Ecology

Ecology

Study Areas

Macroecology, species diversity, biogeography, species distribution or niche modeling, ecoinformatics, global change, community and population ecology, endangered species, and geographic information systems.

Background

I am also a PhD candidate in natural resources and ecology at the University of Arizona, where I conduct research that broadly centers on the topics of biogeography, biodiversity, and macroecology, through my studies of species diversity patterns, determinants of geographic range boundaries, and species distribution modeling. I am particularly interested in how the geographic distributions of species are influenced by climate and climate change. While some of my work is continental in scale across diverse organisms, a significant component is also targeted at understanding the limits of the distribution of Sonoran desert and Mojave Desert plant species.

As part of my research, I helped support the Botanical Inventory and Ecology Network (BIEN) project (an NCEAS funded working group) through previous roles managing the geographic coordinate validation effort as a Research Intern in Bioinformatics and Geospatial Analysis for an iPlant Seed Project on Botanical Geospatial Diversity Cyberinfrastructure [pdf], and a later role in managing the BIEN species distribution modeling efforts.

NCEAS Working Groups

I worked as part of the Botanical Information and Ecology Network (BIEN), funded by the National Center for Ecological Analysis and Synthesis (NCEAS). The BIEN project aims to combine existing sets of vegetation data for the New World into a database of several million species occurrence records (actually 25+ million and growing). The database forms the largest assembly of data on plant diversity and distribution for both tropical and temperate plant species, and it allows us to address very large-scale questions about how climate and climate change influence species range sizes, abundance and extinction risk.

I also participated in an NCEAS funded project, named Climate and Organisms, that seeks to understand how the environment controls species distributions by assembling a state-of-the-art set of environmental layers that incorporate well-known but rarely used measures having direct links to physiological processes like frost, water stress, growing season, soil properties, drainage properties, etc. The group is assembling these variables into a unified, global, gridded, high resolution GIS data set that will be made available to the public. Finally the group is using this data to explore what factors are actually the most important and most predictive in determining where a species lives and examining questions about the nature of links between the environment and the distribution of organisms.

>>  View my Academic Tree

>>  View my Research Gate Portfolio

Research

One of the main goals of my current research program is examining how aspects of climate influence the geographic distributions of species across scales, so that we may begin to understand how those distributions may be affected by climate change. With this in mind, I am currently focusing on several lines of research that include:

  • Assessing the best to define a species’ geographic range size: there are several methods used in scientific literature without consensus as to which methods are better than others.
  • Examining the relationship between climate variability and geographic range size.
  • Testing the climate envelope assumption that the geographic ranges of many species may shift higher in latitude and elevation as a generic response to a warming climate.
  • Investigating whether climate may regulate landscape-level processes, such as maximal woody cover in North American savanna systems.

Education

  • PhD Candidate, Natural Resources, Ecology & Evolutionary Biology, University of Arizona
  • Masters of Business Administration (GIS Emphasis), University of Redlands
  • Certificate in GIS, with Honors, University of California Riverside Extension
  • B.A., withHonors, Geography, California State University, San Bernardino
  • B.A., with Honors, Environmental Studies, California State University, San Bernardino
  • A.A., with Honors, Anthropology, San Bernardino Valley College

Publications

Book Chapters

  • Rosenzweig, M.L., J.C. Donoghue II, M.L., Yue, C. Yuan. Estimating Species Diversity. 2010. Pages 276-288 in McGill, B.J., Magurran, A.E., editors Biological Diversity Frontiers in Measurement and Assessment. Oxford University Press, New York New York, USA.

Abstracts

Donoghue II, J.C., N. Morueta-Holme, B. Boyle, L.L. Sloat, B.J. Enquist, B.J. McGill, J.C. Svenning, R. Condit. 2012. Quantifying the fundamental unit of biogeography: Assessing different methods to measure geographic range size and why it matters. 97th Annual Meeting of the Ecological Society of America. Portland, OR.

Articles

Benjamin Blonder, David Nogué S-Bravo, Michael K Borregaard, John C Donoghue II, Peter M Jørgensen, Nathan J B Kraft, Jean-Philippe Lessard, Naia Morueta-Holme, Brody Sandel, Jens-Christian Svenning, Cyrille Violle, Carsten Rahbek, Brian J Enquist, Linking environmental filtering and disequilibrium to biogeography with a community climate framework (2015), Ecology 96(4):972-985. doi: 10.1890/14-0589.1

Irena Šímová, Cyrille Violle, Nathan J. B. Kraft, David Storch, Jens‐Christian Svenning, Brad Boyle, John C. Donoghue, Peter Jørgensen, Brian J. McGill, Naia Morueta‐Holme, William H. Piel, Robert K. Peet, Jim Regetz, Mark Schildhauer, Nick Spencer, Barbara Thiers, Susan Wiser, Brian J. Enquist, Shifts in trait means and variances in North American tree assemblages: species richness patterns are loosely related to the functional space (2015). Ecography 11/2014; doi:10.1111/ecog.00867

Christine Lamanna, Benjamin Blonder, Cyrille Violle, Nathan J B Kraft, Brody Sandel, Irena Símová, John C Donoghue II, Jens-Christian Svenning, Brian J Mcgill, Brad Boyle, […], Aaron Marcuse-Kubitza, Naia Morueta-Holme, Robert K Peet, William H Piel, James Regetz, Mark Schildhauer, Nick Spencer, Barbara Thiers, Susan K Wiser, Brian J Enquist. Functional trait space and the latitudinal diversity gradient (2014). Proceedings of the National Academy of Sciences 09/2014; 111(38):13745-13750. doi:10.1073/pnas.1317722111

Morueta-Holme, N., Enquist, B. J., McGill, B. J., Boyle, B., Jørgensen, P. M., Ott, J. E., Peet, R. K., Šímová, I., Sloat, L. L., Thiers, B., Violle, C., Wiser, S. K., Dolins, S., Donoghue, J. C., Kraft, N. J. B., Regetz, J., Schildhauer, M., Spencer, N., Svenning, J.-C. (2013), Habitat area and climate stability determine geographical variation in plant species range sizes. Ecology Letters. doi: 10.1111/ele.12184

Michael Rosenzweig, Vanessa Buzzard, John Donoghue II, Gavin Lehr, Natasha Mazumdar, Haley M Rasmussen, Irena Simova, Scott Trageser, Heather Wernett, Jingzi Xu. Patterns in the Diversity of the World’s Land Vertebrate Genera (2013). Evolutionary ecology research 11/2013

Donoghue II, J.C 2001. Improving Code Enforcement Using GIS. ArcUser Magazine. 4:18-21.

PRESENTATIONS

Enquist, B.J., B. Boyle, J.C. Donoghue II, B. Thiers, P. Jorgensen, B.J. McGill, J.C. Svenning, R. Condit, N. Morueta-Holme, L.L. Sloat, R. Peet, and The BIEN Working Group. The commonness and distribution of rarity: Quantifying the botanical diversity of all plant species in the Americas. International Biodiversity Society Sixth Biennial Conference. Miami, FL.

Enquist, B.J., B. Boyle, J.C. Donoghue II, B. Thiers, P. Jorgensen, B.J. McGill, J.C. Svenning, R. Condit, N. Morueta-Holme, L.L. Sloat, BIEN Working Group. 2012. The commonness and distribution of rarity: Quantifying the botanical diversity of all plant species in the Americas. 97th Annual Meeting of the Ecological Society of America. Portland, OR.

Donoghue II, J.C. 2011. Does the climatic variability hypothesis explain the longitudinal range size gradient in North American trees? University of Arizona GradBlitz, Tucson, AZ.

Donoghue II, J.C., 2011. Using GIS to Automate Distribution Models for New World Trees. ESRI User Conference, San Diego, CA.

Donoghue II, J.C. 2007. Improving Public Information Websites through Interactive Website Technologies.  American Association of Airport Executives Noise Mitigation Symposium, San Diego, CA.

Donoghue II, J.C. 2006. Implementing an As-built Drawing Database and Search Engine Using GIS. Southwest GIS User Group Conference, Flagstaff, AZ.

POSTERS

Donoghue II, J.C., N. Moreta-Home, B. Boyle, L.L. Sloat, B.J. Enquist, B.J. McGill, J.C. Svenning, and The BIEN Working Group. Quantifying the fundamental unit of biogeography: Assessing different methods to measure geographic range size and why it matters. International Biodiversity Society Sixth Biennial Conference. Miami, FL.

Assembly of plant communities in climate space, Benjamin Blonder, D. Nogués-Bravo, C. Rahbek, B.J. Enquist, B. Boyle, J. Donoghue, R. Condit, R.K. Peet, S. Dolins, M. Schildhauer, B. McGill, P. Jorgenson, M. Narro, J. Regetz, C. Violle, L. Sloat, B. Piel, N. Kraft, J.C. Svenning, B. Theirs, I. Simova, N. Morueta-Holme, N. Spensor, S. Wiser, J. Ott, B. Dobrin, S. Andelman, and K. Engemann Jensen. International Biodiversity Society Sixth Biennial Conference. Miami, FL.

Simova, I., C. Violle, N.J.B. Kraft , D. Storch, B. Boyle, J.C. Donoghue II, B.J. Enquist. 2012. Scale-dependent trait filtering of woody diversity in North America. 97th Annual Meeting of the Ecological Society of America. Portland, OR.

Donoghue II, J.C. 2011. Does the climatic variability hypothesis explain the longitudinal range size gradient in North American trees? 96th Annual Meeting of the Ecological Society of America, Austin, TX.

Donoghue II, J.C. 2011. The longitudinal range size gradient in North American trees. ESRI User Conference, San Diego, CA.

Training

  • Certified Geographic Information Systems Professional (GISP)
  • 38 hour course in Army Corps of Engineers Wetland Delineation Training
  • Introduction to Desert Tortoise Surveying, Monitoring and Handling Workshop 

Links

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