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 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.
Mol versus classical.doc
Description: MS-Word document
