Sleepless nights- Molecular versus classical taxonomy

Sleepless nights : Attachments (1)

I am sharing herewith an article which appeared in Taxon in 2014 on the above subject. I request you all to kindly comment and give your valuable opinion and suggestions which will enrich our knowledge.

Interesting article and a real message and warning of a sort. Molecular studies are helpful in certain cases, but they need to be associated with some morphological features, which workers in the field (and our group, Flowers of India and several online Forums have shown that these should not be exclusive trained taxonomists, but any lover of plants who knows how to recognise plants like we have Dinesh ji, Garg ji, Prashant ji and others on our forum). I was skeptical when I published a new species Tragopogon kashmirianus from Kashmir in 1976, and thought same two parents may be involved as gave rise to American T. mirus, both allotetraploids. It was a great relief when molecular studies showed that Kashmir plant was distinct from American T. mirus and that Kashmir T. dubius may be different from Europaean T. dubius (one of the parents).

http://2006.botanyconference.org/engine/search/index.php?func=detail&aid=544

There are few things to understand about describing a new species based on DNA data.

HOW DO THEY DO IT?

They sequence the DNA and try to match with existing sequences of related species in GENBANK or BOLD or any other sources not known to me. The sequence dont match and hence they describe the new species.

WHY SEQUENCES DON’T USUALLY MATCH?

Because all species on earth have not been sequenced. How many species from India have been sequenced? may be 10%…… so other 90% of the species will not match with any existing DNA sequences.

DNA IS A TOOL AND TAXONOMY CAN BE CALLED SCIENCE OR OPINION BASED SCIENCE.

DNA is a tool that can help in improvising your taxonomic skills, but just DNA is nothing, but a sequence.

FUNGI

Fungi are a bit different as most of the times you may not be able to see their fruiting body and hence not easy to describe unless you see it. Hence people use DNA data to describe new species among this group.

MORPHOLOGY OVER DNA OR DNA OVER MORPHOLOGY?

At many instances you may not be able to differentiate species based on morphology so easily because changes in DNA may bring changes in phenology that may not be undetectable by eye.

DNA SCIENCE IS STILL DEVELOPING.

DNA science is still evolving and we have not yet understood the full utility of it. Hence it can just be considered as utility. Why? because in every 4-5 years scientists come out with different sequences to use for differentiation. So far there is no universal marker for all species, not even for just all plants. May be in future we will have such sequences.

RELIABILITY ON DNA SEQUENCES

How much can we rely on DNA sequences is a matter of judgement. I have been working on it, and sorry to say but I have felt many times that i cant rely on it. I sequenced my known and well identified plants and many of the sequences matched with sequences of totally different and absurd species. Forget about species, some of my orchid sequences matched with sequences of FUNGI….. NOT A JOKE.

On a friendly note, i just got a manuscript for review from Molecular Ecology where scientists (GOOD TAXONOMISTS) have sequenced all the tuberous orchids of the region (multiple sequences of same species) so that it will aid in identification of orchid tubers in trade. This is one such first study which is surely going to have a great impact for future. So now, if someone is describing a new species and especially of the same subfamily of orchids, then these sequences will be of great help.

Few years back few of our own members published an article in Nature. Title was very good but the content shocked me.

“India needs more plant taxonomists”

India, with its wide range of geographical and climatic conditions, has a rich and varied flora of some 45,000 species — almost 7% of the world’s flowering plants. But their documentation is seriously compromised by the country’s dearth of plant taxonomists. Although DNA sequence data and barcoding are well on the way to being accepted as the global standard for species identification, India’s plant taxonomists are struggling to keep up. A lack of proper training and infrastructure hampers molecular-systematics studies, so the evolutionary lineages of most of the country’s plants remain poorly understood. India’s many outstanding botanists, familiar with regional flora, must help plant taxonomists to advance molecular-systematics studies and improve the evolutionary understanding of the country’s rich biodiversity.

But their documentation is seriously compromised by the country’s dearth of plant taxonomists. – ONE OF THE AUTHOR HAS WORKED WITH BSI.

DNA sequence data and barcoding are well on the way to being accepted as the global standard for species identification, India’s plant taxonomists are struggling to keep up. NO, DNA SEQUENCING AND BARCODING IS A TOOL AND CAN AID IN SPECIES IDENTIFICATION BUT CAN’T SOLELY DO SPECIES IDENTIFICATION. ALL THE NEW SPECIES I HAVE DESCRIBED SO FAR, I HAVE NEVER USED DNA DATA, EXCEPT FOR MY NEXT SPECIES WHICH WILL BE PUBLISHED SOON. BUT YOU WILL SEE IN IT, ABOUT HOW AND WHY MY OPINION DOESNT MATCH WITH THE EXISTING DNA DATA.

India’s many outstanding botanists, familiar with regional flora, must help plant taxonomists to advance molecular-systematics studies and improve the evolutionary understanding of the country’s rich biodiversity. – IT GIVES A FEELING THAT THE AUTHORS THOUGHT THAT ONLY THOSE ARE TAXONOMISTS WHO KNOW MOLECULAR SYSTEMATICS AND REST ARE BOTANISTS, WHICH IS WRONG. INFACT WHEN I HAD A CHAT WITH MY FRIEND WHO IS ONE OF THE AUTHORS, HE SAID HE DIDNT MEAN THAT!!

I attended the International Barcoding of life conference two years back where those barcoding Canadians recommended that we dont even have to name new species, just give them codes, because we dont have trained taxonomists. I would say WE DO HAVE TRAINED TAXONOMISTS, YOU NEED TO GIVE THEM A CHANCE. YOU DONT FUND THEM, YOU DONT SPONSOR THEM, YOU DONT PROVIDE JOB TO THEM, THEN YOU MAKE A HUE AND CRY THAT THERE ARE NOT ENOUGH TAXONOMISTS??? WHEN THERE WAS JOB CUT AT KEW, MOST OF THE PEOPLE WHO LOST THEIR JOBS WERE ACTUALLY TAXONOMISTS.

India already has lot of plant taxonomists who go unrecognised and are jobless and many of them left the country because taxonomists lack the recognition. New generation of students find taxonomy to be a mediocre subject and hesitate to undertake such studies. DNA barcoding will certainly help in better understanding of species, but DNA barcoding is not the standard to describe a new species.

India is one of the very very few countries in the world where they have an organisation called BSI who hire ONLY taxonomists. We should be proud of it and we should make it stronger.

These are my personal views. The authors of the nature article are my good friends, and I know both of you will be offended, so I say sorry in advance……

Interesting discussions.

Thanks Tapas Ji for sharing the interesting article… The authors proposed policy lines (proposals) for describing new taxa, of course it is required to set the guidelines. As Pankaj Ji have told, it is still too early to base the taxonomic affinities entirely on DNA, and giving only codes as per the other article is also not going to make the things more scientific, rather will add to the complexity…

I also join Pankaj Ji to agree that we have a large number of taxonomists and dedicated field workers, who are doing wonderful work in all corners of our country of a large geographical area and one of the richest biodiversity spots on earth.

Hopefully, the article, as expected by the authors, will be discussed for future discussions on the Code.

Thanks again Tapas Ji for this link, and the acknowledgement revealed how a sleepless night ended with these discussions…!!

Just reflecting on this statement,

PK: “How much can we rely on DNA sequences is a matter of judgement. I have been working on it, and sorry to say but I have felt many times that i cant rely on it. I sequenced my known and well identified plants and many of the sequences matched with sequences of totally different and absurd species. Forget about species, some of my orchid sequences matched with sequences of FUNGI….. NOT A JOKE.”

RB: I guess the percentage match is important? Human genome too matches with fungi to the tune of 25% and matches 98% with Chimpazees https://www.koshland-science-museum.org/sites/all/exhibits/exhibitdna/intro03.jsp

Although we humans match our DNA 100% with each other what makes us different then (or for that matter makes every sea squirt different from every other sea-squirt)?

Well there are very small differences in spite of the 100% match. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC534664/

I know about the confidence percentage. But in that case, should I describe them as new species? And yes the percentage was sometimes above 95, up to 98% in many cases. How many times do you really get a 100% match? Two accessions of same species with correct id, same sequence length, but from India and China, may not show 100% match either.

Secondly, how come a sequence of angiosperm (orchid) matched with a fungi? To me, even at 50% match is absurd.

I also understand that its a matter of misidentification and that was my point, that many of the so called barcoding experts ARE NOT WELL TRAINED TAXONOMISTS!!

Barcoding is a tool which you can learn in 1 month training. Taxonomy comes from within and takes years of training and understanding.

Kindly look at the attachment which I support. Attachments (1)

– Mol versus classical.doc

Here is the one line reply from an eminent taxonomist:

Taxonomy is already difficult and why such attempts to create more problems? May God help the future botanists especially florists of India. Whatsoever the developments, a hand lens will continue to serve as the basic tool for identification.