Ecology

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 fund

ed 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.

>>  View my Academic Tree

>>  View my Research Gate Portfolio

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 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

  • 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., 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)
  • Certified ArcGIS Desktop Professional
  • 38 hour course in Army Corps of Engineers Wetland Delineation Training
  • Introduction to Desert Tortoise Surveying, Monitoring and Handling Workshop 

Links

Recent Posts

Re-­engineering the Business Process of Desert Tortoise Data Collection

John Donoghue, Former Technology Manager at Ironwood Consulting

Ironwood Consulting Inc. (Ironwood) is a biological resources consulting firm in Southern California, and specializes in biological resource management, including desert tortoise permitting and mitigation. Ironwood is known for its successful work on large-­scale solar development projects in the Mojave Desert. Most recently, Ironwood was responsible for the pre-­project surveys, permitting, relocation, and monitoring of tortoises on four large-­scale solar energy projects: Desert Sunlight (3,000 acres), Silver State South (2,400 acres with 104 tortoises), Stateline (1,500 acres with 41 tortoises), and Dry Lake SEZ (serving three solar energy developer clients over a combined 2,000 acres with 45 tortoises). These projects combined required the successful translocation and monitoring of over 200 desert tortoises.

The problem
The large-­scale solar development projects Ironwood was managing required collecting a great deal of field data. During active desert tortoise field seasons, over 70 biologists would be collecting location, health, and other data on desert tortoises moving throughout project sites and offsite mitigation areas. This data was used to determine each tortoise’s territory, ascertain its health and identify other tortoises it may be interacting with. The information was necessary to help plan and ensure the successful translocation of tortoises from the project development site to nearby mitigation preserves, where tortoises would continue to be monitored to confirm they were adjusting to their new homes after the move.

Field biologists worked in remote locations that were often out of cellular voice and data access most of the time. Historically, field biologists collected data on paper forms that were later transcribed into Excel for analysis and reporting. Later, Ironwood adopted a system that used Pendragon Forms for offline field-­based digital data entry. This data was later synced through a server into a Microsoft Access database for storage and use. While the Pendragon Forms system accelerated the process of collecting and digitizing field data, biologists were aggravated by its antiquated interface and wanted forms that worked like the other iOS and Android applications they regularly used, with features that included scrolling pages, advanced data entry constraints on fields, photographs, GPS support and more.

Problems

  • Previous interface lacked modern features and user experience
  • Some data was entered into more than one form to record a single activity
  • Data entry errors were common
  • Data required time-­consuming and expensive manual QA/QC
  • Data available to system users was not relational and could not easily address questions asked by project managers
  • Projects hosted in separate databases with different schemas
  • Lack of standard database schema hampered efforts to gain efficiencies and prevented meta-­analyses across projects

The Pendragon/Microsoft Access system also required field biologists to enter some of the same data into different Pendragon forms, which resulted in many data entry errors and required a great deal of oversight and time-­consuming manual QA/QC. With Ironwood simultaneously managing multiple large-­scale solar projects, the time consuming manual processes that the Pendragon/Microsoft Access system required became very costly. Furthermore, the system wasn’t designed to support multiple end users, and the data products produced by the system were not designed to quickly answer the questions project managers were regularly asked by the solar development clients and agencies. Since each project was hosted in its own separate Access database with varying schemas to accommodate the peculiarities of each project, the absence of a standardized multi-­project database made analyses across projects impractical.

Developing a New Solution
To address these limitations, Ironwood decided to design an entirely new system that could support hosting multiple projects with multiple simultaneous users, while providing a greater variety of data products to address the different needs of field-­biologists, project managements, clients, and agencies. Ironwood began by meeting with their biologists in charge of desert tortoise management to review the shortcomings of the current system and discuss the envision the opportunities a new system could generate. The information from this and subsequent meetings resulted in a new database design that comprised a core set of tables and table fields that were designed to manage the data for multiple projects, and could accommodate all previously collected tortoise data, as well as incoming data for all upcoming desert tortoise projects. To ensure the database could support multiple simultaneous internal and external users working on different projects, the new database was implemented in Microsoft SQL Server. This also provided a foundation to support integrations with GIS other business systems.

iFormBuilder
In looking to replace Pendragon Forms, Ironwood reviewed a number of alternative iOS and Android applications for field-­based data entry. Ultimately, iFormBuilder was selected because it provided several benefits: there were iFormBuilder applications for both iOS and Android; the form building process in iFormBuilder was very intuitive, and the resulting forms had the modern user interface and user experience the field biologists desired. iFormBuilder forms also offered many features Ironwood needed, such as data entry constraints, data input masks, context sensitive field visibility, field validation, GPS support and in-form photos. Finally, the field biologist workflows were often best implemented as sub-­forms, and iFormBuilder sub-­forms were more intuitive to field biologists than the previous Pendragon Forms.

Integrating iFormBuilder and SQL Server
A fundamental goal for Ironwood’s new system was automating previously manual processes, and automating the transfer of data from iFormBuilder’ forms to Ironwood’s SQL Server database was a critical component. Fortunately, iFormBuilder offered an XML Post Data feature that pushes a copy of each record’s data from iFormBuilder to a user defined web page every time a new record is successfully uploaded to the iFormBuilder server.

Ironwood developed an ASP.net web application that contained a set of URL endpoints to receive XML data posted from iFormBuilder. The ASP.net application parsed the incoming XML data and inserted data as new records into Ironwood’s SQL Server database. During this process, the ASP.net application also performed QA/QC on incoming data, standardized data formats, and transformed the location information contained in the posted data into Open Geospatial Consortium (OCG) compliant spatial data for use in Ironwood’s ArcGIS system and other applications. Finally, the ASP.net application sent each user synching data to iFormBuilder an email that informed them of their successful data sync and identified any potential data errors found by the QA/QC processes.

Another goal of the new system was to re-­engineer the data collection business processes to remove duplicate data entry processes and reduce the number of digital forms needed. The previous Pendragon forms were designed to populate single database tables. Field biologists often had to enter some of the same data into different Pendragon forms as they performed a single activity, such as a health assessment – in which biologists completed one Pendragon form to record a tortoise location, and another Pendragon form to record tortoise health data.

In contrast, Ironwood designed its iFormBuilder forms around the activities biologists performed during their tortoise survey and monitoring work. As the data was received by Ironwood’s ASP.net application during syncing, the ASP.net application would automatically populate the appropriate tables. Therefore, a field biologist could use an activity specific iForm to record data for multiple associated activities, and the ASP.net application would sort the received data and populate the data into each relevant table.

Leveraging Better Data
To help provide more expedient and broader access to the data gathered in iFormBuilder, Ironwood also developed an ASP.net website that served as a central hub for field biologists, project managers, clients, and agencies. The resulting web portal supported multiple users and projects, and provided access to data as soon as it was synced from iFormBuilder and pushed into Ironwood’s SQL Server database. The web portal provided dashboards where users could view tortoise statistics and interactive maps of tortoise locations that were dynamically generated from the database using data from the most recent iFormBuilder application sync.

The web portal provided data in different formats for the various types of users the system supported. Field biologists and agencies accessed the portal to download dynamically generated Excel and GPX files that contained the most recently recorded tortoise locations and other information. Project Managers and Clients downloaded dynamically generated KML data for mapping in Google Earth, and viewed dynamic charts and statistics to review project’s status and look for potential issues. Unpublished URL endpoints allowed the data to be brought into ArcGIS Online, Google Earth and other systems.

In addition, by storing the location data as OGC compliant spatial points, the database could be directly accessed by GIS systems, and was persistently linked to Ironwood’s esri ArcGIS system where Python scripts automated daily cartographic quality maps used by field biologists, project managers, and clients.

Results
The better data input constraints provided in iFormBuilder significantly reduced Ironwood’s QA/QC needs. Despite having developed an automated backend QA/QC process, Ironwood later found that 95% of the data pushed into its database had no potential QA/QC issues identified by that process as the errors were constrained during data-­entry in iForms.

Field biologists were especially pleased with the new system. The iFormBuilder forms provided a modern user interface and user experience they expected, and iFormBuilder features such as designating the default device keyboard for fields, data input masks, and context sensitive field visibility, significantly increased the speed with which biologists could enter data into iForms, while being confident that data was accurate.

Results

  • Considerably fewer data errors
  • Increased adoption of digital forms
  • Greater trust in data
  • Much faster data turn-­around
  • Significantly lower data management costs
  • Improved client confidence in data management process
  • Increased client satisfaction
  • Improved agency cooperation
  • Stronger client relationships

The iFormBuilder XML Push workflow has greatly benefited field biologists by ensuring that the data the biologists recorded and synched was instantly added to Ironwood’s SQL Server database and biologists were immediately informed of its availability.

By developing a data portal website, Ironwood was able to leverage iFormBuilder and SQL Server to provide biologists, project managers, clients and agencies with access to all data anytime they needed it. Clients have praised the system and are using it regularly to keep informed on the progress of the mitigation programs for their projects. By making data collection processes transparent and providing clients with readily accessible data in the formats they needed, Ironwood was able to better communicate the data collection effort with its clients which reinforced the client’s trust in Ironwood’s data collection processes.

Though considerable effort was involved in reaching agreement with on a new database design and data input forms that bridged the gap between the needs of the field biologists and Ironwood’s end-­users, by implementing an integrated iFormBuilder, SQL Server and ASP.net solution, Ironwood was able to reengineer the business process of desert tortoise data collection. While the entire system took time to develop, the major benefits were realized when the system was fully implemented on multiple projects, where it essentially ran itself with very little intervention, resulting in significantly reduced data management and reporting costs, ultimately transforming a once cost-­intensive activity into a financial and practical benefit to Ironwood’s clients.

  1. Some Coveted Programming Skills Leave a reply
  2. Social Networks and Ecological Food Webs Leave a reply
  3. A Maxent Script Tool for ArcGIS 17 Replies
  4. Speedy Attribute Editing with a Custom ArcMap Add-In 2 Replies
  5. Landing a GIS Job and GIS Skills Development in 2013 39 Replies
  6. Les Miserables Look Down, Look Down the PhD Version 2 Replies
  7. Creating a Video of Vegetative Cover Sampling Leave a reply
  8. Desert Tortoise Training Leave a reply
  9. A Species Diversity Map for 88,000 New World Species Leave a reply