Extinctions are occurring at an unprecedented rate as a consequence of human activities. Vertebrates constitute the best-known group of animals, and thus the group for which there are more accurate estimates of extinctions. Among them, freshwater fishes are particularly threatened and many species are declining. Here we report the extinction of an endemic freshwater fish of Mexico, the Catarina pupfish Megupsilon aporus, the sole species of the genus Megupsilon. We present a synopsis of the discovery and description of the species, the threats to, and degradation of, its habitat, and the efforts to maintain the species in captivity before it became extinct in 2014. The loss of the Catarina pupfish has evolutionary and ecological implications, and highlights the crisis of freshwater fish extinctions. It is a warning of the likely fate of more than 200 freshwater fish species threatened with extinction in Mexico. To save these species, the country urgently needs a national strategy to articulate a bold conservation effort, with better policies on ecosystem management and water use.

Many species are poorly known, with the sum of our knowledge represented by specimens in museums. For assessment of conservation status the most enigmatic and challenging species are probably those known only from a single specimen. We examine the potential persistence of such species using the orchid flora of Madagascar as a case study. We apply a statistical method that tests the likelihood of species presence in relation to the time when a species was collected and a measure of annual collection effort, calculated in three ways based on specimen collection over time. The results suggest that as of 2000 up to nine of the 236 orchid species known from a single specimen may be inferred to be extinct under at least one of the three methods of estimating collection effort and extinction. In addition, up to two additional species are likely to be extinct by 2018 assuming no new collections were made by that time. Substantial collection effort and/or additional evidence will be needed to reach a decision on the persistence of more recently observed species known only from a single collection. This represents a challenge for conservation practitioners.

The impact of fisheries on marine megafauna is widely known but most studies have focused on commercial fisheries, overlooking the effect of local recreational fisheries. This is particularly important for marine turtles in near-shore habitats that overlap with recreational fisheries. We assessed the effect of recreational scallop fisheries on the distribution and behaviour of foraging marine turtles in the coastal waters of the upper Eastern Gulf of Mexico. Before and during the scallop season we quantified the density and overlap of marine turtles and vessels sighted, and satellite tracked four turtles to assess their distribution and behaviour. The relative distribution of marine turtles sighted during the scallop season overlapped with 48% of the area most frequently used by harvesters, and marine turtle activity hotspots shifted between seasons. In addition, during the scallop season the home range size of individual turtles appeared to decrease, and turtles displayed frequent changes in travel speed and directionality. We hypothesize that such changes are probably related to the distribution and movement of vessels and the abundant presence of people in the water. Our study highlights the importance of considering recreational fisheries and their local effect on marine megafauna for informing future adaptive management practices. However, further studies are needed to quantify the direct and indirect impacts of recreational fisheries and to assess the degree of risk of associated activities to marine turtle populations.

Habitat degradation and fragmentation have heightened the importance of understanding human tolerance towards wildlife, as the fate of wildlife in multi-use landscapes depends on people's capacity for coexistence. We applied the wildlife tolerance model to examine drivers of tolerance towards Asian elephants Elephas maximus in rural Bangladesh, interviewing local people in 17 villages. We used structural equation modelling to identify causal pathways in which elephant-related exposure, positive and negative interactions, costs and benefits (tangible and intangible) contributed to tolerance. Contrary to expectations, monetary costs were non-significant in shaping tolerance despite major impacts on livelihoods. Instead, intangible costs and intangible benefits were significant factors determining tolerance. Furthermore, reducing people's exposure to elephants would not necessarily affect tolerance, nor would increasing positive interactions. We discuss how the socio-economic and bio-cultural dynamics of local communities can explain these results, and demonstrate how our model can be used to incorporate such complexities into conservation decision-making. For instance, compensation schemes aim to recompense monetary losses and direct damages, to improve tolerance, whereas our results suggest a more effective approach would be to enhance resilience to non-monetary costs and improve perceived benefits. We conclude that future studies should pay increased attention to intangible costs and consider the less direct drivers of tolerance. Through repeated testing of universal models such as that presented here, broad trends may emerge that will facilitate the application of policies across contexts and landscapes.

There is critical need for more information on the status of forests in Central Asia, to inform conservation management. Here we assess the status and use of the globally important, threatened walnut–fruit forests of Dashtijum Nature Reserve, Tajikistan. We use a mixed methods approach combining a semi-structured interview based socio-economic survey with statistical analysis. Thirty-three tree species were recorded, with Rosaceae the most common family. The mean basal area of the forest was 20.8 m2 per ha and most tree species exhibited stable population structures. Resource use was prevalent throughout the community; most households harvested at least one fruit or nut species (78%), firewood (88%) and grazed livestock (85%). Most respondents noted declines in availability of fruits, nuts and firewood and reported a decrease in the overall area and quality of grazing. Statistical analysis and machine learning identified that distance to nearest settlement significantly affected forest total basal area, tree species richness and the Shannon index, a metric of diversity sensitive to rare species. Our results suggest that conservation management by the government and NGOs is partly effective but there is a need for increased enforcement of grazing restrictions, to prevent further forest degradation.

Pongo pygmaeus pygmaeus is a subspecies of Bornean orangutan whose distribution is restricted to the northern part of the Kapuas River, West Kalimantan, and is categorized as Critically Endangered. In October 2017 we carried out a survey to estimate orangutan density in the peat-swamp forests of the Sungai Palin watershed, of the upper Kapuas river, Kapuas Hulu, West Kalimantan, Indonesia. Surveys for orangutans in 1991, in nearby Nanga Awen, had indicated the presence of orangutans in the peat-swamp forests of this area. We used distance sampling techniques to estimate orangutan densities from nest observations. We recorded 76 orangutan nests along 4.5 km transects in Sungai Palin in 2017, and 71 orangutan nests were observed along 4.3 km transects in Nanga Awen in 1991, giving densities of 1.29 and 2.62 individuals/km2, respectively. The results of this orangutan survey can be used as a baseline for monitoring of orangutan populations for conservation and management of this watershed landscape.

Genetic data on threatened plant populations can facilitate the development of adequate conservation strategies to reduce extinction risk. Such data are particularly important for species affected by habitat fragmentation such as Magnolia cubensis subsp. acunae, a Critically Endangered magnolia subspecies endemic to Cuba. Using genetic data from 67 individuals, we aimed to evaluate the effect of habitat fragmentation on two subpopulations in the Guamuhaya mountain range, in Topes de Collantes Protected Natural Landscape and Lomas de Banao Ecological Reserve. We characterize the structure and genetic diversity of these subpopulations, with the objective of managing their conservation more effectively. We used Landsat satellite images to determine land-cover types at the two locations and calculated indices of habitat fragmentation. For genetic analyses, we extracted DNA from the leaf tissue of individuals from the two subpopulations and used 11 microsatellite markers to genotype them. We calculated heterozygosity, allelic richness and the F-statistics, to evaluate genetic variability. The montane rainforest in Topes de Collantes was most affected by habitat fragmentation, with smaller patches of more irregular shapes, compared to submontane forest at this location and both montane and submontane forests in Lomas de Banao. Genetic diversity was higher in Topes de Collantes, but we found no genetic differentiation between subpopulations. Our findings suggest the two subpopulations can be considered a single evolutionary unit and conservation entity. We propose to use individuals from both subpopulations for reinforcement to increase the overall genetic diversity of the subspecies.

All gibbon species are declining throughout South and South-east Asia because of habitat loss and human activities such as hunting. Lao still contains a relatively large area of forest habitat suitable for gibbons, but their status in the country remains poorly known. Here we present the first density estimate of the Critically Endangered northern white-cheeked gibbon Nomascus leucogenys in Nam Et-Phou Louey National Protected Area, northern Lao. We conducted gibbon surveys using an auditory sampling technique during May–August 2014 and May 2015, at 40 sites, covering 125.6 km2. We applied N-mixture models to analyse group counts, investigating which landscape and human disturbance covariates influenced the spatial variation of gibbon abundance across the study area. We estimated the average gibbon density to be 0.4 groups/km2. Gibbon density was higher in mixed deciduous forest (0.74 groups/km2) than in evergreen forest (0.09 groups/km2), which could be a result of long-term hunting in evergreen forest areas. Thus, future gibbon protection plans should consider not only evergreen forest as priority habitat, but also deciduous forest, which tends to receive less attention in conservation planning. We also highlight key areas containing gibbons where law enforcement patrols should be focussed, to limit threats such as poaching. Future forest management plans should aim to maximize the size and connectivity of suitable gibbon habitat, to enable exchange between subpopulations.

This study assesses the patterns of crop damage by elephants Loxodonta africana in areas adjacent to the Rungwa, Kizigo and Muhesi Game Reserves in Tanzania. We used a questionnaire survey to collect data from a total of 210 household heads from seven villages, with 30 household heads in each village, during June–August 2015. Proximity was a significant factor influencing losses, with crop farms within < 1 km from the reserves having higher losses, followed by those 1–5 km and > 5 km distant. Most households (81.0%) < 1 km from a reserve reported crop damage whereas those within 1–5 km (65.9%) and > 5 km (20.0%) reported less damage. Most of the losses (79.8%) occurred in the first half of the year (the wet season). Immigrants reported higher average losses to crops than Indigenous respondents. Noise making, flashlights, setting fire around fields and disturbance by shooting were the methods used to deter elephants from entering crop fields. We recommend that communities around these game reserves avoid areas that are < 1 km from the reserve boundary, plant crops such as chilli, use honeybee Apis mellifera fences to deter elephants from their crops, and receive education on available mitigation methods, to help minimize crop losses to elephants.

Extinction is a profound biological event, yet despite its finality it can be difficult to verify and many frameworks have been proposed to define formally that extinction has occurred. For most taxonomic groups and regions there is no reliable list of species considered to be probably or possibly extinct. The record of plant extinctions in Australia is no exception, characterized by high turn-over within lists, low transparency of attribution and lack of consistency between jurisdictions. This makes it impossible to evaluate how many plant taxa have become extinct in Australia. We present an ecological framework for assessing the likelihood of plant extinctions, based on taxonomic soundness, degree of habitat modification, detectability and search effort, underpinned by the best available expert knowledge. We show that, in sharp contrast to both the fate of the Australian fauna and prevailing assumptions, only 12 of 71 plant taxa currently listed as or assumed to be extinct are considered probably extinct, and a further 21 possibly extinct. Twenty taxa listed as or assumed to be extinct have dubious taxonomy or occurrence in Australia, and the remaining 18 taxa are considered possibly extant and further surveys are required to ascertain their status. The list of probably and possibly extinct plants is dwarfed by the number thought extinct but rediscovered since 1980. Our method can be used for vascular floras in other regions characterized by well-documented and curated floras and high levels of expert knowledge, and provides a transparent platform for assessing changes in the status of biodiversity.

For many species abundance data from across their entire range are incomplete, and therefore it is difficult to accurately assess their conservation status. Even for species that are large, charismatic and relatively easy to study, conservation assessments are often hampered by lack of data. Here we report a marked, previously undescribed, increase in numbers at a breeding colony of the loggerhead turtle Caretta caretta, a species that is Critically Endangered in several parts of its range, and place this report in the global context for this species. We present a 10-year (2008–2017) dataset of nesting activities for this species on the island of Sal, one of the Cape Verde islands in the Atlantic Ocean. Foot patrols recorded 21,938 nests during the study period. We estimate that the annual number of nests on Sal increased from 506 in 2008 to 7,771 in 2017. Taking into account that there are only two known loggerhead turtle rookeries (on Masirah Island, Oman, and in Florida, USA) with > 50,000 nests reported annually, and few with > 1,000 nests per year, our results suggest that Sal is one of the 10 largest loggerhead turtle rookeries globally. Our work highlights the conservation significance of reporting trends in abundance at breeding sites for marine turtles and other taxa.

The cao vit gibbon Nomascus nasutus, also known as eastern black crested gibbon, is categorized as Critically Endangered on the IUCN Red List and was considered one of the world's 25 most threatened primates. The only known population occurs along the border between China and Viet Nam. Accurate information on population size and dynamics is critical for the species’ conservation, but population surveys conducted in only one country may over- or underestimate total population size because the home ranges of cao vit gibbon groups often cross the international border. In 2007 and 2016 we conducted two collaborative transboundary censuses of the cao vit gibbon populations in the Trung Khanh Cao Vit Gibbon Species and Habitat Conservation Area in Viet Nam and the Bangliang Gibbon National Nature Reserve in China. The results showed a population size of 102–110 in 2007, which increased to 107–136 in 2016. Our results indicate that previous surveys conducted separately in Viet Nam and China underestimated the global population size of this species. According to our more comprehensive surveys, the gibbon population is increasing slowly. The gibbons and their habitat are legally protected in both countries. Hunting and charcoal making have not been reported in this area since 2007. As habitat carrying capacity is a limiting factor, habitat restoration is required. However, lack of funding to protect the cao vit gibbon remains a challenge.

The South Pacific subpopulation of the loggerhead turtle Caretta caretta is categorized as Critically Endangered on the IUCN Red List because of significant population declines. Five Queensland beaches support high-density nesting of this subpopulation, but egg and hatchling survival are low at some beaches because of feral and native terrestrial predators. We quantified predation of loggerhead turtle eggs by two species of goanna, Varanus panoptes and Varanus varius, at Wreck Rock beach, one of the turtle's major nesting beaches. In addition, we conducted an experiment to determine the efficacy of a nest protection device. Predation rates at Wreck Rock beach were 15.2% for treatment and 45.8% for non-treatment clutches during the 2013–2014 nesting season. A higher probability of predation (64%) was predicted for the northern beach. Although nests were only partially predated (16.4% of the total number of eggs), nest loss to predators and beach erosion (caused by a cyclone) was 91.7%. If left unmanaged, the cumulative impact of predation and other threats, including those exacerbated by climate change, can cause unsustainable loss of loggerhead turtle nests. This study provides one of the first quantitative data sets on rates of loggerhead turtle clutch predation in the South Pacific. It enhances our understanding of goanna predation impacts and identifies an efficient predator exclusion device for mitigating the effects of terrestrial predators at Wreck Rock beach, and for protecting marine turtle nests across northern Australia and globally.

Parakmeria omeiensis is a Critically Endangered tree species in the family Magnoliaceae, endemic to south-west China. The tree is functionally dioecious, but little is known about the species’ status in the wild. We investigated the range, population size, age structure, habitat characteristics and threats to P. omeiensis. We located a total of 74 individuals in two populations on the steep slopes of Mount Emei, Sichuan province, growing under the canopy of evergreen broadleaved forest in well-drained gravel soil. A male-biased sex ratio, lack of effective pollinating insects, and habitat destruction result in low seed set and poor seedling survival in the wild. We have adopted an integrated conservation approach, including strengthening in situ conservation, cultivation of saplings, ex situ conservation and reintroduction, to protect this species. The successful conservation of P. omeiensis has important implications for the conservation of the genus Parakmeria and the family Magnoliaceae.

The Annamite mountains of Viet Nam and the Lao People's Democratic Republic (Lao) are an area of exceptional mammalian endemism but intensive poaching has defaunated much of the region, creating an extinction crisis for the endemic species. To make efficient use of limited conservation resources, it is imperative that conservation stakeholders obtain basic information about poorly known and threatened endemics. We present the first comprehensive information on the ecology, distribution and status of the little-known endemic Annamite striped rabbit Nesolagus timminsi. We used a systematic camera-trapping design to study the species in five areas in Viet Nam and Lao. In 29,180 camera-trap-nights we recorded 152 independent events at 36 of 266 stations. We obtained an additional 143 independent detections across 12 stations from a supplementary non-systematic survey. We analysed activity patterns and social behaviour. We also used single-species occupancy models to assess factors that influence occupancy at the landscape scale. We used N-mixture models to obtain local abundance estimates in one target area. The Annamite striped rabbit was found to be nocturnal and primarily solitary. Species occupancy was best explained by a proxy for past hunting pressure, with no significant relationships to current anthropogenic or environmental factors. Local abundance was 0.57 individuals per camera-trap station for one of our sites, and estimated to be zero at the other site where hunting appears to have been more intense. Our results provide information on priority areas for targeted anti-poaching efforts and give the first conservation baseline for the species.

Humans have lived alongside and interacted with wild animals throughout evolutionary history. Even though wild animals can damage property, or injure humans and domesticated animals, not all interactions between humans and wildlife are negative. Yet, research has tended to focus disproportionately on negative interactions leading to negative outcomes, labelling this human–wildlife conflict. Studies have identified several factors, ranging from gender, religion, socio-economics and literacy, which influence people's responses to wildlife. We used the ISI Web of Knowledge database to assess quantitatively how human–wildlife interactions are framed in the scientific literature and to understand the hypotheses that have been invoked to explain these. We found that the predominant focus of research was on human–wildlife conflict (71%), with little coverage of coexistence (2%) or neutral interactions (8%). We suggest that such a framing is problematic as it can lead to biases in conservation planning by failing to consider the nuances of people's relationships with wildlife and the opportunities that exist for conservation. We propose a typology of human responses to wildlife impacts, ranging from negative to positive, to help moderate the disproportionate focus on conflict. We suggest that standardizing terminology and considering interactions beyond those that are negative can lead to a more nuanced understanding of human–wildlife relations and help promote greater coexistence between people and wildlife. We also list the various influential factors that are reported to shape human–wildlife interactions and, to generate further hypotheses and research, classify them into 55 proximate (correlates) and five ultimate (mechanisms) factors.