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.
On Fri, Jul 15, 2016 at 4:13 PM, J.M. Garg <[email protected]> wrote: > Thanks, Tapas ji. > > On 15 July 2016 at 15:12, Tapas Chakrabarty <[email protected]> wrote: > >> Kindly look at the attachment which I support. >> >> On Fri, Jul 15, 2016 at 2:10 PM, Pankaj Kumar <[email protected]> >> wrote: >> >>> 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 email to [email protected]. >>> Visit this group at https://groups.google.com/group/indiantreepix. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> -- >> 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. >> > > > > -- > With regards, > J.M.Garg > > 'Creating awareness of Indian Flora & Fauna' > <http://en.wikipedia.org/wiki/User:Jmgarg1> > > Winner of Wipro-NFS Sparrow Awards 2014 for efloraofindia > <https://sites.google.com/site/efloraofindia/award-for-efloraofindia>. > > For identification, learning, discussion & documentation of Indian Flora, > please visit/ join our Efloraofindia Google e-group > <https://groups.google.com/forum/#!forum/indiantreepix> (largest in the > world- around 2700 members & 2,40,000 messages on 31.3.16) or Efloraofindia > website <https://sites.google.com/site/efloraofindia/> (with a species > database of more than 11,000 species & 2,20,000 images). > > The whole world uses my Image Resource > <http://commons.wikimedia.org/wiki/Category:J.M.Garg> of more than a > thousand species & eight thousand images of Birds, Butterflies, Plants etc. > (arranged alphabetically & place-wise). You can also use them for free as > per Creative Commons license attached with each image. > > Also author of 'A Photoguide to the Birds of Kolkata & Common Birds of > India'. > -- 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.
