By Crystal Sobel
Carter Lear and Jaiden Maksagak (left to right) venturing across the tundra in search of insects
PHOTO CREDIT: Andrea Dobrescu
What do you think of when you hear the word ‘Arctic’? Do you picture snow and ice, freezing temperatures, vibrant communities, and animals like the polar bear and Arctic fox?
Not everyone is able to experience first-hand the vast tundra or see people fishing for Arctic char as they travel down the river to the ocean. I hope to share my impressions as a visitor to the Arctic, through my fieldwork as a research technician for the Arctic BIOSCAN (ARCBIO) project.
ARCBIO is a partnership between the Centre for Biodiversity Genomics (CBG) at the University of Guelph and Polar Knowledge Canada (POLAR) that aims to carry out biodiversity assessments in the Kitikmeot Region of Nunavut. Teams of researchers and technicians have been sent from the CBG to Nunavut for eight weeks spanning July and August in the summer to collect and catalogue plants and animals.
I play a major role in the planning and logistics for ARCBIO’s field expedition which includes working out how to transport and assemble the equipment required to collect and catalog insects, plants, and small mammals for an entire field season involving more than 14 researchers. Careful planning is crucial to order and organize the more than 70 different pieces of equipment — Malaise traps, sifters, nets, forceps, camera gear, labels, collecting bottles, etc. — as it all needs to be in place at our research sites in time for our arrival at the start of field season.
Flying to Nunavut from Ontario involves three flights over two days. But once you arrive, the land is truly a sight to behold. It is like no other place on Earth; its beauty magnified by the midnight sun and the countless tundra flowers covering the landscape.
In 2018 and 2019, my Arctic travels were focused in Iqaluktuuttiaq (Cambridge Bay), Nunavut whose location on Victoria Island along the Northwest Passage has made it a key port for passengers and research vessels. The Inuit have been residing in this region for over 4,000 years, naming the area Iqaluktuuttiaq meaning ‘good fishing place’ in Inuinnaqtun, the traditional language of the area, for its abundance in Arctic char.
My colleagues and I worked at the magnificent new Canadian High Arctic Research Station (CHARS). Run by POLAR staff, the station has several research and teaching spaces including a very impressive necropsy lab that has enough space to dissect whales. Dorm style lodgings are available for visiting researchers, with a facility building full of fieldwork equipment from ATVs to scuba gear to snowmobile suits.
Photo credit: Crystal Sobel
We were also very fortunate to have hired two youth in Cambridge Bay for our 2019 field season. Jaiden Maksagak and Carter Lear helped with insect monitoring by setting up traps, collecting samples, and recording data. Having a keen interest in the sciences, they were eager to gain experience by working with us.
Our team also conducted field work in Kugluktuk for the 2019 summer field season. Kugluktuk, meaning ‘place of moving water’, is situated on the northern edge of the mainland of Canada and is the westernmost community in Nunavut. Here, we worked with two wildlife guides, Thomas Bolt and Dettrick Hokanak whom helped with monitoring for bear activity and site set up as well as with servicing of the insect traps.
In both Iqaluktuuttiaq and Kugluktuk, we sought guidance from Nunavut’s Hunters and Trappers Organization (HTO) who provided us with local wildlife guides, bear monitoring services, and recommended great science-minded youth from the community who worked with us as science rangers. We were grateful for the knowledge they shared with us and for the opportunity to share aspects of our research work with their communities on Nunavut Day.
The kids enjoyed our giveaways which included informational pamphlets, bookmarks, postcards, buttons and other fun items about animals and how DNA barcoding works. I enjoyed learning a few words in Inuktitut from them, such as nuna for land, tuluaq for crow, and hikhik for ground squirrels. I believe that it’s very important to democratize science, involve local communities in research projects, and make data available to the public including the people making decisions that could impact ecosystems and their biodiversity. We need sensitive tools to understand how Arctic environments are changing and give us insights into what we can do to solve problems. DNA barcoding arctic diversity, this is what ARCBIO is all about.
Written by
Research Technician, Collections Unit, Centre for Biodiversity Genomics
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Nee Soon Swamp Forest, Singapore
PHOTO CREDIT: Wang Luan Keng
Benthic macroinvertebrates – those animals that live at the bottoms of water bodies – are abundant, diverse, relatively immobile, and responsive to environmental stresses, and these traits make them ideal indicators of the quality of aquatic ecosystems. Our study demonstrates the utility of Next-Generation Sequencing (NGS) platforms as an efficient and rapid tool for monitoring efforts.
In freshwater ecosystems, non-biting midges (Diptera: Chironomidae) often constitute the majority of diversity and biomass with different chironomid species varying in their sensitivity to environmental changes. But, when monitoring these habitats, chironomids are either ignored entirely or not studied at a species-level because morphological assessments are expensive and laborious, and the identification literature is based on adults while larvae are most often collected.
Bilge Baloglu sampling water DNA from Singapore’s largest swamp forest remnant.
PHOTO CREDIT: Dickson Ng
We generated DNA barcodes using NGS to study chironomids among the natural swamp forest Nee Soon and three adjacent man-made reservoirs. We wanted to understand the effects of urbanization and to know whether the chironomid fauna of Nee Soon is resistant to, that is, minimally impacted by, the adjacent reservoirs. We sampled >14,000 chironomid specimens (both adults and larvae) as part of a freshwater quality monitoring program, and quantified species richness and compositional changes using NGS and DNA barcoding.
Our study showed that Singapore’s biggest swamp forest remnant maintains a rich and largely unique fauna of about 350 species. The minimal species overlap between sites indicated that the Nee Soon swamp forest is resistant against the invasion of species from surrounding artificial reservoirs.
These findings suggest that even small or fragmented swamp forests can be suitable habitats for chironomids, shedding light on many other swamp forests in Southeast Asia that collectively occupy a much larger area and that are threatened by destruction for oil palm plantations and paper pulp production. Overall, our study exposes the enormous power of NGS and DNA barcoding in ecological research to study ecosystem health, biological diversity, and habitat conservation.
1. Brodin Y, Ejdung G, Strandberg J, Lyrholm T (2013) Improving environmental and biodiversity monitoring in the Baltic Sea using DNA barcoding of Chironomidae (Diptera). Molecular Ecology Resources 13:996–1004.
2. Montagna M, Mereghetti V, Lencioni V, Rossaro B (2016) Integrated taxonomy and DNA barcoding of alpine midges (Diptera: Chironomidae). PLoS One 11:e0149673
3. Posa MR (2011) Peat swamp forest avifauna of Central Kalimantan, Indonesia: Effects of habitat loss and degradation. Biological Conservation 144(10):2548-2556.
4. Hooijer A, Page S, Canadell JG, Silvius M, Kwadijk J, Wösten H, Jauhiainen J (2010) Current and future CO2 emissions from drained peatlands in Southeast Asia. Biogeosciences 7:1505–1514
For full details, please refer to the publication in Frontiers in Zoology.
Written by
Centre for Biodiversity Genomics, Guelph, ON, Canada
doi: 10.21083/ibol.v9i1.5525
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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
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
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
Centre for Biodiversity Genomics, Guelph, ON, Canada
General Manager: Savanna and Arid Research Unit, South Africa
doi: 10.21083/ibol.v9i1.5471
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Monitoring life within large bodies of water – those species that should and shouldn’t live there – can be very expensive and time consuming. To overcome these limitations, efforts in many temperate regions employ methods that use environmental DNA (eDNA), enabling effective and targeted detection of invasive and resident endangered species.
Our study is the first to demonstrate that eDNA-based monitoring can be successfully applied to target the whole fish community in a tropical freshwater system and its adjacent wetlands.
Between 1980 -1990, eDNA was the term introduced to define particulate DNA and it was used to detect and describe microbial communities in marine sediments and phytoplankton communities in the water column1. However, eDNA is presently defined as the genetic material left behind by eukaryotic organisms in the environment, reflecting a rise in the use of eDNA for the detection of vertebrate and invertebrate species in aquatic systems1. The popularity of using eDNA has increased following the development of next-generation sequencing, advances in quantitative PCR (qPCR), and the growth of DNA barcodes libraries such as the Barcode of Life Data System (BOLD), providing a quicker and more taxonomically comprehensive tool for biodiversity assessments.
South end of lake Bacalar with the sinkhole Cenote Azul.
PHOTO CREDIT: Manuel Elías-Gutiérrez
Lake Bacalar is the largest epicontinental habitat in Mexico’s Yucatan Peninsula, and it is renowned for its striking blue color, clarity of the water, and for the world’s largest occurrence of living stromatolites, a calcareous mound built up of layers of lime-secreting cyanobacteria. Due to the presence of sediments derived from karst limestone, it represents the world’s largest fresh groundwater-feed ecosystem. The northern part of Lake Bacalar is connected to a complex system of lagoons and the southern part has an indirect connection to the sea via a wetland system that connects with Hondo River and enters Chetumal Bay. This river has been heavily impacted by the discharge of organic waste and pesticides, by vegetation clearing, and by the introduction of invasive fish such as tilapia and the Amazon sailfin catfish (Pterygoplichthys pardalis) 2-4, first detected in 2013 4. The Amazon sailfin catfish is a serious threat to the fragile stromatolite ecosystem due to its burrowing habits and competition with local fish. The impact of declining water quality and the rise of invasive species on the native fish fauna needs to be carefully monitored in aid of conservation efforts of Lake Bacalar.
A team of researchers from the Instituto Tecnológico de Chetumal and El Colegio de la Frontera Sur sampled eight localities in December 2015, and January and April 2016. After each of 14 sampling events, water and sediment samples were immediately placed on ice before transportation to the lab in Chetumal. To minimize eDNA degradation, we filtered water samples within seven hours of collection. All filters and sediments were stored at -18°C before being transported on ice from Chetumal to the Centre for Biodiversity Genomics in Guelph, Canada, where DNA extraction was undertaken.
Water sampling between stromatolites.
PHOTO CREDIT: Miguel Valadez
We sequenced short fragments (<200 bp) of the cytochrome c oxidase I (COI) gene on Ion Torrent PGM or S5 platforms. In total, we recovered eDNA sequences from 75 species of vertebrates including 47 fishes, 15 birds, seven mammals, five reptiles, and one amphibian. Although all species are known from this region, six fish species represent new records for the study area, while two require verification (Vieja fenestrata and Cyprinodon beltrani /simus), because their presence is unlikely in this ecosystem. While there were species (two birds, two mammals, one reptile) only detected from sediments, water samples recovered a much higher diversity (52 species), indicating better eDNA preservation in the slightly alkaline Bacalar water. Because DNA from the Amazon sailfin catfish was not detected, we used a mock eDNA experiment that confirmed our methods were effective.
Interesting findings include the detection of rare species, such as an anteater Tamandua mexicana, which was detected by both PGM and S5 instruments from a river sample (Juan Sarabia), and migratory birds, such as warbler Oreothlypis peregrina known to overwinter in the Yucatan Peninsula.
Docks in front of Bacalar town
PHOTO CREDIT: Miguel Valadez
Our study indicates that eDNA can be successfully applied to monitor vertebrates in a tropical oligotrophic lake as well as more eutrophic (higher primary production) wetlands and can aid conservation and monitoring programs in tropical areas by improving our capacity to map occurrence records for resident and invasive species.
Our next step is to convince Mexican and international stakeholders to implement these methodologies and establish a permanent biomonitoring system for this and other pristine freshwater ecosystems found in Yucatan Peninsula. This work is necessary to detect effects of climate change, declining water quality, and the increasing tourism activities in this region.
1. Díaz-Ferguson EE, Moyer GR (2014) History, applications, methodological issues and perspectives for the use of environmental DNA (eDNA) in marine and freshwater environments. Revista de Biología Tropical 62: 1273-1284. DOI: 10.15517/RBT.V62I4.13231
2. Wakida-Kusunoki AT, Luis Enrique Amador-del Ángel (2011) Aspectos biológicos del pleco invasor Pterygoplichthys pardalis (Teleostei : Loricariidae) en el río Palizada, Campeche, México. Revista Mexicana de Biodiversidad 82: 870-878
3. Alfaro REM, Fisher JP, Courtenay W, Ramírez Martínez C, Orbe-Mendoza A, Escalera Gallardo C, et al. (2009) Armored catfish (Loricariidae) trinational risk assessment guidlines for aquatic alien invasive species. Test cases for the snakeheads (Channidae) and armored catfishes (Loricariidae) in North American inland waters. Montreal, Canada: Commission for Environmental Cooperation. pp. 25-49.
4. Schmitter-Soto JJ, Quintana R, Valdéz-Moreno ME, Herrera-Pavón RL, Esselman PC (2015) Armoured catfish (Pterygoplichthys pardalis) in the Hondo River basin, Mexico-Belize. Mesoamericana 19: 9-19.
Written by
Centre for Biodiversity Genomics, Guelph, ON, Canada
El Colegio de la Frontera Sur, Unidad Chetumal, Chetumal, Mexico
El Colegio de la Frontera Sur, Unidad Chetumal, Chetumal, Mexico
doi: 10.21083/ibol.v9i1.5474
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