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1.  Integrating field surveys and remote sensing data to study distribution, habitat use and conservation status of the herpetofauna of the Comoro Islands 
ZooKeys  2011;21-78.
We studied the non-marine reptile and amphibian species of the volcanic Comoro archipelago in the Western Indian Ocean, a poorly known island herpetofauna comprising numerous microendemic species of potentially high extinction risk and widespread, non-endemic and often invasive taxa. According to our data, the Comoro islands are inhabited by two amphibian species and at least 28 species of reptiles although ongoing genetic studies and unconfirmed historical records suggest an even higher species diversity. 14 of the 28 currently recognized species of terrestrial reptiles (50%) and the two amphibians are endemic to a single island or to the Comoro archipelago. The majority of species are most abundant at low elevation. However, a few endemic species, like the gekkonid lizards Paroedura sanctijohannis and Phelsuma nigristriata, are more common in or even confined to higher altitudes. We created habitat maps from remotely sensed data in combination with detailed species distribution maps produced using comprehensive data from field surveys between 2000 and 2010, literature, and historical locality records based on specimens in zoological collections. Using these data, we assessed the conservation status of the endemic terrestrial reptiles and amphibians according to the IUCN Red List criteria. Our results show that although little area of natural forest remains on the Comoros, many species are abundant in degraded forest or plantations. Competition and predation by invasive species appears to be the most important threat factor for the endemic herpetofauna, together with habitat degradation and destruction, which further favours invasive species. We propose the status Endangered for three species, Vulnerable for one species, Near Threatened for six species, Least Concern for four and Data Deficient for two species. The endemic subspecies Oplurus cuvieri comorensis is proposed for the status Critically Endangered. Based on the results of this study, seven areas of importance for reptile and amphibian conservation on the Comoros are identified. This study shows how remote sensing data can contribute to increasing accuracy and objectiveness of conservation assessments.
doi:10.3897/zookeys.144.1648
PMCID: PMC3233692  PMID: 22207785
amphibians; area of occupancy; conservation planning; IUCN Red List; Landsat; protected areas; reptiles; satellite imagery; Western Indian Ocean
2.  Global Assessment of Extinction Risk to Populations of Sockeye Salmon Oncorhynchus nerka 
PLoS ONE  2012;7(4):e34065.
Background
Concern about the decline of wild salmon has attracted the attention of the International Union for the Conservation of Nature (IUCN). The IUCN applies quantitative criteria to assess risk of extinction and publishes its results on the Red List of Threatened Species. However, the focus is on the species level and thus may fail to show the risk to populations. The IUCN has adapted their criteria to apply to populations but there exist few examples of this type of assessment. We assessed the status of sockeye salmon Oncorhynchus nerka as a model for application of the IUCN population-level assessments and to provide the first global assessment of the status of an anadromous Pacific salmon.
Methods/Principal Findings
We found from demographic data that the sockeye salmon species is not presently at risk of extinction. We identified 98 independent populations with varying levels of risk within the species' range. Of these, 5 (5%) are already extinct. We analyzed the risk for 62 out of 93 extant populations (67%) and found that 17 of these (27%) are at risk of extinction. The greatest number and concentration of extinct and threatened populations is in the southern part of the North American range, primarily due to overfishing, freshwater habitat loss, dams, hatcheries, and changing ocean conditions.
Conclusions/Significance
Although sockeye salmon are not at risk at the species-level, about one-third of the populations that we analyzed are at risk or already extinct. Without an understanding of risk to biodiversity at the level of populations, the biodiversity loss in salmon would be greatly underrepresented on the Red List. We urge government, conservation organizations, scientists and the public to recognize this limitation of the Red List. We also urge recognition that about one-third of sockeye salmon global population diversity is at risk of extinction or already extinct.
doi:10.1371/journal.pone.0034065
PMCID: PMC3325247  PMID: 22511930
3.  Comprehensive Red List Assessment Reveals Exceptionally High Extinction Risk to Madagascar Palms 
PLoS ONE  2014;9(7):e103684.
The establishment of baseline IUCN Red List assessments for plants is a crucial step in conservation planning. Nowhere is this more important than in biodiversity hotspots that are subject to significant anthropogenic pressures, such as Madagascar. Here, all Madagascar palm species are assessed using the IUCN Red List categories and criteria, version 3.1. Our results indicate that 83% of the 192 endemic species are threatened, nearly four times the proportion estimated for plants globally and exceeding estimates for all other comprehensively evaluated plant groups in Madagascar. Compared with a previous assessment in 1995, the number of Endangered and Critically Endangered species has substantially increased, due to the discovery of 28 new species since 1995, most of which are highly threatened. The conservation status of most species included in both the 1995 and the current assessments has not changed. Where change occurred, more species have moved to lower threat categories than to higher categories, because of improved knowledge of species and their distributions, rather than a decrease in extinction risk. However, some cases of genuine deterioration in conservation status were also identified. Palms in Madagascar are primarily threatened by habitat loss due to agriculture and biological resource use through direct exploitation or collateral damage. The recent extension of Madagascar’s protected area network is highly beneficial for palms, substantially increasing the number of threatened species populations included within reserves. Notably, three of the eight most important protected areas for palms are newly designated. However, 28 threatened and data deficient species are not protected by the expanded network, including some Critically Endangered species. Moreover, many species occurring in protected areas are still threatened, indicating that threatening processes persist even in reserves. Definitive implementation of the new protected areas combined with local community engagement are essential for the survival of Madagascar’s palms.
doi:10.1371/journal.pone.0103684
PMCID: PMC4116232  PMID: 25075612
4.  Unveiling the Conservation Biogeography of a Data-Deficient Endangered Bird Species under Climate Change 
PLoS ONE  2014;9(1):e84529.
It remains a challenge to identify the geographical patterns and underlying environmental associations of species with unique ecological niches and distinct behaviors. This in turn hinders our understanding of the ecology as well as effective conservation management of threatened species. The white-eared night heron (Gorsachius magnificus) is a non-migratory nocturnal bird species that has a patchy distribution in the mountainous forests of East Asia. It is currently categorized as “Endangered” on the IUCN Red List, primarily due to its restricted range and fragmented habitat. To improve our knowledge of the biogeography and conservation of this species, we modeled the geographical pattern of its suitable habitat and evaluated the potential impacts of climate change using ecological niche modeling with a maximum entropy approach implemented in Maxent. Our results indicated that the amount of suitable habitat in all of East Asia was about 130 000 km2, which can be spatially subdivided into several mountain ranges in southern and southwestern China and northern Vietnam. The extent of suitable habitat range may shrink by more than 35% under a predicted changing climate when assuming the most pessimistic condition of dispersal, while some more suitable habitat would be available if the heron could disperse unrestrainedly. The significant future changes in habitat suitability suggested for Gorsachius magnificus urge caution in any downgrading of Red List status that may be considered. Our results also discern potentially suitable areas for future survey efforts on new populations. Overall, this study demonstrates that ecological niche modeling offers an important tool for evaluating the habitat suitability and potential impacts of climate change on an enigmatic and endangered species based on limited presence data.
doi:10.1371/journal.pone.0084529
PMCID: PMC3880300  PMID: 24404169
5.  Measuring Global Trends in the Status of Biodiversity: Red List Indices for Birds 
PLoS Biology  2004;2(12):e383.
The rapid destruction of the planet's biodiversity has prompted the nations of the world to set a target of achieving a significant reduction in the rate of loss of biodiversity by 2010. However, we do not yet have an adequate way of monitoring progress towards achieving this target. Here we present a method for producing indices based on the IUCN Red List to chart the overall threat status (projected relative extinction risk) of all the world's bird species from 1988 to 2004. Red List Indices (RLIs) are based on the number of species in each Red List category, and on the number changing categories between assessments as a result of genuine improvement or deterioration in status. The RLI for all bird species shows that their overall threat status has continued to deteriorate since 1988. Disaggregated indices show that deteriorations have occurred worldwide and in all major ecosystems, but with particularly steep declines in the indices for Indo-Malayan birds (driven by intensifying deforestation of the Sundaic lowlands) and for albatrosses and petrels (driven by incidental mortality in commercial longline fisheries). RLIs complement indicators based on species population trends and habitat extent for quantifying global trends in the status of biodiversity. Their main weaknesses are that the resolution of status changes is fairly coarse and that delays may occur before some status changes are detected. Their greatest strength is that they are based on information from nearly all species in a taxonomic group worldwide, rather than a potentially biased subset. At present, suitable data are only available for birds, but indices for other taxonomic groups are in development, as is a sampled index based on a stratified sample from all major taxonomic groups.
An index is developed from the IUCN Red List that measures the overall threat status of taxa and reveals that the status of the world's birds has deteriorated since 1988
doi:10.1371/journal.pbio.0020383
PMCID: PMC524254  PMID: 15510230
6.  Allozyme Variation in the Three Extant Populations of the Narrowly Endemic Cycad Dioon angustifolium Miq. (Zamiaceae) from North-eastern Mexico 
Annals of Botany  2005;95(6):999-1007.
• Background and Aims Dioon angustifolium was considered within D. edule. Recent morphometric and allozyme studies on D. edule have shown that D. angustifolium has originated from geographic isolation and is therefore considered to be a separate species. This cycad is endemic to north-eastern Mexico and is known only from three populations in the Sierra Madre Oriental mountain chain. Its populations are small when compared with its southern relative D. edule. In this study, genetic variation was determined within and between populations of D. angustifolium and the genetic consequences of habitat fragmentation and isolation of populations of this species were assessed.
• Methods Allozyme electrophoresis of 14 presumptive loci was used. The data were analysed with statistical approximations for estimating genetic diversity, structure, gene flow and recent genetic bottlenecks.
• Key Results Means and standard deviations of genetic diversity estimators were: number of alleles per locus (A = 1·67 ± 0·23), percentage of polymorphic loci (P = 52·4 ± 23 %) and expected heterozygosity (HE = 0·218 ± 0·093). The genetic variation attributable to differences among populations was 16·7 %. Mean gene flow between paired populations was Nm = 1·55 ± 0·67, which is similar to that reported for endemic plant species of narrow geographical distribution and species with gravity-dispersed seed. A recent bottleneck is detected in the populations studied.
• Conclusions Dioon angustifolium presents high levels of genetic diversity compared with other cycad species, in spite of small population sizes. The recent bottleneck effect did not effectively reduce the genetic variation to the extent of eliminating these populations. The distribution of D. angustifolium appears to be the result of historical biogeographical effects related to the Pleistocene glaciations. It is recommended that this species be catalogued in the IUCN Red List of Threatened Species and conservation efforts be made to preserve it.
doi:10.1093/aob/mci106
PMCID: PMC4246753  PMID: 15760914
Conservation; cycads; endemic narrow distribution; genetic bottleneck; genetic structure; Mexico; Pleistocene refugia; population genetics
7.  Conservation Priorities in a Biodiversity Hotspot: Analysis of Narrow Endemic Plant Species in New Caledonia 
PLoS ONE  2013;8(9):e73371.
New Caledonia is a global biodiversity hotspot facing extreme environmental degradation. Given the urgent need for conservation prioritisation, we have made a first-pass quantitative assessment of the distribution of Narrow Endemic Species (NES) in the flora to identify species and sites that are potentially important for conservation action. We assessed the distributional status of all angiosperm and gymnosperm species using data from taxonomic descriptions and herbarium samples. We characterised species as being NES if they occurred in 3 or fewer locations. In total, 635 of the 2930 assessed species were classed as NES, of which only 150 have been subjected to the IUCN conservation assessment. As the distributional patterns of un-assessed species from one or two locations correspond well with assessed species which have been classified as Critically Endangered or Endangered respectively, we suggest that our distributional data can be used to prioritise species for IUCN assessment. We also used the distributional data to produce a map of “Hotspots of Plant Narrow Endemism” (HPNE). Combined, we used these data to evaluate the coincidence of NES with mining activities (a major source of threat on New Caledonia) and also areas of conservation protection. This is to identify species and locations in most urgent need of further conservation assessment and subsequent action. Finally, we grouped the NES based on the environments they occurred in and modelled the habitat distribution of these groups with a Maximum Entropy Species Distribution Model (MaxEnt). The NES were separable into three different groups based primarily on geological differences. The distribution of the habitat types for each group coincide partially with the HPNE described above and also indicates some areas which have high habitat suitability but few recorded NES. Some of these areas may represent under-sampled hotspots of narrow endemism and are priorities for further field work.
doi:10.1371/journal.pone.0073371
PMCID: PMC3776834  PMID: 24058470
8.  Plant and animal endemism in the eastern Andean slope: challenges to conservation 
BMC Ecology  2012;12:1.
Background
The Andes-Amazon basin of Peru and Bolivia is one of the most data-poor, biologically rich, and rapidly changing areas of the world. Conservation scientists agree that this area hosts extremely high endemism, perhaps the highest in the world, yet we know little about the geographic distributions of these species and ecosystems within country boundaries. To address this need, we have developed conservation data on endemic biodiversity (~800 species of birds, mammals, amphibians, and plants) and terrestrial ecological systems (~90; groups of vegetation communities resulting from the action of ecological processes, substrates, and/or environmental gradients) with which we conduct a fine scale conservation prioritization across the Amazon watershed of Peru and Bolivia. We modelled the geographic distributions of 435 endemic plants and all 347 endemic vertebrate species, from existing museum and herbaria specimens at a regional conservation practitioner's scale (1:250,000-1:1,000,000), based on the best available tools and geographic data. We mapped ecological systems, endemic species concentrations, and irreplaceable areas with respect to national level protected areas.
Results
We found that sizes of endemic species distributions ranged widely (< 20 km2 to > 200,000 km2) across the study area. Bird and mammal endemic species richness was greatest within a narrow 2500-3000 m elevation band along the length of the Andes Mountains. Endemic amphibian richness was highest at 1000-1500 m elevation and concentrated in the southern half of the study area. Geographical distribution of plant endemism was highly taxon-dependent. Irreplaceable areas, defined as locations with the highest number of species with narrow ranges, overlapped slightly with areas of high endemism, yet generally exhibited unique patterns across the study area by species group. We found that many endemic species and ecological systems are lacking national-level protection; a third of endemic species have distributions completely outside of national protected areas. Protected areas cover only 20% of areas of high endemism and 20% of irreplaceable areas. Almost 40% of the 91 ecological systems are in serious need of protection (= < 2% of their ranges protected).
Conclusions
We identify for the first time, areas of high endemic species concentrations and high irreplaceability that have only been roughly indicated in the past at the continental scale. We conclude that new complementary protected areas are needed to safeguard these endemics and ecosystems. An expansion in protected areas will be challenged by geographically isolated micro-endemics, varied endemic patterns among taxa, increasing deforestation, resource extraction, and changes in climate. Relying on pre-existing collections, publically accessible datasets and tools, this working framework is exportable to other regions plagued by incomplete conservation data.
doi:10.1186/1472-6785-12-1
PMCID: PMC3311091  PMID: 22284854
Andes-Amazon; conservation planning; ecological systems; endemic species richness; irreplaceability; Latin America
9.  The World's Most Isolated and Distinct Whale Population? Humpback Whales of the Arabian Sea 
PLoS ONE  2014;9(12):e114162.
A clear understanding of population structure is essential for assessing conservation status and implementing management strategies. A small, non-migratory population of humpback whales in the Arabian Sea is classified as “Endangered” on the IUCN Red List of Threatened Species, an assessment constrained by a lack of data, including limited understanding of its relationship to other populations. We analysed 11 microsatellite markers and mitochondrial DNA sequences extracted from 67 Arabian Sea humpback whale tissue samples and compared them to equivalent datasets from the Southern Hemisphere and North Pacific. Results show that the Arabian Sea population is highly distinct; estimates of gene flow and divergence times suggest a Southern Indian Ocean origin but indicate that it has been isolated for approximately 70,000 years, remarkable for a species that is typically highly migratory. Genetic diversity values are significantly lower than those obtained for Southern Hemisphere populations and signatures of ancient and recent genetic bottlenecks were identified. Our findings suggest this is the world's most isolated humpback whale population, which, when combined with low population abundance estimates and anthropogenic threats, raises concern for its survival. We recommend an amendment of the status of the population to “Critically Endangered” on the IUCN Red List.
doi:10.1371/journal.pone.0114162
PMCID: PMC4254934  PMID: 25470144
10.  Conservation Actions Based on Red Lists Do Not Capture the Functional and Phylogenetic Diversity of Birds in Brazil 
PLoS ONE  2013;8(9):e73431.
Red Lists of threatened species play a critical role in conservation science and practice. However, policy-making based on Red Lists ignores ecological and evolutionary consequences of losing biodiversity because these lists focus on species alone. To decide if relying on Red Lists alone can help to conserve communities’ functional (FD) and phylogenetic (PD) diversity, it is useful to evaluate whether Red List categories represent species with diverse ecological traits and evolutionary histories. Additionally, local scale analyses using regional Red Lists should represent more realistic pools of co-occurring species and thereby better capture eventual losses of FD and PD. Here, we used 21 life-history traits and a phylogeny for all Brazilian birds to determine whether species assigned under the IUCN global Red List, the Brazilian national, and regional Red Lists capture more FD and PD than expected by chance. We also built local Red Lists and analysed if they capture more FD and PD at the local scale. Further, we investigated whether individual threat categories have species with greater FD and PD than expected by chance. At any given scale, threat categories did not capture greater FD or PD than expected by chance. Indeed, mostly categories captured equal or less FD or PD than expected by chance. These findings would not have great consequences if Red Lists were not often considered as a major decision support tool for policy-making. Our results challenge the practice of investing conservation resources based only on species Red Lists because, from an ecological and evolutionary point of view, this would be the same as protecting similar or random sets of species. Thus, new prioritization methods, such as the EDGE of Existence initiative, should be developed and applied to conserve species’ ecological traits and evolutionary histories at different spatial scales.
doi:10.1371/journal.pone.0073431
PMCID: PMC3767746  PMID: 24039939
11.  Extinction Risks and the Conservation of Madagascar's Reptiles 
PLoS ONE  2014;9(8):e100173.
Background
An understanding of the conservation status of Madagascar's endemic reptile species is needed to underpin conservation planning and priority setting in this global biodiversity hotspot, and to complement existing information on the island's mammals, birds and amphibians. We report here on the first systematic assessment of the extinction risk of endemic and native non-marine Malagasy snakes, lizards, turtles and tortoises.
Methodology/Principal Findings
Species range maps from The IUCN Red List of Threatened Species were analysed to determine patterns in the distribution of threatened reptile species. These data, in addition to information on threats, were used to identify priority areas and actions for conservation. Thirty-nine percent of the data-sufficient Malagasy reptiles in our analyses are threatened with extinction. Areas in the north, west and south-east were identified as having more threatened species than expected and are therefore conservation priorities. Habitat degradation caused by wood harvesting and non-timber crops was the most pervasive threat. The direct removal of reptiles for international trade and human consumption threatened relatively few species, but were the primary threats for tortoises. Nine threatened reptile species are endemic to recently created protected areas.
Conclusions/Significance
With a few alarming exceptions, the threatened endemic reptiles of Madagascar occur within the national network of protected areas, including some taxa that are only found in new protected areas. Threats to these species, however, operate inside and outside protected area boundaries. This analysis has identified priority sites for reptile conservation and completes the conservation assessment of terrestrial vertebrates in Madagascar which will facilitate conservation planning, monitoring and wise-decision making. In sharp contrast with the amphibians, there is significant reptile diversity and regional endemism in the southern and western regions of Madagascar and this study highlights the importance of these arid regions to conserving the island's biodiversity.
doi:10.1371/journal.pone.0100173
PMCID: PMC4128600  PMID: 25111137
12.  Using Red List Indices to measure progress towards the 2010 target and beyond 
The World Conservation Union (IUCN) Red List is widely recognized as the most authoritative and objective system for classifying species by their risk of extinction. Red List Indices (RLIs) illustrate the relative rate at which a particular set of species change in overall threat status (i.e. projected relative extinction-risk), based on population and range size and trends as quantified by Red List categories. RLIs can be calculated for any representative set of species that has been fully assessed at least twice. They are based on the number of species in each Red List category, and the number changing categories between assessments as a result of genuine improvement or deterioration in status. RLIs show a fairly coarse level of resolution, but for fully assessed taxonomic groups they are highly representative, being based on information from a high proportion of species worldwide. The RLI for the world's birds shows that that their overall threat status has deteriorated steadily during the years 1988–2004 in all biogeographic realms and ecosystems. A preliminary RLI for amphibians for 1980–2004 shows similar rates of decline. RLIs are in development for other groups. In addition, a sampled index is being developed, based on a stratified sample of species from all major taxonomic groups, realms and ecosystems. This will provide extinction-risk trends that are more representative of all biodiversity.
doi:10.1098/rstb.2004.1583
PMCID: PMC1569445  PMID: 15814344
indicators; birds; amphibians; IUCN Red List; threatened species; extinction-risk
13.  Scientific Foundations for an IUCN Red List of Ecosystems 
PLoS ONE  2013;8(5):e62111.
An understanding of risks to biodiversity is needed for planning action to slow current rates of decline and secure ecosystem services for future human use. Although the IUCN Red List criteria provide an effective assessment protocol for species, a standard global assessment of risks to higher levels of biodiversity is currently limited. In 2008, IUCN initiated development of risk assessment criteria to support a global Red List of ecosystems. We present a new conceptual model for ecosystem risk assessment founded on a synthesis of relevant ecological theories. To support the model, we review key elements of ecosystem definition and introduce the concept of ecosystem collapse, an analogue of species extinction. The model identifies four distributional and functional symptoms of ecosystem risk as a basis for assessment criteria: A) rates of decline in ecosystem distribution; B) restricted distributions with continuing declines or threats; C) rates of environmental (abiotic) degradation; and D) rates of disruption to biotic processes. A fifth criterion, E) quantitative estimates of the risk of ecosystem collapse, enables integrated assessment of multiple processes and provides a conceptual anchor for the other criteria. We present the theoretical rationale for the construction and interpretation of each criterion. The assessment protocol and threat categories mirror those of the IUCN Red List of species. A trial of the protocol on terrestrial, subterranean, freshwater and marine ecosystems from around the world shows that its concepts are workable and its outcomes are robust, that required data are available, and that results are consistent with assessments carried out by local experts and authorities. The new protocol provides a consistent, practical and theoretically grounded framework for establishing a systematic Red List of the world’s ecosystems. This will complement the Red List of species and strengthen global capacity to report on and monitor the status of biodiversity
doi:10.1371/journal.pone.0062111
PMCID: PMC3648534  PMID: 23667454
14.  Extinction Risk and Diversification Are Linked in a Plant Biodiversity Hotspot 
PLoS Biology  2011;9(5):e1000620.
Plant extinction risks in the Cape, South Africa differ from those for vertebrates worldwide, with young and fast-evolving plant lineages marching towards extinction at the fastest rate, but independently of human effects.
It is widely recognized that we are entering an extinction event on a scale approaching the mass extinctions seen in the fossil record. Present-day rates of extinction are estimated to be several orders of magnitude greater than background rates and are projected to increase further if current trends continue. In vertebrates, species traits, such as body size, fecundity, and geographic range, are important predictors of vulnerability. Although plants are the basis for life on Earth, our knowledge of plant extinctions and vulnerabilities is lagging. Here, we disentangle the underlying drivers of extinction risk in plants, focusing on the Cape of South Africa, a global biodiversity hotspot. By comparing Red List data for the British and South African floras, we demonstrate that the taxonomic distribution of extinction risk differs significantly between regions, inconsistent with a simple, trait-based model of extinction. Using a comprehensive phylogenetic tree for the Cape, we reveal a phylogenetic signal in the distribution of plant extinction risks but show that the most threatened species cluster within short branches at the tips of the phylogeny—opposite to trends in mammals. From analyzing the distribution of threatened species across 11 exemplar clades, we suggest that mode of speciation best explains the unusual phylogenetic structure of extinction risks in plants of the Cape. Our results demonstrate that explanations for elevated extinction risk in plants of the Cape flora differ dramatically from those recognized for vertebrates. In the Cape, extinction risk is higher for young and fast-evolving plant lineages and cannot be explained by correlations with simple biological traits. Critically, we find that the most vulnerable plant species are nonetheless marching towards extinction at a more rapid pace but, surprisingly, independently from anthropogenic effects. Our results have important implications for conservation priorities and cast doubts on the utility of current Red List criteria for plants in regions such as the Cape, where speciation has been rapid, if our aim is to maximize the preservation of the tree-of-life.
Author Summary
The rapid loss of biodiversity is the most significant ecological challenge we face today. Over the past few years, the International Union for Conservation of Nature has published Red Lists documenting the inexorable slide towards extinction of species; recent losses include the Hawaiian crow, golden toad, Baiji dolphin, and the West African black rhino. In groups we know well, such as mammals, the risk of extinction has been related to biology, with the most vulnerable species tending to be large, slow breeding, and narrowly distributed. Although plants are the basis for life on Earth, our knowledge of the drivers of plant extinctions is poor. Here, we disentangle the causes of plant extinctions. We show that the processes linked with extinction risks in plants of the Cape, South Africa differ from those for vertebrates more generally. The most vulnerable species are found within young and fast-evolving plant lineages, opposite to patterns in vertebrates. Our results illustrate the intricate link between the processes of speciation and extinction. We also show that the most threatened species are marching towards extinction at faster rates, but surprisingly, the risk appears independent of human effects.
doi:10.1371/journal.pbio.1000620
PMCID: PMC3101198  PMID: 21629678
15.  At the Heart of the Industrial Boom: Australian Snubfin Dolphins in the Capricorn Coast, Queensland, Need Urgent Conservation Action 
PLoS ONE  2013;8(2):e56729.
The recent industrial boom along the Australian coastline has increased concerns about the long term conservation of snubfin dolphins along the Queensland coast. National assessment of the conservation status and management of the Australian snubfin dolphin is currently hindered by the lack of adequate biological and ecological information throughout most of its range. In response to the issue of determining the conservation status of species with broad ranges, the IUCN has provided a framework for assessing the threatened status of regional populations. In this study we assessed the conservation status of a small geographically isolated population of snubfin dolphins living in the Fitzroy River region, Queensland, Australia, against the IUCN criteria for regional populations. A review of all available sightings data and stranding information indicates that this is the southernmost resident population of snubfin dolphins in Australian waters. The Fitzroy River snubfin dolphin population is composed of less than 100 individuals, with a representative range and core area of less than 400 and 300 km2 respectively. The area most often used by snubfin dolphins within the representative range and core area was estimated to be about 292 and 191 km2, respectively. A decrease in representative range, core area and preferred habitat between 14 and 25% is projected to occur if a planned industrial port development were to occur. These results are robust to uncertainty and considering the low level of formal protection and future threats, a classification of this subpopulation under the IUCN Red List as “Endangered” is appropriate.
doi:10.1371/journal.pone.0056729
PMCID: PMC3577743  PMID: 23437225
16.  Population Differentiation and Hybridisation of Australian Snubfin (Orcaella heinsohni) and Indo-Pacific Humpback (Sousa chinensis) Dolphins in North-Western Australia 
PLoS ONE  2014;9(7):e101427.
Little is known about the Australian snubfin (Orcaella heinsohni) and Indo-Pacific humpback (Sousa chinensis) dolphins (‘snubfin’ and ‘humpback dolphins’, hereafter) of north-western Australia. While both species are listed as ‘near threatened’ by the IUCN, data deficiencies are impeding rigorous assessment of their conservation status across Australia. Understanding the genetic structure of populations, including levels of gene flow among populations, is important for the assessment of conservation status and the effective management of a species. Using nuclear and mitochondrial DNA markers, we assessed population genetic diversity and differentiation between snubfin dolphins from Cygnet (n = 32) and Roebuck Bays (n = 25), and humpback dolphins from the Dampier Archipelago (n = 19) and the North West Cape (n = 18). All sampling locations were separated by geographic distances >200 km. For each species, we found significant genetic differentiation between sampling locations based on 12 (for snubfin dolphins) and 13 (for humpback dolphins) microsatellite loci (FST = 0.05–0.09; P<0.001) and a 422 bp sequence of the mitochondrial control region (FST = 0.50–0.70; P<0.001). The estimated proportion of migrants in a population ranged from 0.01 (95% CI 0.00–0.06) to 0.13 (0.03–0.24). These are the first estimates of genetic diversity and differentiation for snubfin and humpback dolphins in Western Australia, providing valuable information towards the assessment of their conservation status in this rapidly developing region. Our results suggest that north-western Australian snubfin and humpback dolphins may exist as metapopulations of small, largely isolated population fragments, and should be managed accordingly. Management plans should seek to maintain effective population size and gene flow. Additionally, while interactions of a socio-sexual nature between these two species have been observed previously, here we provide strong evidence for the first documented case of hybridisation between a female snubfin dolphin and a male humpback dolphin.
doi:10.1371/journal.pone.0101427
PMCID: PMC4079686  PMID: 24988113
17.  Comparative population genetics and evolutionary history of two commonly misidentified billfishes of management and conservation concern 
BMC Genetics  2014;15(1):141.
Background
Misidentifications between exploited species may lead to inaccuracies in population assessments, with potentially irreversible conservation ramifications if overexploitation of either species is occurring. A notable showcase is provided by the realization that the roundscale spearfish (Tetrapturus georgii), a recently validated species, has been historically misidentified as the morphologically very similar and severely overfished white marlin (Kajikia albida) (IUCN listing: Vulnerable). In effect, no information exists on the population status and evolutionary history of the enigmatic roundscale spearfish, a large, highly vagile and broadly distributed pelagic species. We provide the first population genetic evaluation of the roundscale spearfish, utilizing nuclear microsatellite and mitochondrial DNA sequence markers. Furthermore, we re-evaluated existing white marlin mitochondrial genetic data and present our findings in a comparative context to the roundscale spearfish.
Results
Microsatellite and mitochondrial (control region) DNA markers provided mixed evidence for roundscale spearfish population differentiation between the western north and south Atlantic regions, depending on marker-statistical analysis combination used. Mitochondrial DNA analyses provided strong signals of historical population growth for both white marlin and roundscale spearfish, but higher genetic diversity and effective female population size (1.5-1.9X) for white marlin.
Conclusions
The equivocal indications of roundscale spearfish population structure, combined with a smaller effective female population size compared to the white marlin, already a species of concern, suggests that a species-specific and precautionary management strategy recognizing two management units is prudent for this newly validated billfish.
Electronic supplementary material
The online version of this article (doi:10.1186/s12863-014-0141-4) contains supplementary material, which is available to authorized users.
doi:10.1186/s12863-014-0141-4
PMCID: PMC4278234  PMID: 25494814
Roundscale spearfish; White marlin; Genetic population structure; Genetic diversity; Effective population size; Tetrapturus georgii; Kajikia albida
18.  Monitoring change in the abundance and distribution of insects using butterflies and other indicator groups 
Conservative estimates suggest that 50–90% of the existing insect species on Earth have still to be discovered, yet the named insects alone comprise more than half of all known species of organism. With such poor baseline knowledge, monitoring change in insect diversity poses a formidable challenge to scientists and most attempts to generalize involve large extrapolations from a few well-studied taxa. Butterflies are often the only group for which accurate measures of change can be obtained. Four schemes, used successfully to assess change in British butterflies, that are increasingly being applied across the world are described: Red Data Books (RDB) list the best judgements of experts of the conservation status of species in their field of expertise; mapping schemes plot the changing distributions of species at scales of 1–100 km2; transect monitoring schemes generate time series of changes in abundance in sample populations of species on fixed sites across the UK; and occasional surveys measure the number, boundaries and size of all populations of a (usually RDB) species at intervals of 10–30 years. All schemes describe consistent patterns of change, but if they are to be more generally useful, it is important to understand how well butterflies are representative of other taxa. Comparisons with similarly measured changes in native bird and plant species suggest that butterflies have declined more rapidly that these other groups in Britain; it should soon be possible to test whether this pattern exists elsewhere. It is also demonstrated that extinction rates in British butterflies are similar to those in a range of other insect groups over 100 years once recording bias is accounted for, although probably lower than in aquatic or parasitic taxa. It is concluded that butterflies represent adequate indicators of change for many terrestrial insect groups, but recommended that similar schemes be extended to other popular groups, especially dragonflies, bumblebees, hoverflies and ants. Given institutional backing, similar projects could be employed internationally and standardized. Finally, a range of schemes designed to monitor change in communities of aquatic macro-invertebrates is described. Although designed to use invertebrates as a bio-indicator of water quality for human use, these programmes could be extended to monitor the 2010 biodiversity targets of the World Summit on Sustainable Development.
doi:10.1098/rstb.2004.1585
PMCID: PMC1569450  PMID: 15814349
biodiversity; extinction; habitat loss; climate change; 2010 World Summit on Sustainable Development
19.  Ethnobotanical survey of cooling herbal drinks from southern China 
Background
Liáng chá (“cooling tea”, “herbal tea” or “cool tisane” in Chinese) are herbal drinks widely produced in southern China and consumed by billions of people worldwide to prevent and treat internal heat as well as a range of associated health conditions. Globalization and renewed interest in botanical remedies has attracted growing attention in cooling herbal drinks by industry, scientists and consumers. However, there is a knowledge gap on the plant species used and commercialized for cooling herbal drinks in southern China and their associated ethnobotanical use, habitat and conservation status. This is the first study to document plant species used and commercialized as liáng chá in southern China’s Lingnan region and associated ethnomedical function, preparation methods, habitat and conservation status.
Methods
Three hundred market surveys were conducted between 2010-2012 in the largest herbal drink producing region of China to record plants used for liáng chá and to document knowledge on their medicinal function, habitat and conservation status. Product samples and voucher specimens were collected for taxonomic identification.
Results
All informants harvest and cultivate plants for preparing herbal drinks for their medicinal, cultural and economic values. A total of 222 ethnotaxa corresponded to 238 botanical taxa (species, varieties or subspecies) belonging to 86 families and 209 genera were recorded as liáng chá to treat health conditions in the study area. Recorded remedies consisted of one or several plant species to treat conditions classified into 27 major health conditions with clearing internal heat being the most common medicinal function. The habitat types of plants documented for use as liáng chá include 112 wild harvested species, 51 species that are either wild harvested or cultivated, 57 cultivated species, and 2 naturalized species. According to China’s Red List and CITES on conservation status, one of these species is endangered, one species is critically endangered, eight species are vulnerable, one is listed in CITES II, three are listed in Regional Red Data Book and the remaining 224 species are in the least concerned conservation category.
Conclusions
The liáng chá industry of southern China reflects the plant species richness and cultural diversity of the region. Future research on safety and efficacy of herbal drinks as well as ecological and cultural conservation efforts are needed for the sustainable growth of China’s botanical industry.
doi:10.1186/1746-4269-9-82
PMCID: PMC3926322  PMID: 24354903
liáng chá; Cooling tea; Ethnomedicine; Botanical industry
20.  The Likelihood of Extinction of Iconic and Dominant Herbivores and Detritivores of Coral Reefs: The Parrotfishes and Surgeonfishes 
PLoS ONE  2012;7(7):e39825.
Parrotfishes and surgeonfishes perform important functional roles in the dynamics of coral reef systems. This is a consequence of their varied feeding behaviors ranging from targeted consumption of living plant material (primarily surgeonfishes) to feeding on detrital aggregates that are either scraped from the reef surface or excavated from the deeper reef substratum (primarily parrotfishes). Increased fishing pressure and widespread habitat destruction have led to population declines for several species of these two groups. Species-specific data on global distribution, population status, life history characteristics, and major threats were compiled for each of the 179 known species of parrotfishes and surgeonfishes to determine the likelihood of extinction of each species under the Categories and Criteria of the IUCN Red List of Threatened Species. Due in part to the extensive distributions of most species and the life history traits exhibited in these two families, only three (1.7%) of the species are listed at an elevated risk of global extinction. The majority of the parrotfishes and surgeonfishes (86%) are listed as Least Concern, 10% are listed as Data Deficient and 1% are listed as Near Threatened. The risk of localized extinction, however, is higher in some areas, particularly in the Coral Triangle region. The relatively low proportion of species globally listed in threatened Categories is highly encouraging, and some conservation successes are attributed to concentrated conservation efforts. However, with the growing realization of man's profound impact on the planet, conservation actions such as improved marine reserve networks, more stringent fishing regulations, and continued monitoring of the population status at the species and community levels are imperative for the prevention of species loss in these groups of important and iconic coral reef fishes.
doi:10.1371/journal.pone.0039825
PMCID: PMC3394754  PMID: 22808066
21.  Rewilding the tropics, and other conservation translocations strategies in the tropical Asia-Pacific region 
Ecology and Evolution  2014;4(22):4380-4398.
Alarm over the prospects for survival of species in a rapidly changing world has encouraged discussion of translocation conservation strategies that move beyond the focus of ‘at-risk’ species. These approaches consider larger spatial and temporal scales than customary, with the aim of recreating functioning ecosystems through a combination of large-scale ecological restoration and species introductions. The term ‘rewilding’ has come to apply to this large-scale ecosystem restoration program. While reintroductions of species within their historical ranges have become standard conservation tools, introductions within known paleontological ranges—but outside historical ranges—are more controversial, as is the use of taxon substitutions for extinct species. Here, we consider possible conservation translocations for nine large-bodied taxa in tropical Asia-Pacific. We consider the entire spectrum of conservation translocation strategies as defined by the IUCN in addition to rewilding. The taxa considered are spread across diverse taxonomic and ecological spectra and all are listed as ‘endangered’ or ‘critically endangered’ by the IUCN in our region of study. They all have a written and fossil record that is sufficient to assess past changes in range, as well as ecological and environmental preferences, and the reasons for their decline, and they have all suffered massive range restrictions since the late Pleistocene. General principles, problems, and benefits of translocation strategies are reviewed as case studies. These allowed us to develop a conservation translocation matrix, with taxa scored for risk, benefit, and feasibility. Comparisons between taxa across this matrix indicated that orangutans, tapirs, Tasmanian devils, and perhaps tortoises are the most viable taxa for translocations. However, overall the case studies revealed a need for more data and research for all taxa, and their ecological and environmental needs. Rewilding the Asian-Pacific tropics remains a controversial conservation strategy, and would be difficult in what is largely a highly fragmented area geographically.
doi:10.1002/ece3.1287
PMCID: PMC4267875  PMID: 25540698
Australia; conservation; extinction; mammal; Pleistocene; Southeast Asia; tortoise
22.  Toward a DNA Taxonomy of Alpine Rhithrogena (Ephemeroptera: Heptageniidae) Using a Mixed Yule-Coalescent Analysis of Mitochondrial and Nuclear DNA 
PLoS ONE  2011;6(5):e19728.
Aquatic larvae of many Rhithrogena mayflies (Ephemeroptera) inhabit sensitive Alpine environments. A number of species are on the IUCN Red List and many recognized species have restricted distributions and are of conservation interest. Despite their ecological and conservation importance, ambiguous morphological differences among closely related species suggest that the current taxonomy may not accurately reflect the evolutionary diversity of the group. Here we examined the species status of nearly 50% of European Rhithrogena diversity using a widespread sampling scheme of Alpine species that included 22 type localities, general mixed Yule-coalescent (GMYC) model analysis of one standard mtDNA marker and one newly developed nDNA marker, and morphological identification where possible. Using sequences from 533 individuals from 144 sampling localities, we observed significant clustering of the mitochondrial (cox1) marker into 31 GMYC species. Twenty-one of these could be identified based on the presence of topotypes (expertly identified specimens from the species' type locality) or unambiguous morphology. These results strongly suggest the presence of both cryptic diversity and taxonomic oversplitting in Rhithrogena. Significant clustering was not detected with protein-coding nuclear PEPCK, although nine GMYC species were congruent with well supported terminal clusters of nDNA. Lack of greater congruence in the two data sets may be the result of incomplete sorting of ancestral polymorphism. Bayesian phylogenetic analyses of both gene regions recovered four of the six recognized Rhithrogena species groups in our samples as monophyletic. Future development of more nuclear markers would facilitate multi-locus analysis of unresolved, closely related species pairs. The DNA taxonomy developed here lays the groundwork for a future revision of the important but cryptic Rhithrogena genus in Europe.
doi:10.1371/journal.pone.0019728
PMCID: PMC3096624  PMID: 21611178
23.  A Biodiversity Indicators Dashboard: Addressing Challenges to Monitoring Progress towards the Aichi Biodiversity Targets Using Disaggregated Global Data 
PLoS ONE  2014;9(11):e112046.
Recognizing the imperiled status of biodiversity and its benefit to human well-being, the world's governments committed in 2010 to take effective and urgent action to halt biodiversity loss through the Convention on Biological Diversity's “Aichi Targets”. These targets, and many conservation programs, require monitoring to assess progress toward specific goals. However, comprehensive and easily understood information on biodiversity trends at appropriate spatial scales is often not available to the policy makers, managers, and scientists who require it. We surveyed conservation stakeholders in three geographically diverse regions of critical biodiversity concern (the Tropical Andes, the African Great Lakes, and the Greater Mekong) and found high demand for biodiversity indicator information but uneven availability. To begin to address this need, we present a biodiversity “dashboard” – a visualization of biodiversity indicators designed to enable tracking of biodiversity and conservation performance data in a clear, user-friendly format. This builds on previous, more conceptual, indicator work to create an operationalized online interface communicating multiple indicators at multiple spatial scales. We structured this dashboard around the Pressure-State-Response-Benefit framework, selecting four indicators to measure pressure on biodiversity (deforestation rate), state of species (Red List Index), conservation response (protection of key biodiversity areas), and benefits to human populations (freshwater provision). Disaggregating global data, we present dashboard maps and graphics for the three regions surveyed and their component countries. These visualizations provide charts showing regional and national trends and lay the foundation for a web-enabled, interactive biodiversity indicators dashboard. This new tool can help track progress toward the Aichi Targets, support national monitoring and reporting, and inform outcome-based policy-making for the protection of natural resources.
doi:10.1371/journal.pone.0112046
PMCID: PMC4237332  PMID: 25409183
24.  Ethnomedicinal and ecological status of plants in Garhwal Himalaya, India 
Background
The northern part of India harbours a great diversity of medicinal plants due to its distinct geography and ecological marginal conditions. The traditional medical systems of northern India are part of a time tested culture and honored still by people today. These traditional systems have been curing complex disease for more than 3,000 years. With rapidly growing demand for these medicinal plants, most of the plant populations have been depleted, indicating a lack of ecological knowledge among communities using the plants. Thus, an attempt was made in this study to focus on the ecological status of ethnomedicinal plants, to determine their availability in the growing sites, and to inform the communities about the sustainable exploitation of medicinal plants in the wild.
Methods
The ecological information regarding ethnomedicinal plants was collected in three different climatic regions (tropical, sub-tropical and temperate) for species composition in different forest layers. The ecological information was assessed using the quadrate sampling method. A total of 25 quadrats, 10 × 10 m were laid out at random in order to sample trees and shrubs, and 40 quadrats of 1 × 1 m for herbaceous plants. In each climatic region, three vegetation sites were selected for ecological information; the mean values of density, basal cover, and the importance value index from all sites of each region were used to interpret the final data. Ethnomedicinal uses were collected from informants of adjacent villages. About 10% of inhabitants (older, experienced men and women) were interviewed about their use of medicinal plants. A consensus analysis of medicinal plant use between the different populations was conducted.
Results
Across the different climatic regions a total of 57 species of plants were reported: 14 tree species, 10 shrub species, and 33 herb species. In the tropical and sub-tropical regions, Acacia catechu was the dominant tree while Ougeinia oojeinensis in the tropical region and Terminalia belerica in the sub-tropical region were least dominant reported. In the temperate region, Quercus leucotrichophora was the dominant tree and Pyrus pashia the least dominant tree. A total of 10 shrubs were recorded in all three regions: Adhatoda vasica was common species in the tropical and sub-tropical regions however, Rhus parviflora was common species in the sub-tropical and temperate regions. Among the 33 herbs, Sida cordifolia was dominant in the tropical and sub-tropical regions, while Barleria prionitis the least dominant in tropical and Phyllanthus amarus in the sub-tropical region. In temperate region, Vernonia anthelmintica was dominant and Imperata cylindrica least dominant. The consensus survey indicated that the inhabitants have a high level of agreement regarding the usages of single plant. The index value was high (1.0) for warts, vomiting, carminative, pain, boils and antiseptic uses, and lowest index value (0.33) was found for bronchitis.
Conclusion
The medicinal plants treated various ailments. These included diarrhea, dysentery, bronchitis, menstrual disorders, gonorrhea, pulmonary affections, migraines, leprosy. The ecological studies showed that the tree density and total basal cover increased from the tropical region to sub-tropical and temperate regions. The species composition changed with climatic conditions. Among the localities used for data collection in each climatic region, many had very poor vegetation cover. The herbaceous layer decreased with increasing altitude, which might be an indication that communities at higher elevations were harvesting more herbaceous medicinal plants, due to the lack of basic health care facilities. Therefore, special attention needs to be given to the conservation of medicinal plants in order to ensure their long-term availability to the local inhabitants. Data on the use of individual species of medicinal plants is needed to provide an in-depth assessment of the plants availability in order to design conservation strategies to protect individual species.
doi:10.1186/1746-4269-7-32
PMCID: PMC3212913  PMID: 22011477
25.  FBIS: A regional DNA barcode archival & analysis system for Indian fishes 
Bioinformation  2012;8(10):483-488.
DNA barcode is a new tool for taxon recognition and classification of biological organisms based on sequence of a fragment of mitochondrial gene, cytochrome c oxidase I (COI). In view of the growing importance of the fish DNA barcoding for species identification, molecular taxonomy and fish diversity conservation, we developed a Fish Barcode Information System (FBIS) for Indian fishes, which will serve as a regional DNA barcode archival and analysis system. The database presently contains 2334 sequence records of COI gene for 472 aquatic species belonging to 39 orders and 136 families, collected from available published data sources. Additionally, it contains information on phenotype, distribution and IUCN Red List status of fishes. The web version of FBIS was designed using MySQL, Perl and PHP under Linux operating platform to (a) store and manage the acquisition (b) analyze and explore DNA barcode records (c) identify species and estimate genetic divergence. FBIS has also been integrated with appropriate tools for retrieving and viewing information about the database statistics and taxonomy. It is expected that FBIS would be useful as a potent information system in fish molecular taxonomy, phylogeny and genomics.
Availability
The database is available for free at http://mail.nbfgr.res.in/fbis/
doi:10.6026/97320630008483
PMCID: PMC3374360  PMID: 22715304
Genetic Divergence; Fish; LAMP; Phylogeny; Phylogeography; Taxonomy

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