New Lichen Web Resources

The New York Botanical Garden has recently made available a set of excellent web resources for the study of lichens in North America.  Here is the announcement sent out by James Lendemer:

"

We are pleased to announce that two new lichen websites have been posted that can be accessed via the NYBG Virtual Herbarium (http://sciweb.nybg.org/science2/VirtualHerbarium.asp). These websites treat the lichen biotas of two large biogeographic regions of North America: the Ozarks and the southeastern Coastal Plain.

1) Lichens of the Ozarks - http://sweetgum.nybg.org/ozarklichens/

This website presents the results of Richard Harris and Doug Ladd's research on the lichen biota of the Ozark Ecoregion in central North America. Highlights of the website include a dynamic specimen-based checklist, dynamic literature listings including linked pdfs when applicable, and a pdf of the keys to Ozark lichens produced for the Tuckerman Workshop in Eureka Springs, Arkansas.

2) Lichens of the Southeastern Coastal Plain - http://sweetgum.nybg.org/southeastlichens/index.php

This website is an ongoing effort intended to present the results of our continuing research on the lichen biota of the Coastal Plain of southeastern North America.

We welcome all comments, corrections, and suggestions. These should be sent to jlendemer@nybg.org

"

The southeastern Coastal Plain project builds on the research and collecting done by Richard Harris for the classic works Some Florida Lichens (Harris 1990) and More Florida Lichens (Harris 1995).  Currently, we are actively working further north in the Coastal Plain, conducting inventories (e.g., Hodkinson & Case 2008, Hodkinson et al. 2009, Lendemer & Hodkinson in prep), elucidating distributional patterns (Lendemer & Hodkinson 2009, 2009a), and describing new species that occur in the region (e.g., Lendemer & Hodkinson 2010, in prep).  

Those who are attending the Botany 2010 conference in Rhode Island will have an opportunity to see a talk by James Lendemer on the progress of the work so far in the southeastern Coastal Plain (Lendemer et al. 2010).  At the upcoming conference, I will be co-leading a workshop on an integrated approach to lichen systematics (Lendemer et al. 2010a), presenting a poster on semi-cryptic species (Hodkinson & Lendemer 2010, 2010a), and giving a talk on 'rhizobes' associated with lichens (Hodkinson & Lutzoni 2010).  Hopefully, I will see some of you there!

- Brendan

[Research on the lichens of the Ozarks was supported by NSF Grant DEB-0206023.]

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References:

Harris, R. C. 1990. Some Florida Lichens. Published by the author. Bronx, NY. 109 pp.

Harris, R. C. 1995. More Florida Lichens, including the 10 cent tour of the pyrenolichens. Published by the author. Bronx, NY. 192 pp.

Download publication (PDF file)

Harris, R. C., and D. Ladd. 2005. Ozark lichens; Enumerating the lichens of the Ozark Highlands of Arkansas, Kansas, Illinois, Missouri, and Oklahoma. Published by the authors. Bronx, NY. 249 pp.

Download publication (PDF fie)

Hodkinson, B. P., and M. A. Case. 2008. A lichen survey of Williamsburg, Virginia. Banisteria 31: 24-30.
Download publication (PDF file)

Hodkinson, B. P., R. C. Harris, and M. A. Case. 2009. A Checklist of Virginia Lichens. Evansia 26(2): 64-88.
Download publication (PDF file)
View authors' updated checklist (website)

Hodkinson, B. P., and J. C. Lendemer. 2010. Molecular analyses reveal semi-cryptic species in Xanthoparmelia tasmanica. Bibliotheca Lichenologica: in press.
Download draft (PDF file)
Download alignment (NEXUS file)

Hodkinson, B. P., and J. C. Lendemer. 2010a. How do you solve a problem like Xanthoparmelia? Molecular analyses reveal semi-cryptic species in an Australasian-American 'disjunct' taxon. Botany 2010, abs. 355.
View abstract (website)

Hodkinson, B. P., and F. Lutzoni. 2010. Do lichens harbor their own 'rhizobia'? A large-scale phylogenetic survey of lichen-associated bacteria from the order Rhizobiales. Botany 2010, abs. 347.
View abstract (website)

Lendemer, J. C., and B. P. Hodkinson. 2009. The Wisdom of Fools: new molecular and morphological insights into the North American apodetiate species of Cladonia. Opuscula Philolichenum 7: 79-100.
Download publication (PDF file)
Download alignment (NEXUS file)
 
Lendemer, J. C., and B. P. Hodkinson. 2009a. Stretching the boundaries: A range extension for Buellia wheeleri R.C. Harris. Evansia 26(4): 172-176.
Download publication (PDF file)
View dynamic range map of Buellia wheeleri (google map)
 

Lendemer, J. C., and B. P. Hodkinson. 2010. A new perspective on Punctelia subrudecta in North America: previously-rejected morphological characters corroborate molecular phylogenetic evidence and provide insight into an old problem. Lichenologist 42(4): 405-421.
Download publication (PDF file)
Download alignment (NEXUS file)

Lendemer, J. C., R. C. Harris, and B. P. Hodkinson. 2010. Connecting the dots: progress and problems in assessing lichen biodiversity and biogeography in the coastal plain of southeastern North America. Botany 2010, abs. 30.
View abstract (website) 

Lendemer, J. C., B. P. Hodkinson, and M. Piercey-Normore. 2010. Cladonia Systematics: What can we infer from morphology and molecules? Botany 2010, abs. 1052.
View abstract (website)

Lichens of Nome, Alaska

Lichens of Alaska, Part III: Nome

Pannaria pezizoides surrounded by Stereocaulon sp.

Candelariella aurella with Lecanora sp. and unknown Collemataceae.

Bryocaulon divergens with Alectoria ochroleuca  and Cladonia spp.

Lichen-covered igloo mounds on the tundra.

Ochrolechia upsaliensis with Flavocetraria spp. and Cladonia sp.

Xanthoria-covered rocks overhanging clear waters.

Thanks for all the interest in my photos.  A nice field photo accompanied by a good specimen can have great scientific and educational value, so I encourage everyone to snap and collect (with permission, of course)!

-Brendan

[Funding provided by NSF Award DEB-0640956.]

MSA 2010

Last week I attended the annual meeting of the Mycological Society of America, which was in Lexington, Kentucky, the heart of Horse Country and the land of Bourbon Whiskey. I gave a talk on lichen-associated bacteria (Hodkinson & Lutzoni 2010) and it was quite well-received. There were some great talks, and I enjoyed having an opportunity to catch up with fellow friends of fungi!

One of the great things about the MSA meetings is that there's always a jam session at night, and since I play guitar, I'm always excited to join in. Here is a video of part of a long slow jam to the tune House of the Rising Sun:

We played a real variety of tunes from old-time to punk to country to rock, etc., on into the night.

At the end of the conference there was a final banquet and auction, where I made out with a hefty stack of great old mycological books and papers (thanks to Betsy Arnold for her work on the auction)! There were also some more whimsical items. Here you can see the distinguished Dr. Methven sporting some newly-acquired mycological apparel that he won at the auction.

I would encourage anyone who has an interest in fungi to join the society. There are ten different types of membership, so there's a place for everyone! I'm certainly looking forward to the next meeting!

-Brendan

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Reference:

Hodkinson, B. P., and F. Lutzoni. 2010. Do lichens harbor their own rhizobia? A large-scale phylogenetic survey of lichen-associated bacteria from the order Rhizobiales. Inoculum 61(4): 55-56.
View Inoculum issue (PDF file)

Punctelia caseana Lendemer & Hodkinson sp. nov.

Recently, James Lendemer (of the New York Botanical Garden) and I put together a paper on the North American sorediate species in the genus Punctelia with lecanoric acid and a pale underside. In North America, these species have generally been called Punctelia subrudecta (a European name), but it was discovered more recently that the conidia do not match the European species. Incidentally, the European species P. perreticulata and P. jeckeri (syn. P. ulophylla) have been reported rarely in different parts of the North American continent. For reasons outlined in our recent paper (Lendemer & Hodkinson 2010; see the official website here), P. perreticulata became the accepted name for all three of these species in North America during the past few years. However, our observations in the field and lab told us that there was more than one entity here in North America. Therefore, we decided to generate rDNA internal transcribed spacer (ITS) sequence data from morphologically and geographically disparate populations to see if the observed morphotypes correlated with genetically-distinct entities.

In Eastern North America, we found that the species so long confused with Punctelia subrudecta actually seemed to be an undescribed species, which we named after my undergraduate advisor (Dr. Martha Case of the College of William & Mary):

Punctelia caseana Lendemer & Hodkinson sp. nov. A & B, thallus margin, ×0.5; A (top), morphotype 1; B (bottom), morphotype 2; C & D, soralia, ×1; C (top), morphotype 1; D (bottom), morphotype 2; E & F, epruinose lobe tips, ×3;E (top), morphotype 1; F (bottom), morphotype 2; G, geographic distribution based on herbarium material at CANL and NY; shaded region approximates to the eastern range mapped by Brodo et al. (2001)). Images of morphotype 1 are from Lendemer 12205 (NY) and morphotype 2 are from Harris 54826 (NY).

Punctelia caseana encompasses at least two morphotypes, illustrated in the figure above. However, one of the morphotypes is potentially paraphyletic based on our molecular phylogenetic analyses, leading us to recognize both morphotypes under a single name for the time being. Some additional photos of this species can be seen here (Sharnoff) and here (Mushroom Observer).

In western North America, we found that all of the lichens had a haze of pruina on at least some of the lobe tips, which is often difficult to discern, but immediately made me think of Punctelia jeckeri (syn. P. ulophylla). Of course, it seemed unlikely that the species dominating western North America was the same as the European P. jeckeri (especially given the mantra that pruinosity is not a good taxonomic character). However, we were quite excited to find that the ITS sequences of western North American material were indistinguishable from European P. jeckeri sequences! 

Punctelia jeckeri. (Lendemer 14695, NY). A & B, pruinose lobe tips with arrows highlighting position of the pruina, ×5; C, geographic distribution based on selected herbarium material at NY, shaded regions correspond to western populations mapped by Brodo et al. (2001); note that several populations in Canada are not mapped due to space constraints; D, thallus margin, ×0.5; E, soralia, ×1.

Even though the ITS sequences match up perfectly with European material, we refer to the western North American material as Punctelia jeckeri s. lat., since the conidia do not exactly match P. jeckeri as formally defined. However, we put forth the hypothesis that there may actually be two species in Europe with pruinose lobe tips, but different conidia. This hypothesis will need to be tested with rigorous sampling from throughout Europe.

The third species that we found in North America represented the 'real' Punctelia perreticulata as originally defined. P. perreticulata is the only species with a distinctly scrobiculate upper surface, and its distribution is centered in the Ozark Ecoregion.

Punctelia perreticulata. (Lendemer 7230, NY). A, soralia, ×1; B, thallus margin, ×0.5; C, pruinose lobe margin, ×4; D, geographic distribution based on herbarium material at CANL and NY.

Our paper also provides a key to the genus Punctelia in North America. Anyone who has tried to identify a species in this group should have a look. For those interested in the molecular data or the nitty-gritty of phylogenetic methods, links to the ITS sequences with full GenBank records can be found here and we have also posted the analyzed alignment file (NEXUS).

While there are surely further questions to be answered regarding the genus Punctelia, it is satisfying to have some degree of resolution in this often-misunderstood group of species!

-Brendan

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Works Cited:

Lendemer, J. C., and B. P. Hodkinson. 2010. A new perspective on Punctelia subrudecta in North America: previously-rejected morphological characters corroborate molecular phylogenetic evidence and provide insight into an old problem. Lichenologist 42(4): 405-421.
View publication (website)
Download publication (PDF file)
Download alignment (NEXUS file)

Blomquist Foray

About two years ago now, I had the opportunity to help plan and lead the Hugo L. Blomquist Bryological and Lichenological Foray.  At the time, I was putting the finishing touches on the first edition of the Virginia Lichen Checklist (Hodkinson et al. 2009; http://www.duke.edu/~bph8/VirginiaLichens/checklist.html), so I decided to take the opportunity to bring a group of lichenologists to Virginia for a final collecting blitz!  While there were plenty of areas throughout the state that still required further collecting, southwestern Virginia seemed sufficiently unexplored (especially in terms of crustose lichens) and provided nice opportunities for lodging and easy fieldwork.

We were certainly rewarded with some great discoveries!  Collectively, we identified 41 state records, and had some especially significant findings, including:
Sphaerellothecium coniodes - a lichenicolous fungus that was not previously known to exist in North America;
Hypotrachyna lividescens - a primarily neotropical macrolichen that has not previously been reported from North America;
Pycnora praestabilis - a lignicolous crust not previously reported from any other location in eastern North America;
Heterodermia erecta - a foliose lichen previously known in the world only from a single small region of Georgia/North Carolina, and
Psilolechia clavulifera - a crustose lichen taxon previously reported from only one other location in eastern North America.

In addition, there were specimens that spurred on further studies.  For example, one species listed here, 'Punctelia caseana Lendemer & Hodkinson' (previously known either as Punctelia subrudecta or Punctelia perreticulata), was investigated using molecular tools and formally defined after these collections were made (for more on this new species, see Lendemer & Hodkinson 2010).  Also, specimens that were tentatively called 'Cladonia caespiticia ?' led us to re-evaluate the characters used to circumscribe this species (Lendemer & Hodkinson 2009).

It was only after the foray that I found out that the area is one of only a few parts of the country that is considered a true 'biodiversity hotspot' when diversity calculations are rarity-weighted.  The sheer diversity of lichens, along with the number of rare and/or potentially endangered taxa, highlights the need for continued preservation efforts in MRNRA and the southern Appalachian Mountains in general.

The discoveries made on the Foray are all outlined in an article that recently came out in the journal Castanea (Hodkinson 2010).  The publisher's website for the article can be found here, and a PDF of the article is available on my website.  Some photos of the foray are online in this album.

I encourage anyone who has a serious interest in lichens to please join us on the next Blomquist or Tuckerman Foray!

-Brendan

The Foray's official logo, designed by Donald M. Ziegler.

Acknowledgments: Many thanks are due to all of those who participated in the 2008 Blomquist Foray, especially those who submitted lists of identified specimens (J.G. Guccion, G. Perlmutter, W.R. Buck, R.C. Harris). I thank Richard C. Harris and James C. Lendemer for graciously verifying or identifying the majority of the collections, and Othmar Breuss for examining specimens representing Verrucariaceae. Kerry Knudsen is thanked both for reviewing this manuscript and for examining the collections of Acarospora sp. The author is grateful to Sarah Hodkinson for her assistance with Foray business, and with the collecting and cataloging of specimens. The author also thanks Fred Huber for showing us some of the best collection spots in MRNRA and giving us permission to collect lichens and mosses, Mike Donohue for assisting with field work, Jon Shaw for assisting with general Foray organization, and Blanka Shaw for coordinating communication and housing arrangements.

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Works Cited:

Hodkinson, B. P. 2010. A First Assessment of Lichen Diversity for One of North America's 'Biodiversity Hotspots' in the Southern Appalachians of Virginia. Castanea 75(1): 126-133.
Download publication (PDF file)

Hodkinson, B. P., R. C. Harris, and M. A. Case. 2009. A Checklist of Virginia Lichens. Evansia 26(2): 64-88.
Download publication (PDF file)
View authors' updated checklist (website)

Lendemer, J. C., and B. P. Hodkinson. 2010. A new perspective on Punctelia subrudecta in North America: previously-rejected morphological characters corroborate molecular phylogenetic evidence and provide insight into an old problem. Lichenologist 42(4): 405-421.
Download publication (PDF file)
Download alignment (NEXUS file)

Lendemer, J. C., and B. P. Hodkinson. 2009. The Wisdom of Fools: new molecular and morphological insights into the North American apodetiate species of Cladonia. Opuscula Philolichenum 7: 79-100.
Download publication (PDF file)
Download alignment (NEXUS file)

Lichen Walk

Last weekend, the Ellerbe Creek Watershed Association (ECWA) gave me an opportunity to lead a local 'Lichen Walk'. Members of the community came out to take a hike through the ECWA-managed Glennstone Nature Preserve and learn about lichens in the process. The Preserve had a great variety of lichens for everyone to see, and I had a great time raising lichen awareness!

Thanks to ECWA for arranging the event! For those of you in the area, I hope to see you at the next one; for the lichenologists who live elsewhere, this is a really nice, simple way to reach out locally and get people thinking about lichens!

- Brendan

[Additional thanks are due to Sarah Hodkinson for assistance with the walk, and to the National Science Foundation for funding my research and associated outreach through a Doctoral Dissertation Improvement Grant: DEB-1011504.] 

Lichens of Denali, Alaska

Alaska Lichen Photo Series, Part II: Lichens of Denali

Vulpicida tilesii

Sphaerophorus fragilis

Ochrolechia upsaliensis

Physconia muscigena

Xanthoria elegans


 
[All photos by Brendan Hodkinson]
[Funded by NSF Award DEB-0640956.] 

Gymnosporangium

I was driving along today and saw a particularly striking example of Gymnosporangium juniperi-virginianae (cedar-apple rust) in action!  I saw at least three trees in the area with this amazing bright orange fungus, but one of them was completely covered!  Here are a few photos that I took:

A side view of one of the fungal fruiting bodies progressing through the stages of maturity.

A particularly juicy fruiting body as seen from below.

A small portion of the tree covered in the fungus.


[Photos by Brendan Hodkinson.]

Lichen Photomorphs in Costa Rica

Last year I traveled to Costa Rica in search of lichens. One of the most exciting lichenological phenomena that I observed was the presence of 'photomorphs' in the lichen-forming fungal genus Sticta. Photomorphs (a.k.a., photosymbiodemes) are created when the same fungus associates with two entirely different photobionts (most noticeable when one photobiont is a green alga and the other is a cyanobacterium). I observed this in several species of Sticta while in Costa Rica. This photo shows one example, where the bright green lobes are associated with a green alga and the darker brown lobes are associated with a cyanobacterium:

Some other nice photos from my trip include a moth disguising itself as a lichen...

...and a rainbow over some lichen-covered fence posts by the side of the highway near Cerro de la Muerte.

Costa Rica is beautiful; I look forward to returning some day!

- Brendan


[Travel and research expenses for the field component of this trip were covered by a handful of small grants: Christiane and Christopher Tyson OTS Research Fellowship, Lewis and Clark Fund for Exploration and Field Research Grant, Sally Hughes-Schrader Travel Grant, & Explorers Club Diversa Award.]

Lichens in the Community

Haven't you always wanted to go to a festival and find an exhibit all about lichens?!  This weekend I was lucky enough to have an opportunity to participate in the 10th Annual WOODSmont Children's Festival sponsored by Duke University's Wilderness Outdoor Opportunities for Durham Students ('WOODS').  I set up a table with a full exhibit including 'touch and feel' lichens, a microscope (so that children could see the lichens up close), a collage of amazing photos of lichens from around the world (thanks to Robert Lücking for compiling these), and 'pet lichens' for children to take home. Here is a photo of the exhibit itself:

This picture shows an action shot of some local children becoming aware of the lichens in their neighborhood:

It was a great day, and I look forward to more opportunities for this type of outreach!

-Brendan

[Many thanks to the National Science Foundation for funding my research and associated outreach through a recent Doctoral Dissertation Improvement Grant: DEB-1011504.]

Submitting to GenBank

Anyone who does much in the way of DNA sequencing/analysis eventually has to deal with depositing sequences in GenBank.  For a sequence or two, it is relatively simple to use the online 'BankIt' submission system.  However, for larger batches it becomes necessary to take advantage of the batch functions available with the 'Sequin' program.  To get to the point of being able to submit large batches each containing multiple 'features', there is quite a steep learning curve (especially if you are trying to teach yourself).  Unfortunately, the web-pages on the NCBI website do not seem quite sufficient to make submission a simple process.  While submitting sequences for a number of recent papers (e.g., Hodkinson & Lutzoni 2009, Hodkinson & Lendemer 2010, Lendemer & Hodkinson 2009, 2010), I wrote myself a tutorial on how to submit RNA-encoding sequences (rRNA, introns, transcribed spacers, etc.) to GenBank.  Most of this will apply to all sequence types, but getting the information for protein-coding sequences correct might still be an issue requiring some extra assistance.  In the 16-step outline below, the most difficult and problematic aspect (i.e., annotating multiple sequence features) is emphasized and greater detail is given in this area.

GenBank Submission Using SEQUIN:
1)  Make a FASTA+GAP file with bracketed modifiers for all basic info that varies between sequences (e.g., organism, isolate, specimen-voucher, etc.; for basic formatting see http://www.ncbi.nlm.nih.gov/Sequin/QuickGuide/sequin.htm#AlignmentFormats; for appropriate modifiers see http://www.ncbi.nlm.nih.gov/Sequin/QuickGuide/sequin.htm#DefinitionLine).
2) Run SEQUIN and type in the authorship, contact, and citation information that applies to all sequences.
3) Import file into SEQUIN as a 'Phylogenetic Study' set in 'FASTA+GAP' format.
4) Click 'Edit' 'Alignment Assistant...'.
5) Click 'Features' 'Apply To Alignment >' 'RNA'.
6) For the feature that you wish to annotate, be sure to check the box saying if the 5' or 3' end is partial, if either one is.
7) Type in the alignment coordinates of the particular feature that you are annotating.
8) In the 'RNA Type' box, pick the type of feature (e.g., 'misc_RNA' for ITS1 and ITS2, or 'rRNA' for 18S, 5.8S, or 28S).
9) In the field next to 'RNA Name', put in the specific type of RNA (18S ribosomal RNA, internal transcribed spacer 1, etc.).
10) Click 'Accept.'
11) Repeat steps 5-10 for each section of RNA in the sequence set.
12) In the 'Alignment Assistant' window, go to the 'File' menu and click 'Close'.
13) To check/edit your work: next to 'Target Sequence' choose 'ALL SEQUENCES' and next to 'Format' choose 'Graphic' (double-click on any particular feature annotation to see details and/or make changes; if a particular annotation is entirely erronious, highlight the annotation and go to 'Edit' then 'Clear').
14) Click 'Done' on the main viewing window.
15) When it asks 'Are you ready to save the record?' click 'Yes'.
16) Save the file to the hard drive and email it to 'gb-sub@ncbi.nlm.nih.gov'.

I have been told that this protocol is helpful in getting Sequin to 'work'.  I hope that posting it here will help even more people!

- Brendan


[If you found this post to be a useful guide, and employed the information found here as part of the GenBank submission process, please cite this work as follows:

Hodkinson, B. P. 2010. Submitting to GenBank. Squamules Unlimited, Durham, NC. http://squamules.blogspot.com/2010/04/submitting-to-genbank.html

Many thanks!]

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Works Cited:

Hodkinson, B. P., and F. Lutzoni. 2009. A microbiotic survey of lichen-associated bacteria reveals a new lineage from the Rhizobiales. Symbiosis 49: 163-180.
Download publication (PDF file)
Download alignment (NEXUS file)

Hodkinson, B. P., and J. C. Lendemer. In press. Molecular analyses reveal semi-cryptic species in Xanthoparmelia tasmanica. Bibliotheca Lichenologica.
Download draft (PDF file)
Download alignment (NEXUS file)

Lendemer, J. C., and B. P. Hodkinson. 2009. The Wisdom of Fools: new molecular and morphological insights into the North American apodetiate species of Cladonia. Opuscula Philolichenum 7: 79-100.
Download publication (PDF file)
Download alignment (NEXUS file)

Lendemer, J. C., and B. P. Hodkinson. 2010. A new perspective on Punctelia subrudecta in North America: previously-rejected morphological characters corroborate molecular phylogenetic evidence and provide insight into an old problem. The Lichenologist 42(4): 405-421.
Download publication (PDF file)
Download alignment (NEXUS file)

Eagle Summit, Alaska

The summer before last I traveled to Alaska in search of lichens.  It was an amazing trip!  There were lichens aplenty (in terms of biomass); however, there was noticeably less diversity than one might find in temperate regions or, of course, tropical regions.  This did not diminish my excitement when I saw the lichens of the tundra piled high on top of one another all along the ground.  Here are just a few photos of the amazing lichens of Eagle Summit, near Fairbanks, Alaska:

Masonhalea richardsonii

Solorina crocea



Ophioparma ventosa

Dactylina arctica



Alectoria ochroleuca

Flavocetraria cucullata



Thamnolia vermicularis



Cladonia pleurota



Sphaerophorus globosus


Stay tuned for more photos from some of the other sites that I visited in Alaska!

-Brendan

[Funding for this excursion was provided by NSF Award DEB-0640956.]

Cladonia stipitata Lendemer & Hodkinson, a new species (with squamules!)

I recently worked with James Lendemer of the New York Botanical Garden on a paper that sorts out the taxonomy of the Cladonia lichens in eastern North America that carry out a full sexual life cycle without ever producing podetia (Lendemer & Hodkinson 2009).  Since podetial morphology is typically the most informative character (or set of characters) used for identifying Cladonia specimens, this group has previously been either neglected or treated in a very incomplete manner.  We used a combination of molecular and morphological analyses to better define the morphological/ecological/biogeographical boundaries of several named species, and were able to describe an entirely new species that is well-supported by morphology, ecology, chemistry, and gene sequence data.  The new species is known as Cladonia stipitata Lendemer & Hodkinson.  It has an interesting morphology that includes a narrow, blackened stipe upon which the squamules sit.  The underside of some extremely well-developed specimens on barren rock can have a substantial mass of these distinct thin black stipes, something quite unique in the genus Cladonia.

Plate 5 (Lendemer & Hodkinson 2009). Cladonia stipitata. Figure 1, thallus (Harris 30810, scale = 5 mm). Figure 2, detail of the primary squamules (Harris 38010, scale = 1mm). Figure 3, typical habitat (Jackson Co., North Carolina, USA, photo by E.A. Tripp). Figure 4, detail of apothecium (Lendemer 7615, scale = 2 mm). 
     
In the paper, we also provide a key to the typically sterile Cladonia lichens in eastern North America (which includes many species that have their reproductive structures on podetia, but only rarely reproduce sexually and are therefore without podietia in most collections) and briefly discuss some of the potential forces at work in the evolution of fungal introns.  The title of the work is "The Wisdom of Fools: new molecular and morphological insights into the North American apodetiate species of Cladonia", and it is derived from a quote by Dr. Richard C. Harris ("Dick", from the New York Botanical Garden) stating that "the common wisdom [is] that only fools collect sterile Cladonia" (Harris 1992; note: species that complete the sexual lifecycle without producing podetia are typically grouped in with the 'sterile' species due to their odd mode of reproduction).  Feel free to read our paper here, or check it out in volume 7 of Opuscula Philolichenum (Festschrift für Richard C. Harris). 

-Brendan Hodkinson, Duke University

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Works Cited:

Harris, R. C. 1992. Cladonia petrophila, a new species from eastern North America. Brittonia 44(3): 326-330.

Lendemer, J. C., and B. P. Hodkinson. 2009. The Wisdom of Fools: new molecular and morphological insights into the North American apodetiate species of Cladonia. Opuscula Philolichenum 7: 79-100.
Download publication (PDF file)

What is a species?

Those who belong to the official lichen listserve, 'LICHENS-L', may remember a few months ago when someone threw out the fact that some biologists have adopted the notion that "There is nothing unique or special about the 'species' as a taxonomic rank".  This idea is not in any way unique to lichenology, but within that forum I gave the following response:

"
There is no question that genetic recombination creates forces that maintain uniformity and keep members of 'species' morphologically and molecularly similar to one another; this is not the case for higher taxonomic ranks, where similarity within a group can generally be attributed only to common ancestry or ecology.  When these forces break down permanently because of some reproductive barrier, we generally call that a 'speciation' event.  This is obviously based on a Biological Species Concept (BSC) which says that a 'species' is essentially a group of interbreeding individuals reproductively isolated from other such groups.  From my perspective, that is the only 'real,' justifiable species concept.  However, other species concepts (e.g., phylogenetic, morphological) are perfectly valid in that they provide excellent insight into what the groups of interbreeding individuals are likely to be (this is usually very hard to demonstrate experimentally, so the BSC is often not practical from a scientific standpoint).

Of course, this leaves out asexual organisms, and those must be pigeon-holed because the species are not 'real' (i.e., they do not represent anything uniquely different from any other taxonomic rank).  In these cases, species merely become names for phylogenetic entities possessing shared innovations that have altered the course of their evolutionary history (still valid, but no different from genera, families, etc.).

We must also not forget hybridization, polyploidy, etc., which can throw a wrench into the system.  These events can have major effects and cause instant 'speciation' (reproductive isolation) even though they are seemingly quite rare.  In some cases you can get new species with multiple progenitor species.  We have good examples of this in plants, but I really wouldn't be surprised to find all sorts of crazy things that we just do not know about yet happening in the fungi!

If your perspective is only phylogenetic, then it is true that 'species' often do not show up clearly and distinctly as special units per se.  However, if you can analyze a combination of molecular, morphological, ecological, and geographical features of organisms, then you can begin to infer 'biological species' by assuming that there are forces maintaining some degree of uniformity within each unit (but as I implied above, this is not always a sound assumption).
"

There is no doubt that the question of 'what makes a species' is a difficult one (the evidence for this is in the fact there there are so many well-accepted 'species concepts'), but it does not mean that we should throw out our species concepts and simply say that 'species' is just another taxonomic rank like any other.  If we do this, we are likely to miss the significance of certain phenomena that take place all around us in the natural world.

-Brendan Hodkinson, Duke University

Top Lichens

Dr. Robert Lücking (Field Museum, Chicago) recently asked lichenologists to send in a list of their top 5-20 favorite lichen species.  Along with Dr. Thorsten Lumbsch (also of the Field Museum) and others, he plans to assemble a list of 100 lichens, and eventually each will be featured on a website with its own page full of photos and information about the species.  Feel free to peruse my current top 20 lichens; each name has a link to a photograph of the species.


Arthonia caesia
Brigantiaea leucoxantha
Calicium trabinellum
Chaenotheca furfuracea
Cladonia bellidiflora
Conotrema urceolatum
Dibaeis baeomyces
Glyphis cicatricosa
Gyalideopsis buckii
Herpothallon rubrocinctum
Masonhalea richardsonii
Niebla cephalota
Ochrolechia oregonensis
Pilophorus clavatus
Placopsis lambii
Solorina crocea
Sphaerophorus globosus
Stereocaulon ramulosum
Umbilicaria cylindrica
Usnea longissima

I look forward to seeing how this project evolves!  It will be a great way to reach out to those outside of the field of lichenology and demonstrate the beauty and diversity of lichen-forming fungi!

- Brendan

Tasty Fungi

Over the past few days I've been trying out some new recipes with my wife and we came up with this one that seemed to be worth sharing!  It's loosely based on a recipe from a 2003 issue of Vegetarian Times, picked up from a library book sale (though we have so altered it that I'm not sure that it would be clear what it's based on anyway!).  The dish is called 'Mushroom Couscous Cakes' and it ended up being much better than either of us expected.  My wife made it clear from the start that she was skeptical, since she says that she does not like fungi, but once she tasted it she changed her mind!

This recipe seems to work best in a less formal setting, since the cakes are amazing when they first come off of the skillet, and it may be best for some people to start eating while others are waiting for their cakes to be prepared.  I highly recommend porcini mushrooms in the cakes, but the mushroom mix that goes on top could be made with any number of different types of fungi (e.g., chanterelles, morels, creminis/portobellos, etc.... I wonder if it could work with Umbilicaria....); we had shiitakes in our kitchen and they were great!


Mushroom Couscous Cakes

Serves 4

Cakes:
1/4 oz. dried porcini mushrooms
1/2 cup couscous
1/2 onion, chopped
1/2 tsp. salt
1 egg
1 Tbs. all-purpose flour
Extra virgin olive oil, as needed

Mushroom Mixture:
1 Tbs. extra virgin olive oil
1/2 lb. cleaned, dried shiitake mushrooms
Salt and freshly-ground pepper to taste
1/2 onion, finely chopped
1 clove garlic, finely chopped
1/3 cup dry white wine
1 Tbs. butter
1/4 tsp. Cavender's All-Purpose Greek Seasoning (a mix of salt, pepper, corn starch, garlic, MSG, and oregano)

To prepare dried mushrooms:
Put each type of mushroom in its own separate bowl, fill each bowl with warm water, squeeze mushrooms, pour off water, and repeat several times until mushrooms are reconstituted and the water remains somewhat clear when mushrooms are squeezed.

To make batter for cakes:
Chop porcini mushrooms very fine. Place couscous, 1/2 onion, salt, chopped porcini mushrooms, and 1 cup of water in a small saucepan.  Bring to a simmer, cover and reduce heat. Cook for 25 minutes or until couscous absorbs all liquid.  Transfer to mixing bowl and cool.  Stir in egg and flour.

To make mushroom mix:
Heat olive oil in large skillet over medium-high heat.  Add mushrooms, season with salt and cook, tossing from time to time, until mushrooms release moisture and begin to brown.  Add onions and garlic, cook 1 minute more and add wine.  Continue to cook until only a small bit of liquid remains.  Stir in butter and seasoning mix.  Transfer to bowl/saucepan and keep warm while making cakes. 

To make cakes:
Pour 1/8 inch layer of olive oil into a large skillet and heat over medium heat.  When oil is hot, drop in 2 tablespoon-sized mounds of couscous batter and flatten slightly (if they are too flat, they might start to come apart, but then you can make 'couscous cracklins' which are probably very good too!).  Cook until browned on bottoms, flip and brown top (we almost set off the fire alarm during this step!).  Repeat with remaining batter until used up.

To serve:
Toss each cake onto a small plate and top with a couple of tablespoons of the mushroom mixture.

My preferred way to eat them is to toss them onto a few napkins and squeeze the oil out of them before topping them with a handful of mushrooms.  This allows you to get the nice fried flavor with a little less fat, but it does somewhat deform the cakes!

I hope some of you reading this get a chance to try it!  Please let me know if you do!

- Brendan