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

Don't Miss Out!

Subscribe to the iBOL Barcode Bulletin for updates on DNA barcoding efforts, the iBOL Consortium, and more.

comment on this article

The Barcode Bulletin moderates comments to promote an informed and courteous conversation. Abusive, profane, self-promotional, or incoherent comments will be rejected. 

Discovering ten new species of Paramyia Williston (Diptera: Milichiidae) in North America using DNA barcoding

Discovering ten new species of Paramyia Williston (Diptera: Milichiidae) in North America using DNA barcoding

Discovering ten new species of Paramyia Williston (Diptera: Milichiidae) in North America using DNA barcoding

Making the process of species identification more efficient by focusing morphological efforts using DNA-based tools

Flowering plant visited by Paramyia sp.
PHOTO CREDIT: Steve A. Marshall

The process of discovering and describing new species – the job of taxonomists – is time-consuming. To tackle the challenge, one must become an expert on a specific group in order to notice those rarities among the masses. This is without counting the added challenges of cryptic groups where the external morphology is of limited help as individuals often appear to belong to the same species despite being genetically distinct. In many cases, the taxonomist has to dissect hundreds of specimens to detect slight differences in their genitalia which are usually unique for each species. DNA barcoding can greatly assist any taxonomist by speeding up this laborious identification process, particularly with small flies like Paramyia Williston (Diptera: Milichiidae).

Flowering plant visited by Paramyia sp.

PHOTO CREDIT: Steve A. Marshall

Paramyia, a kleptoparasitic genus well represented worldwide, provides a perfect example of joining DNA barcoding and traditional taxonomy. Paramyia is a small genus, with under 30 described species, of tiny blackish flies, usually under 2mm long, with very similar external morphology. In the Nearctic, it was only represented by one species, P. nitens Loew. With that knowledge in mind, no particular attention was given to specimens collected in that geographic range. That is until multiple Barcode Index Numbers (BIN) were found on the Barcode of Life Data System (BOLD) under the same species name. This strongly indicated that multiple undescribed species may have been placed under one species – P. nitens. A closer look at their genitalia revealed this to be true, and so a revision of the genus was then needed.

Paramyia sp. displaying kleptoparasitism, that is, feeding on the captured prey (stink bug) of another predator (spider)

PHOTO CREDIT: Steve A. Marshall

As with any revision, I first acquired multiple loans from large museum collections to compare and study the many diverse and variable specimens from a specific geographic range, in this case, North America. Then, I studied the morphology of these specimens in-depth to detect variation between those grouped together based on their similarities (i.e, morphs) and dissected the genitalia to confirm if they were indeed new species. With a genus like Paramyia, most helpful characters to differentiate between the species are genitalic, which means that good dissection skills are essential. The skill needed to dissect the genitalia of such small flies is comparable to performing surgery on a baby’s tooth. Important to note, there are no morphology characters to split the females of most species apart.

This is where DNA barcoding comes in handy. I sequenced specimens from my different morphs, and then dissect males grouped in the same BIN to verify the correspondence between the BIN and the species concept. When the molecular and the morphological analysis align perfectly, females can get correctly associates with their male counterpart, which would have otherwise been impossible. Hence, the species description can be more complete and the sequences are available to be used by other researchers to correctly identified that group, e.g. in monitoring programs. I applied this process in the Nearctic revision of Paramyia and described 10 new species! Future revisions tackling the remaining geographic regions can build from this work.

Comparative morphology between the new species P. pseudonitens and P. brevikeraia with a body profile, frontal head and genitalia photos (top to bottom)

PHOTO CREDIT: Valerie Levesque-Beaudin

The taxonomic impediment coupled with the current rate of species extinction is making the job of the taxonomist increasingly more difficult and yet, there’s an urgent need to record species before they disappear. As this study demonstrates, by quickly sorting specimens based on morphology and sequencing representative of each group, the number of undescribed species can be assessed and the amount of dissection needed to make such a discovery can be managed. The focus can then be on the morphology and genitalia of the different BINs, hence speeding up the process of species identification.

For full details, please refer to the publication in Zootaxa.

Written by

Valerie Levesque-Beaudin

Valerie Levesque-Beaudin

Taxonomic Specialist – Diptera, Centre for Biodiversity Genomics

February 27, 2020
https://doi.org/10.21083/ibol.v10i1.6081

Don't Miss Out!

Subscribe to the iBOL Barcode Bulletin for updates on DNA barcoding efforts, the iBOL Consortium, and more.

Related articles

DNA BARCODING WILD FLORA IN PAKISTAN’S FORESTS

by Nazeer Ahmed | Apr 7, 2019 | Research

DNA BARCODING AND GENOMICS IN THE MEGADIVERSE AMAZON ALTITUDE FIELDS

by Guilherme Oliveira, Gisele Nunes, Rafael Valadares, Ronnie Alves and Santelmo Vasconcelos | Apr 7, 2019

comment on this article

The Barcode Bulletin moderates comments to promote an informed and courteous conversation. Abusive, profane, self-promotional, or incoherent comments will be rejected. 

BIOSCAN: Illuminating biodiversity and supporting sustainability

BIOSCAN: Illuminating biodiversity and supporting sustainability

BIOSCAN: Illuminating biodiversity and supporting sustainability

The iBOL Consortium launches a research program that seeks to discover species and reveal their interactions and dynamics

BIOSCAN: Illuminating biodiversity and supporting sustainability

The iBOL Consortium launches a research program that seeks to discover species and reveal their interactions and dynamics

Written by

Donald Hobern

Donald Hobern

Executive Secretary, International Barcode of Life Consortium

October 2, 2019
https://doi.org/10.21083/ibol.v9i1.5527

Newsletter

Get the Barcode Bulletin delivered to your inbox

The International Barcode of Life Consortium (iBOL) launched its new research program BIOSCAN in June 2019, to scale up its efforts to inventory life on Earth at a time when an ecological crisis is threatening the planet.

Recent reports from the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) and the Intergovernmental Panel on Climate Change (IPCC) have highlighted the scale of the pressures that threaten the environment and that are triggering a massive extinction event. Public awareness of these issues is growing and there are increasing demands for policymakers to work to support the environment and to focus on sustainable solutions.

Large-scale datasets are key to empowering societies and politicians to make these changes. Such data are available for some global systems, such as climate and land cover, and national scale datasets are often available for agriculture, human population, and land use. However, at present, biodiversity is not represented at the level of detail or at the scale and frequency required to support decision-making.

 

The International Barcode of Life Consortium (iBOL) launched its new research program BIOSCAN in June 2019, to scale up its efforts to inventory life on Earth at a time when an ecological crisis is threatening the planet.

Recent reports from the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) and the Intergovernmental Panel on Climate Change (IPCC) have highlighted the scale of the pressures that threaten the environment and that are triggering a massive extinction event. Public awareness of these issues is growing and there are increasing demands for policymakers to work to support the environment and to focus on sustainable solutions.

Large-scale datasets are key to empowering societies and politicians to make these changes. Such data are available for some global systems, such as climate and land cover, and national scale datasets are often available for agriculture, human population, and land use. However, at present, biodiversity is not represented at the level of detail or at the scale and frequency required to support decision-making.

 

iBOL has been acquiring growing volumes of data on species and their distributions since 2010 with their first research program BARCODE 500K. By 2015, the program had delivered DNA barcodes representing 500,000 species via its online database called the Barcode of Life Data System (BOLD). These standardized reference sequences have offered researchers everywhere a transformational tool for rapid species identification as well as range of applications across taxonomy, biogeography, ecology, biosecurity, and conservation. The benefits to researchers, policymakers, and the wider public are likely to be even greater through widespread adoption of metabarcoding as a survey tool. Metabarcoding uses DNA barcodes for cheap and efficient assessment of which species are found in a bulk sample or have left residual traces of their DNA in water, soil, and other substrates (“environmental DNA” or eDNA).

Species identification has always been a central challenge for biological research, a task that has relied on the skill-base of the international taxonomic community and the deep and complex foundation of a quarter millennium of work naming and describing species. The importance and difficulty of being able to assign a name to any arbitrary organism of interest and the shortage of trained taxonomists and curators to do this work has become known as the taxonomic impediment and is recognized as an international problem. DNA barcoding has already revolutionized approaches and expectations around detection and diagnosis of species of interest. These changes have been most significant in contexts where morphological taxonomy has been most difficult, such as separation of cryptic species, identification of fragments or products derived from organisms, and recognition of species from poorly-characterized life stages.

BIOSCAN is accelerating support for reviewing and describing the millions of species still lacking scientific names. The Barcode Index Number (BIN) system offered by BOLD simplifies analysis and presentation of well-defined sets of specimens as diagnosable units of biodiversity. Each BIN represents a cluster of individuals that show minimal variation in the standard barcode markers and, in many cases, these clusters will correspond to different species that live and reproduce separately in the environment.

 

The BARCODE 500K research program established the sequencing facilities, analytical protocols, informatics platforms, and international collaboration needed to build the DNA barcode reference library. Building on this success, BIOSCAN launched in June 2019 to scan life and codify species interactions while expanding the reference library and demonstrating its utility. BIOSCAN will be the foundation for the Planetary Biodiversity Mission, a mission to save our living planet.

BIOSCAN is accelerating support for reviewing and describing the millions of species still lacking scientific names. The Barcode Index Number (BIN) system offered by BOLD simplifies analysis and presentation of well-defined sets of specimens as diagnosable units of biodiversity. Each BIN represents a cluster of individuals that show minimal variation in the standard barcode markers and, in many cases, these clusters will correspond to different species that live and reproduce separately in the environment.

 

Since organisms can be assigned to a BIN even when no scientific name is available and even when the exact taxonomic significance of the BIN is unclear, the expanded collecting and sequencing effort planned for BIOSCAN can both assist taxonomists to work more rapidly and efficiently and can offer an interim framework for categorizing and mapping taxonomic units pending full taxonomic review. The significance of such a framework cannot be underestimated. Without a proper and timely catalogue of the units of biodiversity, we cannot fully study or understand the species with which we share the planet and with which our own future is intertwined.

As a result of delivering an efficient tool for identifying and classifying any organism, we gain the ability to explore and track the patterns of communities and ecosystems through time and space. This is especially important for understanding hyperdiverse groups and megadiverse regions. Detailed community analysis is unachievable, or at least unscalable when it depends on sorting and identifying thousands of cryptic organisms, which is the situation for most insects, fungi or marine organisms. As sequencing technologies and bioinformatics capabilities continue to advance, these same difficult groups can be routinely and regularly sampled and described. This offers whole new windows into the structure, ecology, and dynamics of each ecosystem, opening up unprecedented opportunities to understand and respond to biological systems. Perhaps most importantly of all, high-bandwidth DNA-based monitoring of biodiversity can support intelligent approaches to landscape-level conservation, agriculture and pest management, and response to climate change.

BIOSCAN will lay the foundation for an earth observation system. It will examine biological communities from at least half the world’s ecoregions to begin the task of compiling comprehensive biodiversity baselines.

BIOSCAN comes at a time when technological advances are combining with the rich data held in BOLD to increase the cost-effectiveness of barcoding and metabarcoding. The iBOL community internationally, and particularly the Centre for Biodiversity Genomics (CBG) at Guelph, are at the forefront in exploiting next-generation sequencing. iBOL’s approach is to use the power and scale of these platforms to focus on a narrow subset of each species’ genome as the tool that cheaply permits the broadest possible detection and identification of any species.

 

Going even further, the sensitivity of these platforms is unlocking the often-hidden relationships between species, allowing us to document these interactions and clarify their role in structuring biological communities. Every organism interacts with representatives of other species as hosts or food and itself supports or contains a universe of parasites and microbes. These relationships have complex effects on the role that each species plays in each ecosystem. In the past, these associated species have often been detected as a source of potential confusion while deriving reference barcodes from specimens. Increased sensitivity from sequencing platforms will allow BIOSCAN to start treating these intermingled sequences not as noise but as a tool to document the set of species associated with a specimen, the organism’s symbiome.

BIOSCAN will use taxonomically targeted primer sets on the DNA extract from single specimens to reveal their commensals, mutualists, parasites and parasitoids – the symbiome.

Going even further, the sensitivity of these platforms is unlocking the often hidden relationships between species, allowing us to document these interactions and clarify their role in structuring biological communities. Every organism interacts with representatives of other species as hosts or food and itself supports or contains a universe of parasites and microbes. These relationships have complex effects on the role that each species plays in each ecosystem. In the past, these associated species have often been detected as a source of potential confusion while deriving reference barcodes from specimens. Increased sensitivity from sequencing platforms will allow BIOSCAN to start treating these intermingled sequences not as noise but as a tool to document the set of species associated with a specimen, the organism’s symbiome.

iBOL’s new program will use these advances to build on the foundations of BARCODE 500K and deliver the reference data, tools, and processes that will allow the world to survey and monitor all life. BIOSCAN’s three main research themes aim to (1) increase the coverage of the barcode reference library to at least two million species, (2) exploit the power of new sequencing platforms to survey species communities at thousands of sites across different ecoregions and (3) to probe the biotic associations of millions of individual organisms. The CBG team has invested not only in upgrading sequencing hardware to support the scale and complexity of BIOSCAN but also in the informatics capability required to support it, now available as the Multiplex Barcode Research and Visualization Environment (mBRAVE). iBOL will also use this program to address outstanding issues around marker genes and sequencing protocols for challenging taxonomic groups and to standardize approaches to sampling taxa in different environments and ecosystems.

The efficiency of barcoding as a tool for identifying species or for validating other identifications also positions BIOSCAN as an essential activity in support of other genomics activities. The Earth Biogenome Project (EBP) and a suite of taxon-specific genomics networks aim to sequence full genomes or significant portions of the genome for many or all the world’s species. A significant challenge for these major projects will be to locate high-quality genetic material to represent each of these species. By building the reference library of DNA barcodes, each accompanied by vouchered specimens and extracted DNA, BIOSCAN’s collecting activities can also enable these projects to proceed rapidly and with high confidence. The deliverables of BIOSCAN are fully complementary to those of EBP and similar efforts. BIOSCAN will deliver the reliable look-up mechanisms that verify the identifications associated with more extensive sequencing and will also deliver the biogeographic information to understand the distribution and variation for each species, along with their interactions. Complete-genome efforts will complement this with extensive additional data from examples of each species, enabling us to explore how species function and how evolution has shaped them.

 

By deep sequencing tens of millions of DNA extracts from single specimens and metabarcoding more than 100 million specimens from 2,000 sites spanning half the world’s ecoregions, BIOSCAN will expose countless undescribed species and reveal their distributions, dynamics and hidden interactions. Although BIOSCAN will not register all species or fully reveal their dynamics and interactions, it will be the foundation for a 20-year mission that will achieve these goals. Along the way, the aim is to develop the network to include practitioners and projects in all regions.

Participation is sought from researchers in all countries to expand iBOL’s coalition and explore multi-cellular diversity throughout the world’s ecosystems. iBOL welcomes comments and online discussion on the draft Strategic Plan for BIOSCAN.

We share our planet with more diversity than we yet recognise. This diversity drives the systems that keep the planet habitable for our species and those on which we depend. Now is the time to understand and monitor biodiversity everywhere. BIOSCAN is a key opportunity to make this happen.

Please check out the following resources and contribute to delivering BIOSCAN.

Written by

Donald Hobern

Donald Hobern

Executive Secretary, International Barcode of Life Consortium

October 2, 2019
https://doi.org/10.21083/ibol.v9i1.5527

Newsletter

Get the Barcode Bulletin delivered to your inbox

Don't Miss Out!

Subscribe to the iBOL Barcode Bulletin for updates on DNA barcoding efforts, the iBOL Consortium, and more.

Also in BIOSCAN

INSECTS DON’T TALK, BUT NEW DNA-BASED TECHNOLOGIES ARE HELPING TO TELL THEIR STORIES

by Christina Lynggaard, Martin Nielsen, Luisa Santos-Bay, Markus Gastauer, Guilherme Oliveira and Kristine Bohmann | Oct 16, 2019 

HOW A TROPICAL COUNTRY CAN DNA BARCODE ITSELF

by Dan Janzen and Winnie Hallwachs | Oct 2, 2019

comment on this article

The Barcode Bulletin moderates comments to promote an informed and courteous conversation. Abusive, profane, self-promotional, or incoherent comments will be rejected.