Poemules

Those involved in Southeastern U.S. licheneering have probably met Sean Q. Beeching on a foray. His knowledge of the local lichen flora of Georgia and neighboring states surpasses that of most lichenologists for any region. He even has a species named after him: Megalaria beechingii (Lendemer 2007). He has also authored a book of essays... I highly recommend the fascinatingly-titled: "'I Like You But What Can You Do, Can You Be a Bird?': Adventures In The Lichen Trade." Page 3 of this bulletin provides a review of the book that gives some clues as to what kinds of essays you will find between the covers.

I recently received a message from Sean regarding the video of James Lendemer on the NPR website and some of the thoughts that it inspired in him:

"
I sent James's lichen video, by way of your blog, to a friend of mine, the botanist Lisa Kruse, and she, being sharper than me, noticed that the narrator says that the lichen fungus eats the algae. She then asked me if that is true because her understanding, and mine, was that the fungus appropriates from the algae, in one way or another, its nutrients without actually consuming the little green fellows. Instead of answering the question I sent her these three poems, or perhaps, poemules, would more accurately describe them. And thus I send them to you in the hope that you find them amusing.... on the other hand, if recent investigations have determined that the fungus does indeed devour the algae, I would like to know about that.

Three rhymes on the lichen symbiosis occasioned by a lichen video’s narrator having said that the lichen fungus eats the lichen algae.

Were I to venture to explain
How doth the fungus entertain,
I’d not have said he eats his guests
But rather shares in their bequests.

If to me the burden fell,
To illustrate the lichen, well,
More like the cow-maid, I would hold,
The fungus cultivates her fold,
She slaughters not her gentle beasts,
But rather milks them by their teats.

How doth the lichen food obtain?
The fungus, I would ascertain,
The alga probes with fingers shrewd.
His ticklish damsels something lewd,
And makes the ladies to surrender,
Unto its hands the purloined provender.
"

My only thoughts on the issue of whether the fungus 'eats' the algae are that [1] the fungi eat the products made by the algae (and they often even seem to enhance the production of food by the algae) and [2] the fungi presumably must devour the carcasses of the dead algae. Whether or not the fungi may, under certain conditions, 'kill' some of the algae or speed along their ultimate demise is not something that I think is known, although I would welcome additional commentary on the matter!

- Brendan

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Works Cited:
Lendemer, J.C. 2007. Megalaria beechingii, a new species from the southern Appalachian Mountains of eastern North America. Opuscula Philolichenum 4: 41-44.
Download publication (PDF file)

PICS-Ord

Just this week I had a 'methodology' article published in BMC Bioinformatics.  Robert Lücking of the Field Museum was the first author, and we worked with Alexis Stamatakis (of RAxML fame) and Reed Cartwright (creator of Ngila and Dawg).  The paper is entitled "PICS-Ord: Unlimited Coding of Ambiguous Regions by Pairwise Identity and Cost Scores Ordination" and it presents a method for encoding data found in ambiguously-aligned regions of multiple sequence alignments in a way that makes it possible to integrate such data into standard molecular phylogenetic analyses.  Most researchers simply exclude data found in ambiguously-aligned regions of nucleotide or amino-acid alignments when conducting phylogenetic inferences.  While such practices are perfectly sound, a large amount of potentially informative data is subsequently left out of downstream analyses.  However, using a method to recode these regions and integrate the data into phylogenetic analyses allows one to consider all of the data present in the larger molecular regions being analyzed.

Until PICS-Ord, no method had been devised for properly integrating this type of data into likelihood-based analyses (e.g., ML, Bayesian).  INAASE (Lutzoni et al. 2000) is a program that recodes ambiguously-aligned regions, but since the distances between different sequence types are encoded as cost matrices, its utility is limited to parsimony-based analyses.  It also has a finite number of symbols, making it impractical for large data sets.  For each ambiguously-aligned region, PICS-Ord uses ordination of scores (which are based on pairwise alignments between the sequences for each taxon) to create a series of axes that are converted to discreet characters which can be appended to a multiple sequence alignment.  The matrix of the sequence alignment plus the recoded characters can then be analyzed phylogenetically based on any number of criteria, including maximum likelihood (ML) and Bayesian inference.

PICS-Ord is available here as an R-based program.  As academic software goes, it's pretty friendly, but please let us know if you run into any troubles.  The publication of this method along with a program for implementation represents a great leap forward in phylogenetics, with the ability to finally integrate data from ambiguously-aligned regions into likelihood-based analyses!

-Brendan

P.S. Find out more about PICS-Ord here on Reed Cartwright's blog:
http://pandasthumb.org/archives/2011/01/pics-ord-unlimi.html

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Works Cited:

Lücking, R., B. P. Hodkinson, A. Stamatakis, and R. A. Cartwright. 2011. PICS-Ord: Unlimited Coding of Ambiguous Regions by Pairwise Identity and Cost Scores Ordination. BMC Bioinformatics 12: 10.
Download publication (PDF file)
Download R-based PICS-Ord program (zipped program package)
View program wiki (website)

Lutzoni, F., P. Wagner, V. Reeb, and S. Zoller. 2000. Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology. Systematic Biology 49: 628-651.
Download publication (PDF file)
Download Java-based INAASE program (zipped program package)