UC Davis at ESA 2017

UC Davis will make a strong showing for the 102nd meeting of the Ecological Society of America in Portland, OR this year! We have 78 students, postdocs, faculty, and recent graduates giving 1st author oral or poster presentations. Come see your talented colleagues showcase the variety of fascinating ecology research they’ve been up to recently.

If you’re on twitter, be sure to follow the #ESA2017 hashtag (and the @davis_egsa account!) for a whole new way to experience conferences. We’ll also be sending out tweet reminders about these UC Davis affiliated talks and posters about an hour or two before they start.

Don’t forget to join us for the annual UC Davis Ecology mixer on Wednesday starting at 6:30 PM PDT. The venue is Room A109 right in the Oregon Conference Center (the same venue as the Meeting). Hope to see you there!

Demystifying the hosting duties for the UC Davis Ecology & Evolution Weekly Seminar Series

Demystifying the hosting duties for the UC Davis Ecology & Evolution Weekly Seminar Series

By Michael Koontz, Allison Dedrick, and Helen Killeen

The EEB Seminar Series is a weekly opportunity to fortify the ecology and evolution community at Davis. We see cutting edge research by individuals holding positions that we one day hope to attain, we interact with those individuals in casual and professional settings, and we build our academic network in the proces. Students have an awesome opportunity to shape the lineup of speakers by nominating and hosting people of their choosing. When students are more involved in hosting speakers, it is more likely that the diversity of the speakers will reflect the breadth of interests, backgrounds, and future goals of the student body. As best as I (Mike) can tell, 2 students hosted speakers the first year I was at UC Davis (2014-2015), and 4 students hosted speakers the next year. However, 9 out of 28 speakers were hosted by students this year! This is great to see, and hopefully it marks the start of a reenergized seminar series.

Hosting a speaker for the EEB Seminar Series is a great experience. It can be daunting, so we wanted to shed some light on the process in the hopes of persuading more folks (especially students!) to nominate and invite scholars that would best serve their goals for their research training.

Why host?

  • Great way to meet people you might want to collaborate with or postdoc with in the future (broaden your network)
  • Can be a way to meet others on campus who have similar interests as you who you might not have encountered before
  • Have heard anecdotally from a couple of people that they are more likely to accept invitations to speak when invited by a student
  • A chance to advocate for/represent your particular sub-discipline to your peers and colleagues

Tips before hosting

  • Go to a student lunch with a seminar speaker before it is your turn to host to see what it’s like (they’re super informal and a great way to interact with the speaker and stay in touch with your colleagues)
  • Go to a no-host dinner with a seminar speaker before it is your turn to host
  • Enlist the help of your labmates to host someone
  • The official email to introduce the community to the next speaker goes out the Friday before the speaker visits, but there’s no need to wait until then to start planning their schedule! See if your labmates and other folks in the GGE might be interested in a 30 minute, 1-on-1 meeting in advance.
  • Make a schedule for your guest’s visit in 30-minute blocks. Use a Google Sheet so the schedule will be easy to see and modify, and everyone with access will be able to see the most up-to-date information. Be sure to include room locations for each meeting. Here’s the format Mike used when he hosted: https://docs.google.com/spreadsheets/d/1OtuTG5aR1LwSb9xOU71sPjbMMN4oBvnGhkh5rCo1jfM/edit?usp=sharing
  • Visit the seminar room before the day of the talk to make sure you know how to work the projector, lights, etc. Arrange to have a clicker/laser pointer available for the speaker to use if they want.
  • (more of a tip for nominating): If your speaker is coming from far away, think about other funding sources that might help get them here (like if you already know they’ll be in the area for another reason and this visit could get added into that). Or reach out to other groups on campus – like Bodega Marine Lab or Coastal Marine Sciences Institute — to see if they might be willing to share costs or co-sponsor the visit.

Tips during hosting

  • Tell your guest to have some questions ready for the students during the student lunch, so that your guest will have some time to eat
  • Tell each person on the 1-on-1 schedule to escort the speaker to their next meeting (this is why it is key to have “location” on the schedule!)
  • To avoid low turn-out at either the student lunch or the no-host dinner, individually invite people who you think might be particularly interested in the speaker (especially students not in the GGE who might otherwise not realize the speaker is coming)
  • Ask the speaker if there are any people at Davis they particularly want to meet with during their visit, contact those people first about meetings when setting up the schedule
  • The email to hosts often doesn’t go out until just before the start of the quarter but start planning the visit before then. As the host, you are in charge of connecting with the speaker and the relevant admin people to book flights, hotels, etc. — if your speaker is early in the quarter, don’t wait for the host reminder email.

UC Davis at ESA 2016

UC Davis will make a strong showing for the 101st meeting of the Ecological Society of America in Ft. Lauderdale, FL this year! We have 30 students, postdocs, faculty, and recent graduates giving 1st author oral or poster presentations. Come see your talented colleagues showcase the variety of fascinating ecology research they’ve been up to recently. Click on any talk title below to go to the full abstract, time and location in the ESA program. The full program can be found here.

If you’re on twitter, be sure to follow the #ESA2016 hashtag (and the @davis_egsa account!) for a whole new way to experience conferences. We’ll also be sending out tweet reminders about these UC Davis affiliated talks and posters about an hour or two before they start.

Don’t forget to join us for the annual UC Davis Ecology mixer on Wednesday starting at 6:30 PM EDT. The venue is Grille 66 & Bar, which is about a half mile walk from the ESA conference venue. Details can be found on the Facebook event page. Hope to see you there!

Monday, August 8th

Name Title/Link
Meredith Cenzer Natural selection and maladaptive plasticity counteract each other on a native and invasive host plant in soapberry bugs
Toby Maxwell Soil properties drive carbon-water relations across a climate gradient in Sierra Nevada forests
Ash Zemenick A picture of nectar: Do pollinators and nectar robbers vector unique microbe communities to columbine (Aquilegia formosa) nectar?
Nick Rasmussen Determining the consequences of phenological shifts for plant-herbivore interactions: An experimental approach

Tuesday, August 9th

Name Title/Link
Noam Ross Joint circulation of viral diseases in a bat population
Lucas Silva The strength of weak ties: The influence of soil-plant interactions on ecosystem restoration trajectories
Daniel Karp Co-managing fresh produce for nature conservation and food safety in California’s Central Coast
Rebecca Hernandez Organic and inorganic soil carbon in global aridlands
Jordan Hollarsmith Short-term estuarine acidification: Spatially complex impacts of upwelling and run-off on oyster growth and water chemistry in a Northern California estuary
Meghan Skaer Thomason Hydrologic variation drives dynamics of invasive aquatic plant spread at three spatial scales in a managed river
Kara Moore Experimental ecology and evolution in the field: A unique course for upper-level undergraduates and instructors
Kate Tiedeman Experimental ecology and evolution in the field: A unique course for upper-level undergraduates and instructors

Wednesday, August 10th

Name Title/Link
Alan Hastings Challenges in applying tipping point concepts to social-ecological systems
Julea Shaw Patch size effect on a native plant community within a grassland restoration setting
David Spiller Predators suppress herbivore outbreaks and enhance plant recovery following hurricanes
Swati Patel The stabilizing and destabilizing effects of eco-evolutionary feedbacks
Grace Charles Impacts of different large herbivores on ecosystem function: Cattle increase mean productivity, and wild herbivores reduce variability around the mean

Thursday, August 11th

Name Title/Link
Keely Roth Exploring drivers of spectral variation at landscape scale: Structure, composition and function
Susan Ustin Mapping vegetation of the Sacramento Delta with AVIRIS-ng
Jay Stachowicz Genetic diversity, relatedness, and trait variation as determinants of plant coexistence and ecosystem functioning
Juan Ruiz Guajardo Host quality impacts colony-level aggression, survival, and the effectiveness of the defensive mutualism between Crematogaster mimosae (Santschi) and its host tree Acacia drepanolobium
Allison Dedrick Quantifying the interactions between management practices and the portfolio effect in salmon
Moria Robinson From soils to webs: Effects of environmental heterogeneity on specialization of plant-herbivore-parasitoid ecological networks
Andrew Siefert Testing the roles of niche differences and rhizobial mutualists in stabilizing coexistence of congeneric legumes
Jason Sadowski The influence of biological invasions and climate change on non-consumptive effects

Friday, August 12th

Name Title/Link
Val Eviner New mechanisms governing plant-soil feedbacks of native vs. exotic grassland species: Soil carbon depth distribution alters rooting distribution and seed production in a moisture-limited grassland
Jens Stevens The biogeography of fire regimes: A trait-based approach
Allison Simler Seedling regeneration dynamics following compounded disturbances: Wildfire and sudden oak death alter recruitment, mortality, and growth
Evan Batzer Perennial grasses in annual-dominated communities: Tradeoffs between invasive species suppression and fecundity
Chuanwu Chen The effects of seasonal changes and migratory versus resident status on the spatial structure of bird communities

Davis at ESA 2015

Like every year, the GGE will be out in force at the Ecological Society of America’s meeting! If you’re in Baltimore for #ESA100, come and see the many talks by students in the Ecology and Population Biology graduate groups, as well as many other professors and researchers from Davis. Click on any talk title below to go to the full abstract, time and location in the ESA program.

Also, if you’re coming to ESA, don’t forget to come by the Davis Mixer on Wednesday Evening!

GGE and Population Biology Students and Recent Graduates

Name Title/Link
Max Castorani Connectivity structures local population dynamics: A long-term empirical test in a large metapopulation network
Allison G. Dedrick Quantifying the interactions among ocean acidification, temperature, and fishing for marine invertebrates
Kelly Gravuer Trait-based ecological strategies explain microbial responses to environmental change
David J. Harris Estimating species interactions from observational data with Markov networks
Vadim A. Karatayev Density-dependent maturation regulates overcompensation and increases persistence in harvested populations
Alex J. Klein Interacting effects of vegetation and hydrogeomorphic complexity on nitrate in agricultural waterways
Anne Marie Panetta Migration and adaptation in response to natural and experimental climate gradients: Implications for species’ responses to climate change from a field transplant experiment
Noam Ross Managing fungal diseases with optimal control methods and individual-based models
Jonathan Salerno Quantitative evaluation of conservation strategies in Tanzania: Household livelihoods and wildlife conflict in community-based management areas
Allison Simler Resprouting and disease dynamics in forests impacted by compounded disturbances: Wildfire and sudden oak death in Big Sur, CA
Jens T. Stevens Multi-scale effects of fire severity on snowpack dynamics in montane coniferous forest
Elise M. Tulloss Tracking the fate of nitrogen deposition in a spatially heterogeneous savanna landscape: A short-term 15N labeling experiment
Jennifer I. VanWyk Wet meadow restoration buffers the impact of climate change: pollinator resilience during the California drought
Benjamin Waitman Ectomycorrhizal enzyme production is largely resilient to N-deposition in a Mediterranean forest system
Robert Walsh What 100+ amino acid isotope (CSIA-AA) studies reveal about tracing organismal ecology: Roles of trophic interactions, phylogeny, and environment
Alexandra M. Weill Fire regimes and functional traits: Adaptation and population resilience in obligate reseeding shrubs
Matthew A. Williamson Preliminary assessment of opportunities and obstacles for climate information use in resource management decisions in the Southwest
Joy B. Winbourne Controls on free-living nitrogen fixation during decomposition of leaf litter across a soil-age gradient
Lauren Yamane Differences in response to environmental variability across Pacific salmon species
K. Ash Zemenick Do flower visitors introduce unique nectar microbial communities to strawberry flowers?
Easton R White The inevitable partial collapse of an American pika metapopulation

Faculty, postocs and other students and researchers from Davis

Name Title/Link
Kendra M. Chan Effect of species and genotypic diversity on eelgrass detrital systems
Richard C. Cobb The potential of tree resistance to Phytophthora ramorum as an alternative to scorched earth eradication measures on tribal lands
Howard V. Cornell How are regional species pools used in community ecology?
Christopher R. Dillis Phenological and population responses of the invasive pioneer tree, Bellucia pentamera (Melastomataceae) to selective logging disturbance at Gunung Palung National Park, Indonesia
Katherine A. Dynarski Role of bedrock nitrogen in regulating asymbiotic nitrogen fixation and plant tissue chemistry
Anu Eskelinen Multiple resource limitation interacts with plant functional traits to drive productivity and diversity responses to climate
Valerie T. Eviner Opportunities and challenges in linking ecological science, policy and management to address current and future environmental issues
Eugenia Gonzalez Integration of carbon fluxes and ground-based broadband vegetation indices (VIs) in a tropical dry forest in Western Mexico
Elise S. Gornish Defoliation and habitat effects on Medusahead demography
Jennifer R. Gremer Gambling in the desert: Bet hedging in Sonoran Desert winter annual plants
Juan C Ruiz Guajardo Density manipulations influence colony aggression, expansion, and survival success of the mutualistic ant-acacia species Crematogaster mimosae (Santschi)
Susan Harrison Declining diversity in response to intensifying midwinter drought in a Californian grassland
Alan Hastings Residence time and turnover times in a changing environment
Alan Hastings Population ecology: Prediction is harder than understanding
Kristin Hulvey Using forest-based carbon programs to conserve biodiversity
Ermias Kebreab Livestock’s role in rural development – the case of Vietnam
Alexander Koltunov Reconstructing 20+ year history of subpixel forest canopy cover, structure, and disturbances at 30-meter scale with a suite of advanced Landsat image processing systems
Adam Lampert Social-ecological challenges for cost-effective restoration of degraded ecosystems
Andrew M. Latimer Evolutionary relationships of functional trait and environmental variation: Gene expression variation across the range of a plant species
Alejandra Martinez-Berdeja Effects of variation at flowering and dormancy loci on life history and fitness responses of Arabidopsis thaliana to different precipitation regimes
Mariah H. Meek Protecting life history diversity: Using genomics to aid conservation of imperiled salmon
Kara A. Moore Ecological drivers of rare desert milkweed persistence amid utility-scale solar energy
Bryan N. Nguyen Effects of wrack composition, age, and cover on the spatial distribution of beach arthropods
Joshua M. Rapp Increase the mean, reduce the variance, or bet on a bonanza: How should plants respond to environmental variability in pollen receipt?
Nick L Rasmussen Consequences of shifts in the mean and variation in prey phenology for predator-prey interactions
Pamela L. Reynolds Global seagrass ecology: Biogeography of Zostera marina community dynamics
Keely L. Roth Relationships among leaf traits and leaf spectra: Prediction, clustering and functional types
M. Rei Scampavia A novel mechanism of pesticide exposure to a cavity-nesting solitary bee: Can residues in nesting material affect female selectivity and reproductive performance?
Sebastian J. Schreiber Short term climatic rescue of an endangered species? The interactive effects of climate and a pathogen on the demography of Menzies’ wallflower
Mark W. Schwartz Science, education and management to redress ongoing losses of biodiversity
Mark W. Schwartz Integrating conservation practice into ecology education for students seeking non-academic careers
Andrew Siefert Soil mutualists mediate interactions of Trifolium species: Implications for fine-scale co-occurrence
David R. Smart Biological nitrogen fixation by biocrusts and contribution to N flows in a grazed grassland ecosystem in Northern Mexico
Joanna P. Solins Influences of urban hydrology and channel morphology on the dry-season water status of riparian trees in a Mediterranean climate
David A. Spiller Multiple effects of hurricane-induced marine subsides on island food webs
Sharon Y. Strauss Experiments and observations within the full dimensionality of field niches reveal a nonlinear relationship between ecological similarity and phlyogenetic distance between species
Katie Stuble Above and belowground impacts of climatic warming drive rates of decomposition in a grassland ecosystem
Susan Ustin Can plant traits be used to classify functionality in remote sensing data
Rachel Vannette Microbes: Essential mediators of plant-animal interactions?
Truman P. Young Every restoration is unique: Testing priority effects, year effects, and site effects as determinants of initial restoration trajectories

Data management – actually easier than herding cats

It’s a new year, new grant cycle, time to think about everyone’s favorite topic – Data management! OK, it’s probably not the most fun thing you will ever do. If you really love databases, Endnote libraries, data dictionaries, and quality assurance plans, you will have great job security later in life. However, if you are like me you started grad school with a vague proficiency in Excel and some idea that you should take good lab notes. Managing data in any organized fashion was never as fun or interesting as collecting it. I was sure to remember what I did, why I did it, and where I put it, right?

You can get away with sloppy data management with a small project, but you should start good habits early. Even that pilot study needs a little help from the data organization cat!

No. Not really. It is amazing how difficult it is to remember why I didn’t catch any mice at Big Marshy Lake, or what LITTER stood for when I came up with that acronym. If you want to produce useful data that allows you to write scientifically defensible publications and share your data with others, you need a data management plan.

Not convinced? Well, more to the point, many funding agencies now require a data management section in grant proposals where you describe your plans to efficiently collect, QC, analyze, store, and share your data.

So what is data management? I recently attended two sessions at ESA in Sacramento on tools and tips for managing ecological data. The organizers were from DataONE,  (Data Observation Network for Earth) which is an organization that searches data stored across many different data repositories and organizes multiple tools and resources for managing and analyzing data. They broke down the process of data management and introduced tools to make it easier. I have attempted to compile their work into guidelines for your own data/cat management plans.

The data management life cycle, from USGS's data management website.

The data management life cycle, from USGS’s data management website.

Step 1: Plan

Plan your data collection and management before you start. You will undoubtedly make changes as you go, but starting with a plan will prevent avoidable mistakes.

Developing your data management plan is hard work. It should be done in a very comfortable chair.

  • Start by looking at the whole data life cycle, you want to plan every step before you collect your first data point. Check out https://dmptool.org/dashboard  , it’s like TurboTax for data management plans. They even include specific requirements that funding agencies require in management plans for their grant proposals.
  • What protocols will you use? Your data should be comparable with others, so try to use established protocols and methods when you can instead of developing your own from scratch.
  • What format will you use to record the data? Will you use paper data sheets or direct computer entry?
  • Who will collect your data? Training interns/kittens before you start to make sure everyone is interpreting and recordings things the same way will help avoid errors. Training them in good data management skills is also critical  (I wish I had told my kittens to always write the date on their data sheets… I have no memory of when we collected those hairballs at the neighbors catnip patch).
  • Start metadata early! Make a “data dictionary” of common terms and abbreviations that you can refer to in the field.
  •  It is important to think how others might use the data, so include anything that might seem redundant or unnecessary to record for a single study, but puts the data in context with other studies of its type.
  • Where will the data be stored? Decide on a repository and whether you will have to put any restrictions on its use (see Preservation section below).

Step 2: Acquire

Along the way: Manage quality

(also known as Quality Assurance/Quality Control, or QA/QC)

This cat makes a fatal mistake in quality control. Never shred your mistakes. Fix them or omit them from analysis, but keep a record of the original version.

  • QA/QC begins in the planning stage and follows you throughout the data life cycle.
  • Do most of the work before data are collected:
    • Assign responsibility for quality control to one cat in the lab/field
    • Define and enforce data collection standards
    • Minimize repeat entries
    • Learn to use databases effectively (Most felines don’t really know how relational databases work). Using relational databases minimizes repetition and allows you to query the information you need for analysis in the correct format quickly and easily.
  • Use tools such as forms and data-checking techniques in most database programs
  • If you are managing a large group of kittens, perform data or lab audits to make sure all felines are collecting data the same way
  • Bring in an expert to check your work, or send a certain percentage of your samples to an alternate lab for confirmation.
  • Search data for outliers before analysis. Some techniques for finding outliers include basic graphic techniques such as histograms, scatter plots, and quantitative checks such as comparing median with the mean.
  • Deal with outliers on a case-by-case basis
  • Always document changes made to the data.

Along the way: Describe your data (Metadata!)

  •  Metadata is the who, what, where, when, why and how of your data. Like QA/QC, this should follow you throughout the data life cycle
  •  Record your planning process
  • Record what protocols were used to collect all your data, who collected it, when it was collected, and where it was collected
  • Record what quality control procedures were used on it, and any changes made after data was collected
  •  Record where the data will be stored and who will be allowed access to it.
  • A document with all of these metadata should be included with your data whenever you do anything!
  • This tool can help you put your metadata into a standardized format and stop you from forgetting anything: https://knb.ecoinformatics.org/#tools/morpho

Along the way: Back up and Secure

  • Your data is precious. Do not leave your entire dissertation sitting on a thumb drive that gets lost in a hole in your pocket. Do not trust it to your hard drive. Keep it in multiple locations, one of which should be an on-line service that is accessible anywhere.
  • Scan or make copies of paper data sheets
  • Back up your files in non-proprietary formats such as .csv and .txt. This will make it easier for others to use and will add to its longevity.
  • Store metadata with your data.

Step 3 and 4: Process and analyze your data

Don’t forget to record exactly when and where cats fell asleep on your laptop during the data analysis stage.

  •  Hopefully you planned what transformations and statistical analyses you are going to do in the planning part of the data life cycle.  Now is the time to get cracking!
  • Do not neglect your metadata during this stage in the process. Record what analyses you tried that did not work out as well as the ones you plan on using so that you do not repeat your mistakes.
  • I won’t go further into how to do data analysis here, that’s a whole ‘nother bag of cats…

Step 5: Preserve

  • If you have been backing up your data regularly, you should be half-way there. However, back-ups are designed to restore what you are working on in case you lose it, while archives and repositories are built for long-term storage and reuse by others.

Choose your data storage wisely.

  • Re-evaluate your documentation. Would an outside researcher be able to recreate what you did? Is there sufficient information to place your data in context?
  • Store your data in an on-line repository and include a data attribution file with full information on who produced the data set and who should be contacted for more information.  These repositories also provide a  DOI (Digital Object Identifier), to make your data easier to cite and discover.  Repositories include:
  • Consider licensing and legal issues. For example, many federally funded projects require data to be publicly available. Some open-access journals (PLOS and others) also require data to be publicly available. However, data concerning human subjects or location data on species of special concern may be sensitive. (more on legal and privacy issues from DataOne’s policy guide)

DOIs allow other people who use your data to cite it properly.

Step 6: Share your data

  • Just because your data is up in a publicly available repository doesn’t mean people will be able to find it or use it.
  • Include information on where your data can be found in any publications you produce using it.
  • Submit your dataset to Data Portals and Catalogs to them more visible and more likely to be employed by others. Data Catalogs and Portals (Like DataOne) provide searchable directories of data and usually include many data repositories.
  • Tweet it! Facebook it! Social media is the way of the future!

 

Lots of scientists use twitter these days to publicize new publications, including data sets.

 

More resources on data management:

USGS data management website:

http://www.usgs.gov/datamanagement/index.php

Cool paper on data collection:

http://www.esajournals.org/doi/pdf/10.1890/0012-9623-90.2.205

Data Management Plan Tool:

https://dmptool.org/dashboard

Data management best practices:

https://www.dataone.org/sites/all/documents/DataONE_BP_Primer_020212.pdf