Is the painted frog Discoglossus pictus a declining species in Italy? On the reliability of a distributional atlas approach

Peru hosts a rich amphibian fauna with approximately 571 species described to date. Many of these species have been formally described only recently, and many more remain to be discovered and recognized. Despite the increase in the number of known species, some reports indicate recent, and in some cases enigmatic, loss of species richness at several sites in the Peruvian Andes. Similar population declines have been observed in neighboring Andean countries. The pathogenic fungus Batrachochytrium dendrobatidis is associated with some of these declines, and we include a timeline of records of this pathogen in Peruvian amphibians. However, the paucity of standardized, long-term surveys limits our ability to understand the causes of declines and to assess the conservation status of Peruvian amphibians. Here we provide updated information on the conservation status of amphibians in Peru, and we discuss the possible causes of the observed declines. Furthermore, we discuss present and future threats to amphibian biodiversity, and we outline actions needed to promote the survival of this globally endangered group. We include a list of candidate sites for long-term surveys.

Some interior areas of Sindh are poorly studied previously which are considered as main sites for present investigation. For the study of ignored amphibian fauna, we conducted a survey to observe the environmental condition of amphibian habitats. The physical characteristics of habitat such as types of vegetation and presence of predators were observed, while water samples were collected from all aquatic habitats for analysis of parameters i.e. pH, electric conductivity, total dissolved solids, total hardness, chloride, sulphate, phosphate, nitrite and nitrate as well as carbon dioxide. All the habitats were analyzed thoroughly and designated as highly contaminated and unfavorable especially for spawns and larvae and their conservation status was found entirely deteriorated, though abundance of vegetation was observed alongwith availability of potential predators.

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The Sierra Madre del Sur (SMS) is a biologically diverse biogeographic province found in south-central Mexico. It is therefore an area of interest from a conservation standpoint. Here we examine the diversity and conservation status of the amphibians and reptiles of the SMS and its subprovinces and determine their similarity with neighboring provinces. We compiled a list of the species of amphibians and reptiles occurring in the SMS and its neighboring provinces from the available literature and gathered information on their conservation status. We also compiled the herpetofauna of the three subprovinces of the SMS (Western, Central, and Eastern). The SMS houses 186 species of amphibians, of which 89% are endemic to Mexico and 53% endemic to the SMS. The SMS also contains 331 reptile species, of which 72% are endemic to Mexico and 23% are endemic to the SMS. The amphibian and reptile diversity of the SMS is concentrated in the Eastern subprovince. The significant number of amphibian and reptile species endemic to the SMS highlights its importance for conservation. Comparison with neighboring provinces shows that the SMS shares 33% of its species with the Transvolcanic Belt, 25% with the Pacific Lowlands and Balsas Basin, and 19% with Veracruzan. The SMS shares 52% of its reptile species with the Transvolcanic Belt, 42% with the Pacific Lowlands, 40% with the Balsas Basin, and 33% with the Veracruzan. The results of a cluster analyses suggest that the SMS does not represent a single unit in terms of its herpetofauna, since the three subprovinces do not cluster together. The Western and Central subprovinces cluster with the Balsas Basin and the Pacific Lowlands, whereas the Eastern subprovince clusters separately. We found that 25.7% of the evaluated amphibian and reptile species in the SMS are included in the International Union for Conservation of Nature’s (IUCN) Red List in some category of conservation concern (amphibians: 54.9%; reptiles: 6.8%). The Eastern subprovince hosts the highest proportion of species of conservation concern (93.8%). It is important to increase the number of areas protected by federal and state governments, especially in the Eastern subprovince, and to promote protections driven by local communities. These actions could help protect the herpetofauna of the SMS, especially the Eastern subprovince, which harbors a unique fauna and deserves special consideration from a conservation standpoint.

Monitoring of habitat types conservation status is an essential task in the frame of the European policy for biodiversity conservation. The parameters to be assessed for the purposes of habitat types’ conservation status assessment are described in several European documents, but the methodology for their determination has not yet been standardized or optimized. This study presents methods for the assessment of the actual status and the future prospects of structure and functions of habitat types. Specifically, it presents a bottom–up approach for the assessment of these two parameters at different spatial scales. In the proposed method, conservation status assessment is based on a classification of habitat types to subtypes, with the latter representing the basic monitoring entities. The conservation status is assessed by recording: (i) the presence/absence of specific indicators of structure and functions per habitat type, and (ii) the presence/absence, abundance, and vitality of the typical species of the habitat subtypes. The typical species are determined objectively using algorithms and fidelity coefficient values. The conservation status and future prospects of structure and functions (including the typical species) are estimated quantitatively with the help of numerical methods and algorithms, but their assignment to conservation status classes is based on thresholds defined by experts. Assessments are made at the local scale, but can be upscaled to coarser ones (up to the national level). The proposed methods have been applied in Greece and were effective both in terms of results obtained and costs needed.

Lipidomics is a younger member of the "omics" family. It aims to profile lipidome alterations occurring in biological systems. Similar to the other "omics", lipidomic data is highly dimensional and contains a massive amount of information awaiting deciphering and data mining. Currently, the available bioinformatic tools targeting lipidomic data processing and lipid pathway analysis are limited. A few tools designed for lipidomic analysis perform only basic statistical analyses, and lipid pathway analyses rely heavily on public databases (KEGG, Reactome, and HMDB). Due to the inadequate understanding of lipid signaling and metabolism, the use of public databases for lipid pathway analysis can be biased and misleading. Instead of using public databases to interpret lipidomic ontology, the authors introduce an intra-omic integrative correlation strategy for lipidomic data mining. Such an intra-omic strategy allows researchers to unscramble and predict lipid biological functions from correlated genomic ontological results using statistical approaches. To simplify and improve the lipidomic data processing experience, they designed an interactive web-based tool: LINT-web (http://www.lintwebomics.info/) to perform the intra-omic analysis strategy, and validated the functions of LINT-web using two biological systems. Users without sophisticated statistical experience can easily process lipidomic datasets and predict the potential lipid biological functions using LINT-web.

Conservation status and threat assessments evaluate species’ relative risks of extinction globally, regionally, nationally, or locally and estimate the degree to which populations of species are already safeguarded in existing conservation systems, with the aim of exposing the critical gaps in current conservation. Results of the assessments can therefore aid in directing limited conservation resources to the species and populations that are most at-risk. This chapter introduces the roles of conservation status and threat assessments in informing conservation priorities for crop wild relatives in North America and provides an overview of the current results for US taxa. Methods to assess the conservation status and to perform threat assessments for North American crop wild relatives are well developed via NatureServe and the International Union for Conservation of Nature (IUCN) Red List, and the essential infrastructure to perform these analyses is present, at least in Canada and the US. Current conservation assessments for North American wild relatives need updating but already reveal a landscape of multiple complex threats and major gaps in the ex situ and in situ conservation of prioritized species. Further resources and concerted efforts are needed to update conservation assessments and then to use the results to inform efforts to fill the critical gaps in conservation.

ESR Endangered Species Research Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials ESR 14:61-68 (2011) - DOI: https://doi.org/10.3354/esr00345 Rediscovery, conservation status and taxonomic assessment of Melicope degeneri (Rutaceae), Kaua‘i, Hawai‘i Kenneth R. Wood* National Tropical Botanical Garden, Kala–heo, Hawai‘i 96741, USA *Email: kwood@ntbg.org ABSTRACT: Melicope degeneri (B. Stone) T. Hartley & B. Stone is endemic to the island of Kaua‘i and is one of Hawai‘i’s rare members of the Rutaceae. Rediscovered in 1993 after not being documented for 67 yr, it is currently known from only 22 individuals. Data concerning its morphology, distribution, and ecological preferences are presented in this paper in order to contribute to the Global Strategy for Plant Conservation (GSPC) goals and to assist biologists and land managers in monitoring and protecting this species from extinction. A formal IUCN assessment of the species has been completed and is reported here as Critically Endangered (CR B2ab(iii,v); D). KEY WORDS: Melicope degeneri · Rutaceae · Hawaiian Islands · Prevention of extinction · Distribution · Ecological preferences · IUCN Red List Category · Critically Endangered Full text in pdf format PreviousNextCite this article as: Wood KR (2011) Rediscovery, conservation status and taxonomic assessment of Melicope degeneri (Rutaceae), Kaua‘i, Hawai‘i. Endang Species Res 14:61-68. https://doi.org/10.3354/esr00345 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in ESR Vol. 14, No. 1. Online publication date: May 06, 2011 Print ISSN: 1863-5407; Online ISSN: 1613-4796 Copyright © 2011 Inter-Research.

South America is considered a world biodiversity hotspot, especially for freshwater ecosystems where there is significant biodiversity and endemism across different taxonomic groups. Native South American crayfishes are characterized by small range distributions, high levels of endemism and specific habitat requirements.Although this group may be considered one of the most threatened among South American freshwater crustaceans, IUCN Red List assessments for most of these species are ‘data deficient’. IUCN assessments are technical evaluations of species risk of extinction based on biological indicators of population features, thereby providing a ‘conservation status’ for each species based on common and international standards.Attempts to assess the conservation status of native South American crayfishes have been limited mainly owing to a lack of fundamental data and also misinterpretations of present information. Thus, a revision of the state of knowledge of native South American crayfishes (taxonomy, phylogeny and distribution, genetics, ecology and threats) was carried out coupled with IUCN assessments of conservation status.Globally, the lack of information on the biology of these species is still the major obstacle to making reliable conservation status assessments. For this reason, the Data Deficient (DD) category is still appropriate for many species. However, based on the Extent of Occurrence (EOO) and severely fragmented populations, number of locations and decline in area, extent or quality of habitat, it is recommended that some species (especiallyVirilastacusspp.) should be moved to threatened categories (VU, EN or CR). The data suggest that others are appropriately in the Near Threatened (NT) category, because they almost reach the thresholds for threatened categories.The assessment of conservation status is essential to support future conservation actions, especially for species allocated to threatened categories. This study has identified new species under threat and also areas for future study to provide relevant data for conservation assessment for ‘data deficient’ species.Copyright © 2014 John Wiley & Sons, Ltd.

Planning the future of plant systematics: Report on a special colloquium at the Royal Netherlands Academy of Arts and Sciences.

Errors in the interpretation of copy number variations due to the use of public databases as a reference

In spite of the increasing importance of information technology, there are several example of failures. Systems are built with unrealistic assumptions about individual and organizational behavior. Public databases are important mediators of information. We use a media metaphor for databases to derive a model where we can identify a series of conditions for the well-functioning of public databases. These conditions are not easily met in practical work with such databases. One should therefore be careful with ambitions regarding the design, use and impact of information technology.

To explore a noninvasive method for diagnosis of SEA-thalassemia and to investigate whether the regional factors affect the accuracy of this method. The method involved using a public database and bioinformatics software to construct parental haplotypes for proband and predicting fetal genotypes using relative haplotype dosage. We screened and downloaded sequencing data of couples who were both SEA-thalassemia carriers from the China National Genebank public data platform, and matched the sequencing data format with that of the reference panel using Ubuntu system tools. We then used Beagle software to construct parental haplotypes, predicted fetal haplotypes by relative haplotype dosage. Finally, we used Hidden Markov Model and Viterbi algorithm to determine fetal pathogenic haplotypes. All noninvasive fetal genotype diagnosis results were compared with gold standard gap-PCR electrophoresis results. Our method was successful in diagnosing 13 families with SEA-thalassemia carriers. The best diagnostic results were obtained when Southern Chinese Han was used as the reference panel, and 10 families showed full agreement between our noninvasive diagnostic results and the gap-PCR electrophoresis results. The accuracy of our method was higher when using a Chinese Han as the reference panel for haplotype construction in the Southern Chinese Han region as opposed to Beijing Chinese region. The combined use of public databases and relative haplotype dosage for diagnosing SEA-thalassemia is a feasible approach. Our method produces the best noninvasive diagnostic results when the test samples and population reference panel are closely matched in both ethnicity and geography. When constructing parental haplotypes with our method, it is important to consider the effect of region in addition to population background alone.

Even in Europe, where database rights(Sui Generis Database Rights) were first created, questions about the utility of these rights have been raised and discussions for revision is going on. We, who benchmarked these European cases at the time, also need to pay attention to the changes in EU. Therefore, in this study, the problems of the database rights were analyzed and future improvement tasks were derived. The results of the s tudy a re a s follows. First, the EU is changing the criteria for judging database rights infringement through the CJEU decision. In order to accommodate the innovation of data, the creation of added value through reuse of users and competitors and the possibility of innovation are accepted as the criteria for judging infringement. We also need to take this into account in our “significant investment” and “determination of infringement”. Second, it is necessary to think about the extension of the exception range of the database right. In Europe, through a separate legislative measure called the Data Act, a wide range of exceptions are being allowed by excluding the database right for databases acquired or created by the use of products or services. This is premised on the premise that the establishment and utilization of databases in various artificial intelligence services, including IoT, is essential anyway, so there is no need to induce investment by guaranteeing sui generis rights. As such, in certain cases, it is necessary to review the introduction of regulations that restrict database rights. Third, like public works, free use of public databases needs to be introduced. Public databases are already trying to create added value through private use through other individual laws. In addition, it is questionable whether the criteria for judging infringement, such as ‘significant investment’ and ‘risk of recovery of investment’, can be applied to the act of creating a database funded by the state finances. Therefore, it is necessary to review the introduction of database rights restrictions on public works.

BackgroundThe pathogenicity of many Mendelian variants has been challenged by large-scale sequencing efforts. However, many rare and benign “disease mutations” are difficult to analyze due to their rarity. The Saudi Arabian variome is enriched for homozygosity due to inbreeding, a key advantage that can be exploited for the critical examination of previously published variants.ResultsWe collated all “disease-related mutations” listed in the Human Gene Mutation Database (HGMD) and ClinVar, including “variants of uncertain significance” (VOUS). We find that the use of public databases including 1000 Genomes, ExAC, and Kaviar can reclassify many of these variants as likely benign. Our Saudi Human Genome Program (SHGP) can reclassify many variants that are rare in public databases. Furthermore, SGPD allows us to observe many previously reported variants in the homozygous state and our extensive phenotyping of participants makes it possible to demonstrate the lack of phenotype for these variants, thus challenging their pathogenicity despite their rarity. We also find that 18 VOUS BRCA1 and BRCA2 variants that are listed in BRCA Exchange are present at least once in the homozygous state in patients who lack features of Fanconi anemia. Reassuringly, we could reciprocally demonstrate that none of those labeled as “pathogenic” were observed in the homozygous statue in individuals who lack Fanconi phenotype in our database.ConclusionOur study shows the importance of revisiting disease-related databases using public resources as well as of population-specific resources to improve the specificity of the morbid genome of Mendelian diseases in humans.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1102-1) contains supplementary material, which is available to authorized users.