natal philopathy. A total of 69 analyzed specimens revealed individual and significant genetic differentiation between the sampled locations. ST (0.12), PCA, DAPC and Bayesian analyses of the genetic population structure revealed at least two distinct genetic R. bonasus groupings. IBD tests were significant, indicating a correlation between genetic and geographical distance among populations, which can be explained by reproductive philopatric behavior. Philopatric behavior associated with R. bonasus mobility may influence the differentiation values observed for all loci in the investigated samples.

RESUMO Rhinoptera bonasus é uma espécie bento-pelágica e altamente migratória, que ocorre do sul dos Estados Unidos ao norte da Argentina. Devido aos efeitos da sobrepesca, R. bonasus está atualmente em risco, classificada pela Lista Vermelha da IUCN como vulnerável. Considerando a falta de dados moleculares disponíveis para R. bonasus, este estudo teve como objetivo descrever a variabilidade genética e estrutura populacional de espécimes amostrados em três ecorregiões do litoral brasileiro (Ecorregião Amazônica, Pará; Ecorregião Nordeste, Pernambuco e Ecorregião Sudeste, Rio de Janeiro, São Paulo e Santa Catarina), por meio de cinco marcadores microssatélites polimórficos. Assim, testaremos as hipóteses de panmixia e filopatria natal. Um total de 69 espécimes analisados revelou diferenciação genética individual e significativa entre os locais amostrados. As análises de ST (0,12), PCA, DAPC e Bayesiana revelaram pelo menos dois agrupamentos genéticos distintos de R. bonasus. Os testes de IBD foram significativos, indicando uma correlação entre a distância genética e geográfica entre as populações, o que pode ser explicado pelo comportamento filopátrico reprodutivo. O comportamento filopátrico associado à mobilidade de R. bonasus pode influenciar os valores de diferenciação observados para todos os loci nas amostras investigadas.

Assessment of Yangtze sturgeon as recipient for the production of American paddlefish gametes through spermatogonia transplantation.

The Chinese paddlefish (Psephurus gladius), one of the world's largest freshwater fish, was last seen alive in 2003; they are presumed now to be extinct. In fish, germ cell transplantation is currently known as one of the most powerful assisted reproductive technologies for the conservation of endangered species. In the event that a Chinese paddlefish is unexpectedly caught in the near future, we aimed to develop an experimental strategy to produce paddlefish gametes in the gonads of surrogate sturgeon. Spermatogonia were collected from the testes of 2.5-year-old immature male American paddlefish (Polyodon spathula), the species most closely related to the Chinese paddlefish, by Percoll gradient centrifugation, and transplanted into the peritoneal cavity of Yangtze sturgeon (Acipenser dabryanus) larvae at 7-8 days post-hatch. At two months post-transplantation, donor-derived spermatogonia had efficiently colonized in the recipient gonads and proliferated. A PCR analysis developed to detect xenogenic donor-derived mtDNA sequences in recipient gonads revealed that American paddlefish germ cells survived for at least seven months after transplantation in the gonads of Yangtze sturgeon recipients. These results show that the somatic microenvironment of Yangtze sturgeon gonads was able to support the colonization, proliferation, and survival of xenogeneic germ cells from a different taxonomic family. This study provides key information that could lead to future restoration of Chinese paddlefish using germ cell transplantation.

Extinction risk assessment of a Patagonian ungulate using population dynamics models under climate change scenarios.

Climate change affects population cycles of several species, threatening biodiversity. However, there are few long-term studies on species with conservation issues and restricted distributions. Huemul is a deer endemic to the southern Andes in South America and it is considered endangered mostly due to a 50% reduction of its distribution over the last 500 years. To assess environmental variables potentially affecting huemul population viability and the impact of climate change, we developed population dynamics models. We used a 14-year survey data from Bernardo O'Higgins National Park, coastal Chilean Patagonia. We used Ricker models considering winter and spring temperatures and precipitation as variables influencing huemul population dynamics. We used the Bayesian information criterion (BIC) to select models with the greatest predictive power. The two best models (ΔBIC < 2) included winter temperature and density-dependence population growth drivers. The best model considered a lateral effect, where winter temperature influences carrying capacity and the second best a vertical effect with winter temperature influencing Rmax and carrying capacity. Population viability was evaluated using those models, projecting them over a 100-year period: (a) under current conditions and (b) under conditions estimated by Global Climate Models for 2050 and 2070. The extinction risk and quasi-extinction were estimated for this population considering two critical huemul abundance levels (15 and 30 individuals) for persistence. The population is currently in a quasi-extinction process, with extinction probabilities increasing with climate change. These results are crucial for conservation of species like huemul that have low densities and are threatened by climate change.