Significant ‘developments’ this last few days associated with how we use lands #evidence #synthesis

This last week has been busy with numerous evidence syntheses highlighting that location, location, location and land use patterns are critical issues.

(1) ‘North American diets require more lands than we have’ was published in PLOS ONE and discussed widely. A compelling map of land spared showed little remains.

(2) On the other side of the coin, retiring lands because of water regulations, limitations, and drought are an opportunity for conservation and restoration was published in Ecosphere. Tools mapped for California studying three endangered animal species highlighted that we do know enough to begin to make evidence-based decisions for strategic retirement.

(3) A compelling map of how America uses land was published at Bloomberg.

(4) Hydraulic fracking is now being considered in the region used a case study for the retired land synthesis in #2 listed above including a map of proposed lands open for leasing.

Implications

(a) Scientific synthesis rapidly advances the big picture and both different synthesis tools (maps, systematic reviews, and ideally meta-analyses too) and syntheses with different purposes facilitate a more balanced weighting of issues. Even better, reproducible syntheses provided by different sets of stakeholders would elevate discussion and decision making.

(b) Agriculture, restoration, and energy development (both sustainable and non) must be better balanced through contrasted, transparently aggregated evidence.

(c) The ecological services and functions we get from lands ‘for free’ are precarious and precious.

(d) Whilst we cannot ignore human needs (and their likelihood of continued increases),  it is hard not to imagine that a buffer for other living creatures should also be factored into proposed land use trajectories.

(e) Ecology, socioeconomics, and other fields need to much more rapidly crunch current evidence because the clock is ticking.

 

Ecological network flavors: many-to-many, few-to-many, and few-to-many spatially

Recent conference attendance inspired me to do a quick typology of networks that were presented in various talks. All were done in R using a few different packages.
All were interested in diversity patterns.
None were food webs.

Networks

many-to-many: many plant species and many pollinators for instance

few-to-many: mapping the associated set of pollinators to one flowering species

few-to-many: replicated mapping of diversity for one taxa to a single species of another either nested or spatially contrasted.

 

Network analyses are amazing. I need to learn more!

Can you also map interactions onto other interactions?

 

 

Hacking the principles of #openscience #workshops

In a previous post, I discussed the key elements that really stood out for me in recent workshops associated with open science, data science, and ecology. Summer workshop season is upon us, and here are some principles to consider that can be used to hack a workshop. These hacks can be applied a priori as an instructor or in situ as a participant or instructor by engaging with the context from a pragmatic, problem-solving perspective.

Principles

1. Embrace open pedagogy.
2. Use and current best practices from traditional teaching contexts.
3. Be learner centered.
4. Speak less, do more.
5. Solve authentic challenges.

Hacks (for each principle)

1. Prepare learning outcomes for every lesson.

2. Identify solve-a-problem opportunities in advance and be open to ones that emerge organically during the workshop.

3. Use no slide decks. This challenges the instructor to more directly engage with the students and participants in the workshop and leaves space for students to shape content and narrative to some extent. Decks lock all of us in. This is appropriate for some contexts such as conference presentations, but workshops can be more fluid and open.

4. Plan pauses. Prepare your lessons with gaps for contributions.  Prepare a list of questions to offer up for every lesson and provide time for discussion of solutions.

5. Use real evidence/data to answer a compelling question (scale can be limited, approach beta as long as an answer is provided, and the challenge can emerge if teaching is open and space provided for the workshop participants to ideate).

Final hack that is a more general teaching principle, consider keeping all teaching materials within a single ecosystem that then references outwards only as needed. For me, this has become all content prepared in RStudio, knitted to html, then pushed to GitHub gh-pages for sharing as a webpage (or site). Then participants can engage in all ideas and content including code, data, ideas in one place.

 

Fix-it Facilitation: additional resources

A super fun process exploring how empirical contributions can reshape and embrace theory by addressing gaps in better designs and clear interpretations of findings.

Fix-it Felix: advances in testing plant facilitation as a restoration tool in Applied Vegetation Science.

The original contribution was longer with a more complete set of resources. Here is the full citation list that framed and supported the story and discussion.

Literature cited

Badano, E.I., Bustamante, R.O., Villarroel, E., Marquet, P.A. & Cavieres, L.A. 2015. Facilitation by nurse plants regulates community invasibility in harsh environments. Journal of Vegetation Science: 756-767.

Badano, E.I., Samour-Nieva, O.R., Flores, J., Flores-Flores, J.L., Flores-Cano, J.A. & Rodas-Ortíz, J.P. 2016. Facilitation by nurse plants contributes to vegetation recovery in human-disturbed desert ecosystems. Journal of Plant Ecology 9: 485-497.

Barney, J.N. 2016. Invasive plant management must be driven by a holistic understanding of invader impacts. Applied Vegetation Science 19: 183-184.

Bertness, M.D. & Callaway, R. 1994. Positive interactions in communities. Trends in Ecology and Evolution 9: 191-193.

Bronstein, J.L. 2009. The evolution of facilitation and mutualism. Journal of Ecology 97: 1160-1170.

Bruno, J.F., Stachowicz, J.J. & Bertness, M.D. 2003. Inclusion of facilitation into ecological theory. Trends in Ecology and Evolution 18: 119-125.

Bulleri, F., Bruno, J.F., Silliman, B.R. & Stachowicz, J.J. 2016. Facilitation and the niche: implications for coexistence, range shifts and ecosystem functioning. Functional Ecology 30: 70-78.

Callaway, R.M. 1998. Are positive interactions species-specific? Oikos 82: 202-207.

Chamberlain, S.A., Bronstein, J.L. & Rudgers, J.A. 2014. How context dependent are species interactions? Ecology Letters 17: 881-890.

Filazzola, A. & Lortie, C.J. 2014. A systematic review and conceptual framework for the mechanistic pathways of nurse plants. Global Ecology and Biogeography 23: 1335-1345.

Gomez-Aparicio, L., Zamora, R., Gomez, J.M., Hodar, J.A., Castro, J. & Baraza, E. 2004. Applying plant facilitation to forest restoration: a meta-analysis of the use of shrubs as nurse plants. Ecological Applications 14: 1128-1138.

Holmgren, M. & Scheffer, M. 2010. Strong facilitation in mild environments: the stress gradient hypothesis revisited. Journal of Ecology 98: 1269-1275.

James, J.J., Rinella, M.J. & Svejcar, T. 2012. Grass Seedling Demography and Sagebrush Steppe Restoration. Rangeland Ecology & Management 65: 409-417.

Lortie, C.J., Filazzola, A., Welham, C. & Turkington, R. 2016. A cost–benefit model for plant–plant interactions: a density-series tool to detect facilitation. Plant Ecology: 1-15.

Macek, P., Schöb, C., Núñez-Ávila, M., Hernández Gentina, I.R., Pugnaire, F.I. & Armesto, J.J. 2017. Shrub facilitation drives tree establishment in a semiarid fog-dependent ecosystem. Applied Vegetation Science.

Malanson, G.P. & Resler, L.M. 2015. Neighborhood functions alter unbalanced facilitation on a stress gradient. Journal of Theoretical Biology 365: 76-83.

McIntire, E. & Fajardo, A. 2011. Facilitation within species: a possible origin of group-selected superoorganisms. American Naturalist 178: 88-97.

McIntire, E.J.B. & Fajardo, A. 2014. Facilitation as a ubiquitous driver of biodiversity. New Phytologist 201: 403-416.

Michalet, R., Brooker, R.W., Cavieres, L.A., Kikvidze, Z., Lortie, C.J., Pugnaire, F.I., Valiente‐Banuet, A. & Callaway, R.M. 2006. Do biotic interactions shape both sides of the humped‐back model of species richness in plant communities? Ecology Letters 9: 767-773.

Michalet, R., Le Bagousse-Pinguet, Y., Maalouf, J.-P. & Lortie, C.J. 2014. Two alternatives to the stress-gradient hypothesis at the edge of life: the collapse of facilitation and the switch from facilitation to competition. Journal of Vegetation Science 25: 609-613.

Noumi, Z., Chaieb, M., Michalet, R. & Touzard, B. 2015. Limitations to the use of facilitation as a restoration tool in arid grazed savanna: a case study. Applied Vegetation Science 18: 391-401.

O’Brien, M.J., Pugnaire, F.I., Armas, C., Rodríguez-Echeverría, S. & Schöb, C. 2017. The shift from plant–plant facilitation to competition under severe water deficit is spatially explicit. Ecology and Evolution 7: 2441-2448.

Pescador, D.S., Chacón-Labella, J., de la Cruz, M. & Escudero, A. 2014. Maintaining distances with the engineer: patterns of coexistence in plant communities beyond the patch-bare dichotomy. New Phytologist 204: 140-148.

Rydgren, K., Hagen, D., Rosef, L., Pedersen, B. & Aradottir, A.L. 2017. Designing seed mixtures for restoration on alpine soils: who should your neighbours be? Applied Vegetation Science.

Sheley, R.L. & James, J.J. 2014. Simultaneous intraspecific facilitation and interspecific competition between native and annual grasses. Journal of Arid Environments 104: 80-87.

Silliman, B.R., Schrack, E., He, Q., Cope, R., Santoni, A., van der Heide, T., Jacobi, R., Jacobi, M. & van de Koppel, J. 2015. Facilitation shifts paradigms and can amplify coastal restoration efforts. Proceedings of the National Academy of Sciences 112: 14295-14300.

Stachowicz, J.J. 2001. Mutualism, facilitation, and the structure of ecological communities. Bioscience 51: 235-246.

von Gillhaussen, P., Rascher, U., Jablonowski, N.D., Plückers, C., Beierkuhnlein, C. & Temperton, V.M. 2014. Priority Effects of Time of Arrival of Plant Functional Groups Override Sowing Interval or Density Effects: A Grassland Experiment. PLoS ONE 9: e86906.

Went, F.W. 1942. The dependence of certain annual plants on shrubs in southern California deserts. Bulletin of the Torrey Botanical Club 69: 100-114.

Xiao, S. & Michalet, R. 2013. Do indirect interactions always contribute to net indirect facilitation? Ecological Modelling 268: 1-8.

Overdispersion tests in #rstats

A brief note on overdispersion

Assumptions

Poisson distribution assume variance is equal to the mean.

Quasi-poisson model assumes variance is a linear function of mean.

Negative binomial model assumes variance is a quadratic function of the mean.

rstats implementation

#to test you need to fit a poisson GLM then apply function to this model

library(AER)

dispersiontest(object, trafo = NULL, alternative = c(“greater”, “two.sided”, “less”))

trafo = 1 is linear testing for quasipoisson or you can fit linear equation to trafo as well

#interpretation

c = 0 equidispersion

c > 0 is overdispersed

Resources

  1. Function description from vignette for AER package.
  2. Excellent StatsExchange description of interpretation.