Fwd: [diybio-boston] botany

[Bryan Bishop]

---------- Forwarded message ----------
From: DonLubin <donl...@comcast.net>
Date: Tue, Apr 27, 2010 at 11:40 AM
Subject: [diybio-boston] botany
To: diybio-boston <diybio...@googlegroups.com>


Hi folks, I just signed up.

I wonder whether this group has any suggestions for plant
identification technology.

I lead field trips and workshops, mostly for the New England Wild
Flower Society, on identifying native pteridophyte plants (ferns,
horsetails, club-mosses, etc.)  I grow 44 fern taxa in my small city
yard, survey pteridophyte florae in conservation areas, and maintain a
website at NEfern.info

I wonder whether anyone has ideas about low-tech chromosome squashing
techniques, or useful chromatography procedures. Differentiating
ploidy levels would be useful.

 - Don Lubin

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- Bryan
http://heybryan.org/
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[Forrest Flanagan]

Has anyone ever thought about a DIY fastprep machine? I think they're just glorified paint shakers.

[Tristan Eversole]

Hey! I'm new at this too, but this is exactly the kind of task I'm interested in. It's my general hope that cheap molecular biology will assist in surveying existing species and discovering new ones.

I have to admit that I hadn't heard of chromosome squashing before. The only plant protocols I can find for it (e.g. http://www.le.ac.uk/biology/phh4/prosquash.htm ) don't seem especially amateur-friendly. I'll keep looking.

I've checked out a few other identification methods. If you're set up for PCR, DNA barcodes exist for some of the plant species you list on your website:

Adiantum pedatum
Asplenium platyneuron
Athyrium filix-femina
Botrychium virginianum
Cystopteris fragilis
Dryopteris carthusiana
Equisetum arvense
Equisetum fluviatile
Equisetum palustre
Equisetum pratense
Equisetum scirpoides
Equisetum variegatum
Gymnocarpium dryopteris
Onoclea sensibilis
Osmunda regalis
Phegopteris connectilis
Thelypteris palustris
Woodsia glabella

You can find the relevant sequences here: http://www.boldsystems.org/views/taxbrowser_root.php

It also looks as if they're working on a number of other species that overlap with your list, but don't have sequences for them yet:

Asplenium scolopendrium
Asplenium trichomanes
Azolla sp.
Blechnum occidentale
Cystopteris bulbifera
Davallia pyxidiata
Dennstaedtia punctilobula
Dryopteris intermedia
Dryopteris marginalis
Equisetum hyemale
Equisetum sylvaticum
Gymnocarpium robertianum
Osmunda cinnamomea
Osmunda claytoniana
Pellaea atropurpurea
Pellaea glabella
Polypodium appalachianum
Polypodium virginianum
Polystichum acrostichoides
Pteridium aquilinum
Salvinia sp.
Thelypteris noveboracensis
Woodsia alpina
Woodsia ilvensis

I was disappointed to discover that the Molecular Ecology Resources Primer Database (http://tomato.biol.trinity.edu/ ) lacks sequences for most Pteridophytes. They have ten primers for Polystichum filix-mas, but that's not a species you're interested in, and they're only SNPs, rather than more useful microsatellite regions. Nonetheless, new primers might show up there in the future, so you may want to hang on to the link.

Automated species identification seems to be in the works. Smithsonian researchers are working on an iPhone app out there that can identify plants from a photograph of a leaf, as discussed in this New York Times article: http://www.nytimes.com/2009/05/10/business/10novel.html?_r=1 News reports on this subject date from nearly a year ago, but I can't find the actual software on the iPhone app store.

The Smithsonian also has a largish collection of botanical type specimens online, with images: http://botany.si.edu/types/ . I haven't looked at it in any extensive way, but they appear to have a lot of images for the Pteridaceae, for example.

I'm sorry if this reply isn't too helpful. This is my general area of interest, but I've only just started looking into it. (I'm not too great with plants, alas; my interests run more towards marine invertebrates.) If you'd like, I could keep looking for, say, chromatography techniques.

Nonetheless: Computational and molecular biological approaches to species identification and field study are massively parallelizable— the research subjects are readily available (instructions: go outside), the relevant protocols are straightforward, and programs for sequence alignment (innumerable), tree building (MrBayes, PhyML, PHYLIP— if only we had a PAUP equivalent....), and statistical analysis (R) are free. Projects like the Encyclopedia of Life appear to be warming up to the idea of amateur contributions, and biodiversity informatics is coming along. Watch this space!