O'Grady Lab
  • Home
  • News and Events
  • People
    • Current Members
    • Undergraduate Research
    • Past Members
  • Research
  • Publications
  • Data
    • Mitochondrial Primers
    • Nuclear Primers
    • Accession Numbers
  • Photos
  • Courses
  • Educational Outreach
  • Links

On barcoding, bandwagons and the nature of scientific revolutions

10/12/2012

1 Comment

 
Several recent events have me reflecting on how science is done and how different schools of scientific thought turn over through time.  I'm teaching a grad class in phylogenetic methods for the first time since 2007 and I've noticed a big difference in the students.  In the past, their emphasis has been on understanding the nuts and bolts of how to generate phylogenies.  While the students this year are still interested in building trees, I'm getting the sense that they view tree building as a means to an end, rather than a valid activity in and of itself.  Student interest seems to have shifted more towards using trees to test evolutionary hypotheses.  While the sample size is small, this echoes what I've heard from colleagues about two courses taught in integrative biology, IB200A (phylogenetic reconstruction) and IB200B (phylogenetic hypothesis testing).  Enrollment in 200A is dropping relative to 200B.  

It's an interesting phenomenon and makes me think we may be in the midst of another paradigm shift (albeit a small one) in how systematics is done.  Looking back over the years, you can clearly see turnovers in schools of scientific inquiry.  Here's a short list:

Numerical Taxonomy
Starting in the early 1960s, numerical taxonomists brought a quantitative approach to taxonomy and systematics that previously been absent.  This was driven largely by statisticians (Sokal, Sneath) and the notion that careful measurements could lead to improved taxonomic hierarchies.  During the 1970s this field fractured into phenetics and cladistics.  Then the cladists ate all the pheneticists. 

Cladistics (and cladists)
While cladistics and cladists are tightly linked, not all people who practice cladistics are cladists and not all cladists always employ a strictly cladistic approach.  In essence, it's a semantic argument, something that all good cladists enjoy.  I define cladists as those followers of Willi Hennig who espouse a parsimony-only approach to systematics.  They aggressively routed the numerical taxonomists in the 70s and then stuck around to rail against likelihood, Bayesian analysis, and, in some cases, evolutionary inference itself.  For more detail on this era of systematics, check out the chapter in Joe Felsenstein's Inferring Phylogenies book.

Molecules vs. morphology
Starting in the mid-1980s, the introduction of PCR led to a technical revolution in systematics.  Suddenly, everyone was scrambling to sequence DNA in his or her favorite organism and use it to generate phylogenies.  Like most of the previous theoretical and technical advances in systematics, DNA promised to "fix everything."  This, of course, hasn't come to pass and, even now that we can sequence entire genomes, some systematic questions remain difficult to approach.  What did happen was a massive shift in resources, both in terms of grant funding and jobs offered, with the traditional morphologists being on the losing end of things.  This led to a lot of animosity - I can still remember being called a "moleculoid" by some of my older colleagues.  Luckily, this has largely blown over and most systematists take a holistic approach to understanding relationships in their focal taxa.

DNA barcoding
In some ways barcoding is a spin off of the molecules vs. morphology debate.  The notion here is that taxonomy isn't really needed now that we can use DNA sequence to uniquely identify (or barcode) species.  While DNA approaches are important techniques to have in your taxonomic toolkit, throwing out all by a single character system (the COI gene if you work on animals) in your taxonomy is ridiculous.  And many people have pointed this out before.  The initial DNA barcoding push was really more of a marketing campaign than a novel scientific approach and, once again, a more inclusive approach is being taken.   

Statistical phylogenetics
The idea that phylogenies are statistical statements about evolutionary history and can not only be viewed as hypotheses but also used to test hypotheses is the predominant paradigm in modern systematics.  More advanced analytical techniques, increased processor speed, and the introduction of model-based approaches have all helped shaped modern phylogeneic systematics.  Powerful statistical methods are currently causing an expansion of systematics and driving the "use of trees" over the "building of trees."  I think this is a normal, natural outgrowth of the field and will hopefully continue to drive it forward. 

My own work is moving away from tree building and more into the area of community assembly and interaction so I've been reading a lot about phylogenetic community ecology (PCE from here on out - too much to write) as a way to merge the fields.  I ran across this interesting blog post a few days back where the author, Jeremy Fox, makes the case that PCE is a "bandwagon." He makes bring up some good points (although he uses a pseudo-subjective literature review to do so) and the post is worth a read.

This all leaves me wondering, however, if there's really anything wrong with any one field or subfield jumping on a bandwagon.  This is, at least if you take an historical perspective, how science moves forward.  For example, organismal biology jumped hard on the DNA bandwagon in the late 1980s/early 1990s, eliminating entire -ologies in the rush to capitalize on the new technology.  Within 10 years, however, people began to realize that you couldn't place those DNA-based phylogenies in context without some knowledge of basic biology so the field corrected itself, including the new theories and technologies.  I imagine this is what will happen as a result of the current push for hypothesis testing in phylogenetics.


Patrick O'Grady
1 Comment

Biodiversity of Hawaiian Fungi: A Brief History

9/14/2012

1 Comment

 
Picture
Yeasts and other fungi are important components of decomposer commnunities and may have large impacts on rates of diversification in saprophagous insect taxa. Two Drosophila systems have been investigated in detail; morning glories in the Hawaiian Islands and the  cacti in the southwesten United States.  These two systems are the best understood examples of symbiotic relationships among flies, their host plants and the microbes that make the plant tissue suitable for larval development.  

Herman Phaff began surveying Hawaiian yeasts in collaboration with William B. Heed (Speith 1981).  Heed had worked on the ecological associations of Hawaiian Drosophilidae, focusing mainly on rearing flies from various host plants (Heed 1968; 1971).  He was interested in delving into more detail on this system as part of his sabbatical at UC Davis.  During this time he also worked with Phaff on the cactophilic Drosophila in the southwesten United States. The Phaff Collection at Davis still consists of many of the yeasts discovered as part of this research.

Lachance, Starmer and their colleagues (Lachance et al. 1990; 2001; 2003; 2005) picked up where Phaff and Heed left off, describing many yeast species present in Hawaii, as well as their specific interactions with plants and insects.  They studied the relatively simple flower-yeast-insect systems using culture dependent approaches.  Recently, several studies (Ort, et al. 2012; Zimmerman and Vitousek 2012) have expanded our knowledge of Hawaiian fungal and yeast systems, using culture-independent, DNA sequence-based approaches to examine communities in several native plant genera (e.g., Metrosideros, Clermontia, Pisonia, Acacia, Cheirodendron).

Research on Hawaiian fungi are still in the descriptive stage but once these systems are better understood, a wealth hypotheses addressing biogeography, coevolution and adaptive radiation, and community assembly can be tested.  

Patrick O'Grady

1 Comment

Scaptomyza Collecting - Marin and Sonoma

6/27/2012

0 Comments

 
Rick Lapoint is back in town this week collecting Scaptomyza for his postdoctoral research.  We went out to several locations in Marin and Sonoma counties looking for the elusive members of this genus.  We got several species, updates to follow, and almost died only once.  We'll have to wait and see how many complaints Rick gets about his driving....
Picture
Picture
Picture
0 Comments

Eel River Trip

6/22/2012

0 Comments

 
Picture
Collecting in the South Fork of the Eel River
Mike, Brian and I traveled to Angelo Coast Reserve on the 19th to do some collecting.  Our goals were to collect some aquatic insects in the Eel River and look for Scaptomyza species in the surrounding riparian zones.  We didn't see any Scaptomyza but we got a great sample of aquatics, including lots of Dicosmoecus, Neophylax and Calineuria.  

Picture
Merganzer Pool, South Fork, Eel River
Picture
Mike Peterson
0 Comments

Yeast Paper Accepted

6/8/2012

6 Comments

 
Picture
Figure 1
Our paper on "Fungal diversity associated with Hawaiian Drosophila host plants" has been accepted in PLoS ONE.  Congratulations to Brian Ort for leading this effort, along with two undergraduate researchers in the lab, Norma Pantoja and Roxanne Bantay!

6 Comments

Field Work - Russian River Watershed

6/8/2012

2 Comments

 
Picture
Brian collecting in Dutch Bill Creek
This week we made two short field trips to collect aquatic insects.  On Tuesday we worked northwest of Sebastapol. Brian and I visited several sites we had collected last fall. Our first stop was Pyrrington Creek on Graton Road, followed by Dutch Bill Creek along the Occidental Highway.  We stopped for lunch at Stumptown Brewpub in Guerneville.  After lunch we drove north of the Russian River to Austin Creek near the town of Cazadero. Our last stop of the day was Salmon Creek, northwest of the town of Bodega.  

Thursday we did a half day trip to two streams in Marin County, Lagunitas Creek and Pine Gulch Creek in Bolinas.  Thanks to Sarah Hake for allowing us access to Pine Gulch Creek!  We collected Neophylax here, as well as three species of Scaptomyza!!

Picture
Lagunitas Creek
Picture
Lagunitas Creek
Picture
Bolinas Lagoon
Picture
Lunch at Stumptown Brew Pub
Picture
Neophylax rickeri
Picture
Pine Gulch Creek flowing through the Hake Farm
2 Comments

Field Work

5/22/2012

0 Comments

 
Picture
Collecting aquatic insects in Yolo, Napa and Lake counties. 

Picture
Picture
Picture
0 Comments

New Publication!!

5/21/2012

0 Comments

 
Picture
We have a critical review of Michael Heads' new book on Molecular Panbiogeography of the Tropics in the June issue of Taxon.  My favorite part is the quote that leads off the review:

“Or they asserted that all those landlubbery creatures had walked dry-shod across a natural bridge, or had swum short distances between stepping stones, and that one such formation or another had since disappeared beneath the waves.  But scientists using their big brains and cunning instruments had by 1986 made maps of the ocean floor.  There wasn’t a trace, they said, of an intervening land mass of any kind.”

                                                                               Kurt Vonnegut, Galápagos (1985)



0 Comments

Graduation

5/21/2012

0 Comments

 
Picture
Gordon, Crystal and Patrick
Congratulations to all the lab members who are graduating this year.  Gordon received his PhD and will be moving on to a postdoctoral position in Nancy Moran's Lab at Yale.  Crystal got her Bachelor's degree in Molecular Toxicology and is applying to Pharmacy School.  Best of luck to you both in the future! 
Picture
Dr. Gordon Bennett
Picture
Isn't he so cute?
Picture
You know dad, you're not the only one who gets to play dress up...
0 Comments

Jiji Foundation Grant Funded

1/25/2012

1 Comment

 
The lab was just awarded a $3500 grant to do barcoding of aquatic insects in Northern California. Congrats to Brian for all his hard work on this project.
1 Comment
<<Previous
Forward>>

    Patrick

    Professor
    Cornell University

    Archives

    April 2018
    March 2018
    August 2017
    March 2017
    January 2017
    September 2015
    May 2015
    March 2015
    January 2015
    October 2014
    April 2014
    March 2014
    February 2014
    September 2013
    May 2013
    April 2013
    February 2013
    January 2013
    November 2012
    October 2012
    September 2012
    August 2012
    July 2012
    June 2012
    May 2012
    January 2012
    November 2011
    October 2011
    May 2011
    February 2011

    Categories

    All
    1090
    1091
    Alumni
    Aquatic Insects
    Arizona
    Asteia
    Barcoding
    Bennett
    Blog
    Career
    Celebrations
    Chelsea
    Climate Change
    Cornell
    Craft
    Dicranota
    Dolichopodidae
    Drosophila
    Ephydra
    Ephydridae
    Field Work
    Funding
    Goodman
    Hawaiian Drosophila
    Keys
    Kidwell
    Lapoint
    Limonia
    Magnacca
    Marrack
    Montana
    Nesophrosyne
    New Species
    Ogrady
    Ort
    Paceyn
    Pak
    Panbiogeography
    Pediciidae
    Peterson
    Phylogenetic Methods
    Publications
    Readings
    Rhaphidolabis
    Scaptomyza
    Scatella
    Schedule
    Stauffer
    Sylvain
    Talks
    Taxonomy
    Tipula
    Undergraduates
    Unicorns
    Whiteman Lab
    Wojciechowski
    Wolbachia
    Wyoming
    Yeast And Fungi

    RSS Feed

Powered by Create your own unique website with customizable templates.