Liselotte Wesley Andersen
Department of Wildlife Ecology and Biodiversity, Danish National Environmental Research Institute, University of Aarhus
Possible applications of DNA-barcoding in nature management: pros and cons
In connection with the implementation of the EU-Habitats Directive in Denmark and the following protection of the species on Annex II and IV, the Danish National Environmental Research Institute initiated genetic research to evaluate the conservation status of vulnerable species and hence, support management decisions. The definitions of DNA-barcoding spans widely. Both the more traditional view of sequencing conserved genes as CO1 or CytB for species-identification combined with the available knowledge and hypothesis addressed for the particular specimen will be discussed together with individual DNA-barcoding using several genetic markers for individual identification. Both examples of DNA-barcoding have been used in Danish nature management. Case-studies involving the European otter (Lutra lutra) and European tree frog (Hyla arborea) will be used to illustrate the DNA-barcoding application and its advantages and pitfalls.
Curator of Division of Invertebrate Zoology, American Museum of Natural History
|The Use of DNA Barcoding in Taxonomy|
Recent excitement over the development of an initiative to generate DNA sequences for all named species on the planet has igenerated areas of contention as to how this 'DNA barcoding' initiative should proceed. It is critical that these issues are clarified and resolved, before the use of DNA as a tool for taxonomy and species delimitation can be universalized. Currently, many of the published studies under this initiative have used tree building methods and more precisely distance approaches to the construction of the trees that are used to place certain DNA sequences into a taxonomic context. The classical taxonomic approach and the DNA approach will need to be reconciled in order for the 'DNA barcoding' initiative to proceed with any kind of community acceptance. In this talk we will discuss these major concerns generated around the DNA barcoding initiative and attempt to present a phylogenetic systematic framework for an improved barcoder as well as a taxonomic framework for interweaving classical taxonomy with the goals of 'DNA barcoding'.
Section of Natural History, Museum of Natural History and Archaeology, Trondheim, Norway
|DNA Barcoding: a valuable tool in taxonomy and identification of non-biting midges|
Torbjørn Ekrem, Endre Willassen & Elisabeth Stur
Non-biting midges (Diptera: Chironomidae) usually are the most abundant and species rich insects in freshwater ecosystems and they are frequently used as indicators of environmental conditions in biological monitoring of freshwaters. However, limited knowledge of larval taxonomy, restricted access to taxonomic expertise, and meticulous procedures for species identification are impediments both for the detailed knowledge on the biology of these insects and for the potentially wider use of chironomids in monitoring of fresh water resources. Consequently, a system for rapid species identification and life stage association by comparisons of short gene sequences (i.e. DNA barcoding) would be useful to both systematic and ecological studies on Chironomidae.
This talk will present results from a recent study where we explored the prospects of DNA barcoding on non-biting midges. Our results show that COI from 98% of the sampled specimens could be amplified from different life stages using the standard Folmer et al. (1994) primers (LCO1490 & HCO2198) and that interspecific genetic distances exceeded intraspecific distances for all species. Thus, DNA barcodes can be used to identify species that are already in a COI library. However, the results from the neighbour joining and parsimony analyses did not otherwise reflect trustworthy phylogenetic relationships between the species examined, and DNA barcodes appeared unreliable for approximate identification when sequences of the unknown taxon are absent from the COI library. Nevertheless, it would be relatively quick and inexpensive to create a COI library of the most common chironomid species. Once established, a library of DNA barcodes will not only assist in rapid and accurate identification of chironomid larvae, but also in identifying taxonomic entities that deserve more thorough morphological, ecological and genetic analyses by an integrative approach.
We are now in the process of generating a DNA library of European and Canadian non-biting midges. Our projects currently hold about 500 sequences of approximately 200 species. We have already recognized several species that putatively are new to science and also taxonomic groups that are in desperate need of revision.
Canadian Barcode of Life Network
Biodiversity Institute of Ontario &
Department of Integrative Biology
University of Guelph
|A New Paradigm for Natural History Collections|
Biological specimen collections exist for many reasons, from museum voucher specimens documenting the application of names, to commercial and industrial collections that underpin modern biotechnology. With today’s technology, they all represent potentially accessible “genetic resource collections” awaiting characterization. DNA sequencing offers an efficient means of direct comparison across all such collections, a process that could bring systematic breadth and rigor to genetic databases, drive digitization of collection records and generate libraries of reference sequences for species identification. This talk will examine the role of emerging genetic characterization, annotation and information dissemination standards for developing an accessible network of biorepositories capable of supporting multidisciplinary research. Broad-based implementation of such standards would benefit the user community by creating an index of taxonomically validated genetic resources, while also enabling calculation of a repository impact factor to justify ongoing support of the collections. While traditional collections can be valuable sources of genetic data, natural history museums must also consider the collection, preservation and archival of genomic resources as an integral part of their mission to document life on earth.
The Mandahl-Barth Research Centre for Biodiversity and Health, DBL - Centre for Health Research and Development,
Institute of Veterinary Pathobiology,
Faculty of Life Sciences, University of Copenhagen
|DNA barcoding of schistosome intermediate host snails – the CONTRAST project|
Schistosomiasis (snail fever) infects app. 200 million people in Africa, Eastern Asia and South America and is caused by parasitic trematodes in the genus Schistosoma. To complete their lifecycle the parasites need intermediate snail hosts for the development of miracidia into cercaria. Both prosobranch and pulmonate snails can act as intermediate hosts. In Africa only pulmonate snails in the genera Biomphalaria and Bulinus act as intermediate hosts of Schistosoma.
Biomphalaria and Bulinus belong to two distant evolutionary lineages of planorbid snails (Planorbinae and Bulininae) and are infected by different species of schistosomes.
In Africa Biomphalaria currently has 12 recognized species, which can all be intermediate host for the Schistosoma mansoni parasite. Two major evolutionary lineages are currently recognized with 1-2 species in the B. pfeifferi species group and the rest in the Nilotic species complex. The species show relatively little interspecific DNA sequence variation, convergent shell evolution and the capacity of reproduction by self-fertilization. Within the six species of the Nilotic species complex currently investigated the maximum COI sequence variation is 3.3%, and the COI variation between the two evolutionary lineages is up to 6.5%. The intraspecific variation has only been estimated for 16S (0.4%) and ND1 (2.3%) in Biomphalaria pfeifferi.
Bulinus currently consists of app. 30 recognized species in four major evolutionary lineages and not all species act as intermediate hosts of Schistosoma parasites. The Bulinus species show pronounced plasticity of the shells. Most, if not all, species of Bulinus have the capacity of reproduction by self-fertilization. Within Bulinus DNA sequences of internal transcribed spacer (ITS), 16S rDNA and a small (400 bp) fragment of COI have been used for preliminary species discrimination. The COI sequence variation of the Bulinus reticulatus species group is unknown. The average COI sequence variation within the Bulinus africanus and the B. forskalii species groups are 11.3% and 12.2%, respectively. However, the Bulinus truncatus/tropicus species complex show low COI sequence variation (average 2.9% with a maximum of 9.4%) and might be a recently evolved group. This complex has many examples of speciation by ploidy and the taxonomy has been further complicated by the recognition of species described mainly on enzyme electrophoretic evidence. The degree of intraspecific variation has not been estimated and analyses of COI sequences from GenBank result in some non-monophyletic species. However, the four major evolutionary lineages are inferred by both COI and 16S.
In October 2006 CONTRAST, a large EU funded project, was launched with one of its workpackages focusing on DNA barcoding of schistosomes and intermediate host snails in Africa. During the CONTRAST project Biomphalaria and Bulinus snails will be extensively collected in Cameroon, Kenya, Senegal, Tanzania, Uganda and Zambia, and these collections will be supplemented by the collections held at DBL and The Natural History Museum, London. The main objective of the snail work of CONTRAST is to create an international standardized molecular nomenclature based upon DNA barcoding and selected microsatellite loci for classification of genetic variation within schistosome snail hosts.
Éamonn Ó Tuama
DK-2100 Copenhagen Ø
|DNA Barcoding and GBIF - Linking Barcode Information to Specimen Data|
The vision of the Global Biodiversity Information Facility (GBIF) is to make the world's biodiversity data freely accessible and universally available to all. It achieves this by establishing and promoting an ever-growing network of data-contributing participant nodes distributed around the world and maintaining a central indexing service which provides the core functionality for the GBIF Data Portal and various web services which rely on the central index.
In its first development phase (2001-2006), GBIF concentrated on primary species-occurrence data, that is, specimens held in museum and other collections, as well as observational records. As of April 2007, GBIF is serving more than 120,000,000 records from 1017 collections managed by 199 data providers. Now, as it moves into its next phase, GBIF has prioritised particular areas for development, amongst which are the inclusion of other data types within the GBIF Data Portal. These include both genomic and ecosystem data. DNA barcode data is thus a very appropriate resource for integration into the GBIF portal where it can be cross-referenced to other species data and also provide a novel and valuable contribution to integrative taxonomy.
This presentation provides an overview of the GBIF information architecture and the services built upon it. It emphasises the importance of community standards for biodiversity data, particularly those developed under the aegis of the Biodiversity Information Standards (TDWG) group. It examines the proposed standard from the Database Working Group for the Consortium for the Barcode of Life (CBOL) for dealing with barcode records held in the International Nucleotide Sequence Database Collaboration and their linkage to voucher specimens through use of a Globally Unique Identifier (GUID) system. Life Science Identifiers (LSIDs) are highlighted as one particular GUID standard promoted by BIS(TDWG) and GBIF that provide persistent, globally unique identifiers for biological data thus facilitating sharing and re-use. Their integration in the BARCODE record system is explored.
|Gitte Petersen &
Natural History Museum of Denmark, University of Copenhagen
|How many genes does it take to barcode a plant?|
At present there is no standard protocol for barcoding land plants. COI and all other mitochondrial genes are highly conserved across land plants, thus providing limited discriminative power. The most variable sequences in land plants are probably found in the nucleus: However, the high frequency of polyploidy or other partial duplications of the genome, and the unlikely possibility of producing universal primers will make it highly problematic to develop an easily applicable system for amplification of unique nuclear sequences. Therefore, efforts are focused on sequences from the plastid genome. However, no single plastid sequence is variable enough in all lineages of land plants to facilitate species recognition. A novel suggestion, which will be submitted to CBOL, proposes a “triplet” plant barcode consisting of three sequences. At least in some lineages it is shown that the most variable protein coding sequences are more variable than non-coding regions. Being less prone to length mutations, protein coding sequences also have analytical advantages. Thus, the triplet will either include only protein coding sequences, or include two coding and one non-coding region. However, in some genera not even three sequences will be enough to distinguish all species.
Swedish Museum of Natural History, Stockholm,
|DNA Barcoding and the Swedish Taxonomy Initiative|
The Swedish Taxonomy Initiative (Svenska Artprojektet), launched in 2002, aims to complete the inventory of the Swedish fauna and flora within 20 years. The project involves massive collecting efforts, taxonomic research, and the production of a comprehensive national biodiversity encyclopedia (Nationalnyckeln till Sveriges Flora och Fauna). Two large field inventories are underway: A survey of Swedish marine habitats and a terrestrial Malaise trapping project. These, and other activities within the Swedish Taxonomy Initiative, now provide access to fresh material of a large portion of the Swedish flora and fauna. Although this creates an ideal opportunity for DNA barcoding, this is not a given priority within the project. First, effective selection of specimens for DNA barcoding requires traditional taxonomic work, so barcoding does not speed up the inventory. Second, although DNA barcoding is a powerful resource for
species identification, it is not foolproof so, again, it needs to be complemented with more traditional identification aids. Third, future monitoring of the Swedish flora and fauna will
undoubtedly remain, to a large extent, in the hands of amateur naturalists. They seem unlikely to have access to DNA barcoding equipment in the near future; in fact, even if cheap DNA barcoders became available, they would probably still prefer traditional identification aids because of the intellectual satisfaction involved in species recognition.
Program for the Human Environment
The Rockefeller University
New York, NY
|All Birds Barcoding Initiative (ABBI) update|
Birds are among the most conspicuous and well-studied groups of animals, yet genetic surveys including with DNA barcoding suggest there are hundreds of as yet undescribed species. All Birds Barcoding Initiative (ABBI) aims to collect DNA barcodes from the approximately 10,000 species of known birds and speed discovery of new species, establishing an electronic library that links barcodes, reference specimens in collections, and associated collection data. As of May 2007 there are over 8000 barcodes representing 1700 species deposited in Barcode of Life Database (BOLD), including most North American species, with recent infusion of barcodes contributed by institutions in Central and South America. Interest from individuals and institutions in Europe, Africa, East and Southeast Asia promise additional growth. Surprisingly, over 3000 world birds are not represented in existing avian tissue collections, particularly Afrotropical and Indomalayan avifauna, but also Palearctic and Nearctic species. The avian barcode library will be a valuable resource for conservation planners, ornithologists, ecologists, public health officials, and the interested public. Once the library is established, DNA barcoding can be applied by interested persons to confirm identification regardless of age, sex, or plumage, including from individual feathers. Comparison of avian barcode data with that from other vertebrate and invertebrate taxa suggests common patterns of diversity. Mapping a single locus across the diversity of animal life, ie DNA barcoding, may provide new insights into processes that form and maintain species.
|Malin Strand & Per Sundberg
Göteborg University, Department of Zoology, Systematics and Biodiversity, Box 463 Göteborg, Sweden
|Marine inventories and DNA barcoding|
The Swedish Taxonomy Initiative is currently undertaking marine inventories in its effort to catalogue the Swedish fauna. Marine fauna consists of many phyla, which poses problems when it comes to identifying the collected specimens. Since it is impossible to have experts covering all possible taxa on board the ship, one often has to rely on post identification of preserved material. For many taxonomic groups this make identification difficult or in some cases impossible. It is therefore common in marine monitoring programmes to see that animals are only identified to phylum. This will of course give an inaccurate measurement of biodiversity, and will also risk hiding changes in the faunal composition.
We discuss whether DNA barcoding could be used for identifying species in preserved bulk samples, and show an example of how it can work. We furthermore discuss potential problems with barcoding of marine invertebrates.
Finnish Museum of Natural History
Barcoding and COI sequence variability: examples from flies and mayflies
Studies to test the utility and informativeness of COI sequences for morphologically similar species groups in different genera of Diptera (Syrphidae) and Ephemeroptera (Baetidae) are presented. For Syrphidae, a 750 bp fragment of the 3’-end of COI has routinely been used for taxonomic purposes. The sequence variability of equally large sequence fragments of both the 5’ and 3’ end of COI were hence compared for particular species groups. Internal Transcribed Spacer 2 sequences were generated as additional barcodes. COI hypotheses were evaluated against morphological species concepts, but taxonomic decisions integrated all available characters. In cases where morphological species could not be diagnosed due to invariant COI sequences, or numbers of COI haplotypes was large and/or partially informative, ITS2 sequences often proved informative. Molecular data were invaluable in assisting taxonomic decision-making, but it is evident that both taxonomic studies and identification of taxa based on DNA sequences (barcodes) benefits highly from extensive back-ground studies screening specimens over wide geographic distributions.
|Robert D. Ward
CSIRO Marine and Atmospheric Research
GPO Box 1538
|FISH-BOL (A Network to Assemble DNA Barcodes for ‘All Fishes’) – Prospects, Goals and Societal Importance|
The Fish Barcode of Life campaign, FISH-BOL (www.fishbol.org), is a global effort to assembly a standardised searchable web-based DNA sequence library for all fish species, derived from voucher specimens with authoritative taxonomic identifications. The benefits of barcoding fishes include facilitating species identification for all potential users, including taxonomists, highlighting specimens that represent a range expansion of known species, flagging previously unrecognised species, and perhaps most importantly, enabling identifications where traditional methods are not readily applicable. The latter include identifications of fillets, fins, eggs and larvae.
There are about 30,000 species of fish world-wide, about 16,000 marine and 13,000 freshwater. The FISH-BOL campaign began in 2005 and has thus far barcoded some 18,000 individuals from nearly 4,000 species. Of the first 500 Australian fish species examined, only two pairs of species could not be discriminated. These rare instances either reflect imperfect taxonomy (i.e. the characteristics used to separate these taxa do not reflect true species differentiation), hybridisation, or very recent speciation.
This talk will describe the aims and organization of FISH-BOL, and will demonstrate some of its achievements. Examples will be given of likely species discovery triggered by barcoding results, and its uses in fisheries management. The latter examples will focus on the ability of barcoding to discriminate among species of tuna that can be difficult to identify morphologically, and its use in identifying shark species from confiscated catches of illegally-taken shark fins. The FISH-BOL campaign is a public-good project will benefit conservation, fisheries management, fish retailing, and fisheries and marine ecology.
|Quentin D. Wheeler
International Institute for Species Exploration
Arizona State University, Tempe
|DNA Barcoding and Integrative Taxonomy|
What is the appropriate relation between DNA barcoding and taxonomy? Is DNA barcoding best regarded as a component of an integrated approach to taxonomy or as a replacement or surrogate for taxonomy? To answer these questions, it is appropriate that we ask some even more fundamental questions about the goals of taxonomy and the factors that make taxonomy in general “good” or “bad”. Given a clear concept of what “good” taxonomy looks like, it is possible to assess the logical contributions and potential roles of DNA barcoding within taxonomy. It is concluded that the urgent need for rapid and accurate species identifications by fields outside taxonomy indicates the need to invest in “good” fundamental taxonomy and to avoid overextending the reach of any single technique or data source. Increasing demand for new applied taxonomy (identification) tools is a justification to expand support for integrative taxonomy, not an excuse to supplant “good” taxonomy with expedient alternatives.
Centre for Ancient Genetics,
University of Copenhagen
|Ancient DNA and Barcoding|
DNA barcoding should provide rapid, accurate and automatable species identifications by using a standardized DNA region as a tag. However, this is difficult to find especially when dealing with fossil remains where the DNA is highly degraded. Here I evaluate the plant chloroplast trnL intron P6 loop, (10-143 bp) as a possible ancient DNA barcoding marker. Based on sequences available in GenBank and sequences produced using a new “universal” primer set, the species resolution is found to be about 19.5%. The resolution is much higher in specific contexts such as species originating from a single ecosystem, or commonly eaten plants. For the Arctic community, where we have recently reproducibly sequenced the whole chloroplast trnL (UAA) intron (254-767 bp) for about 763 specimens (737 different taxa, 246 genera) the species resolution for P6 is about 50%. If amplification and identification based on the P6 loop is followed by that targeting of specific substitution in the trnL (UAA) intron the species ID could increase to maybe 80% (rough estimate). Thus, the trnL intron P6 loop gives a much higher resolution than the chloroplast rbcl region commonly used in ancient DNA studies.
Page last modified: 11/04/2008