naming of plants

aaron floden
Sat, 09 Jan 2016 06:30:06 PST
The old taxonomists using morphology were often correct. Look at Aster which is now split back into many genera. Many of those are old names resurrected based on more recent molecular data. Same for Saxifraga, and many other genera. From the 1930-1970's it seems there was a movement to recognize very broad species concepts and taxonomists started lumping species and genera together. While I think new species descriptions should include more than morphology the science is that people collected something, they questioned what it was, compared it to what they thought it was, and eventually described it. In the paper this is all reduced down to "the plant in questions was compared to ...... and determined to be a new species." Where the flora is relatively unknown and understudied that is often sufficient, but here in North America there should be other sources of data in addition to morphology, though some people doubt anything new is still present in eastern North America. Most botanists I know don't rush into describing a species because they consider alternatives. I sat on Dirca decipiens for 10 years! Then It finally got published with molecular. habitat, and extensive morphological data and someone immediately put it in synonymy with D. palustris on their Wikipedia page. Now whole chloroplast data of all the known populations (4) clearly places it sister to D. mexicana. 

There are many species definitions outside that one on Wikipedia. Some taxonomists often used several in validating a novel species whereas others don't even bother.
 Next generation sequencing (NGS) has given us the ability to get a lot of data, but we still don't know what the functions of all the genes in the chloroplast are! Getting to the mitochondrion, and the extensive nuclear genome will take a long time. That said, there was a recent paper on the genome size in the tribe Paridae (=Trilliaceae) that looked into why that group relative to the remaining Melanthiaceae had such large genomes. It might have been nice to have NGS data for everything in the tree and the comparison of gene presence/absence before and after the genome size increase. Was it an increase in functional genes or just duplications and spacers? Before you can ask the big questions you have to know what you are looking at and often those people asking the larger questions don't know or understand the organism. If I had focused on large questions first in Polygonatum I probably would have missed some things. There have been 8 new species described since 2014. There are still others and trying to understand the verticillate species in southwest China is another project all together. 

  The one or two locus molecular analyses are common, but recent NGS publications are showing that comparison of the nuclear ribosomal ITS + a chloroplast locus or maybe two provide the same topology and occasionaly branch support as 100k base pairs. So is it worth the extra money to a researcher to get many loci vs. a few? I have whole chloroplasts for 24 Polygonatum and numerous nuclear and mitochondrial loci. The tree for those from that dataset is identical to Sanger sequenced nuclear ETS (ca. 400 bp) and 1200 bp of the chloroplast. More molecular data is not always better. 

 Taxonomists used to get tenure. Now taxonomists struggle to get jobs. There is very little money in it and getting money for fieldwork is even harder. Some money has to go to getting papers published, especially if you want open access or a higher caliber journal. Open access cost by some publishers for a paper of any length is $2000. Others are free, some are only $20/page. The trickle-down effect to other plant related industries takes a long time. Getting books published on new species might only be a photo of a new plant in a specialist gardening book, not a gardeners monograph.


      From: Robin Graham Bell <>
 To: Pacific Bulb Society <> 
 Sent: Wednesday, January 6, 2016 4:03 PM
 Subject: Re: [pbs] naming of plants
Of course taxonomists had nothing other than structure to work with originally & they did what they could, that's not really the problem. The problem is how this was all done, a series of measurements does not constitute an experiment or a proof, no matter whether you're measuring one or many characters. One can say two plants, populations or whatever, are different, using whatever measurements you want, but does that mean they are different species? How do you know, which should mean how do you prove it. At the moment it rests on someone's authority/respect/standing. Alternative explanations are virtually never considered.That is not science. I wonder how many species a taxonomist might have found with Mendel's peas?
    Why should one care? Well, there is a strong tendency in botany to treat the designation of a new species as the end of the road, it is catalogued, pigeonholed, a new monograph is written, superseding the previous one & that is the end of that. In my view this is a strong impediment to understanding anything. Or conducting any insightful biology. For example, I would like to know why plants need so many genes, humans, for example, have ~24.000 but at least some plants have well into the 40,0000 range. Even something as manifestly simple as Arabidopsis has more genes than humans, & Paris japonica has the largest known genome. I'm sure you know all this stuff, but answers as to why it should be, seem rare, even questions seem rare.
    Not only that, but questions about what might be rapidly evolving plants in any geographic area are submerged when they are all assigned species status, game over, we understand that lot.
    The DNA analysis & comparison seems more & more to be based on one or two genes, & not necessarily even the whole gene. Genome screening of a putative new species consists of finding a gene that is "informative" that is, conforms to ones expectations; just like looking for an anatomic difference in earlier times. We ignore & reduce the significance of all that is indistinguishable, even if this could be over 99% of structure.This is simply fishing for a confirmation of hypothesis, same as the old taxonomy, find a difference & you've got it, new species! It seems that the DNA work has successfully shown that taxonomy was often in error in the past, but at the other end it is simply becoming the "new" taxonomy.
    Finally, while you may not personally benefit from the discovery of a new species, people do benefit from these discoveries,  taxonomists get tenure, publishers get books, nurserymen get plants, often expensive ones, people underwrite discovery expeditions & gardeners want to have them & other people become experts. Although definitely modest & pretty harmless, species discovery would appear to have many of the hallmarks of an industry. Wild plants also suffer as folks go out & dig the new discoveries up to have or to sell. That's not a plus.
    I hope this clarifies my comments a bit.
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