A Comprehensive Quantitative Assessment of Bird Extinction Risk in Brazil

In an effort to avoid species loss, scientists have focused their efforts on the mechanisms making some species more prone to extinction than others. However, species show different responses to threats given their evolutionary history, behavior, and intrinsic biological features. We used bird biological features and external threats to (1) understand the multiple pathways driving Brazilian bird species to extinction, (2) to investigate if and how extinction risk is geographically structured, and (3) to quantify how much diversity is currently represented inside protected areas. We modeled the extinction risk of 1557 birds using classification trees and evaluated the relative contribution of each biological feature and external threat in predicting extinction risk. We also quantified the proportion of species and their geographic range currently protected by the network of Brazilian protected areas. The optimal classification tree showed different pathways to bird extinction. Habitat conversion was the most important predictor driving extinction risk though other variables, such as geographic range size, type of habitat, hunting or trapping and trophic guild, were also relevant in our models. Species under higher extinction risk were concentrated mainly in the Cerrado Biodiversity Hotspot and were not quite represented inside protected areas, neither in richness nor range. Predictive models could assist conservation actions, and this study could contribute by highlighting the importance of natural history and ecology in these actions.     

Application of IUCN criteria and Red List categories to species of five Anacardiaceae genera in Madagascar

The conservation status of five genera of Anacardiaceae in Madagascarwas determined by applying IUCN risk assessment criteria to recent taxonomicrevisions and available specimen data. A major problem in establishing protocolsfor efficiently protecting and conserving Madagascar's biodiversity is the lackof essential biological information. In light of this, primary occurrence dataappears to be an invaluable tool for assessing both current and historic speciesdistributions. GIS technology was used to create species distribution maps forhistoric vs. recent occurrence data to analyze the change in conservationstatus, extent of occurrence, and area of occupancy for each of the targetspecies. A GAP analysis reveals that 14 (100%) of the target species for whichdata were available are considered threatened by IUCN standards. Furthermore, 11(79%) species showed a decrease both in the number of subpopulations and theirextent of occurrence when compared to historic distributions. This studyhighlights the importance of two factors necessary to address modernconservation questions. Sound conclusions regarding the conservation status ofindividual species requires a strong taxonomic framework and good collectiondata for a species distribution. However, because specimen data are very oftenincomplete and biased both geographically and taxonomically, reaching soundconclusions requires field knowledge of individual species to compensate forthese limitations.     

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.     

Assessment of Extinction Risk and Reasons for Decline in Sturgeon

Sturgeon populations in the Danube River have been affected by a combination of hydropower development, over-harvesting, habitat degradation from agricultural and industrial practices and from urbanization. The effects of these changes have been monitored on six sturgeon species inhabiting the Danube River. Two of them are resident species, while the other four migrate to the river for spawning. Atlantic sturgeon (Acipenser sturio) has completely disappeared from this region. Ship sturgeon (Acipenser nudiventris) is very rare in professional fishing catches. Beluga (Huso huso), Russian sturgeon (Acipenser gueldenstaedtii), stellate sturgeon (Acipenser stellatus) and sterlet (Acipenser ruthenus) are endangered with different levels of extinction risk. Here, we model the time dependence of the beluga and Russian sturgeon catch in the Serbian part of the Danube River. Predicted extinction of Russian sturgeon was estimated to fall around the middle of the century, and for beluga approximately at middle of the millennium. Suggestions for sturgeon conservation measures on a national level and coordination of all relevant institutions in Serbia are also presented.     

High Risk Population Isolate Reveals Low Frequency Variants Predisposing to Intracranial Aneurysms

3% of the population develops saccular intracranial aneurysms (sIAs), a complex trait, with a sporadic and a familial form. Subarachnoid hemorrhage from sIA (sIA-SAH) is a devastating form of stroke. Certain rare genetic variants are enriched in the Finns, a population isolate with a small founder population and bottleneck events. As the sIA-SAH incidence in Finland is >2× increased, such variants may associate with sIA in the Finnish population. We tested 9.4 million variants for association in 760 Finnish sIA patients (enriched for familial sIA), and in 2,513 matched controls with case-control status and with the number of sIAs. The most promising loci (p<5E-6) were replicated in 858 Finnish sIA patients and 4,048 controls. The frequencies and effect sizes of the replicated variants were compared to a continental European population using 717 Dutch cases and 3,004 controls. We discovered four new high-risk loci with low frequency lead variants. Three were associated with the case-control status: 2q23.3 (MAF 2.1%, OR 1.89, p 1.42×10-9); 5q31.3 (MAF 2.7%, OR 1.66, p 3.17×10-8); 6q24.2 (MAF 2.6%, OR 1.87, p 1.87×10-11) and one with the number of sIAs: 7p22.1 (MAF 3.3%, RR 1.59, p 6.08×-9). Two of the associations (5q31.3, 6q24.2) replicated in the Dutch sample. The 7p22.1 locus was strongly differentiated; the lead variant was more frequent in Finland (4.6%) than in the Netherlands (0.3%). Additionally, we replicated a previously inconclusive locus on 2q33.1 in all samples tested (OR 1.27, p 1.87×10-12). The five loci explain 2.1% of the sIA heritability in Finland, and may relate to, but not explain, the increased incidence of sIA-SAH in Finland. This study illustrates the utility of population isolates, familial enrichment, dense genotype imputation and alternate phenotyping in search for variants associated with complex diseases.     

Improvements to the Red List Index

The Red List Index uses information from the IUCN Red List to track trends in the projected overall extinction risk of sets of species. It has been widely recognised as an important component of the suite of indicators needed to measure progress towards the international target of significantly reducing the rate of biodiversity loss by 2010. However, further application of the RLI (to non-avian taxa in particular) has revealed some shortcomings in the original formula and approach: It performs inappropriately when a value of zero is reached; RLI values are affected by the frequency of assessments; and newly evaluated species may introduce bias. Here we propose a revision to the formula, and recommend how it should be applied in order to overcome these shortcomings. Two additional advantages of the revisions are that assessment errors are not propagated through time, and the overall level extinction risk can be determined as well as trends in this over time.     

Assessment of Hebei flora against the IUCN Red List Criteria in China

Some plants of Hebei Province in China are under threat from human activities, such as over-herding and over-exploitation of wild medicinal plants and industrial plants, etc. To identify the plants in danger in the province and to inspect the quality of the environment encompassing Beijing and Tianjin, a red list of the threatened flora of Hebei Province was produced by using the IUCN Red List Criteria (version 3.1) and its guidelines (version 6.2). Some 262 species were assessed and the results were as follows: (1) the threatened flora include 211 species, accounting for 7.95% of the total native vascular plants. Among them, 44 are Critically Endangered, 80 Endangered and 87 Vulnerable; (2) the destruction of the habitat caused by human activities and the actual or potential exploitation of the plants themselves were the main threat factors of Hebei flora; (3) most of the threatened plants are located in the western, northern and northeastern mountainous regions, namely the key regions of Hebei plant diversity; the endemic and regionally endemic species are severely threatened. Consequently, the assessment not only presented the threatened status of Hebei flora but also indicated the relatively fragile health status of the environment of Beijing and Tianjin. Thus, it is suggested that the application of the IUCN Red List Criteria at the regional level, as an index, could reflect the health status of the local ecosystem. In addition, more concrete measures are needed to conserve the plant diversity and the natural ecosystem of Hebei Province and even the whole region encompassing Beijing and Tianjin.     

Assessment of Hebei flora against the IUCN Red List Criteria in China

Some plants of Hebei Province in China are under threat from human activities,such as over-herding and over-exploitation of wild medicinal plants and industrial plants,etc.To identify the plants in danger in the province and to inspect the quality of the environment encompassing Beijing and Tianjin,a red list of the threatened flora of Hebei Province was produced by using the IUCN Red List Criteria (version 3.1) and its guidelines (version 6.2).Some 262 species were assessed and the results were as follows:(1) the threatened flora include 211 species,accounting for 7.95% of the total native vascular plants.Among them,44 are Critically Endangered,80 Endangered and 87 Vulnerable;(2) the destruction of the habitat caused by human activities and the actual or potential exploitation of the plants themselves were the main threat factors of Hebei flora;(3) most of the threatened plants are located in the western,northern and northeastern mountainous regions,namely the key regions of Hebei plant diversity;the endemic and regionally endemic species are severely threatened.Consequently,the assessment not only presented the threatened status of Hebei flora but also indicated the relatively fragile health status of the environment of Beijing and Tianjin.Thus,it is suggested that the application of the IUCN Red List Criteria at the regional level,as an index,could reflect the health status of the local ecosystem,In addition,more concrete measures are needed to conserve the plant diversity and the natural ecosystem of Hebei Province and even the whole region encompassing Beijing and Tianjin.     

Sportsfish Consumption Surveys: A Risk Assessment Practitioner's Wish List

In the United States, risk assessments that include sportsfish consumption often rely on default values derived by the USEPA. However, local, regional, and cultural differences can result in substantial differences in consumption rates, species of fish caught, parts of fish consumed, and fish preparation methods—all of which contribute to the extent of contaminant exposure. Because of these differences, site-specific data are important for the reliable prediction of exposure. This article reviews the types of information important to a risk assessor to enhance the applicability of the exposure assessment to the population being evaluated. It provides a method for setting priorities based on the sensitivity of the exposure assessment to each type of information. Consumption rate and parts of fish consumed are the most important information to obtain. This information should be obtained for each fish species consumed, and should be obtained for both children and adults. Body weight and exposure duration have the next level of priority, and cooking method has the lowest level of priority. Results from surveys should be presented in a manner that allows the reader to understand the variability observed in the data and the survey questions that were asked. Correlations between variables should be evaluated and presented.     

Health Risk Assessment Due to Groundwater Arsenic Contamination: Children Are at High Risk

Health risk assessment due to groundwater As contamination was conducted in two As-prone panchayats, Rampur Diara (RD) and Haldichapra (HC) of the Maner block of the Patna district, Bihar (India). All 100% of the water samples surveyed were found to be contaminated with As with a mean value of 52 μg/L (n = 10) in RD and 231 μg/L (n = 10) in HC, both exceeding the World Health Organization (WHO) guideline of 10 μg/L and the Bureau of Indian Standards (BIS) standard of 50 μg/L, respectively. The average calculated per capita consumption of As through drinking water in RD ranged from 120 μg/day for 5–10-year-old children to 320 μg/day for adults older than 41 years, while in HC the average calculated As through consumption ranged from 580 μg/day for 5–10-year-old children to 1470 μg/day for adults older than 41 years. Hazard quotients were calculated to be between 12.1 to 41.6 for the RD population and 58.3 to 192.5 for the HC population, both exceeding the typical toxic risk index 1. In addition, cancer risk of 19 per 1000 was found for RD children and 87 per 1000 for HC children. Visible symptoms of Arsenicosis were also observed in the area.     

Green Plants in the Red: A Baseline Global Assessment for the IUCN Sampled Red List Index for Plants

Plants provide fundamental support systems for life on Earth and are the basis for all terrestrial ecosystems; a decline in plant diversity will be detrimental to all other groups of organisms including humans. Decline in plant diversity has been hard to quantify, due to the huge numbers of known and yet to be discovered species and the lack of an adequate baseline assessment of extinction risk against which to track changes. The biodiversity of many remote parts of the world remains poorly known, and the rate of new assessments of extinction risk for individual plant species approximates the rate at which new plant species are described. Thus the question ‘How threatened are plants?’ is still very difficult to answer accurately. While completing assessments for each species of plant remains a distant prospect, by assessing a randomly selected sample of species the Sampled Red List Index for Plants gives, for the first time, an accurate view of how threatened plants are across the world. It represents the first key phase of ongoing efforts to monitor the status of the world’s plants. More than 20% of plant species assessed are threatened with extinction, and the habitat with the most threatened species is overwhelmingly tropical rain forest, where the greatest threat to plants is anthropogenic habitat conversion, for arable and livestock agriculture, and harvesting of natural resources. Gymnosperms (e.g. conifers and cycads) are the most threatened group, while a third of plant species included in this study have yet to receive an assessment or are so poorly known that we cannot yet ascertain whether they are threatened or not. This study provides a baseline assessment from which trends in the status of plant biodiversity can be measured and periodically reassessed.     

Adaptation to High Ethanol Reveals Complex Evolutionary Pathways

Tolerance to high levels of ethanol is an ecologically and industrially relevant phenotype of microbes, but the molecular mechanisms underlying this complex trait remain largely unknown. Here, we use long-term experimental evolution of isogenic yeast populations of different initial ploidy to study adaptation to increasing levels of ethanol. Whole-genome sequencing of more than 30 evolved populations and over 100 adapted clones isolated throughout this two-year evolution experiment revealed how a complex interplay of de novo single nucleotide mutations, copy number variation, ploidy changes, mutator phenotypes, and clonal interference led to a significant increase in ethanol tolerance. Although the specific mutations differ between different evolved lineages, application of a novel computational pipeline, PheNetic, revealed that many mutations target functional modules involved in stress response, cell cycle regulation, DNA repair and respiration. Measuring the fitness effects of selected mutations introduced in non-evolved ethanol-sensitive cells revealed several adaptive mutations that had previously not been implicated in ethanol tolerance, including mutations in PRT1, VPS70 and MEX67. Interestingly, variation in VPS70 was recently identified as a QTL for ethanol tolerance in an industrial bio-ethanol strain. Taken together, our results show how, in contrast to adaptation to some other stresses, adaptation to a continuous complex and severe stress involves interplay of different evolutionary mechanisms. In addition, our study reveals functional modules involved in ethanol resistance and identifies several mutations that could help to improve the ethanol tolerance of industrial yeasts.     

Using the IUCN Red List to determine effective conservation strategies

Threatened species lists continue to grow while the world’s governments fail to meet biodiversity conservation goals. Clearly, we are failing in our attempts to conserve biodiversity. Yet 37 mammal species genuinely improved in status in the 2009 IUCN Red List, suggesting there are ways to successfully conserve biodiversity. Here, I compare the threats and conservation actions (proposed and implemented) by the expert assessors of the Red List of improving species to a further 144 declining mammal species to determine whether specific threats were more easily remedied, and whether certain conservation actions were more successful than others. Declining species were faced with different threatening processes to mammals improving in status suggesting some threats were easier to treat (e.g. hunting) than others (climate change, invasive species). Declining species had different proposed and implemented conservation actions than improving species suggesting some actions are more successful than others. Threatened species were invariably found in conservation areas, suggesting protected area creation alone is not an overly successful strategy for species at risk of extinction. Conservation actions were more frequently implemented for improving than declining species suggesting active conservation is effective in improving the status of biodiversity. There were significant differences between proposed and implemented conservation actions suggesting some actions are easier to implement than others. Reintroduction, captive breeding and hunting restriction were more effective in conserving mammals than site creation and invasive species control. These findings highlight effective conservation actions for mammals worldwide and allow the rationalisation of threat mitigation measures to ensure economically justifiable biodiversity conservation strategies.     

Birds to watch: a Red Data List for East Africa

Bennun, L.A., Njoroge, P. & Pomeroy, D. 2000. Birds to watch: a Red Data List for East Africa. Ostrich 71 (1 & 2): 310–314.

The value of Red Data books and lists is well established; there has been much recent work on improving the criteria for listing species of conservation concern. So far these have been applied mainly at the global level. Regional lists can be useful, however, in improving the resolution of conservation priorities and setting an agenda for research, monitoring and conservation, especially where data are collected by amateur naturalists. A Red Data list for East African birds has been drawn up following an eight-month process that involved wide consultation within the region, defined as Uganda, Rwanda, Tanzania, Kenya and Burundi. The criteria for listing were based on those defined by IUCN, and summarised in a single, simple table that could be used for screening large numbers of species. A criterion based on geographic range eliminated from consideration vagrant species or those on the extreme edge of their range. A separate Near Threatened category (Lower Risk but very close to Vulnerable) proved useful. An additional category of Regional Responsibility captured species that are entirely or mainly confiied to East Africa, or to three habitats where the region has special responsibility: coastal forests, Albertine Rift forests, and papyrus swamps. A total of 107 species (about 8% of the regional avifauna) were listed as regionally threatened. This includes four Critical, 18 Endangered and 85 Vulnerable species, proportions very close to those expected from the theoretical probabilities of extinction in each case. One hundred and four species were listed as Near-threatened and 153 as Regional Responsibility, 87 of which are not under threat. Placing a species in a particular category of threat, for explicit reasons, poses an hypothesis about its status that can be tested with additional data. This process is now under way with the compilation of a more detailed, annotated list.     

High Diversity in Cretaceous Ichthyosaurs from Europe Prior to Their Extinction

Background

Ichthyosaurs are reptiles that inhabited the marine realm during most of the Mesozoic. Their Cretaceous representatives have traditionally been considered as the last survivors of a group declining since the Jurassic. Recently, however, an unexpected diversity has been described in Upper Jurassic–Lower Cretaceous deposits, but is widely spread across time and space, giving small clues on the adaptive potential and ecosystem control of the last ichthyosaurs. The famous but little studied English Gault Formation and ‘greensands’ deposits (the Upper Greensand Formation and the Cambridge Greensand Member of the Lower Chalk Formation) offer an unprecedented opportunity to investigate this topic, containing thousands of ichthyosaur remains spanning the Early–Late Cretaceous boundary.

Methodology/Principal Findings

To assess the diversity of the ichthyosaur assemblage from these sedimentary bodies, we recognized morphotypes within each type of bones. We grouped these morphotypes together, when possible, by using articulated specimens from the same formations and from new localities in the Vocontian Basin (France); a revised taxonomic scheme is proposed. We recognize the following taxa in the ‘greensands’: the platypterygiines ‘Platypterygius’ sp. and Sisteronia seeleyi gen. et sp. nov., indeterminate ophthalmosaurines and the rare incertae sedis Cetarthrosaurus walkeri. The taxonomic diversity of late Albian ichthyosaurs now matches that of older, well-known intervals such as the Toarcian or the Tithonian. Contrasting tooth shapes and wear patterns suggest that these ichthyosaurs colonized three distinct feeding guilds, despite the presence of numerous plesiosaur taxa.

Conclusion/Significance

Western Europe was a diversity hot-spot for ichthyosaurs a few million years prior to their final extinction. By contrast, the low diversity in Australia and U.S.A. suggests strong geographical disparities in the diversity pattern of Albian–early Cenomanian ichthyosaurs. This provides a whole new context to investigate the extinction of these successful marine reptiles, at the end of the Cenomanian.