My post-iEvoBio Meeting emotional outburst

I have just come back from the iEvoBio Meeting in Norman, Oklahoma. This is the first time ever I didn't quite mind to be stuck in a place in the middle of nowhere (seriously!) because my fellow prisoners were actually pretty entertaining.  This is what I love about iEvoBio. It does NOT bore you and it keeps you awake despite the heavy drinking session of the previous night; and for someone like me, with ADD, the constant flow of information, often delivered in 5 minutes slots, is just perfect (it's like watching great superbowl-style commercials!). The meeting format offered a little bit for every taste, from more focused presentations to fairly short discussion sessions. What do we get from short discussion sessions? Well, how about a set of quickly vomited ideas, needs, wish-lists, from a variety of people with often different backgrounds, seeds to bring home and plant to see whether anything germinates, either in your lab or someone else's. This is what's fun in science! I just love to be there and watch what will happen next, e.g. next year at iEvoBio.  We really need iEvoBio to remind us every year of the status quo in evolutionary informatics, what's cooking, what are the missing ingredients, the limitation and potential of the tools we build, and the beauty is we don't really need a week to catch-up.  Two intense days (and nights :-) are actually great!  Last year in Portland, OR, the meeting was fantastic, but this year I enjoyed it no less! For a great list of projects and new tools presented see Recology blogpost. Just a few of my favorites include Map of Life, TreeBASE with an R interface, Phenoscape, Ontogrator, and BirdVis. Of course, we presented our BiSciCol prototype and our slides are up in slideshare now. We didn't win the challenge though, despite me trying to cheat the system by voting from different browsers (I couldn't help it, it was more of an experiment, really ;-) but BiSciCol is still in its infancy stage and we will present a more mature product at the next TDWG meeting in New Orleans, so stay tuned!
Can't wait for next iEvoBio meeting in Ottawa! In the meanwhile I am charged-up and super ready to go back to work!

Talking about names....

A new Angiosperm phylogeny paper is finally out!  It clarifies relationships at some of the deeper messier nodes and reinforces our previous knowledge of some others.  The point I want to make here is that the authors use phylogenetic nomenclature to name major clades.  They state:

"For higher clades, we consistently use PhyloCode names (see Cantino et al., 2007 ) whenever these are available; these names are always in italics (e.g., Pentapetalae, Mesangiopsermae, Rosidae, Fabidae, Malvidae). Note that Rosidae (sensu Cantino et al., 2007 ) does include Vitaceae. Our use of family and ordinal names follows APG III (2009) as a formal point of reference; for Caryophyllales, we follow Cantino et al. (2007; hence, the use of italics), which matches the APG III circumscription. For additional recent discussion on families and their status, see the Angiosperm Phylogeny Website (Stevens, 2001 onward). We recognize that some broader family circumscriptions favored in APG III are controversial and can obscure underlying diversity (e.g., Passifloraceae s.l.), which would be evident with narrower circumscriptions."

I hear left and right how the PhyloCode is going to bring a mess in the field of Biology by changing all names and reshaping the Classification (impossible, as it is just a nomenclatural tool). Well, here it is, another shocking paper that imposes so many new names to the community. The way I see it, we now have some pretty well refined concepts attached to names, the same names that have been previously used idiosyncratically. Names that won't change even if the clade content does change. Names that will always refer to the same ancestors. Names that we could actually query and be happy with what we retrieve. That would be indeed a breath of fresh air.

BSA/ASPT 2011 Meeting

Our lab submitted 3 abstracts to the upcoming Botany 2011 Meeting:


Evolution and biogeography of endemic taxa within the Roucela aggregate (Campanulaceae: Campanuloideae) in the Eastern Mediterranean region.

The phylogenetic utility of low-copy nuclear genes in Campanuloideae (Campanulaceae) with special focus on the evolution of NW Alpine Campanula endemics.

How floristic data can inform historical biogeography: an example from the Caucasian monocot, gymnosperm and pteridophyte flora.

PPR gene family

While generating more GapC and NIA sequences, we have now successfully amplified three PPR alleles and from preliminary runs they seem to be very informative too at species level in Campanulaceae. To make everything even more appealing, cloning is indeed not necessary.  Quick and cheaper results. What's not to love about the nuclear genome! So far, so still excellent!

Low-copy genes

How can something low makes you feel so high?!  Our first test run with low-copy gene sequences gave excellent (better than expected!) results.  A well resolved topology with great support!  Can't wait to show some results.  We are now working on a paper that focuses on alpine taxa and we will show the first Campanuloideae tree generated with low-copy nuclear genes.

Oxford Journals, please take my money!!

How hard can it be to renew a Journal subscription? Well, looks like Oxford Journal is gifting me with a pain in the rear.  I have tried to give them my money since end of 2010.  The renewal site turns down all my credit cards.  Obviously, I had to call in. I spoke to a lady, gave her my membership number and credit card details and hung up happy.  She also confirmed that their on-line system is not performing very well.   Guess what?  That didn't work either.  More than a month later I receive a notice of renewal by mail.  I tried to call the North Carolina office multiple times with no luck, so I am now filling a form by hand.  I have spent enough time on this! Please, take my money!!

Herbaria are a major frontier for species discovery

A very nice article published in PNAS enhancing the role of herbaria (and other museum collections, really!) in biodiversity research. Of all the new species I have described, only one I found in the field.  Discoveries are really made around the corner...in many cases.  The statistics presented is really interesting! Great read!  See paper here