Squamules

Darwin Day

2012-02-12T20:17:00.000-08:00

Today my family and I attended a celebration of Darwin's 203rd birthday hosted by the Metropolitan Society of Natural Historians! As part of the birthday party, there was a cake contest.

My wife's entry (which won first place!) was a series of cupcakes illustrating the evolution of mankind, beginning with an ancestral primate akin to a shy, nocturnal aye-aye, moving through our common ancestors with the monkeys and great apes, and culminating in Darwin himself:

The Descent of Man

My entry was a bit more cryptic, but got to the heart of one of the most important aspects of evolution: the fact that individuals within a species vary. Without this, evolution would not be possible. I think that many of the misunderstandings about what evolution is, and how it works, among the general public seem to stem from the under-appreciation of this fact. So I created a group of cupcakes that showed the variation within one species:

Variation Within Species

Happy Darwin Day!

- Brendan

Lepidostroma vilgalysii

2012-02-07T09:09:00.000-08:00

I recently had a paper published in Mycological Progress with Jessie Uehling and Matt Smith in which we described a new species of lichen. This is a special lichen because it is one of the few species in the Basidiomycetes that forms an intimate association with an alga (note that >98% of lichen-forming fungi belong to the Ascomycetes). The species was first collected by Rytas Vilgalys of Duke University, so naturally we named it Lepidostroma vilgalysii. There is a "DukeTODAY" post about the species, which was followed up by a podcast. Also, an announcement was posted in The Herald-Sun.

Here's a shot of the species in the field:

Notice the yellow clubs (these are the fungal reproductive structures) and the tiny light-green white-rimmed squamules on the soil (these are the lichenized part with the sterile fungus and the algae).

- Brendan

--------------------------

References

Hodkinson, B. P., J. K. Uehling, and M. E. Smith. 2012. Lepidostroma vilgalysii, a new basidiolichen from the New World. Mycological Progress doi:10.1007/s11557-011-0800-z.
View publication (website)

Hodkinson, B. P., J. K. Uehling, and M. E. Smith. 2012. Data from: Lepidostroma vilgalysii, a new basidiolichen from the New World. Dryad Digital Repository doi:10.5061/dryad.j1g5dh23.
View data and analysis file webportal (website)

-------------------------

P.S. I found this interesting blog post that gives the Lepidostroma vilgalysii article as an example for citation of data packages associated with articles. The public archiving of all data and analysis files associated with published results is extremely important (but often neglected), and is analogous to the archiving of physical resources such as specimens and cultures.

NYBG Lichenology - Year in Review

2012-02-01T00:52:00.000-08:00

Recently, Bill Buck of the New York Botanical Garden wrote up a summary of the past year in cryptogamic botany at NYBG. A portion of this was specifically on lichenology, which I have reproduced below:

"This was a monumental year at New York for lichenology. Several things all came together. First, our lichenologists, led by graduate student James Lendemer, have prepared a manuscript on the lichens of the Great Smoky Mountains National Park, based on their own recent collections and increasing the lichens known from the park by over 60%! This will be published in the Garden’s Memoir series. Next, we received a National Science Foundation grant to digitize our North American bryophytes and lichens. As part of this project we brought to New York Dr. Brendan Hodkinson, who just finished his Ph.D. at Duke University looking at the role that bacteria play in the lichen symbiosis. He is organizing the project and coordinating with other centers of the project. Next, we heard from Dr. Jonathan Dey, at Illinois Wesleyan University, that he would donate his private lichen herbarium to NYBG. Since his thesis was on the lichens of the higher elevations of the Appalachian Mountains, this was a wonderful addition to our holdings of lichens from the Great Smoky Mountains National Park. Although we are still processing this amazing gift, it appears to be about 30,000 specimens! Next, Brendan Hodkinson and James Lendemer applied to the National Science Foundation to inventory the lichens of the mid-Atlantic coastal plain (southern New Jersey to southern Georgia), as postdoctoral students of our lichenologist, Dr. Richard Harris. Much to our delight, this project was fully funded and will begin later this month. In addition to funding the two postdocs, the grant will also cover the expenses of a new graduate student. So, we will continue to have lichenology here at New York for some time to come. Brendan will move off of his administrative role in the one grant and onto the other."

So within the coming weeks, I will officially become the PI on this new grant, entitled "Lichen biodiversity of the threatened North American Middle Atlantic Coastal Plain: Improving classification, conservation, and communication." I can't wait to get started!

- Brendan

Lichenology Conference in Thailand

2012-01-24T19:37:00.001-08:00

I recently attended the 7th International Association for Lichenology Symposium in Bangkok, Thailand. It was a great conference with many exciting presentations about the most cutting-edge lichen research! Besides networking, presenting, and listening to talks, I also took a few hours to do some sightseeing around the city. Here are some photos:

See more photos from the conference here!

- Brendan

Lichen Taxonomy

2012-01-05T17:45:00.000-08:00

This week a new issue of the journal Opuscula Philolichenum came out. It contains two pieces to which I contributed. The first is an announcement of the new International Committee for the Nomenclature of Lichens and Allied Fungi (ICNLAF), which was formed only very recently (Lendemer et al. 2012). The second is an annotated phylogenetically based summary of lichen taxonomy that I have put together based on the system in use at the New York Botanical Garden (NYBG) (Hodkinson 2012). This will be up on the internet in a format that can be continually updated as our understanding of the organisms evolves. Hopefully it can serve as a useful guide for lichen herbarium/data managers wishing to arrange taxa within a higher-level framework.

Here is the official announcement from the editor:
"The latest issue (volume 11, number 1) of Opuscula Philolichenum is now available online at http://sweetgum.nybg.org/philolichenum/ free of charge as is tradition. This is the first volume to be published in the new age of electronic publication as sanctioned in Melbourne last year. As was noted in the previous issue, the journal has ceased its print run (although one copy is still deposited in the library at NYBG). Volumes will also now consist of multiple numbers, published throughout the year.

"The current issue comprises five contributions covering a diverse array of topics. This includes a higher level taxonomic scheme for lichen-forming fungi that synthesizes current literature. The system may be particularly useful to those wishing to organize herbaria using a phylogenetic system as is common practice in vascular plants. Also included are contributions to our understanding of Hypogymnia in eastern Asia, Parmeliella in South America, and Acarospora in South America. Those who have been following the changes in generic concepts in Acarosporaceae, particularly pertaining to Silobia, will be interested in the discovery by Linda in Arcadia and Kerry Knudsen that Myriospora is actually an earlier available name for Silobia. The authors make the appropriate new combinations and place the taxa previously assigned to Myriospora in a new genus.

"In addition to the above contributions the issue contains the notice of the formation of an International Committee for the Nomenclature of Lichens and Allied Fungi. A group that that aims to work with IAL and various bodies (ICNF, NCF) in the event that matters of nomenclatural governance are formally delegated to special committees by the IBC/IAPT."

-------------------------------------

References

Hodkinson, B. P. 2012. An evolving phylogenetically based taxonomy of lichens and allied fungi. Opuscula Philolichenum 11: 4-10.
Download publication (PDF file)

Lendemer, J. C., M. N. Benatti, T. L. Esslinger, J. Hafellner, B. P. Hodkinson, K. Knudsen, and J. Kocourková. 2012. Notice of the formation of the International Committee for the Nomenclature of Lichens and Allied Fungi (ICNLAF). Opuscula Philolichenum 11: 1-3.
Download publication (PDF file)

Environmental Microbiology

2012-01-03T21:49:00.000-08:00

Just yesterday I had an article come out in print in Environmental Microbiology (Hodkinson et al. 2012a) that represents the central chapter of my doctoral dissertation (Hodkinson 2011). It has been published as part of a special issue on 'Omics' and their utility in environmental microbiology and microbial ecology. The study uses 16S rRNA gene sequence data (generated both through molecular cloning and pyrosequencing) to illuminate the bacterial diversity found in lichens. There are a number of interesting discoveries presented, e.g.:
- lichens harbor complex, diverse bacterial communities
- mycobiont, photobiont, and geography are all significant factors in determining bacterial community composition in lichens
- the most taxonomically diverse group is the order Rhizobiales (which contains many symbiotic nitrogen fixers... and many of the groups found within lichens have members that are symbiotic nitrogen fixers)
- the LAR1 (Lichen-Associated Rhizobiales #1; Hodkinson & Lutzoni 2009) lineage is one of the most abundant lineages and seems to be nearly exclusive to lichens
- Acidobacteria is also extremely common, which could potentially be a result of the abundant acidic secondary compounds produced by lichens.

In addition to the above findings (along with the exciting future directions that they point to!), the paper presents many scripts and protocols for managing and analyzing large 16S rRNA gene sequence data sets (Hodkinson et al. 2011). Many of the scripts and protocols that I have posted elsewhere on this blog were derived from the studies that led to this publication. For much of my future research I plan to tweak these scripts and re-purpose them for all sorts of exciting and interesting new applications!

I'll be giving a talk next Monday on this work at the International Association for Lichenology conference (IAL-7) in Bangkok, Thailand (Hodkinson et al. 2012b). I hope to see some of you there!

- Brendan

--------------------------------------------

References

Hodkinson, B. P. 2011. A phylogenetic, ecological, and functional characterization of non-photoautotrophic bacteria in the lichen microbiome. Doctoral Dissertation, Duke University, Durham, NC.
Downl oad Dissertation (PDF file)

Hodkinson, B. P., and F. Lutzoni. 2009. A microbiotic survey of lichen-associated bacteria reveals a new lineage from the Rhizobiales. Symbiosis 49(3): 163-180.
Download publication (PDF file)
Download nucleotide alignment (NEXUS file)
View Dryad data package (website)

Hodkinson, B. P., N. R. Gottel, C. W. Schadt, and F. Lutzoni. 2011. Data from: Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome. Dryad Digital Repository. doi:10.5061/dryad.t99b1

Hodkinson, B. P., N. R. Gottel, C. W. Schadt, and F. Lutzoni. 2012a. Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome. Environmental Microbiology 14(1): 147-161. [doi:10.1111/j.1462-2920.2011.02560.x]
Download publication (PDF file)
Download supplementary phylogeny (PDF file)
View data and analysis file webportal (website)
Download data and analysis file archive (ZIP file)

Hodkinson, B. P., N. R. Gottel, C. W. Schadt, and F. Lutzoni. 2012b. Pyrosequencing reveals previously unknown phylogenetic, metabolic and ecological complexity within the lichen microbiome. In: IAL-7, International Association for Lichenology, Bangkok, Thailand, in press.

Using R for community analyses

2011-12-16T14:09:00.000-08:00

For the central chapter of my doctoral dissertation (published in Environmental Microbiology), I wanted to visualize similarities and differences between lichen-associated bacterial communities, find which factors were most strongly correlated with community differences, and determine the significance of these correlations. When communities are characterized using large sets of DNA sequence data, this can be achieved by using both genetic measures (e.g., UniFrac distance) and taxon-based measures (e.g., Bray-Curtis OTU-based dissimilarity).

This post gives an example of a script (or a series of commands) to be run with the R statistical package (R Development Core Team 2010) for performing ANOSIM and NMDS analyses of (1) an OTU-based relative abundance matrix derived from a set of clone libraries and (2) a UniFrac distance matrix derived from a 454 amplicon library (see example files at the bottom of this post). These examples are derived from Hodkinson et al. (2012), although the scripts and example files shown here are abbreviated in order to save space. Full example files can be downloaded from the Dryad data package associated with this publication [Hodkinson et al. 2011; http://dx.doi.org/10.5061/dryad.t99b1]. The matrices were obtained using the Fast UniFrac program (see instructions here) and Mothur (using the get.relabund command; for the full pipeline that I authored to process these data, see the Dryad data package). Some minor modifications were required to get the matrices into the precise format needed for R (edits were performed in Microsoft Excel and files were saved in .csv format... note that all of the spaces/tabs in the examples below would actually be commas in the raw text versions of the files).

Running the script as it is presented below (with hash marks in front of the 'plot' commands) will allow one to obtain an output file with the numerical results of all analyses. However, in order to visualize the NMDS plots, one can run each of the commands line-by-line in the R-GUI (of course, all 'anosim' commands can be ignored if the only goal is NMDS), removing the hash marks in front of the plot commands (note that R has many fancy options for visualization using 'plot'; these may be worth investigating further for your own purposes). Here is a link to the version of R that I used for these analyses: http://cran.r-project.org/bin/windows/base/old/2.12.0/. Once R is installed, you can call the script with a command like this one:
C:\\"Program Files"\R\R-2.12.0\bin\i386\Rterm.exe --verbose --no-restore --file=C:\\ANOSIM_NMDS_Clon_454_win.R > C:\\ANOSIM_NMDS_Clon_454_win.out

Here is the script, named 'ANOSIM_NMDS_Clon_454_win.R' (abbreviated example script; full file available at http://dx.doi.org/10.5061/dryad.t99b1):

# load the necessary libraries
library(ecodist)
library(vegan)
# set the output file
sink("ANOSIM_nmds.out", append=TRUE, split=TRUE)
# load the clone data set
samplesClon<-read.csv("C:\\SamplesClon.csv", header=TRUE)
samplesClon
# load the Bray-Curtis OTU-based matrix
OTUsClon<-read.csv("C:\\HodkinsonClon16S_OTUs_1per_171.csv", head = FALSE, row.names = 1)
# transform the OTU matrix into a Bray-Curtis matrix
OTUsClon.dist<-vegdist(OTUsClon, "bray")
# run Bray-Curtis OTU-based ANOSIM
anosim(dis = OTUsClon.dist, grouping = samplesClon$Photobiont, strata = samplesClon$Site)
anosim(dis = OTUsClon.dist, grouping = samplesClon$Mycobiont, strata = samplesClon$Site)
anosim(dis = OTUsClon.dist, grouping = samplesClon$Mycobiont, strata = samplesClon$Photobiont)
anosim(dis = OTUsClon.dist, grouping = samplesClon$Site, strata = samplesClon$Photobiont)
anosim(dis = OTUsClon.dist, grouping = samplesClon$Site, strata = samplesClon$Mycobiont)
# run Bray-Curtis OTU-based NMDS
nmds <- nmds(as.dist(OTUsClon.dist))
nmin <- nmds.min(nmds)
nmin
#plot(nmin, pch=as.numeric(samplesClon$Photobiont))
#plot(nmin, pch=as.numeric(samplesClon$Mycobiont))
#plot(nmin, pch=as.numeric(samplesClon$Site))
# load the 454 data set
samples454<-read.csv("C:\\Samples454.csv", header=TRUE)
samples454
# load the normalized weighted UniFrac matrix
unifracnw454<-read.csv("C:\\DistUFnw454.csv", head = FALSE, row.names = 1)
# run normalized weighted UniFrac ANOSIM
anosim(dat = as.dist(unifracnw454), grouping = samples454$Photobiont, strata = samples454$Site)
anosim(dat = as.dist(unifracnw454), grouping = samples454$Site, strata = samples454$Mycobiont)
anosim(dat = as.dist(unifracnw454), grouping = samples454$Site, strata = samples454$Photobiont)
anosim(dat = as.dist(unifracnw454), grouping = samples454$Mycobiont, strata = samples454$Photobiont)
anosim(dat = as.dist(unifracnw454), grouping = samples454$Mycobiont, strata = samples454$Site)
# run normalized weighted UniFrac NMDS
nmds <- nmds(as.dist(unifracnw454))
nmin <- nmds.min(nmds)
nmin
#plot(nmin, pch=as.numeric(samples454$Photobiont))
#plot(nmin, pch=as.numeric(samples454$Mycobiont))
#plot(nmin, pch=as.numeric(samples454$Site))
# close the output file
sink()
# unload the libraries
detach("package:ecodist")
detach("package:vegan")

Samples454.csv (referenced in the above script)

SampleID	Photobiont	Site	Mycobiont
CLCl	Ch	C	Cl
CLDi	Cy	C	Di
CLLe	Cy	C	Le
CLPe	Cy	C	Pe
CLSt	Cy	C	St
CLUs	Ch	C	Us
ELCl	Ch	E	Cl
ELFl	Ch	E	Fl
ELOp	Ch	E	Op
ELPe	Cy	E	Pe
ELUm	Ch	E	Um
HLCl	Ch	H	Cl
HLLe	Cy	H	Le
HLPe	Cy	H	Pe
HLSt	Cy	H	St
HLUs	Ch	H	Us
NLCl	Ch	N	Cl
NLFl	Ch	N	Fl
NLOp	Ch	N	Op
NLPe	Cy	N	Pe
NLUm	Ch	N	Um

DistUFnw454.csv (referenced in the above script; full file available at http://dx.doi.org/10.5061/dryad.t99b1)

CLCl		0.16	0.17	0.11	0.08	0.12	...
CLDi	0.16		0.24	0.18	0.13	0.18	...
CLLe	0.17	0.24		0.11	0.16	0.20	...
CLPe	0.11	0.18	0.11		0.10	0.18	...
CLSt	0.08	0.13	0.16	0.10		0.13	...
CLUs	0.12	0.18	0.20	0.18	0.13		...
ELCl	0.20	0.22	0.30	0.25	0.19	0.17
ELFl	0.14	0.18	0.24	0.19	0.14	0.15	...
ELOp	0.33	0.35	0.40	0.37	0.34	0.31	...
ELPe	0.16	0.21	0.24	0.19	0.15	0.19	...
ELUm	0.22	0.24	0.32	0.27	0.22	0.22	...
HLCl	0.19	0.18	0.27	0.24	0.17	0.15	...
HLLe	0.13	0.16	0.20	0.15	0.11	0.12	...
HLPe	0.09	0.17	0.15	0.11	0.11	0.16	...
HLSt	0.14	0.16	0.21	0.18	0.12	0.13	...
HLUs	0.10	0.20	0.18	0.15	0.14	0.11	...
NLCl	0.19	0.21	0.28	0.25	0.19	0.15	...
NLFl	0.18	0.21	0.27	0.24	0.19	0.15	...
NLOp	0.24	0.27	0.32	0.29	0.25	0.25	...
NLPe	0.10	0.18	0.13	0.09	0.10	0.14	...
NLUm	0.09	0.18	0.21	0.15	0.13	0.16	...

SamplesClon.csv (referenced in the above script)

SampleID	Photobiont	Site	Mycobiont
CL01	Cy	C	Peltigera
CL02	Ch	C	Alectoria
CL03	Ch	C	Cladonia
CL04	Tr	C	Placopsis
CL05	Cy	C	Erioderma
CL06	Cy	C	Sticta
CL07	Cy	C	Dictyonema
CL08	Cy	C	Leptogium
CL09	Tr	C	Stereocaulon
CL10	Ch	C	Usnea
EL01	Cy	E	Peltigera
EL01t	Tr	E	Peltigera
EL02	Ch	E	Alectoria
EL03	Ch	E	Cladonia
EL04	Ch	E	Rhizocarpon
EL05	Ch	E	Ophioparma
EL06	Ch	E	Flavocetraria
EL07	Ch	E	Arctoparmelia
EL08	Ch	E	Umbilicaria
EL09	Ch	E	Masonhalea
EL10	Ch	E	Dactylina
HL01	Cy	H	Peltigera
HL02	Ch	H	Platismatia
HL03	Ch	H	Cladonia
HL04	Ch	H	Parmotrema
HL05	Ch	H	Flavoparmelia
HL06	Cy	H	Sticta
HL07	Ch	H	Xanthoparmelia
HL08	Cy	H	Leptogium
HL09	Tr	H	Stereocaulon
HL10	Ch	H	Usnea
NL01	Cy	N	Peltigera
NL01t	Tr	N	Peltigera
NL03	Ch	N	Cladonia
NL04	Tr	N	Amygdalaria
NL05	Ch	N	Ophioparma
NL06	Ch	N	Flavocetraria
NL07	Ch	N	Parmelia
NL08	Ch	N	Umbilicaria
NL09	Tr	N	Stereocaulon
NL10	Ch	N	Cetraria

HodkinsonClon16S_OTUS_1per_171.csv (referenced in the above script; full file available at http://dx.doi.org/10.5061/dryad.t99b1)

CL01	0.00	0.00	0.00	0.00	0.00	0.00	...
CL02	0.00	0.00	0.00	0.00	0.00	0.00	...
CL03	0.00	0.25	0.00	0.00	0.00	0.00	...
CL04	0.11	0.00	0.00	0.00	0.00	0.00	...
CL05	0.00	0.03	0.34	0.05	0.00	0.00	...
CL06	0.00	0.10	0.02	0.03	0.00	0.02	...
CL07	0.00	0.56	0.00	0.00	0.00	0.19	...
CL08	0.00	0.03	0.00	0.00	0.00	0.00	...
CL09	0.02	0.13	0.06	0.15	0.00	0.00	...
CL10	0.00	0.00	0.00	0.00	0.00	0.00	...
EL01	0.00	0.00	0.00	0.00	0.00	0.17	...
EL01t	0.00	0.00	0.00	0.00	0.00	0.31	...
EL02	0.00	0.26	0.00	0.00	0.00	0.00	...
EL03	0.00	0.03	0.00	0.00	0.00	0.00	...
EL04	0.00	0.10	0.00	0.00	0.00	0.00	...
EL05	0.00	0.04	0.00	0.00	0.00	0.00	...
EL06	0.00	0.07	0.00	0.00	0.00	0.00	...
EL07	0.00	0.00	0.00	0.00	0.00	0.00	...
EL08	0.00	0.34	0.00	0.00	0.00	0.00	...
EL09	0.00	0.21	0.00	0.00	0.00	0.00	...
EL10	0.00	0.21	0.00	0.00	0.04	0.00	...
HL01	0.00	0.00	0.00	0.00	0.00	0.00	...
HL02	0.13	0.00	0.00	0.00	0.00	0.00	...
HL03	0.00	0.00	0.00	0.00	0.00	0.00	...
HL04	0.06	0.00	0.00	0.00	0.00	0.00	...
HL05	0.00	0.03	0.00	0.00	0.00	0.00	...
HL06	0.00	0.00	0.00	0.06	0.00	0.00	...
HL07	0.00	0.14	0.00	0.00	0.00	0.00	...
HL08	0.00	0.00	0.00	0.00	0.00	0.00	...
HL09	0.00	0.00	0.00	0.00	0.00	0.00	...
HL10	0.00	0.02	0.00	0.00	0.00	0.00	...
NL01	0.00	0.15	0.00	0.00	0.00	0.00	...
NL01t	0.00	0.00	0.00	0.00	0.00	0.15	...
NL03	0.00	0.00	0.00	0.00	0.00	0.00	...
NL04	0.00	0.15	0.00	0.00	0.00	0.00	...
NL05	0.00	0.17	0.00	0.00	0.00	0.00	...
NL06	0.00	0.02	0.00	0.00	0.00	0.00	...
NL07	0.00	0.33	0.00	0.00	0.00	0.00	...
NL08	0.00	0.80	0.00	0.00	0.00	0.00	...
NL09	0.00	0.00	0.00	0.00	0.00	0.00	...
NL10	0.00	0.05	0.00	0.00	0.00	0.00	...

Here are some examples of non-metric multidimensional scaling plots produced from OTU-based Bray-Curtis dissimilarities between lichen-associated bacterial communities (Hodkinson et al. 2012). Photobiont is indicated by color (light green = green algae; dark blue = Cyanobacteria; black = Tripartite), while the site is indicated with symbols (• = Eagle Summit, AK; + = Nome, AK; x = Highlands, NC, and * = Cerro de la Muerte, CR). Numbers indicate the identity of different mycobiont types (see associated publication for details). Continuous lines act as visual aids to delimit communities associated with the two major photobiont-types, whereas dashed lines delimit communities associated with chlorolichens from northern versus southern sites.

Plot A shows results obtained from clone library data of 16S sequences from the order Rhizobiales.

Plot B was produced from 454 barcoded 16S amplicon data (representing approximately half the number of samples as the clone library set but ~100 times as many sequences from a much wider range of bacterial diversity; since this plot was produced through OTU-based methods it does not precisely correlate with what would be produced through the abbreviated script above, which uses UniFrac distances to generate NMDS plots based on 454 data).

For additional information and documentation, including results of ANOSIM analyses, please see the references below!

- Brendan

---------------------------------------

References

Hodkinson, B. P. 2011. A phylogenetic, ecological, and functional characterization of non-photoautotrophic bacteria in the lichen microbiome. Doctoral Dissertation, Duke University, Durham, NC.
Download Dissertation (PDF file)

Hodkinson, B. P., N. R. Gottel, C. W. Schadt, and F. Lutzoni. 2012. Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome. Environmental Microbiology 14(1): 147-161. [doi:10.1111/j.1462-2920.2011.02560.x]
Download publication (PDF file)
Download supplementary phylogeny (PDF file)
View data and analysis file webportal (website)
Download data and analysis file archive (ZIP file)

Hodkinson, B. P., N. R. Gottel, C. W. Schadt, and F. Lutzoni. 2011. Data from: Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome. Dryad Digital Repository. doi:10.5061/dryad.t99b1

R Development Core Team. 2010. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. http://www.r-project.org/

Editor's Pick

2011-12-08T07:08:00.000-08:00

I recently received an email notifying me that the journal The Lichenologist had just released a compilation of papers entitled 'Editor's Pick of Papers: from Genome to Ecosystems.' This group consists of the editor's top 15 articles published in the journal over the past two years (volumes 42 and 43), during which well over 100 works have been published in The Lichenologist. I was excited to see that one of my papers was selected! To read my previous blog post outlining the content of the paper, please click here. Many thanks to Peter Crittenden for his work as editor-in-chief and to the British Lichen Society for publishing the journal!

- Brendan

Two new orders of fungi

2011-12-06T21:29:00.000-08:00

This week I had a manuscript published in which two entirely new orders of fungi were established! They are Sarrameanales and Trapeliales, and they both belong to the subclass Ostropomycetidae in the class Lecanoromycetes (the main class of lichen-forming fungi). To read more about the taxonomy of these two orders, see the publication in the December 2011 issue of Phytologia. This research can partly be seen as a taxonomic extension of the NSF-funded Assembling the Fungal Tree of Life project, since the distinctness of these orders was only recognized as a result of multi-gene phylogenetic analyses conducted as part of this effort.

We are making progress taxonomically, but even the higher-level work is not done yet; there are still many groups of 'incertae sedis' fungi out there and probably many more legitimate orders to be described... which means that there's plenty more exciting work to be done in the future!

- Brendan

------------------------------------

Reference

Hodkinson, B. P., and J. C. Lendemer. 2011. The orders of Ostropomycetidae (Lecanoromycetes, Ascomycota): Recognition of Sarrameanales and Trapeliales with a request to retain Pertusariales over Agyriales. Phytologia 93(3): 407-412.
Download publication (PDF file)

My New Supercomputing Center

2011-11-20T20:13:00.000-08:00

Recently I applied for and received an XSEDE (Extreme Science and Engineering Discovery Environment) Startup Allocation Award (DEB-110024), allowing me to use the San Diego Supercomputing Center (SDSC) Trestles cluster. The cluster itself contains over 10,000 processor cores; you can read more about it here. While there are many different types of research being conducted using this cluster, my work focuses on ecological and evolutionary analyses of molecular sequence data. Previously I conducted my computationally-intensive analyses using the Duke Shared Cluster Resource (DSCR). However, since leaving Duke University a few months ago, I have been without a cluster. I am happy to say that I now have access to a cluster once more! Let the supercomputing resume!

- Brendan

Outreach and training through Youtube videos

2011-11-10T19:02:00.000-08:00

Over the past few months I have acted as the New York Botanical Garden's Workflow Coordinator for the NSF-funded "Digitization TCN Collaborative Research: North American Lichens and Bryophytes: Sensitive Indicators of Environmental Quality and Change" (EF-1115086). This project is a collaboration between multiple institutions across North America and is aimed at cataloging label data from the vast majority of North American lichen and bryophyte specimens. Recently, as part of this project, we at NYBG released two videos on Youtube. The first acts as an introduction to the project for the general public and gives some of the rationale behind it:

The second is a training video that can be used by members of the partner institutions or others who are thinking about taking on similar projects:

As you will probably notice from the videos themselves, Charlie Zimmerman, the imager that I have supervised for this project here at the garden, was the one who did most of the writing, filming and editing... and we greatly appreciate all of his work!

Please enjoy the videos!

- Brendan

Building linkage-probability-based RNA secondary structure models for phylogenetic inference

2011-11-06T19:36:00.000-08:00

RNA secondary structure models are increasingly being integrated into likelihood-based phylogenetic inferences, but the dynamic structure of functional RNA molecules makes any single structural inference necessarily inaccurate. In this post I present an objective method for determining which elements of secondary structure are most stable based on the statistical significance of linkage probabilities between sites on a given RNA molecule. I briefly outline how this information can be integrated into a phylogenetic analysis by creating an input file that contains these statistically significant structural elements.

For some additional background on RNA secondary structure, see this previous post:
http://squamules.blogspot.com/2011/08/its-rna-secondary-structure.html

Functional RNA molecules include pairs of nucleotide sites that are linked to one another physically, resulting in specific secondary structures that define the shape of each molecule. This linkage causes certain sites to evolve in tandem with their counterparts. As such, the secondary structure of RNA molecules has been recognized for some time as a significant consideration in the inference of phylogenies from functional RNA-encoding genes (Kimura 1985, Tillier and Collins 1995). Typically, RNA secondary structure is used to optimize multiple-sequence-alignment accuracy for functional RNA-encoding genes (Gutell et al. 1992, Kjer 1995, Lendemer and Hodkinson 2009). However, in recent years, the use of secondary structure in modeling evolution for likelihood-based phylogenetic inferences has begun to gain popularity (Hodkinson and Lendemer in review, Savill et al. 2001, Telford et al. 2005). This approach requires defining the pairs of linked sites on the encoded RNA molecule and treating these pairs as states that are separate from the standard independent nucleotide states (A, C, T, G) in a phylogenetic inference. This method allows one to properly account for the interdependency of interacting nucleotides, since paired RNA nucleotides are no longer required to be treated as independent sites, leading to a more accurate approach for modeling sequence evolution.

Current protocols for integrating RNA secondary structure data into phylogenetic analyses require a single hypothetical structure to be used as an input. Structures are typically inferred using algorithms that minimize free energy or use other thermodynamic considerations to produce the best single structural inference (Mathews & Turner 2006). However, RNA secondary structure is dynamic, frequently changing in the cell as RNA catalyzes reactions and performs various cellular functions. When RNA molecules encounter certain enzymes and cellular components, the thermodynamic rules that previously favored one structure might strongly favor another. Additionally, different methods of structural inference are not always comparable, and small differences in algorithms can favor significantly different structures; the use of differing structural models in a phylogenetic context can have consequences in terms of both topology inference and the calculation of support (Ullrich et al. 2010).

These problems can largely be solved by removing statistically non-significant linkages from phylogenetic analyses, leaving only the most probable structural elements to be incorporated into downstream inferences. The determination of which RNA secondary structural elements are supported with statistical significance is often overlooked and is certainly not a standard part of the current work flow for scientists integrating secondary structural data into phylogenetic analyses.

Since RNA secondary structure can serve as such a useful tool for revealing the evolutionary history of certain groups, it is essential that objective criteria be established for incorporating structural elements into phylogenetic inferences. The simple method outlined here allows one (a) to evaluate the probability that each site on an RNA-encoding gene is linked to each other site and (b) to produce an 'elemental' secondary structure model for phylogenetic inference containing only the statistically-supported elements of the structure.

The UNAFold package provides a particularly useful set of tools for exploring various aspects of RNA secondary structure (Markham and Zuker 2008). UNAFold's 'hybrid-ss.exe' yields a set of '.plot' files that give the probability of each base binding to each other base for all reasonable pairings. After installing UNAFold and running 'hybrid-ss.exe' on a FASTA-formatted sequence, one can choose the '.plot' file with the number that most closely approximates the typical cellular temperature (in degrees Celsius) of the organism from which the sequence is derived. This '.plot' file can be modified in Excel by sorting according to 'P(i,j)' values (the probability of pairing) and isolating only the rows for which 'P(i,j)' is above 0.95. This stringent 95% pairing probability cut-off seems most easily justifiable; however, other cut-off values could potentially be used in the context of this method.

For integrating this type of data into a phylogenetic analysis (e.g., using RAxML 7.2.8; http://wwwkramer.in.tum.de/exelixis/software.html; Stamatakis 2006), the standard 'Vienna' dot-bracket notation is used (Hofacker et al. 1994). Any standard secondary structure inference program can be used to create an initial structure that may serve as a template; parentheses can be converted to periods using a standard text-editor or secondary structure editing program (e.g., 4SALE; http://4sale.bioapps.biozentrum.uni-wuerzburg.de/; Seibel et al. 2006) for sites whose linkage is statistically non-significant. These procedures will produce a secondary structure model that includes only the statistically supported elements of structure. When this 'elemental' secondary structure model is incorporated into phylogenetic analyses, it could serve to decrease the degree of uncertainty inserted into the standard secondary structure-based inferences.

Future advances may allow the integration of various intermediate linkage probabilities to be considered in the calculation of tree likelihoods. However, it seems that certain theoretical hurdles remain to be overcome before this type of analysis can be possible. Meanwhile, a methodology like the one outlined here could be beneficial if one wishes to reduce the amount of chance introduced into phylogenetic analyses while still accounting for the fact that certain sites are inextricably linked.

- Brendan

---------------------------------------------------

References

Gutell, R. R., A. Power, G. Z. Hertz, E. J. Putz, and G. D. Stormo. 1992. Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods. Nucleic Acids Research 20(21): 5785–5795.

Hodkinson, B. P., and J. C. Lendemer. In review. Systematics of a enigmatic sterile crustose lichen.

Hofacker, I. L., W. Fontana, P. F. Stadler, S. Bonhoeffer, M. Tacker, and P. Schuster. 1994. Fast folding and comparison of RNA secondary structures. Monatshefte für Chemie / Chemical Monthly 125: 167-188.

Kimura, M. 1985. The role of compensatory neutral mutations in molecular evolution. Journal of Genetics 64(1):7-19.

Kjer, K. M. 1995. Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from frogs. Molecular Phylogenetics and Evolution 4: 314-330.

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.

Markham, N., and M. Zuker. 2008. UNAFold: software for nucleic acid folding and hybridization. Methods in Molecular Biology 453: 3-31.

Mathews, D. H., and D. H. Turner. 2006. Prediction of RNA secondary structure by free energy minimization. Journal of Molecular Biology 16(3): 270-278.

Savill N. J., D. C. Hoyle, and P. G. Higgs. 2001. RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximum likelihood methods. Genetics 157: 399-411.

Seibel P. N., T. Müller, T. Dandekar, J. Schultz, and M. Wolf. 2006. 4SALE - A tool for synchronous RNA sequence and secondary structure alignment and editing. BMC Bioinformatics 7: 498.

Stamatakis, A. 2006. RAxML-VI-HPC: maximum likelihood- based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.

Telford, M., M. Wise, and V. Gowri-Shankar. 2005. Consideration of RNA secondary structure significantly improves likelihood-based estimates of phylogeny: examples from the Bilateria. Molecular Biology and Evolution 22: 1129-1136.

Tillier, E. R. M., and R. A. Collins. 1995. Neighbor-joining and maximum likelihood with RNA sequences: addressing interdependence of sites. Molecular Biology and Evolution 12: 7-15.

Ullrich, B., K. Reinhold, O. Niehuis, and B. Misof. 2010. Secondary structure and phylogenetic analysis of the internal transcribed spacers 1 and 2 of bush crickets (Orthoptera: Tettigoniidae: Barbitistini). Journal of Zoological Systematics and Evolutionary Research 48(3): 219-228.

---------------------------------------------------

This article can be cited as:
Hodkinson, B. P. 2011. Building linkage-probability-based RNA secondary structure models for phylogenetic inference. Squamules Unlimited, New York. [Available at: http://squamules.blogspot.com/2011/11/building-linkage-probability-based-rna.html]

Visiting Harvard

2011-10-31T22:42:00.001-07:00

Last week I visited Harvard University and gave a talk on my research into the consortia of bacteria associated with lichens. I was invited by Anne Pringle and was really excited to see some of the great research going on in her lab. One highlight of the visit was a tour of the Farlow Herbarium with Don Pfister. It was interesting to discuss how the herbarium would implement procedures for the NSF-funded TCN North American Lichens and Bryophytes project, for which I am the coodinator at the New York Botanical Garden (NSF Awards - NYBG: EF-1115086; Harvard: EF-1114957). Soon we will be putting online YouTube videos detailing procedures and workflows for this project, which will hopefully help other institutions such as the Farlow Herbarium to get the project up and running quickly once they are ready to begin. I hope that this visit will represent the first step in establishing lasting collaborations with some of the biologists at Harvard!

- Brendan

Lichen Conservation

2011-10-13T20:39:00.000-07:00

I saw this story in the news and thought that it was interesting:
http://www.bbc.co.uk/news/uk-wales-south-west-wales-15180179
It talks about cutting down trees at a location in Wales in order to engineer a park so that it will remain an optimal location for lichen growth. I am very interested in lichen conservation, but I typically take the stance that we should just "leave it alone" (i.e., let the preserved places evolve naturally) rather than actively attempting to create, maintain, or otherwise engineer a suitable habitat for lichens. But perhaps in parts of the world where there are only a few small, fragmented pieces of land on which lichens can thrive, a different approach must be taken (so that the preserved places remain more or less static instead of evolving naturally into old-growth habitats). It's not something that I would jump into without reservations, but perhaps this instance will be a good test case. I still instinctively remain wary of anything that could set off a chain of interventions that may lead us where we never intended to go! What are your thoughts?

- Brendan

Unravelling Lecidea

2011-09-27T12:26:00.000-07:00

Recently, I co-authored a paper (Schmull et al. 2011) in which we presented the results of analyses aimed at determining the phylogenetic placement of numerous lineages of lichen-forming fungi that were previously placed in the genus Lecidea based solely on morphology. For a long time, it has been known that the assemblage of species placed in Lecidea by Zahlbruckner did not form a single evolutionary lineage. However, placing all of the species in known families has been problematic. For our paper, we conducted two separate 6-gene analyses of lichen-forming fungi in the class Lecanoromycetes in order to infer the placement of twenty-five Lecidea taxa. Most species fell within three families: Lecanoraceae, Pilocarpaceae, and Lecideaceae (the familiy of the 'real' Lecidea). Those within the first two families will unquestionably need to be given new generic names in the near future. The main story that I hope will come out of this paper is that there is much more work to be done! We have used molecular data to demonstrate the scope of the problem with the genus Lecidea, but the definitive placement of all described species will require a great deal of additional study. I'm looking forward to continuing work on this group in the future!

- Brendan

-----------------------------------------------

Reference

Schmull, M., J. Miadlikowska, M. Pelzer, E. Stocker-Wörgötter, V. Hofstetter, E. Fraker, B. P. Hodkinson, V. Reeb, M. Kukwa, H. T. Lumbsch, F. Kauff, and F. Lutzoni. 2011. Phylogenetic affiliations of members of the heterogeneous lichen-forming genus Lecidea sensu Zahlbruckner (Lecanoromycetes, Ascomycota). Mycologia 103(5): 983-1003.
Download publication (PDF file)
Download nucleotide alignment (NEXUS file)
Download supplementary data table 1 (PDF file)
Download supplementary data table 2 (PDF file)

Musical Lichenology

2011-09-14T20:29:00.000-07:00

I recently received an email from Sean Beeching, famous to readers of this blog for his poetry (click here and here for samples). This is what he wrote:

"Here is a video that Nancy Lowe of discoverlife shot during our lichen workshop [http://www.youtube.com/watch?v=rvxnv-6Z6rg]. I am sawing up branches to show the students the lichens that were growing on them in time to Tommy [Jordan]'s banjo playing. He and I play together in the evenings during the workshop. You might also have a look at the lichen key I made for our students at discoverlife, go to the nature guides at the discoverlife.org website and then page down to 'Lichens, Georgia.' The site just passed a billion hits."

For anyone in the southeastern US interested in learning a thing or two about lichens, I would highly recommend any workshop with Sean!

- Brendan

Diversity of Lichenology

2011-09-07T20:35:00.000-07:00

Not too long ago I reviewed the 100th anniversary issue of the journal/book series Bibliotheca Lichenologica for The Bryologist. Here is what I wrote:

The 100th volume of Bibliotheca Lichenologica (‘‘Diversity of Lichenology — Anniversary Volume’’) provides important contributions to the field and gives us further insights into the biology of lichens while connecting us to our historical roots. While the volumes of this series have taken many different forms, this edition appears as a standard journal volume, with 18 scientific and historical articles from a total of 37 authors representing a diverse array of lichenologists. It should be noted that the emphasis is on lichens of Eurasia and/or the Southern Hemisphere; however, many of the articles will appeal to a general, worldwide audience.

In terms of taxonomy, this volume will be of particular interest to those following the changes in the family Teloschistaceae. Kondratyuk et al. describe 35 new species in the family. Many of these are known only from the type locality, or a small handful of specimens, making further evaluation of some of the taxa difficult, although the authors are to be commended for providing excellent color photographs of the thalli. The work by Fedorenko et al. focusing on the phylogeny of ‘xanthorioid’ lichens represents a significant contribution in terms of both the data generated and the provisional generic concepts articulated. However, both of the aforementioned works seem to highlight the fact that the largest task still remains: an integrated systematic revision of the family Teloschistaceae that includes crustose, foliose, and fruticose forms. In different ways, these works both improve our understanding of this family for which the taxonomy continues to evolve.

This volume also includes important insights into the taxonomy of the oft-neglected lichenicolous fungi. Hafellner presents an excellent ‘traditional’ treatment of the lichenicolous genera Phacothecium and Phacographa. The work is notably thorough, articulating precisely what is known about the genera, while highlighting areas where additional data and analyses are needed. The author also provides a useful key to opegraphoid lichenicolous fungi with widely exposed hymenia, along with a summary table of the phenotypic characters separating the five opegraphoid arthonialean genera with lichenicolous members discussed in the text (i.e., Opegrapha, Lecanographa, Phacothecium, Phacographa, and Plectocarpon).

Among the works that will appeal to a broader audience is Kärnefelt’s contribution entitled ‘‘Fifty influential lichenologists.’’ This portion of the volume provides a veritable ‘‘Who’s Who’’ of lichenology. The careers of some of the world’s major players in our field, both modern and historical, are briefly summarized, starting with ‘‘the father of lichenology,’’ Erik Acharius. Another work with broad appeal is by Lücking et al., entitled ‘‘How many tropical lichens are there… really?’’ This piece discusses the various factors involved in calculating a ‘ballpark’ estimate of the overall diversity of lichens in the neotropics, the tropics in general, and the globe as a whole (the estimate for the latter comes in at 28,000 species!). Although any estimate is subjective in nature, various points that have not been explicitly integrated into previous estimates are considered (e.g., taxonomic ‘orphans,’ species pairs, photosymbiodemes, chemotypes, and cryptic species). Another portion of the volume that will appeal to amateurs and professionals alike is the section by Randlane et al., which provides what is undoubtedly the best synthetic work on the species of Usnea for the continent of Europe. Range maps and photographs of small-scale features make this section both informative and interesting.

Reading this volume also makes it apparent that the changing landscape of lichenological research has led to certain problems that require special attention. Many of the problematic issues plaguing our field seem to be associated with the process of adjusting to the molecular age. A number of the studies published herein leave the reader wanting to know more, especially in terms of molecular data and how they were analyzed (or how they could be analyzed differently). Beyond the simple deposition of sequences in a public repository, alignments must be reviewed and made available if alignment-based phylogenetic analyses are to be reproducible. Authors will find that making their assembled molecular datasets freely available to readers (on their own personal websites if necessary) increases the impact and relevance of their work by permitting others to easily build on their studies. Ultimately, this practice will allow our field to advance more quickly and will raise the bar in terms of research quality. In summary, this volume of Bibliotheca Lichenologica, as its title suggest, provides an excellent picture of the diversity of lichenology and represents quite well the overall state of the field as we enter this next decade. Many of the works contained in this anniversary edition provide important contributions, and any lichenologist’s collection would be enriched by the addition of this volume.

- Brendan

-----------------------------

Citation:
Hodkinson, B. P. 2010. Lichenological Diversity. The Bryologist 113(4): 828-829.

ITS RNA secondary structure

2011-08-31T23:58:00.000-07:00

I have recently been conducting phylogenetic and taxonomic studies of selected groups of lichen-forming fungi using sequences from the quickly evolving nuclear ribosomal ITS (internal transcribed spacer) region to examine relationships within and between species (e.g., Hodkinson & Lendemer 2011, Hodkinson et al. 2010, Lendemer & Hodkinson 2009, 2010, in prep). In order to properly analyze the evolutionary relationships between the organisms from which these molecules were derived, I built secondary structure models for the RNA molecules encoded by ITS1 and ITS2 (the two rapidly evolving sections of the ITS region) for some of the groups.

The ITS1 and ITS2 spacer regions encode stretches of RNA that fold up in specific conformations and help to assemble the ribosomes (the pieces of cellular machinery that build protein molecules based on specific messenger RNA sequences transcribed from DNA). The particular folding pattern is referred to as the molecule's "secondary structure." Here is an example of a secondary structure model that I put together for ITS2 of Parmotrema perforatum:

Notice the A(adenine)-U(uracil) pairings and the G(guanine)-C(cytosine) pairings, just like the complementary strands of DNA (except that with DNA you have T for thymine instead of U for uracil).

There are two main reasons that one might want to have a secondary structure model when inferring phylogeny:

[1] Nucleotide Alignment - An understanding of the overall structure of the molecule can aid in discerning which sets of sites in different organisms actually represent the same character when they have different states and there are adjacent nucleotides that have been inserted or deleted in some taxa (Kjer 1995). Many studies use principles of secondary structure to aid in alignment.

[2] Phylogenetic Inference - Since paired sites in some sense evolve in tandem (if one nucleotide changes, the linked nucleotide will often change to compensate over evolutionary time), it is most appropriate within a likelihood framework to apply a different model of evolution to the paired nucleotides so that this can be taken into consideration. This type of inference can be done with RAxML (Stamatakis 2006) and I have recently integrated this into my workflow (Hodkinson & Lendemer in prep).

The really interesting thing to think about is the fact that this type of macromolecule needs to be able to move in order to function, which means that the structure is not actually static, but dynamic. While we usually use the 'best' structure for phylogenetic inference, there are actually many structures that are nearly equally good, and the molecule actually changes its conformation through space and time, flipping between these different conformations in order to perform its functions in the cell. To drive the point home, here is a quick video I made of the ITS2 molecule of Cladonia stipitata Lendemer & Hodkinson (2009) shifting between different likely conformations:

------------------------------

Sources cited:

Hodkinson, B. P., and J. C. Lendemer. 2011. Molecular analyses reveal semi-cryptic species in Xanthoparmelia tasmanica. Bibliotheca Lichenologica 106: 115-126.
Download publication (PDF file)
Download nucleotide alignment (NEXUS file)

Hodkinson, B. P., and J. C. Lendemer. In prep. Systematics of a enigmatic sterile crustose lichen.

Hodkinson, B. P., J. C. Lendemer, and T. L. Esslinger. 2010. Parmelia barrenoae, a macrolichen new to North America and Africa. North American Fungi 5(3): 1-5.
Download publication (PDF file)

Kjer, K. M. 1995. Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs. Molecular Phylogenetics and Evolution 4: 314–330.

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)
Download nucleotide 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 nucleotide alignment (NEXUS file)

Stamatakis, A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688–2690.

Taxonomy: Art or Science?

2011-08-17T12:52:00.000-07:00

When Googling "science definition," the first thing that came up was "The intellectual and practical activity encompassing the systematic study of the structure and behavior of the physical and natural world through observation and experiment." After a little more research, I was surprised to see that this seems to be one of the stricter definitions of science (others may be as broad as "the state of knowing" or some such...), but it is one with which I can get on board. I tend to think of science itself in a very strict sense, as the process of developing and testing hypotheses. However, my big caveat is that there are many activities that are involved in (and are absolutely essential to) the practice of science that are not science per se according to that definition. This does not diminish their value to science. Some of this has to do with the acquisition of background knowledge that informs the hypotheses to be tested, while some of it is associated with making the results of inquiry available and comprehensible to the scientific community and the public.

So then is taxonomy art or science? With taxonomy, there is not a "right" answer, although there are plenty of wrong answers if one wishes to have a system that is informed by the results of scientific inquiry. Taxonomic units are all in some sense arbitrary. Although a group of organisms may form a "clade," whether we recognize that clade with a certain name is somewhat arbitrary. I personally like to think of taxonomic units being defined by specific innovations (morphological, molecular, ecological, etc.) that have changed the evolutionary trajectory of a group, but that rule is certainly not universally applied, and there could certainly be many alternative taxonomies even if such standards were applied.

For me, the argument for taxonomy as an art does not actually diminish taxonomy in any way as part of what we must do in order to be effective and responsible scientists. In fact, having this perspective on taxonomy can help to enhance the understanding of the significance of taxonomy for science. As scientists, we must use what we discover through the scientific process to help facilitate communication about natural phenomena. Taxonomy is a tool that we use to communicate ideas about organisms, so taxonomy is an absolutely necessary part of the pursuit of scientific truth, even if it is not "science" itself.

One test for me of whether taxonomy is itself a science in the very strictest sense of the word is whether it is directly involved in the process of hypothesis testing. One can use principles of phylogenetics, ecology, or molecular biology to test hypotheses, but taxonomic principles would not be used. When we begin to dissect some of the scientific questions that are often deemed "taxonomic questions," it can be argued that they are not actually taxonomic in nature, and that the taxonomic repercussions would really only be a byproduct of obtaining results through scientific inquiry. For instance, a question like "Is this a good genus?" is really asking something like "Do the species form a distinct clade?", which is a question that is evolutionary in nature. Likewise, the question "Do these individuals make up one species?" is perhaps just a way of saying "How can we properly apply a biological, morphological, chemical, ecological, and/or phylogenetic species concept to this group of individuals?", a question that draws on different fields of biology.

I can see that many systematists would hesitate to state that taxonomy is an art, because of what it implies. If it is an art, then it opens the door for people to say that people who do taxonomy are not really scientists at all. But a consummate scientist is not just someone who constantly tests hypotheses one after another without consideration for anything else. To be a scientist, one must also lay the groundwork for scientific pursuits, and defining the terms used to communicate ideas about specific units of the tree of life (whether or not it is itself an artistic pursuit) is crucial to the advancement of science.

- Brendan

Using Sequencher for Multiple Sequence Alignments

2011-08-04T23:09:00.000-07:00

Much of the molecular research that I have done over the years has involved working with DNA sequences generated through Sanger sequencing. These sequences are never perfect, and always require manual correction. It is especially helpful to correct sequences and align them to other similar sequences simultaneously. In this way, alignment and structural data can be taken into consideration when interpreting the chromatograms for the DNA sequences.

So I wrote a couple of simple Perl scripts that would allow me to make my alignments in Sequencher (the standard program for editing raw sequence reads) and easily move it over to Mesquite or MacClade (standard programs for assembling data matrices for downstream phylogenetic analyses) so that it could be joined with a reference alignment that I had made previously. In this way, I could avoid completely realigning all sequences to one another through an automatic alignment program, thereby preserving certain sequence alignment patterns (note that I often deal with over 1000 sequences at a time). If you use Linux or Macintosh, running a Perl script is generally a pretty simple matter (since Perl interpreters are typically built into the operating system). If you use Windows, you will probably need to download an interpreter like Strawberry Perl or ActivePerl.

The type of data that I was dealing with was a set of bidirectional Sanger sequences (one forward, one reverse primer for each sequence) of fragments ~650 bp in length. These sequences were cloned and therefore had vector overhang on both ends of both strands, which had to be deleted. If you have data that are similar, here is a procedure that can be used to preserve the Sequencher alignment pattern and bring it into MacClade/Mesquite (potentially for merging with a curated reference alignment, if you have one of these):

[a] In the Sequencher alignment, make sure at least one sequencing strand of each pair of strands (from the bidirectionally-sequenced pool of DNA fragments) has all of the corrected bases, and delete the second strand for each pair. This gives an alignment with one strand for each sequence. [This Sequencher alignment can be tweaked visually to align with a reference set that is already pre-aligned by introducing gaps into the Sequencher alignment to accommodate the gaps in the reference alignment.]
[b] The Sequencher alignment can then be exported as a contig in aligned fasta format and subsequently opened in MacClade/Mesquite. [Note: If you have exported the sequences from Sequencher as a concatenated set of sequence fragments, it might use ':' instead of '-' to represent the gaps; make sure all of the gaps are changed to '-' for integration into MacClade or Mesquite (this can be done as a simple search and replace with any text editor).]

For my particular sequences, I had to deal with the issue of all of the sequence names being proceeded by my initials and having strand-specific information tacked on to the end (both standard pieces of information added by the sequencing facility). Here is another blog post with the Perl script that I wrote for editing the fasta file to extract the 10-digit alpha-numeric code used to identify my sequences. Also, I had to line my sequence block up with the portion of my reference alignment with which it correlated. In my particular situation, the block of sequences that I had aligned began 488 bases into the reference alignment. Here is the script that I used to add 488 bases to the front of each sequence in the fasta file (this script relies on having a 10-digit code name for each sequence):

#!/usr/bin/perl

print "\nPlease type the name of your input file: ";
my $filename = <STDIN>;
chomp $filename;
open (FASTA, $filename);
        {
        if ($filename =~ /(.*)\.[^.]*/)
                {
                open OUT, ">$1.ed.fasta";
                }
        }
while (<FASTA>)
        {
       if ($_ =~ /^>(..........)/)
                {
                print OUT "\r>$1\r\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\n";
                }
       else
                {
                print OUT $_;
                }
       }

The final step was to simply open up my reference alignment in MacClade and import the newly-generated fasta file of aligned cloned sequences... and they lined up perfectly! I then tweaked exclusion sets, saved the full alignment, and was ready for downstream phylogenetic analyses.

Even though MacClade and Mesquite are very good programs overall for alignment, aligning a set of 1000+ sequences is extremely cumbersome, and Sequencher can be much faster and easier as long as the sequences are relatively conserved. With this set of Perl scripts discussed above, hopefully researchers will no longer perceive impediments or inefficiency in a process that includes aligning and correcting relatively conserved sequences in Sequencher (with all of the raw sequence data) before moving them over to MacClade/Mesquite for final data set assembly and formatting.

- Brendan

----------------------------------------------

References

The above protocols are published in the following sources:

Hodkinson, B. P. 2011. A Phylogenetic, Ecological, and Functional Characterization of Non-Photoautotrophic Bacteria in the Lichen Microbiome. Doctoral Dissertation, Duke University, Durham, NC.
Download Dissertation (PDF file)

Hodkinson, B. P., N. R. Gottel, C. W. Schadt, and F. Lutzoni. 2011. Data from: Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome. Dryad Digital Repository doi:10.5061/dryad.t99b1.

Hodkinson, B. P., N. R. Gottel, C. W. Schadt, and F. Lutzoni. In press. Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome. Environmental Microbiology.

----------------------------------------------

This work was funded in part by NSF DEB-1011504.

Taxonomy as Wastewater Treatment

2011-07-25T21:55:00.000-07:00

I was thinking about taxonomic treatments of specific groups of organisms; in some cases a 'treatment' is essentially a rehash and synthesis of what has been published previously (but just for a specific subregion, etc). While focusing on the mechanistic details of how my colleagues and I put together treatments (not through rehashing), I thought of the process by which sewage is treated. So I did a Google image search for "taxonomic treatment," and basically got a bunch of photos of journal pages/covers, some phylogenetic trees, and some photos of organisms. I think that's pretty much how most people see biological taxonomy, which explains a lot about why taxonomy is often seen as dull and sometimes (even worse) unscientific. But then I did a Google image search for "wastewater treatment" and I was amazed to see that the images there generally matched my concept of how to do a taxonomic treatment much better than what I saw in the previous search! What I saw were mainly flowcharts... they showed processes like screening, pre-treatment, cleaning, clarification, digestion, storage, disposal... and the processes all flowed into one another and ended up making products for public consumption! Yes! This is it! This is how we really need to be doing taxonomy! Instead of perpetuating the problems that exist, take them head on... get the junk out of the way, and make something that people can use. Many researchers seem to be of the mind that if it's mostly right, it's good enough; but as any wastewater treatment plant manager will tell you, even if it's only 10-20% sewage, it's not fit for public consumption. Let us view our taxonomy in the same manner!

Lichenologist James Lendemer is famously quoted as saying "I think of myself as a bounty hunter." Perhaps I should think of myself as a manager of a wastewater treatment plant. Maybe that's not as glorious, but it certainly is important. So much work remains to be done before we get close to having a reasonable set of names for the organisms on the Earth. As long as humans are involved, our nomenclatural system will be imperfect and will require constant cleaning, management, and enforcement of standards... and there I will stand, ready to take on the nastiest and dirtiest of the problems!

- Brendan

P.S. Some recent big news in the NYC area has been the big fire at a wastewater treatment plant that sent sewage spewing into the Hudson River. Thought exercise for taxonomists: Can you think of any events like this one (speaking metaphorically) that affected your particular group of organisms?

Man It Feels Good 2 B A Lichen

2011-07-12T08:29:00.000-07:00

Recently I was thinking about the plight of the sterile crustose lichens, specifically those in Eastern North America. One could feel sorry for them, being so taxonomically neglected and underrepresented in all major surveys of biodiversity. But in a certain kind of way, I think that they must be very proud. It's certainly amazing how they've been able to get by on so little (so little sex, so little attention from humans). Inspired by the story of the sterile crusts, I decided to write some lyrics, which I entitled "Man, It Feels Good 2 B A Lichen," and set the words to the music of the similarly-titled song (made famous by the movie Office Space) by the Geto Boys, about being a gangsta, not a lichen. Some people have said that it's groundbreaking... that it's a whole new genre (known as "Lichen Rap" or, more commonly, "Lich-Hop")... I just like to think of it as one of the products resulting from the inspiration that I get from the amazing organisms that I study!

Please press play above (or download here)

Man, It Feels Good 2 B A Lichen (a sterile crust’s song)

Man, it feels good to be a lichen

Live sterile crust lichens ain’t indoors

Real sterile crust lichens are hard to identify

‘cause sterile crust lichens don’t make spores

Man, it feels good to be a lichen

I mean one that you don’t really know

Livin’ as a sterile crust, drivin’ people crazy

‘cause I can’t be identified for sho’

Now sterile crust lichens come in all shapes and colors

Some got killed in the past

But if NSF could just get their back with some fundin’

We could study them and hopefully they’ll last

Now all I gotta say to you

Sexually-reproducin’ lichen-formin’ fungi recombinin’

When your spore can’t find no algae what you think you gonna do?

Man, it feels good to be a lichen

Flying round on the currents all day

‘cause when a sterile crust lichen goes and tries to reproduce

It bundles up the partners and it blows away

Now when a lichen like this one is livin’ in your ‘hood

It’s most likely that you ain’t gonna know

‘cause lots of sterile crust lichens are small and inconspicuous

But under UV they might glow

Now all I gotta say to you

Sexually-reproducin’ lichen-formin’ fungi recombinin’

When your spore can’t find no algae what you think you gonna do?

Man, it feels good to be a lichen

Stay tuned for news about the record release party in the Bronx, to take place later this year!

- Brendan

Perl: Renaming DNA Sequences

2011-07-05T22:30:00.000-07:00

When I began my dissertation studies, I did not know the wonders of the Perl programming language. However, within the past year, it has proven to be an invaluable tool for manipulating DNA sequence data sets and helping me to tackle projects that once seemed too large in scope. In this post I will just give one example of a Perl script that I wrote after getting some training from Dr. Bob Thomson, who I met at the NSF-Sponsored "Fast, Free Phylogenies" workshop at NIMBioS (Knoxville, TN).

When processing large numbers of DNA sequences, it always helps to have a standardized naming system so that the sequences can be handled in an automated way during downstream analyses. For a recent large-scale cloning experiment that involved picking 2880 clonal bacterial colonies (to amplify and sequence a vector-inserted 16S gene fragment from each), I developed a 10-digit alpha-numeric code that allowed me to encode all of the necessary data about my sequences into each specific sequence identifier. However, the sequencing facility also needed to use its own codes to keep track of my sequences, so I ended up with long names that had my own codes in the middle with information identifying them as my sequences in front and information about the individual sequence reads themselves tacked on at the end. Therefore, to recover the names (without retaining the sequencing facility's additions) in an automated way, I wrote a simple Perl script to edit a fasta file containing the sequences (this was run after the process of manual sequence correction had been finished).

The following script (‘Clon_16S_fasta_renamer.pl’) allowed me to extract the 10-digit alpha-numeric codes that I used in my dissertation studies (Hodkinson 2011) from the long names (with extraneous information) that come from the sequencing facility. It creates a new fasta file with these modified identifiers. Specifically, it takes sequences that have "BH_" (my initials), followed by a 10-digit code, followed by additional characters, and simply renames each sequence using just the 10-digit code (effectively stripping out "BH_" at the beginning and and extra characters at the end). The new file will have the same name, but the extension will be replaced by ".ed.fasta". This can be easily modified for any set of sequences that are identified using a standardized naming scheme.

#!/usr/bin/perl

print "\nPlease type the name of your input file: ";

my $filename = <STDIN>;

chomp $filename;

open (FASTA, $filename);

{

if ($filename =~ /(.*)\.[^.]*/)

{

open OUT, ">$1.ed.fasta";

}

while (<FASTA>)

{

if ($_ =~ /^>BH\_(..........)/)

{

print OUT ">$1\n";

}

if ($_ =~ /^[A,C,G,T,R,Y,K,M,S,W,B,D,H,V,N,:,-][A,C,G,T,R,Y,K,M,S,W,B,D,H,V,N,:,-][A,C,G,T,R,Y,K,M,S,W,B,D,H,V,N,:,-][A,C,G,T,R,Y,K,M,S,W,B,D,H,V,N,:,-]*/)

{

print OUT $_;

}

if ($_ =~ /^[A,C,G,T,R,Y,K,M,S,W,B,D,H,V,N,:,-][A,C,G,T,R,Y,K,M,S,W,B,D,H,V,N,:,-]$/)

{

print OUT $_;

}

if ($_ =~ /^[A,C,G,T,R,Y,K,M,S,W,B,D,H,V,N,:,-]$/)

{

print OUT $_;

}

If you need to know how to run a Perl script, you can look it up on Google, but here is one example of how to run a Perl script using Windows (it's actually easier on almost any other type of operating system). Since I was performing a simple task with a very specific data set, it was easy for me to use basic Perl commands. However, for more complex sequence manipulations, BioPerl provides an excellent collection of Perl modules for biological applications.

- Brendan

----------------------------------------------

References

The above script is published in the following sources:

Hodkinson, B. P. 2011. A Phylogenetic, Ecological, and Functional Characterization of Non-Photoautotrophic Bacteria in the Lichen Microbiome. Doctoral Dissertation, Duke University, Durham, NC.
Download Dissertation (PDF file)

Hodkinson, B. P., N. R. Gottel, C. W. Schadt, and F. Lutzoni. 2011. Data from: Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome. Dryad Digital Repository doi:10.5061/dryad.t99b1.

Hodkinson, B. P., N. R. Gottel, C. W. Schadt, and F. Lutzoni. In press. Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome. Environmental Microbiology.

----------------------------------------------

This work was funded in part by NSF DEB-1011504 and EF-0832858.

Molecular Phylogenetics Workshop

2011-06-18T02:31:00.000-07:00

Next week I will be running a short Molecular Phylogenetics Workshop at Roan Mountain State Park in Tennessee (June 22, 10:30-2:00; see announcement on this page). The workshop coincides with the meeting of the American Bryological and Lichenological Society, but I will be presenting general principles of molecular evolution and phylogenetic inference that are applicable to any set of organisms.

Here is the abstract:
"Cryptogams are notorious for their paucity of morphological characters when compared with higher plants and animals. As a result, an understanding of molecular data and what they can reveal in terms of evolution is perhaps more crucial in these organisms than in many others. Workshop participants will explore principles of molecular phylogenetics and learn basic protocols for running phylogenetic analyses. The main objectives will be (1) to promote an understanding of how events in the course of molecular sequence evolution affect phylogenetic inference, (2) to explore the advantages and disadvantages of different phylogenetic methods, and (3) to facilitate sound research into the phylogenetic history of life. The workshop will include both lecture and discussion. Participants are invited to bring their own data sets for more detailed evaluation at the conclusion of the workshop."

For those scheduled to attend, I look forward to seeing you there! For those not attending, I hope to see you at a future workshop!

- Brendan

----------------------------------------------

This work was was made possible in part by NSF (DEB-1011504) and the American Bryological and Lichenological Society.

Writing a Phycas Script

2011-06-17T11:27:00.000-07:00

For a while I have been wary of phylogenetic results supported only by Bayesian analyses, because of the so-called 'star-tree paradox' that haunts MrBayes and even some other programs like it. As I have mentioned previously, one of the best features of the Bayesian phylogenetic program Phycas is that it gives one the opportunity to allow polytomies in the trees sampled as part of the posterior (which can often deflate the inflated posterior probability values seen with programs like MrBayes). The specific command for this is:
"mcmc.allow_polytomies = True"

To run Phycas, it is best to write a script to go with a standard NEXUS-formatted sequence alignment. There is some basic information on how to install and run Phycas in my previous post:
http://squamules.blogspot.com/2011/06/installing-and-running-phycas.html
However, that post does not go into any of the details of scripting for Phycas. Recently, I ran a multigene analysis with mtSSU, ITS1, 5.8S, and ITS2 in different partitions, with a different evolutionary model for each. Here is what my Phycas script looked like:

from phycas import *
setMasterSeed(98765)
mcmc.data_source = 'Input_file_name.nex'
mcmc.out.log = 'Output_file_name.log'
mcmc.out.log.mode = REPLACE
mcmc.allow_polytomies = True
mcmc.polytomy_prior = False
mcmc.topo_prior_C = 1.0
mcmc.out.trees.prefix = 'Output_file_name'
mcmc.out.params.prefix = 'Output_file_name'
mcmc.ncycles = 50000
mcmc.sample_every = 10
# Set up the K80+I model for 5pt8S
model.type="hky"
model.state_freqs = [0.25, 0.25, 0.25, 0.25]
model.fix_freqs = True
model.kappa = 2.0
model.kappa_prior = BetaPrime(1.0, 1.0)
model.pinvar_model = True
# Save the K80+I model for 5pt8S
m3 = model()
# Set up the GTR+I model for mtSSU
model.type="gtr"
model.state_freqs = [0.3338, 0.1493, 0.1983, 0.3187]
model.fix_freqs = False
model.relrates = [1.4783, 5.8050, 3.3222, 0.6768, 7.6674, 1.0000]
model.pinvar_model = True
# Save the GTR+I model for mtSSU
m1 = model()
# Set up the HKY+G model for ITS1
model.type="hky"
model.state_freqs = [0.1487, 0.3566, 0.2704, 0.2244]
model.fix_freqs = False
model.kappa = 2.0
model.kappa_prior = BetaPrime(1.0, 1.0)
model.num_rates = 4
model.gamma_shape = 0.5
model.gamma_shape_prior = Exponential(1.0)
model.pinvar_model = False
# Save the HKY+G model for ITS1
m2 = model()
# Set up the HKY+G model for ITS2
model.state_freqs = [0.1419, 0.3069, 0.3199, 0.2314]
# Save the HKY+G model for ITS2
m4 = model()
# Define partition subsets
mtssu = subset(1, 1080)
its1 = subset(1081, 1607)
fivept8S = subset(1608, 1768)
its2 = subset(1769, 2041)
# Assign partition models to subsets
partition.addSubset(mtssu, m1, "mtSSU")
partition.addSubset(its1, m2, "ITS1")
partition.addSubset(fivept8S, m3, "5pt8S")
partition.addSubset(its2, m4, "ITS2")
partition()
# Start the run
mcmc()
# Summarize the posterior
sumt.trees = 'trees.t'
sumt.burnin = 500
sumt.tree_credible_prob = 1.0
sumt()

Although I have some notes within the script, please see the Phycas manual for instructions on what each of the individual commands does. Hopefully more people will be using Phycas (and allowing polytomies!) in the future!

- Brendan

Note: One question that I had about running Phycas was how to define exclusion sets; however, Phycas apparently can read the EXSET line of the ASSUMPTIONS block of the NEXUS file in the same way that Mesquite, MacClade, and PAUP* can.

Installing and Running Phycas

2011-06-14T21:02:00.000-07:00

Phycas has recently earned a high spot on my short list of favorite computer programs for phylogenetics. Phycas is the amazing program that can run a Bayesian phylogenetic inference without being susceptible to the 'star-tree paradox' because it allows for the existence of polytomies in the sampled trees.

From an academic perspective, Phycas is actually a pretty easy program to run and install. Still, some additional notes on tricks and tips for running it were beneficial to one of my colleagues who was really having trouble getting it to go. Here were my instructions for installing Phycas on a Windows machine:

1) Install Python 2.7. [I use the Enthought Python Distribution, available here: http://www.enthought.com/products/epd.php. Everything is bundled together so components like SciPy, NumPy, etc., never need to be installed individually and the different versions of the components are all guaranteed to play well together.]

2) Follow the instructions here:
http://hydrodictyon.eeb.uconn.edu/projects/phycas/index.php/Telling_Windows_where_to_find_Python
to append Python27 (different from the versions they have listed there) to your PATH (I guess if your PATH is truly empty then you will just leave out the semi-colon; otherwise, keep whatever's already in your PATH in there, but just add ;C:\Python27 to the end of it it). [It might also be important to make sure that the PYTHON-STARTUP environmental variable says C:\Python27 (if you have that variable... mine was still set to 2.6, meaning that the wrong version of Python would likely open up by default), and that this is all being done for the system level and the user level... I was only doing it for the user level for a while and it got me mixed up.]

3) Do the 4-step Phycas installation as outlined on the "Windows XP/Windows Vista/Windows 7" section of this website (the manual itself is apparently wrong, so be careful here).

4) For your own particular analysis, put the NEXUS-formatted alignment file ('.nex') and the phycas script file ('.py') on the Desktop where you have the shortcut to the '.bat' file. [For more on writing a Phycas script, stay turned to this blog!]

5) Drag and drop the phycas script file (.py) onto 'Shortcut to phycas.bat'.

I'll have another blog post that goes more into the details of Phycas scripting, but I hope this post helps jump-start some of those eager to deflate their inflated posterior probability values!

- Brendan

A New Home

2011-06-13T18:05:00.000-07:00

I have relocated and am finally settled in New York! I will be doing my post-doctoral work at the New York Botanical Garden (NYBG) using advanced bioinformatics tools to study lichen ecology and evolution with Richard C. Harris and James C. Lendemer. Here is my new address:

International Plant Science Center
The New York Botanical Garden
2900 Southern Blvd.
Bronx, NY 10458-5126

NYBG has an amazing research program that is not typical for a botanical garden. The departments within the International Plant Science Center include the following: Institute of Systematic Botany, Cullman Program for Molecular Systematics, Plant Research Laboratory, NY Plant Genomics Consortium, Steere Herbarium, Graduate Studies, Mertz Library, and NYBG Press (plus more). My research will likely connect in some way with all of these departments, which is why NYBG is a perfect environment for my post-doctoral research.

Those who have been following my research closely might say "obviously you study diverse organisms from across the tree of life, but since when do you study plants?" Since the concept of "plants" once included fungi, the "plant" research program at NYBG (which began taking shape over 100 years ago) provides amazing resources for the study of fungal biology as well. Of course, I will specifically be focusing my energy on the lichen-forming fungi.

Please stay tuned for more on my research as it unfolds in New York City!

- Brendan

Graduation/Dissertation

2011-05-23T23:48:00.000-07:00

Upon my graduation, I thought I'd give a little update. The thesis defense last month was successful and the final draft of my dissertation has been submitted! My thesis was on the communities of non-photoautotrophic bacteria associated with lichens. This research broke a lot of new ground in terms of using high-throughput pyrosequencing and cutting-edge bioinformatics to examine the phylogenetic, ecological, and functional complexity of the lichen microbiome. My hope is that my dissertation will contribute to science through both the data that I have generated and the set of tools that I have developed. I have talked a little about some of the bioinformatics tools that I have developed in previous posts here, but I will continue to post additional elements of my thesis, especially as they are published in peer-reviewed journals.

The graduation itself gave me a final chance to reflect on the great opportunities that have been made available to me at Duke University. Here you can see me chillin' out after the hooding ceremony:

This week I'm in the process of moving up to NY to start my postdoctoral research on the systematics of lichen-forming fungi at the New York Botanical Garden. I will be working with Dr. Richard C. Harris and James Lendemer, focusing on long-standing problems in Eastern North American lichen taxonomy, while testing a number of specific ecological and biogeographical hypotheses. Addressing many of these issues will require cutting-edge bioinformatics tools that I have developed or am in the process of developing with a network of collaborators in diverse fields.

- Brendan

This graduation account is recommended and promoted by Online PhD.

Investing in Science

2011-05-16T12:27:00.000-07:00

Several months back I worked with a group of other student members of the Botanical Society of America (BSA) to draft an open letter to lawmakers to express our hope that policymakers in Washington, DC, would sustain a national commitment to invest in our nation's scientific research, development, and education. This has now evolved into a petition. Please read the email below from the BSA student representatives to find out more about this effort:

"
Attention Students: Ask Lawmakers to Support Science Education and Research
First, we'd like to thank all of you who have taken action and responded to this call. Please take the extra step and ask your friends to consider doing so as well.
The end of the academic year is quickly approaching. Before you venture off for the summer research season or for a short break from classes, you have one more assignment. I am writing to ask that you join with other science students from across the country to sign an online petition to lawmakers. This statement reminds our elected leaders that scientific research and education are keys to our future and asks them to continue to make important investments in the scientific programs that will support your education and preparation for future careers in research, teaching, or the myriad fields that grow and benefit from scientific research.
We already have more than 2,750 signatures, but we would like to have more than 5,000 by the end of May. So, if you have not already signed this online petition, please do so today at http://www.aibs.org/public-policy/science_students_letter.html. You may also sign the petition and encourage your friends to sign via Facebook -- http://www.facebook.com/pages/Students-Sign-the-Open-Letter-to-Policymakers-About-Investments-in-Science/183684855001704.
Thank you for your time and support!
Sincerely,
Botanical Society of America Student Representatives, Marian Chau (University of Hawai`i at Manoa) and Rachel Meyer (New York Botanical Garden)
"

Punctelia eganii Hodkinson & Lendemer, sp. nov., a rare chemical oddity

2011-05-13T20:50:00.000-07:00

Just today I had an article published in the journal Opuscula Philolichenum in which I, along with James Lendemer, describe a new species in the genus Punctelia that has only been found once and contains a chemical compound (lichexanthone) that has otherwise not been seen in this genus. The species was collected along the Alabama River in historic Monroe County, Alabama, near Monroeville (childhood home of Harper Lee and Truman Capote; "the literary capital of Alabama").

Under an ultraviolet light, it makes pin-pricks of bright light across the surface (due to the localized presence of lichexanthone). The species is named Punctelia eganii, after Dr. Bob Egan of the University of Nebraska at Omaha, who first collected the species and brought it to our attention. The paper ends with a discussion of 'chemotaxonomy' and the evolving views on the role of secondary chemistry in lichen taxonomy.

- Brendan

--------------------------------------------------------------

Reference:
Hodkinson, B. P., and J. C. Lendemer. 2011. Punctelia eganii, a new species in the P. rudecta group with a novel secondary compound for the genus. Opuscula Philolichenum 9: 35-38.
Download publication (PDF file)

PICS-Ord Tricks

2011-05-10T22:32:00.000-07:00

Those who have ever used the R statistical package know that it can be a bit tricky, especially if you're first starting out.

The R-based PICS-Ord program (developed to recode ambiguously-aligned regions for phylogenetic analyses; see here and here and here for more information) was written to be as simple as possible while remaining flexible and adjustable. A set of pretty comprehensive instructions was produced to facilitate analyses and provide recommendations for basic use (see 'manual.pdf' available here). The manual is where everyone should look first for help with PICS-Ord. However, those who are not experts in R and/or the command line may benefit from some additional information on how to implement PICS-Ord without really having to know much background information on the R statistical package. Therefore, the goal of this post is to detail one relatively simple way of implementing the PICS-Ord program on a PC.

Here are instructions for one way of running PICS-Ord on Microsoft Windows. Note that these instructions will only work with installations of the Windows version of R (try 2.12.0; the most recent version of R did not work at the time that this was last updated) [ http://cran.r-project.org/bin/windows/base/old/2.12.0/ ] and the Ngila Windows executable [ http://scit.us/projects/ngila/ ] (for the latter, choose the option of putting Ngila in your PATH upon installation).
1) Place picsord.R (found in the picsord.zip archive) in the same folder as ngila.exe (probably C:\\"Program Files"\Ngila\bin\).
[Note: If Ngila is not in your path, you can go into the picsord.R file and change "ngila" (the one in quotes) to "ngila.exe" in the first line that is not preceded by a hash mark (#), or you can type out the full path (but this will not be necessary if you are following the rest of this procedure). Some users have manually edited picsord.R by deleting the first line (the line specifying the location of Rscript); this seems unnecessary but may be worthwhile on certain machines.]
2) Save/copy the input fasta file to a directory (e.g., your home directory, Desktop, or C:\).
3) In the Command Prompt window, use the 'cd' or 'chdir' command to navigate to the directory in which the input fasta file is stored (or simply put the input fasta file in the home directory so that navigation is not necessary), then type the following (this line can be modified based on the version of R being used or the specific location on the drive where Rscript and picsord.R are located):
C:\\"Program Files"\R\R-2.12.0\bin\Rscript.exe C:\\"Program Files"\Ngila\bin\picsord.R input.fas > output.phy

After this, the output phylip file should appear in the working directory.

Multiple regions can be processed by running the command in step 3 separately for each region, or one can use the .bat file that comes as part of the PICS-Ord package (use of the .bat file is outlined in the manual). After this, the phylip-formatted PICS-Ord alignment portions can be pasted at the end of the original nucleotide alignment alongside the unambiguously-aligned sites. Please see the manual for further recommendations regarding implementation.

-Brendan

References:

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)

Semi-Cryptic Species

2011-05-08T23:41:00.000-07:00

Last week the most recent volume of Bibliotheca Lichenologica (dedicated to Tom Nash) was released. There were 33 peer-reviewed contributions by 70 authors, and one of these contributions was a paper that I wrote with James Lendemer of the New York Botanical Garden. In short, the paper demonstrates with molecular data that the species Xanthoparmelia tasmanica (Parmeliaceae) contains at least two species that cannot be differentiated based on any known morphological or chemical characters. However, the two species belong to two larger clades within the genus Xanthoparmelia, one of which seems to be exclusively Australasian, and the other of which is distributed across the Earth's other continents.

The evolutionary pattern seen here is strikingly similar to what is found in placental mammals and marsupial mammals, with two larger clades of organisms (one of which is almost exclusively Australasian) in which certain pairs of species have converged on similar morphologies. The pair of Xanthoparmelia tasmanica and Xanthoparmelia hypofusca (the new name of the other species, which we sampled in North America) is interesting because it is the first known example of complete convergence in this group, where no distinguishing morphological or chemical characters could be identified for two species found to be in these two major clades. However, we use the term 'semi-cryptic' (as opposed to 'cryptic') to describe the pair of species, since geography would seem to indicate which species is represented by any given sample.

A press release came out from Duke for this story. The following list represents a handful of websites that have covered the story:
http://today.duke.edu/2011/05/lichen
http://www.evoscience.com/2423/lichen-could-be-a-fungal-equivalent-at-least-evolutionarily/
http://www.sciencedaily.com/releases/2011/05/110502110622.htm
http://www.biologynews.net/archives/2011/05/02/lichen_evolved_on_2_tracks_like_marsupials_and_mammals.html
http://archaeologynewsnetwork.blogspot.com/2011/05/lichen-evolved-on-2-tracks-like.html
http://anpron.eu/?p=2023
http://scienceblog.com/44922/lichen-evolved-on-2-tracks-like-marsupials-and-mammals/
http://www.geneticarchaeology.com/research/Lichen_evolved_on_2_tracks_like_marsupials_and_mammals.asp
http://www.australasianscience.com.au/news/may-2011/lichen-evolved-two-tracks-marsupials-and-mammals.html
http://feelsynapsis.com/pg/blog/read/64210/the-lichens-are-a-good-example-of-convergent-evolution
http://www.noodls.com/viewNoodl/9870752/duke-university/lichen-evolved-on-two-tracks-like-mammals-and-marsupials
http://7thspace.com/headlines/381043/lichen_that_seem_identical_in_all_outward_appearances_are_in_fact_two_different_species.html
http://esciencenews.com/articles/2011/05/02/lichen.evolved.2.tracks.marsupials.and.mammals
http://pda.physorg.com/news/2011-05-lichen-evolved-tracks-marsupials-mammals.html
http://www.uux.cn/viewnews-27222.html
http://www.cnfossil.com/?action-viewnews-itemid-205
http://tieba.baidu.com/f?kz=1070028772
http://www.nigpas.cas.cn/kxcb/kpwz/201105/t20110506_3128772.html
http://www.uua.cn/news/show-11534-1.html
http://www.sciencetechmag.com/lichen-evolved-on-two-tracks-like-marsupials-and-mammals.html
http://www.ebionews.com/news-center/general-research/evolution/37344-lichen-evolved-on-two-tracks-like-marsupials-and-mammals.html
http://www.astrobio.net/pressrelease/3948/lichens-two-track-evolution
http://www.eurekalert.org/pub_releases/2011-05/du-leo050211.php
http://forum.grasscity.com/science-nature/806894-evolution-action-convergent-species.html
http://www.labspaces.net/110538/Lichen_evolved_on___tracks__like_marsupials_and_mammals
http://pda.physorg.com/news/2011-05-lichen-evolved-tracks-marsupials-mammals.html
http://www.verticalnews.com/premium_newsletters/Journal-of-Technology-and-Science/2011-05-22/213JTS.html
http://www.solociencia.com/biologia/11061009.htm [In Spanish]
http://www.firstscience.com/home/news/breaking-news-all-topics/lichen-evolved-on-2-tracks-like-marsupials-and-mammals_104827.html
http://www.irlab.org/now/GetSummary.do?id=3590
http://www.bioquicknews.com/node/494
http://i.bioknow.cn/portal/root/rsp/zx_nr.jsp?id=64585741
http://www.noticias21.com/node/3503 [In Spanish]
http://riktningnews.bio-medicine.org/biology-news-1/Lichen-evolved-on-2-tracks--like-marsupials-and-mammals-19054-1/
http://www.sciencenewsline.com/biology/2011050313000026.html?continue=y
http://www.sciencecodex.com/lichen_evolved_on_2_tracks_like_marsupials_and_mammals
http://www.onenewspage.com/news/Science/20110503/21924744/Lichen-Evolved-On-Tracks-Like-Marsupials-And.htm
http://www.astrobio.net/pdffiles/news_3948.pdf
http://chemical-and-chemistry.verticalnews.com/articles/5287667.html
http://www.freeusenetnewsgroup.com/lichen-evolved-on-2-tracks-like-marsupials-and-mammals.html
http://foronatura.mforos.com/1926434/10384172-2-sp-de-liquen-transformadas-en-una-sola-a-efectos-practicos/ [In Spanish]
http://newswithscience.blogspot.com/2011/05/lichen-evolved-on-2-tracks-like.html
http://i-science77.blogspot.com/2011/05/lichens-two-track-evolution.html
http://www.sciguru.com/newsitem/8367/lichen-evolved-on-two-tracks-like-marsupials-and-mammals
http://www.sciencenewsworld.com/science-articles/lichen-evolved-on-2-tracks-like-marsupials-and-mammals.html

- Brendan

-------------------------------

CITATIONS:
Hodkinson, B. P., and J. C. Lendemer. 2011. Molecular analyses reveal semi-cryptic species in Xanthoparmelia tasmanica. Bibliotheca Lichenologica 106: 115-126.
Download publication (PDF file)
Download nucleotide alignment (NEXUS file)

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

-------------------------------

UPDATE:

I even found a site that tries to use my article to disprove evolution!
http://www.evolutionnews.org/2011/05/convergent_genetic_evolution_i046651.html
I consider it to be a badge of honor. As an evolutionary biologist, when the intelligent design people start paying attention to your work, I think that it's an indication that you've "arrived"!

WOODSmont #2 - Continuing Outreach

2011-04-13T01:32:00.000-07:00

I recently set up an exhibit all about lichens at my second WOODSmont Childrens' Festival. Some readers may recall my post about last year's event. Once again, it was a great success; it was both a lot of fun and a great chance to expose people to lichens at a young age!

The festival was sponsored by Duke University's Wilderness Outdoor Opportunities for Durham Students ('WOODS'). My table included 'touch and feel' lichens, a dissecting scope (so that children could see the lichens up close), and samples of local lichens for children to take home. I also had opportunities to interact with people of all ages from the local community and a number of K-12 educators.

There were many lichens to put under the scope.

I was sure to accommodate even the smallest of lichen observers.

The whole family can learn to love lichens!

A lesson on minute graphids.

Phylogenetic tree editing: Reinserting removed identical sequences

2011-04-02T20:20:00.000-07:00

In phylogenetic analyses, a large number of identical sequences can sometimes prove to be problematic. This post outlines a protocol for creating and running a customized Unix shell script that reinserts identical sequences into a phylogenetic tree file (NEWICK or NEXUS format), for situations in which identical sequences were removed pre-analysis.

Identical sequences may have been removed using the Mothur 'unique.seqs' function (in which case a '.names' file would have been generated, storing the information about which sequences were removed) or RAxML (which generates a '.reduced.phy' file for phylogenetic analysis and a log file that contains a list of the removed sequences and their remaining representatives in a format that can be easily extracted using Unix or Microsoft Excel). The protocol described here relies on using a '.names' file. If sequences were not removed using Mothur, the '.names' file can be manually generated (here are notes on the basic format: http://www.mothur.org/wiki/Names_file ), or the original sequence file can be processed using the Mothur 'unique.seqs' function.

This script will need to be built from the ground up as a customized Unix shell script for your sequence set. This can be assembled easily in Microsoft Excel or one of its clones:

Column A: 'sed -i s/' all the way down the column
Column B: sequence IDs for representative sequences (Column 1 of the '.names' file)
Column C: backslashes all the way down the column
Column D: lists of sequences represented by each representative sequence (including the representative itself) separated by commas; each line must correlate with the Column B identifiers (Column D corresponds to Column 2 of the Mothur '.names' file)
Column E: '/g file_name.tre' all the way down the column

After this is put together, save it as tab-delimited text, open it with an advanced text editor (one that can perform a search and replace on tabs, e.g., TextWrangler or TextPad), remove all tabs (search for tabs and replace them with nothing), and add the first few lines manually to make it a working script. [Note: If one sequence name anywhere in the tree file or '.names' file is nested within another (e.g., 'bacterium' and 'bacterium2'), a colon can be added immediately after the name of the representative sequence with the shorter name, as long as a colon is added after the list of sequences being represented by that sequence.] The script can now be run on the original tree file and it will transform it into a tree file containing all of the sequences in the original sequence set (before removing identical sequences).

Here's an example:

#!/bin/bash

#$ -S /bin/bash

#$ -cwd

#$ -o search_replace.log -j y

sed -i s/5005c2/5005c2,HL06C03c12/g RAxML_bipartitions.Rhizo_RAxML_topo_BP_50plus.tre

sed -i s/5005c4/5005c4,CL08C02c09,uncultured_bacterium_FD01A08,uncultured_bacterium_FD04E06/g RAxML_bipartitions.Rhizo_RAxML_topo_BP_50plus.tre

sed -i s/5015c31/5015c31,EL02B02c77,EL02C01c63,EL02C02c85,EL02C03c68,EL04C01c65,EL04C01c68,EL04C01c71,EL04C01c72,EL05B03c02,EL06C03c65,EL06C03f17,EL08B01c10,EL08B01c13,EL08B03c17,EL08B03c19,EL09A01c65,EL09A01c67,EL09A01c68,EL09A01c70,EL09A03c19,EL09A03c20,EL09B02c36,EL09B02c39,EL10B01c41,HL10A02c32,NL07B01c12,NL08C03c25,NL08C03f89,NL08C03f90,NL08C03f93/g RAxML_bipartitions.Rhizo_RAxML_topo_BP_50plus.tre

sed -i s/5027c58/5027c58,EL08B01c09/g RAxML_bipartitions.Rhizo_RAxML_topo_BP_50plus.tre

sed -i s/uncultured_bacterium:/uncultured_bacterium,HL08B03c26:/g RAxML_bipartitions.Rhizo_RAxML_topo_BP_50plus.tre

sed -i s/uncultured_bacterium_5C231311/uncultured_bacterium_5C231311,GQ109020/g RAxML_bipartitions.Rhizo_RAxML_topo_BP_50plus.tre

sed -i s/uncultured_bacterium_FD02D06/uncultured_bacterium_FD02D06,EL02C01c61,EL02C02c84,EL02C03c67,EL08C01c23,EL08C03c09,EL10C03c15,NL01B03c63,NL07B01c10,NL07B01d89,NL07B03d84,NL10A02c32/g RAxML_bipartitions.Rhizo_RAxML_topo_BP_50plus.tre

sed -i s/uncultured_bacterium_nbw397h09c1/uncultured_bacterium_nbw397h09c1,HL05A03c20/g RAxML_bipartitions.Rhizo_RAxML_topo_BP_50plus.tre

sed -i s/uncultured_bacterium_Sed3/uncultured_bacterium_Sed3,EF064161/g RAxML_bipartitions.Rhizo_RAxML_topo_BP_50plus.tre

This information and many more bioinformatics tricks, tips, and scripts can be found in my doctoral dissertation (Hodkinson 2011), which will be coming out soon!

- Brendan

Update: These instructions are now published as part of a paper in Environmental Microbiology (Hodkinson et al. in press) and the data/analysis/instruction files are available from the Dryad data repository (Hodkinson et al. 2011).

----------------------------------------------

References

The above instructions are published in the following sources:

Hodkinson, B. P. 2011. A phylogenetic, ecological, and functional characterization of non-photoautotrophic bacteria in the lichen microbiome. Doctoral Dissertation, Duke University, Durham, NC.
Download Dissertation (PDF file)

Hodkinson, B. P., N. R. Gottel, C. W. Schadt, and F. Lutzoni. 2011. Data from: Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome. Dryad Digital Repository doi:10.5061/dryad.t99b1.

Hodkinson, B. P., N. R. Gottel, C. W. Schadt, and F. Lutzoni. In press. Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome. Environmental Microbiology.

----------------------------------------------

This work was funded in part by NSF DEB-1011504.

Even More Florida Lichens

2011-03-20T00:04:00.000-07:00

Two years ago the Tuckerman Foray and Workshop was held in southern Florida. 'The Tuckerman,' as it's often called, was begun by Dick Harris, and is best summarized in his own words:

"This series of workshops, aimed at amateurs interested in lichens, was initiated because of a concern over the decline in organismal lichenology in North America. The workshops were begun as a way to pass along knowledge about lichens as living organisms and their systematics to a group of amateurs who could then keep the knowledge alive until academia once again becomes interested. The first workshop in 1994 had only about 10 participants. However, as the reputation of the workshops grew, and the original participants acted as teachers themselves, the workshops grew to 30-40 participants. The 19th workshop was held in 2010 in Georgia. For several of the workshops, major keys or other publications have been written and distributed to the participants. For the first several workshops I was the only mentor, but through the years the workshops have attracted other professionals who welcome the opportunity to interact, and learn (!), from enthusiastic amateurs. There are no registration fees for the workshops and all professionals pay their own expenses." (excerpted from Harris's own NSF biographical sketch)

In 2001, Dick won the first Peter Raven Award (American Society of Plant Taxonomists), for public outreach to nonscientists, for organizing the Tuckerman Workshops. In an age when morphological studies of organisms are out of fashion, it is important to keep these traditions alive. Once the initial pizazz of molecular studies wears off (perhaps it already has?), we will really only be able to break significant new ground in lichenology if we have an integrated approach that utilizes both the old and the new. I am very much with E.S. Luttrell when he says that:

"Little progress can be made if new techniques are used only to replace, rather than complement, the old" (E.S. Luttrell, 1989).

So the Tuckerman Foray keeps some of the old traditions and techniques alive in lichenology. At the particular one referenced in this post, we had a great time exploring Fakahatchee Strand near the Everglades and collecting an amazing diversity of lichens! Over a dozen new species are described as part of the final field trip publication (Lücking et al. 2011) and nearly 100 species are newly reported for North America. Be sure to check out the amazing supplementary photos!

I'm currently working on finishing up my dissertation on lichen-associated bacteria so I might not write for a while... the defense is April 1st!

- Brendan

*UPDATE*
This article has been featured on sciencedaily.com and earthsky.org!

------------------------------------------------
Citation:

Lücking, R., F. Seavey, R. S. Common, S. Q. Beeching, O. Breuss, W. R. Buck, L. Crane, M. Hodges, B. P. Hodkinson, E. Lay, J. C. Lendemer, R. T. McMullin, J. A. Mercado-Díaz, M. P. Nelsen, E. Rivas Plata, W. Safranek, W. B. Sanders, H. P. Schaefer Jr. and J. Seavey. 2011. The lichens of Fakahatchee Strand Preserve State Park, Florida: Proceedings from the 18^th Tuckerman Workshop. Bulletin of the Florida Museum of Natural History 49(4):127-186.
Publication: http://www.flmnh.ufl.edu/bulletin/vol49no4/vol49no4.pdf
Supplementary photos: http://www.flmnh.ufl.edu/bulletin/vol49no4supplmats.htm

Lichen Research in Science News

2011-03-14T09:27:00.000-07:00

OK, so I guess this is old news, but maybe it'll be new to you! The Lutzoni Lab was featured a couple of years back in Science News. You can check out the article here:
http://www.sciencenewsdigital.org/sciencenews/20091107?pg=20#pg18
If for nothing else, have a look at the great spread of photos by Stephen Sharnoff!

- Brendan

Usnea Launch Project

2011-03-04T20:39:00.000-08:00

Certain lichens need a little help. That's the philosophy behind the Usnea Launch Project out in the Pacific Northwest region of the United States. Their motto is "A Better Future for Usnea longissima." From what I can glean from the promotional film, the project entails taking fallen lichens, packing them up in little latex capsules with plenty of water, and launching them high into the trees using a giant 3-person catapult.

If you haven't gotten a chance to see it yet, have a look at the video. It will show you some of the lengths that lichenologists go to for conservation!

- Brendan

The Licheniad

2011-02-25T22:58:00.000-08:00

The Licheniad

by Sean Q. Beeching

Canto I

A lichen, one may theorize,
When on the future casts his eyes,
His dear descendants he descries.

Eternal life, so it appears,
And a youth that lasts a thousand years,
The lichen spurns as cause for tears.

He dreams, or she, perhaps I’ll say,
Of numerous, happy, progeny,
With whom it would, perforce, parté.

The truth to which one must attest,
Is that our lives may not be blest,
And nuclear winter may end the fest.

In which event the lichen too,
Will perish along with me and you,
Unless a lifeboat he can constue.

But how to effect the goal sublime?
To reproduce two souls entwined,
Involves a course most labyrinthine.

Too sadly he must bid ado,
To sex, I’m sorry, but it’s true,
The ordinary method won’t work for two.

By sex what here we represent,
Does not demand adult consent,
Simple meiosis is all that’s meant.

These poor dears, for aught we know,
Lack the genders and hence forgo,
What here to say would not be apropos.

And had they genders, why they’d be four,
Two for the fungus, for the alga two more,
As state of affairs one would deplore.

It would lead to confusion,
To mishap and exclusion,
And not, in fine, to the hoped for diffusion.

One half, if the better, I’ll not say,
May be engendered in the usual way,
What results, I’m afraid, is a lichen manqué.

Oft tales are told of the sailing spores,
Which travel the heavens beyond our shores
And by means unknown the lichen restores.

Yet how the bionts reunite,
On what rare moonlit starry night;
It remains conjecture, that secret rite.

Yet how the lichen reunites,
By what fantastic arcane rites
Remains unknown, they’re unseen sights.

(Betwixt the preceding tercets twain
Neither of the other could the advantage gain,
I’ve left them both as a short refrain.)

Though it may happen, it seems farfetched,
Belief must needs be sorely stretched,
To credit the procedure I have thus far sketched.

Instead the lichen puts his trust,
In structures far removed from lust;
They seem to us no more than dust.

Within the thallus, all unseen,
Assembles the lichen his breeding machine,
As in an ant hill he were the queen.

At length the surface of its skin,
Reveals the tumult deep within,
It writhes and wrinkles and waxes thin.

Upon its face begin to vent,
Depending on the creature’s bent,
Features odd but of small extent.

Their smallness is indeed a test
Of our student’s eyesight. They protest,
And think our labels a cruel jest.

They’re each quite different, we declare,
Which drives them all to black despair,
As at the mocking plants they stare.

And truth to tell not even we,
Are always sure which one we see,
Isidia, soredia, which could it be?

Regardless which these fly aloft,
Both symbionts combined but soft,
They fall to earth, not seldom but oft.

Back on the earth, behold, it sprouts,
It lives, it breathes, convention flouts,
And grows to manhood, or thereabouts.

Thus, dear readers, have you now heard,
A tale as marvelous but far less blurred,
Than that of the logos, the living word.

Should that comparison seem extreme;
By it am I seen to blaspheme:
It’s nothing, I assure you, but blown off steam.

Fast UniFrac for barcoded 454 16S amplicons

2011-02-22T10:35:00.000-08:00

When analyzing large 16S sequence data sets from multiple samples to infer community patterns, one of the best analytical methods available is Fast UniFrac. Barcoded 454 sequencing (a type of 'pyrosequencing') is quickly becoming the method of choice for generating the data for these types of analyses, and Fast UniFrac has been built especially to handle the large data sets generated using this method. However, there are simple data management issues that can keep researchers from using this methodology. One major hindrance with Fast UniFrac is that, if one wants to take advantage of the 16S reference tree that is built in to the program (something that becomes almost obligatory with sufficiently large data sets), it is necessary to put all of the sequence names in a specific format that reveals the sample of origin while preserving the individual sequence identifiers. Below I describe two distinct procedures that I developed for assembling the input file for the first step of the Fast UniFrac pyrosequencing analysis procedure. I have tested the first procedure on a data set of ~120,000 sequences (this required sending an email to request a higher Fast UniFrac quota, which is typically capped at 100,000 sequences) of ~500bp in length and the second procedure on a data set of ~40,000 sequences of the same approximate length.

Files needed:
Sequence files ('.fna'+'.qual' or '.sff' or '.fasta'+'.groups') with sequence names that are all the same length (standard for 454 data)
Oligos file with primers and barcodes for each sample (for use with Mothur) [http://www.mothur.org/wiki/Trim.seqs]

Special programs needed:
Mothur
A text editor that can perform search and replace on returns (e.g., TextWrangler for Macintosh or TextPad for Windows)
Microsoft Excel 2008 (previous versions max out at ~65000 rows and may do other unexpected things to large data sets)
BLAST (local)
PyCogent
Enthought Python Distribution (I used v6.3) (alternatively, you can download Python and Numpy, but the EPD has versions of these that play well together and should hopefully work with PyCogent as long as they are first in your path... getting Python, Numpy, and PyCogent to talk can be more complicated than it would seem)

Method #1 (no UNIX scripting required):

1) Take the '.fna' (fasta) and '.qual' (quality) files (or alternatively the '.sff' file) plus the manually-produced '.oligos' file for your data set and process them with Mothur using the 'trim.seqs' function [http://www.mothur.org/wiki/Trim.seqs]. This will produce a '.fasta' file with your sequences and a '.groups' file that shows which sequences come from which samples ('environments' in the language of UniFrac). I recommend using the many functions of Mothur to further cull your data set; however, the amazing power of Mothur will be the subject of future posts. If you do decide to change the composition of the '.fasta' file in any way (this is always necessary at least to some degree), you can use the Mothur 'list.seqs' function (performed on the finalized '.fasta' file) to generate an '.accnos' file, then follow that by the 'get.seqs' function (performed on the '.accnos' file and the original '.groups' file) to generate a finalized '.groups' file that correlates with the finalized '.fasta' file.

2) Open the '.groups' file in Microsoft Excel and edit the file to create a four-column spreadsheet: (A) '>' on every row; (B) sample names; (C) delimiter (I use '#') on every row, and (D) sequence names. Highlight all four columns and sort ascending according to column D (sequence names). This is done by going to 'Data' > 'Sort' > 'Column D', 'ascending'. Save as 'file1.csv' (comma-delimited text).

3) Open the new 'file1.csv' file in a text editor and remove all commas (this can be easily done in TextWrangler for Mac by opening the file and going to 'Search' > 'Find', putting ',' in the 'Find:' box, typing nothing in the 'Replace:' box, and clicking 'Replace All'). Save as 'file2.txt' (plain text).

4) Open the '.fasta' file with a text editor (e.g., TextWrangler). Remove all returns (e.g., Find: '\r', Replace: '' in TextWrangler with the 'Grep' box checked on the Find/Replace screen). Replace all instances of '>' with a return and '>' (e.g., '\r>'; remember that 'Grep' must be checked if you are using TextWrangler). Now the first line is empty; manually delete that line. Save as 'file3.txt' (plain text).

5) Import 'file2.txt' into the first column of Microsoft Excel (column A). On the same spreadsheet, import the names and sequences from file3.txt to the second and third columns (columns B and C) by clicking on cell B1 (column B, row 1) and importing 'file3.txt' as a text file with 'fixed width'; set the field width for the column break manually at the interface between the sequence name and the beginning of the nucleotide sequence (for my data, it was around the 15th place; if this doesn't work with the text import wizard, fixed-width delimitation can be performed under 'Text to Columns...' in the 'Data' menu). Highlight columns B and C *only* (if you highlight column A as well, this will not work). Go to 'Data' > 'Sort' > 'Column B', 'ascending'. At this point, you should have rows that look something like: '>CLSt#GR5DBVW03HJKND' '>GR5DBVW03HJKND' 'TACGATCGATCGATCAGCATCGATCA...' where the columns are correlated with one another and reading across a row should show the same identifier in column A as in column B. Be sure that this is the case throughout the spreadsheet. Now delete column B (the one with the identifiers from the imported fasta file). Save as 'file4.csv' (comma-delimited text).

6) Open 'file4.csv' with a text editor. Replace all instances of ',,' with a single return (e.g., find ',,' and replace with '\r' in TextWrangler... remember to have the 'Grep' box checked). Save as 'file5.fasta'.

7) Follow the instructions for "The BLAST to GreenGenes protocol" and 1-7 of the "Steps" in the Fast UniFrac tutorial (download raw pairwise distance matrices for further analyses), all found here:
http://bmf2.colorado.edu/fastunifrac/tutorial.psp

Method #2 (simpler overall, but requires assembling and running a customized UNIX shell script):

1) Take the '.fna' (fasta) and '.qual' (quality) files (or alternatively the '.sff' file) plus the manually-produced '.oligos' file for your data set and process them with Mothur using the 'trim.seqs' function [http://www.mothur.org/wiki/Trim.seqs]. This will produce a '.fasta' file with your sequences and a '.groups' file that shows which sequences come from which samples ('environments' in the language of UniFrac). I recommend using the many functions of Mothur to further cull your data set; however, the amazing power of Mothur will be the subject of future posts. If you do decide to change the composition of the '.fasta' file in any way (this is always necessary at least to some degree), you can use the Mothur 'list.seqs' function (performed on the finalized '.fasta' file) to generate an '.accnos' file, then follow that by the 'get.seqs' function (performed on the '.accnos' file and the original '.groups' file) to generate a finalized '.groups' file that correlates with the finalized '.fasta' file.

2) Create and run a shell script on the '.fasta' file that looks something like this:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -o search_replace.log -j y

sed -i s/GMQ03P202B3SVL/MID08#GMQ03P202B3SVL/g file_name.fasta
sed -i s/GMQ03P202BTOMD/MID08#GMQ03P202BTOMD/g file_name.fasta
sed -i s/GMQ03P202CGYZW/MID08#GMQ03P202CGYZW/g file_name.fasta
sed -i s/GMQ03P202BT4E9/MID08#GMQ03P202BT4E9/g file_name.fasta
sed -i s/GMQ03P202BXELV/MID08#GMQ03P202BXELV/g file_name.fasta

It will have to contain a row for every sequence. This sort of thing can be assembled in Microsoft Excel:
Column A: 'sed -i s/' all the way down the column
Column B: sequence IDs (from a Mothur '.groups' file)
Column C: backslashes all the way down the column
Column D: sample identifiers (correlated with the sequence IDs... easily done if the sequence IDs and sample identifiers are both taken from a Mothur '.groups' file and the order is preserved)
Column E: delimiter (e.g., #) all the way down the column
Column F: identical to column B
Column G: '/g file_name.fasta' all the way down the column
After that is put together, save it as comma-delimited text, open it with a text editor, remove all commas, add the first few lines manually to make it a working script, and run.

3) Follow the instructions for "The BLAST to GreenGenes protocol" and 1-7 of the "Steps" in the Fast UniFrac tutorial (download raw pairwise distance matrices for further analyses), all found here: http://bmf2.colorado.edu/fastunifrac/tutorial.psp

Once you have the raw pairwise distance matrices, they can be analyzed in R or another statistical package/program. This will be the subject of a later post. As part of the Fast UniFrac protocol (when using the GreenGeenes core backbone tree), it will be necessary to use PyCogent. If you have trouble with PyCogent itself (or the command-line in general), please see my earlier post with some tricks and tips on getting that part of the Fast UniFrac 'BLAST-to-GreenGenes' protocol to work. Hopefully the current post can help someone in constructing the initial input file for the first part of the Fast UniFrac procedure!

- Brendan

P.S. This procedure places '#' in the sequence names as the delimiter. This information will be needed during the PyCogent-dependent portion of the Fast UniFrac protocol. Here is an example of what I type in the command line once I have navigated to the folder where I have placed the 'create_unifrac_env_file_BLAST.py' python script and the 'blast_output...' file (the confusing thing with my nomenclature is that the Python input is named 'output' because it is the BLAST output, while the Python output is named 'input' because it becomes the Fast UniFrac input; the logic behind this is that the essence of this step is the transformation of the BLAST output file into the Fast UniFrac input file):

python create_unifrac_env_file_BLAST.py blast_output_allreplaced_ready4python.txt fastunifrac_input_file.txt #

Update: These instructions are now published as part of my dissertation (Hodkinson 2011) and an article in Environmental Microbiology (Hodkinson et al. in press); the supporting data/analysis/instruction files for the latter are available from the Dryad data repository (Hodkinson et al. 2011).

----------------------------------------------

References

The above instructions are published in the following sources:

Hodkinson, B. P. 2011. A phylogenetic, ecological, and functional characterization of non-photoautotrophic bacteria in the lichen microbiome. Doctoral Dissertation, Duke University, Durham, NC.
Download Dissertation (PDF file)

Hodkinson, B. P., N. R. Gottel, C. W. Schadt, and F. Lutzoni. 2011. Data from: Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome. Dryad Digital Repository doi:10.5061/dryad.t99b1.

Hodkinson, B. P., N. R. Gottel, C. W. Schadt, and F. Lutzoni. In press. Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome. Environmental Microbiology.

----------------------------------------------

The development of the above protocols was supported in part by NSF (DEB-1011504) and the US Department of Energy.

PyCogent for Fast UniFrac

2011-02-10T23:01:00.000-08:00

As someone studying the composition of lichen-associated bacterial communities, I have generated several data sets of 16S rRNA gene sequences from bacteria that live in this specialized niche. Beyond the simple question of "who lives there?" we can start to use phylogenetic inferences to examine the ecology of this niche by comparing sets of 16S sequences from different communities and taking into account where the different members fall in a phylogeny. UniFrac is a tool that allows the integration of phylogenetic information into ecological comparative community analyses, and its hip new cousin Fast UniFrac is all the rage these days. But, alas, fully utilizing the special features of Fast UniFrac (such as mapping pyrosequencing reads to a reference phylogeny) requires PyCogent, the installation of which has given me much grief recently.

PyCogent is a great Python-based toolkit that can be used for conducting a number of analyses on biological sequence data (DNA, RNA, proteins); it is billed as "making sense from sequence" (Knight et al. 2007). There is a good guide to PyCogent known as the PyCogent Cookbook. Some programs/packages/pipelines that depend on PyCogent include QIIME and Fast UniFrac (for the latter, PyCogent is required only if you have a large 16S data set that requires a guide tree).

I have had trouble getting the different versions of Python, NumPy, and PyCogent to communicate with one another through UNIX (on both CentOS and MacOSX... although all of the various versions of the different dependencies may have been an issue, since I do not own the machines and I run several versions of Python myself locally), but I ran through the simple 2-step protocol listed below on Windows XP and Windows 7 and it worked very well for running the Python script associated with the Fast UniFrac 'BLAST-to-GreenGenes' protocol. This is a little odd since it is written that installation of PyCogent by itself is not supported for Windows... and the procedure that I outline below seems to be a pretty simple way to get it installed.

Installing and running PyCogent requires using the command line. If you would like to do this on a Windows machine and you are unfamiliar with the Windows command line, you can google tutorials on "MS-DOS" and/or "command prompt". There is a decent introductory guide here. The instructions below are written in a broad, inclusive way so that they should work with a UNIX-based system as well (including Macintosh; if you are a Mac user and are unfamiliar with the command line, you can google something like "Mac OSX Terminal" or find a good beginners' tutorial here).

Whatever type of system it is, the PATH variables must be set correctly so that the programs can find one another. As long as you do not have previous versions of Python, NumPy, or PyCogent installed, Windows should automatically set the environmental variables so that this protocol will work without a hitch (Macintosh most likely will not set the variables automatically because it usually comes with a pre-installed Python that it will always want to use). Click here to see a post that further addresses one of the issues with the wrong version of Python/NumPy getting in the way.

Here is my simplistic protocol for getting PyCogent moving enough to run the Python script mentioned above (I should note that this protocol is not approved by the makers of PyCogent, since it may not produce a fully-functional package, but it does allow me to run the script):

1) Installing Python, NumPy, etc.:
Install the most recent version of the Enthought Python Distribution package (free for academics).

2) Installing PyCogent:

Download the most recent version of PyCogent ('.tgz' file).
Unzip the folder (using, e.g., WinRAR, WinZip, or 7-Zip; an automatic partial unzip might leave it as '.gz' but one of the previously mentioned programs will allow you to unzip it fully and you can drag the folder to your desktop if necessary).

In the command line, navigate to the PyCogent directory.
Type in the command line:

python setup.py install

There are some further notes on installation here and in the README, but please note that it was the fact that these instructions didn't quite get me to where I was going that inspired me to write this post. Still, they are likely to provide exactly what is needed for most situations.

Depending on the sort of jobs you need to run using PyCogent, a single computer may or may not have enough computing power. I have an interest in PyCogent because I need it to run the aforementioned script that makes the Fast UniFrac '.env' input file (see the Fast UniFrac tutorial for more details on how this fits into the overall Fast UniFrac protocol). A single computer processor has more than enough computing power to handle this job, but some of the more advanced QIIME functions will certainly require greater power for sufficiently large data sets.

Hopefully the notes here can make Fast UniFrac more accessible to more people (specifically, when the mapping of pyrosequencing reads to a reference tree is required), since the various errors that may occur with PyCogent, NumPy, Python, etc. can be difficult. If you wish to use PyCogent directly, you will probably have to be somewhat familiar with the Python programming language, although the cookbook has enough examples that one may be able to stumble through it naively (not that I would recommend it). If you're like me, and only use PyCogent so that you can map sequences to a reference tree for Fast UniFrac, then everything else you'll need to know can probably be found in the excellent Fast UniFrac tutorial. The Fast UniFrac 'BLAST-to-GreenGenes' procedure also requires a local installation of BLAST (installation instructions for PC, Mac, Linux, etc.). Making the initial input file for this specific type of Fast UniFrac analysis can require some creative thinking, and will be the subject of a future post.

- Brendan

Poemules

2011-01-23T02:39:00.000-08:00

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

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

2011-01-08T23:32:00.000-08:00

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

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)

Snow Camp Lichens

2010-12-31T16:52:00.000-08:00

A few years back I stopped into a little town called Snow Camp, NC, and saw some amazing rooftops with wooden shingles filled with Cladonia lichens! I had never seen colonies so large in this region before. Recently, I realized that I would be passing by the town again and decided to take some photographs of this phenomenon. I had to do some acrobatics to get close-ups of them. You can click on the photos to see greater detail!

Standing on the back of a car to photograph the lowest of the Cladonia-filled rooftops.

One half of a roof almost entirely covered with lichens.

A roof corner with Cladonia cristatella and other species.

A close-up of just one shingle.

Happy New Year!

- Brendan

Our Lady of Lichens

2010-12-16T12:50:00.000-08:00

This statue of Mary sits in a graveyard near our home. Notice all of the beautiful orange lichens that cover her!

Have a merry Christmas!

- Brendan

Lichens in the Media

2010-11-29T19:33:00.000-08:00

Recently, National Public Radio (NPR) interviewed James Lendemer of the New York Botanical Garden for a portion of the "Science Friday" program about lichens. The primary product that resulted from this interview was a video that they posted on their website:
http://www.sciencefriday.com/videos/watch/10336
My favorite part of the video occurs when they show James hiking through the forest hunting for lichens and there is a voice-over of James saying "I think of myself as a bounty hunter." On the weekly national broadcast they did a five-minute piece in which they briefly discussed lichens and heavily referenced the above video. Online there is a transcript and a link to an mp3 of the broadcast. There are also some lichen photos that viewers/listeners sent in to NPR after hearing the program:
http://www.sciencefriday.com/newsbriefs/read/203

Lepraria hodkinsoniana (photo taken by an NPR listener)

It's great to see a piece like this promoting lichenology in the media!

-Brendan

USA Science

2010-11-14T17:13:00.000-08:00

Last month I volunteered to take part in the USA Science and Engineering Festival Expo in our nation's capital, Washington D.C.! There were all kinds of exhibits hosted by agencies, professional science organizations, and businesses like NASA, the American Society for Microbiology, and Lockheed Martin.

"
Mission:
Our mission is to re-invigorate the interest of our nation’s youth in science, technology, engineering and math (STEM) by producing and presenting the most compelling, exciting, educational and entertaining science gatherings in the United States.
"

If the powers that be decide to throw this festival a second time, it would be great to have a representation of the country's leading lichenological, bryological, and mycological societies. I'll keep an eye on future plans!

- Brendan

Beneficial Microbes

2010-11-01T17:14:00.000-07:00

Recently I attended the American Society for Microbiology's 3rd Conference on Beneficial Microbes, which was held in Miami, FL. It was great to meet so many people using techniques similar to the ones that I am using for my research into the bacteria of the lichen microbiome. I was especially excited to go to the session entitled 'Ecology and evolution of microbial communities' since this is one of the major topics that interests me. There were talks by some of the stars of microbial community ecology (e.g., Dr. Rob Knight and Dr. Ruth Ley) and other great talks as well. There were certainly other sessions with interesting talks, too, including one by Dr. Giles Oldroyd on 'Reprogramming Plant Cells for Endosymbiosis.'

Here is a short description of the conference:
"Biologists are becoming increasingly aware that animals and plants have coevolved with diverse assemblages of microorganisms that are required for normal health and development. Not surprisingly, the activity of these symbiont communities is also likely to profoundly affect all aspects of the host’s physiology. An understanding of these complex interactions requires contributions from a diverse, multidisciplinary group of researchers, including microbial ecologists and geneticists. The goal of this conference is to bring together a wide array of scientific expertise to foster the development of this rapidly expanding field of biology."

I returned excited to continue my research on the lichen microbiome, and I look forward to speaking again with some of the people that I met!

- Brendan

Tennessee Journey

2010-10-19T20:01:00.000-07:00

Over the past couple of weeks I've been in Tennessee working at the Oak Ridge National Laboratory and attending a class on High Performance Computing for Phylogenetics at the University of Tennessee. My family came along, and since we were staying in Knoxville, which is only an hour from the Great Smoky Mountains, we spent one Saturday visiting the G.S.M. National Park. We happened to be there right in the peak of fall color season and had a great time looking at the foliage and exploring the amazing diversity of lichens in and around the park!

An official park stamp with Cladonia apodocarpa.

Traveling companions.

Checking out the lichen diversity!

-Brendan

NC Science Festival

2010-10-05T18:27:00.000-07:00

A little over a week ago, I participated in a Science Expo that was one of the culminating events of the North Carolina Science Festival. It was great fun to bring my traveling lichen show, complete with real lichens, microscopes, and plenty of amazing lichen photos. I was also sure to engage passersby and answer any questions that they might have about lichen biology and the science of lichenology. While my table was one of the only 'natural history' type displays, there were all sorts of science demos, hands-on activities, lab tours and talks. It was a great time!

- Brendan

Bayesian reversible-jump MCMC: deflating inflated support values

2010-09-22T23:22:00.000-07:00

Recently, on the Botanical Society of America Student ListServ, commonly-used phylogenetic methods were being discussed, and a specific problem was raised with regard to Bayesian phylogenetic inference: it has been documented that, within a Bayesian framework, support values (in the form of posterior probabilities) can become inflated or skewed. This is an issue of special interest to me, since I commonly use Bayesian inference alongside other phylogenetic methods in my research (e.g., Hodkinson & Lendemer 2010, Hodkinson & Lutzoni 2009, Miadlikowska et al. 2006). I decided to contribute to the discussion by sending the following message to the ListServ:

"
I have found that Bayesian phylogenetic inference methods can do amazing things (like finding the same topology with one gene that only emerges with two or three genes in an analysis based on maximum parsimony (MP) or maximum likelihood (ML)). However, this problem of Bayesian methods inflating support (especially at short internodes) makes me feel very suspicious of any given Bayesian posterior probability value. Therefore, if I want to evaluate support, I always look at MP- and/or ML-bootstrap proportions. The Bayesian problem that we're talking about has been discussed by Lewis et al. (2005), and they state that the solution is to use reversible-jump MCMC (rjMCMC). However, I have wondered myself how I could actually implement this.

I recently found an article that clearly stated the fact that MrBayes and BEAST cannot perform rjMCMC (Kodandaramaiah et al. 2010): http://dx.doi.org/10.1016/j.ympev.2009.08.012
In this article, they used Phycas for their rjMCMC analyses.

So I went to the Phycas manual (Lewis et al. 2010), and found that it does give the nitty-gritty of how to implement this (see section 2.3 on 'Polytomy Priors'):
http://phylo.bio.ku.edu/phycas/manual.pdf
I have not yet done it myself, but I am very excited to try it out! Perhaps now I will have more faith in my posterior probabilities!
"

The Phycas manual gives the best, most concise summary of the issue that I have seen anywhere:

"
A solution to the 'Star Tree Paradox' problem was proposed by Lewis, Holder, and Holsinger (2005). Their solution was to use reversible-jump MCMC to allow unresolved tree topologies to be sampled during the course of a Bayesian phylogenetic analysis in addition to fully-resolved tree topologies. If the time between speciation events is so short (or the substitution rate so low) that no substitutions occurred along a particular internal edge in the true tree, then use of the polytomy prior proposed by Lewis, Holder, and Holsinger (2005) can improve inference by giving the Bayesian model a 'way out.' That is, it is not required to find a fully resolved tree, but is allowed to place a lot of posterior probability mass on a less-than-fully-resolved topology. Please refer to the Lewis, Holder, and Holsinger (2005) paper for details.
"

Please post comments here if you have performed these types of analyses and have any additional insights!

-Brendan

P.S. Please see my more recent posts for the details of using Phycas:
http://squamules.blogspot.com/2011/06/installing-and-running-phycas.html
http://squamules.blogspot.com/2011/06/writing-phycas-script.html

Works Cited:

Hodkinson, B. P., and J. C. Lendemer. 2011. Molecular analyses reveal semi-cryptic species in Xanthoparmelia tasmanica. Bibliotheca Lichenologica 106: 115-126.
Download draft (PDF file)
Download alignment (NEXUS file)

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)

Kodandaramaiah U., C. Pena, M. F. Braby, R. Grund, C. J. Muller, S. Nylin, and N. Wahlberg. 2010. Phylogenetics of Coenonymphina (Nymphalidae: Satyrinae) and the problem of rooting rapid radiations. Molecular Phylogenetics and Evolution 54(2): 386-394.
View Publication (webpage)

Lewis, P. O., M. T. Holder, and K. E. Holsinger. 2005. Polytomies and Bayesian phylogenetic inference. Systematic Biology 54(2): 241-253
View Publication (webpage)

Lewis, P. O., M. T. Holder, and D. L. Swofford. 2010. Phycas User Manual, Version 1.2.0.
View Manual (PDF file)

Miadlikowska, J., F. Kauff, V. Hofstetter, E. Fraker, M. Grube, J. Hafellner, V. Reeb, B. P. Hodkinson, M. Kukwa, R. Lücking, G. Hestmark, M. Garcia Otalora, A. Rauhut, B. Büdel, C. Scheidegger, E. Timdal, S. Stenroos, I. Brodo, G. Perlmutter, D. Ertz, P. Diederich, J. C. Lendemer, P. May, C. L. Schoch, A. E. Arnold, C. Gueidan, E. Tripp, R. Yahr, C. Robertson, and F. Lutzoni. 2006. New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes. Mycologia 98: 1088-1103.
Download publication (PDF file)
Download supplement (PDF file)
Download alignment (zipped NEXUS file)

A recipe with fungi and algae!

2010-09-11T02:00:00.000-07:00

I have never actually eaten a lichen, but I was thinking the other day about how I do like to eat both fungi and algae, especially together. Several years ago, my wife and I took a Korean cooking class, where we learned some great recipes. The one that we enjoy cooking the most is Bee-bim Bop, a dish with all kinds of veggies served over rice. We usually serve it like a salad bar, where people can put whatever items they want on their rice then mix it themselves. In addition to the veggies, both fungi (mushrooms) and algae (seaweed) are a traditional part of the dish, and help to form a flavor symbiosis of sorts.

Here's our recipe for Bee-bim Bop:

Ingredients (you can vary the quantities of each vegetable depending on your preference)
Rice (cook ~1/2 cup per person)
Shiitake mushrooms
Bean Sprouts (~1 cup)
Eggs (to be whipped, fried, and sliced; we use 3 eggs)
Carrots (to be cut into matchsticks and fried; 1 big carrot should do it)
Onion (to be chopped and fried)
Cucumber (to be cut into matchsticks)
Lettuce (1 small head or less)
Tofu (firm, cubed; ~ 1 cup)
green onion tops for garnish
Seasonings: salt, garlic, sesame oil, sesame seeds, sugar, soy sauce, and cayenne pepper

Now there is a lot of vegetable chopping to be done!

Directions:
1. Soak dried mushrooms at least 30 minutes
2. Wash and get rice cooking.
3. Prepare marinade sauce for mushrooms and tofu: 1t salt, 1/2t garlic, and 1t sesame oil (make as much as you need using those proportions). Put the tofu (raw) in a bowl with some of the sauce to marinate while you do the next few steps.
3. Wash the bean sprouts and put them in a pot with a little water (not quite covering them) and a pinch of salt. Cook them, covered, about 15 minutes on medium-high heat, then drain and place in a bowl.
4. Heat some sesame oil in a frying pan for the eggs. Mix the eggs and a dash of salt vigorously with a fork and then pour them into the hot pan. Let it spread out as much as possible. Flip it after a couple minutes, and when the "pancake" is cooked through, take it out of the frying pan and slice it into long, thin strips.
5. Cut the carrots and onions into thin pieces and fry them (with salt) in the hot oil until the carrots are tender.
6. Drain the re-hydrated mushrooms and squeeze excess water out of them. Mix them with some of the sauce from step 3 and fry.
7. Fry the tofu in hot oil with black pepper.
8. Drain the cooked bean sprouts and season them with a little bit of salt, garlic, sesame seeds, and sesame oil.
9. Cut the cucumber and lettuce into long thin strips.
10. Prepare Goo Choo Chang sauce: mix 1/2t cayenne pepper, 1/2t garlic, 1t sesame seeds, 1T soy sauce, 1T sugar, and 1T sesame oil. You'll want to put this in a little container for pouring at the dinner table.

When you have it all ready, you should have on the table a big bowl of rice and small bowls with the mushrooms, sprouts, egg strips, carrots & onions, tofu, cucumber, and lettuce.

To Serve:
Put cooked rice into individual serving bowls.
Put vegetables, eggs, tofu, and mushrooms on top of the rice.
Pour Go Choo Chang sauce over bowl.
Mix thoroughly, and add more sesame oil to the mixture depending on your preference.
Serve with Kim Chee and Laver seaweed (thin and crispy... not sushi nori).

The ingredients on display (with a small one who is quite excited about the algae)!

The final product, with algae around the edges and fungi in the mix with the rest.

All that's left at this point is to give your hands a thorough washing and dig in; we typically eat this by using the little sheets of laver as our utensils!

Enjoy!

-Brendan

Virginia Lichen Checklist

2010-08-28T22:37:00.000-07:00

Back in 2004 I began assembling the first checklist of Virginia lichen taxa. The first draft of this work consisted of a literature review plus an inventory of Virginia specimens held by the DUKE Cryptogamic Herbarium (DUKE) and various herbaria with publicly-accessible databases. However, I decided not to publish any of that work, instead favoring an approach that would produce a list of expert-verified taxa for the state. I did this because I was in a unique position to correct some of the taxonomic problems that have arisen over the years, and a literature review with an herbarium inventory would only perpetuate previous errors.

Beginning in 2006, I worked primarily with Dr. Richard C. Harris ('Dick') of the New York Botanical Garden to assemble the lichen checklist for the state, and ensured that Dick verified at least one specimen for each taxon in the list. This resulted in the first checklist of Virginia lichens, lichenicolous fungi, and allied taxa, published last year in Evansia (Hodkinson et al. 2009). However, taxonomy is ever-evolving, and new species are constantly being discovered. To address this issue, I have designed a website that can be updated at any time to reflect changes in our understanding of the Virginia lichen flora:
http://www.duke.edu/~bph8/VirginiaLichens/checklist.html

Virginia’s physiographic provinces

The most recent addition to the list, from just this week, is the lichenicolous fungus Skyttea radiatilis (Tuck.) R.Sant., Etayo & Diederich, identified by James Lendemer. The species was described just within the past decade; it seemingly grows only on a single sterile crustose lichen species, and is probably not rare, even though it is seldom collected and identified. In order to understand why it is so seldom seen, one must simply ask: 'How many people are collecting and carefully examining sick-looking sterile crustose lichens?' (Hint: not many). Additions like this have brought the total number of verified taxa for the state to just over 600, and additional collecting work that I have recently done in the outer Coastal Plain of Virginia has revealed many more (keep an eye out for this work, to be published sometime next year).

I welcome any comments or corrections to the Virginia Lichen Checklist. Let us not forget that, since so much remains to be discovered about the diversity of lichenized fungi, regional inventories like this one are still crucial for the advancement of the field!

-Brendan

References:

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)

Hodkinson, B. P., R. C. Harris, and M. A. Case. 2010. A Checklist of Virginia Lichens. http://www.duke.edu/~bph8/VirginiaLichens/checklist.html [updated: 25 August 2010].
View authors' updated checklist (website)

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

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)

Parmelia barrenoae

2010-08-16T21:47:00.000-07:00

Recently I published an article in the journal North American Fungi on the distribution and morphology of the foliose lichen Parmelia barrenoae (Hodkinson et al. 2010). One significant aspect of this paper is that it highlights the importance of good herbarium collections. Bill and Chicita Culberson traveled to Morocco in 1971, and to Calfornia in 1972; on both trips, they collected generally, and happened to pick up specimens of P. barrenoae without knowing it (since the species was not yet described). However, when I went into the DUKE herbarium to look for specimens, I found two continental records (for both Africa and North America) just sitting there!

The species was described from Spain a few years back (Divakar et al. 2005), but the emphasis of the originial paper was on the molecular phylogeny and the fact that this distinctive species was differentiated by having simple rhizines (as opposed to the squarrose rhizines seen in the closely-related Parmelia sulcata). An examination of the herbarium material from a broader geographic range allowed us to additionally highlight the fact that the species has distinct soralia that are erose, instead of the more erumpent soralia seen in Parmelia sulcata.

Figure 1. Parmelia barrenoae (A-E; all from Lendemer 19720) and comparison of rhizines with P. sulcata (F, from McGarrity s.n.). A, lobe morphology (scale = 2.0 mm). B, detail of lobe tip (scale = 0.5 mm). C, young soralium (scale = 0.5 mm). D, soralia (scale = 1.0 mm). E-F, comparison of rhizines in P. barrenoae (E) and P. sulcata (F) (scale = 0.2 and 0.5 mm respectively).

Several lichenologists (e.g., Trevor Goward and Ernie Brodo) had recognized this entity in western North America as a species not on the continental checklist (N.A. lichen checklist), but Ted Esslinger recognized it as P. barrenoae and James Lendemer generated the ITS rDNA sequence data confirming it. Additional ITS rDNA sequences from this species recently deposited in GenBank from Morocco and Turkey (previously deposited sequences were from Spain, and ours from California) give molecular barcode sequence data from throughout the species's known worldwide range. Now there is at least one ITS sequence (the more-or-less 'official' fungal barcode) from each of the continents from which the species has been reported, giving a good sampling of the sequence diversity found across its range.

For another nice set of photos of this species, check out these ones on MushroomObserver.com!

-Brendan

Works Cited:

Divakar, P. K., M. C. Molina, H. T. Lumbsch, and A. Crespo. 2005. Parmelia barrenoae, a new lichen species related to Parmelia sulcata (Parmeliaceae) based on molecular and morphological data. Lichenologist 37: 37-46.

Hodkinson, B. P., J. C. Lendemer, and T. L. Esslinger. 2010. Parmelia barrenoae, a macrolichen new to North America and Africa. North American Fungi 5(3): 1-5.
Download publication (PDF file)
View journal volume (website)
View sequence data (NCBI website)

After posting this, I was alerted to the following article in Spanish, which gives some additional discussion of morphology and ecology, with some nice micrographs:
Barreno, E., and M. A. Herrera-Campos. 2009. Parmelia barrenoae Divakar, MC. Molina & A. Crespo un liquen nuevo para la flora asturiana. Bol. Cien. Nat. R.I.D.E.A. 50: 333-341.
Download publication (PDF file)

New Lichen Web Resources

2010-07-21T22:20:00.000-07:00

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.]

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

2010-07-09T14:30:00.000-07:00

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

2010-07-05T19:34:00.000-07:00

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

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.

2010-06-17T21:14:00.000-07:00

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

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

2010-06-06T22:31:00.000-07:00

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.

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)