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.
Acknowledge but propose a solution for those lands to better recognize the diversity of peoples associated with its present and past.
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.
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.
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.
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.
Scientists take a lot of pictures, or at least, we should. We travel to unusual places, do unusual activities, and see unusual things, all of which can often be displayed excellently in a photograph. Before cameras, many scientists were also supreme artists. They would document the real world (and the subjects of their studies) in drawings or paintings, and the line between scientific data and artistic expression was blurry. This skill was necessary for the dispersal of information, and more information on a place or a organism can often be expressed per page in a picture than in text. A collection of dozens of paintings or drawings could represent a lifetime’s work and only exist in a handful of prints. Now, with digital photography, we can take hundreds of high-quality photos in minutes with infinite, diverse data and immediately share them with the world. But all these photos can be difficult to manage, particularly as your collection grows. So let’s talk about how we can more effectively manage our photographic
Most science-pics can fit into at least one of four categories: 1) Aesthetic, 2) Exhibitory, 3) Methodological, and 4) Systematic. Aesthetic photos should be consciously composed and executed, and serve as an artistic representation of a subject. Handy for presentations and exhibits, these can be infinitely elevated and the principles that make a quality photograph can be incorporated into any picture, scientific or not. Exhibitory photos are particularly useful to scientists seeking to communicate natural phenomenon. If we carry a camera with us while we’re in the field, we can catch examples of our study topic in action. For example, a photo of a bird eating a bug on a cactus can help you explain the idea of indirect facilitation. Again, these types of photos are useful for presentations, teaching, and publication, but do not necessarily have to be artfully composed (though an attractive photo can make your presentation stronger and more professional). Methodological photos are unique, but are present across many disciplines, as a tool or resource for explaining a protocol. For us ecologists, these photos are usually of a researcher conducting their experiment or of equipment in the field. A photo like this can help your audience better understand what exactly you were doing, especially if they are outside of your field. And finally, systematic photos are those which are taken as a part of the protocol. Just like any other measurement in a study, these photos should be taken at regular intervals, be they spatial, temporal, or event-based. These photos are often not aestetic at all, but rather are primarily functional. One should never permanently delete these photos just are you wouldn’t delete other observations–they are a part of the dataset. Indeed, this category is usually the type of photo that requries the most management, and is most likely to make your hair fall out. Large file sizes make it hard to save on your personal machine or online platform not specifically designed for uploading many photos at once (looking at you, google drive). That’s why I’m going to tell you a bit about a platform that we can use to more effectively backup, share, and manage our science-pics: Flickr.
Flickr, an online photo sharing platform, is similar to many other databases were one can have their own personal account, be on a team account, create groups, tag photos, and make your photos public or private. Free for your first 1000 photos and $50/year for unlimited uploads, the real beauty comes in it’s file management. And lucky for us, it has both a desktop and mobile version. Just like any platform, however, it has it’s disadvantages. Without careful monitoring and guidelines, it can become just as unorganized and hence unusable as any sharing platform. To benefit from Flickr’s system, you have to establish a system among your team, and make sure to follow it. Here, I’m going to walk you through uploading a photo, creating an album, and managing those photos in a clean and effective way.
Once you’ve signed in you, you can explore your profile page, which has different tabs for the different elements of your page. This is pretty self explanatory; the only part that may seem confusing is the Photostream element, which is simply a list of all public photos you’ve uploaded in order of recentness. Private photos won’t show up here.
Our profile page won’t be very interesting, however, until we start to populate our account by uploading photos. To do this, notice the cloud and arrow in the top right corner and choose “Upload”.
Now, to upload new photos, simply follow the prompts and fill out the left hand tabs with descriptions or tags, and chose/create the appropriate the album. You don’t need to choose an album, if you don’t, it’ll simply go to your camera roll and (if public) your photostream. However, we should always try to maintain order by depositing photos into albums, especially on a shared account.
But the real power comes when we want to upload multiple photos at once. Unlike other photo sharing platforms and most personal machine file management systems, you can edit multiple files and assign names/descriptions/tags/people/albums to multiple files at once, easily selecting all or some of the photos you’re interested in.
Now, if you are working on a project that includes systematically taken photos, a team Flickr account can support it. It’s important to establish certain guidelines for the publication for all albums with multiple contributors, but especially for photos a part of a dataset. As an example, our lab is cataloging photos of trees on York University’s campus, and we would like to include photos of every tree in an album on Flickr. We might use the following guidelines to make sure all photos are properly documented:
Album title should be descriptive of the project and include the year.
Only systematic photos should be included in the album, methodological and fun photos should be in a separate album.
The photo title should be the Unique ID that the tree is recorded as in the dataset. If we have multiple photos for one tree, that’s fine! Maintain the
The description should include any details that distinguish it from other photos of the same tree (e.g. you might take a photo of the entire tree, a photo of a bird in the tree, and some damage to the bark, so include that detail in the description). Try to use the same one or two words if you are taking the same photos (e.g. “whole tree”, “bird”, “damage”, etc.). It should also include the photographer, the date the photo was taken, and the treatment we are interested in (for this project, it might be disturbance level).
We should include general tags on every photo that strangers may wish to find (e.g., science, ecology, nature, explorer, tree, bird, insect, etc.), but also a project-specific tag that includes systematic and other photos from the project.
The members working on the project should be added to “people”, particularly those who were collecting the data (even if they weren’t the photographer)
This is only one example, but it can be modified for all sorts of albums and projects. In fact, it doesn’t have to only be for specific projects! How often have you been working on a presentation and realized you never did take a photo of your study site? Instead of trying to track down anyone with a photo of the place (or being asked to wade through your phone’s camera roll), we can have a place to put them all immediately and know exactly who to credit (don’t forget to credit photographers!) When we systematically organize our photos, we can quickly find and share them among our peers. Much like sharing our code, our research plan, or our datasets, sharing our photos can help cultivate a culture of open science and provide resources within our own research group and beyond! Now, go follow us on Flickr, @ecoblender_lab! 🙂
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.
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.
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.
Disclaimer Preferences from a week of work on reading and writing with an attempted laser-beam focus.
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.
Publications describing the fine-scale annual plant neighbourhood concept
In collaboration with Professor Katie O’Meara, an architect, Professor Zaitchik, an Earth Scientist, and researcher Claire Moriarty, we are examining the use of drones to map keystone species in extreme environments such as cushion plants in Patagonia or shrubs in deserts. This is just a pilot experiment (haha, get it), and we need a graduate student for 2020 to dig in and ground-truth the metrics we will derive from imagery. The focus will be structure and architecture in natural systems.
All field scientists know that getting out into nature to do your work means problem solving. Usually, you have to do this on the fly and with limited time, internet, communication… limited everything basically. But that’s where the creativity and decision making skills come in handy. Sometimes it’s a simple obstacle like breaking your tape measure or cactus spines lodged in your shoes. But then other times, it’s a seemingly catastrophic event—like flash floods destroying your study species, or political unrest in your study area—that disrupts your plan. Or, if you’re me, cold weather delaying cactus blooming in a cactus flower experiment.
This winter in the Mojave was unusually cold and rainy. The average high in January 2019 was 10.5°F—normally it’s a high of 57°F. Rain is great for flowers, it means there will be much more of them when they bloom. But cold means delayed blooms. And this Spring, it was delayed by about a month. Four weeks was how long I had planned to be in the desert, so after about two weeks of no flowers and a chilly forecast, I knew we needed to come up with some solutions.
The most obvious: stay longer. Duh. But this wouldn’t help if the cacti never bloomed, and I had to be back in Toronto to TA eventually. So I planned to hang out in the desert (no complaints here, it’s beautiful out there), but I knew we needed more options. Hire help? Working with birds means access to a large pool of citizen scientists who would give their time to look at birds in a place they otherwise couldn’t go. And I could hire a paid assistant from the area. These two options seemed great, but getting anything done with the public takes several months advanced notice, and there simply wasn’t any interest in my for-hire ad. So help was out. I kept thinking, and waiting, and hoping the flowers would just bloom and I could work extra long days and get it done. But that didn’t happen.
I had one last idea. Perhaps it was my most hair-brained scheme: use fake flowers (more appropriately called mimic flowers). After all, the problem was there were no flowers, and the end goal was to have flowers. A few papers had studied bird (hummingbird, specifically) visits to mimic flowers, and had success. This idea, which we didn’t know would even work, required a lot of experimental design rewiring. Two semester’s worth of planning and design scrapped and reinvented in a hour was terrifying. Whoever I told about my woes all echoed the same reaction, “That’s field ecology for you!” For a worrier and a planner like me, it’s a nerve-wracking line of work.
But I had to do something. I’d finished walking transects to look at birds and needed to start an experiment, any experiment. So I bought a bunch of fake flowers at Michael’s (Michael’s, would you like to sponsor an up-and-coming ecologist??) that looked like the Buckhorn Cholla’s flowers I’d seen on google, and pinned them onto the un-opened buds of my focal cacti. I had four levels of manipulations, set out camera traps, and watched for an hour. I was on the edge of my camping-chair-seat for the first session. There were thirty flowers pinned on this plant, my highest volume of flowers. Would they come? I needed proof of concept, proof that the birds would visit these cacti in some capacity, or else my findings are nothing but “birds don’t visit cacti”. Nothing wrong with this from a scientific perspective, but there’s not much to explore after the fact. A huge part of my Master’s relied on this next hour.
I was lucky. Within seven minutes, a Costa’s Hummingbird visited the cactus and attempted to pollinate the fake flowers. And then 6 more did the same over that hour. Funnily enough, this would be my busiest session for the rest of the field season. But it was peace of mind—the birds came, and no matter what else happened for the rest of the Spring, I had something to compare all my results to. After the 10 day experiment observing these mimic flowers, they finally began to bloom. The flowers really did look similar to the mimics, and I figured next we could see how different concentrations of real flowers on a cactus influenced bird behavior.
The experimental design for the real flowers was exactly the same as the mimic flowers, but this time, there were real flowers on the plants instead of fake ones. So I watched and waited, this time with less anxiety. But the first day passed, and no birds visited the cacti. Strange, but it was a particularly hot day, perhaps they just weren’t out and about. The next day came and went, and still, no birds at the cacti. This stayed true for the rest of the experiment. Birds were still coming to the procedural control (a poll with 30 mimic flowers glued to the top), but not to the real flowers. Not even once in the 10 day experiment. And just like that, the experiment ended. Science waits for no one.
Now, I’m back in Toronto. Data analysis is next up on the docket, but one thing is clear even without the statistics: birds will pollinate flowers on a cactus, just not the flowers that a cactus actually produces. It’s not the entire structure of the cactus that deters birds, but something about the flower itself that tells them not to come.
We know that most cacti are primarily pollinated by bees, and now we can say, at least for Buckhorn Cholla, they are absolutely not pollinated by birds. Could the flower have ultraviolet patterns advertising to the birds that this flower is not for them? Or perhaps a chemical signal from the flower deters them? Essentially, what is the mechanism associated with the flower that keeps birds away?
But perhaps even more interesting is this: what is the cactus flower actually saying to different pollinators? Two signal options exists, exclusionary or inclusionary. The flowers may signal that birds should not come here. Or perhaps, the flowers signal that the nectar is explicitly for bees. Imagine a sign outside a young boys treehouse saying, “No girls allowed.” This is an exclusionary signal, telling girls that they cannot come in (but I mean, smash the patriarchy). Now consider a “Man Cave” sign outside a basement. This is an inclusionary signal, suggesting that this space is for men. In the end, these signs have the same outcome: no women are in the space. An observer who cannot read English could observe that no women entered either of these spaces, but would need to be able to interpret the signs to know whether the signal is exclusionary or inclusionary.
This is fascinating, because in our human signage example, the interaction individuals of men, women, and sign-maker all are the same species speaking the same language. But in our bird-bee-cactus scenerio, we have three extremely different taxa (a plant, an insect, and a vertebrate) all possibly “reading” the same language. And they do all this interspecific signalling avoid niche overlap and wasted energy.
Now, we just got to test it. Easier said than done.
All these questions were… not what I was expecting to come home with at the start of my field season. Had the flowers bloomed when I arrived, I would have performed our original experiment manipulating the number of flowers on different sized cacti. And I would’ve gotten a whole lot of nothing. I’m a scientist, so I don’t like to say fate had a hand in this, but it was some good luck that I was so unlucky.