Monday, May 23, 2011

Graduation/Dissertation

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

Monday, May 16, 2011

Investing in Science

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)
"

Friday, May 13, 2011

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

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)

Tuesday, May 10, 2011

PICS-Ord Tricks

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:

L├╝cking, 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)

Sunday, May 8, 2011

Semi-Cryptic Species

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://dukemagazine.duke.edu/article/symbiotic-association
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"!