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]. 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