Long-term population trends of Sooty Terns <Emphasis Type="Italic">Onychoprion fuscatus</Emphasis>: implications for conservation status

Seabirds have suffered dramatic declines in population over recent decades. The most abundant seabirds of tropical oceans are Sooty Terns Onychoprion fuscatus and they have an IUCN Red List category of ‘Least Concern’. Ascension Island has the largest colony of Sooty Terns in the Atlantic Ocean and censuses between 1990 and 2013 have shown that its population size is static. In this study we have used historical data and recent censuses to describe the population status of Sooty Terns on Ascension Island over a century. We show that the breeding population contained over 2 million individuals in the 1870s and remained at this level for at least 70 years. However, the population declined from >2 million birds in 1942 to 350,000 birds by 1990. The population trend spanning a period equivalent to three generations of the species (63 years; 1942–2005) showed an approximate 84% decline in population size. Using IUCN criteria this suggests that Sooty Terns on Ascension could be considered ‘Critically Endangered’. We conclude that a re-evaluation of Sooty Tern conservation status is necessary at the local level and possibly globally. Our study highlights that for long-lived species historic demographic data should be considered when determining conservation status.     

Papyrus swamp drainage and the conservation status of their avifauna

Papyrus Cyperus papyrus swamps sustain the livelihoods of millions of people, but threats to this habitat have never been quantified formally. Birds are useful indicators of threats that cannot be measured directly. Using satellite imagery classification and habitat associated modelling, we quantify drainage and present International Union for Conservation of Nature (IUCN) Red List assessments for the eight taxa most closely associated with this habitat. We show that, between 1984–1987 and 1999–2001 the areal extent of papyrus declined by 6.7 % from 1,643 to 1,532 km². Papyrus-specialist avifauna has undergone much greater declines, due in part to fragmentation effects and in part to geographical overlap between areas of highest population densities and areas that have experienced greatest habitat loss. Our assessment does not alter the IUCN Red List status of any full species, but it improves current knowledge of the drivers of their extinction risk. Papyrus gonolek Laniarius mufumbiri should remain at least near threatened, but on the basis of population decline rather than a purported small and decreasing range size, and papyrus yellow warbler Chloropeta gracilirostris should remain vulnerable, but again due to declines rather than on the basis of previous under-estimates of population size. Other species should remain listed as least concern. However, taxonomically, likely specifically, distinct populations of papyrus yellow warbler in Zambia and Kenya are highly threatened and should be listed as endangered and critically endangered respectively. We propose several conservation priorities and discuss means of achieving these in a manner consistent with maintaining the livelihoods of people.     

Estimating the rate of increase for the finless porpoise with special attention to predictions for the Inland Sea population in Japan

The finless porpoise Neophocaena asiaeorientalis inhabits coastal waters and rivers in East Asia and is exposed to various human activities. This species is listed on the IUCN Red List of Threatened Species due to a reduction in abundance. Although human-induced mortality can be a threat to porpoise populations, future anthropogenic impacts have not been quantitatively evaluated due to lack of demographic information. Adequate future population projections are needed to form the basis for conservation measures before the population declines to critical levels. We conducted a population viability analysis for the population of finless porpoise in the Inland Sea, Japan using a Leslie matrix model composed of age-specific survival and fertility rates. We described the uncertainty in the annual rate of increase (λ) for the finless porpoise using randomly sampled estimates of survival rate for other cetaceans with similar life histories. Plausible median estimates of λ ranged from 1.041 (age at first reproduction [AFR] = 7) to 1.056 (AFR = 5). Future population changes and extinction probabilities were predicted after combining these estimates with a predicted human-induced mortality rate (M) and available abundance estimates. The extinction probability after 100 years was 0 %. However, the probability of the quasi-extinction (<100 individuals) was as high as 79.0 % after 100 years. The results also suggest that the persistence of the finless porpoise population could be achieved with a small effort to reduce anthropogenic mortality.     

How closely do measures of mitochondrial DNA control region diversity reflect recent trajectories of population decline in birds?

Monitoring levels of genetic diversity in wildlife species is important for understanding population status and trajectory. Knowledge of the distribution and level of genetic diversity in a population is essential to inform conservation management, and help alleviate detrimental genetic impacts associated with recent population bottlenecking. Mitochondrial DNA (mtDNA) markers such as the control region have become a common means of surveying for within-population genetic diversity and detecting signatures of recent population decline. Nevertheless, little attention has been given to examining the mtDNA control region’s sensitivity and performance at detecting instances of population decline. We review genetic studies of bird populations published since 1993 that have used the mtDNA control region and reported haplotype diversity, number of haplotypes and nucleotide diversity as measures of within-population variability. We examined the extent to which these measures reflect differences in known demographic parameters such as current population size, severity of any recent bottleneck and IUCN Red List status. Overall, significant relationships were observed between two measures of genetic diversity (haplotype diversity and the number of haplotypes), and population size across a number of comparisons. Both measures gave a more accurate reflection of recent population history in comparison to nucleotide diversity, for which no significant associations were found. Importantly, levels of diversity only correlated with demographic declines where population sizes were known to have fallen below 500 individuals. This finding suggests that measures of mtDNA control region diversity should be used with a degree of caution when inferring demographic history, particularly bottleneck events at population sizes above N = 500.     

The Sampled Red List Index for Plants,phase II: ground-truthing specimen-based conservation assessments

The IUCN Sampled Red List Index (SRLI) is a policy response by biodiversity scientists to the need to estimate trends in extinction risk of the world''s diminishing biological diversity. Assessments of plant species for the SRLI project rely predominantly on herbarium specimen data from natural history collections, in the overwhelming absence of accurate population data or detailed distribution maps for the vast majority of plant species. This creates difficulties in re-assessing these species so as to measure genuine changes in conservation status, which must be observed under the same Red List criteria in order to be distinguished from an increase in the knowledge available for that species, and thus re-calculate the SRLI. However, the same specimen data identify precise localities where threatened species have previously been collected and can be used to model species ranges and to target fieldwork in order to test specimen-based range estimates and collect population data for SRLI plant species. Here, we outline a strategy for prioritizing fieldwork efforts in order to apply a wider range of IUCN Red List criteria to assessments of plant species, or any taxa with detailed locality or natural history specimen data, to produce a more robust estimation of the SRLI.     

Found again: the extremely rare <Emphasis Type="Italic">Codonorchis canisioi</Emphasis> (Orchidaceae: Codonorchideae) reappears after being missing for 78 years

To date, the endangered terrestrial orchid Codonorchis canisioi was only known from two collections at its type locality. This plant has not been collected since 1935 and is currently considered as Critically Endangered in the Brazilian list of threatened flora. We recently found two small populations about 174 km from the type locality. We thus seized the opportunity to make a complete record of morphological traits, aiming to fill the gaps of the short and non-illustrated protologue. Plant, flower (including details of column and pollinarium) and fruit features are here illustrated and discussed in detail. Overall, plant and flower features are similar to those of the widespread Patagonian C. lessonii. Yet, both species can be separated by a number of vegetative and floral features. Female Augochlorine Halictidae bees were recorded as pollinators. Fruits mature quickly (15–19 days after pollination). Plants wither by middle October, resting underground as very small (3–5 mm diameter) roundish tubers. The two newly found populations are in privately owned areas and prone to both fire and cattle grazing. Due to the small size of each population (estimated in less than 200 individuals), it is likely that this species would still be considered as CR (Critically Endangered) when formally and properly surveyed under the IUCN criteria. Since plants are small and strongly seasonal, more field surveys are necessary to locate other potentially overlooked populations.     

Extinction risk assessments at the population and species level: implications for amphibian conservation

Amphibian populations are declining worldwide and this is causing growing concern. High levels of population declines followed by the expansion of red lists are creating demands for effective strategies to maximize conservation efforts for amphibians. Ideally, integrated and comprehensive strategies should be based on complementary information of population and species extinction risk. Here we evaluate the congruence between amphibian extinction risk assessments at the population level (Declining Amphibian Database––DAPTF) and at species level (GAA––IUCN Red List). We used the Declining Amphibian Database––DAPTF that covers 967 time-series records of amphibian population declines assigned into four levels of declines. We assigned each of its corresponding species into GAA––IUCN red list status, discriminated each species developmental mode, and obtained their geographic range size as well. Extinction risk assessments at the population and species level do not fully coincide across geographic realms or countries. In Paleartic, Neartic and Indo-Malayan realms less than 25% of species with reported population declines are formally classified as threatened. In contrast, more than 60% of all species with reported population declines that occur in Australasia and the Neotropics are indeed threatened according to the GAA––IUCN Red List. Species with aquatic development presented proportionally higher extinction risks at both population and species level than those with terrestrial development, being this pattern more prominent at Australasia, Paleartic, and Neartic realms. Central American countries, Venezuela, Mexico and Australia presented the highest congruence between both population and species risk. We address that amphibian conservation strategies could be improved by using complementary information on time-series population trends and species threat. Whenever feasible, conservation assessments should also include life-history traits in order to improve its effectiveness.     

Conserving Europe’s most endangered butterfly: the Macedonian Grayling (Pseudochazara cingovskii)

The Macedonian Grayling is listed as critically endangered in the recent IUCN Red List of European butterflies because of its extreme rarity and habitat loss due to quarrying. This categorisation was, however, based on rather limited knowledge on its actual distribution, population size and habitat requirements. In 2012, we conducted field surveys to acquire more information. We found the species at six new sites extending its known range of suitable habitat to just under 10 km². The daily population size was estimated using capture-mark-recapture method in the most densely populated part of the Pletvar pass site at more than 650 individuals. Adults proved to be extremely sedentary, not moving far even within the continuous habitat on the same slope. Oviposition was observed on dry plant material and in a rock crevice close to the potential larval host plant Festuca sp. Quarrying is confirmed to be the main threat to the habitat of the Macedonian Grayling with five out of seven populated sites containing active marble quarries. Due to the enlargement of the known area of occupancy, its threat status would now be estimated at endangered. Despite the restricted knowledge about its distribution and trends in the population size, the IUCN criteria proved to be applicable to determine the threat status of a rare and localized butterfly such as Pseudochazara cingovskii. Its original assessment of being called the most threatened butterfly in Europe resulted in immediate research project and subsequent actions that will undoubtedly help to conserve it in the future.     

Conus: First Comprehensive Conservation Red List Assessment of a Marine Gastropod Mollusc Genus

Marine molluscs represent an estimated 23% of all extant marine taxa, but research into their conservation status has so far failed to reflect this importance, with minimal inclusion on the authoritative Red List of the International Union for the Conservation of Nature (IUCN). We assessed the status of all 632 valid species of the tropical marine gastropod mollusc, Conus (cone snails), using Red List standards and procedures to lay the groundwork for future decadal monitoring, one of the first fully comprehensive global assessments of a marine taxon. Three-quarters (75.6%) of species were not currently considered at risk of extinction owing to their wide distribution and perceived abundance. However, 6.5% were considered threatened with extinction with a further 4.1% near threatened. Data deficiency prevented 13.8% of species from being categorised although they also possess characteristics that signal concern. Where hotspots of endemism occur, most notably in the Eastern Atlantic, 42.9% of the 98 species from that biogeographical region were classified as threatened or near threatened with extinction. All 14 species included in the highest categories of Critically Endangered and Endangered are endemic to either Cape Verde or Senegal, with each of the three Critically Endangered species restricted to single islands in Cape Verde. Threats to all these species are driven by habitat loss and anthropogenic disturbance, in particular from urban pollution, tourism and coastal development. Our findings show that levels of extinction risk to which cone snails are exposed are of a similar magnitude to those seen in many fully assessed terrestrial taxa. The widely held view that marine species are less at risk is not upheld.     

Conservation genetics of the short-beaked common dolphin (<Emphasis Type="Italic">Delphinus delphis</Emphasis>) in the Mediterranean Sea and in the eastern North Atlantic Ocean

Mediterranean Sea common dolphins have recently been listed as ‘endangered’ in the IUCN Red list, due to their reported decline since the middle of the 20th century. However, little is know about the number or distribution of populations in this region. We analysed 118 samples from the Black Sea, Mediterranean Sea and eastern North Atlantic at nine microsatellite nuclear loci and for 428 bps of the mtDNA control region. We found small but significant population differentiation across the basin between the eastern and the western Mediterranean populations at both nuclear and mtDNA markers (microsatellite F _ST = 0.052, mtDNA F _ST = 0.107, P values ≤ 0.001). This matched the differential distribution and habitat use patterns exhibited by this species in the eastern and the western parts of the Mediterranean Sea. The assignment test of a small number of samples from the central Mediterranean could not exclude further population structure in the central area of the basin. No significant genetic differentiation at either marker was observed among the eastern north Atlantic populations, though the Alboran population (inhabiting the Mediterranean waters immediately adjacent the Atlantic ocean) showed significant mtDNA genetic differentiation compared to the Atlantic populations. Directional estimates of gene flow suggested movement of females out of the Mediterranean, which may be relevant to the population decline. Phylogenetic analysis suggested that the observed population structure evolved recently.     

关于物种濒危等级标准之探讨--对IUCN物种濒危等级的思考

为了保存地球上的生物多样性,我们需要根据物种的种群数量与分布、种群数量波动与分布区下降速率来评定濒危物种的濒危等级,并针对物种的濒危等级提出具体的保护措施。1994年11月,IUCN第40次理事会会议正式通过了经过修订的Mace-Lande物种濒危等级标准作为IUCN物种濒危等级标准。IUCN濒危物种红色名录虽然不是国际法和国家法律,但是对于政府间组织、非政府组织的保护决策以及各国的自然法律法规的制定有着深远的影响,在保护生物学理论研究中也发挥了一定作用。我们在研究制定中国水生野生生物濒危等级标准时发现,如果直接应用IUCN物种濒危等级标准评定水生野生生物濒危等级将存在一些问题。如：(1)如何区别对待那些本来就数量稀少、分布区狭窄的物种和那些由于人类活动而导致其种群数量与生境面积急剧下降的物种?(2)不同的动物类群能否应用同一濒危标准尺度?(3)如何区别对待物种边缘分布区和核心分布区的种群数量与密度的差异?(4)如何处理种群的局部灭绝、局部濒危?(5)一些濒危物种在野生环境中濒危,但是这些物种可以人工繁殖,如何处理可以人工繁殖的濒危物种?(6)如果没有种群与栖息地的精确历史资料和统计数据,怎样应用物种的濒危标准评估其濒危等级?在实践中,我们针对这些问题提出了解决方案。考虑与国际流行的IUCN物种濒危等级标准接轨,我们提出来一个由“无危”、“值得关注”、“受胁”、“濒危”和“灭绝”等5个级构成的濒危等级系统,其中“值得关注”、“受胁”、“濒危”又分为“一般”与“高度”两个亚等级。我们提出应区分“生态濒危物种”、“进化濒危物种”;对于不同生物类群,应区分物种的生活史对策,制定不同生活史物种的濒危标准。对于r-对策物种,引入“经济灭绝”这一等级,将这一等级对应于“受胁”等级,以解决缺少物种数量的统计数据和历史数据这一难题;区别对待特有物种,将其濒危等级提升一等;引进集合种群(metapopulation)概念,将集合种群的局域种群(local population)作为“个体”对待。     

Conservation genetics of the endangered terrestrial orchid Liparis japonica in Northeast China based on AFLP markers

Levels of genetic diversity and population genetic structure of the rare, endangered terrestrial orchid Liparis japonica were examined for eight natural populations (n = 185) in Northeast China using six AFLP primer pairs, where this species has experienced severe habitat loss and fragmentation. Based on 406 DNA bands, a high level of genetic diversity was found at the species level with the PPB of 85.47 %, while the genetic diversity at the population level was low (PPB = 47.48 %). A significantly high degree of population differentiation was found with 42.69 % variation existed among populations as measured by AMOVA, indicating potential restricted gene flow. The genetic distances between populations were independent of the corresponding geographic distances, and the genetic relationship of individuals had no significant correlation with their spatial distribution. The restricted gene flow might be impacted by reduced population size, habitat destruction and fragmentation. The results in this study suggested that habitat protection and keeping a stable environment are critical for the conservation of L. japonica species.     

Redlistr: tools for the IUCN Red Lists of ecosystems and threatened species in R

The International Union for the Conservation of Nature (IUCN) Red List of ecosystems and Red List of threatened species are global standards for assessing risks of ecosystem collapse and species extinction. However, misconceptions of the Red List assessment process, along with its technically demanding nature, can result in the misapplication of their criteria, leading to inconsistent and potentially unreliable assessments. To address this problem, we developed redlistr, an R package aiding in the production of consistent species and ecosystem Red List assessments. Redlistr's features include methods to calculate 1) area from spatial data, 2) range size metrics, 3) rates of change of distributions or populations, and 4) distribution or population at another time from these rates. A key feature of the package is the systematic approach used to eliminate geometric uncertainty when estimating area of occupancy. Here, we develop two case studies to demonstrate the functionalities of redlistr with typical workflows for both species and ecosystems. Redlistr was developed to be accessible to users with a broad range of experience in programming for spatial and temporal data analysis, and sufficiently flexible to allow users to parameterise functions and select equations to fit their purposes. The package specifically aims to assist researchers and conservation practitioners to conduct robust and transparent risk assessments of ecosystems and species under the IUCN Red List criteria but is also useful for other studies requiring analyses of range size, area change and calculations of rates of change.     

Life history and seasonal occurrence of the spotted eagle ray,Aetobatus narinari,in the eastern Gulf of Mexico

The spotted eagle ray, Aetobatus narinari, is listed on the IUCN Red List of Threatened Species as Near Threatened with a decreasing population trend, but many aspects of this ray’s biology and population status are unknown. Aerial and on-water surveys were conducted in the eastern Gulf of Mexico off southwest Florida 2008–2013, to document seasonal occurrence and life history characteristics of this species. Aerial surveys documented spotted eagle rays mostly in spring, summer, and autumn months with larger aggregations observed near inlet passes. Boat-based surveys documented rays on 152 out of 176 survey days, mostly as solitary individuals but sometimes in aggregations of up to 60. More rays were observed when water temperatures were 23-31?ºC. A total of 393 rays (231 males, 161 females, 1 unrecorded sex) were captured, measured, sampled, tagged, and released. Sizes ranged 41.4–203.0 cm disc width (DW) and weight 1.1–105.5 kg. Male size at 50 % maturity was 127 cm DW. Five percent (19) of tagged rays were recaptured after 5–1,293 days at liberty and recaptured rays exhibited faster growth than previously estimated from vertebral readings. Based on observations of rays relative to survey effort, numbers of observed rays declined after 2009 for reasons not yet understood. This observation, together with concerns about sustainability of fisheries targeting these rays in nearby Mexico and Cuba, underscore the need for investigations into stock structure, population trends, growth, and critical habitat of spotted eagle rays throughout the Gulf of Mexico, Caribbean Sea, and elsewhere in their range.     

Population genetics and distribution data reveal conservation concerns to the sky island endemic <Emphasis Type="Italic">Pithecopus megacephalus</Emphasis> (Anura,Phyllomedusidae)

Pithecopus megacephalus is a reticulated monkey–frog species endemic to the highlands of the Espinhaço Mountain Range in southeastern Brazil, an important centre of endemism in South America. This species has a discontinuous distribution and is considered “data-deficient” by the IUCN Red List, raising concerns about its conservation. Understanding the historical dynamics and connectivity of P. megacephalus populations can provide guidelines for preservation of this species in the wild. To investigate the population dynamics of P. megacephalus, we obtained multilocus DNA data for 55 individuals from different locations along the species’ known distribution. Spatial population structure, genetic diversity and demographic parameters were evaluated using population genetic and phylogeographical tools. We also evaluated its extent of occurrence and area of occupancy to investigate extinction risk of this species. We found genetic structure along P. megacephalus’ spatial distribution in the South Espinhaço Mountain Range corresponding to three population groups: northern, central and southern. Our results could provide important data on geographic distribution and population dynamics for a Data Deficient species. Therefore, we suggest these population data, together with the species’ limited occurrence in sky island environments could be used for a more accurate classification of P. megacephalus in the IUCN list, and conservation strategies for the species should be planned accordingly.     

Emergence pattern,microhabitat choice,and population structure of the Maghribian endemic Gomphus lucasii Selys, 1849 (Odonata: Gomphidae) in northeastern Algeria

Emergence of Gomphus lucasii Selys, 1849, an unstudied Maghreb endemic, was synchronised by overwintering in the final stadium in the Seybouse River in northeastern Algeria. Regular collections revealed that half of the annual population emerged during 10 days, showing a typical ‘spring species’ emergence pattern. Sex ratio was slightly male biased (51%). Males and females did not differ in vertical stratification. Emergence support choice was not random, but rather depended on support height, body size, and daily population density. Mortality was caused mainly by ants, although deformity of tenerals and bird predation were also important factors. Gomphus lucasii has been assessed as vulnerable (International Union for Conservation of Nature (IUCN) Red List), and the information provided in our study will be helpful in future conservation efforts.     

Population trends in a substantial colony of Little Penguins: three independent measures over three decades

Estimating long-term population trends is vital for the conservation and management of species, yet few trends exist and fewer still are verified with independent measures. We compared three independent measures of change in population size over 27 years (1984–2011) for a significant Little Penguin Eudyptula minor colony in south-eastern Australia: (1) a series of 13 colony-wide surveys conducted in eight separate years, (2) mean nightly counts of penguins returning to breeding sites (365 counts × 27 years) and (3) population growth rates from a demographic model based on survival and recruitment rates measured at three sites each year. Colony-wide surveys of burrows were used as a benchmark of change in population size in the 8 years they were conducted as they were a robust measure of population size corrected for intra-annual variation in burrow occupancy using mark-recapture modelling at six reference sites. However, the demographic model matched the trend from colony-wide surveys with greater resolution in years and with less effort. Beach counts were unreliable for monitoring trends for the entire population due to its singular and peripheral location in the colony. Trends indicate a doubling of the population from 1984 to 2011 despite a marked population contraction linked to a mass mortality of a key prey species. The colony appears secure but remains subject to changes in the marine and terrestrial environments in the longer term.     

A third microendemic to the Iwokrama Mountains of central Guyana: a new “cryptic” species of Allobates Zimmerman and Zimmerman, 1988 (Anura: Aromobatidae)

The aromobatid frog Allobates amissibilis sp. nov. is described from a very limited area in the Iwokrama Mountains at elevations between 160 and 950 m, in central Guyana, South America. The new taxon is diagnosed from other Allobates species by morphology, bioacoustics, and genetics, and can be distinguished readily from known congeners by cryptic colouration, small size (16.3–17.8 mm snout-vent length), absence of distinct dorsal pattern in living adult individuals, presence of a distinctly enlarged tubercle on each eyelid, diffuse broad oblique lateral stripe extending from groin to about midbody length, sexually dimorphic throat colouration (pinkish grey, suffused with dark pigment in male, immaculate cream to yellow in female), belly cream to yellow in both sexes, and distinct vocalisation formed by calls of usually 9–12 notes emitted between silent intervals of usually ca. 2–6 s, with a dominant frequency ranging from 5,064 to 5,845 Hz. The new species is the third microendemic reported from the Iwokrama Mountains together with the caecilian Caecilita iwokramae and the lizard Gonatodes timidus. We recommend considering the conservation status of the new species as Data Deficient, and highlight that environmental impact assessments are needed to refine its IUCN threat status.