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.
On Fri, Jul 15, 2016 at 4:28 PM, Rakesh Biswas <[email protected]> wrote: > 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/ > > best, > > rb > > On Fri, Jul 15, 2016 at 6:56 AM, Dr Pankaj Kumar <[email protected]> > wrote: > >> 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...... >> >> >> >> >> >> On Friday, 15 July 2016 01:08:10 UTC+8, tchakrab wrote: >>> >>> Respected/Dear All, >>> >>> 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. >>> With kind regards, >>> Tapas. >>> >> -- >> You received this message because you are subscribed to the Google Groups >> "efloraofindia" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To post to this group, send email to [email protected]. >> Visit this group at https://groups.google.com/group/indiantreepix. >> For more options, visit https://groups.google.com/d/optout. >> > > -- ****************************************************** **************************************************************** *Pankaj Kumar*, Ph.D. *IUCN-SSC Orchid Specialist Group Asia* *Office*: Conservation Officer Orchid Conservation Section Flora Conservation Department Kadoorie Farm and Botanic Garden (KFBG) Corporation Lam Kam Road, Tai Po, New Territories, Hong Kong. *Residence*: House no. 39, 2nd Floor, Shui Wo Tsuen Lam Tsuen, Tai Po, New Territories, Hong Kong. *email*: [email protected]; [email protected] *Phone*: +852 2483 7128 (office - 8:30am to 5:00pm); +852 9436 6251 (mobile); *Fax*: +852 2483 7194 -- You received this message because you are subscribed to the Google Groups "efloraofindia" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send an email to [email protected]. Visit this group at https://groups.google.com/group/indiantreepix. For more options, visit https://groups.google.com/d/optout.
