Jabberwocky Ecology

Ph.D Student Opening in Weecology


The Ernest Lab at the University of Florida has an opening for a Ph.D student interested in research in the area of community ecology, forecasting, and/or temporal dynamics to start fall 2020.  The student will participate in the collection of small mammal and plant data at our long-term site in southeastern Arizona which will be used as part of our recently funded NSF grant to tackle challenges associated with ecological forecasting under novel conditions. While participation in the field data collection at the long-term site is expected, students in the Ernest Lab are free to develop their own research projects depending on their interests. The Ernest lab is interested in general questions about the processes that structure communities, with a particular focus on understanding when and how ecological communities change through time and how we can forecast those changes. Examples of research that students in the Ernest lab have pursued as part of their dissertation include: Does long-term change in communities occur through gradual species replacements or rapid reorganization events?, Are biodiversity patterns sensitive to changes in biotic interactions?, Do disturbances impact species populations and community-level properties similarly?, and How does the colonization of new species impact habitat patch preferences?

The Ernest Lab is part of the Weecology research group, Weecology is a partnership between the Ernest Lab, which tends to be more field and community ecology oriented and the White Lab, which tends to be more quantitatively and computationally oriented. The Weecology group supports and encourages students interested in a variety of career paths. Former weecologists are currently employed in the tech industry, with the National Ecological Observatory Network, at teaching-focused colleges, and as postdocs in major research groups. We are also committed to supporting and training a diverse scientific workforce. Current and former group members encompass a variety of racial and ethnic backgrounds from the U.S. and other countries, members of the LGBTQIA+ community, military veterans, people with disabilities, and students who are the first generation in their family to go to college. We work hard to create a supportive and inclusive lab environment and expect all members of Weecology to abide by the lab code of conduct.

More information about the Ernest lab and Weecology research group is available at: (https://weecology.org). You can also check out the blog for our long-term study (https://portalproject.wordpress.com) and our lab blog (https://jabberwocky.weecology.org; if you’re reading the ad here, you’ve found it already!).

Interested students should contact Dr. Morgan Ernest (skmorgane@ufl.edu) by Oct 15th, 2019 to start a dialogue about the position and receive further information about the next steps in the application process.

Way too many examples of graduate students not getting their paychecks

It’s not uncommon to hear stories of mistakes resulting in graduates students missing paychecks. This is a major problem because most students live month-to-month and can’t wait for a missed check to be fixed in the next pay cycle. Despite the commonness and dramatic impact of missed pay in graduate school*, it’s common to see these issues written off as isolated incidents and not part of a more systematic problem. As a counterpoint to this idea, here are just some of the responses to a single tweet about this problem.

If you’d like to add your own experiences either post them to Twitter (responding to or quote tweeting the original tweet or tagging me @ethanwhite; I’ll keep updating this post as new experiences come in) or post a comment on this blog post.



*As a number of folks have noted this issue is also a real challenge for lots of folks both at universities (adjuncts, postdocs, and even professors) and beyond. I couldn’t agree more. That said I think there are some unique things related to graduate students that make the occurrence of these mistakes more common (like the fact that at many universities they are “hired” at least once and often 2-3 times/year; more on this soon) and I also think it’s OK to highlight and attempt to fix general issues within specific populations.

Weecology at #ESA2018 [updated]

The weecology group is coming in force to the annual meeting of the Ecological Society of America which is being held in New Orleans next week. We’ve been up to a quite diversified list of things over the past year ranging from temporal dynamics of communities to forecasting and remote sensing. We also have people involved in a number of outreach or training events this year. We’re super proud of all the work everyone has been doing – both on the science end of things and the culture of science end of things. The Weecologists involved with each presentation/event are highlighted in electric blue with links to either their web page or google scholar profile so you can learn more about them. Talk or event titles link to the relevant listing in the ESA program.



10:15-11:30 Special Session: Path to being a strong ally in science. Location: Convention Center 238-239. (Juniper Simonis is involved in this session)

11:30-1:15 Workshop: NEON Resources for Your Research. Location: Convention Center 238-239 (Ethan White is on the panel).

1:50-2:10 Weak impacts of climatic factors on intraspecific body size variation in endothermic species. Kristina Riemer, Narayani Barve, Brian Stucky, Stephen Mayor, Robert Guralnick, Ethan White. Location: Convention Center Rm 356.

3:20-3:40 The influence of data type, functional traits, and ecoregion on native bee phenology. Joan Meiners, Michael Orr, Kristina Riemer, Shawn Taylor, Terry Griswold. Location: Convention Center – R05

3:30-5:00 INSPIRE Session on Rapid Ecological Transitions: Synthesizing Concepts about Abrupt State Changes in Nature. Organized by SK Morgan Ernest, Christie Bahlai, Kendi Davies, and Sarah Elmendorf. Location: Convention Center – Rm 243

3:30 Rapid Ecological Transitions: A state space of concepts and ideas. SK Morgan Ernest. Location: Convention Center – Rm 243

4:40-5:00 Prediction and forecasting of Portal fauna via particle filtration. Juniper Simonis, Glenda Yenni, Shawn Taylor, Erica Christensen, Ellen Bledsoe, Ethan White, SK Morgan Ernest. Location: Convention Center Rm 355.


2:00-2:30 Evidence of rapid transitions in long-term community data. Erica Christensen, David Harris, Renata Diaz, SK Morgan Ernest. Location: Marriott – River Bend 1

3:10-3:40 Dynamic indicators of ecosystem resilience. Hao Ye, Erica Christensen, SK Morgan Ernest, Juniper Simonis, Ethan White. Location: Marriott – River Bend 1

5:00-6:00 during the poster session Juniper Simonis will hold an informal chat for those interested in knowing more about starting your own consulting business (likely in the poster hall, assuming there’s room). For more information, contact Juniper on Twitter @DapperStats

6:30-8:00 Long-term Studies and Paleoecology Mixer. Location: Rusty Nail Bar (SK Morgan Ernest is the chair of the Long-term Studies Section. If you like talking about temporal dynamics or want to learn more about paleoecology, come join us!).


10:50-11:10 Heterogeneity in competitors affects patch preference in the same extrinsic environment. Ellen Bledsoe, SK Morgan Ernest. Location: Convention Center Rm 356.

11:30-12:30 during lunch Juniper Simonis will hold another informal chat for those interested in knowing more about starting their own consulting business (location not yet determined). For more information, contact Juniper on Twitter @DapperStats

3:30-5:00 Software skills for reproducible data-intensive research. Ethan White. Location: Convention Center Rm 243.

4:20-4:40 Scaling up remote sensing fundamental unit: from pixels to crowns. Sergio Marconi, Sarah Graves, Stephanie Bohlman, Jeremy Lichstein, Aditya Singh, Ethan White. Location: Convention Center 338


1:30-2:30 Getting a handle on your data with the dplyr R Package. Shawn Taylor . At the Data Help Desk in the Poster/Exhibit Hall.

4:30-6:30 Evaluating a near-term ecological forecast of plant phenology. Shawn Taylor, Ethan White. Location: Poster 110, Exhibit Hall


A Julia Package for the Data Retriever

We are excited to announce the first release of a new Julia package that let’s you run our Data Retriever software with a native Julia interface.

For those of you not familiar with Julia it is a new programming language that is similar to R and Python, has a central focus on data analysis, and is designed from the ground up to be fast. It is an emerging scientific programming and data analysis language. Tim Poisot and his lab have been leaders in introducing Julia to the ecology community (thanks to them you can access GBIF data, analyze ecological networks, and more) and we’re pleased to start following his lead.

After installing the Python package getting your favorite dataset into Julia involves opening Julia and running:

julia> Pkg.add("Retriever")
julia> using Retriever
julia> iris_data = Retriever.install_csv("iris")
julia> iris_data = readcsv("iris_Iris.csv")

Like the Python and R versions of the retriever the Julia version also lets you install into a number of different database management systems and formats to meet your needs including PostgreSQL, MySQL, SQLite, JSON, and XML. So if you need to install a large dataset and access if from the database you can do that:

julia> Pkg.add("SQLite")
julia> using SQLite
julia> Retriever.install_sqlite("breed-bird-survey", file="bbs.sqlite")
julia> db = SQLite.DB("bbs.sqlite")
julia> SQLite.query(db, "SELECT * FROM breed_bird_survey_counts LIMIT 10")

We use the PyCall package to directly run the Python code from the main retriever package. Cross-language support like this is really useful for letting difficult to develop core code be easily used in different languages and it’s great that this is a core feature of Julia.

The development of this package was lead by Shivam Negi, a fantastic Google Summer of Code student with us last year, and our amazing senior software developer Henry Senyondo.

This is our first Julia package and so there are sure to be lots of things to improve (starting with the documentation). If you use Julia, or are interested in experimenting with it, we’d love feedback, issues, and pull requests. We’re always enthusiastic to have new contributors and help everyone get started, especially if they’re just learning. For more information see:


Data science competition for converting remote sensing to ecological data

Scaling-up ecological patterns and processes is crucial to understanding the effects of environmental change on natural systems and human society. We are piloting a Data Science Challenge where multiple groups attempt to use the same remote sensing data from low flying airplanes to infer the location and type of trees in forests. This will allow forests to be studied in detail at much larger scales than is currently possible. This kind of collaborative data analysis challenge has proven highly effective in other fields for quickly improving methods for converting image data to useful information.

There are three sets of tasks: 1) identifying individual trees in remote sensing images; 2) aligning ground data with remote sensing data; and 3) classifying trees into species.

Screen Shot 2017-11-06 at 10.33.22 AM

Teams (or individuals) can participate in all of them or just pick the tasks they are most interested in. Tasks 2 and 3 can be accomplished using just tabular data. Task 1 requires working directly with spatial data. Details of the different tasks and links to the data are available at the challenge website:


We plan to write a general paper about the competition, the data, and the performance of the different methods used. Individual participants will be invited to write and publish associated short papers on the methods they used and results they produced. We already have a journal that has agreed to publishing all of these related contributions together into a collection (pending review of course).

The challenge is already open and the deadline for submissions is December 15th. Once you sign up on the website you will receive an email with some additional details. If you have any questions feel free to respond to that email or checkout the FAQ to see if they have already been answered.

This challenge is sponsored by the National Institute of Standards Technology as part of it’s Data Science Evaluation series and is also partially supported by he Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative through grant GBMF4563.It uses data from the National Ecological Observatory Network in addition to data collected by the organizers. It is being organized by the Data Science Research lab, the Weecology lab, and Stephanie Bohlman’s lab all at the University of Florida.

Data Retriever 2.1: Python Interface, Autocomplete & More

EcoData Retriever logo

We are exited to announce a new release of the Data Retriever, our software for making it quick and easy to get clean, ready to analyze, data.

The Data Retriever, automates the downloading, cleaning, and installing of data into your choice of databases and flat file formats. Instead of hours tracking down the data on the web, downloading it, trying to import it, running into issues, fixing one problem, and then encountering the next, all you need to do is run a single command from the command line, R, or (now!!) Python:

$ retriever install csv iris
> portal_data <- rdataretriever::fetch('portal')
In [1]: import retriever as rt
In [2]: rt.install_postgres('breed-bird-survey')

Major changes

  • Python interface: While the retriever is written in Python the package previously only had a command line interface. Now you can access the full power of the retriever from directly inside Python. See the full tutorial for more details.
  • Conda packaging: The conda package manager has become one of the two main ways to install Python packages. You can now install the retriever using
conda install retriever -c conda-forge
  • Command line autocomplete: As the number of datasets and backends supported by the retriever goes it can be difficult to remember specific names. Using Tab will now autocomplete retriever commands, backends, and dataset names. (Currently only available of OSX and Linux)


  • We also made some changes to the metadata script system so if you’ve previously installed the retriever you should update your scripts using:
retriever reset scripts
retriever update

Find out more

To find out more about the Data Retriever checkout the:


Ongoing work on the Data Retriever lead by Henry Senyondo is made possible by the generous support of the Gordon and Betty Moore Foundation’s Data Driven Discovery Initiative. This kind of active support for the development and maintenance of research oriented software makes sustainable software development at universities possible. Shivam Negi developed the Python interface as part of his Google Summer of Code project. You can read more about his time in GSOC at his blog.

Twelve different folks contributed code to this release. A big thanks to Henry Senyondo, Ethan White, Shivam Negi, Andrew Zhang, Kapil Kumar, Kunal Pal, Amritanshu Jain, Kevin Amipara, David LeBauer, Amritanshu Jain, Goel Akash, and
Parth-25m for making the retriever better.

The Portal Weather Station

How has our collection of weather data at the Portal Project changed through time? Weecology Project Manager Glenda Yenni recounts the saga of the weather stations.

The Portal Project

For the history of the project, weather monitoring has always accompanied the collection of rodent, plant, and ant data. At first, this was done manually. Portalites from 1980 to 1989 measured rain in a rain gauge, and used something called a hygrothermograph to measure temperature and humidity.

hygrothermograph Hygrothermograph

Then things started to get fancy. In 1989, an automated weather station was installed. This is the desert though, and leaving expensive toys out in the rain, dust and lightning takes it’s toll.

Sunset in the desert jungle At least the lightning storms leave us with some nice scenery after they try to blow up our weather station.

All things considered, our weather stations have stood up pretty well. The first lasted from 1989 until 2002. And the station from 2002 is still limping along, although it’s had its moments (it tends to have a bit of a tantrum after being struck by lightning). We connected to…

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A Vegetation History

Today’s reblog from the Portal Project is a piece by Tom Valone how the site inspired him to ponder vegetation change.

The Portal Project

My Portal story begins in 1991 when Jim Brown offered me the opportunity to be the Portal postdoc. Among other things, this meant I organized the yearly ant census in which we spent about 2 weeks counting the abundance of ant colonies on the experimental plots. In one of my first summers, I hired Don Sias to help with the census. Don was a non-traditional student and had previously traveled extensively throughout the southwest. One day he mentioned to me that the vegetation in the San Simon valley looked pretty “beat up”. By that he meant the vegetation, dominated by shrubs, had the look of a grassland that had become desertified.

August 2015

I was intrigued by Don’s comment for two reasons. First, Brown and Heske (1990) had recently described a significant increase in grass cover on Portal plots that removed kangaroo rats and mentioned that the site was “near the zone…

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Portal: Then and Now

Love to see paired photos of places in the past and now? My PhD student Erica Christensen has a treat for you. Here’s a post about her attempts to reshoot old photos from the site.

The Portal Project

A lot can change in 40 years.  This is perhaps never more apparent than when you find a box of old photographs, and start comparing then to now.  When the Weecology lab immigrated from Utah to Florida in 2015, just such a box surfaced: a glimpse back in time to the beginning of the portal project.  I did my best to re-create some of these photographs—trying to line up horizons and mountains—to show how the site has changed over 40 years.

One thing is immediately apparent: the shrubs have grown up.  The left side of these photographs were taken in 1977 (photographer unknown), and the right side in 2015 (photographer Erica Christensen).  What happened to the rows upon rows of aluminum flashing, indicating the location of the rodent fences?  I assure you the fences are still there, they’re just obscured by the jungle.

The fact that you used to be…

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2017 Summer Plant Census

Someone (**cough** **cough** Morgan) fell down on their job rebloging the Portal Project 40th anniversary posts to Jabberwocky. But that means this week is the week o’ Portal as we reblog the various posts from the past few weeks. First up, what happens when we go out in the summer to count plants?

The Portal Project

Twice a year the Portal crew gets a little larger, and spends a few extra days, and we count plants on all 384 quadrats. Despite some of us being in our second decade of visiting the site, and everyone on the plant crew being intimately familiar with most of the species at the site, and that the rodent RA has been watching the plants grow and giving us monthly updates, we still never really know what we’re going to find once we get out there. The desert does what it wants.

The uncertainty seems especially high for the summer plant community. Some years we arrive to an ocean of grass, waving in the breeze. Those are the years we spend a lot of ‘quality time’ with each quadrat. Other years we arrive to a dustbowl. We walk around the site laying our PVC quadrat down and picking it back up…

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Ode to six-legged wonder

While the Portal Project focuses primarily on rodents and plants, there is more to our ecosystem than just those taxa. This week’s Portal Project post focuses on some insect work at the site.

The Portal Project

If four legs are great, six legs are better. Right? For forty years now, the Portal Project has primarily focused on two-legged creatures trapping, studying, and sometimes cuddling small, furry four-legged creatures. But we haven’t ignored the six-legged inhabitants of our long-term research site, and I am going to tell you more about them now.

roachantmouse Which one of these is least like the other?

I am the Ernest lab entomologist, who doesn’t consider herself an entomologist. I am interested in biodiversity, community, and macroecological patterns like those studied by generations of Portal rodent researchers. I just happen to study them using bees. There are over twenty thousand species of bees in the world, and about four thousand in North America. My research so far has focused on the community ecology of native bees in a global hotspot of bee diversity in California. But as fate or luck would have it…

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The Spectabulous Spectabs of Portal

The latest installment from the Portal Project Blog on the watch for Banner-tailed Kangaroo Rats

The Portal Project

Much beloved by those who have worked at the Portal Project, the banner-tailed kangaroo rat (Dipodomys spectabilis) is one of the most charismatic rodents at the site (for us smammal lovers who think rodents can be charismatic, anyway). The fact that they have a nickname—spectabs—attests to this fondness. Look at that mighty tufted tail! Those giant, majestic furred feet! Weighing in at over 100 grams as adults, they are twice the size of our other kangaroo rat species (D. ordii and D. merriami). What’s not to love?

8067256761_6ab7d78602_zDipodomys spectabilis

As avid readers of the Portal blog might recall, the site used to be much grassier back in the day. At the start of the project in 1977, spectabs were running the show at Portal; we even had some plots that excluded only D. spectabilis because they were so dominant! For the spectabs, this was a desert…

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