Biodiversity encompasses all varieties of life, from the level of ecosystems (such as water, forest, soil) to the diversity of species and the diversity of genes within a species. Switzerland’s topographical, geographical and climatic characteristics make Switzerland particularly rich in terms of species numbers and therefore particularly responsible for the documentation of species diversity and the protection of biodiversity.

Imagining the determination of the species present at a specific place at a given moment in a fast and reliable way is now possible. The Swiss reference genetic catalog is helping to establish a species identification tool and contributes to the global need to increase documentation of species.

The biodiversity in Switzerland

Thanks to its particular topography, its important elevation gradients and its central location in Europe, Switzerland hosts high levels of biodiversity. Despite its small size, 45,000 species have been recorded in Switzerland (state 2014) and according to specialists current estimates, the number of known species could be 70,000. Among this wealth, Switzerland has more than 100 species that live strictly in Switzerland (endemic to Switzerland) or that are restricted to Switzerland and its bordering regions (shared endemic).

Today we are witnesses of a decline in the overall state of biodiversity in Switzerland, with more than a third of plant, animal and fungal species considered endangered. The measures taken so far to safeguard specific diversity are not enough and Switzerland needs to redouble efforts to reduce species regression. In addition, Switzerland has an additional responsibility for the 39 endemic species, the disappearance of which on its territory would mean their disappearance on a worldwide scale.

An inventory as comprehensive as possible of Swiss biodiversity is an integral part of the species conservation and protection strategy. While such inventories have historically depended on traditional taxonomic methods, genetic cataloging techniques are increasingly being used to document species. The various biodiversity monitoring programs set up in Switzerland can thus benefit from a quick and reliable tool for identifying species, in addition to traditional taxonomy.

The genetic cataloguing

Our main goal is to create a genetic reference encyclopedia for all species in Switzerland. This genetic encyclopedia is made up of DNA sequences obtained from correctly determined reference specimens. The aim is to create a unique genetic profile for each species, which will later allow to determine by comparison the identity of any unidentified specimen complete or not.

The genetic profile may consist of the sequence of a single DNA fragment, ideally the official DNA barcode, or DNA sequences of a wider variety of genetic markers.

An ideal DNA barcode marker must meet a number of prerequisites: 1) be stable within a species, but variable between species; 2) be amenable to amplification with universal primers — primers conserved at both ends of the targeted gene so that the same primer pairs can be used for a wide range of organisms; 3) be easy to align, which facilitates the identification of specimens by using neighbor-joining trees. The CoI marker is currently recognized as the official barcode for animals. In addition, two markers located in the chloroplast genome are recognized as official barcodes for plants — rbcL and matK — and it is the nuclear marker ITS1/2 that serves as the official barcode for fungi.

Evolutionary histories of organisms have a great influence on the ability of the selected marker to fulfill its unique identifier role for each species. Thus, by increasing the number and diversity of markers targeted for the creation of a species’ genetic profile, the various biases related to the unique barcode are reduced. While traditional Sanger sequencing can target a single marker at a time, next-generation technologies can sequence dozens of markers at the same time and at the same cost.

Whether based on one or more sequences, the Swiss genetic reference catalog must above all compile quality genetic information on species. This database consists of DNA sequences generated from specimens determined by recognized experts for the treated groups. In addition, the Swiss reference genetic catalog is a tool for determining the identity of specimens, the sequence of an unidentified specimen being comparable to the sequences already recorded in the database.

Genetic cataloguing methods follow a precise protocol:

  1. A specimen is collected. The specimen is documented with the standard chorological information (who collected the specimen, where, when, etc.);
  2. The specimen is put in collection. The voucher is deposited in a public collection, such as a museum or a herbarium;
  3. Tissue is removed. A piece of tissue that contains DNA (muscle, piece of leaf, hair follicle, pollen grain) is taken from the specimen;
  4. The DNA is extracted. Several methods of DNA extraction exist but they all pass through the same steps: i) the cells of the tissue are lysed, ii) the lipids and proteins are removed, iii) the DNA molecules are precipitated and isolated. DNA extractions are stored under stable conditions in the long-term;
  5. Genetic markers are sequenced. From the DNA extraction and either using standard amplification and sequencing techniques or using modern genomic techniques, the sequences of the targeted markers are obtained;

The information is entered and linked. Information about each stage of the process is recorded according to the parameters required by the relevant databases. The links between the whole information, the specimen itself, the DNA extracts and the sequences generated are guaranteed by SwissBOL. Publication of the sequences in the international databases BOLD SYSTEMS and GenBank is also planned.

The practical applications

The genetic catalog of biodiversity is a valuable tool for identifying specimens. The data and information it contains are particularly useful for:

  • conservation. Species identification underpins all conservation efforts, and DNA sequences accelerate and facilitate this task, providing a basis for biodiversity monitoring, habitat protection and environmental risk assessment.

  • discerning cryptic species. Cryptic species are species that do not interbreed, but whose morphology is almost identical, making their distinction difficult or impossible on the sole basis of morphological criteria. DNA sequences, particularly official DNA barcodes, have revealed cryptic species in various groups including butterflies, algae, orchids and mollusks.
  • the identification of incomplete specimens. If only part of a specimen is available, such as a leaf fragment, a pollen grain, leg of an insect, or a tuft of hair, species identification based on morphology alone is very difficult, if not impossible. It is however possible, by using the genetic catalog and by comparison to the DNA sequences already referenced, to identify the species to which the biological element belongs.
  • associating males and females of the same species. In certain groups, males and females are dimorphic (i.e. they are not alike). Despite their external differences, males and females of a single species share the same genetic profile for most of the genome, at least for markers officially recognized as DNA barcodes. The DNA sequences thus make it possible to assign males and females to the correct species.
  • associating different stages of development of the same species. In some groups immature stages are phenotypically very different from adults of the same species. As for dimorphic males and females, assignment of immature stage specimens to correct species is possible based on DNA sequence comparison.
  • the identification of invasive species. Species introduced accidentally (or sometimes deliberately) into an area where they are naturally absent can result in significant economic losses and have considerable ecological impacts if they are a threat to native species. They are then called “invasive”. Genetic data, including DNA barcodes, can play a crucial role in the early detection of these species, fundamentally important to both outbreak prediction and prevention of attacks on both wild and cultivated species.
  • forensics. Criminal investigations often rely on the identification of insect larvae or fragments of plant material to determine when and where a crime was committed. In cases where such elements are difficult to identify by morphology, the use of DNA sequences is an effective alternative way to achieve this.
  • international trade regulation. Products made from illegally obtained materials (ivory, hides, horns, precious woods) are widely available on the international market. The source and origin of these materials are often difficult to identify, making it difficult to prevent the traffic of such products. DNA sequences, particularly DNA barcodes, can be used to determine the identity and source of such materials and thus contribute to the protection and control of the movement of these goods on the market.
  • food safety. The contents of products found in the supermarket may be impossible to determine, especially if the products have been processed in any way. DNA sequencing is a means of reliably identifying the contents of such products. Recent investigations using this technique revealed that certain products, including natural health products and frozen ready-made meals, contained ingredients that did not match their packaging labels. Other studies have uncovered extensive fraud in the seafood market, with cheaper fish being sold under the label of more expensive varieties to increase their retail value.

Documentation