Research and CV

Study Areas

Biogeography, macroecology, species diversity, species distribution/niche modeling, suitability modeling, ecoinformatics, global change, population ecology, endangered species, and GIS.

Academic Background

I have a Master of Science degree in natural resources at the University of Arizona, where I conducted research that broadly centers on the topics of biogeography, biodiversity, and macroecology, through 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

BIEN Raw Diversity Sample

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.

Research

One of the main goals of my 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 focus on several lines of research that include:

  • Assessing various definitions of a species’ geographic range size: there are several methods used in scientific literature without consensus as to which methods are better than others. How accurate are various computational methods when compared to expert range estimates?
  • Examining the relationship between climate variability and geographic range size. The common perception is that plants with large geographic ranges occupy a broader climatic regime than plants with smaller geographic ranges. Is this true?
  • 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

  • M.S., Natural Resources, University of Arizona
  • M.B.A (GIS Emphasis), University of Redlands
  • Certificate in GIS, with Honors, University of California Riverside Extension
  • B.A., with Honors, 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.

Thesis

Donoghue, John. (2016). Geographic Range Size: Measuring The Fundamental Unit Of Biogeography and Evaluating Climatic Factors That May Influence Longitudinal Range Size Gradients In North American Trees.

Articles

Enquist, Brian & Feng, Xiao & Boyle, Brad & Maitner, Brian & Newman, Erica & Jørgensen, Peter & Roehrdanz, Patrick & Thiers, Barbara & Burger, Joseph & Corlett, R. & Couvreur, Thomas & Dauby, Gilles & Donoghue, John & Foden, Wendy & Lovett, Jon & Marquet, Pablo & Merow, Cory & Midgley, Guy & Morueta-Holme, Naia & Mcgill, Brian. (2019). The commonness of rarity: Global and future distribution of rarity across land plants. Science Advances. 5. eaaz0414. 10.1126/sciadv.aaz0414.

Enquist, Brian & Feng, Xiao & Boyle, Brad & Maitner, Brian & Newman, Erica & Jørgensen, Peter & Roehrdanz, Patrick & Thiers, Barbara & Burger, Joseph & Corlett, Richard & Donoghue, John & Foden, Wendy & Lovett, Jon & Marquet, Pablo & Merow, Cory & Morueta-Holme, Naia & Kraft, Nathan & Park, Daniel & Peet, Robert & Mcgill, Brian. (2019). The commonness of rarity: Global and future distribution of rarity across land plants. 10.32942/osf.io/qfpa9. (preprint)

Maitner, Brian & Boyle, Brad & Casler, Nathan & Condit, Rick & Donoghue, John & Durán, Sandra & Guaderrama, Daniel & Hinchliff, Cody & Jørgensen, Peter & Kraft, Nathan & McGill, Brian & Merow, Cory & Morueta-Holme, Naia & Peet, Robert & Sandel, Brody & Schildhauer, Mark & Smith, Stephen & Svenning, Jens-Christian & Thiers, Barbara & Enquist, Brian. (2017). The bien r package: A tool to access the Botanical Information and Ecology Network (BIEN) database. Methods in Ecology and Evolution. 9. 10.1111/2041-210x.12861.

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

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.

SCHOLARSHIPS AND FELLOWSHIPS

  • Pistor-Stanley Scholarships in Agriculture (2013), $800
  • Agriculture and Life Sciences Graduate Tuition Scholarship (2011), $2,101
  • NCEAS Research Assistantship (2010), $1500
  • Tuition and Registration Scholarship (2010), $1223
  • Agriculture and Life Sciences Graduate Tuition Scholarship (2009), $4,000

HONORS AND AWARDS

  • Banta Center for Business, Ethics and Society, Case Study Award, Univ. of Redlands (2006)
  • University Honors, 1998, University of California Riverside Extension.
  • University Honors, 1995, California State University San Bernardino.
  • Graduated with Distinction, 1990, San Bernardino Valley College.

GRANTS AWARDED
(from prior work in conservation)

Grants Authored

  • California Office of Historic Preservation: Historic Resources Inventory Database Phase II Enhancement Project, 2000 ($ 16,500)
  • Environmental Protection Agency and California State Water Resources Control Board: Upper Santa Ana Watershed-Wide Invasive Species Eradication and Public Outreach Plan, 1997 ($ 191,830)
  • Environmental Protection Agency and California State Water Quality Control Board: Alternative Dairy Waste Management Practices, 1996 ($ 504,000)
  • Environmental Protection Agency and California State Water Quality Control Board: Mill Creek Watershed Protection Program, 1994 ($ 255,000)
  • California Department of Agriculture Fertilizer Research and Education Program (FREP): Managing Agricultural Non-Point Source Pollution, 1994 ($105,000)

Grants Co-authored

  • Environmental Protection Agency: Wild About Wetlands, 1997
  • South Coast Air Quality Management District: Smog Busters, 1997
  • California Department of Education: Nature Discovery Improvement Project, 1996
  • Environmental Protection Agency: Santa Ana Watershed Enhancement Project, 1996
  • Phillips Petroleum Company: Habitat Discovery Trail, 1995
  • California Department of Parks and Recreation: Glen Helen Habitat Trail, 1994
  • California Department of Transportation: Devore Road Restoration Program, 1994

CERTIFICATIONS HELD

  • Certified ArcGIS Desktop Professional, ESRI.
  • Certified Geographic Information Systems Professional (GISP), GIS Certification Institute.

TECHNICAL SKILLS

ArcGIS Desktop, ArcGIS Pro, Collector, Survey 123, ArcGIS Online/Enterprise, QGIS, R, SQL Server, Microsoft Access, Python, C# ASP.net (MVC), Visual Basic .net, HTML, CSS, XML, Trimble GPS, Windows, MacOS, and Linux.

Links

Recent Posts

CNPS Online Inventory of Rare Plants v9.0

For the past year, while working for Rincon Consultants, I have been working with two colleagues, Andrew Walter of The Jones Payne Group, and Mark Naftzger of Studio Simple, to develop the latest version of the California Native Plant Society’s Online Inventory of Rare Plants.

The new CNPS Online Rare Plant Inventory (Inventory) is the latest evolution of an effort CNPS started in 1974. Since that time, CNPS produced six printed editions from 1974 to 2001, when the first online edition was launched. The previous inventory were composed of three elements: A Microsoft Access database that CNPS staff used to maintain the names and status attributes of rare plants, and an online database managed by another individual, and a public-facing website. This architecture required regularly transferring files from MS Access to the online database manager for processing into the database powering the public site.

The new version redeveloped the back-end plant management features of the MS Access database with the public-facing search and status information and a single comprehensive database. This version also includes a modern, streamlined, and mobile-friendly interface and a new underlying architecture that creates the foundation for future enhancements to take advantage of modern web technologies, including potential Application Programming Interfaces (APIs) and geospatial integrations.

CNPS is the leading voice in plant science and conservation in California and one of the foremost native plant organizations in the world (CNPS, 2019). The new Inventory is a widely used resource that directly guides rare plant protection, conservation planning, land acquisition, and management in California. It is considered the authoritative source for rare plant information and used every day by agencies, consultants (including Rincon and our competitors), and conservationists to determine the potential for rare plant resource conflicts, develop project-specific lists of rare plants to target during botanical surveys, and help prepare and review environmental documents and public testimony to influence decision-makers.

For this version, Andrew was responsible for the database design, including the tables, views, triggers, and stored procedures that power many functions in the database. Mark created a brilliant, mobile-friendly Bootstrap template for the public and back-end pages. Finally, I developed the .Net MVC C# and JavaScript coding in Visual Studio.

It was an interesting project for a noteworthy organization and we all learned a a great deal more about our respective disciplines while pushing our personal envelopes to deliver a product worthy of its history and one we hope our CNPS predecessors would be proud of.

Our work to build this new version is the culmination of a 7-year effort by CNPS’ Rare Plant Manager, Aaron Simms, who has been great to work with.

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