Tag: DNA

A primer in access and benefit-sharing for DNA barcoders

New open access book provides essential background for molecular biodiversity researchers on international policy regarding use and transfer of genetic materials

Molecular biology approaches, such as DNA barcoding, have become part of the standard toolkit for a growing number of biodiversity researchers and practitioners, with an increasing scope of applications in important areas, such as environmental assessment, food inspection, disease control and public education.

Globalization and the advent of bioinformatics are rapidly changing the landscape of international scientific collaborations, which now often span multiple jurisdictions and increase the volume of international data exchange and transactions of biological materials. At the same time, researchers engaging in such partnerships are often unaware of the complex policy frameworks governing such transactions, which may carry reputational and even legal liabilities.

The United Nations Convention on Biological Diversity (1992) and its supplementary agreement, the Nagoya Protocol (ratified in 2014), are the most prominent international treaties designed to provide a legal framework for ensuring the fair and equitable sharing of the benefits arising from research activities involving genetic resources. Although often challenging and, at times, frustrating, it is important for researchers to understand the ramifications of these international agreements, to ensure that their scientific reputations are not tainted with allegations of unfair or unethical practices.

The recent book by Canadian ABS consultant and advisor to Botanic Gardens Conservation International, Kate Davis, and University of Guelph, Canada, researcher and international development expert, Alex Borisenko, offers a perspective on the ramifications of the Convention and the Nagoya Protocol on molecular biodiversity research.

Titled ‘Introduction to Access and Benefit-Sharing and the Nagoya Protocol: What DNA Barcoding Researchers Need to Know‘, it is openly available from Pensoft as an advanced book or PDF document under Creative Commons License.

This contribution is specifically geared towards researchers and practitioners working in the field of DNA barcoding – an actively developing field of biology that advances molecular tools for fast, reliable identification and discovery of species by analyzing short standardized DNA fragments, known as ‘DNA barcode regions’.

This approach, lying at the interface between genomics and biodiversity science, is creating the global knowledge base needed to assess ecosystem services and detect emerging environmental threats, while addressing the imperative of preserving the world’s biodiversity. Carrying out this mission demands close partnerships between biodiversity researchers worldwide, and also relies on large molecular facilities to provide timely, cost-effective and high-quality analytical services, thereby involving active international transactions of biological materials.

Furthermore, the utility of DNA barcoding depends on active open data sharing in ways similar to those established by the medical community for human genomic information.

The book is prefaced by the Executive Secretary of the Convention on Biological Diversity, Dr. Cristiana Pa?ca Palmer. It provides a brief introduction to the Convention and the Nagoya Protocol, and reviews some of their key legal definitions (e.g., ‘genetic resources’, ‘access’, and ‘utilization’). These definitions are considered within the context of terms more familiar to researchers (e.g., tissue samples, DNA extracts, PCR products, trace files) and their daily activities (e.g., field collecting, molecular analysis, DNA sequence assembly).

The main chapters provide further insights into the structure and function of the access and benefit-sharing mechanism at the international policy level and its possible ramifications in form of national laws and institutional requirements.

The text concludes with a set of practical guidelines for researchers and practitioners on the steps that should be taken to ensure due diligence when working with internationally-sourced biological samples. Adhering to these best practices would help build trust and sustain research collegiality among partners involved in international collaboration.

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Original source:

Davis K, Borisenko A (2017) Introduction to Access and Benefit-Sharing and the Nagoya Protocol: What DNA Barcoding Researchers Need to Know. Advanced Books. https://doi.org/10.3897/ab.e22579

Origins of an enigmatic genus of Asian butterflies carrying mythological names decoded

A group of rare Asian butterflies which have once inspired an association with Hindu mythological creatures have been quite a chaos for the experts. In fact, their systematics turned out so confusing that in order to decode their taxonomic placement, scientists had to dig up their roots some 43 million years back.

Now, having shed new light on their ancestors, a team of researchers from the Biodiversity Institute of Ontario at University of Guelph, Agriculture and Agri-Food Canada and University of Vienna, published their findings in the open access journal Zoosystematics and Evolution.

CalinagaTogether, Drs. Valentina Todisco, Vazrick Nazari and Paul Hebert arrived at the conclusion that the enigmatic genus (Calinaga) originated in southeast Tibet in the Eocene as a result of the immense geological and environmental impact caused by the collision between the Indian and Asian subcontinents. However, the diversification within the lineage was far from over at that point. In the following epochs, the butterflies had to adapt to major changes when Indochina drifted away, leading to the isolation of numerous populations; and then again, when the Pleistocene climatic changes took their own toll.

To make their conclusions, the scientists studied 51 specimens collected from a wide range of localities spanning across India, South China, Laos, Vietnam, Myanmar and Thailand. For the first time for the genus, the authors conducted molecular data and combined it with an examination of both genitalia and wing patterns – distinct morphological characters in butterflies. While previous estimates had reported existence of anywhere between one and eleven species in the genus, the present study identified only four, while confirming how easy it is to mislabel samples based on earlier descriptions.

However, the researchers note that they have not sampled specimens from all species listed throughout the years under the name of the genus, so they need additional data to confirm the actual number of valid Calinaga species. The authors are to enrich this preliminary study in the near future, analysing both a larger dataset and type specimens in collaboration with the Natural History Museum of London that holds the largest Calinaga collection.

Despite being beautiful butterflies, the examined species belong to a genus whose name derives from the Hindu mythical reptilian creatures Nāga and a particular one of them – Kaliya, which is believed to live in Yamuna river, Uttar Pradesh, and is notorious for its poison. According to the Hindu myths, no sooner than Kaliya was confronted by the major deity Krishna, did it surrender.

“It seems that the modern taxonomy of Calinaga is in need of a Krishna to conquer these superfluous names and cleanse its taxonomy albeit after careful examination of the types and sequencing of additional material,” comment the authors.

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Original source:

Todisco V, Nazari V, Hebert PDN (2017) Preliminary molecular phylogeny and biogeography of the monobasic subfamily Calinaginae (Lepidoptera, Nymphalidae). Zoosystematics and Evolution 93(2): 255-264. https://doi.org/10.3897/zse.93.10744

Bush Blitz: The largest Australian nature discovery project finds 4 new bee species

Four new native bee species were recognised as part of the largest Australian nature discovery project, called ‘Bush Blitz‘. The South Australian bee specialists used molecular and morphological evidence to prove them as new. Three of the species had narrow heads and long mouth parts – adaptations to foraging on flowers of emu-bushes, which have narrow constrictions at the base. The new species are described in the open access journal ZooKeys.

Bees are important pollinators of crops and native plants, but habitat loss and pesticides are proved to be causing a serious decline in their populations in Europe and the United States of America. Meanwhile, the conservation status of native Australian bees is largely unknown because solid baseline data are unavailable and about one third of the species are as yet unknown to science. Furthermore, identification of Australian bees is hampered by a lack of keys for about half of the named species.

With their present publication, bee specialists Katja Hogendoorn (University of Adelaide), Remko Leijs and Mark Stevens (South Australian Museum) are now trying to make Australian native bees more accessible to the scientific community. The study introduces a new Barcoding of Life project, ‘AUSBS‘, which will be built to contain the barcode sequences of the identified Australian native bees.

In future, this database can help scientists who have molecular tools, but insufficient knowledge of bees, to identify known species. Yet, that is not the only use of the database. “Bee taxonomists can access and use the molecular information to answer specific problems, for example, how certain species are related or whether or not a male and female belong to the same species”, says Dr. Hogendoorn. “And combined with morphological information, the molecular database can help to identify new species”, she adds.

In their publication, the researchers demonstrate the utility of the database. After careful evaluation of the DNA sequence data and subsequent morphological comparison of the collected bees to museum type specimens, they recognised four new species in the genusEuhesma, which they subsequently described.

Three of the species belong to the group of bees that specialise on the flowers of emu-bushes. These bees have evolved narrow faces and very long mouth parts to collect the nectar through a narrow constriction at the base of the flowers. A similar evolution has been already observed in other groups of bees. The fourth species belongs to a different group within this large genus and has a normally shaped head.

So far, the project includes 271 sequences of 120 species that were collected during the Bush Blitz surveys, Australia’s largest nature discovery project. The researchers intend to build on the existing DNA database to cover as many as possible of the Australian species. “It is hoped that this will stimulate native bee research”, says Dr. Hogendoorn. “With about 750 Australian bee species still undescribed and many groups in need of revision there is an enormous job to do”, she concludes.

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Original source:

Hogendoorn K, Stevens M, Leijs R (2015) DNA barcoding of euryglossine bees and the description of new species of Euhesma Michener (Hymenoptera, Colletidae, Euryglossinae).ZooKeys 520: 41-59.doi: 10.3897/zookeys.520.6185

The four-letter code: How DNA barcoding can accelerate biodiversity inventories

With unprecedented biodiversity loss occurring, we must determine how many species we share the planet with. This can start in our backyards, but speed is critical. A new study shows how biodiversity inventories can be accelerated with DNA barcoding and rapid publishing techniques, making it possible to survey a nature reserve in just four months. The final inventory of 3,500 species was written, released and published in the Biodiversity Data Journal in under one week.

To assess how quickly and effectively DNA barcoding could aid in quantifying biodiversity on a massive scale, the Biodiversity Institute of Ontario partnered with the rare Charitable Research Reserve, a 365+ hectare land reserve located in Ontario, Canada, in an attempt to expand the reserve’s existing species inventory list. To complement this speed in surveying, the two partners also used cutting edge tools and venues for data release and publishing to rapidly disseminate the results.

Surveys of different habitats on the reserve were conducted over four months and culminated in a bioblitz, at which point delegates of the 6th International Barcode of Life Conference joined the effort. “These experts possess invaluable skills that enabled us to identify so many species,” Angela Telfer, University of Guelph, comments in hindsight. “It was a great chance to marry barcoding data with taxonomic data and further our efforts to build a DNA barcode reference library.”

The use of DNA barcoding to conduct this inventory greatly improved the speed at which the results were made available to the public. For the 3,502 specimens barcoded from the bioblitz, the data were generated at an impressive time scale – samples went through lysis, DNA extraction and PCR, sequencing and validation within 72 hours of their collection. Using the BOLD barcode reference library, taxonomy was applied and these results were uploaded to the Global Biodiversity Information Facility (GBIF) via Canadensys within 96 hours of their collection.

Even the choice of journal for publication contributed to the rapid process. The manuscript preparation and submission took considerably less time due to the online writing platform and pre-submission peer-review offered by the Biodiversity Data Journal, used for the first time in this survey. This allowed the 100+ co-authors of this study to all provide input, and reviewers were able to discuss and comment on the paper during the authoring process. All data are now publicly accessible, through the journal article and the various repositories above, and all specimens have been deposited in the Biodiversity Institute of Ontario’s natural history collection and herbarium.

Over the span of four months, the two-staged survey produced a total of 28,916 specimens barcoded or observed across 14 phyla, 29 classes, 117 orders, and 531 families of animals, plants, fungi and lichens. A total of 1,102 species were recorded for the first time for the nature reserve, expanding its existing inventory by 49%.

The results from this mass data collection uncovered abundant biodiversity in taxa that were previously understudied. For example, there were no previous records of spiders at the reserve, but the team’s efforts added an impressive 181 species to the inventory list, three of which were new to the province.

“The survey at rare Charitable Research Reserve is unique to other studies in that within four months – plus a single day of a concentrated bioblitz – more than 25,000 specimens and 3,500 species were recovered, often by non-experts,” explains Connor Warne, a co-author on the paper and specialist in ants. “This model of assessment has the potential to revolutionize the way we uncover diversity in our world. With a coordinated effort, we could implement this model in parks, conservation areas and reserves across the world and take a much needed step in filling in the blank pages of the story of life on earth.”

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Original source:

Telfer A, Young M, Quinn J, Perez K, Sobel C, Sones J, Levesque-Beaudin V, Derbyshire R, Fernandez-Triana J, Rougerie R, Thevanayagam A, Boskovic A, Borisenko A, Cadel A, Brown A, Pages A, Castillo A, Nicolai A, Glenn Mockford B, Bukowski B, Wilson B, Trojahn B, Lacroix C, Brimblecombe C, Hay C, Ho C, Steinke C, Warne C, Garrido Cortes C, Engelking D, Wright D, Lijtmaer D, Gascoigne D, Hernandez Martich D, Morningstar D, Neumann D, Steinke D, Marco DeBruin D, Dobias D, Sears E, Richard E, Damstra E, Zakharov E, Laberge F, Collins G, Blagoev G, Grainge G, Ansell G, Meredith G, Hogg I, McKeown J, Topan J, Bracey J, Guenther J, Sills-Gilligan J, Addesi J, Persi J, Layton K, D’Souza K, Dorji K, Grundy K, Nghidinwa K, Ronnenberg K, Lee K, Xie L, Lu L, Penev L, Gonzalez M, Rosati M, Kekkonen M, Kuzmina M, Iskandar M, Mutanen M, Fatahi M, Pentinsaari M, Bauman M, Nikolova N, Ivanova N, Jones N, Weerasuriya N, Monkhouse N, Lavinia P, Jannetta P, Hanisch P, McMullin R, Ojeda Flores R, Mouttet R, Vender R, Labbee R, Forsyth R, Lauder R, Dickson R, Kroft R, Miller S, MacDonald S, Panthi S, Pedersen S, Sobek-Swant S, Naik S, Lipinskaya T, Eagalle T, Decaëns T, Kosuth T, Braukmann T, Woodcock T, Roslin T, Zammit T, Campbell V, Dinca V, Peneva V, Hebert P, deWaard J (2015) Biodiversity inventories in high gear: DNA barcoding facilitates a rapid biotic survey of a temperate nature reserve. Biodiversity Data Journal 3: e6313. doi: 10.3897/BDJ.3.e6313