Land Acknowledgments

Recent talks I have attended mentioned indigenous histories at their research sites. This is a positive form of provenance not just of the site or place but of the sense of its ecology. Nonetheless, it has been proposed that talk is cheap. There at least five major implications of this premise.

  1. Acknowledge but propose a solution for those lands to better recognize the diversity of peoples associated with its present and past.
  2. Similar to prepping a data management plan, prepare a land and research provenance management plan that includes sharing and communicating results to current and past stakeholders within the region.
  3. Provide the audience or readers with an opportunity to contribute to this recognition process. This can include mechanisms such as an NPO or charity to support associated with the land use culture and peoples, a mailing address or contact details for more information, a link to additional resources or the site for deeper reflection, and finally lead by example and mention how your research process incorporated provenance.
  4. Revisit the culture, history, and ecology at the end of the talk by reconnecting with its peoples. In many of the systems we work in as a team in Central California, Ephedra californica is a foundation plant species. This plant has a long history of use and management by many. Mention this as a key connector to the ecology that we now study. These ephedra parklands reflect many processes of change including active management.
  5. The written word is powerful. In the standard ‘study site’ description included in the Methods section of field ecology papers, consider a statement describing and citing work on the indigenous people and culture that supported your study site.

Campus tree project 2020

Two super experiments.

  1. Exotic animal responses to trees and disturbance.
  2. Individual tree and patch-level dynamic responses to disturbance.
  3. Post hoc synthesis and contrast of interaction pathways.

Sample academic plans

Table, list, freeform, calendar, all good. Match your modality or even use more than one mechanism to support your journey this Fall and beyond.

Journey rabbit


Read Spatio-temporal statistics with R

Read Advanced R (skim some bits, functions)


Rangeland brome papers x2

Scientific synthesis paper

Editorial on distributed learning

Dream on – notes on how to do experiments into paper

Magic paper with Mario

Synthesis papers with Mario, Nargol, and Malory


Teach BIOl3250

Review apps for Diol grad committee

Support team in papers and planning


Seminars on experimental science

Connect with USAID folks



YUFA to write a book

Journey army ants

1) Apply for NSERC and other grants

2) Readings list for PhD project

3) Select committee Members 

4) Come up with a few thesis questions

a. Possibly run a meta/Systematic review (Would need to make a super clear one though)

b. Continue with density? Maybe make areas with a bunch of replicate shrubs and see what happens. Or cut some shrubs down and see what happens

c. Maybe look at how density of shrubs has an impact on invasive grasses?

d. Maybe look at one specific animal species and compare density of that specific species to density of shrubs?

e. Or maybe take a completely new route on thing.

5) Brainstorm possible field projects for PhD (When we are going, manipulative for experiments, timeframes, etc.)

6) Work on posters and other outside projects/research papers

Journey salamander

Read “Fundamentals of Statistics” Aug 2020

Research possible committee members and reach out Oct 2020

Select a committee member Dec 2020

Come up with a thesis question Dec 2020

Field Work/Data Collection Apr 2020 – Aug 2020

Data Analysis Fall 2021

Reading list for research Winter 2020

Take remote sensing course? Winter 2020

Thesis Writing Winter 2022

Hugh C. Morris Experiential Learning Fellowship application February 15, 2021

Scholarship/fellowship research Oct 1, 2020

Ontario Graduate Scholarships (OGS) application Dec 1, 2020

Journey chipmunk

Not including how ongoing work is structured.. mostly deadlines, hopeful progress and some milestones


Decide on topic

Find committee

Submit NSERC/OGS application

Transfer final insect survey specimens to ethanol

Some progress on synthesis


Come up with a review/meta

Come up with 1or 2 new chapters on top of lizard diet

Progress report

Mail first run of samples to Mark


Field planning

Resurrect and write-up spatial veg finally

Apply for permits if needed

Work through a review

Compile taxonomist list


Family level data input

Second round of specimens sent to Mark

Review data extracted – what is the story?

Do I need to get additional data?

Get into grad level GIS course


Learn simulations 


Research evaluation meeting

Submit thesis proposal to FGS


Submit interim report to BLM

My Q: 

How focused does a topic need to be? How related are chapters?

How do expectations differ for phd from msc

Journey hellgrammite

1) Apply for NSERC and other grants

2) Readings list for PhD project

3) Select committee Members 

4) Come up with a few thesis questions

a. Possibly run a meta/Systematic review (Would need to make a super clear one though)

b. Continue with density? Maybe make areas with a bunch of replicate shrubs and see what happens. Or cut some shrubs down and see what happens

c. Maybe look at how density of shrubs has an impact on invasive grasses?

d. Maybe look at one specific animal species and compare density of that specific species to density of shrubs?

e. e. Or maybe take a completely new route on thing.

5) Brainstorm possible field projects for PhD (When we are going, manipulative for experiments, timeframes, etc.)

6) Work on posters and other outside projects/research papers

Journey capybara

Largest focus on teaching for the fall term. Followed by restarting the greenhouse experiment and finishing seeds in October. Two papers are currently submitted and going through review, with another manuscript in preparation.

Journey kangaroo

-September’s end: finalize rough research questions and ideas to explore for PhD (human-wildlife conflict, trampling, and facilitation)-October 20th: confirm committee members-October: Collect reading list, get seeds and scale from lab to continue seed allocation side project-October 15th: Confirm all AIF Climate Activist Videos online-November: Work through reading list & submit grants (National Geogrpahic Explorer Grant, MITACS?, other small grants). Seed allocation data analyses-December 1st: first progress report-December: Continue working through reading lists, add to lists as necessary. -December’s end: Finish full draft of seed allocation paper-January: Determine 2 cognates and begin drafting cognate literature reviews-March: Finish up first full draft of proposal (due beginning of May)

Fall 2020 goals


  1. Stay healthy.
  2. Be safe.
  3. Connect with team.
  4. Learn something new.


  1. Academic plan.
  2. MSc and PhD committees built and summoned.
  3. Read a pile of papers on existing focus and begin a new direction too.
  4. Proposal.
  5. Complete and submit outstanding synthesis papers.
  6. Book and schedule progress reports.
  7. Prep deck and present at report meeting.


  1. Set hard and soft deadlines.
  2. Populate google calendar.
  3. Identify stepping stones to larger goals and make lists breaking each deliverable down.
  4. Select someone to be accountable to.
  5. Identify collaborations and update them on stepping stones.
  6. Keep track of progress (Gantt charts, notes, meetings, GitHub repos with issues to track).
  7. Plan breaks from the screen.
get the lands out so you have the mana to spend


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.

Desert arthropod diversity patterns in California.

Camera traps and birds of the deserts.

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!

Proposed guidelines for presentation of ecological community responses to a key factor (or set thereof)

Observations on accessibility of evidence and coherence in reported findings

In collaboratively writing this week as a team and in reviewing the literature with a specific meta-question in mind (how best to present community ecology, today, for the specific papers we are working on), we have a formula for a REALLY solid and clear presentation of results for some papers to consider – primarily for those that examined the response of a community (animals, birds, pollinators, etc.) to a key factor such as shrubs, shelters, water, light, or density to name a few ideas. This trend in reporting included competition and facilitation papers not just keystone plant species effects on other species.

FIG 1. Gift to the reader.

Surprise, this is for you. Thank you for getting this far into the paper or even scrolling to a figure. No sarcasm here – everyone busy and there a lot of potential papers to read in ecology and evolution.

This figure is thus the MAIN POINT of paper.
Show them the hypothesis ‘worked’! We defined ‘worked’ as including enough complexity to address how well and when (i.e. community response by phylum or season). So, reading a paper on light and competition on COMMUNITIES (plants or any taxa), we skim to the first figure and EXPECT to see, well you guessed it, light on x-axis then y-some measure of how the community responded – big picture results. We also expected to see some facet or color in data or some level illustrating how well the factor worked so to speak. Is light level always important? Or, does it depend on something?  Almost ALL current papers include that second factor.

Like this or even better really.

The reader is like ‘OH I got it’. Density is important or microhabitat important, but it depends on season because birds fly around a lot and migrate too.

FIG 2. Show something about the species in community.

Imagine a reviewer for a journal such as Journal of Animal Ecology or really any eco-journal.  The editor will try for an ecologist that knows something about desert mammals, birds, or the bees if the paper is about those communities. These readers will expect a second plot to be about composition or show species. Bird people (plant people too when we read community response papers about plants) want to be able see a plot and go OHYA I know that species OR aha I suspected NOT all species responded the exact same way to this key driver.

There are least three options for a STRONG second plot about species.

a. Relative frequencies.
A stacked bar or line plot or something that lists out species and shows their relative frequencies by at least one, prefereably two, key level(s). Rank abundance plots nice but not so common now.

b. A composition plot from an ordination analysis
One that shows something really deep about community OR actually shows species in the ordination plots with labels.

c. A cool species network plot
A plot that shows not only the species BUT how their connections changes based on the key factor(s).

FIG 3. Mechanism or other key ecological context that illuminates WHY the community responded to key factor(s).

Optional (and depends on study of course) but can illustrate how another key moderator IF needed such as RDM, temperature, etc mediates the community outcomes. OR, show the mechanism that explains fig 1 and 2. OR, zoom in on a key finding such as species by functional group, migratory status, etc.


Fig 1 – Main finding with enough detail to encompass predictions or how well and when hypothesis works (or not).
Fig 2 – Show composition or species because this is a community response paper.
Fig 3 – Show mechanism, zoom in on how community responded (functional groups), or show a really important finding that is strongly related to Fig 1 but you did not want clutter up or make it even more complex.

Preferences from a week of work on reading and writing with an attempted laser-beam focus.

Annual plant neighbourhoods

As a team, we are discussing the fine-scale grain of sampling for estimating annual-annual plant interactions in deserts. We are particularly interested in the Mojave Desert to examine pollinator-herbivore interactions with annuals that are mediated by the other immediately adjacent congeneric species. Here is a brief compilation of key papers examining this challenge.

scale matters, a plant’s eye view

Publications describing the fine-scale annual plant neighbourhood concept

Mack, R. N. and Harper, J. L. 1977. Interference in dune annuals: spatial pattern and neighbourhood effects. – Journal of Ecology 65: 345-363.

Holzapfel, C. and Mahall, B. E. 1999. Bidirectional facilitation and interference between shrubs and annuals in the Mojave desert. – Ecology 80: 1747-1761.

Schiffers, K. and Tielbörger, K. 2006. Ontogenetic Shifts in Interactions among Annual Plants. – Journal of Ecology 94: 336-341.

Lortie, C. J. and Turkington, R. 2008. Species-specific positive effects in an annual plant community. – Oikos 117: 1511-1521.

Emery, N. C., Stanton, M. L. and Rice, K. J. 2009. Factors driving distribution limits in an annual plant community. – New Phytologist 181: 734-747.

Luzuriaga, A. L., Sánchez, A. M., Maestre, F. T. and Escudero, A. 2012. Assemblage of a Semi-Arid Annual Plant Community: Abiotic and Biotic Filters Act Hierarchically. – PLOS ONE 7: e41270.

Underwood, N., Inouye, B. D. and Hambäck, P. A. 2014. A Conceptual Framework for Associational Effects: When Do Neighbors Matter and How Would We Know? – The Quarterly Review of Biology 89: 1-19.

Underwood, N., Hambäck, P. A. and Inouye, B. D. 2020. Pollinators, Herbivores, and Plant Neighborhood Effects. – The Quarterly Review of Biology 95: 37-57.

Personal vote

I am a fan of the 15cm scale for fine-scale but often sample with a 15cm ring nested within a second 30cm metal ring. I construct using wire.