{"id":615,"date":"2018-05-21T08:30:00","date_gmt":"2018-05-21T12:30:00","guid":{"rendered":"http:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/?p=615"},"modified":"2018-05-20T12:53:13","modified_gmt":"2018-05-20T16:53:13","slug":"causal-inference-in-ecology-setting-the-stage-for-the-rubin-causal-model","status":"publish","type":"post","link":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/blog\/2018\/05\/21\/causal-inference-in-ecology-setting-the-stage-for-the-rubin-causal-model\/","title":{"rendered":"Causal inference in ecology – Setting the stage for the Rubin causal model"},"content":{"rendered":"

Causal inference in ecology – links to the series<\/a><\/p>\n

If you\u2019ve been following along, you realize by now that it\u2019s not easy to infer the cause of a phenomenon, even in a well-controlled experiment. What about observational experiments, which are what many ecologists and evolutionary biologists have? Take one paper of mine that I\u2019m reasonably happy with (PLoS One<\/em> e52035; 2012. doi: 10.1371\/journal.pone.0052035<\/a>). One part of that paper included an experiment of sorts. We1<\/a><\/sup> established experimental gardens at the Kirstenbosch National Botanical Garden<\/a> and at a mid-elevation site on Jonaskop mountain<\/a> about 100km due east of Kirstenbosch. Among other things we were interested both in how certain traits in newly formed leaves (specific leaf area, stomatal pore index, and leaf area) differed depending on the age of the plant and on the garden in which they were grown.<\/p>\n

This part of the paper is analogous to the thought experiment on corn that we\u2019ve discussed so far. Since the plants were grown from wild-collected seedlings, we obviously couldn\u2019t duplicate genotypes across gardens. We also didn\u2019t have enough seed from individual maternal plants to replicate families across the gardens. So we did the best we could. We randomized seedlings within populations and split populations across gardens. You\u2019ll see the results from this part of the analysis in the figure below.<\/p>\n

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Figure 4 from PLoS One<\/em> e52035; 2012. doi: 10.1371\/journal.pone.0052035<\/a><\/p><\/div>\n

The trends with plant age are clear.2<\/a><\/sup> Specific leaf area (SLA) declines with plant age, stomatal pore index increases with plant age, and leaf area increases with plant age. Given that the trends are consistent across species and gardens, I\u2019m reasonably confident that plant age influences these traits in this group of Protea<\/strong><\/em>.3<\/a><\/sup> Notice that I wrote \u201cinfluences\u201d, which is a short way (for me) of writing that plant age is a<\/strong><\/em> causal factor that influences the traits but that I am not claiming that it is the<\/strong><\/em> causal factor.4<\/a><\/sup><\/p>\n

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Figure 3 from PLoS One<\/em> e52035; 2012. doi: 10.1371\/journal.pone.0052035<\/a><\/p><\/div>\n

Similarly, the figure above makes it clear that which garden the plants are grown in influences these (and other) traits. These results won\u2019t surprise anyone whose worked with plants. The traits plants have depend both on how old the plant is and on where its grown. So far a reasonably straightforward experiment, but how about this? We also wanted to know whether the amount of change in leaf traits depended on measures of resource availability and rainfall seasonality in the places that seeds were collected from. Here we\u2019re asking a more complicated question.<\/p>\n

Take SLA, for example, and imagine that we\u2019re asking the question just about changes in SLA for plants grown at Jonaskop. Now the fully fleshed out the question is something like this:<\/p>\n