CSEE 2017 Highlights

This year the ecoblender lab attended CSEE 2017. The conference was great and covered four days of talks, workshops, and networking events. I attended a free workshop that taught some basics in mapping spatial data and different packages to use in R. There was also a wide range of talks that mostly seemed interdisciplinary. This included discussions of uncertainty in ecology, estimate the value of natural resources, and developing models of habitat selection. Here are some of the highlights I took away from the conference:

Modelling:

There was discussion over the usage and power of mechanistic vs. phenomenological models. This is a topic discussed often in ecology (see of that discourse here), but can be defined here as:

mechanistic: includes a process (physical, biological, chemical, etc) that can be predicted and described.

phenomenological: Is a correlative model that describes trends in associated data but not the mechanism linking them.

The discussion mostly described the relationship between phenomenological and Mechanistic models as not binary and rather a gradient of different models that describe varying amounts of a particular system. However, it did touch upon models such as GARP and MaxEnt that are often used for habitat selection or SDM but neglect the mechanism that is driving species occurrence. Two techniques I would like to learn more about are Line Search MCMC and HMSC which is a newly developed method for conducting joint species distribution models.

Camera traps:

There was also a morning session that described benefits and tools for using camera traps. These sessions are always great as they give a chance to see some wildlife without disturbance. Topics focus around deer over abundance harming caribou populations, how wildlife bridges do not increase predation through the Prey-Trap Hypothesis and techniques for using wildlife cameras or drones. One talk that was particularly interested used call back messages when triggered to see how animals respond to noises such as human’s talking or a mating call.

One of the more useful things I believe to have taken out of the session is how to estimate animal abundance and movement when the animals in your camera traps are unmarked. One modelling technique using Bayesian modelling and was found to be equivalent to genetic surveys of animal fur for estimating animal abundance. This is in contrast to the more frequent spatial capture-recapture (SCR) methods that either mark individuals or supplement camera trap data with other surveys. I also discovered there the eMammal project at the Smithsonian that is an Open Access project for the management and storage of camera trap data.

Ecology and climate change:

Climate change as always is a big topic at these conferences. There was a good meta-analysis out of the Vellend lab that show artificial warming of plant communities does not result in significant species loss. However, there was evidence that changes in precipitation does significant impact plant communities. The results are very preliminary, but I look forward to seeing more about it in the future. I also liked a talk that is now a paper in Nature that models networks in the context of climate change. The punchline of the results being that species composition in communities is dependent on dispersal, and high dispersal rates can maintain network structure although members of the community may change.

I presented results from our upcoming paper modelling positive interactions in desert ecosystems:

Overall I learned a lot from the CSEE 2017 conference and thought it was a health balance of size and events. Victoria was also a great city and made hosting the conference very easy. Next year it will in the GTA and I plan on connecting with the organization committee to potentially host an R workshop at the beginning of the conference. Until then!

MSc or PhD for Canadians to do research in desert ecology or open science in California

Great news, we have had some funding come through for some research in California.

Two options, MSc or PhD.

Desert ecology research

The primary focus of the research is exploring how we might better use positive interactions between plants for restoration and management of arid systems. In particular, we want to examine influences on other taxa such as insects (including pollinators), endangered animal species (such as leopard lizards and kangaroo rats – cute), and on community biodiversity dynamics.

Details

Graduate-level research with The Nature Conservancy in Carrizo National Monument of positive-plant animal interactions.

GPA for YorkU Biology is A-, A.

Need to be able to drive.

Competent in R.

Admission Requirements

Open science research

Graduate-level research on open scientific synthesis. The goal is to explore existing data in high-stress ecosystems such as deserts and do synthesis. Data aggregation, systematic reviews, and meta-analyses to explore the importance of foundation species and biodiversity. This is a unique opportunity because this person can also collaborate with NCEAS to explore teaching open scientific synthesis, develop materials, and do research with the process of doing open science for synthesis.

Details

Excited about open and team science.

Competent in R.

Excited to work with big data, access data repositories, and do synthesis.

Excited to become an educator and contribute to positive change by developing materials (code, packages, guidelines, etc) that use these approaches.

Same admission requirements as first position.

Start date is Sept 1, 2017 for both/either opportunity.

http://futurestudents.yorku.ca/graduate/apply-now

I recommend you pop me an email too if you are interested: lortieATyorku.ca

Ecoblender hosting a workshop: An Introduction to R and Generalized Linear Models

Full details are provided here.
https://afilazzola.github.io//YorkU.GLM.2017-04-28/

General Information

The purpose of this workshop is to provide tools for a new/novice analyst to more effectively and efficiently analyse their data in R. This hands-on workshop will introduce the basic concepts of R and use of generalized linear models in R to describe patterns. Participants will be encouraged to help one another and to apply what they have learned to their own problems.

Who: The course is aimed at R beginners and novice to intermediate analysts. You do not need to have any previous knowledge of the tools that will be presented at the workshop.

Where: 88 Pond Road, York University. Room 2114 DB (TEL). Google maps

Requirements: Participants should bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) with administrative privileges. If you want to work along during tutorial, you must have R studio installed on your own computer. However, you are still welcome to attend because all examples will be presented via a projector in the classroom. Coffees and cookies provided for free.

 

How we use a handheld soil moisture probe to supplement in situ plant ecology sampling

It is best to deploy loggers with appropriate sensors to capture an environmental signal within a set of study sites. Nonetheless, when actively sampling for plant-plant interactions dynamics,  an estimate of soil moisture at that particular point in time and space precisely is useful (at least as a covariate). We use the Delta-T SM-150 handheld unit to complement our long-term logging arrays.

Here is a brief summary of the settings/methodology we use.

Method

  1. Push right button to activate unit.
  2. Repeatedly depress right button to cycle through modes until you reach ‘organic’.
  3. Insert probe into ground and ensure that metal conductors are fully embedded in ground with ceramic/plastic unit flush with ground surface.
  4. Left button to measure. Typically, it should take only 1-2 seconds.
  5. Avoid rocks and voids in the ground when inserting probe.

Comments: Ranges you can expect at least in arid and semi-arid systems we have tested within California are between 1-40% but most frequently < 10%.  The unit is durable, and the control unit is ‘water resistant’. However, when the controller gets wet in the rain, it stops working until it drys out again (typically at least a day later). The cable is not that robust, and to be safe, we insert/push the sensors into the ground using the ceramic casing.

 

Microenvironmental change in Cuyama Valley 2017.2 goals

In 2016, we deployed micro-environmental data logger arrays to monitor global change dynamics at very fine scales. We also structured measurements to ensure we can infer and link to a biotic interaction signal between common plants within this region.

This is very important region to study for at least two reasons ecologically.

(1) Water issues with people, plants, and agricultural are critical here.

(2) Cuyama Valley is an excellent set of sites or mesocosm for the San Joaquin Valley at large. The San Joaquin Valley is still sinking (NASA report). We need to understand temperature, precipitation, and soil moisture availability patterns at many scales within the region.

This season, 2017, is a relative boom year in terms of precipitation. Here are the immediate sampling goals for this season.

1. April (mid). At peak flowering, count burrows, re-measure shrub sizes, sample annual vegetation, and collect biomass.
2. May (mid). Retrieve all logger units, download data, and check functionality. These data capture two growing seasons – one drought, one wet.
3. May (mid). Re-deploy and re-initialize loggers. Rationale – need data on shrub effects when it matters for animals like lizards and hoppers etc and when it is really hot.
4. Sept (end). Retrieve loggers and sensors, download data, end experiment.
5. Oct. Design and test a missing-data strategy to address missing sensor and logger failures. I will likely implement a within-site, resampling data strategy associated with central tendency measures to fill gaps.

mini-reviews

Mini-reviews are shorter and more focused than traditional literature reviews. Their specific format varies between journals, however they all have a few things in common: They are topical, concise and specialized, rather than being exhaustive. They quickly bring the reader up to speed on current research in a field, particularly when there has been a major change in thinking. This is in contrast to major reviews, which provide a comprehensive overview of a subfield.

Mini-reviews often synthesize recent research, offering insight and new direction in an important emerging research area. They ideally propose new ideas and hypotheses that arise from the synthesis. Challenging current views in ecology and embracing a bit of controversy is welcome. Despite being called minor, these reviews may garner higher readership and impact than major reviews, due to their conciseness, readability and relevance. I think they are particularly suited to interdisciplinary synthesis, as they do not require writing an exhaustive background from each field, making it easier to communicate the interesting or important aspects of the crossover to a wider audience.

While only a handful of ecology journal explicitly provide guidelines for a mini-review, but quite a few impose a shorter word limit (< 3000 – 5000) and limit references to around 40, essentially requiring a mini-review. Other keywords I have noted are ‘topical’, ‘specialized’, ‘research reviews’, ‘briefings’ and ‘question-based’.

They following ecology-related journals either publish mini-reviews by name, have previously published mini-reviews or their submission guidelines strongly suggest that they welcome the format:

  • Journal of Ecology
  • Methods in Evolution and Ecology
  • New Phytologist
  • Annals of Botany (Botanical Briefings)
  • Frontiers in Ecology and the Environment
  • Global Ecology and Biogeography
  • Conservation Letters
  • PLoS Computational Biology
  • Insect Conservation and Diversity
  • Basic and Applied Ecology
  • Functional Ecology (question-based)
  • Ecosystems (invited only)

Mojave Desert Site Selection

I recently had the chance to spend a few days exploring in the Mojave National Preserve in California to select new study sites for my study of plant-plant-pollinator positive interactions. Sunset Cove, located in the UCNRS Sweeney Granite Mountains Desert Research Centre, is host to an incredible diversity of shrubs and cacti. The two foundational species I will be studying are creosote bush (Larrea tridentata) and buckhorn cholla (Cylindropuntia acanthocarpa), which are codominant in this site.

Annuals were germinating all over the site, however they are still incredibly tiny. Both creosote bush and buckthorn were showing facilitation, with higher abundances of germinants under the shrubs than in open areas. Finally, one cool observation was that 100% of the buckhorns surveyed were growing in close association with another codominant, but only 70% of creosote bush were growing with a codominant, suggesting cacti have some interesting interactions in this area. Finally, this area has been experiencing winter rainfall leading to optimism about flowering this spring.