Multi-Proxy Paleoecological Analysis Using R

Johanna Bosch

2024-03-05

Welcome!

This book can be used to learn how to conduct a paleoecological analysis in R. The project methods described here are formally reviewed and cited in the following paper:

Bosch J, Álvarez-Manzaneda I, Smol J, Michelutti N, Robertson GJ, Wilhelm SI, Montevecchi WA. 2024 Blending census and paleolimnological data allows for tracking the establishment and growth of a major gannet colony over several centuries. Proceedings of the Royal Society B [in review].

0.1 Study Methods

For this study, we gathered sediment records from a pond situated 240m upwind of the northern gannet (Morus bassanus) colony in Cape St Mary’s Ecological Reserve (Newfoundland, CA) that receives seabird nutrients. We reconstructed the population trends of the gannets using multiple proxies (δ15N, chlorophyll a, phosphorus, cadmium, zinc, ornithogenic diatoms) related to seabird nutrient inputs into freshwater catchments. By aligning shifts in seabird-related proxies to historical census data, we reveal how paleo-reconstructions can accurately follow known population counts.

0.2 Study Site Description

Samples were taken from Cape St. Mary’s Ecological Reserve, in Newfoundland. The main nesting site within the Reserve is named Bird Rock. A review of the paleolimnological process at play are shown in the graphical abstract below. Two sediment cores were obtained for the study, one from the impacted pond (ID: CSM-IMP-2) ~240 m away from the colony, and another from a reference pond (study control, ID: CSM-REF-3) more than 1 km away from the colony.

Figure 0.1: [Bosch et al. 2024]: Seabird nutrient transfer from Bird Rock, in Cape St. Mary’s Ecological Reserve (Newfoundland) to a pond nearby the seabird colony. Seen in the illustration are northern gannets (Morus bassanus) and black-legged kittiwakes (Rissa tridactyla), which both nest within the Reserve on an annual basis.

Figure 0.2: [Bosch et al. 2024]: Map of sampling locations relative to Bird Rock

0.3 Resources

0.3.1 Download data

Download some of the example data from my github repo - Paleo_Analysis_Using_R

0.3.2 Install packages

Install all of the packages used in this analysis:

REQUIRED:

• Tidyverse - Wickham H, Averick M, Bryan J, Chang W, McGowan LD, François R, Grolemund G, Hayes A, Henry L, Hester J, Kuhn M, Pedersen TL, Miller E, Bache SM, Müller K, Ooms J, Robinson D, Seidel DP, Spinu V, Takahashi K, Vaughan D, Wilke C, Woo K, Yutani H (2019). “Welcome to the tidyverse.” Journal of Open Source Software, 4(43), 1686.

• Tidypaleo:Dunnington DW, Libera N, Kurek J, Spooner IS, Gagnon GA (2022). “tidypaleo: Visualizing Paleoenvironmental Archives Using ggplot2.” Journal of Statistical Software, 101(7), 1–20.

• Vegan- Oksanen J, Simpson G, Blanchet F, Kindt R, Legendre P, Minchin P et al. (2022). vegan: Community Ecology Package. R package version 2.6-4

• Ggplot2and Ggpubr- Wickham H (2016). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. ISBN 978-3-319-24277-4,

• Dplyr- Wickham H, François R, Henry L, Müller K, Vaughan D (2023). dplyr: A Grammar of Data Manipulation. R package version 1.1.4

• Viridis- Garnier, Simon, Ross, Noam, Rudis, Robert, Camargo, Pedro A, Sciaini, Marco, Scherer, Cédric (2024). viridis(Lite) - Colorblind-Friendly Color Maps for R. doi:10.5281/zenodo.4679423, viridis package version 0.6.5

Note that installation may differ depending on the type of operating system you’re using.

# to install the tidy packages on Ubuntu, start by opening your terminal and installing Libcurl and Vegan

sudo apt-get install -y libxml2-dev libcurl4-openssl-dev libssl-dev libv8-dev
sudo apt-get install -y r-cran-vegan