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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ABOL BioBlitz: DNA barcoding safeguards taxonomic knowledge

ABOL BioBlitz: DNA barcoding safeguards taxonomic knowledge

ABOL BioBlitz: DNA barcoding safeguards taxonomic knowledge

The Austrian Barcode of Life (ABOL) initiative uses DNA barcoding to safeguard and make publicly accessible rare knowledge on biodiversity generated in the course of local BioBlitz events
Local fisher presents catch of the day from lake Millstatt PHOTO CREDIT: Susanne Glatz-Jorde, Biosphere Reserve Nockberge

A BioBlitz is an event organized to survey the biodiversity of a designated area as fast and as comprehensively as possible1. Along with the general public, taxonomic experts from various fields, whether laymen or academics, swarm a location to record every identifiable species, usually within 24 hours.

The primary goal of these events is to increase bioliteracy—awareness of biodiversity and its importance for healthy, functioning ecosystems. We believe increased bioliteracy could transform societal perceptions of nature and, ultimately, humanity’s relationship with other species. Consequently, we deem it a prerequisite in our arsenal to abate the dramatic loss of biodiversity2. Additionally, the BioBlitz approach is becoming increasingly important for conservation efforts as it generates high-quality biodiversity data while simultaneously enhancing research capacity3.

In 2019, the Austrian Barcode of Life Initiative (ABOL) successfully introduced a new extended BioBlitz format to Austria—the ABOL BioBlitz—which combines existing collecting events with DNA barcoding. The organisms acquired and identified by experts during BioBlitz events are subsequently DNA barcoded. Importantly, specimens are photographed and stored in a scientific collection along with their associated metadata to be fully compliant with DNA barcoding standards for reference sequences.

The Great Lakes

Locations of the ‘Days of Biodiversity’ 2019 in Austria. The logos represent the organizing institutions.

Base map from d-maps.com

Although running for the first time, the ABOL BioBlitz efforts were very well received and highly successful. From 2000 individuals comprising 1400 taxa, approximately 1500 DNA barcodes were obtained and these data are now available on BOLD.

The number of individuals per higher taxon provided for DNA barcode analysis in the course of the ABOL BioBlitzes 2019. Sites indicated by colours.

Images from ClipArt ETC

In 2019, ABOL joined six ‘Days of Biodiversity’ with ABOL BioBlitzes in five different federal states of Austria. These events covered very different habitat types, from an organic farmstead in Upper Austria, a valley in the mountainous area in Tyrol, to annually organized events in protected areas like National Park Hohe Tauern or the Biosphere Reserves of Nockberge and Wienerwald. It is important to note that these events are only possible with the generosity and cooperation of the institutional hosts to whom we wish to extend our deepest thanks.

In total 54 taxonomic experts joined our efforts at these events. They not only provided us with samples from their collected material, along with the respective metadata and photos, but they also prepared reference individuals and assured their appropriate storage in public collections. After receiving samples from the experts, the ABOL team transferred tissue into microplates and shipped them to the Canadian Centre for DNA Barcoding (CCDB) in Canada for barcode analysis. We thank all the experts for their incredible efforts as well as staff at the CCDB for their obligingness and cooperation.

Day of Nature in the Biosphere Reserve Nockberge

The 4th Day of Nature named ‘Shores and mountain slopes of Lake Millstatt in Carinthia’ in the Biosphere Reserve Nockberge contributed substantially to the species inventory of the Carinthian part of the Biosphere Reserve. 45 taxonomic experts recorded 1166 species, some rare while others new records for the Biosphere Reserve Nockberge and for Carinthia. The event was organized by the team at the Biosphere Reserve, together with two ecological agencies, Ökoteam and E.C.O.

IMAGE: Local fisher presents catch of the day from lake Millstatt
CREDIT: Susanne Glatz-Jorde, Biosphere Reserve Nockberge

Day of Biodiversity in Upper Austria

The Day of Biodiversity in Upper Austria, organized by the Naturschutzbund Oberösterreich and the Biologiezentrum of the Upper Austrian State museums, took place around the Mühlbergerhof, an organic farmstead covering around 20 ha of species-rich grassland, pastures, and deciduous forest. In addition to the species inventory, excursions with different topics (e.g. moths and bats, plants, fungi and lichens, insects) were offered to the public.

IMAGE: Members of the ABOL coordination team examine collected insects from Mühlbergerhof
CREDIT: Heidi Kurz, Naturschutzbund OÖ

Day of Biodiversity in the Biosphere Reserve Wienerwald

The annual Day of Biodiversity in the Biosphere Reserve Wienerwald took place in 2019 in Pressbaum, Lower Austria. Within 24 hours, 1151 species were recorded. This data forms a valuable basis for scientific research and nature conservation activities in the Biosphere Reserve. Excursions led by experts explored water insects, plants, and birds. More than 30 stands provided information on various topics for adults and children. The festival of biodiversity was completed with regional food, kid’s programs and an open-air concert.

IMAGE: ABOL information stand at the festival of biodiversity in Pressbaum
CREDIT: Michaela Sonnleitner

Day of Biodiversity in Vienna

The Day of Biodiversity in Vienna was the 1st transnational event of its kind within the Interreg project CITY NATURE jointly organized by the Vienna municipality (MA22), the University of Natural Resources & Life Sciences (BOKU), and Bratislava, Slovakia. The collecting event around the BOKU area was complemented by excursions exploring birds, plants, insects & mammals.

IMAGE: Group photo from the closing event with project partner from Bratislava at the Day of Biodiversity in Vienna CREDIT: Barbara Reinwein, MA22

Day of Biodiversity in Tyrol

During the Day of Biodiversity in Tyrol, the Brandenberg Valley attracted many experts and visitors with its diverse natural habitat. A highlight of the event was the demonstration of different types of light traps catching night-active insects. Experts held lectures on butterflies, which fascinated children and adults. Arctia matronula, a rare and locally distributed Noctuidae was among the observed species. The days of biodiversity in Tyrol are organized by the Tyrolean State Museums, the University of Innsbruck and the State of Tyrol.

IMAGE: Expert demonstrates light traps and explains nocturnal butterflies
CREDIT: Michaela Sonnleitner

Day of Biodiversity in the National Park Hohe Tauern

The motto of the 13th Day of Biodiversity in the National Park Hohe Tauern was Summit of biodiversity at the foot of the Großglockner (the highest mountain in Austria). More than 60 experts investigated the species inventory of the Gössnitztal, an elongated alpine valley up to more than 2000 m and the surroundings of Heiligenblut in Carinthia. In addition to plants, insects, birds etc., bats were observed in different altitudes and their call sequences recorded. The event was perfectly organized by the Team of the National Park.

IMAGE: Group photo from the Day of Biodiversity in the National Park Hohe Tauern in Heiligenblut with Großglockner in the background.
CREDIT: Manfred Schmucker

Due to the current Coronavirus pandemic, some of the 2020 ‘Days of Biodiversity’ were cancelled or postponed to 2021, while some will take place but with great care. For the future, we hope to be able to increase the number of participants and, ultimately, the data collected.

The concerted actions of the ABOL team at the ‘Days of Biodiversity’ significantly enhance the value and reach of these local BioBlitz events. For example, our efforts contribute to the completion of DNA barcode reference databases, important resources for society in the long term. They also support taxonomic research by providing the genetic resources important to the morphological determination of species. Additionally, we significantly promote these events amongst the public, raise awareness of the importance of biodiversity as well as build and strengthen bonds within the biodiversity community by enabling a process of mutual learning between cross-disciplinary experts.

As events this past year have shown, combining a BioBlitz with DNA barcoding is a very successful way to obtain both taxonomic and barcode data as well as integrate experts, especially for national DNA barcoding initiatives, which are not always fully funded, as is the case in Austria.

These events also foster a greater appreciation of biodiversity and ecosystems amongst the public and, therefore, are a very successful approach to increase bioliteracy. The currently ongoing biodiversity crisis implies rapidly growing importance of biodiversity data. As taxonomic expertise is increasingly rare in the academic environment, it is becoming more dependent on nature enthusiasts. This knowledge of biodiversity has always received too little attention, although a substantial part of it is held outside of academic institutions. Therefore, we wish to emphasize, that increased appreciation of nature should go hand in hand with that of private taxonomic expertise. ABOL BioBlitzes take all this into account.

References:

1. Baker G.M., Duncan N., Gostomski T., Horner M.A., Manski D. (2014). The bioblitz: Good science, good outreach, good fun. Park Science 31(1): 39–45.
2. IPBES (2019). Global assessment report on biodiversity and ecosystem services of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services. E. S. Brondizio, J. Settele, S. Díaz and H. T. Ngo (eds.) Bonn, IPBES secretariat.
3. Parker S.S., Pauly G.B., Moore J., Fraga N.S., Knapp J.J., Principe Z., Brown B.V., Randall J.M., Cohen B.S. Wake T.A. (2018). Adapting the bioblitz to meet conservation needs. Conservation Biology 32(5): 1007–1019. https://doi.org/10.1111/cobi.13103

Written by

Michaela Sonnleitner

Michaela Sonnleitner

Sabine Schoder

Sabine Schoder

Oliver Macek

Oliver Macek

Nikolaus U. Szucsich

Nikolaus U. Szucsich

Natural History Museum Vienna, Austria

August 24, 2020

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Local wildlife enthusiasts drive DNA barcode library building in the UK

Local wildlife enthusiasts drive DNA barcode library building in the UK

Local wildlife enthusiasts drive DNA barcode library building in the UK

Researchers in the UK are spearheading a number of high-profile initiatives designed to populate and fill gaps in the national DNA barcode library

Distribution of DNA barcode records for the United Kingdom.

IMAGE: BOLD Sytems 2020-03-10

Despite some notable achievements, such as a complete DNA barcode library for the native plants of Wales, the UK has lagged behind other European countries when it comes to growing its DNA barcode library. On BOLD there are 24,555 DNA barcode records for specimens collected in the UK (from 5,484 species) which is very similar to Austria (24,513 records, from 5,375 species), a landlocked country with roughly one third the land area and one seventh the human population. Germany leads Europe with 167,458 records from 14,805 species.

    The UK is working to catch-up through a number of high-profile initiatives designed to populate and fill gaps in the UK’s DNA barcode library and, in particular, bring BIOSCAN to UK insects.

    Distribution of DNA barcodes records for the United Kingdom.
    IMAGE: BOLD Systems from 2020-03-10

    The Darwin Tree of Life project is being led by the Wellcome Sanger Institute and involves a consortium of institutes, universities, museums, and agencies, including the Natural History Museum and Royal Botanical Gardens Kew. The project aims to deliver public DNA barcodes for 10,000 species by 2023 and ultimately sequence the genomes of all 66,000 species of plants, fungi, protozoa, and animals that are found in the UK.

    DEFRA (the Department for Environment, Food & Rural Affairs) has established a Centre of Excellence for Environmental Genomic Applications. This virtual centre recognises the absolute necessity of DNA barcode libraries to meet its aims of “applying genomics methods (eDNA and metabarcoding) to detect rare and invasive species, evaluate the effectiveness of conservation interventions, monitor the status and trends for key assemblages and taxa, and assess ecosystem health, functioning, and resilience”1.

    What is special about these initiatives is that they capitalize on the UK’s large community of local wildlife enthusiasts. A recent workshop organised by BugLife (the Invertebrate Conservation Trust) and Natural England (the UK government’s adviser for the natural environment in England) to examine “gaps” in BOLD for “key English invertebrates” brought together members of the Caddisfly Recording Scheme, Cranefly Recording Scheme, the British Dragonfly Society, the Amateur Entomologists’ Society, amongst others. The UK’s exceptional network of dedicated volunteer wildlife recorders already contribute thousands of records to taxon-focussed databases such as the UK Butterfly Monitoring Scheme (UKBMS), Local Record Centres, and through apps such as iSpot and iRecord which transmit data to the NBN (National Biodiversity Network) Atlas.

    Ainsdale Sand Dunes National Nature Reserve, one of the most important wildlife sites in England.
    PHOTO CREDIT: Gary Hedges

    The Darwin Tree of Life project kicked off last summer about 25 km north of Liverpool at Ainsdale Sand Dunes National Nature Reserve with a DNA Bioblitz attended by a team of local recorders including National Museums Liverpool entomologists. These local experts are passionate, driven and keen to contribute to DNA barcode libraries, but don’t necessarily have background knowledge in molecular biology or a basic skill set in “wet” lab techniques.

    Participants during the World Museum DNA Barcoding Workshop in February 2020.
    PHOTO CREDIT: Leanna Dixon

    To address this we recently ran a DNA barcoding workshop at World Museum Liverpool for eleven prominent local recorders connected with the Tanyptera Project. The Tanyptera Project is a seven-year initiative funded by the Tanyptera Trust to promote the study and conservation of insects and other invertebrates in the Lancashire and Cheshire region of Northwest England. To our knowledge this was one of the first DNA barcoding workshops run solely for non-professional scientists.

    Sphecodes ferruginatus female blood bee collected in Cheshire, England.
    PHOTO CREDIT: Chloe Aldridge

    The 1.5-day workshop covered the key steps in DNA barcoding from lab to BOLD2. Participants brought along their own invertebrates collected during recent local fieldwork and all successfully produced DNA barcodes for their specimens, which included springtails, bees, a cranefly, other flies, beetles, and spiders. The specimens have been vouchered into World Museum Liverpool’s National Entomology Collection which includes over 1 million specimens, and the sequences have been submitted to BOLD. One participant was able to confirm the first record of a Nationally Scarce blood bee in Cheshire – Sphecodes ferruginatus – raising interesting hypotheses about its potential host species.

    At National Museums Liverpool, together with the Tanyptera Project, we are committed to continue developing our DNA barcoding educational offering for local wildlife enthusiasts and supporting their work driving forward national initiatives to get more UK barcodes onto BOLD.

    References:

    1. Nelson M, Woodcock P, Maggs C (2018) Using eDNA and metabarcoding for nature conservation. Joint Nature Conservation Committee (JNCC 18 25). Available at http://data.jncc.gov.uk/data/99e1f69f-c438-439f-8401-dd8a6ce17320/JNCC18-25-Using-eDNA-and-Metabarcoding-for-Nature-Conservation.pdf

    2. Wilson JJ, Sing KW, Jaturas N (2019) DNA barcoding: Bioinformatics workflows for beginners. In Bioinformatics and Computational Biology. The A to Z of Bioinformatics. Ranganathan S, Nakai K, Gribskov M & Schönbach C, Eds. Elsevier Ltd., Oxford.

    Written by

    John-James Wilson

    John-James Wilson

    Vertebrate Zoology at World Museum, National Museums Liverpool, United Kingdom

    Leanna Dixon

    Leanna Dixon

    Tanyptera Project, National Museums Liverpool, United Kingdom

    Gary Hedges

    Gary Hedges

    Tanyptera Project, National Museums Liverpool, United Kingdom

    March 20, 2020

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