From concern to action: The Silicon Valley Barcode of Life

From concern to action: The Silicon Valley Barcode of Life

From concern to action: The Silicon Valley Barcode of Life

A new project empowers local citizens to catalog biodiversity to understand and protect nature in Silicon Valley.

 Volunteers at DNA Barcoding Bioblitz, Hidden Villa Farm and Wilderness Center, June 2018. PHOTO CREDIT: Dan Quinn

Human destabilization of climate with its current and future costs and suffering make headlines daily. Related yet to some extent independent, the most current mass extinction—the seventh1 event of its kind in the nearly four billion years since life appeared on Earth—with potentially greater adverse impacts2 receives severalfold less attention3. We began the Silicon Valley Barcode of Life to further iBOL’s work to address this imbalance.

 

We grew up in Palo Alto, exploring nature in our yard, on the nearby 8,800 acre Stanford University campus, and in regional open space spanning San Francisco Bay marshes, Coast Range grassland, chaparral, and redwood forests, and Pacific Coast beaches. From an early age we participated in, and more recently we’ve led others in habitat stewardship fieldwork.

Songbirds like the hooded oriole (Icterus cucullatus) and cedar waxwing (Bombycilla cedrorum), once common visitors to our yard, now come rarely if at all.

We’ve observed firsthand how humans are diminishing biodiversity. As property owners in our community have covered more land with buildings and paving, they’ve reduced and fragmented habitat4. Songbirds like the hooded oriole (Icterus cucullatus) and cedar waxwing (Bombycilla cedrorum), once common visitors to our yard, now come rarely if at all. As we and those around us have relied increasingly upon products imported from around the world, we’ve introduced pests and invasive species that disrupt long-standing ecological relationships5. Oak Sudden Death, caused by a water mold (Phytophthora ramorum) thought to have entered the United States via the nursery plant trade, has killed tanoak (Notholithocarpus densiflorus) and coast live oak (Quercus agrifolia) in some of our favorite hiking spots and far beyond.

PHOTO CREDIT: Jen Bayer

Feeling concern about losing the living nature we love, we’re acting to preserve it. In 2018, inspired by conservationists Daniel Janzen’s and Winnie Hallwachs’ biodiversity protection and advocacy in Årea de Conservación Guanacaste, and San Diego Barcode of Life founder Bradley Zlotnick’s biodiversity cataloging and education achievements in Southern California, we launched the Silicon Valley Barcode of Life with the purpose of using DNA barcoding to engage people in cataloging biodiversity, in learning about the importance of biodiversity to human well-being and about threats to it, and in acting to conserve it.

Taxonomy wheel graphic

Taxonomic distribution of biodiversity collected at Hidden Villa DNA Barcoding Bioblitz, June 2018. Colors in the heat tree indicate the number of samples detected.

IMAGE CREDIT: Hilary Bayer

To date we’ve actively engaged more than a hundred volunteers, directly addressed more than a thousand people in-person (pre-pandemic) and subsequent online events, and indirectly addressed several thousands more in published writing and through our website. We’ve also hand-collected 600 specimens from diverse ecosystems in Santa Clara and San Mateo counties, and collected nearly 30,000 additional specimens from Malaise traps deployed in partnership with Stanford University’s Fukami Lab, the City of Palo Alto, and Hidden Villa Organic Farm and Wilderness Center.

In 2021 we were offered an opportunity to partner with the Mono Lake Committee to study arthropods of the Mono Basin. Though Mono Lake is several hundred miles across California from the Silicon Valley, we’ve vacationed in the Sierra Nevada with our family for as long as we can remember, and we’re grateful to be able to contribute to protecting its biodiversity.

In our first round of collections, we gathered 250 unique specimens within a 50-mile radius of Mono Lake by hand. With pit traps and a Malaise trap on Mono Lake Committee properties, including the Outdoor Education Center visited by hundreds of students annually, we gathered about 4,000 additional specimens.

Mantidfly

Mantidfly, family Mantispidae.
PHOTO CREDIT: Jen Bayer

Scarabeidae beetle

Monkey beetle, genus Hoplia, family Scarabaeidae PHOTO CREDIT: Jen Bayer

In 2022 we’re continuing to catalog arthropods of Silicon Valley and of the Mono Basin. In both places we have plans to deploy additional Malaise traps in partnership with local conservation and educational organizations and proceed with hand collection, engaging volunteers in these activities and in specimen processing.

We’re demonstrating how DNA barcoding can be a means to quickly and cost-effectively catalog biodiversity and thereby contribute to global and local libraries of life—a resource on which many can rely to inform science-based stewardship and enrich educational programs.

“We’re demonstrating how DNA barcoding can be a means to quickly and cost-effectively catalogue biodiversity and thereby contribute to global and local libraries of life—a resource on which many can rely to inform science-based stewardship and enrich educational programs.”

Jen and Hilary Bayer, co-founders of
Silicon Valley Barcode of Life, in front of
their first Malaise trap.

We’re looking for partners.

Silicon Valley Barcode of Life is an all-volunteer endeavor made possible by dedicated advisors, generous donors, institutional partners who share our goals, and volunteers.

Please contact us if you’re interested in assisting Silicon Valley Barcode of Life with funding, macro photography, graphic design, data uploading, Malaise trap servicing, or hand collection.

You can reach us at svbarcodeoflife@gmail.com

We gratefully acknowledge the Consulate of Canada in San Diego for kindly supporting us in facilitating this partnership with the International Barcode of Life Consortium, and the staff at the Centre for Biodiversity Genomics for the ways they’ve assisted us in learning and contributing.

References:

1. Michael R. Rampino & Shu-Zhong Shen (2019): The end-Guadalupian (259.8 Ma) biodiversity crisis: the sixth major mass extinction? Historical Biology 33(1):1-7. DOI: 10.1080/08912963.2019.1658096

2. Cardinale BJ et al (2012) Biodiversity loss and its impact on humanity. Nature 486(7401):59-67. DOI: 10.1038/nature11148.

3. Legagneux1 P et al (2018) Our house is burning: Discrepancy in climate change vs. biodiversity coverage in the media as compared to scientific literature. Front. Ecol. Evol. 5:175. doi: 10.3389/fevo.2017.00175

4. University of Exeter. (2018, April 13). Crowded urban areas have fewer songbirds per person. ScienceDaily. Retrieved  from https://www.sciencedaily.com/releases/2018/04/180413093836.htm

5. Dawson W et al (2017). Global hotspots and correlates of alien species richness across taxonomic groups. Nature Ecology and Evolution 1: 0186. DOI: 10.1038/s41559-017-0186.

Written by

Jen Bayer

Jen Bayer

Silicon Valley Barcode of Life
Palo Alto, USA
Hilary Bayer

Hilary Bayer

Silicon Valley Barcode of Life
Palo Alto, USA
March 14, 2022

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Arctic BIOSCAN: Tracking biodiversity in Canada’s Middle Arctic using DNA

Arctic BIOSCAN: Tracking biodiversity in Canada’s Middle Arctic using DNA

Arctic BIOSCAN: Tracking biodiversity in Canada’s Middle Arctic using DNA

Danielle ‘Dani’ Nowosad wildflower hunting for the regional herbarium

Written by

DANIELLE NOWOSAD

The University of Guelph, Department of Integrative Biology

All photos credited to Dani unless specified otherwise

DNA barcoding is a molecular technique used globally to discover new species and assess biodiversity quickly and inexpensively. As it is based on standardized fragments of DNA, it can also be used to trace colonization patterns on Turtle Island (North America). My work is using DNA barcode data to quantify biodiversity and document colonization patterns in the Canadian Middle Arctic which would establish critical baseline data for future studies and enable us to monitor biological changes in response to climate change.

Cabin featuring the Nunavut flag on the shores of the Arctic Ocean.

DNA-based research in the Canadian Arctic

Seasonal camp in the Intensive Monitoring Area of Kilinoyak.

My research in the Iqaluktuttiaq (Cambridge Bay) region of Kilinoyak (Victoria Island), Nunavut, is in conjunction with the Arctic BIOSCAN (ARCBIO) project. ARCBIO, spearheaded by the Centre for Biodiversity Genomics (CBG) at the University of Guelph, aims to document all Arctic life using DNA barcodesshort pieces of DNA that are specific to each species. Funded by Polar Knowledge Canada (POLAR), ARCBIO is in its third year with at least four more years to go.

ARCBIO’s research base in Nunavut is in Iqaluktuttiaq (Ekaluktutiak or Ikaluktutiak, depending on who you’re talking with), a community of 1,600, located in Inuit Nunangat (the Inuit homeland). Iqaluktuttiaq also happens to be the site of the state-of-the-art Canadian High Arctic Research Station (CHARS) which opened its doors in August 2019.

Dani setting up a Malaise trap in front of the Canadian High Arctic Research Station (CHARS).

Located above the treeline on Kilinoyak’s southern edge, Iqaluktuttiaq is a polar desert with 24-hour daylight in the summertime. This region features stunning landscapes and prolific freshwater bodies of all sizes that are culturally, spiritually, and economically important to Inuit in this region. Many locals spend summer seasons fishing for Arctic char and trout, which use freshwater to spawn. Iqaluktuttiaq in the Inuinnaqtun dialect means “a good fishing place”. Arctic char has been harvested for generations for sustenance and now supports a local export industry.

Ice melting on the Arctic Ocean.

My research examines these water bodies and contributes an important resource to ARCBIO’s goals by establishing a DNA sequence catalogue of freshwater invertebrates for southern Kilinoyak. This will support future studies on biodiversity and allow us to monitor changes in freshwater ecosystems.

There is not enough local baseline data on biodiversity and abiotic variables such as water chemistry to track how climate change is altering the region. It is crucial to understand and mitigate changes to Arctic environments as these changes will have severe consequences globally including sea-level rise and unpredictable fluctuations in methane and carbon cycling1-3.

Dani collecting aquatic invertebrate samples on a helicopter trip near Wellington Bay.

Species found on Kilinoyak likely arrived within the last 7,500 years as the Laurentide ice sheet receded4. Some species might have managed to survive the last ice age in glacial refugia5, that is, regions largely in an ice-free state during the last ice age.

By analyzing the percentage of genetic divergence from local source populations, we can get closer to determining if this is the case. Taxa found in Iqaluktuttiaq that show a low percentage of genetic variance from taxa found elsewhere on Turtle Island could reveal interesting colonization patterns. For example, studies on small crustacean (Branchiopoda) in Churchill, Manitoba have shown multiple sources of origin from high Arctic regions in the north to Mexico in the south6. Apart from uncovering historical patterns, these data can inform models predicting the risk associated with invasive species to the region.

Dani assisting with a plant phenology/insect pollinator research project near CHARS.

The freshwater invertebrate catalogue currently consists of approximately 2,500 records from two summer sample collecting seasons. Most of these records include insects and crustacean (Arthropoda), of which many are flies (Diptera) and tiny water fleas (Anomopoda). Of these, just under 900 are of sufficient quality to obtain a standard DNA barcode. It is becoming clear with this early work that more sampling is needed to obtain a more comprehensive understanding of freshwater invertebrates in the Canadian Middle Arctic. Nevertheless, once sequences have been quality checked, researchers will release these data to the public via the standardized online DNA barcode library called BOLD.

BOLDthe Barcode of Life Data Systemsis an online, openly accessible repository for DNA sequence data and metadata. It allows users to create biogeographic maps, species accumulation curves, geo-distance correlations, biodiversity measures, and phylogenetic trees, among various other functions.

Haplotaxida

Daphniidae

Polyartemiella hazeni

Bosminidae

IMAGE CREDIT: CBG Imaging lab

My experience with BOLD and the DNA barcode pipeline began in the CBG’s Collections laba well-oiled machine where staff take gathered specimens, sort them, and input all their metadata (location, collection method, team members, etc.) into BOLD. Then, specimens are photographed, sent through automated DNA sequencing machinery, and finally, each sequence obtained is run through algorithms resulting in a BIN (Barcode Index Number) which is a proxy for species.

Fishing on the Arctic Ocean

With millions of records now accessible online, there is no question that DNA barcoding has contributed an incredible amount of knowledge and information to global biodiversity.

An important aspect and often interesting challenge in generating these data are sharing it in meaningful ways with local communities and the public.

Connecting the local community to DNA-based tools and technologies

View of the coast from Long Point

Committing resources and time to monitor environmental change in the Arctic is critical, but responsible research must prioritize integrating different voices from the community. As First Nations and Inuit communities in northern Canada7 are directly impacted, it is of the utmost importance to conduct this research in collaboration with local communities. This means listening to, including, and supporting Indigenous voices. Stitching together local Inuit’s experiences and traditional knowledge (otherwise known as IQ – Inuit qaujimajatuqangit) with climate change and scientific data in the region will only strengthen our understanding of these shared challenges and better position us to garner support for environmental protections.

ARCBIO offers several opportunities to fundamentally engage with local communities in ways that are not possible with one-off, short-term studies.  As part of early sampling efforts, CBG hired two full-time Junior Science Rangers from the local community for the summer field season in 2019. This created summer jobs for local high school students who were paid for their expert knowledge of the land. Through working with CBG collections staff, they learned scientific methods for sampling invertebrates such as pitfall trapping, Malaise traps, plankton tows, and D-net sampling.

The CBG is also preparing a community report that will be released to locals this spring, just ahead of the 2021 field season. The community report will provide an overview of the ARCBIO project, its goals, and a description of DNA barcoding and methods used to assess biodiversity. It will be made available online through the ARCBIO website and social media.

Beyond these efforts, I have been exploring other ways to connect with the community. The pandemic has complicated in-person plans which had included a workshop held in conjunction with POLAR and the local high school, a knowledge-sharing wetland walk, and a freshwater-themed photo contest funded by POLAR. 

Inukshuk with a view of town behind

Alternative outreach methods are being explored, taking into consideration the slower internet connectivity issues experienced by many Northerners. One possible method includes connecting with the local radio station that many locals tune into regularly to discuss research and generate conversations about science, increase awareness about projects, and put calls out for collaboration. The radio station communication strategy has been identified by locals in many northern communities as an excellent way to reach out8. Recently, a group of Inuit youth from various regions in Nunavut developed a concept they dubbed ScIQ (science + Inuit qaujimajatuqangit) in an effort to close the gap between attempts from external researchers to engage communities, and respectful inclusion8.

Monitoring equipment set up in the Intensive Monitoring Area, with Uvayuk (glacial esker) behind

One of the significant challenges ARCBIO will face is in finding ways to share barcode data with communities that are meaningful and useful. While data will be publicly available on BOLD, it is very likely that few, if any, locals will use the platform.

Sharing ARCBIO results with the local community in Cambridge Bay and other Northerners could be facilitated by a relatively new digital app called SIKU: the Indigenous Knowledge Sharing Network. This app was specifically designed by the Arctic Eider Society for Northerners. One might compare SIKU to iNaturalist, but specifically tailored for Northern hunters.  It allows users to log ice and land conditions, animal sightings, hunting experiences, among other things in a privacy-protected space. App users can also submit plant and animal observations, including arthropod orders that are prolific across Northern Canada, such as caddisflies, mayflies, copepods, and beetles.

The SIKU mobile app and web platform by and for Inuit provides tools and services for ice safety, language preservation and weather. IMAGE CREDIT: siku.org

Part of the network is a “Projects” section, which lists various research initiatives such as government projects like Department of Fisheries and Oceans fish surveys, climate change studies, and other weather, climate, and wildlife-related studies. Principal Investigators can list a description of the project under this section as well as contact information and URLs. I believe this is a huge opportunity to communicate with the people who are most impacted and stand the most to gain by data that ARCBIO generates.

Unlike Facebook or any other mainstream social media platform, SIKU users can be assured that any information they share on the app remains their own. Due to these properties, SIKU may be a perfect avenue to share the ARCBIO project outcomes with local people who could benefit directly from the project’s data. I was first made aware of SIKU during the ArcticNet 2019 Annual Scientific Meeting, where the Arctic Eider Society did a public launch of the platform in a plenary session. Since the launch, Siku has gained popularity across Arctic Canada.

So far, our meetings with SIKU’s developers have explored the types of information that Northerners might find useful. Discussions have revolved around biogeographical figures, time series, and other such accumulations of data. Although this pipeline will require significant computational and technological power, I believe in years to come, it will result in user-generated research questions in which Southern researchers can assist locals in answering.

Moving Forward

Once the DNA barcode data is established, we as researchers must ask ourselves which information is relevant and important to locals. The public requires more than access to ARCBIO’s raw data. While ARCBIO is increasing barcode coverage for Arctic species, I believe that by developing a direct pipeline from BOLD to SIKUwith community consultationARCBIO can disseminate meaningful data for local benefit.  Inuit have been explicit in their expectations for external researchers to approach science in the North with compassion, understanding of Northern cultures and lifestyles, respect, and inclusion. This doesn’t simply mean sending an academic publication of the results from a study to the communityit means developing relationships with community members, behaving in ways that are respectful to local culture, creating research questions with input from locals, and continuous communication throughout the study.

View of the last few pieces of ice before summer on the Arctic Ocean

Long-tailed jaeger

References:

1. Anisimov OA, Vaughan DG, Callaghan TV, Furgal C, Marchant H, Prowse TD, Vilhjálmsson H & Walsh JE (2007) Polar regions (Arctic and Antarctic). Climate Change 2007: Impacts, Adaptation and Vulnerability. Cambridge University Press, Cambridge, 653-685.

2. Prowse T, Bring A, Mård J & Carmack, E. (2015). Arctic freshwater synthesis: Introduction. Journal of Geophysical Research G: Biogeosciences, 120(11): 2121–2131. https://doi.org/10.1002/2015JG003127

3. Hammar J (1989) Freshwater ecosystems of polar regions: vulnerable resources. Ambio, 18(1): 6–22. https://doi.org/10.2307/4313520

4. Arthur D (2004) An outline of North American deglaciation with emphasis on central and northern Canada. Developments in Quaternary Sciences. 2. 10.1016/S1571-0866(04)80209-4.

5. Shafer AB, Cullingham CI, Cote SD & Coltman DW (2010) Of glaciers and refugia: a decade of study sheds new light on the phylogeography of northwestern North America. Molecular Ecology19(21): 4589-4621.

6. Jeffery NW, Elías-Gutiérrez M & Adamowicz SJ (2011) Species diversity and phylogeographical affinities of the Branchiopoda (crustacea) of Churchill, Manitoba, Canada. PLoS ONE, 6(5). https://doi.org/10.1371/journal.pone.0018364

7. Government of Canada; Indigenous and Northern Affairs Canada; Communications Branch. “Climate Change in Indigenous and Northern Communities.” Government of Canada; Indigenous and Northern Affairs Canada; Communications Branch, 19 Jan. 2021, rcaanc-cirnac.gc.ca/eng/1100100034249/1594735106676.

8. Pedersen C, Otokiak M, Koonoo I, Milton J, Maktar E, Anaviapik A, Milton M et al. (2020) ScIQ: an invitation and recommendations to combine science and Inuit Qaujimajatuqangit for meaningful engagement of Inuit communities in research. Arctic Science6(3): 326-339. https://doi.org/10.1139/as-2020-0015

Hunting for a water mite neotype in southern Norway

Hunting for a water mite neotype in southern Norway

Hunting for a water mite neotype in southern Norway

Scientists rediscover lost specimens of water mite in Norway 120 years after they were first described

A stream near the church of Vanse at Lista in southern Norwaythe type locality of Lebertia porosa Thor, 1900.

PHOTO CREDIT: Torbjørn Ekrem

Did you know that scientists can assess natural water quality by monitoring the diversity of aquatic invertebrates? Freshwater insect and arachnid populations are often important indicators of environmental change. This is evident in particularly species-rich groups, such as water mites and biting or non-biting midges, which have great potential for monitoring water quality. The problem is only that they are too difficult and time consuming to identify in routine water quality assessments. This hurdle can be overcome with DNA metabarcoding, but only if a good reference barcode library is available.

Elisabeth Stur of the Norwegian University of Science and Technology (NTNU) University Museum, along with her team, have been doing summer fieldwork for the Water Mites and Midges in southern Norway (Water M&M) project. One of the many goals for this year’s fieldwork was not only to contribute to the reference barcode library, but also to sample the type locality of the water mite Lebertia porosa, described 120 years ago by Sig Thor, a Norwegian priest and acarologist.

The Great Lakes
Phaenopsectra flavipes (Diptera: Chironomidae) with water mite larvae attached. PHOTO CREDIT: Aina Mærk Aspaas, NTNU University Museum

Barcode data indicate that there are at least six cryptic genetic lineages within this species, but it is unknown which of these applies to the nominal species. Since the original type material is lost, re-sampling L. porosa from its type locality is important in designating a neotype that most likely belongs to the species described by Thor in 1900. This way, researchers can stabilize the definition of the L. porosa species name, such that potential new species could be described. This species delineation is part of a MSc. project by Valentina Tyukosova at NTNU: Integrative taxonomy and species delimitation in the Lebertia porosa species complex (Acari, Parasitengona: Hydrachnidia).

The type locality of L. porosa was vaguely described in Thor’s original publication as a “stream near the church of Vanse”. After studying maps of the surrounding area, researchers learned that this church still stands, and were able to locate two nearby streams.

Now they wondered, would these streams still be in good condition 120 years later? As the team of researchers approached what they thought might be the stream in June 2020, they were pleased to see running, clear water under the bridge. Next mystery: could the streams hold a population of L. porosa 120 years after first collection? They found that yes, the waters could, and the water mite populations were bountiful!

The Great Lakes DNA Barcoding Project team

Water mites from the type locality of Lebertia porosa Thor, 1900.
PHOTO CREDIT: Torbjørn Ekrem

Stur and her team are now looking forward to getting these critters under the compound microscope. Using DNA analysis, they hope to identify which barcode clusters they match with, potentially revealing the nominal species of L. porosa. We’re sure that Sig Thor would be thrilled to learn that his identified species is still thriving, 120 years later.

Written by

Katherine Perry

Katherine Perry

Centre for Biodiversity Genomics, Guelph, ON, Canada

July 24, 2020

doi: 10.21083/ibol.v10i1.6243

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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!

Don't Miss Out!

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

comment on this article

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