SC/BIOL 4000 8.0 BIOLOGY HONOURS THESIS

This Fall will be remote for the majority of academic activities. The 8.0 credit honours thesis program is approximately 8mos in duration. The student leads an independent research project. As a team, we would like to work with two individuals on one of the following projects. Each student will work with a graduate student or postdoc and Chris Lortie.

a. Each project is individually implemented by the student safely.
b. Zoom calls with Chris and the co-mentor to ideate, solve, and plan will be used to collaborate in addition to editing datasheets and docs.
c. It will be beneficial for the student to have experience in R and be able to work independently.
d. The pre-reqs are listed online for BIOL4000 are here and currently include students their final year with a BIOL GPA of at least 6.0.

Tree forest dynamics at YorkU

(1) Subway effects on trees and woodlots. A census of tree forest dynamics and individual tree changes on YorkU campus. Jenna Braun, Mike Belanger, and I dug through census records compiled by the YorkU master gardener in 2012 and 2013. Over 5000 trees were tagged on campus and their size and health were recorded. The data are here. This is a fantastic project and opportunity to revisit a superb dataset in R and also resample some or many of the trees. We now have a subway rumbling away underneath campus, and we can check trees near and far from the line and test the hypothesis that disturbance belowground influences tree growth and health.

(2) Other ecological hypotheses relevant to urban forest dynamics (disturbance, new buildings, edge or center of campus etc). There are at least two projects here. The students can work independently and still split up the work of testing more than question or hypothesis. One individual can (re)sample trees from 2012 and 2013 near/far subway lines, and a second student can examine any other ecological question with disturbance, new buildings, or how sets of trees are doing in different ecological contexts on a university campus.

Desert ecology data analyses

We have many open datasets ready to go for deep analysis work if you are competent in R (or Python but we work in R in the lab). Many spatial questions, niche questions, or use or plant and animal survey data and join them to new data on climate or downscaled remote data if you are game for that adventure. Here are a few examples.

Vegetation under shrubs and in the open in the Central California Deserts.
Data.

Desert arthropod diversity patterns in California.
Data.

Camera traps and birds of the deserts.
Data.

In each instance, the workflow will include a few Zooms to plan analyses and additional data lookups, then the student researcher digs in!

To apply

If you meet the pre-reqs and are in your final year in YorkU Biology, please email lortieatyorkudotca, and we will set up an interview with you for the team!

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

Documenting my study of plant interactions

The first of hopefully many more videos documenting my travels throughout the deserts of California studying plant interactions.

Precipitation mediates the mechanism of facilitation in a Californian Desert

ESA 101 at Fort Lauderdale is coming up! I will be presenting on recent findings from an experiment we conducted over two years. I am extremely excited for both the presentation and the results! Here is the slide deck, statistical analyses and program outline.

https://afilazzola.github.io/water.consumer/

Background/Question/Methods
The stress gradient hypothesis original purposed the frequency of plant interactions along countervailing gradients of abiotic stress and consumer pressure. However, research to date has studied these two stressors in isolation rather than together, thereby potentially neglecting the interaction of these factors on plant composition. In the arid central valley of California, we artificially manipulated a soil moisture gradient and erected animal exclosures to examine the interactions between dominant shrubs and the subordinate annual community. We conducted this experiment in an extreme drought year (2014) and a year of above-average rainfall (2016).

Results/Conclusions

Shrubs positive affected the abundance and biomass of the annual community at all levels of soil moisture and consumer pressure. In the drought year, shrub facilitation and water addition produced similar positive effect sizes on plant communities; however, the shrub facilitation effect was significantly greater in watered plots. During the year with higher rainfall, there was no observed water or exclosure effect, but shrubs still significantly increased biomass of the subordinate plants. Shrubs and positive interactions maintain productivity of annual plant communities at environmental extremes despite reductions in droughts stress or consumer pressure and these positive effects are even more pronounced with water addition. The relationship between consumer pressure and abiotic stress on plant interactions is non-linear particularly since shrubs can facilitate understorey plants through a series of different mechanisms.

Loggers, micro-environments and ecology: an ESA 2016 Workshop

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We would like to advertise our ESA workshop: How to Set Up Automated Sensors Arrays for Measuring Micro-Environmental Characteristics and Synthesize to Larger Scales

Abstract: Tracking the consequences of environmental change requires information on both the physical and biological characteristics of ecological systems. Large-scale environmental data are now widely available from many data repositories. However, these data sets often need to be down-scaled in order to be paired with local ecological measurements. Hence, micro-environmental sensors are sometimes useful to integrate scales of ecological information relevant to global change. In this workshop, we will demonstrate the use of all major affordable types of micro-environmental sensors available to collect fine-scale environmental data. Using the R environment, we will also provide the means to analyze these data and also to integrate this information with ecological data and macro-environmental data streams. The overall purpose of this workshop is to provide attendees with hands on experience on the use of automated sensors of micro-environmental variables, their appropriate deployment in the field in relation to ecological questions, and an introduction to the integration of micro-scale data to larger environmental datasets. This workshop will also serve to launch MicroNet. This is an open-source, collaborative network of micro-environmental sensors deployed globally.

 

And this is the link to the ESA Programme: https://eco.confex.com/eco/2016/webprogram/Session11870.html

 

The workshop will take place on Monday August 12 at room 304 of the Fort Lauderdale Convention Center, between 11:30am and 1:15 pm.

 

We hope to see you there!

 

Eco-graduate student research seminars @YorkU on Nov 17-2015 #STEM with #STEMDIVERSITY

Many of the graduate students in ecology & evolution are presenting from within the Biology Department @YorkU on Nov 17,2050 from 530-830pm in LSB 105. We will explore whether we can live stream or google hangout share it.  If you are near campus and want to check out some new research in person however, please pop in. Seminars are 12mins in length with a few minutes allotted for questions.

Lineup
Sean Chin
Amanda Liczner
Taylor Noble
Alannah Ruttan
Katrina Gaibisels
Samantha Stefanoff

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#ESA2015 Organized Session: Implications of positive interaction studies to the future of ecological research

We would like to invite you to the ESA 2015 session OOS 37 (quite a few of us from the lab will be in attendance).

Implications of positive interaction studies to the future of ecological

research. The session is on Wednesday, August 12th from 8:00-11:30am.

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The goal of this session is to highlight the current state of

facilitation research and describe the future projections including

available gaps in the literature. Broadly, this session provides a

synthesis of positive interaction studies across different ecosystems with

topics ranging from niche expansion, coexistence, evolutionary adaptation,

and global change. This set of studies showcase the growing importance of

positive interactions for ecological processes and biodiversity

coexistence. We also guarantee that it will be entirely entertaining. We

will be on social media to share and explore questions in real time. We are

encouraging presenters to share in advance as well.

 

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Speakers

8:00 AM – A role for soil microbial communities in plant-plant facilitation

Cristina Armas, Consejo Superior de Investigaciones Científicas; Yudi M.

Lozano, Consejo Superior de Investigaciones Científicas; Sara Hortal,

University of Western Sydney; Susana Rodríguez-Echeverría, Centre for

Functional Ecology; Francisco I. Pugnaire, Consejo Superior de

Investigaciones Científicas

8:20 AM – Positive interactions expand habitat use and the realized niches

of sympatric species

Sinead M. Crotty, Brown University; Mark D. Bertness, Brown University

8:40 AM – Facilitation in plant communities: Driver of evolutionary

adaptation?

Christian Smit, University of Groningen

9:00 AM – The future of gradient studies in examining plant-plant

interactions for the next 100 years

Chris Lortie, York University

9:20 AM – The consequences of plant–plant interactions at the community

level: A niche-based approach

Christian Schöb, University of Zurich; Sara Hortal, University of Western

Sydney; Alison J. Karley, The James Hutton Institute; Luna Morcillo,

Universitat d’Alacant; Andrian C. Newton, The James Hutton Institute; Robin

J. Pakeman, The James Hutton Institute; Jeff R. Powell, University of

Western Sydney; Ian Anderson, University of Western Sydney; Rob W. Brooker,

The James Hutton Institute

9:40 AM – Break

9:50 AM – The competition cascade: Indirect facilitation emerges as a key

driver of species richness under neutral, niche or individual difference

Eliot J. B. McIntire, Natural Resources Canada

10:10 AM – Positive species interactions and climate change at global scales

Qiang He, Duke University; Brian R. Silliman, Duke University

The session is on room 314 of the Baltimore Convention Center. We hope to

see you there!

 

Abstracts

http://eco.confex.com/eco/2015/webprogram/Session10663.html

Little data, big data, & equipment archival goals & guidelines

I have been thinking about our goals to get all data entered within a few weeks of completion of field season. Also, we have added a new set of animal cams, loggers, etc to our lab inventory.

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Little data
Goal:
At the end of the 2016 season, I want to take a shot at doing what I proposed in the NSERC grant. Aggregating the little data into big data for the San Joaquin Valley Region from our lab. I see connecting shrub data, subordinate plant data, seedbank data, crickets, leopard lizards, and pollinators as opportunities for connection. I propose we get all little data (individual sampling events and experiments), archived appropriately with meta-data. Each instance is georeferenced and time stamped.  If it is a two-phase structured experiment (shrub-open), perfect. I will then collapse each instance at that level into effect size estimates for comparison. I will not use Rii but instead Hedge’s d or LRR for instance. Alternate approach, secure common measures such as density (abundance of whatever taxa was sampled) and load up micro-environmental estimates (smoothed) and run an SEM.

Worflow:
Use the google drive. Same format as usual.
(1) Cut and paste from primary data files into google sheet to preserve formatting and ensure version control from that point forward.
(2) Tabs for site data, primary data, meta-data, derived estimates such as aggregated means or effect size estimates, and other ancillary data.

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Big data
Goal:
At the end of this season, by Sept 2015, explore the capacity to mine big data in the form of animal cam pictures (Amanda from Panoche and Taylor from Carrizo Plain National Monument) and pollinator videos (primary Ally).  I see a nice opportunity for some code from Alex, a workflow and semantic development on how to integrate, and the derivation of common measures across all big data in this form. We can also explore bulk processing of all imagery via algorithms or mechanical turks. Output, big data how to paper, primary papers for each study, then a synthesis paper across all big data out there on this topic.

Workflow:
(1) Amanda – archive all animal cam pics on Flickr. Done! yahoo. Use albums, tags, and explore enabling easy mining. Develop clean signal to communicate collaboration and sharing and not my name, ie ecoblender.
(2) Ally – use youtube or the same Flickr account. Put all 2015 videos up asap in albums with tagging emulating decisions by Amanda.
(3) Diego – same approach for pollinator videos.
(4) Taylor – animal cam pics on Flickr for now.
(5) Ally – then begin backloading up older pollinator video libraries asap including alpine sets.

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Equipment
Goal:
Keep track of equipment and preemptive this upcoming season to avoid last minute ordering. Also, align equipment usage and purchasing more effectively with collaborators.

Workflow:
1. Use existing google sheet on drive within ecoblender ‘logistics’ folder entitled ‘ecoblender equipment’.  I copied the 2014 tab and generated a new one for 2015.
2. Collapse previous equipment usage for 2015 into this new doc and include column for grant (NSERC or BLM), principal investigator on equipment, and condition.
3. Sharing and sampling duration are now included as well if we are able to share certain individual items collaboratively.

 

#phenology with plant-animal update for California Deserts

Panoche Hills Ecological Reserve & Carrizo Plains National Monument are fascinating this year (as in highly variable rainfall patters, temperature, and responses by the biota).  Updates continue.
(1) Blunt-nosed leopard lizards are out at several deserts.  This is up to 6-weeks earlier than long-term patterns.

(2) Numerous insects are up and running at Carrizo Plains National Monument (but limited bees). This is still two-weeks later than flowering plants but the mismatch is less pronounced now.

(3) In an addition experiment of native seed to explore restoration at Panoche Hills Ecological Reserve, we saw very limited ‘establishment’ i.e. the mode of germination was < 1% for all three species tested. There is little evidence that these plants will reach flowering before the temperatures get too high.

Scroll to bottom for a few surprises spotted by collaborator Michael Powers (all photos courtesy of his mid-season census).

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