Case Studies in DNA Barcoding

 

The Consortium for the Barcode of Life (CBOL) invites researchers to submit brief abstracts of “case studies” of DNA barcoding. Please refer to the instructions for information on how to prepare your case study. Case studies can be submitted for proposed projects or projects that are underway. If you would like to initiate a barcoding project but you are missing a key ingredient (e.g., access to lab facilities, samples, expert identifications), submitting a Case Study can help you locate these resources.

In submitting this case study, you are authorizing CBOL to post a summary of your project on the CBOL website and to send the full case study text to people who ask for a copy. For this reason, do not include any information that you wish to keep out of the public domain.

Case Studies can be devoted to:

  • Collecting barcode data from new taxonomic groups and/or geographic areas,
  • Building libraries of barcode data for groups from which some barcode data has already been obtained, and/or
  • Applying barcode data to applied problems (e.g., agriculture, public health, conservation).

These one-page documents will:

  • Help submitters and researchers interested in participating in barcode projects to find each other;
  • Provide CBOL with an assessment of the current and projected needs among barcode researchers;
  • Help CBOL in its efforts to identify sources of support for specific barcoding projects and for the barcode initiative in general, and
  • Give policy-makers and funding agencies a clearer picture of the potential impact of DNA barcoding.

Case studies can be submitted by:

  • Systematists and molecular biologists who are gathering or intend to gather barcode data as part of their taxonomic research;
  • Ecologists, ecosystem scientists, researchers doing biodiversity inventories, oceanographers, and other non-systematists who need access to species identifications based on DNA barcodes for their research; and
  • Applied scientists, government agencies, conservation organizations and non-researchers who want to use DNA barcodes gathered by others to address practical problems.

Questions concerning CBOL Case Studies can be directed to cbolinfo@si.edu.
Technical questions about this website can be directed here.

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Submitted By

Name: Susie Wood
Institution: University of Bristol
Country: United Kingdom
Email: Susie.Wood@bristolalumni.org.uk

Title & Categories

Case Study Title: Use DNA Barcoding Techniques to Identify Flowering Plants in San Rafael National Park, Paraguay
Focus Theme: Adding barcodes to a large survey of a taxonomic group, Biotic inventory of multiple taxa in a region or habitat
Geographic Region: South America
Habitat Type: Terrestrial temperate forest, Terrestrial tropical forest
Taxonomic Group: c: Magnoliophyta, c: PLANTS

Scope

Investigate, identify and document flowering plants in a floristically rich, under researched and threatened part of the Atlantic Forest.

The study of flowering plants will be conducted at Ecosara Reserve in San Rafael National Park, Paraguay – an area of approximately 73,000 hectares. 

Data will be collected for all angiosperms that are observed within the park. It is anticipated that data will be restricted to taking digital images, small samples of plant material suitable for DNA extraction and barcoding and that no plant specimens will be taken at this stage. 

 

The number of species is difficult to quantify, but is crudely estimated at 180- 850; the calculation is derived from the Paraguay specimen total currently available from the Royal Botanic Gardens Herbarium on-line catalogue.

Purpose

The project will promote the use of DNA barcodes as an identification key for plant species. Using barcodes will help minimise the impact on fragile ecosystems by reducing and / or eliminating the number of specimens ‘collected’ from their natural environment.

The project aims are to:

 

  • Conduct a scientific investigation of flora in San Rafael National park and establish a biodiversity inventory.
  • Establish a plant photographic database
  • Design and develop identification keys for the plant groups
  • Publish findings across a broad scientific and non-scientific community
  • Ally Ecosara with conservation organisations in other countries.

This provides the opportunity to initiate a DNA barcoding project in Paraguay using DNA to identify the flowering plants in San Rafael National Park. 

The aims of Ecosara support CBOL’s mission to promote the exploration and development of DNA barcoding as a global standard for species identification, specifically the following goals: 

  • involvement of researchers and users of barcode data from all regions of the world, especially those with high biodiversity
  • rapid compilation of high-quality DNA barcode records in a public library
  • participation of taxonomists and research organizations in all regions and countries
  • use of barcode data for the benefit of science and society
  • development of intellectual activity involving DNA barcode data in the wider academic community among diverse users throughout society
  • greater awareness of DNA barcoding beyond taxonomic researchers.

Background

Paraguay is home to a wealth of floristic diversity, yet there is a paucity of available data; most of the botanical collections and literature is over a hundred years old. Research is needed to investigate, identify, document and preserve the country’s under-studied flora.

ECOSARA, (Estación Ecológica de San Rafael) is a research station aimed at saving one of the world’s most important, but little known Atlantic Forest Reserves – San Rafael National Park in Paraguay.The Forest once covered about one million square kilometres of Paraguay, Brazil and Argentina. Today, only 7 to 10% remains. Conservation International describes the Atlantic Forest as one of the most important ecosystems on the planet being of “critical importance for global biodiversity” and, because of the level of threat and endemism, has selected it as a Biodiversity Hotspot.

Deforestation continues at a high rate, yet Eastern Paraguay retains a large area of the Upper Paraná region, much of it degraded and in dispersed fragments, placing it amongst the most endangered ecosystems in the world. Estimates indicate that 40% of the thousands of plant species in the Upper Paraná are endemic to the region with many known for their medicinal properties.

In 1992 the government, recognising the area as a top conservation priority in Paraguay, designated 73,000 hectares as San Rafael National Park. Located in the south eastern departments of Caazapá and Itapúa, it is the most complete example of the diverse species and is the largest continuous block of the Upper Paraná Atlantic Forest in Paraguay.

Logistics

The project is at the preliminary stage, with no resources yet having been identified. Ecosara is a non-profit ecological station, staffed by professionals yet also heavily reliant on a constant stream of volunteers, so timescales are uncertain. The project can start when resources become available.

However, before data collection can proceed, it is necessary to ascertain whether or not actual plant specimens are required as voucher evidence; The Royal Botanic Gardens Kew will be contacted to discuss the feasibility of accepting photographic evidence in combination with the DNA barcode, their advice will be sought on what data needs to be captured and how it will be preserved and stored. 

 

A decision has been reached on which loci should be designated as the universal DNA barcode for plants. Formal acceptance by CBoL is awaited. Data collection is not dependent on this acceptance. 

Each plant will be photographed in situ using a digital camera; multiple images will be obtained to show sufficient plant characteristics enabling species identification; comprehensive data is needed to provide a photographic voucher for each specimen. 

 

In order to create a barcoding identification key, DNA material needs to be extracted from plant specimens currently held in herbaria. The cooperation of Missouri Botanical Garden and Royal Botanic Gardens Kew will be sought for their collaboration in accomplishing this.