Unraveling the rapid radiation of crested newts, Triturus cristatus superspecies, using complete mitogenomic sequences

Background - The rapid radiation of crested newts (Triturus cristatus superspecies) comprises four morphotypes: 1) the T. karelinii group, 2) T. carnifex - T. macedonicus, 3) T. cristatus and 4) T. dobrogicus. These vary in body build and the number of rib-bearing pre-sacral vertebrae (NRBV). The phylogenetic relationships of the morphotypes have not yet been settled, despite several previous attempts, employing a variety of molecular markers. We here resolve the crested newt phylogeny by using complete mitochondrial genome sequences. Results - Bayesian inference based on the mitogenomic data yields a fully bifurcating, significantly supported tree, though Maximum Likelihood inference yields low support values. The internal branches connecting the morphotypes are short relative to the terminal branches. Seen from the root of Triturus (NRBV = 13), a basal dichotomy separates the T. karelinii group (NRBV = 13) from the remaining crested newts. The next split divides the latter assortment into T. carnifex - T. macedonicus (NRBV = 14) versus T. cristatus (NRBV = 15) and T. dobrogicus (NRBV = 16 or 17). Conclusions - We argue that the Bayesian full mitochondrial DNA phylogeny is superior to previous attempts aiming to recover the crested newt species tree. Furthermore, our new phylogeny involves a maximally parsimonious interpretation of NRBV evolution. Calibrating the phylogeny allows us to evaluate potential drivers for crested newt cladogenesis. The split between the T. karelinii group and the three other morphotypes, at ca. 10.4 Ma, is associated with the separation of the Balkan and Anatolian landmasses (12-9 Ma). No currently known vicariant events can be ascribed to the other two splits, first at ca. 9.3 Ma, separating T. carnifex - T. macedonicus, and second at ca. 8.8 Ma, splitting T. cristatus and T. dobrogicus. The crested newt morphotypes differ in the duration of their annual aquatic period. We speculate on the role that this ecological differentiation could have played during speciatio

Non-native Amphibian Pet Trade via Internet in Poland

Overharvesting and trade in amphibian populations is one of the causes of their global decline. Online trade not only encourages the exploitation of an increasing number of rare and endangered amphibian species from all over the world but also influences the spread of invasive species. The aim of our research was to investigate the amphibian pet trade conducted in online stores and portals in Poland and determine its potential impact on native species. Between November 2013 and October 2014, we regularly (on a monthly basis) checked sale offers on the websites of the 18 biggest pet shops in the country specialised in exotic animals, on a nationwide auction portal and on three exotic pet fan portals. During the study, we reported 486 offers of 112 amphibian species in online stores and on portals. Most of the offers involved one of the four families of amphibians: poison dart frogs (Dendrobatidae), tree frogs (Hylidae), true toads (Bufonidae) and true salamanders (Salamandridae). Our data show increased interest in amphibians as pets in Poland. At least half of the offered species are possible hosts for the chytrid fungus Batrachochytrium dendrobatidis. However, only one species, the American bullfrog Lithobates catesbeianus (Shaw, 1802), appears to be a potential invasive species. To summarise, the species offered in Poland that are characterised as threatened are predominantly those that are relatively easy to breed and that are popular as pets. Further studies are required to investigate the real threat to wild amphibian populations caused by the pet trade

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

The SWISS-PROT protein knowledgebase (http://www.expasy.org/sprot/ and http://www.ebi.ac.uk/swissprot/) connects amino acid sequences with the current knowledge in the Life Sciences. Each protein entry provides an interdisciplinary overview of relevant information by bringing together experimental results, computed features and sometimes even contradictory conclusions. Detailed expertise that goes beyond the scope of SWISS-PROT is made available via direct links to specialised databases. SWISS-PROT provides annotated entries for all species, but concentrates on the annotation of entries from human (the HPI project) and other model organisms to ensure the presence of high quality annotation for representative members of all protein families. Part of the annotation can be transferred to other family members, as is already done for microbes by the High-quality Automated and Manual Annotation of microbial Proteomes (HAMAP) project. Protein families and groups of proteins are regularly reviewed to keep up with current scientific findings. Complementarily, TrEMBL strives to comprise all protein sequences that are not yet represented in SWISS-PROT, by incorporating a perpetually increasing level of mostly automated annotation. Researchers are welcome to contribute their knowledge to the scientific community by submitting relevant findings to SWISS-PROT at [email protected]

An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ(TM)

BACKGROUND: Proteomics continues to play a critical role in post-genomic science as continued advances in mass spectrometry and analytical chemistry support the separation and identification of increasing numbers of peptides and proteins from their characteristic mass spectra. In order to facilitate the sharing of this data, various standard formats have been, and continue to be, developed. Still not fully mature however, these are not yet able to cope with the increasing number of quantitative proteomic technologies that are being developed. RESULTS: We propose an extension to the PRIDE and mzData XML schema to accommodate the concept of multiple samples per experiment, and in addition, capture the intensities of the iTRAQ(TM )reporter ions in the entry. A simple Java-client has been developed to capture and convert the raw data from common spectral file formats, which also uses a third-party open source tool for the generation of iTRAQ(TM) reported intensities from Mascot output, into a valid PRIDE XML entry. CONCLUSION: We describe an extension to the PRIDE and mzData schemas to enable the capture of quantitative data. Currently this is limited to iTRAQ(TM) data but is readily extensible for other quantitative proteomic technologies. Furthermore, a software tool has been developed which enables conversion from various mass spectrum file formats and corresponding Mascot peptide identifications to PRIDE formatted XML. The tool represents a simple approach to preparing quantitative and qualitative data for submission to repositories such as PRIDE, which is necessary to facilitate data deposition and sharing in public domain database. The software is freely available from

PRIDE: new developments and new datasets

The PRIDE (http://www.ebi.ac.uk/pride) database of protein and peptide identifications was previously described in the NAR Database Special Edition in 2006. Since this publication, the volume of public data in the PRIDE relational database has increased by more than an order of magnitude. Several significant public datasets have been added, including identifications and processed mass spectra generated by the HUPO Brain Proteome Project and the HUPO Liver Proteome Project. The PRIDE software development team has made several significant changes and additions to the user interface and tool set associated with PRIDE. The focus of these changes has been to facilitate the submission process and to improve the mechanisms by which PRIDE can be queried. The PRIDE team has developed a Microsoft Excel workbook that allows the required data to be collated in a series of relatively simple spreadsheets, with automatic generation of PRIDE XML at the end of the process. The ability to query PRIDE has been augmented by the addition of a BioMart interface allowing complex queries to be constructed. Collaboration with groups outside the EBI has been fruitful in extending PRIDE, including an approach to encode iTRAQ quantitative data in PRIDE XML

PRIDE: a public repository of protein and peptide identifications for the proteomics community

PRIDE, the ‘PRoteomics IDEntifications database’ () is a database of protein and peptide identifications that have been described in the scientific literature. These identifications will typically be from specific species, tissues and sub-cellular locations, perhaps under specific disease conditions. Any post-translational modifications that have been identified on individual peptides can be described. These identifications may be annotated with supporting mass spectra. At the time of writing, PRIDE includes the full set of identifications as submitted by individual laboratories participating in the HUPO Plasma Proteome Project and a profile of the human platelet proteome submitted by the University of Ghent in Belgium. By late 2005 PRIDE is expected to contain the identifications and spectra generated by the HUPO Brain Proteome Project. Proteomics laboratories are encouraged to submit their identifications and spectra to PRIDE to support their manuscript submissions to proteomics journals. Data can be submitted in PRIDE XML format if identifications are included or mzData format if the submitter is depositing mass spectra without identifications. PRIDE is a web application, so submission, searching and data retrieval can all be performed using an internet browser. PRIDE can be searched by experiment accession number, protein accession number, literature reference and sample parameters including species, tissue, sub-cellular location and disease state. Data can be retrieved as machine-readable PRIDE or mzData XML (the latter for mass spectra without identifications), or as human-readable HTML

Evaluation of DNA barcode libraries used in the UK and developing an action plan to fill priority gaps

There are approximately 76,000 eukaryote species recognised in the UK, and while we know some of them in great detail, the majority of these species are poorly known, and hundreds of new species are discovered each year. DNA barcoding uses a short, standardised segment of an organism’s genome for identification by comparison to a reference library; however, the UK lags behind several countries in Europe and North America in that we lack trusted, reliable and openly accessible reference sequences for key UK taxa. This report is the first step in rectifying this by engaging diverse stakeholders to facilitate collaboration and coordination; providing robust stakeholder-based and independent assessment of the current state of reference libraries available for all known UK taxa; and prioritising key taxa. A survey was developed and shared with the UK research and end user community, receiving 80 responses from a wide range of stakeholders and covering the focal taxa / assemblages and habitats; the DNA reference libraries in use, their quality assurance and perceived coverage. A formal gap analysis of the public DNA data in major DNA reference libraries highlighted that an estimated 52% of UK species have publicly available DNA data of some sort; however, coverage in gene specific reference libraries varies greatly (eg 2 – 52%), as does the associated quality assurance. Priority taxa highlighted by end users had coverage in reference libraries ranging from almost complete, in the case of known invasive non-native species, to significant coverage (71%) for taxa with conservation designations. However, these data also vary by kingdom and reference library, as does the associated quality assurance. If taking a strict requirement of DNA data provided by UK specimens and held in UK repositories, for robust QC and QA, then the proportion of UK species with public DNA data in reference libraries falls to less than 4% in the largest reference library assessed (BOLD). While standard genes for DNA-based identification have essentially been established, more work is required to establish the priority taxa required for regulatory delivery in contrast to taxa that are surveyed in a non-regulatory framework. Several barriers to the development of barcode libraries were highlighted, the most relevant being sustained large scale funding, expertise, capacity, laboratory skills and equipment, quality control and assurance, collecting logistics (eg permits and access) and communication. Significant opportunities identified include a large network of interested experts, several organisations with significant delivery capabilities, current large-scale projects and funding opportunities, emerging technologies and the economy of scale for DNA sequencing. Following a stakeholder workshop, we have outlined a concise action plan to provide reliable, open access reference sequences, linked to open access vouchers, identified by known experts, to facilitate UK academic and regulatory aims.This report is published by Natural England under the Open Government Licence - OGLv3.0 for public sector information. You are encouraged to use, and reuse, information subject to certain conditions. For details of the licence visit Copyright. Natural England photographs are only available for non-commercial purposes. If any other information such as maps or data cannot be used commercially this will be made clear within the report. ISBN 978-1-78354-671-8 © Natural England and other parties 2020 © Trustees of the Natural History Museum, Londo