Biological Diversity


How many species are there? This seemingly simple question is fundamental to much of ecology and conservation. Yet typically we can not directly count all the organisms in a community. Instead we must rely upon sampling to make inferences about how many species there are. Sampling efforts are often difficult to standardize across habitats. Given these challenges, how can we compare biodiversity between habitats in a robust way? Here, we'll use rock pools on the James River to learn how to quantify biodiversity. This approach could easily be adapted to other systems, terrestrial and aquatic. Our exploration is couched within the framework of island biogeography theory and aims to examine one of the most tested patterns observed in ecological systems, the species area relationship. Specifically, we will sample organisms from a set of rock pools that vary in size and then use these data to estimate the overall diversity of each pool. We can then plot our estimates of the estimate total diversity of individual rock pools by rock pool size. 

Read more about our collaborative research, education & outreach in the wonderful Belle Island rock pool system here.

Day 1 - Introduction to the ideas and system & data collection

We'll meet in the Life Science Building for initial lectures on the conceptual background, study system, and rock pool organisms. Please read the Kraus study to gain familiarly with the spatial aspects of this system. Also look over the James River Park System's Science in the Park Rock pool resources. We'll then relocate to the study area on the Southside of Belle Island and navigate to specific pools using Collector for ArcGIS. You should download this app onto your phone, we'll provide login detail in class.  After watching a demo on how to sample rock pools, student will work in pairs to collect data from 1-2 additional pools. Each rock pool sampled will have a data sheet. Lunch may be in the field. Upon return we'll enter the groups data into a Google Sheets. Come with grippy shoes that can get wet. Be prepared for rain, wading, poison ivy and general muddiness.

Day 2 - Lecture & discussion of Gotelli & Colwell (2001) & Data Analysis

Armed with our data we can estimate species richness for each pool and compare pool diversity across pool sizes. To accomplish this in a robust manner, we need to be aware of the issues discussed in the class review paper by Gotelli & Colwell (2001). Read this article carefully several times. Also read the associated intervew to get some of the "back story" on the making of this citation classic.

We will conduct our analyses using the software R. You'll need to download this powerful open source analysis tool onto your laptop. You'll also need to install the R packages "Rcmdr" and "BiodiversityR".  The latter can sometimes be a little tricky, as there are many supporting packages which it requires. Generally go ahead and install any additional packages prompted. This website also has some help directions for getting R and packages installed on various platforms - there are some specific directions for varios Mac OSs (and I am a PC guy - so you Mac folks will need to largely figure this out for yourselves - I wont be that much help).




James Vonesh


Office Information
Room 226
Phone: (804)827-8596

Research Interests
Community ecology
Predator-prey ecology
Conservation biology

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