Genomic Signatures Suggest Convergent Evolution
LeBlanc (CompSci), Dyer (Bio), Kahn (Stats)
Professors Betsey Dyer, Mike Kahn, and Mark LeBlanc recently published Classification and regression tree (CART) analyses of genomic signatures reveal sets of tetramers that discriminate temperature optima of archaea and bacteria. Archaea 2:159-167.
What was the gist of this publication?
We used a technique of 'genomic signature' to differentiate the genomes of organisms who love hot environments from the genomes of organisms who thrive in other temperatures. 
Finding genomic signatures across entire genomes is similar to identifying types of patterns used by a particular author in authorship attribution studies, e.g., did John Donne really write this poem? Although genomic signatures have been used typically to classify divergences between genomes (think evolutionary tree), in this case convergent evolution of genomes was the focus. Because we had good success using genomic signature to differentiate hyperthermophiles (think Yellowstone mats of bacteria) from thermophiles from mesophiles (think E.coli in your gut), our work suggests that pervasive (non-linear) qualities of genomes may reflect certain environmental conditions (such as temperature) in which those genomes evolved.
What was part of the motivation for your latest study?
From the beginning of the Wheaton Genomics Group (1998), we have been influenced by and made great use of language as a metaphor for thinking about and explaining work in genomics. It was, of course, Erwin Chargaff who first noticed the ratios of nucleotides in DNA and reported the similar frequencies of adenine and thymine and of cytosine and guanine in his influential 1949 paper.
"I knew that a great deal can be learned about an unknown language through a study of its phonemes, their frequency, distribution density, and allophonic relationships." (pg. 130)
What are some of the challenges of temperature classifications for microorganisms?
The division of microorganisms into four categories based on optimal growth temperatures, psychrophile (cold), mesophile, thermophile, and hyperthermophile (very hot), owes much to the fact that mesophiles are so well studied, especially symbionts or pathogens of mesophilic humans, thriving at the body temperatures of humans. Furthermore, the range of temperatures on the classification scale has been modified over the years as organisms at extreme temperatures have not only been discovered but also found to be common, at least in certain habitats. The present system of temperature classification is by no means settled and has some hallmarks of having been decided by a committee. New input includes discoveries of microbes at extreme temperatures and attempts to even out the temperature intervals. Meanwhile, the previous temperature classification system (still the template for the new one) is strongly biased toward mesophilic pathogens.
You have a decade-long history of interdisciplinary teaching and research. Describe how your use of a lingustic metaphor influences your work?
The statistical method we used in this study to differentiate genomes based on the relative frequencies of their 'words' is an indexing tool. As noted by many professional indexers (or cataloguers) of books, an index (or catalogue) is limited only by the interests, assumptions, and imagination of the indexer. An index, whether of a book or a genome, is the creative product bearing the imprint of the indexer. On the topic of the London Library catalogue system, A.S. Byatt (2001) wrote:
"It represents order-it is helpful, it leads you to what you were trying to find, and also to what you needed, but did not know you needed to find. It also has the delightfully mad quality of heterogeneous things linked violently together by the arbitrary order of the alphabet."
What books have you been reading lately
We are big fans of Bernd Heinrich's works. We are currently passing around the Wheaton Library's new copy of Heinrich's
The Snoring Bird: My Family's Journey Through a Century of Biology (Ecco Publishing, 2007).
From air battles in World War I to a frantic flight during World War II to resettlement in rural Maine, Heinrich shares the true story of his Papa Gerd's relentless and systematic pursuit of wasps in the family Ichneumonidae. With uncanny honesty, Heinrich shares the influences and results of growing up within a family where science is king.
Dr. Betsey Dyer's Personal Profile.
Biology.
Dr. Michael J. Kahn's Personal Profile.
Mathematics.
Dr. Mark D. LeBlanc's Personal Profile.
Computer Science.