Thursday, 17 August 2017

DNA sequencing - the solution to recording problems?

There was a bit of controversy on the UK Hoverflies Facebook page yesterday. Debate about the ethics and/or importance of retaining specimens led to an assertion by one contributor that collecting for recording was an anachronism and that it could be replaced by DNA analysis of a leg taken from a live insect!

The concept provides rich food for thought. Are we at that stage yet? If so, is it or will it be a viable option?

As far as I am aware, we are a long way off having a full database of DNA sequences for many animals and the prospects of assembling such sequences for bigger Orders such as the Diptera are a very long way away. There are initiatives to start the process, but they are fraught with problems; not least that traditional killing agents degrade DNA, so the only viable option is to take fresh specimens and freeze them. That is relatively simple for easily recognised species, but once one enters the realm of difficult taxa it is likely to lead to the need to take and kill very large numbers of individuals to track down the missing pieces. The sheer scale of the job is immense and is not going to be achieved in the near future. It is further complicated because the specimens must be stored in close to pure ethanol – which is not readily available to anyone other than registered labs.

That starts the thread of a bigger problem

Which gene sequences are the most useful for separating particular taxa? There has been a lot of work on the CO1 gene in hoverflies, but this gene is not without its limitations. I suspect there is a lot more to do before we can reliably separate some species using DNA sequencing.

BUT, I think the most worrying complication is the degree to which identification errors are already entering the system. Dipterists in the UK have been shocked by some examples of gene sequencing from other parts of the World, with the authors describing sequences for what are clearly species within a different FAMILY let alone genus! The genie is out of the bottle and it is going to take a fair while to put it back and then release it under control.

What about DNA as a way of recording?

The idea is great. You buy your portanble gene-sequencer and catch insects that go into the sequencer and out pops a record! What happens to the insect? I suspect early sequencers will be fairly invasive and the animal will suffer serious injury or death. The idea of removing a leg from a fly 3mm long whilst keeping the animal alive is going to be dependent upon the dexterity of the operator. I suspect there will be large numbers of maimed and dying insects! Why not the old system of hand lens and holding the insect in ones fingers as specialists do at the moment for moderately doable species?

I suspect what is more likely is that in time it will be possible to put an insect soup into a sequencer and get a long species list of those that can be identified, plus a tail of question marks that cannot be identified and will never be identified because the animal has been liquidised!

What is the way forward?

There is no doubt that there is a need for a major gene sequecing programme, and that existing specialists will need to engage in the process. Many of us have already done so in some capacity. It remains to be seen how fast progress is made, but the days when there is no need for the microscope and pinned specimens are some way off.

Critically, if DNA sequencing is to be anything more than a dream, we need to grow a new generation of taxonomically competent specialists. They will have to provide the technical know-how in terms of reliable species identifications to confirm what gene-sequencing tells us. Traditional taxonomists are likely to be needed for a very long way into the future! The Universities are not doing this. I'm not sure they ever did, really. The skill of the taxonomist is the result of many years' work after graduation: getting to know their subject area in intimate detail. Such skills may once have lain in Universities, but to a large extent they were the territory of museums. Those jobs have largely gone too.

In the UK perhaps as much as 80% of the technical know-how resides in the non-vocational sector (amateurs). We must therefore make sure that taxonomic skills survive until Nirvana is attained. The HRS is doing its bit by running training courses and in its use of the UK Hoverflies Facebook page to mentor new taxonomic specialists. Taxonomic expertise is at a premium and needs to be valued and nurtured if the aspiration of developing a complete DNA sequence library is ever to be achieved.

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