Ημερολόγιο της/του wweellll

These are my notes for Usnea in the area, compiled from a few sources in an abbreviated form for quick identification. I wrote some tips below the tables as well.

Abbreviations:

Saxicolous, subalpine-alpine, black stripes on branches: lambii

Apotheciate, no isidia or soredia

These are distinguished by chemistry typically, but in our area location is normally all you need:

• K+Y, P+O, UV- (thamnolic acid, accessory alectorialic acid): florida (probably not in the PNW)
• K+Y-O, P+O, salacinic acid; in California: intermedia
• K-, P-, UV+ (squamatic acid, accessory alectorialic acid): florida (probably not in the PNW)
• K-, P+R, UV- (protocetraric acid); in n. WA, BC: quasirigida

Unusual thallus or axis color:

• axis yellow, cortex with red spots: flavocardia
• axis brown, lacking isidia and soredia: trichodea
• axis red, pinkish brown, rose, cortex with isidia and coarse soredia: ceratina
• cortex red, or red spots, axis white, coastal: rubicunda

Pendulous:

• main branches not dividing: longissima

Cigar shaped branches (all have CMA about 7/31/25 with a very loose medulla):

Tufted with soralia which are strongly concave, wrapping around branches with age, with a recurved cortex:

Photos of this type of soralia

Tufted otherwise:

Tips for good Usnea observations

• Try to find a healthy thallus that is not immature. Necrotic thalli often have colored axes or thalli which might be mistaken for flavocardia or other specially colored species.
• Identify the overall morphology: is it pendant or tufted? Does it have cigar-shaped branches? Is the thallus foveolate or not? Are there many fibrils or is it barely branched like an alectoria?
• Get a good photo of the base: the area above the base might have annular rings, possibly many, or be papillate. Most bases are black or darkening, but a few species never have darkening bases
• Look for soralia; sometimes these are only on smaller branches. Find several; species with soralia which are large will also have smaller, young soralia. Smaller soralia may be the only ones with isidia. Whether or not there are any isidia is often useful.
• Make a cut near but not at the base into the interior and take a CMA measurement (I made a tool for measuring CMA quickly here: https://welliam.github.io/measure-cma/). Recently papers have been referring to M/C and A/M ratios as well, which are just calculated from the CMA measurement (it captures the notion of “medulla thinner than cortex” as a M/C<1 and is apparently a useful characteristic). With a CMA measurement this can be calculated by taking the ratio of the medulla/cortex or axis/medulla percents
• A CMA measurement is not necessary for cigar shaped branches, but it’s still worth revealing the axis to check for flavocardia. Cigar shaped branches are caused by a very loose, thick medulla; if you are unsure about this (it can sometimes be a bit subtle) check if the medulla is over 25% and very loose
• If the axis strangely colored, this may reveal the species immediately (yellow = flavocardia, brown = trichodea, red, pinkish brown, rose = ceratina)
• Shine a UV light at the freshly exposed medulla; there are only a few UV+ species (from squamatic acid). Squamatic acid’s UV+ is bright and obvious; if ambiguous it is UV-
• Consider doing a spot test with the piece you removed taking the CMA measurement. Virtually all species will occasionally lack any secondary metabolites other than usnic acid, so only positive results are useful

Cutting the branch longitudinally for a CMA

This can be a little tricky. Using a double edged razor blade that's been broken in half (like you might use for sectioning apothecia) is best. Find a well exposed, large branch near the base, and make a cut, trying to keep the razor blade level with the branch. If the cut isn't far enough into the branch to cross section the axis, scrape a bit more off. Less is better so you don't cut the branch all the way through (not the end of the world, if you still got a good level section exposed). I find this easier with dry thalli but completely possible with wet thalli too. A 1:1 macro lens with flash should be powerful enough to get a good photo for the CMA measurement. Rotate and crop so the branch makes up the lower 2/3rds of the photo and is horizontal in the frame.

Resources

Bruce McCune and Linda Geiser's Macrolichens of the Pacific Northwest; McCune's website has good photos
Daphne Stone's Usnea in the Pacific Northwest (available here)
Clerc (1987) Systematics of the Usnea fragilescens aggregate and its distribution in Scandinavia. (describes CMA measurements)
Clerc (1987) On the morphology of soralia in the genus Usnea.

iNaturalist currently doesn't have a lot of good observations, and computer vision is almost completely useless for Usnea.

I recently wrote a Python script that reads EXIF data for camera, lens, and focus position and adds a scale bar to the photos: https://gist.github.com/welliam/f1df4594670b4b2165d0661a78b33a24

Here's an example of the result: https://www.inaturalist.org/photos/309888307

How it works

It's written with prime lenses in mind, though other lenses could be adapted to work for it. I didn't attempt a general formula, with my limited understanding of optics. Additionally, most people online say focus distance is not reported accurately from EXIF data at all, so a general formula wouldn't probably work. Even with perfect EXIF data, I'm not sure a general solution is actually possible; real life lenses are complicated.

Instead I manually recorded pixels/mm at various focus distances with the camera, and interpolate between them linearly. (Therefore, it doesn't matter if the EXIF focus distance is actually accurate, just that it's internally consistent.) It's a crude solution but it does seem to work; with test photos of rulers at random focus distances it seems to be reasonably accurate.

Right now it only works with known combinations of lenses and cameras (really just the one I use most often now, my OM-5 with the M.Zuiko 60mm macro lens). It feels like a safe assumption to just go off sensor size for the camera, rather than rely on an individual model, but without more cameras and lenses to try out I'm not confident about any assumptions.

Making this useful for other people

I don't think a Python script is the best way to do this part. I want a sort of webpage that people can quickly add scale bars onto. The automatic derivation from EXIF data part will be hard to get support for without people contributing their own measurements (cameras are pretty expensive!); most likely I'll add an input field for manually specifying pixels/mm at various focus distances, and give people instructions on how to figure that out on their own.

TODOs

• Rotating the scale bar
• Changing scale bar style (color)
• Changing the unit (cm, mm, etc)
• Non-macro or even telephoto distances (issues with focus distance inaccuracy might make this unreasonable: TBD)
• Microscopes: supporting photos taken through a dissecting microscope eyepiece would probably also be useful; these focus by physically moving the microscope up and down, so they'd work a little different (you'd specify the zoom factor). The camera sensor size and resolution would be the only other factors in this situation. Light microscopes would work similarly. Neither are going to be as luxurious as the camera solution, as no information about the microscope would be in the EXIFs
• Resizing: A limitation that might not be reasonable to work around is that you can't resize images before using this tool, as pixels/mm is the magic factor that'd be ruined by resizing (so cropping is ok). I'm not sure resizing is recorded in EXIF data; if it were, it'd be easy to adapt. If not then we're hosed!

Query of all taxa

Queries:

• All observations
• Research grade
• Needs ID

Caveat: this queries for any species listed in WA, OR, BC in any of those areas; if a species is listed in BC but not in WA, observations in WA will still show.

To get this I:

• Downloaded taxa data from https://www.inaturalist.org/taxa/inaturalist-taxonomy.dwca.zip
• Extracted copied taxa.csv from inaturalist-taxonomy.dwca.zip
• Copied listed species from the docx file here: https://northwest-lichenologists.wildapricot.org/page-1854188
• Manually created NAME_MAP by searching for synonyms on inaturalist (there's probably a better way to do this but there were only a few)
• Ran script to get ids from listed_species.txt: https://gist.github.com/welliam/0ca175ad65ed885c565952b28afd8b2c

There's a few taxa I couldn't find on iNat:

• Leptogium umpquaense
• Scytinium quadrifidum

Edit 08/30/2023: Added some previously missing species (Sticta torii, Scytinium siskiyouense)