Monitoring diversity

Bird counts at the San Dieguito River Estuary have been ongoing since 2010. The estuary was the subject of a huge habitat restoration project, and the bird counts are part of the post-restoration monitoring. Information about the surveys can be found here. We have Jayne Lesley, Joni Ciarletta, Mona Baumgartel, and Sue Smith to thank for agreeing to let us use their data for this exercise!

Rather than focusing on a few species, these surveys are designed to document all of the species found within the estuary at the time. A healthy, functioning estuary will provide habitat for a variety of species, from shorebirds (i.e. sandpipers and relatives) that feed on invertebrates on or in the mud, to wading birds (i.e. herons and egretsherons and egrets) that fish in shallow water, to ducks that either dabble (i.e. feed on plants or invertebrates they can reach by tipping into the water without diving, such as mallards) or dive (i.e. mergansers), to birds of prey (e.g. osprey) and terns that plunge into deeper water to catch fish. The individual species matter, and community-level surveys provide abundance data that can be used to asses trends in each species. But, for surveillance monitoring it is also useful to assess the diversity of the community as an indicator of the health of the ecosystem. Ecosystem damage often harms some species more than others, and may even benefit some, so measures of diversity can help identify changes in the relative abundance of species that indicate changes in conditions that are difficult to detect by monitoring individual species.

Diversity is a complex topic, because there are many different ways for an ecosystem to be diverse. We will focus on the most common meaning, species diversity, as well as functional diversity. To address functional diversity, we will identify guilds of species that have a common diet, and will evaluate the diversity of species within each guild, as well as the diversity of the guilds themselves. Guild classifications were obtained from De Graaf et al. 1985. Using a functional characteristic of the species, like diet, helps us understand why a change might be occurring - if, for example, all of the piscivores (i.e. fish-eating birds) are declining we would look for problems in the fish supply.

We will use as our measure of diversity the Shannon index, which balances species richness (i.e. the number of species present) and evenness (i.e. similarity in the relative frequencies of the species present). The Shannon index increases when either more species are added to the community, or when their relative frequencies are more similar - the converse is that Shannon diversity declines either when species are lost, or when the community is disproportionately made up of one or a few of the species present.

The main shortcoming in the Shannon index is that it does not account for changes in the species composition of the community. If all of the native species in the estuary were replaced by invasive exotic species the diversity may not change, but the estuary's bird community would be completely different. Methods that assess changes in species composition seek to

This exercise will be done in R Studio. Start R Studio, start a new project, and download this data file into the project folder. Then download this Rmd file into the project file, and open it in R Studio. The instructions are all within the Rmd file.