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.
Preferences from a week of work on reading and writing with an attempted laser-beam focus.
Lockdown still, but collaborators at local site that manage research reserve kindly agreed to collect native seeds.
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
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.
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.
Panoche Hills Ecological Reserve
Active restoration of native vegetation and seeds.
Contrast with regional patterns of diversity.
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.
York Science Fellow Dr. Jacob Lucero and international collaborator Dr Merav Seifan are launching into 2020 with an ambitious experiment in Israel and California. The purpose is to explore the relative importance of provenance of a highly invasive species of bromus in the deserts of California by comparing performance and key interactions in its home range, Israel, and in its introduced range, California. This is a new direction from previous work published in NeoBiota entitled ‘The dark side of facilitation: native shrubs facilitate exotic annuals more strongly than native annuals’ that demonstrated a very significant effect of bromus on local plant community dynamics.
Sometimes, peer review (and procrastination) help. Other times, the delays generate more net work. I was discussing this workflow with a colleague regarding a paper that was submitted two-years ago, rejected, then we both ran out of steam. This was the gold-standard workflow we proposed (versus reformat and submit to another journal immediately).
- Hit web of science and check for new papers on topic.
- Download the pdfs.
- Read them.
- Think about what to cite or add.
- Add citations and rebuild biblio.
- Update writing to mention new citations especially if they are really relevant (intro and discussion).
- Take whatever pearls of wisdom you can from rejection in first place and revise ideas, plots, or stats.
- Format for new journal.
- Check requirements for that journal.
- Search the table of contents for the journal and check your lit cited to ensure you cite a few papers from that journal – if not, assess whether that the right journal for this contribution.
- Download pdfs from new journal, read, cite, and interpret.
- Then, look up referees and emails.
- Write cover letter.
- Set up account for that new and different annoying journal system – register and wait.
- Fight with system to submit and complete all the little boxes/fields.
No markers go a long way to better meetings!