Over 30,000 species of animals and plants are considered to be potentially at risk of extinction, many of them due to the illegal trade in wildlife. The UK Department for Environment, Food and Rural Affairs ( DEFRA) has been interested for some time in the use of DNA-based tests to aid law enforcement and to help combat this illegal trade. In early 2000 they decided to fund a project to develop methods to first prioritise those species at greatest risk, and then to identify those where DNA markers (characterised differences in DNA used for identity) were not currently available, but could be of potential use in enforcement cases. This list would then be used by DEFRA to fund researchers to develop DNA markers for those species.
A number of organisations which carry out contract research projects were invited to submit proposals. LGC was well placed to tender for this work as the company has expertise not only in forensic analysis but also in the development and application of DNA markers for species identification. Our proposal was well received and we were invited to attend a tender board meeting at DEFRA?s offices in Bristol. I had only recently joined LGC (see box for my earlier career steps), and so presenting an outline of the major features of the project and being questioned by a panel of advisers was one of my first duties in my new role--a slightly nerve-wracking start! However, a few weeks later we heard that we had been successful in our bid and that we could start the project.
The first challenge was honing down those 30,000 ?at risk? species to a manageable top priority list of approximately 100--no mean feat in itself. Bearing in mind that the project was only funded for 1 year and had a fairly tight budget, we really had to make sure that we were searching for information and prioritising species in the most efficient way possible, whilst also trying to be thorough and accurate.
A Helical Career Path
Following a BSc in genetics from Leeds University, I worked as a scientific officer at the Regional Molecular Genetics Lab at St. Mary?s Hospital in Manchester. Whilst there I worked on a research project studying the genetics of inherited deafness and also performed routine genetic screening and prenatal diagnoses for diseases such as Duchenne muscular dystrophy and cystic fibrosis. Studying for a PhD took me back to Leeds, where my research at the department of pathology involved using DNA-based approaches to attempt to identify the causes of Type 1 diabetes.
A postdoc, again in Leeds, in the Unit of Molecular Vascular Medicine, followed. Predisposition to vascular disease was my focus here, using genetic epidemiological studies to identify novel polymorphisms in a range of candidate genes. In 1997, I took up a position as a technology development scientist at AstraZeneca Diagnostics. My role there involved technology development for microarray-based genetic analysis.
I arrived at LGC in May 2000, having been attracted to a company with a wide variety of science going on, and the scope to move between areas.
The project involved a team of people at LGC and I was responsible for its overall management. This involved liaising with DEFRA, ensuring that the work was delivered on time and to cost, that milestones were being met, and work was delivered to the required quality. I also had to make sure that invoices for payment were submitted and that contracts with DEFRA and subcontracts with our collaborators were in place. I was generally the point of contact between all those involved in the project, ensuring that all parties were working together in the most effective way.
Just to add to the pressure of delivering to a tight deadline, this project was one of several that I was required to manage on a day-to-day basis. The others included projects on DNA arrays and novel DNA technology development programmes. Managing a diversity of simultaneous projects is a common experience when you work for an organisation such as LGC.
The wildlife DNA project team consisted of DNA scientists, information specialists, and database designers. We were also able to call upon the expertise of others within LGC who had experience with the use of forensic DNA tests for species identification. The project also benefited from having TRAFFIC International as our partner. TRAFFIC is the wildlife trade-monitoring programme of the World Wide Fund for Nature and the World Conservation Union and aims to help ensure that wildlife trade is at sustainable levels.
The project kicked off with a meeting between LGC and TRAFFIC to finalise the project strategy, co-ordination, and delivery. To begin with we decided to perform an initial filter by focussing primarily on those species that are most protected in law (there are currently five levels of protection according to EU regulations). We also focussed on those considered to be the most endangered according to international classifications.
This initial screen brought the numbers down to a more manageable 350 or so species. For all these 350 species we then had the task of gathering together data on a number of factors which, when considered together, could be used to generate a priority ranking for the species. This involved taking into account the extent of illegal trade, gathered from seizure records and intelligence information, and the form that the species was traded in, for example live animal, parts, or derivatives. The idea was to determine the potential need for DNA-based identification; clearly live animals are easier to identify without the need for DNA analysis than parts or derivatives.
In the next stage of the project we planned to broaden our interests and include markers that were able to distinguish whether a live animal had been taken from the wild or from a captive-bred population, so we were also looking for population, family, and paternity type markers as well. The ability of the species to breed in captivity, based on information gathered from zoo breeding records and captive breeding programmes, was also of interest because easy-to-breed species would be of lower priority when determining where to focus antitrading efforts. TRAFFIC gathered all of this information and fed it into a database designed at LGC.
Finally, we had to search for the current availability of DNA markers. As no search strategy could ever be considered exhaustive, we had to devise a method for gathering the information that was as comprehensive as possible, whilst still achievable within the time and budget constraints of the project. Our strategy involved four stages. The first was to search publicly available databases such as PubMed and GenBank to identify markers or DNA sequences in the published literature. To do this we used the assistance of information specialists at LGC to devise a search strategy. This strategy combined the Latin name of the species (by the end of the project we were all able to recite the Latin names for several hundred species by heart--an unexpected outcome!) with a series of key words related to DNA markers.
The next stage involved feeding those species for which no markers could be identified into a more comprehensive database of published literature, which was available to LGC on a pay-per-go basis. Species for which we still could not identify markers were examined further by performing general Internet searches and looking at the Web sites of wildlife forensics labs and other relevant organisations.
The final stage involved contacting by e-mail experts across the world to ask whether they knew of any information or researchers working on the species in question. Many individuals were already known to LGC. Others were obtained through the literature or Internet searching processes and recommendations from TRAFFIC, DEFRA, or DEFRA-appointed advisers to the project. In all we contacted over 100 individuals or organisations to request information, many of whom were extremely helpful.
The final stage of the project was to feed all of the information into the database and assign scores to represent the information gathered. Once the architecture of the database was in place a ?top 100? priority list was generated.
This was a very rewarding project to work on and was a learning experience for me as, although my background is in genetics and DNA analysis, I had previously concentrated on humans rather than wildlife. However, I was fortunate that within LGC there was a wealth of expertise on hand and many individuals within the organisation provided guidance and support.
A final report, together with the complete database of information about all 350 species, has now been submitted to DEFRA and we are awaiting their feedback. There is a possibility that the database will be hosted on an Internet site so that other researchers in the field can gain access to the information. At the very least, however, we hope that the information will be of use to DEFRA in future research programmes, and that ultimately a few of those 30,000 species will be a little less endangered.