Basic Profile

Name: Paula Mabee

Education: Ph.D. Duke University, 1987 (Zoology)

Home Institution:
The University of South Dakota

NSF Experience/History:

I have been the Division Director of the Division of Environmental Biology in the NSF’s Directorate for Biological Sciences (BIO) since August of 2015, but my history with NSF goes way back. I’ve served on 16 panels and participated in multiple site visits across BIO since 1996, and I have served as an ad hoc reviewer since 1990. I have also been a fortunate NSF awardee. I received my first NSF award – a postdoctoral research fellowship – in 1989, during which I trained in experimental methods in developmental morphology.  This led to my first award as a faculty member at San Diego State University in 1994 for a comparative experimental study of cranial development in teleost fishes.  Following this, I diverged a bit to pursue the development of mobile platform-based field guides with SBIR and STTR funding, leading to the National Geographic Birds birding guide app.  In 2004, NSF supported a collaborative Assembling the Tree of Life (AToL) project for cypriniform fishes (carps, minnows, loaches), for which I was one of the PIs.  Support from the NSF-funded National Evolutionary Synthesis Center for a synthesis working group with the Zebrafish Model Organism Database folks (ZFIN) led to a NSF DBI award in 2007 and another in 2011. These awards supported development of bioinformatics methods to compute across the full range of very diverse anatomical traits and link those traits to candidate developmental genes.  A RCN award in 2010 broadened this type of community-driven data integration by establishing an international Phenotype Research Coordination Network with over 400 participants.

Research Experience/History:

My Ph.D. work and subsequent research focuses on questions at the intersection of evolutionary and developmental biology such as: What is the relationship between developmental and evolutionary change?  What is the genetic basis for anatomical structures that are evolutionarily new? I’ve explored these questions using a variety of experimental and computational approaches, beginning with comparative morphology and phylogenetic systematics, continuing with developmental genetics, and currently bioinformatics. My research contributions include 52 peer-reviewed journal publications, many with student co-authors, and spanning the fields of evolution, phylogenetics, ichthyology, anatomy, bioinformatics, developmental biology, and cross-cutting journals.

Since 2006 my research has been highly collaborative and focused on developing a new bioinformatics approach for connecting the diverse phenotypes of species to the genetic and developmental data from model organisms such as zebrafish and other vertebrates.  Our research team has established methods to connect, search, and compare data from the zebrafish community database (ZFIN) and other vertebrate databases (e.g., Xenbase and MGI).  This has been challenging from the biodiversity phenotype perspective, because in contrast to genomics, where resources are well-developed for computation, it is difficult to render diverse morphological and behavioral features computable.  For example, representing ‘segmented fin rays’ of fishes such that a computer can reason that they are part of fins, composed of bone, and develop from mesoderm, requires a basic logical dictionary of terms called an ontology.  Ontologies appropriate to represent multiple species or phenotypic diversity had not previously been built when we began this research, so we developed these methods and, at the same time, built resources to promote discovery of new knowledge.

The outcome is a resource that combines new software, a database infrastructure, and an interface to serve evolutionary biologists and geneticists.  The connection of genetic, medical, and evolutionary data in one resource –the Phenoscape Knowledgebase (KB)– enables over 500,000 testable hypotheses regarding which specific genes might underlie specific traits in vertebrates and how those traits have changed over time.  For example, modern catfishes do not have tongues and data in the KB implicated a role for the brpf1 gene in evolutionary changes in this trait, a prediction that would have been difficult to formulate without computational methods. Data from our recent wet-lab work validated this prediction [i].

More recently we have used this machine logic to ‘expand’ the trait data available for phylogenetic and evolutionary research [ii].  This is an application of these data that had not been envisioned when we initially planned this research.

What gets me excited about this research is the prospect, some day, of being able to join different data types across environment, ecology, phylogenetics, traits, and genetics to make discoveries that are very difficult at present.

Q&A

Why did you want to work for DEB?

I think that DEB broadly encompasses my scientific home. In the past, I pitched some unconventional ideas and always found they were appreciated in DEB panels. From the outside, the Division seemed to be welcoming to creative research, and now as a NSF insider, I can see that it is.

Of particular interest to me are questions that both enable and require the integration of different kinds of data.  DEB is faced with increasing numbers of projects that require data integration. This is true in both core programs and DEB’s special programs such as Dimensions of Biodiversity and the Long Term Ecological Research program. These projects require that we be able to integrate data across scales. To do this, I think that looking across traditional knowledge domains is critical.

I feel that biologists are at a particularly interesting juncture in comparative work. Although tools are available to aggregate and analyze some data such as genetic sequences, they are only just emerging to integrate other very central pieces such as phenotypes, phylogenies, and environmental variables. An important challenge is to scale up this integrative approach across all extinct and extant biodiversity, enabling visualization of linked data in time and space, and integrating environmental data to produce a fully informed and machine-enabled comparative biology of the future.

Biggest surprise you’ve encountered coming to DEB from the academic world?

Being here has made me realize the extent to which we are living through the Wild West of data. I noticed this first in the Dimensions of Biodiversity program where PIs have been undertaking a lot of one-off processes, without the ease or benefit of standards or best practices. This raises questions about how to use funding to organize the community for greatest efficiency in these early times. DEB funded research has included incredibly heterogeneous data types, so finding effective strategies for integrating data is very challenging.

This leads me to another surprise, which is the level of introspection among DEB Program Officers and staff.  I had no idea the extent to which Program Officers reflected on whether the existing slate of funding mechanisms sufficed to cover the spectrum of science proposed by the PI community.  No one wants a proposal to fall through a gap.  What was not surprising is that DEB Program Officers have a great deal of respect for the PI community.

What would someone find you doing in your down time?

In short, eating and going to art galleries.  Because I’m living in the DC area now, I’m taking full advantage of all it has to offer. It seems there is no end to the variety and deliciousness of area cuisine. I’ve also been enjoying docent tours at the National Gallery of Art and the show currently at the Renwick Gallery.

Simultaneously, I’m reconnecting with colleagues and many old friends. Because of my interdisciplinary, roaming life, I have been a part of several communities that have had little to no interaction, such as evolutionary biology and genetics. When I got involved with data interoperability for example, I didn’t know anyone in that community. Because there are so many meetings and government agencies in DC, people from all of these disciplines come together here.  It is great fun to have the opportunity to be reacquainted with old friends and meet so many new interesting people.

Personally I love to travel, and I love anything having to do with water, from swimming to scuba diving, sailing, and fly-fishing.  Aquatic pursuits are a big part of my life in South Dakota.  I am also enjoying time with my two college-age sons when they visit D.C.

Where should someone go to eat when they visit NSF?

Wow – this the hardest question of all because there are so many awesome places.  I especially love the Spanish and Middle Eastern restaurants.

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[i] Edmunds, R.C., Su, B., Balhoff, J.P., Dahdul, W.M., Lapp, H., Lundberg, J.G., Vision, T.J., Dunham, R.A., Mabee, P.M., Westerfield, M. 2016. Phenoscape: Identifying candidate genes for species-specific phenotypes. Molecular Biology and Evolution 33 (1): 13-24. doi:10.1093/molbev/msv223

[ii] Dececchi, T.A., Mabee, P.M., Blackburn, D. 2016. Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices. PLOS One 11(5): e0155680. doi:10.1371/journal.pone.0155680