Barcoding life to conserve biological diversity: Beyond the taxonomic imperative

Barcoding scientists aspire to adhere to the objectives of the Convention on Biological Diversity by promoting conservation, sustainability, and the equitable sharing of benefits arising from use of genetic resources. (Image: Juan Manuel Escalante, wwww.realitat.com

A New Method for Species Identification via Protein-Coding and Non-Coding DNA Barcodes by Combining Machine Learning with Bioinformatic Methods

Species identification via DNA barcodes is contributing greatly to current bioinventory efforts. The initial, and widely accepted, proposal was to use the protein-coding cytochrome c oxidase subunit I (COI) region as the standard barcode for animals, but recently non-coding internal transcribed spacer (ITS) genes have been proposed as candidate barcodes for both animals and plants. However, achieving a robust alignment for non-coding regions can be problematic. Here we propose two new methods (DV-RBF and FJ-RBF) to address this issue for species assignment by both coding and non-coding sequences that take advantage of the power of machine learning and bioinformatics. We demonstrate the value of the new methods with four empirical datasets, two representing typical protein-coding COI barcode datasets (neotropical bats and marine fish) and two representing non-coding ITS barcodes (rust fungi and brown algae). Using two random sub-sampling approaches, we demonstrate that the new methods significantly outperformed existing Neighbor-joining (NJ) and Maximum likelihood (ML) methods for both coding and non-coding barcodes when there was complete species coverage in the reference dataset. The new methods also out-performed NJ and ML methods for non-coding sequences in circumstances of potentially incomplete species coverage, although then the NJ and ML methods performed slightly better than the new methods for protein-coding barcodes. A 100% success rate of species identification was achieved with the two new methods for 4,122 bat queries and 5,134 fish queries using COI barcodes, with 95% confidence intervals (CI) of 99.75–100%. The new methods also obtained a 96.29% success rate (95%CI: 91.62–98.40%) for 484 rust fungi queries and a 98.50% success rate (95%CI: 96.60–99.37%) for 1094 brown algae queries, both using ITS barcodes

International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database - the quality controlled standard tool for routine identification of human and animal pathogenic fungi

Human and animal fungal pathogens are a growing threat worldwide leading to emerging infections and creating new risks for established ones. There is a growing need for a rapid and accurate identification of pathogens to enable early diagnosis and targeted antifungal therapy. Morphological and biochemical identification methods are time-consuming and require trained experts. Alternatively, molecular methods, such as DNA barcoding, a powerful and easy tool for rapid monophasic identification, offer a practical approach for species identification and less demanding in terms of taxonomical expertise. However, its wide-spread use is still limited by a lack of quality-controlled reference databases and the evolving recognition and definition of new fungal species/complexes. An international consortium of medical mycology laboratories was formed aiming to establish a quality controlled ITS database under the umbrella of the ISHAM working group on "DNA barcoding of human and animal pathogenic fungi." A new database, containing 2800 ITS sequences representing 421 fungal species, providing the medical community with a freely accessible tool at http://www.isham.org and http://its.mycologylab.org/ to rapidly and reliably identify most agents of mycoses, was established. The generated sequences included in the new database were used to evaluate the variation and overall utility of the ITS region for the identification of pathogenic fungi at intra-and interspecies level. The average intraspecies variation ranged from 0 to 2.25%. This highlighted selected pathogenic fungal species, such as the dermatophytes and emerging yeast, for which additional molecular methods/genetic markers are required for their reliable identification from clinical and veterinary specimens.This study was supported by an National Health and Medical Research Council of Australia (NH&MRC) grant [#APP1031952] to W Meyer, S Chen, V Robert, and D Ellis; CNPq [350338/2000-0] and FAPERJ [E-26/103.157/2011] grants to RM Zancope-Oliveira; CNPq [308011/2010-4] and FAPESP [2007/08575-1] Fundacao de Amparo Pesquisa do Estado de So Paulo (FAPESP) grants to AL Colombo; PEst-OE/BIA/UI4050/2014 from Fundacao para a Ciencia e Tecnologia (FCT) to C Pais; the Belgian Science Policy Office (Belspo) to BCCM/IHEM; the MEXBOL program of CONACyT-Mexico, [ref. number: 1228961 to ML Taylor and [122481] to C Toriello; the Institut Pasteur and Institut de Veil le Sanitaire to F Dromer and D Garcia-Hermoso; and the grants from the Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq) and the Fundacao de Amparo a Pesquisa do Estado de Goias (FAPEG) to CM de Almeida Soares and JA Parente Rocha. I Arthur would like to thank G Cherian, A Higgins and the staff of the Molecular Diagnostics Laboratory, Division of Microbiology and Infectious Diseases, Path West, QEII Medial Centre. Dromer would like to thank for the technical help of the sequencing facility and specifically that of I, Diancourt, A-S Delannoy-Vieillard, J-M Thiberge (Genotyping of Pathogens and Public Health, Institut Pasteur). RM Zancope-Oliveira would like to thank the Genomic/DNA Sequencing Platform at Fundacao Oswaldo Cruz-PDTIS/FIOCRUZ [RPT01A], Brazil for the sequencing. B Robbertse and CL Schoch acknowledge support from the Intramural Research Program of the NIH, National Library of Medicine. T Sorrell's work is funded by the NH&MRC of Australia; she is a Sydney Medical School Foundation Fellow.info:eu-repo/semantics/publishedVersio

The next generation of natural history collections.

The last 50 years have witnessed rapid changes in the ways that natural history specimens are collected, preserved, analyzed, and documented. Those changes have produced unprecedented access to specimens, images, and data as well as impressive research results in organismal biology. The stage is now set for a new generation of collecting, preserving, analyzing, and integrating biological samples-a generation devoted to interdisciplinary research into complex biological interactions and processes. Next-generation collections may be essential for breakthrough research on the spread of infectious diseases, feeding Earth's growing population, adapting to climate change, and other grand research challenges. A decade-long investment in research collection infrastructure will be needed

Economic Analyses of Federal Scientific Collections: Methods for Documenting Costs and Benefits

Federal object-based scientific collections have been created to serve agency missions and, in a few cases, to comply with legislative and regulatory mandates. “Project collections” (those managed by the researchers who obtained them for restricted use) and their costs and benefits were considered too varied for standard methodologies that assess costs and benefits. In a few cases, departments and agencies are required by legislation or regulations to retain objects in long-term “institutional collections.” In most cases, decisions to retain objects are based on long-term costs relative to the perceived potential for benefits to taxpayers. Federal collections vary in their philosophies and practices of offsetting operating costs by charging users for access to their collections. Operational costs vary among institutional collections, reflecting differences in the size of collections, types of material they contain, and differences in the services they provide to the agency, extramural users, and society in general. This report describes six general services that federal institutional collections provide. Departments and agencies vary in the number of services they offer and the degree to which these services have been developed. Returns on investment are controlled, in large measure, by decisions about what is accessioned into a collection, policies concerning user fees and access, and the services provided by a collection. Those collections that offer only the basic service of accessioning objects have limited ability to generate benefits because few users will know about and have access to objects in the collection. By offering more services, collections broaden their potential use to: future generations (through proper maintenance and preservation), intramural research and by extramural users (through online documentation and user access programs), users in other disciplines (through data curation), and the general public (through education and outreach). The benefits generated by federal institutional collections can take many forms, both monetary and non-monetary. These benefits are usually indirect and delayed, and the value chains that connect costs to benefits are generally difficult to document. This report describes five methodologies (and their strengths and weaknesses) that are available to federal collections for describing and estimating the benefits they generate. Departments and agencies can use the methods described here for evidence-based decisions concerning policies and management practices for their institutional collections

Collecting event cascade.

<p>Holistic sampling and extended specimens begin with a more comprehensive collecting event that captures multiple specimens, samples, and data about event context. These begin a cascade of subsamples, preparations, and diverse data records that may be located in different collections, institutions, data repositories, and publications. All these descendants and associated derivative data are linked to the original collecting event and, as a result, to each other.</p

The role of natural history biorepositories in pathogen biology and mitigation.

<p>Host–parasite collections provide an exemplar of how museums can stimulate better coordination and participation in pathobiology across multiple institutions. Their roles range from sample providers to sample users (research) to informatics resources and contributing to the mitigation of public health crises. In this model, specimens are provided to natural history repositories by existing public health networks, fieldwork, and rural communities. Frozen and traditional collections become central to pathobiology research aimed at identifying pathogens, discovering zoonotic host associations, and delineating the potential spatial extent of the pathogen. Detailed questions about the pathogen ecology and evolutionary history can then be addressed to provide a framework for more effective public health response in increasingly dynamic environments. Relational web-accessible databases at museums facilitate complex linkages between all associated materials and allow careful tracking of all studies and their derived data (e.g., GenBank).</p

The role of biological collections in integrated pest management.

<p>The process of diagnosing an agricultural pest and then finding, testing, mass-producing, and releasing a control agent takes place in different settings and institutions. For the process to succeed, each participant in the process must be using the same host plants, pest species, and control agent species. Morphological and genetic comparisons with reference collections and databases can reveal the inadvertent introduction of look-alike or cryptic species into the process.</p