The important interactions behind the itch

The important interactions behind the itch

The important interactions behind the itch

The potential consequences of reducing Anopheles gambiae mosquitoes to control Malaria

Ghanaian researchers sorting insect samples at the University of Ghana, Accra, Ghana.

IMAGE CREDIT: Michelle L. D’Souza; PHOTO CREDIT: Lema Concepts Africa

Written by

Talya D. Hackett

Talya D. Hackett

Department of Zoology, University of Oxford, Oxford 

Karen E. Logan

Karen E. Logan

Target Malaria, Dept Life Sciences, Imperial College London, UK

Michelle L. D'Souza

Michelle L. D'Souza

Centre for Biodiversity Genomics, University of Guelph, Guelph, CA

January 27, 2021

doi:10.21083/ibol.v11i1.6267

Only four months after China reported its first COVID-19 case to the World Health Organization (WHO) the virus had spread to every nation on the African continent. Despite being home to 17% of the world’s population, Africa currently accounts for just 2.5% of COVID-19 related deaths1. But the pandemic may well have caused many more to die, not from coronavirus, but from malaria.

The 2020 World Malaria Report warned that disruptions to malaria prevention and treatment caused by the coronavirus could see as many as 100,000 malaria-related deaths in Sub-Saharan Africa2. Similar effects were unfortunately experienced during the 2014-2015 outbreaks of Ebola in West Africa3. While most strategies being employed to control malaria have worked well, progress to reduce its incidence has stagnated. New strategies are needed to prevent the mortality rate from increasing further and to better prepare countries in the face of other unexpected pressures.

With the ambitious goal to create a world free of malaria, one not-for-profit research consortium–Target Malaria–is developing novel technologies using genetic modification to control the numbers of the malaria-transmitting mosquitoes.

The nature of malaria and the microbe responsible

Malaria is a disease that starts with a small single-celled parasite. This microorganism belongs to the genus Plasmodium, and of the four species that threaten humans, P. falciparum and P. vivax are the most common, and the former the most dangerous4.

Female mosquitoes alone spread malaria in nature. An infected mosquito injects a small number of parasites into its victim’s bloodstream while it feeds, and the parasites then travel to the liver where they multiply rapidly before infecting red blood cells. Flu-like symptoms begin when the parasites break out of the blood cells, one to four weeks after the bite.

Of the 229 million confirmed malaria cases worldwide in 2019, 94% occurred in Africa2. Even more devastating, of the 409,000 malaria-associated deaths, 84% occurred in children under the age of five.

While there are more than 3,500 species of mosquito worldwide and 837 in Africa, three very closely related species are responsible for most transmission of the disease: Anopheles gambiae, Anopheles coluzzii, and Anopheles arabiensis. These three species belong to the Anopheles gambiae complex which, if targeted, is likely to have the largest effect on the transmission of malaria. This species complex has tightly evolved with humans and is the key vector for malaria in sub-Saharan Africa.

Current vector control tools such as insecticides, bed nets, and drugs have been effective in reducing malaria cases but not in eradicating the disease. Target Malaria’s approach is meant to be complementary to the existing interventions by focusing on malaria control by mosquito control.

Researchers unify under Target Malaria

In 2003, Prof. Austin Burt published a seminal paper5 describing the principle of genetically modifying a population of mosquitoes for applications in the control of vector-borne diseases. Prof. Burt predicted that malaria-transmitting mosquitoes could potentially disappear in an area within two years when using these novel genetic tools. It was fortuitous that only a few years prior in Imperial College London, where Prof. Burt was working, a team lead by Prof. Andrea Crisanti had created the first reliable system for germline transformation of a malaria-transmitting mosquito6.

The two groups were brought together in 2005 with a grant given as part of the Grand Challenges in Global Health initiative and in a little over a decade the team’s scientific progress had resulted in a new mechanism for genetic control measures within An. gambiae7.

The initial group of researchers has now grown into a team of 180 project members, with collaborating research partners in Africa, Europe, and North America. As the work progressed, the project grew under its new brand–Target Malaria.

Target Malaria is working with five African partner sites.
IMAGE CREDIT: Michelle L. D’Souza

Today, Target Malaria is working with five African partner sites: Burkina Faso, Cape Verde, Ghana, Mali, and Uganda. This work is being headed by Dr. Abdoulaye Diabate at the Institut de Recherche en Sciences de la Santé (Research Institute on Health Sciences), Bobo-Dioulasso, Burkina Faso; Dr. Adilson de Pina at the Instituto Nacional da Saude (National Institute of Public Health, CCS-SIDA), Cape Verde; Dr. Fred Aboagye-Antwi at the University of Ghana, Accra, Ghana; Dr. Mamadou Coulibaly at the University of Bamako Malaria Research and Training Center, Bamako, Mali; and Dr. Jonathan Kayondo at the Uganda Virus Research Institute, Entebbe, Uganda.

Each of the African partners and their teams bring a different skillset to the collaboration, none being able to deliver all key elements independently. A relationship of co-development is fostered within the project with scientists working together across countries and with communities towards a common objective and vision–a world free of malaria.

The three key guiding pillars

Target Malaria’s work is structured around three key pillars: science, stakeholder engagement, and regulatory affairs. Each pillar is essential for the project’s success, supporting responsible research and development of genetic technologies, a commitment to engaging a wide variety of stakeholders, as well as ensuring compliance with all national regulations and laws. 

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Science

To date, Target Malaria has made significant scientific advancements on the path to developing a new tool for vector control for malaria. Researchers have demonstrated the proof of concept in creation of a transgenic sterile male An. gambiae8 strain, demonstration of the ability to modify a laboratory population of An. gambiae mosquitoes to be male biased9, suppression of a small cage population of laboratory reared An. gambiae mosquitoes10, creation of the first gene drive mosquitoes capable of suppressing a laboratory population of An. gambiae mosquitoes11, modelling the potential of genetic control of malaria mosquitoes12, modelling suppression of malaria vector using gene drive13, and the importation of the first genetically modified mosquitoes (a self-limiting sterile male line) into Burkina Faso for contained laboratory use in 2016 and regulatory approval for the subsequent release of the same self-limiting sterile male line in 2019.

Stakeholder engagement

The list of stakeholders is vast, from grass roots, those local communities where the project is working, through to local civil society organizations, regional governing bodies, and the appropriate governmental agencies, all in-country, as well as a range of interested parties outside of the African partner countries. Target Malaria is committed to ensuring that the stakeholders understand the research and long-term goals of the project enabling them to make an informed decision on whether to support the project’s efforts. Engagement also helps ensure that the research is welcomed and useful in the fight against malaria. Most importantly, Target Malaria will learn a lot from their stakeholders through the process.

Regulatory affairs

While an important aspect of Target Malaria’s strategy is to focus on the communities that might benefit from the technology and that are most concerned by the research activities, they also have an ongoing, transparent dialogue with other stakeholders at the national and international level. For example, the project is taking a phased approach to its development pathway in line with guidance from the WHO14.

Technology being developed

The goal is to develop modified mosquitoes that can pass on to their progeny a self-sustaining genetic change, a process aiming to reduce specific mosquito populations to break the malaria transmission cycle. To do so, Target Malaria is using gene drive, a phenomenon that occurs in nature and causes a selected trait to rapidly increase in frequency through a population via sexual reproduction over several generations. Gene drive works by increasing the likelihood–from the usual 50 per cent to greater than 95 per cent–that a modified gene will be inherited by its offspring. This means that over the course of several generations, a selected trait could become increasingly common within a specific species (depending on the specific area and how the animals move around within it).

Researchers are investigating the use of genes that produce enzymes that cut specific sequences of DNA. Called nucleases, these enzymes found in simple single celled organisms can copy themselves from one chromosome to another5. When introduced into the malaria mosquito, the nuclease works by identifying and cutting a selected site within essential genes targeted by researchers, rendering them functionless, such as reproductive genes. The subsequent effects depend on the nature and importance of the gene.

Target Malaria’s goal is to produce modified malaria mosquitoes that can pass these genes on to greater than 95 per cent of their offspring, so the modification is spread throughout the specific population relatively quickly and is effectively “self-sustaining”. This strategy is known as population suppression, and as the mosquitoes themselves do the work of spreading the modification, it makes the reduction of the malaria mosquito population relatively cost effective and simple to implement.

Current gene drive research is at an early stage, and so definitive decisions about gene drive-based tools are premature. Based on current progress, field releases of a gene drive-based tool are many years away. This gives scientists and stakeholders, specifically those from countries where gene drives might one day be employed, valuable time to consider the important questions of regulation, risk assessment, ethics, and engagement, and to prepare for assessing any application related to gene drive mosquitoes and their potential use as a tool for vector control for malaria.

An ecological approach spearheaded in Ghana

As the gene drive approach in development by Target Malaria will specifically target the An. gambiae complex to reduce its population, it is vital to ensure there are no undesirable consequences to the rest of the plant and animal communities. In Ghana, researchers are focusing on the ecological implications of the work; the role of the An. gambiae mosquito in the broader ecosystem. The ongoing research in Ghana aims to predict these potential effects.

 

Researchers setting off to sample the insect community around a Ghanaian village.

PHOTO CREDIT: Michelle L. D’Souza

THE ECOLOGICAL ROLE OF MOSQUITO LARVAE IN AQUATIC ENVIRONMENTS

read more…

WHAT WE KNOW, DON’T KNOW, AND THINK WE KNOW ABOUT THE PREDATORS OF MOSQUITOES

read more…

POLLINATORS OR NECTAR THIEVES? THE ROLE OF MALARIA-TRANSMITTING MOSQUITOES IN POLLINATION

read more…

ECOLOGICAL AND EPIDEMIOLOGICAL INSIGHTS FROM BLOOD MEALS

read more…

While some aspects of An. gambiae ecology is well studied, research in Ghana will provide a more complete picture, specifically determining the interactions between An. gambiae and other mosquito species as well as predators, prey, and vertebrate hosts. In this sense, the research is based on a community ecology approach rather than looking at just mosquito ecology.

Researchers are sampling, as far as they are able, insects from the entire aerial communities across all habitats, not just where they expect to find high numbers of An. gambiae. Equally true for insectivores that might feed on mosquitoes or similar small aerial insects, they are taking fecal samples or stomach contents. In aquatic habitats, they are sampling from a range of water bodies and collecting representatives across all insect and insectivorous groups. And, because adult mosquitoes rely on flower nectar for food, they are sampling the pollinator community as well. Finally, they are looking at the community of biting flies and their vertebrate hosts by determining blood-meal interactions to better understand shared hosts and the potential for zoonotic disease transmission15. Importantly, all methods and target sample numbers have been cleared by independent ethics boards at both the University of Ghana and the University of Oxford to ensure there is no lasting impact on the community of plants and animals where the work takes place.

Insect samples collected around a Ghanaian village using Malaise traps (top) before being sorted and pinned (bottom) at the University of Ghana.
PHOTO CREDIT: Lema Concepts Africa

Using this broad community approach allows researchers not only to describe the role of An. gambiae in the ecosystem but also to predict how the rest of the ecological community would respond to An. gambiae reduction. For example, the data would allow them to determine which insects might face more pressure from predators if those that feed on mosquitoes shifted their feeding behaviour to replace An. gambiae in their diet and how this change might affect the rest of the food web. As there is no known animal or plant that relies solely on An. gambiae16, and food webs tend to rewire following minor perturbations17,18, it is predicted that there will not be any significant effects because of An. gambiae population reduction. Regardless, it is necessary to ensure this is the case and a community ecology approach will make this possible.

Some of the faces of the research team in Ghana. Dr. Fred Aboagye-Antwi (Ghanaian Principle Investigator, top left), Helen Selorm Wohoyie (Assistant Stakeholder Engagement and Communications Advisor, top center), Divine Dzokoto (Senior Stakeholder Engagement and Communications Advisor, top right) and Dr. Talya D. Hackett (project coordinator), Bernard Aiye Adams, Ezekiel Yaw Donkor, and Naa Na Afua Acquaah (laboratory technicians) (bottom, left to right).
PHOTO CREDIT: Lema Concepts Africa

Building a DNA barcode reference library for Ghana

The tools being used to construct the food web are mostly molecular-based, all requiring the creation of a DNA barcode library for insects in the area as the important first step. To this end, researchers in Ghana regularly collected terrestrial insects from villages in the southeast of Ghana for a year.

Once the library is established, they can then start looking at the feces and the gut contents of insectivores and use that library to match and identify prey DNA fragments using DNA metabarcoding.

Researchers are using a similar metabarcoding approach for the aquatic food web while for the pollination network they will use a combination of traditional observational methods and DNA metabarcoding of pollen from caught insects. Finally, for the blood meal analysis, they are metabarcoding the blood meals of fed mosquitoes and other biting flies to identify what has been bitten.

The ecological research in Ghana is a collaboration between Dr. Fred Aboagye-Antwi at the University of Ghana, Prof. Sir Charles Godfray and Prof. Owen Lewis at the University of Oxford, as well as an extensive team of postdoctoral researchers, Ph.D. students, and technicians at both institutions. Part of the UK team, postdoctoral researcher and project coordinator, Dr. Talya D. Hackett is organizing efforts between countries, including a collaboration with the Centre for Biodiversity Genomics (CBG) in Guelph, Canada, global leader in the field of DNA barcoding. Supported by Prof. Paul D. N. Hebert, the Director of CBG, and Dr. Michelle L. D’Souza, samples from Ghana have begun making their way to the large sequencing platforms housed at the CBG.

Dr. Talya D. Hackett (left) and Dr. Michelle L. D’Souza (right) discuss DNA barcode data compatibility across platforms EarthCape and BOLD Systems at the University of Ghana.
PHOTO CREDIT: Lema Concepts Africa

So far, about 3,000 insects have been processed and 530 BINs (species proxies) have been documented, about 70% of which are unique to the project. Efforts will ultimately barcode 100,000 specimens and fill a large gap in barcode data currently missing from West Africa.

Conclusions

Examining diets to determine species-specific interactions in a complex community food web is only possible at this large scale with molecular techniques, and only recently, because the costs of DNA barcoding and metabarcoding techniques have dropped. Even five years ago this sort of a project would not have been feasible.

Apart from building large, comprehensive food webs, these data can further inform our understanding of things like community structure and insect abundances across time and space, the dietary overlap of insectivorous species, and niche overlap of different mosquito species.

All data will be made publicly available. Ultimately, this project is creating a wealth of information, not just for Target Malaria’s research goals, but for the broader scientific community and for other people within Ghana and West Africa.

These efforts are a demonstration of the power of DNA barcoding and its ability to reveal the nature and intensity of interactions among all species. This endeavour, to reveal species interactions to clarify their role in structuring biological communities, is a key research theme of BIOSCAN, iBOL’s new seven-year, $180 million global research program that aims to revolutionize our understanding of biodiversity and our capacity to manage it.

If you would like to know more about Target Malaria, go to www.targetmalaria.org

References:

1. World Health Organization (2020) WHO Coronavirus Disease (COVID-19) Dashboard. Accessible at: https://covid19.who.int/

2. World Health Organization (2020) World malaria report. Accessible at: https://www.who.int/teams/global-malaria-programme/reports/world-malaria-report-2020

3. Wang J et al. (2020) Preparedness is essential for malaria-endemic regions during the COVID-19 pandemic. The Lancet 395(10230), 1094–1096. doi: 10.1016/s0140-6736(20)30561-4

4. Crutcher JM, Hoffman SL. Malaria. In: Baron S, editor. Medical Microbiology. 4th edition. Galveston (TX): University of Texas Medical Branch at Galveston; 1996. Chapter 83.

5. Burt A (2003) Site-specific selfish genes as tools for the control and genetic engineering of natural populations. R. Soc. London. Ser. B Biol. Sci. 270:921–928. doi: 10.1098/rspb.2002.2319

6. Catteruccia F, Nolan T, Loukeris TG, Blass C, Savakis C, Kafatos FC, Crisanti A (2000) Stable germline transformation of the malaria mosquito Anopheles stephensi. Nature 405(6789):959-962. doi: 10.1038/35016096.

7. Windbichler N, Menichelli M, Papathanos PA, Thyme SB, Li H, Ulge UY, Hovde BT, Baker D, Monnat RJ Jr, Burt A, Crisanti A. (2011) A synthetic homing endonuclease-based gene drive system in the human malaria mosquito. Nature. 473(7346):212-215. doi: 10.1038/nature09937.

8. Windbichler N, Papathanos PA, Catteruccia F, Ranson H, Burt A, Crisanti A (2007) Homing endonuclease mediated gene targeting in Anopheles gambiae cells and embryos. Nucleic Acids Res. 35(17):5922-5933. doi:10.1093/nar/gkm632

9. Galizi R, Doyle LA, Menichelli M, Bernardini F, Deredec A, Burt A, et al. (2014) A synthetic sex ratio distortion system for the control of the human malaria mosquito. Commun., 5: 1–8.

10. Hammond AM, Kyrou K, Bruttini M, North A, Galizi R, Karlsson X, et al. (2017). The creation and selection of mutations resistant to a gene drive over multiple generations in the malaria mosquito. PLOS Genet. 13:e1007039.

11. Kyrou K, Hammond AM, Galizi R, Kranjc N, Burt A, Beaghton AK, et al. (2018) A CRISPR–Cas9 gene drive targeting doublesex causes complete population suppression in caged Anopheles gambiae mosquitoes. Biotechnol. 36:1062–1071

12. North AR, Burt A & Godfray HCJ (2019) Modelling the potential of genetic control of malaria mosquitoes at national scale. BMC Biol. 17: 26.

13. North AR, Burt A & Godfray HCJ (2020) Modelling the suppression of a malaria vector using a CRISPR-Cas9 gene drive to reduce female fertility. BMC Biol. 18:98.

14. World Health Organization (2014) Guidance framework for testing of genetically modified mosquitoes. Accessible at: https://www.who.int/tdr/publications/year/2014/en/

15. Bellekom B, Hackett TD & Lewis OT (2021) A Network Perspective on the Vectoring of Human Disease. Trends Parasitol.

16. Collins CM, Bonds JAS, Quinlan MM & Mumford JD (2018) Effects of the removal or reduction in density of the malaria mosquito, Anopheles gambiae s.l., on interacting predators and competitors in local ecosystems. Vet. Entomol. 33(1):1–15. doi: 10.1111/mve.12327

17. Timóteo S, Ramos JA, Vaughan IP & Memmott J (2016) High resilience of seed dispersal webs highlighted by the experimental removal of the dominant disperser. Biol. 26:910–915. doi: 0.1016/j.cub.2016.01.046

18. Bartley TJ, McCann KS, Bieg C, Cazelles K, Granados M, Guzzo MM, et al. (2019) Food web rewiring in a changing world. Ecol. Evol. 3: 345–354. doi: 10.1038/s41559-018-0772-3

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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.

Taxon-based morphology+barcoding inventory

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.

Industrial biomonitoring

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).

Facilitating National Park staff’s biomonitoring efforts

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 (http://phillipsrodriguez@gmail.com) 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 (Robferug2000@gmail.com), 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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Also in BIOSCAN

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

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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.