ABOL BioBlitz: DNA barcoding safeguards taxonomic knowledge

ABOL BioBlitz: DNA barcoding safeguards taxonomic knowledge

ABOL BioBlitz: DNA barcoding safeguards taxonomic knowledge

The Austrian Barcode of Life (ABOL) initiative uses DNA barcoding to safeguard and make publicly accessible rare knowledge on biodiversity generated in the course of local BioBlitz events
Local fisher presents catch of the day from lake Millstatt PHOTO CREDIT: Susanne Glatz-Jorde, Biosphere Reserve Nockberge

A BioBlitz is an event organized to survey the biodiversity of a designated area as fast and as comprehensively as possible1. Along with the general public, taxonomic experts from various fields, whether laymen or academics, swarm a location to record every identifiable species, usually within 24 hours.

The primary goal of these events is to increase bioliteracy—awareness of biodiversity and its importance for healthy, functioning ecosystems. We believe increased bioliteracy could transform societal perceptions of nature and, ultimately, humanity’s relationship with other species. Consequently, we deem it a prerequisite in our arsenal to abate the dramatic loss of biodiversity2. Additionally, the BioBlitz approach is becoming increasingly important for conservation efforts as it generates high-quality biodiversity data while simultaneously enhancing research capacity3.

In 2019, the Austrian Barcode of Life Initiative (ABOL) successfully introduced a new extended BioBlitz format to Austria—the ABOL BioBlitz—which combines existing collecting events with DNA barcoding. The organisms acquired and identified by experts during BioBlitz events are subsequently DNA barcoded. Importantly, specimens are photographed and stored in a scientific collection along with their associated metadata to be fully compliant with DNA barcoding standards for reference sequences.

The Great Lakes

Locations of the ‘Days of Biodiversity’ 2019 in Austria. The logos represent the organizing institutions.

Base map from d-maps.com

Although running for the first time, the ABOL BioBlitz efforts were very well received and highly successful. From 2000 individuals comprising 1400 taxa, approximately 1500 DNA barcodes were obtained and these data are now available on BOLD.

The number of individuals per higher taxon provided for DNA barcode analysis in the course of the ABOL BioBlitzes 2019. Sites indicated by colours.

Images from ClipArt ETC

In 2019, ABOL joined six ‘Days of Biodiversity’ with ABOL BioBlitzes in five different federal states of Austria. These events covered very different habitat types, from an organic farmstead in Upper Austria, a valley in the mountainous area in Tyrol, to annually organized events in protected areas like National Park Hohe Tauern or the Biosphere Reserves of Nockberge and Wienerwald. It is important to note that these events are only possible with the generosity and cooperation of the institutional hosts to whom we wish to extend our deepest thanks.

In total 54 taxonomic experts joined our efforts at these events. They not only provided us with samples from their collected material, along with the respective metadata and photos, but they also prepared reference individuals and assured their appropriate storage in public collections. After receiving samples from the experts, the ABOL team transferred tissue into microplates and shipped them to the Canadian Centre for DNA Barcoding (CCDB) in Canada for barcode analysis. We thank all the experts for their incredible efforts as well as staff at the CCDB for their obligingness and cooperation.

Day of Nature in the Biosphere Reserve Nockberge

The 4th Day of Nature named ‘Shores and mountain slopes of Lake Millstatt in Carinthia’ in the Biosphere Reserve Nockberge contributed substantially to the species inventory of the Carinthian part of the Biosphere Reserve. 45 taxonomic experts recorded 1166 species, some rare while others new records for the Biosphere Reserve Nockberge and for Carinthia. The event was organized by the team at the Biosphere Reserve, together with two ecological agencies, Ökoteam and E.C.O.

IMAGE: Local fisher presents catch of the day from lake Millstatt
CREDIT: Susanne Glatz-Jorde, Biosphere Reserve Nockberge

Day of Biodiversity in Upper Austria

The Day of Biodiversity in Upper Austria, organized by the Naturschutzbund Oberösterreich and the Biologiezentrum of the Upper Austrian State museums, took place around the Mühlbergerhof, an organic farmstead covering around 20 ha of species-rich grassland, pastures, and deciduous forest. In addition to the species inventory, excursions with different topics (e.g. moths and bats, plants, fungi and lichens, insects) were offered to the public.

IMAGE: Members of the ABOL coordination team examine collected insects from Mühlbergerhof
CREDIT: Heidi Kurz, Naturschutzbund OÖ

Day of Biodiversity in the Biosphere Reserve Wienerwald

The annual Day of Biodiversity in the Biosphere Reserve Wienerwald took place in 2019 in Pressbaum, Lower Austria. Within 24 hours, 1151 species were recorded. This data forms a valuable basis for scientific research and nature conservation activities in the Biosphere Reserve. Excursions led by experts explored water insects, plants, and birds. More than 30 stands provided information on various topics for adults and children. The festival of biodiversity was completed with regional food, kid’s programs and an open-air concert.

IMAGE: ABOL information stand at the festival of biodiversity in Pressbaum
CREDIT: Michaela Sonnleitner

Day of Biodiversity in Vienna
The Day of Biodiversity in Vienna was the 1st transnational event of its kind within the Interreg project CITY NATURE jointly organized by the Vienna municipality (MA22), the University of Natural Resources & Life Sciences (BOKU), and Bratislava, Slovakia. The collecting event around the BOKU area was complemented by excursions exploring birds, plants, insects & mammals.

IMAGE: Group photo from the closing event with project partner from Bratislava at the Day of Biodiversity in Vienna CREDIT: Barbara Reinwein, MA22

Day of Biodiversity in Tyrol

During the Day of Biodiversity in Tyrol, the Brandenberg Valley attracted many experts and visitors with its diverse natural habitat. A highlight of the event was the demonstration of different types of light traps catching night-active insects. Experts held lectures on butterflies, which fascinated children and adults. Arctia matronula, a rare and locally distributed Noctuidae was among the observed species. The days of biodiversity in Tyrol are organized by the Tyrolean State Museums, the University of Innsbruck and the State of Tyrol.

IMAGE: Expert demonstrates light traps and explains nocturnal butterflies
CREDIT: Michaela Sonnleitner

Day of Biodiversity in the National Park Hohe Tauern

The motto of the 13th Day of Biodiversity in the National Park Hohe Tauern was Summit of biodiversity at the foot of the Großglockner (the highest mountain in Austria). More than 60 experts investigated the species inventory of the Gössnitztal, an elongated alpine valley up to more than 2000 m and the surroundings of Heiligenblut in Carinthia. In addition to plants, insects, birds etc., bats were observed in different altitudes and their call sequences recorded. The event was perfectly organized by the Team of the National Park.

IMAGE: Group photo from the Day of Biodiversity in the National Park Hohe Tauern in Heiligenblut with Großglockner in the background.
CREDIT: Manfred Schmucker

Due to the current Coronavirus pandemic, some of the 2020 ‘Days of Biodiversity’ were cancelled or postponed to 2021, while some will take place but with great care. For the future, we hope to be able to increase the number of participants and, ultimately, the data collected.

The concerted actions of the ABOL team at the ‘Days of Biodiversity’ significantly enhance the value and reach of these local BioBlitz events. For example, our efforts contribute to the completion of DNA barcode reference databases, important resources for society in the long term. They also support taxonomic research by providing the genetic resources important to the morphological determination of species. Additionally, we significantly promote these events amongst the public, raise awareness of the importance of biodiversity as well as build and strengthen bonds within the biodiversity community by enabling a process of mutual learning between cross-disciplinary experts.

As events this past year have shown, combining a BioBlitz with DNA barcoding is a very successful way to obtain both taxonomic and barcode data as well as integrate experts, especially for national DNA barcoding initiatives, which are not always fully funded, as is the case in Austria.

These events also foster a greater appreciation of biodiversity and ecosystems amongst the public and, therefore, are a very successful approach to increase bioliteracy. The currently ongoing biodiversity crisis implies rapidly growing importance of biodiversity data. As taxonomic expertise is increasingly rare in the academic environment, it is becoming more dependent on nature enthusiasts. This knowledge of biodiversity has always received too little attention, although a substantial part of it is held outside of academic institutions. Therefore, we wish to emphasize, that increased appreciation of nature should go hand in hand with that of private taxonomic expertise. ABOL BioBlitzes take all this into account.

References:

1. Baker G.M., Duncan N., Gostomski T., Horner M.A., Manski D. (2014). The bioblitz: Good science, good outreach, good fun. Park Science 31(1): 39–45.
2. IPBES (2019). Global assessment report on biodiversity and ecosystem services of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services. E. S. Brondizio, J. Settele, S. Díaz and H. T. Ngo (eds.) Bonn, IPBES secretariat.
3. Parker S.S., Pauly G.B., Moore J., Fraga N.S., Knapp J.J., Principe Z., Brown B.V., Randall J.M., Cohen B.S. Wake T.A. (2018). Adapting the bioblitz to meet conservation needs. Conservation Biology 32(5): 1007–1019. https://doi.org/10.1111/cobi.13103

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What can’t be measured won’t be managed: Scientists and U.S. Environmental Protection Agency work together to conserve the Great Lakes

What can’t be measured won’t be managed: Scientists and U.S. Environmental Protection Agency work together to conserve the Great Lakes

What can’t be measured won’t be managed: Scientists and U.S. Environmental Protection Agency work together to conserve the Great Lakes

The Great Lakes DNA Barcoding project brings together several international partners to understand the aquatic invertebrate biodiversity in the Laurentian Great Lakes
The Laurentian Great Lakes from space.

The Laurentian Great Lakes provide extremely valuable ecosystem services to nearly 40 million citizens of Canada and the United States who inhabit the watershed and many other visitors. These lakes are important for commercial navigation and are one of the most valuable freshwater commercial and recreational fisheries in the world. Such heavy use makes them vulnerable to invasive species, of which there are about 180 known to have invaded the five lakes1. However, the lakes’ biodiversity remains startlingly unknown, especially at lower trophic levels, even with strong scientific communities on both sides of the border.

The Great Lakes DNA Barcoding Project is using new and scalable genetic approaches to fill in the gaps in our knowledge of the native aquatic biodiversity of the Great Lakes and to detect previously undiscovered biological invasions. It will provide a baseline against which to monitor future changes in response to unintentional anthropogenic impacts and quantify efforts to restore biodiversity in parts of the lakes where it has declined.
The Great Lakes
The Great Lakes contain 21% of the world’s surface freshwater and are an important resource for agriculture, fishing, recreation, and international shipping. IMAGE CREDIT: 2013 National Geographic Society; Watershed defined by Great Lakes Aquatic Habitat Framework.

Understanding the impacts of anthropogenic changes on freshwater biodiversity is a major challenge with direct relevance to human health and well-being2. Monitoring and managing aquatic biodiversity needs to involve both academic and government institutions as well as stakeholders spanning farmers, fishermen, global transport companies, and policymakers in order to better inform environmental risk assessment, policy development, and natural resource management. Additionally, evaluating and improving private or public efforts to protect biodiversity requires an ability to quantify biodiversity, beginning with species richness.

The lack of scalable tools for assessing biodiversity has been a major impediment when monitoring the health of freshwater ecosystems. These habitats are dominated by small organisms that are difficult to identify and preserve. Species-level identification based on morphology is often impractical or sometimes even impossible. The process involves expert taxonomists and the special treatment of specimens requires significant investments in money, time, and labour. Therefore, when we rely only on these traditional survey practices, many organisms are identified only to genus/subfamily or simply neglected3,4.

DNA barcoding is a useful tool in these situations because the necessary taxonomic resources can be invested in a more targeted approach once a large number of specimens have been assigned a digital species identifier based on its DNA—the DNA barcode—to create a standardized, reproducible, and scalable solution for monitoring, otherwise difficult to quantify species. By digitizing taxonomic information in the form of a barcode, one needs not taxonomic expertise but simply access to sequencing technology for future identification and monitoring requirements. These technologies are becoming more portable and affordable every day and these tools become even more exciting when we apply non-invasive water sampling to monitor entire fauna from the trace amounts of DNA they leave behind (called ‘environmental DNA’)5.

The Great Lakes Barcoding Project, funded by the United States Environmental Protection Agency (EPA), aims to build a comprehensive genetic barcode library for aquatic invertebrates in the Laurentian Great Lakes watershed. The goal is to improve biodiversity monitoring, provide early detection of non-indigenous species, and inform management efforts to protect biodiversity from threats including climate change, pollution, and invasive species.

At the beginning of the project, only limited genetic information was available for many of the Great Lakes species6. The scale of the Great Lakes and its relatively large invertebrate biodiversity requires this research to be highly collaborative. To this end, the project has brought together several taxonomic experts, molecular ecologists, and aquatic biologists across USA and Canada, from the EPA and research institutions including Cornell University, Buffalo State College, University of Notre Dame, Central Michigan University, and the Centre for Biodiversity Genomics at the University of Guelph.

The Great Lakes DNA Barcoding Project team

The Great Lakes DNA Barcoding Project Team: Bret Coggins, Lars Rudstam, Susan Daniel, Adam Frankiewicz, James Watkins, Beth Whitmore, Joe Connolly; bottom row left to right: Sara Westergaard, Michael Pfrender, Bilgenur Baloglu, Kristy Deiner, Ed DeWalt, Alexander Karatayev, Christopher Marshall, Lyubov Burlakova (top to bottom, left to right). In attendance but not pictured: David Lodge, Kara Andres, and Jose Andres. George Rogalskyj and Erik Pilgrim joined electronically.
PHOTO CREDIT: The Great Lakes DNA Barcoding Project

 

At the end of February 2020, scientists as well as EPA representatives managing or participating in the project gathered at the beautiful Biological Field Station at Cornell University in upstate New York. We shared the latest project updates—everything from taxonomy to biodiversity, from ecological analysis to portable DNA sequencing, and the future of DNA-based monitoring. While the project is still in progress with hundreds of more specimens awaiting analysis, so far, our collaboration has resulted in over 1,000 DNA barcodes spanning over 300 invertebrate species.

This diversity includes more than ten taxonomic classes of invertebrates and is a resource that will improve tracking of non-native and native aquatic species, as well as clarify taxonomic inconsistencies or misrepresentations. The project has stimulated collaborations both within and outside of the main group of researchers and the sharing of specimens, resources, and, most importantly, new ideas and research directions has been an extremely encouraging and productive outcome.

Each plate of specimens sent away for DNA barcode analysis also contains a mix of feelings: satisfaction from a job well done, anticipation of the eventual results, and excitement around the new discoveries that may unfold.

References:

1. Great Lakes Aquatic Nonindigenous Species Information System. Retrieved from: www.glerl.noaa.gov/glansis/index.html

2. IPBES (2019) Global assessment report on biodiversity and ecosystem services of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services. ES Brondizio, J Settele, S Díaz and HT Ngo (editors). IPBES secretariat, Bonn, Germany.

3. Baloğlu B, Clews E and Meier R (2018) NGS barcoding reveals high resistance of a hyperdiverse chironomid (Diptera) swamp fauna against invasion from adjacent freshwater reservoirs. Frontiers in Zoology, 15(1)

4. Srivathsan A, Baloğlu B, Wang W, Tan WX, Bertrand D, Ng AH, Boey EJ, Koh JJ, Nagarajan N and Meier R (2018) A MinION™‐based pipeline for fast and cost‐effective DNA barcoding. Molecular Ecology Resources, 18(5): 1035–1049.

5. Deiner K, Bik HM, Mächler E, Seymour M, Lacoursière‐Roussel A, Altermatt F, Creer S, Bista I, Lodge DM, De Vere N and Pfrender ME (2017) Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Molecular Ecology, 26(21): 5872–5895.

6. Trebitz A, Sykes M, Barge J (2019) A reference inventory for aquatic fauna of the Laurentian Great Lakes. J. Great Lakes Res.

this project is supported by the

Great Lakes Restoration Initiative

Written by

Bilgenur Baloğlu

Bilgenur Baloğlu

Centre for Biodiversity Genomics, Guelph, ON, Canada

Christopher C. Marshall

Christopher C. Marshall

Department of Natural Resources, Cornell University, Ithaca, New York, USA

Lars Rudstam

Department of Natural Resources, Cornell University, Ithaca, New York, USA

David M. Lodge

David M. Lodge

Cornell Atkinson Center for Sustainability and Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA

Edward DeWalt

Illinois Natural History Survey, Champaign, Illinois, USA

Paul W. Simonin

Paul W. Simonin

Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA

Elizabeth Whitmore

Elizabeth Whitmore

Department of Natural Resources, Cornell University, Ithaca, New York, USA

Lyubov Burlakova

Great Lakes Center, Buffalo State College, Buffalo, NY, USA

Kristy Deiner

Kristy Deiner

Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland

June 18, 2020

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Local wildlife enthusiasts drive DNA barcode library building in the UK

Local wildlife enthusiasts drive DNA barcode library building in the UK

Local wildlife enthusiasts drive DNA barcode library building in the UK

Researchers in the UK are spearheading a number of high-profile initiatives designed to populate and fill gaps in the national DNA barcode library

Distribution of DNA barcode records for the United Kingdom.

IMAGE: BOLD Sytems 2020-03-10

Despite some notable achievements, such as a complete DNA barcode library for the native plants of Wales, the UK has lagged behind other European countries when it comes to growing its DNA barcode library. On BOLD there are 24,555 DNA barcode records for specimens collected in the UK (from 5,484 species) which is very similar to Austria (24,513 records, from 5,375 species), a landlocked country with roughly one third the land area and one seventh the human population. Germany leads Europe with 167,458 records from 14,805 species.

    The UK is working to catch-up through a number of high-profile initiatives designed to populate and fill gaps in the UK’s DNA barcode library and, in particular, bring BIOSCAN to UK insects.

    Distribution of DNA barcodes records for the United Kingdom.
    IMAGE: BOLD Systems from 2020-03-10

    The Darwin Tree of Life project is being led by the Wellcome Sanger Institute and involves a consortium of institutes, universities, museums, and agencies, including the Natural History Museum and Royal Botanical Gardens Kew. The project aims to deliver public DNA barcodes for 10,000 species by 2023 and ultimately sequence the genomes of all 66,000 species of plants, fungi, protozoa, and animals that are found in the UK.

    DEFRA (the Department for Environment, Food & Rural Affairs) has established a Centre of Excellence for Environmental Genomic Applications. This virtual centre recognises the absolute necessity of DNA barcode libraries to meet its aims of “applying genomics methods (eDNA and metabarcoding) to detect rare and invasive species, evaluate the effectiveness of conservation interventions, monitor the status and trends for key assemblages and taxa, and assess ecosystem health, functioning, and resilience”1.

    What is special about these initiatives is that they capitalize on the UK’s large community of local wildlife enthusiasts. A recent workshop organised by BugLife (the Invertebrate Conservation Trust) and Natural England (the UK government’s adviser for the natural environment in England) to examine “gaps” in BOLD for “key English invertebrates” brought together members of the Caddisfly Recording Scheme, Cranefly Recording Scheme, the British Dragonfly Society, the Amateur Entomologists’ Society, amongst others. The UK’s exceptional network of dedicated volunteer wildlife recorders already contribute thousands of records to taxon-focussed databases such as the UK Butterfly Monitoring Scheme (UKBMS), Local Record Centres, and through apps such as iSpot and iRecord which transmit data to the NBN (National Biodiversity Network) Atlas.

    Ainsdale Sand Dunes National Nature Reserve, one of the most important wildlife sites in England.
    PHOTO CREDIT: Gary Hedges

    The Darwin Tree of Life project kicked off last summer about 25 km north of Liverpool at Ainsdale Sand Dunes National Nature Reserve with a DNA Bioblitz attended by a team of local recorders including National Museums Liverpool entomologists. These local experts are passionate, driven and keen to contribute to DNA barcode libraries, but don’t necessarily have background knowledge in molecular biology or a basic skill set in “wet” lab techniques.

    Participants during the World Museum DNA Barcoding Workshop in February 2020.
    PHOTO CREDIT: Leanna Dixon

    To address this we recently ran a DNA barcoding workshop at World Museum Liverpool for eleven prominent local recorders connected with the Tanyptera Project. The Tanyptera Project is a seven-year initiative funded by the Tanyptera Trust to promote the study and conservation of insects and other invertebrates in the Lancashire and Cheshire region of Northwest England. To our knowledge this was one of the first DNA barcoding workshops run solely for non-professional scientists.

    Sphecodes ferruginatus female blood bee collected in Cheshire, England.
    PHOTO CREDIT: Chloe Aldridge

    The 1.5-day workshop covered the key steps in DNA barcoding from lab to BOLD2. Participants brought along their own invertebrates collected during recent local fieldwork and all successfully produced DNA barcodes for their specimens, which included springtails, bees, a cranefly, other flies, beetles, and spiders. The specimens have been vouchered into World Museum Liverpool’s National Entomology Collection which includes over 1 million specimens, and the sequences have been submitted to BOLD. One participant was able to confirm the first record of a Nationally Scarce blood bee in Cheshire – Sphecodes ferruginatus – raising interesting hypotheses about its potential host species.

    At National Museums Liverpool, together with the Tanyptera Project, we are committed to continue developing our DNA barcoding educational offering for local wildlife enthusiasts and supporting their work driving forward national initiatives to get more UK barcodes onto BOLD.

    References:

    1. Nelson M, Woodcock P, Maggs C (2018) Using eDNA and metabarcoding for nature conservation. Joint Nature Conservation Committee (JNCC 18 25). Available at http://data.jncc.gov.uk/data/99e1f69f-c438-439f-8401-dd8a6ce17320/JNCC18-25-Using-eDNA-and-Metabarcoding-for-Nature-Conservation.pdf

    2. Wilson JJ, Sing KW, Jaturas N (2019) DNA barcoding: Bioinformatics workflows for beginners. In Bioinformatics and Computational Biology. The A to Z of Bioinformatics. Ranganathan S, Nakai K, Gribskov M & Schönbach C, Eds. Elsevier Ltd., Oxford.

    Written by

    John-James Wilson

    John-James Wilson

    Vertebrate Zoology at World Museum, National Museums Liverpool, United Kingdom

    Leanna Dixon

    Leanna Dixon

    Tanyptera Project, National Museums Liverpool, United Kingdom

    Gary Hedges

    Gary Hedges

    Tanyptera Project, National Museums Liverpool, United Kingdom

    March 20, 2020

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    DNA Barcoding at the Iberian Symposium on Marine Biology Studies

    DNA Barcoding at the Iberian Symposium on Marine Biology Studies

    DNA Barcoding at the Iberian Symposium on Marine Biology Studies

    Marking its 20th anniversary, the international Iberian Symposium on Marine Biology Studies took in September 2019 in Braga, Portugal
    Participants to the 20th International Iberian Symposium on Marine Biology Studies, 9-12 September 2019, Braga, Portugal PHOTO CREDIT: Andreia Pacheco
    Marking its 20th anniversary, the international Iberian Symposium on Marine Biology Studies, organized by the University of Minho and the Centre of Molecular and Environmental Biology (CBMA) in Braga, Portugal, took place from September 9-12 this year. Of the 14 plenary sessions, one was dedicated to DNA barcoding and DNA metabarcoding. Plenary speaker and session chair, Mehrdad Hajibabaei, Canada’s iBOL Science Committee member for Centre for Biodiversity Genomics at the University of Guelph in Canada discussed the latest updates on the use of DNA metabarcoding to study biodiversity across all life, from microbes to mammals. The session included five presentations ranging from revealing hidden diversity to the applications of DNA metabarcoding approaches. Discussing research in the Northwest Iberian Peninsula, Maria Fais presented on the assessment of spatio-temporal variation on meiofauna while Barbara Leite focused on investigations in macrozoobenthic communities. With a Mediterranean focus, Adria Antich discussed approaches to evaluate DNA dynamics in the benthic boundary layer between benthos and plankton. Focusing on the use of DNA barcoding to spot hidden diversity, Marcos Teixeira examined diversity in polychaetes from the Phyllodocidae family and David Varros-Garcia explored the deep-sea morid Lepidion lepidion from European waters.
    Congratulations to Barbara Leite for winning the award for the best conference presentation. PHOTO CREDIT: Andreia Pacheco

    Beyond the one session dedicated to DNA barcoding, there were several other sessions and poster talks that focused on the subject. The plenary speaker, Marta Pascual, used the gene COI among other genetic and genomic tools to show different cases of population genetic structure in marine organisms. DNA barcoding was also applied by Xazier Turon et al. to identify invasive ascidians and by myself and colleagues in a comprehensive analysis of DNA barcoding diversity in marine peracarids.

    Two posters discussed the current status of the DNA barcoding reference libraries of non-indigenous marine species: Sofia Duarte et al. focused work in the Azores archipelago while Sofia Duarte et al. examined European coastal regionsSampieri and colleagues used different genetic markers (including COI) to identify a complex of cryptic species along South American estuaries. DNA barcoding was even applied to study the diet of crustaceans.

    Select Abstracts
    Antich et al. Metabarcoding the benthic boundary layer: the role of sampling method and marker characteristics in the DNA signatures obtained at the interface between benthos and plankton. doi:10.3389/conf.fmars.2019.08.00046 Barros-García et al. Phylogeography of the deep-sea morid codling Lepidion lepidion reveals the presence of two ancient Atlantic/Mediterranean lineages. doi:10.3389/conf.fmars.2019.08.00129 Campos et al. Polymerase chain reaction as a promising tool for DNA-based diet studies of crustaceans. doi:10.3389/conf.fmars.2019.08.00104 Duarte et al. Species gap analysis in DNA barcode reference libraries of marine non-indigenous species in the Azores archipelago.  doi:10.3389/conf.fmars.2019.08.00170

    Duarte et al. Current status of the DNA barcode reference library of non-indigenous marine species occurring in European coastal regions. doi:10.3389/conf.fmars.2019.08.00169

    Fais et al. Patterns of spatial and temporal variation in estuarine meiofaunal communities assessed through DNA metabarcoding: a case study in the Lima estuary (NW Portugal). doi:10.3389/conf.fmars.2019.08.00060
    HajibabaeiFrom microbes to mammals: comprehensive analysis of biodiversity using DNA metabarcoding. doi:10.3389/conf.fmars.2019.08.00008 Leite et al. Combining artificial substrates, morphology and DNA metabarcoding for investigating macrozoobenthic communities in NW Iberia. doi:10.3389/conf.fmars.2019.08.00061

    Pascual et al. Population structure in marine organisms: from genetics to genomics. doi:10.3389/conf.fmars.2019.08.00002

    Sampieri et al. Cryptic or cosmopolitan? Unveiling the Laeonereis complex along South American estuaries through DNA barcoding. doi:10.3389/conf.fmars.2019.08.00108

    Teixeira et al. Molecular and morphometric combo reveals extraordinary hidden diversity in European polychaetesfrom the Phyllodocidae family. doi:10.3389/conf.fmars.2019.08.00057

    Turon et al. Population genomics revealed independent colonisation events of a global ascidian invader. doi:10.3389/conf.fmars.2019.08.00043

    Vieira et al. Evolutionary insights derived from comprehensive analyses of DNA barcoding diversity in marine members of the superorder Peracarida (Crustacea: Malacostraca) doi:10.3389/conf.fmars.2019.08.00058

     All conference abstracts were published in Frontiers.

    Written by

    Pedro Vieira

    Pedro Vieira

    University of Minho, Braga, Portugal

    November 28, 2019

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    Fifty years of amphipod meetings and counting!

    Fifty years of amphipod meetings and counting!

    Fifty years of amphipod meetings and counting!

    More than 120 people from 27 countries came together at the end of August to share the latest developments in amphipod research relating to everything from taxonomy to ecology, from physiology to behaviour, from phylogeography to cryptic speciation.

    Created by the Grabowski lab for ICA15 – Poland, 2013

    DESIGN: Karolina Bącela-Spychalska; PHOTO CREDIT: Arthur Anker, Michał Grabowski, Hans Hillewaert, Anna Jażdżewska, Alexander Semenov

    As summer slowly approached its end, Dijon, the beautiful French city surrounded by Burgundy wineries, was suddenly inundated by people dedicated to the study of amphipods – a group of fascinating crustaceans inhabiting all aquatic habitats.

    More than 120 people from 27 countries came together at the end of August to share the latest developments in amphipod research relating to everything from taxonomy to ecology, from physiology to behaviour, from phylogeography to cryptic speciation.

    What started as a meeting dedicated to one taxon (the groundwater genus Niphargus) has become the International Colloquium on Amphipoda (ICA), a meeting that envelops all amphipods from all habitats. It quickly grew into a friendly, informal environment where researchers and students exchange ideas and start new collaborations. A big family that reunites every two to three years in different countries in the Euro-Mediterranean region.

    This year, ICA18 was a particularly special occasion as the group celebrated its 50th anniversary. As plenary speaker José Manuel Guerra-García from the University of Seville put it, “1969 had two major events: the moon landing and ICA1 in Verona, Italy.” His presentation, titled ‘Fifty years of amphipod meetings. Taxonomical, ecological, and behavioural patterns of the amphipodologist community’, detailed the history of this important community of researchers and its rapid growth and diversification during the last decades.

    ICA18, organized by Thierry Rigaud and Rémi Wattier from the University of Burgundy, brought new energy, new graduate students, and early-career researchers looking to understand the incredible diversity of amphipods as well as new ideas for future collaborative projects.  

    Participants to the 18th International Colloquium on Amphipoda, 26-30 August 2019, Dijon, France PHOTO CREDIT: Anna Jażdżewska

    Meeting highlights

    Nicolas Puillandre from the National Museum of Natural History in Paris gave a plenary talk titled, ‘DNA Barcoding, DNA taxonomy, and integrative taxonomy: separating the wheat from the chaff’. He highlighted the history of DNA barcoding and the growth of its applications, from its restricted sense of specimen identification to the wider applications as part of DNA taxonomy and integrative taxonomy. This was the first ICA meeting to have a plenary talk dedicated to DNA barcoding.

    Another first for ICA was the hands-on mini-workshop on BOLD, the online platform that provides an integrated environment for the assembly and use of DNA barcode data, organized by Filipe Costa, iBOL Science Committee member for Portugal, and Pedro Vieira, both from the University of Minho in Portugal; Michał Grabowski, iBOL Science Committee member for Poland, and Tomasz Mamos, both from the University of Łódź in Poland; and myself from the University of Guelph in Canada. After three days of talks and poster presentations, the workshop participants gathered in the beautiful old library room of the Faculty of Sciences and spent an entire Friday afternoon learning about BOLD and how to include it in their workflow so that their data and metadata are stored on a single platform.

    Participants to the BOLD mini-workshop organized on the margins of ICA18 in Dijon, France.

    PHOTO CREDIT: Maria João Gomez

    One of the hottest topics at ICA18 was cryptic speciation, as amphipods are a group known for high intra-specific diversity. The subject triggered an ad-hoc meeting to establish a roadmap for approaches to identifying and describing cryptic species. Due to the complexity of the topic, moderator Michał Grabowski proposed that a core group with representatives from natural history museums, academia, BOLD, and the World Register of Marine Species (WORMS) should continue the discussion online and produce guidelines for the amphipod community to address the topic of cryptic species in the near future.

    Ad hoc meeting on cryptic species in amphipods. PHOTO CREDIT: Adriana Radulovici

    The final session was dedicated to DNA barcoding and the progress made in freshwater, marine and groundwater amphipods. I had the pleasure of closing ICA18 with an overview of current practices in DNA barcoding amphipods inferred from compiling and analyzing all public amphipod barcode data available in BOLD.

    Talks from the final session titled, ‘How many taxa?’

    DNA barcode reference library for European freshwater malacostracans: getting there
    T Mamos, T Rewicz, K Bacela-Spychalska, K Hupalo, A Jablonska, K Zganec, M Jelic, A Wysocka, L Sworobowicz, D Copilas-Ciocianu, A Petrusek, R Wattier, J Hinić, V Slavevska-Stamenković & M Grabowski

    Broad-scale DNA barcode-based meta-species analyses of patterns of molecular variation in Amphipoda from world’s oceans
    PE Vieira, C Gonçalves, P Soares, H Queiroga & FO Costa

    DNA barcode availability for European groundwater macrocrustaceans
    M Zagmajster, Š Borko, T Delić, C Douady, D Eme, C Fišer, F Malard, P Trontelj & A Weigand

    What public data can tell us about current practices in DNA barcoding amphipods
    AE Radulovici

    ICA18 has set the course for a very interesting two years in amphipod research, one that will lead to ICA19 in Tunisia in 2021. I am happy to see more and more people producing DNA barcodes for amphipods which inherently leads to the discovery of new cryptic species (especially in groundwater). Compared to 2010 when I attended ICA14 in Spain, my first amphipod meeting, there is definitely more interest in DNA barcoding, with some research labs widely adopting the tool for their amphipod projects. My biggest hope coming out of ICA18 (and the BOLD mini-workshop) is that amphipodologists will come together to follow best practices when generating DNA barcoding data and metadata so that the entire community will have access to a reliable dataset of amphipod records.

    As always, ICA was inspiring and energizing. And if ICA needed a slogan, the phrase coined by the Grabowski lab in 2013 could very well reflect the belief of people gathered in Dijon – Amphipoda is the way of life!

    Conference Posters

    I highlight some of the poster presentations of interest to the barcoding community. For more information including the authors’ affiliations and abstracts, please refer to the book of abstracts.

    Coloring outside the lines: cryptic diversity in podocerid amphipods
    BC Cummings & G Paulay

    PHOTO CREDIT: Adriana Radulovici

    Combining molecules and morphology to describe cryptic new species – the Bathyceradocus genus case
    L Corbari, A Jażdżewska & A Ziemkiewicz

    Combining artificial substrates, morphology and DNA metabarcoding for investigating marine amphipod communities in NW Iberia
    BR Leite, PE Vieira, JS Troncoso & FO Costa

    DNA sequencing and morphological analysis of an undescribed Salentinella species (Amphipoda, Salentinellidae) from an anchialine cave in Peloponnese, Greece
    D Davolos, C Calcari, E De Matthaeis & C Di Russo

    Estimating the actual biodiversity and evolutionary history of the amphipod genus Eusirus in the Southern Ocean
    L Salabao, B Frédérich, G Lepoint, ML Verheye & I Schön

    First insights into the deep-sea scavengers at hydrothermal vent fields along the Southeast Indian Ridge
    K Kniesz, A Jażdżewska, TC Kihara & PM Arbizu

    Historic Peracarid Crustacea collections in The Natural History Museum, London
    A Herdman, LE Hughes & M Lowe

    Syntopic coexistence of gammarid cryptic lineages: rule or exception?
    A Petrusek, T Rutová, PK Bystřický, M Gajdošová, A Beermann, P Pařil, M Horsák, D Copilas-Ciocianu & F Leese

    The deep-sea Eusiridae from Papua New Guinea waters (SW Pacific Ocean)
    I Frutos, JC Sorbe & L Corbari

    When one becomes 15: Morphological vs. molecular species delimitation in the “Niphargus aquilex” complex
    D Weber, T Brad, A Weigand & J-F Flot

    To keep up with the latest research in amphipods, check out the Amphipod Newsletter.

    Written by

    Adriana Radulovici

    Adriana Radulovici

    Centre for Biodiversity Genomics, University of Guelph, Canada

    November 26, 2019

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    Reflections from a DNA barcoding course in Norway – From sequences to species

    Reflections from a DNA barcoding course in Norway – From sequences to species

    REFLECTIONS FROM A DNA BARCODING COURSE IN NORWAY – FROM SEQUENCES TO SPECIES

    The Norwegian Research School on Biosystematics (ForBio) and the Swedish Taxonomy Initiative (STI) organized a DNA barcoding course welcoming 16 university students from 10 nations to the scenic outer coastline of Central Norway.

    Students and teachers attending the course DNA barcoding – from sequences to species.

    PHOTO CREDIT: Thomas Stur Ekrem

    What exactly is DNA barcoding? What are the major challenges with the identification of species using DNA sequences? How can we evaluate the quality of barcode reference libraries? How will international agreements like the Nagoya protocol influence the use of genetic data to assess and monitor biodiversity? These are a few of the questions that were explored during the recent DNA barcoding course at Sletvik Field Station near Trondheim, Norway.

    The landscape around Sletvik Field Station PHOTO CREDIT: Torbjørn Ekrem

    The Norwegian Research School on Biosystematics (ForBio) and the Swedish Taxonomy Initiative (STI) organized the course welcoming 16 university students from 10 nations to the scenic outer coastline of Central Norway. The students came from universities in Norway and Sweden, and one even travelled all the way from Mozambique. The course was taught and organized by Rakel Blaalid, Norwegian Institute of Nature Research; Filipe O. Costa, CBMA, University of Minho; Torbjørn Ekrem, NTNU University Museum; Galina Gusarova, The Arctic University Museum of Norway; Malin Strand, Swedish University of Agricultural Sciences; and Elisabeth Stur, NTNU University Museum.

    Primarily aimed at PhD students and early career researchers, while still open to nature managers and MSc students, the course focused on increasing the in-depth knowledge of molecular techniques for identification of species. The packed program included four days of lectures, practical exercises and seminars and concluded on day five with a three-hour exam, rewarding students with two European Credit Transfer and Accumulation System (ECTS) credits if they passed. In order to meet the requirements by some universities’ PhD program, an additional ECTS credit was offered to students that opted for a home assignment after the course.

    Even the teabags took active participation in the course. PHOTO CREDIT: Torbjørn Ekrem

    The Sletvik Field Station run by the Norwegian University of Science and Technology was a marvellous and very practical setting for the course with lots of space, nice lecture rooms and a large kitchen where instructors and students prepared meals together and socialized.

    The teachers were impressed by the students’ efforts and active participation. We hope everyone had a good experience and gathered useful knowledge for their current and future careers!

    Daniel Abiriga, Katharina Bading and Misganaw Gessese preparing homemade pizza for 24 people. PHOTO CREDIT: Anna Seniczak

    Reflections from three participants:

    The DNA barcoding course – from sequence to species was really useful for me because although I knew how to clean DNA sequences, I was missing how to do various analyzes in databases such as BOLD. The time spent on each topic was good, but due to poor internet connections, we could have had more time for the practicals. I think that the topics were well covered, and I gained a lot of knowledge on the theory of DNA barcoding and the challenges faced when using barcode sequences to describe new species. The knowledge acquired in this course will help me analyze sequence data for my PhD project on fishes.

    A big challenge for African countries, specifically for Mozambique, is the lack of expert taxonomists working with DNA barcoding. Moreover, the whole process of sample processing is still expensive, and many African species do not have sequences in public reference libraries. My next challenge will be to start a small dataset for the species I’m working on. I already have sequences for some, and I only need to check if they fulfill all the requirements to be deposited on BOLD. Thanks a lot for the opportunity to attend the course. Hope to attend more ForBio courses next year!

    Erica Tovela

    Museu de Historia Natural, Mozambique

    I found the DNA barcoding course very interesting, particularly to a junior researcher like me. Before joining the course, I did not know about the different DNA markers that are widely being used in species delimitation. Through a broad spectrum of experts from different disciplines, e.g., entomology, plant, fungi, and marine invertebrates, we were taken through current applications of DNA barcoding in the various fields. This has greatly enhanced my understanding of DNA barcoding, including its strengths and limitations. Overall, the course was very enlightening, and I would recommend it to fellow junior researchers who employ DNA barcoding in their work.

    Daniel Abiriga

    PhD student, University of South-Eastern Norway

    Tucked away in the fjords of Slettvik, we were a couple dozen scientists discussing the best way to designate barcodes to all of life. What is a species? How do we identify one from another? How different does their DNA need to be to assign this designation? From at least ten different countries and various continents, we (the students) were able to learn from our professors and from each other. Globally, as computing power increases and genetic data becomes easier to sample, DNA barcoding has become more popular. Having a place for systematists—those classifying organisms using a small piece of standardized genetic information—to converge is pretty unique.  At the barcoding course, ForBio brought together researchers from many different silos to explore the intricacies of genetic barcoding as a group.

    Personally, I am particularly interested in understanding species composition in soil samples—metabarcoding. I came to this Forbio course with the expectation of understanding a bit better the best practices of barcoding in the field. We discussed phylogeography, practiced tree making with different parameters, went through workflows in different barcoding databases, and learned about cleaning up datasets. More importantly, however, I now have an understanding of how my work will fit a much larger context: of the past, present, future of molecular sequencing. I understand the implications DNA barcoding work on a global scale; I came away with an understanding of why we have the Nagoya Protocol and how it aims to secure access and benefit sharing of genetic resources. Through structured discussions with my classmates and our teachers we explored the consequences of moving taxonomy toward a more molecular basis and what this means in a global context. Thanks, ForBio for a great course! It is not very often you can get groups of scientists like this outside of their office and into such meaningful discussions.

    Louisa Durkin

    Nordic Academy for Biodiversity Systematics, University of Gothenburg, Gothenburg Global Biodiversity Center, Sweden

    Written by

     Elisabeth Stur

    Elisabeth Stur

    NTNU University Museum

    Torbjørn Ekrem

    Torbjørn Ekrem

    NTNU University Museum

    November 11, 2019

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    Small steps lead to big initiatives: Pakistan reaffirms support for iBOL by launching PakBOL

    Small steps lead to big initiatives: Pakistan reaffirms support for iBOL by launching PakBOL

    Small steps lead to big initiatives: Pakistan reaffirms support for iBOL by launching PakBOL

    From economically important insect species to plants to food security, Pakistani researchers are working to barcode all life in their country through a national initiative - PakBOL.

    PakBOL inauguration with Margaux McDonald, Canada’s Senior Trade Commissioner in Pakistan (left) and Dr. Ghazala Yasmin, Vice Chancellor of Women University Mardan.

    PHOTO CREDIT: Hina Jabeen

    With continued interest in documenting native biodiversity and cognizance about the applications of barcode data, the scientific community in Pakistan has reiterated its support for the iBOL Consortium and its new venture BIOSCAN by launching the national initiative, Pakistan Barcode of Life (PakBOL).

    PakBOL launched in the presence of more than 120 scientists, academicians, students, and other stakeholders in biodiversity and pest management sciences who gathered in Islamabad for the 3rd international conference on “Empowering Nation through Science” organized by the Women University Mardan.

    PakBOL attended by Pakistani representatives from 15 universities and several government and non-government organizations
    PHOTO CREDIT: Hina Jabeen

    The two-day conference was attended by Pakistani representatives from 15 universities and several government and non-government organizations including Higher Education Commission, Directorate of Biodiversity, Ministry of Climate Change, Pakistan Agricultural Research Council, Pakistan Atomic Energy Commission, and Dairy Science Park.

    International delegates were also in attendance, including the Canadian High Commission Islamabad, Oxford Brooks University (UK), International Foundation of Science (Sweden), Organization for Women in Science for Developing Countries (Italy), Centre for Biodiversity Genomics (Canada).

    Pakistan has been an active member of iBOL since it joined the consortium in 2011, generating more than 50,000 barcode records. Over the last eight years, these efforts have provided coverage for 6,300 animal BINs (proxy for species) and 350 plant species.

    Researchers sampling in the foothills of Kashmir, Pakistan.
    PHOTO CREDIT: Muhammad Ashfaq

    But the amount of barcode data generated so far pales in comparison with the species richness and size (882,000 km2) of the country. Most of the barcoding work in Pakistan has been carried out by a few labs with 99% of the generated data representing arthropods.

    The very first barcoding project in Pakistan “Sequencing DNA barcodes of economically important insect species of Pakistan” conducted jointly by the National Institute for Biotechnology and Genetic Engineering, Pakistan, and the University of Guelph, Canada, successfully introduced DNA barcoding to the country producing 5,000 barcodes within the first year of its launch (2010 – 2012).

    Although the resources available for the project were inadequate for large-scale barcode coverage of the country’s arthropod fauna, the project helped to create understanding among local researchers about barcoding science. The subsequent financial support from the International Development Research Centre (IDRC), through the University of Guelph, helped Pakistani researchers expand barcoding activities in the country, generate barcode data from other organisms including plants, and develop national networking opportunities. This helped Pakistan become a National Node in iBOL’s first research program BARCODE 500K and contributed to the documentation of biodiversity on the planet.

    With continued interest in DNA barcoding research, Pakistan has formally joined as a member nation of the iBOL Consortium to participate in its global initiative – BIOSCAN. Pakistan is already participating in the Global Malaise Program led by the Centre for Biodiversity Genomics in Guelph and, with the launch of BIOSCAN, it plans to expand this program to all the ecoregions in the country. 

    Participating in the Global Malaise Program from Lahore, Pakistan.
    PHOTO CREDIT: Shahbaz Ahmad 

    Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta is leading the efforts to organize a network of universities and research organizations; their aim is to promote and strengthen barcoding research in Pakistan to achieve the goal of documenting all fauna and flora in the country.

    Several universities in Pakistan, including BUITEMS, the University of Sargodha, GC University Lahore, University of Swat, University of Sindh Jamshoro, GC University Faisalabad, University of Rawalakot Azad Kashmir, Punjab University Lahore, LCWU Lahore, and Quaid-e-Azam University Islamabad have been involved in barcoding research but lack a common platform to coordinate barcoding activities. PakBOL will provide that platform to the barcoding community in Pakistan to coordinate efforts to achieve their common goal.

    An initiative taken eight years ago with a small project on barcoding pest insects has now expanded to a national effort with a much broader goal – barcoding all life in Pakistan. And PakBOL aims to achieve just that!

    Read more about Pakistan:

    DNA BARCODING WILD FLORA IN PAKISTAN’S FORESTS

    Preserving voucher specimens and creating a virtual herbarium to understand and protect some of the oldest living trees on the planet.

    UNIVERSITY OF SINDH JAMSHORO BARCODES GRASSHOPPERS IN PAKISTAN’S THAR DESERT

    Tracking the shift of non-pests to crop pests, a phenomenon accelerated by anthropogenic pressures in the Thar Desert.

    Written by

    Muhammad Ashfaq

    Muhammad Ashfaq

    Centre for Biodiversity Genomics, University of Guelph

    June 10, 2019

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    Update from the Norwegian Barcode of Life Network (NorBOL)

    Update from the Norwegian Barcode of Life Network (NorBOL)

    Update from the Norwegian Barcode of Life Network (NorBOL)

    Norway is supporting projects to assess and monitor biodiversity in time and space, authenticate various products, and develop new methodologies with DNA barcode data.
    Nereis pelagica barcoded by NorBOL. PHOTO CREDIT: Katrine Kongshavn

    Written by

    Torbjørn Ekrem

    Torbjørn Ekrem

    NTNU University Museum, Coordinator of NorBOL, Trondheim, Norway

    April 7, 2019

    Five years have passed since the Norwegian Barcode of Life (NorBOL) obtained funding from the Norwegian Research Council to develop a national research infrastructure for DNA barcoding in Norway. This funding was the major boost needed to build a barcode reference library for Norwegian and polar biota, but it was also an important driver to ensure knowledge transfer and capacity building for DNA barcoding in Norway.

    A central collaborator and funder over the years has been the Norwegian Taxonomy Initiative run by the Norwegian Biodiversity Information Centre; they are an important reason why we now have almost 19,000 species barcoded from Norway. The positive synergies between DNA barcoding and inventory projects targeting groups of little-known organisms were highlighted at the 7th iBOL Conference in Kruger.

    NorBOL is a geographically distributed infrastructure with four hubs located at the university museums in Bergen, Oslo, Tromsø, and Trondheim. This has made it possible for us to take advantage of existing expertise and be particularly active in some areas. For instance, the University Museum of Bergen is currently the largest contributor to marine bristle worm data in the Barcode of Life Database (BOLD), while the Tromsø Museum is a key player in developing genome skimming of herbarium material to retrieve barcode regions from the chloroplast genome.

    As an established national research infrastructure and member of iBOL, NorBOL continues the collaboration with the Norwegian Taxonomy Initiative and seeks additional funding to fill the gaps in the barcode library of Norwegian species. We will also continue supporting applied projects that use the generated data and knowledge to assess and monitor biodiversity in time and space, authenticate various products, and develop methodology.

     

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