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!

Jacob’s ESA 2020 talk

The annual symposium of the Ecological Society of America (ESA) is 100% virtual this year. My “talk” is available for download below, if you’re feeling curious. Questions and comments welcome!!

The content of the talk is from an article published last month in Diversity and Distributions: https://onlinelibrary.wiley.com/doi/full/10.1111/ddi.13111.

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.

The Beetles and the Bees: Interactions Between Herbivores and Pollinators

Check out our newly published article in the open access journal PeerJ: A systematic review of the direct and indirect effects of herbivory on plant reproduction mediated by pollination.

Figure 2: Mechanisms of damage by herbivores that can impact pollination and therefore seed set.
Solid lines represent direct interactions and dotted lines indirect interactions. The two main pathways are direct (direct damage to floral tissue influences pollinators; shown lighter in orange) and indirect (damage to vegetative tissue indirectly effects floral traits; shown darker in blue). Lines and boxes in black represent interactions and steps shared by both pathways. The dotted lines represent the net indirect interaction of plant damage on pollinators (and pollination) that was the focus of this review.

Any gardener knows the havoc that herbivores can have on their plants; whether it’s the rabbits eating their cabbage or beetles damaging their prized roses. Herbivores can devastate a floral display or chew away at the leaves until a plant is too sickly to produce flowers or fruit. However, a discerning gardener will know that not all insects are bad for their vegetable garden; rather they should hope for some bees if they expect to see a good yield of tomatoes or strawberries. Both herbivores and pollinators can influence the yield of fruits and seeds for many plants worldwide and therefore impact both crop yields and plant reproduction. The effects of both types of interactions have been repeatedly tested by the scientific community; however, by their nature, these types of studies must simplify things in order to isolate the specific effect of one species on another and therefore neglect the multitude of other species present that might change this interaction. A caterpillar may chew the petal of a flower that a bee then passes over because the flower is no longer perfect or a rabbit may eat the leaves of a plant that, in consequence, only produces one small flower that is easily overlooked. Bees and other pollinators make choices when they choose flowers to visit, and damage to the plant (whether the flower or not) can result in flowers that are less attractive to pollinators. Similarly, the part of the plant attacked (i.e. leaves, roots, stem, or flowers) should certainly impact this choice differently. Damaging flowers directly reduces the appeal of the flower, and removing it entirely certainly eliminates the possibility of pollination; but how does damage to the leaves, roots and stem change the flowers? Damage to these parts can reduce the overall quality of a flower, whether the flower is smaller or produces less nectar, or if there are simply fewer flowers overall.

This dance between herbivores and pollinators is the subject of the review we recently published in the journal PeerJ: “A systematic review of the direct and indirect effects of herbivory on plant reproduction mediated by pollination.” We collected peer-reviewed studies that examined the effects of herbivores and pollinators on plant reproduction. One of our conclusions is evident simply by the number of studies we found; out of a total of 4,304 studies that turned up in a search on the search engine Web of Science, only 59 studies fit our criteria. That is, not many studies look at both herbivores and pollination. Half of these studies looked at damage to flowers and only about a third looked at damage to any of leaves, roots, and stems (the remainder looked at general damage to any tissue). When tightening our criteria to studies that compare damage to flowers and other parts of the plant, we only found three studies. In our paper we discuss in depth the ways herbivores and pollinators interact can call for more studies to compare damage to both flowers (direct damage) and other parts of plants (indirect damage).


While Chris (my co-author) has completed and published many systematic reviews, this was my first. Gathering and sifting through this much data was certainly an experience and quite the grind. However, I have learned many lessons from this process, both about systematic reviews in general and about handling data. One lesson is to make sure to well-document everything in your process, because you will end up going back to look, months or even years later. So, document it, organize it, and if you can, automate it! However, the most important lesson I learned was the importance of a clear question and idea in advance. By the time I had collected all my data and knew the studies well, I felt as though I had lost the entire point of the review. I didn’t have a clue what to do next. It took going back to my original notes and having a discussion with Chris to remember why we had started off on this journey to begin with and to identify what questions we were trying to answer.

Overall, this systematic review gave me an excellent insight into the review process, both what to do and what not to do. However, the content itself provided a firm basis for my own practical field research. I have been in the process of implementing some of my own experiments contrasting the effects of damage to different plant tissues both in the field and in the greenhouse.

Collaborative seed collecting

Lockdown still, but collaborators at local site that manage research reserve kindly agreed to collect native seeds.

Do native shrubs facilitate exotic species equally??

I just returned from some exciting desert fieldwork! Last year, I sampled the annual plant community under shrubs and in the open at six sites across the Mojave and San Joaquin Deserts, and here’s the gist of what I found:

RII values (negative values indicate negative associations with native shrubs; positive values indicate positive associations) for nine vegetation measures taken at six study sites across the Mojave (Mesquite, Mojave, and Vegas) and San Joaquin (Panoche, Cuyama, Carrizo) Deserts. Panels are arranged in ascending order of relative aridity. Data currently in review at Diversity and Distributions.

Spatial association with native foundation shrubs strongly and consistently increased the abundance, biomass, cover, and fitness of the dominant invader Bromus rubens but not the native annual community. This is interesting because positive interactions mediated by native species are seldom invoked to explain the success of exotic invaders. Very cool, but what about the system’s many other exotic, invasive species? Is facilitated invasion species-specific?

To tackle this question, I returned to the desert and sampled the annual plant community at nine study sites scattered across the Mojave and San Joaquin Deserts. Six are repeats from last year, three (Yuc, Cna, Hea) are new:

The three leftmost sites are in the San Joaquin Desert. The six rightmost sites are in the Mojave Desert.

At each site, I sampled the annual plant community at 20 pairs of shrub and open microsites with a 0.5m x 0.5m quadrat. Shrub microsites were the area immediately beneath the canopies of foundation shrubs, and open microsites were areas >1m from any shrub canopy. In each microsite, I estimated the abundance of the native annual community as a whole and the exotic annual community as a whole. I collected species-specific measurements for the abundance, biomass, and fitness of the following exotic plant species: Bromus rubens, B. tectorum, B. diandrus, Erodium cicutarium, Schismus spp., and Brassica tournefortii. Each of these exotic invaders can contribute to biodiversity loss and diminished ecosystem function.

Strong facilitation of Bromus rubens near Las Vegas, NV. Bummer, but cool.

We’ll have to wait for the official stats, but it seemed that B. rubens, B. tectorum, and B. diandrus formed strong and consistent positive associations with native shrubs. Each of the other exotic species ( E. cicutarium, Schismus spp., and B. tournefortii ) associated with native shrubs more sporadically. The most interesting observation was this: it seemed that B. rubens controlled the game — when it was super abundant under shrubs, nothing else (except other bromes) strongly associated with shrubs. When it was less abundant, other exotic (and sometimes native!) species apparently associated with shrubs more strongly. This suggests a competitive hierarchy in which exotic bromes, and especially B. rubens, rule the understory, followed by other exotic species, followed by native species. Again, the stats will give us the official story, but I think that’s what I saw! Very cool.

More cool stuff:

There was a crazy flash flood on Tues, April 14. This is the road I was driving on!
That’s 1/2″ of hail. Did it hurt? Hail yes (sorry).
Sunday, April 12 was a glorious morning! Cholla and Fouquieria near Turtle Mountain, NV. Did I mention glorious?

We Want a Shrubbery! The direct and indirect influence of Shrubs on Flowering Annual plants in an Arid Ecosystem

A progress report by Stephanie Haas

Shrubs frequently have positive interactions with annuals in desert ecosystems. This facilitative effect has been seen repeatedly with plant density, but the effect of shrubs on flowering is less studied. Shrubs also impact other species that interact with annuals, including both herbivores and pollinators. These direct and indirect interactions exist in a complex network that we attempt to tease apart through both manipulation and observation.

To see the slide deck click here.

To see the presentation click here.

Climatic scaling effects of foundation plant species interactions with vertebrate species.

Positive interactions are key to many systems worldwide. Foundation species such as shrubs are able to benefit other taxa through various mechanistic pathways. The canopy of these species is also an structural agent, able to reduce light intensity and temperature variation experienced by vertebrates. But, do the instances of animal near a shrub increase as temperature and light intensity increase? Can artificial shelters be as good as shrubs when comes to lowering the variation in the above parameters? Disturbances such as land use and climate change are the current reality of many regions. To be able to artificially restore these systems post-disturbance while new vegetation is grown is thus key.

Click here to find out more!

Panoche Hills, California
(Chateaugrief, 2019)

Shrub-animal density dependence in desert ecosystems

By: Mario Zuliani

Positive interactions between plant and animal species have been reported in most ecosystems globally. Most literature that looks at these interactions, particularly in arid ecosystems, reports the facilitative interactions occurring between shrub and animal species. With these types of interactions being present, one begs to question; does the density of these foundational shrub species have a relationship with the animal abundance present near them? That being said, understanding this relationship could potentially be used for remediation efforts, for many of the animal species using these shrubs.

For access to my March 2020 Progress report presentation click here

For access to the slide show click here