To BOLDly Go

To BOLDly Go

To BOLDly Go

Catalog all of Earth's multicellular lifeforms—tens of millions of species—in one giant DNA library.

November 14, 2019

By Kat Pyne and Josh Silberg, Hakai Institute – hakai.org

Space may be the final frontier, and yet we still have light years to go before we fully understand the rich diversity of life at home. The current mission? Catalog all of Earth’s multicellular lifeforms—tens of millions of species—in one giant DNA library.

Imagine this: just as you would scan a cereal box’s barcode at the grocery store, the same thing could be done with any plant or animal’s DNA to find out its species. It may sound like science fiction, but scientists around the world are working toward that reality. Their goal? To create an international barcode of life!

So just how are scientists stocking the library’s shelves? Come with us to British Columbia and California to find out!

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How a tropical country can DNA barcode itself

How a tropical country can DNA barcode itself

How a tropical country can DNA barcode itself

Costa Rica’s newly started ten-year goal called BioAlfa is DNA barcoding an entire tropical country

Written by

Daniel Janzen and Winnie Hallwachs

Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 and Technical Advisors to Área de Conservación Guanacaste

October 2, 2019
https://doi.org/10.21083/ibol.v9i1.5526

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IBOL’s new research program BIOSCAN has set out to DNA barcode the world (terrestrial invertebrates especially).  This will give us a very broad and paper-thin view. We and the world can do a lot with paper.  A very lot. Especially when it is used to map movements, detect presence, and begin to reveal the linkages among living things, tens of millions of living things.

Costa Rica, a very enthusiastic node in BIOSCAN, has decided instead to go for depth for a place, for its million-plus species of Eukaryota in an area the size of a tiny USA state or a fraction of a Canadian province. There are more eukaryote species within 50 km of our field home in the Area Administrativa of Área de Conservación Guanacaste (ACG) in northwestern Costa Rica1,2 than in all of Europe.

Costa Rica’s newly started ten-year goal is called BioAlfa, as derived from BioAlfabetizada and BioAlfabetización (a.k.a. BioLiterate in another familiar language).

IBOL’s new research program BIOSCAN has set out to DNA barcode the world (terrestrial invertebrates especially).  This will give us a very broad and paper-thin view. We and the world can do a lot with paper.  A very lot. Especially when it is used to map movements, detect presence, and begin to reveal the linkages among living things, tens of millions of living things.

Costa Rica, a very enthusiastic node in BIOSCAN, has decided instead to go for depth for a place, for its million-plus species of Eukaryota in an area the size of a tiny USA state or a fraction of a Canadian province. There are more eukaryote species within 50 km of our field home in the Area Administrativa of Área de Conservación Guanacaste (ACG) in northwestern Costa Rica1,2 than in all of Europe.

Costa Rica’s newly started ten-year goal is called BioAlfa, as derived from BioAlfabetizada and BioAlfabetización (a.k.a. BioLiterate in another familiar language).

BioAlfa aims to document and reveal, for its 5 million people, by those people, with appropriate international collaborations and one major technical advance, the pocket personal reusable cheap barcoder, Costa Rica’s “total multi-cellular biodiversity”. For any species, if you know what it is, if you can read and access it, then humans are quite adroit at deciding how and why they want to conserve it for truly sustainable uses. “Use it or lose it” is a gene complex deeply embedded in our Pleistocene genome. That is the deepest, most selfish driver of BioAlfa.

A thoroughly barcoded national biodiversity will be at the least a major reference baseline for whatever sampling methods BIOSCAN and others employ world-wide. Not only will BioAlfa have repeatedly collected a year of Malaise traps from this or that ecosystem, but it will also come to know what fraction of the trappable and untrappable arthropod fauna is being captured in that or other years, owing to both Malaise trapping and all the other many ways we find invertebrates.

For any organism found in the country, Costa Rica wants to know what it is, where it is, what it does, and how to find it when you want to – for at the least the 25% of the country that is still natural forest – dry forest, rain forest, and (rapidly dwindling) cloud forest. And what is on the agroscape derives from the wild as well, so it will be registered too. BioAlfa’s technical and bio-political goal is to capture those informative items and get them all readably and legally stashed on the internet in the public domain. 

Until the internet, computerization, and DNA barcoding emerged, such a goal would have been only a dream, and restricted largely to what is big enough for you see through your binoculars or in the museum drawer. The latter species are some 2% of Costa Rica’s wild biodiversity, depending on how good and trained your vision, and how many libraries and field guides you have to hand – along with ever-scarcer quality taxonomists. What about the rest of the crops, beauties, wigglies, and dangers in those wild forests and remaining freshwater – 70% arthropods, 19% nematodes, and 9% fungi?

BIOALFA IS MODULAR

BioAlfa is modular. Different modules range from taxon-based morphology+barcoding inventory (e.g., all Hymenoptera, all Lepidoptera) that was initiated decades ago1,3-6, to industrial biomonitoring7 with 6 years (so far) of Malaise traps to determine the impact of a road and geothermal drilling platform on original complex tropical forest, to facilitating staff of Costa Rica’s national parks to set and manage at least a year of Malaise traps in all of Costa Rica’s major ecosystems (including the urban capital San Jose) with their own sweat equity (initiated March 2019 by gov-NGO collaboration), to (taking a note from iBOL’s Canadian efforts) setting rural schools to do their own Malaise trapping. And in all of this, BioAlfa is turning Costa Rica into being a tropical canary in the coal mine, now facing three decades of climate change8.

Image

Taxon-based morphology+barcoding inventory

   BIOALFA module

Hazel Cambronero and Sergio Salas collecting ACG moths from a light trap. Each moth is individually collected into discardable plastic containers so as to minimize DNA contamination among them.  At present, 11,500+ species of ACG Lepidoptera have been barcoded from light-trapped adults since 2004 and reared caterpillars since 1978, for an estimated total of 15,000 species from an area the size of New York and its suburbs (125,000 terrestrial ha of dry forest, rain forest, cloud forest, and intergrades of a 400-year old ranch being restored since 1985.

Image

Industrial biomonitoring

   BIOALFA module

The PL12 geothermal drilling platform in its first year of construction, with a Malaise trap at its margin for biomonitoring (the white spot just to the left of the yellow star).  This trap and its eight companions have been in place since forest clearing began in September 2013. Together these traps continually compare the insect community of the margin with that 50 m and 150 m into the forest behind. This trap collected ~ 80,000 insects of ~8,500 species in its first year, the same year that the platform was carved out of this old-growth forest.  Comparison with the traps 50 and 150 m into the forest showed that as far as their species and seasonal communities were concerned, the drilling platform did not exist. These nine traps in total contributed 11,500+ species barcodes as measured through Barcode Index Numbers.  The actual number once these species are “more known” will be about 13,000. The Centre for Biodiversity Genomics did the barcoding and analyses of seven of the traps in six months with funding from the Japan International Cooperation Agency (JICA) (the other two traps are still in the freezer, awaiting funding for processing).

Image

Facilitating National Park staff's biomonitoring efforts

   BIOALFA module

Two staff of Parque Nacional Tortuguero install their first Malaise trap by themselves following their early March instructive workshop in SINAC’s Parque Ecologico in Santo Domingo de Heredia (outskirts of San Jose).  While the photo appears simply to show two researchers, closer scrutiny shows that they both have guns on their belts.  That is to say, they are simultaneously park guards on the government payroll while now performing biodiversity science.  The trap is about 150 m from the jaguar at the bottom, a screen capture from a video taken by the Costa Rican Minister of the Environment himself, Carlos Manuel Rodriguez, on a visit at about the same time.  The slide itself was created by the trap setters and posted by them, unknown to BioAlfa, on International Forest Day, 21 March 2019.

As BioAlfa takes form, perhaps being a walking organism by January 2020, the modules each move at their own pace according to their technology, biopolitics, and “small” funds to accompany their massive Costa Rican (and on many occasions international) sweat equity. The sweat-equity budget will always characterize sustainable long-term tropical national biodiversity biodevelopment but also is the only way known to have a tropical country itself become truly aware of this vital piece of its socioeconomic fabric.

The modules also fit together according to their development, their discoveries, their small failures, their repairable flat tires. This is planning by doing rather than hewing to a monster complex “plan” or “blueprint” that is long obsolete by the time the rubber hits the road and takes years to create in the first place. It is also evolution, as biologists are very aware. But for other sectors of society, this methodology can be quite novel and even threatening.

There is, however, the reality that the overall cash cost, to match at least a portion of Costa Rica’s sweat equity (coupled with the same from the international community, and especially the taxasphere) will be at least $100 million as a single source spread over ten years and variously front-loaded and pulsed. Of this, $25 million will be needed for a permanent endowment, the income from which will be aimed at perpetuity for all of BioAlfa’s processes – ranging from data and specimen preservation to constant updating of information management for raw information and output formats. Another $25 million will be a slowly sinking fund to facilitate start-ups and start-up processes that build on BioAlfa biodiversity data for biodevelopment of all kinds by all sectors – government, private, commercial, academic, etc.; innovative embedment of wild biodiversity in Costa Rica’s socioeconomic fabric is the goal. And, finally, $50 million is for the actual cost associated with all the mechanics of species sampling (no matter how much sweat equity, there are store-bought costs), laboratory DNA barcoding the samples, and base management of the information and process. Fortunately, BioAlfa has the Centre for Biodiversity Genomics (CBG) backing BIOSCAN. The CBG can also meet the BioAlfa need to DNA barcode at least 10 million specimens that will be generated by BioAlfa over its ten years; the CBG has already barcoded 500,000+ ACG insects of about 45,000 species since ACG offered itself in 2003 to the CBG for this close scrutiny of tropical biodiversity, a level of scrutiny of which we have been innocently ignorant for various centuries.

A magnificent DNA barcode library and its accompanying collateral data and analyses will not, however, truly generate national bioliteracy until every citizen – farmer, schoolchild, housewife, garage mechanic, entrepreneur, and government employee has or can have a dirt-cheap personal barcoder in their pocket, reusable and connected to the internet through Wifi. All of the quasi-analogues that exist today and those envisioned are aimed at the high-end purchaser of both gadgets and supplies. When a cheap alternative comes down the road, there will be billions of buyers and barcodes and collateral information on each species will be the resource in short supply. Until that time, both verified barcodes and the gadget are in short supply.

A bioliterate world will contribute seriously to the global barcode library every time anyone uses the magic gadget. As in literacy, for it to reach its social potential, cheap tools are needed for everyone.

As is known to all, the academic research and discovery community has for a very long time been examining portions of tropical biodiversity for a multitude of reasons, yet also mostly in the fragmented, expeditionary and superficial way common to our northern societies and their tropical acolytes. BioAlfa is philosophically and technically an offspring of those efforts, but in modular outcomes differs in audience and actions.

Here we list just a few as modules of the start-up process. Each document is available on request for updates, if there are, but most are now available on the ACG web site and more will be parked there as available.

1.

On 27 November 2017, the previous Costa Rican government decreed that DNA barcodes from Costa Rican specimens are public domain, and therefore may be harvested (under appropriate government permit from CONAGEBIO, the operational manifestation of Costa Rica’s Ley de Biodiversidad). Costa Rican barcodes can be freely used, published, etc. for biodiversity identification and discovery. This assumes that the barcode itself is not of commercial value, anymore than is a word in a dictionary. Indeed, CONAGEBIO’s headline is “Contributing to the conservation and sustainable uses of biodiversity”. The permitting process basically involves registration of the project coupled with assurances that the actual owner of the organisms is in agreement with the sampling of “his or her” beasts. Simultaneously this decree set in motion the government mechanics of formally bringing BioAlfa to life. Available on request and the ACG web site (decree #40725).

2.

On 17 November 2018, the staff of the Sistema Nacional de Areas de Conservación (SINAC) of the present Costa Rican government of President Carlos Alvarado presented BioAlfa to the global COP meeting of the CBD (Convention for Biological Diversity) in Egypt as part of Costa Rica’s ongoing stock-taking of its biodiversity resources and weaving them into national socioeconomics. A bilingual folder available on request and the ACG web site.

3.

On 4 June 2019, the Costa Rican government officialized BioAlfa and its goals, especially by declaring it to be a process of National Importance, thereby granting even more legitimacy for the government to develop government-NGO-private-commercial-academic collaborations to advance BioAlfa goals (decree #41767). The signing of this decree was the occasion of a sit-down explanatory meeting of BioAlfa with the entire Cabinet and other major sector decision-makers. It is also at the roots of the government of Costa Rica currently constructing a proposal to the government of Norway for major funding of BioAlfa (fingers crossed).

4.

At present, a number of small modules are being initiated or continue with the few resources at hand, while desperately searching for at least enough funding to cover CBG’s sequencing costs that are currently at $3/insect for massive samples and hoped to drop to about $1/insect by January 2020.

  • Expansion of the long-on-going intense inventory of ACG Lepidoptera (adults and caterpillars and their parasitoids) to include the remainder of Costa Rica (estimate at least 25,000 species of Lepidoptera).
  • DNA barcoding the thorough national collection of aquatic insects in ethanol, done a few years earlier by the Universidad de Costa Rica but with no funds for identification.
  • Six years of continued barcoding and analysis of the 9 Malaise trap catches from the geothermal biomonitoring site and at select other National Electric Company (ICE) rural installations7.
  • Setting and managing Malaise traps by park staff, collected weekly for at least a year in 9 national parks (24 traps).
  • Malaise trapping conducted and analysis paid for by commercial ecotourism lodges and hotels in rural areas.
  • Ongoing organizational meetings with the Ministry of Education for the enlistment of select rural highschools to run Malaise traps in their vicinities.
  • Initial conversations with farm owners and government facilitators for combining insect trapping in fields with adjacent wild vegetation.
  • Initiation of conversations for collaborations with image, natural history and genomic aggregators such as GBIF, iNaturalist, and all the other mega-initiatives such as the Earth BioGenome Project (EBP). BioAlfa, just as is the case with BIOSCAN, has much to offer all of them.
  • Initiation of the dedicated BioAlfa web site. This is currently parked on the ACG web site, but that will eventually have its own encyclopedic web site.
  • Initiation of the process of quickly blessing enormous numbers of undescribed species with classical scientific names, and at the same time handling species-level taxonomic information flow and analysis with COI barcodes and BINs. It is a commonplace in the Costa Rican species-rich ecosystems for a BIN to contain several species that can be discriminated both by other subtle (to a human) traits and by clean clustering on both sides of shallow barcode splits.  The latter discrimination is greatly facilitated by large sample sizes accompanied by accumulating collateral information on natural history.
  • Initiation of forming a technical-biopolitical team of seasoned biodiversity managers with basic office facilities in San Jose (actually, Santo Domingo de Heredia in the outskirts of San Jose) and in ACG. On 1 January 2019, the BioAlfa team was joined by Jenny (Eugenie) Phillips Rodriguez the primary Costa Rican microlepidoptera specialist who has dedicated decades to the former INBio collection (now legal property of the Museo Nacional de Costa Rica) and its antecedents and its parataxonomists, and MS Roberto Fernandez Ugalde, formerly a field environmental planner for ICE projects, ecotourist guide and herpetological aficionado.  They are supported by the GDFCF endowment constructed for the specific purpose of supporting the long-term survival of ACG biodiversity, which of course includes its integral role in BioAlfa.
  • And many more at various stages of seeding or growth, but all delayed by the lack of funds for the direct laboratory sequencing to build the Costa Rican DNA barcode public library in BOLD.

In short, BioAlfa is engaging in the technically straightforward task of DNA barcoding an entire tropical country so as to set it up for being sustainably wanted as wild organisms by its own country. This is simultaneously a massively complex collage of technical science embedded in an omnipresent biopolitical socioeconomic context. BioAlfa will only be achievable when actually carried out by the future owners and caretakers of their country, with support from appropriate international collaborations.

References:

1. Janzen DH and Hallwachs W (2016) DNA barcoding the Lepidoptera inventory of a large complex tropical conserved wildland, Area de Conservacion Guanacaste, northwestern Costa Rica. Genome 59:641-660. dx.doi.org/10.1139/gen-2016-0005.

2. http://www.gdfcf.org

3. Fernandez-Triana JL, Whitfield JB, Rodriguez JJ, Smith MA, Janzen DH, Hallwachs W, Hajibabaei M, Burns JM, Solis MA, Brown J, Cardinal S, Goulet H, and Hebert PDN (2014)  Review of Apanteles sensu strictu (Hymenoptera, Braconidae, Microgastrinae) from Area de Conservación Guanacaste, northwestern Costa Rica, with keys to all described species from Mesoamerica.  ZooKeys 383:1-565. doi: 10.3897/zookeys.383.6418

4. Gaston KJ, Gauld ID and Hanson P (1996) The size and composition of the hymenopteran fauna of Costa Rica. Journal of Biogeography 23: 105-113.

5. Gauld ID (2000) The Ichneumonidae of Costa Rica, 3. Memoirs of the American Entomological Institute 63: 1-453.

6. http://janzen.sas.upenn.edu

7. Janzen DH (2017) Final (one year) report to ERM/JICA/ICE from GDFCF with respect to BIO/CBG/Canada laboratory barcoding of PL12 Malaise samples, and then their subsequent analyses by GDFCF for the project entitled  “SAPI for Geothermal Development Loan: Study on improvement of Environmental Monitoring methodologies for geothermal development in Costa Rica Agreement #0328497.”  Unpublished 73 pp. report, available on request from djanzen@sas.upenn.edu (2019-08-08).

8. Janzen DH and Hallwachs W (2019)  Perspective: where might be many tropical insects?  Biological Conservation 233:102-108. https://doi.org/10.1016/j.biocon.2019.02.030

Written by

Daniel Janzen and Winnie Hallwachs

Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 and Technical Advisors to Área de Conservación Guanacaste

October 2, 2019
https://doi.org/10.21083/ibol.v9i1.5526

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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

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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

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Don't Miss Out!

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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

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Starving for data and more: what rangers and scientists stand to learn from one another in South Africa

Starving for data and more: what rangers and scientists stand to learn from one another in South Africa

Starving for data and more: what rangers and scientists stand to learn from one another in South Africa

A one-year pilot biomonitoring program in Kruger National Park, South Africa – the Kruger Malaise Program – reignites rangers' energy about biodiversity conservation.

Silhouette of a giraffe in Kruger National Park, South Africa

PHOTO CREDIT: Michelle D’Souza

Insect biodiversity is understudied and often underappreciated. As evidence for large-scale insect declines emerge, there is an increasing need to address the extreme lack of data on the general ecology and population dynamics of most insect groups. Charismatic species, such as the iconic monarch butterflies (Danaus plexippus) of the Americas, are one of the few exceptions.

Closely related to the migratory Danaus plexippus, the non-migratory monarch species – Danaus chrysippus – is found in the warm climate of the African continent.
PHOTO CREDIT: Johandre van Rooyen

The caterpillars of the Emperor moth (Gonimbrasia belina) are just as iconic and societally relevant on the African continent. Locally referred to as ‘mopane worms’ after the mopane trees upon which they primarily feed, these insects have been a vital source of protein for generations. A mopane caterpillar contains on average 50 per cent protein1, a higher percentage than the average steak.

In recent years, mopane caterpillars have also provided an important source of income for many rural communities. It has been estimated that 9.5 billion caterpillars are harvested annually in Southern Africa’s 20,000 km2 of mopane forest. The ability to predict mopane caterpillar outbreaks in space and time becomes increasingly valuable, particularly for rural communities living along the borders of national parks, who rely heavily on natural resources to supplement their livelihood.

Mopane worm harvest in Kruger National Park, South Africa.
PHOTO CREDIT: Louise Swemmer

Local community members harvesting mopane worms in the Kruger.
PHOTO CREDIT: Louise Swemmer

Since 2010, permit-based harvesting projects have taken place in some South African National parks to share benefits and build positive relationships between the parks and their neighbouring communities. With the declining occurrence of mopane caterpillars outside of protected areas due to habitat change and over-harvesting, and the overall erratic nature of recent outbreaks, neighbouring communities risk losing an important source of food and income.

A better understanding of insect dynamics has the potential to inform the sustainable harvest of natural resources such as the mopane caterpillar, but it also tells us a lot more.

A pilot insect biomonitoring program in Kruger National Park, South Africa – the Kruger Malaise Program – is already demonstrating implications for natural resource harvesting, as well as agricultural pest and disease management. Perhaps even more significant, it has reignited energy in park rangers about biodiversity conservation.

One of 26 Malaise traps sampling insects in Kruger National Park with the Kruger Malaise Program.
PHOTO CREDIT: Ryan Rattray

The Kruger Malaise Program (KMP), a year-long monitoring effort, was undertaken in Kruger Park from May 2018 to June 2019. With the main goal of understanding insect diversity and seasonal variation, the program deployed 26 Malaise traps that sampled the flying insect community in all 22 sections of the park. Traps were set up within each section ranger’s property, and rangers were tasked with organizing and maintaining weekly sample collections. The samples were then retrieved in four large batches over the year by staff from the African Centre for DNA Barcoding (ACDB) in Johannesburg, South Africa, where they were packaged and shipped to the Centre for Biodiversity Genomics (CBG) in Guelph, Ontario, Canada for DNA barcode analysis. This program was only possible due to the collaborative efforts of park rangers and staff, researchers at the Savanna & Arid Research Unit in Skukuza, Kruger, and scientists at the ACDB and CBG.

The African Centre for DNA Barcoding (ACDB) team after collecting the last Malaise trap at the end of the KMP in June 2019: Zandisile Shongwe, Nolo Sello, Michelle van der Bank (ACDB Director), Ross Stewart, Jonathan Davies (top left to right), Johandre van Rooyen (bottom).
PHOTO CREDIT: Nolo Sello

With sampling now complete, analysis has begun in earnest. So far, more than 260,000 specimens have been processed, and 170,000 have been sequenced.  Preliminary results have delivered barcode coverage for 9,000 species including various agricultural pests (e.g., the olive fruit fly (Bactrocera oleae), and the rusty plum aphid (Hysteroneura setariae)) as well as several vector species known to transmit the bluetongue and African horse sickness viruses (e.g., Culicoides imicola) and West Nile Virus (Culex perexiguus). When compared against the DNA barcode database (BOLD Systems) of more than 600,000 species, almost half of the insect diversity uncovered by the program so far is only found in Kruger.

Based on species accumulation rates, it is likely that 25,000 species will be recorded in the park. This number represents more than half of the species previously reported from South Africa2, and quarter of those described in sub-Saharan Africa3.

Selection of specimens collected from the Kruger Malaise Program.
PHOTO CREDIT: CBG Imaging Lab

The Kruger Malaise Program reveals just how quickly DNA barcoding can provide in-depth and broad-scale information for regions where past research has largely been focused on particular taxonomic groups.  While one of the only comprehensive field guides for insects in South Africa contains 1,200 species – those that are ‘abundant, widespread, conspicuous, large or unusual’ – the Kruger Malaise program has largely uncovered the rare, small, inconspicuous, yet ecologically important, species.

In 2013, SANParks developed a biodiversity monitoring strategy but its activation has been very mixed across the 19 parks. Some began their monitoring efforts by focusing on rare species, while others used key indicator groups. But there have been no standardized techniques implemented across all parks, and there has been little monitoring of insects at a large scale, mainly because of the lack of taxonomic expertise. A program involving DNA technology makes large-scale biomonitoring of these national parks possible.

The KMP has been a huge success with the next steps set to fine tune logistics before its expansion to other parks and, ideally, to identify specific sites in Kruger for ongoing monitoring. The program also provided a test bed for TRACE (Tracking the Response of Arthropod Communities to Changing Environments), a major research theme within the 7-year, $180 million BIOSCAN program. Its success has demonstrated the feasibility of extending this work in other national parks within South Africa and on a global scale. In doing so, BIOSCAN will lay the foundation for a DNA-based global biodiversity observation system, similar to the monitoring systems that have been recording weather patterns since the 1800s. BIOSCAN has a grand vision, one that is necessary if we are to truly identify, understand, and manage the global decline in insects.

The park rangers and staff who managed the Malaise traps in Kruger National Park.
PHOTO CREDIT: Michelle D’Souza

But if you ask the people working in Kruger, the KMP was more than a biodiversity monitoring program. Most rangers start out as nature conservation and zoology students, but anti-poaching efforts are so time consuming that their roles have gone from biodiversity managers to single-species protectors. The KMP has not only sparked interest and reignited energy in the park rangers about their conservation work, it has engaged and valued the observational and experiential data that rangers have to offer, such as stories and strategies related to the mopane caterpillars.

In this way, the KMP has made a very big impact – and that is the true beauty of the program – its ability to spur interest in insect life, and the patterns and processes that define our world.

Please feel free to contact Michelle D’Souza, the KMP project manager, if you have any questions about the program: mdsouza@uoguelph.ca

References:

1. Glew RH, Jackson D, Sena L, VanderJagt DJ, Pastuszyn A and Millson M (1999) Gonimbrasia belina (Lepidoptera: Saturniidae): a Nutritional Food Source Rich in Protein, Fatty Acids, and Minerals. American Entomologist 45(4): 250–253

2. Scholtz CH and Chown SL (1995) Insects in southern Africa: how many species are there? South African Journal of Science 91:124–126

3. Miller SE and Rogo LM (2002) Challenges and opportunities in understanding and utilisation of African insect diversity. Cimbebasia 17:197–218

Written by

Michelle L. D'Souza

Michelle L. D'Souza

Centre for Biodiversity Genomics, Guelph, ON, Canada

Danny Govender

Danny Govender

General Manager: Savanna and Arid Research Unit, South Africa

June 12, 2019
PDF
https://doi.org/10.21083/ibol.v9i1.5471

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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.