Multitrophic assembly influences β-diversity across a tripartite system of flowering plants, bees, and bee-gut microbiomes

Theoretical frameworks of terrestrial community assembly often focus on single trophic levels (e.g., plants) without considering how complex interdependencies across different trophic levels influences assembly mechanisms. Yet, when multiple trophic levels are considered (e.g., plant-pollinator, plant-microbe interactions) the focus is typically on network analyses at local spatial scales. As spatial variation in biodiversity (β-diversity) is increasingly being recognized for its relevance in understanding community assembly and conservation, considering how β-diversity at one trophic level may be influenced by assembly processes that alter abundance and composition of interacting communities at a different trophic level (multitrophic dependency) is critical. Here, we build on single trophic level community assembly frameworks to explore the assembly processes affecting β-diversity in multitrophic communities comprising flowering plants, their bee pollinators, and the corresponding bee-..., Study sites
We surveyed two ecological regions: Three islands within the Channel Island archipelago in the coast of California, namely Anacapa, Santa Cruz, and Santa Rosa islands, and five sites in canyon localities near Zuma Canyon and Stunt Ranch, belonging to the Santa Monica Mountains (hereafter SAMO) in California (Figure 2). The Channel Islands archipelago, which includes the aforementioned islands, originated approximately 20 million years ago through a complex interplay of plate tectonics and volcanic activity (Atwater, 1998; National Park Service, 2016). Over time, the islands have undergone dynamic changes influenced by geological processes. During the Pleistocene ice ages, sea levels were lower due to the accumulation of ice in polar regions. This lowered sea level exposed the seafloor between the Channel Islands and allowed them to be connected into a supper-island referred to as Santarosae. Although never connected to the mainland during the Quaternary, this land bridge fac..., , # # README

This folder contains:

1\) Script1.R: Custom R script that allows full reproducibility of the null models for Standardize Size Effect calculations to test if observed β-diversity differed from stochastic assembly (ecological drift).

2\) Script2.R: R script that allows full reproducibility of variation partitioning of β-diversity using dbRDA and the Blanchet et al. (2008) approach. We organized this script in 7 parts which need to be run in order.

3\) Figure3.R: R script to create the NMDS representations portrayed in Figure 3.

4\) Figure4.R: R script to create the observed and SES deviations of β-diversity portrayed in Figure 4.

5\) Figure5.R: R script to create the stacked bar plots portrayed in Figure 5.

6\) env_all_var.csv: File with abiotic environmental variables to use with Script1.R file.

7\) plants-site-all.csv: the plant species matrix. Species names are in the file \"flower-names.xlsx\".

8\) bees-site-all.csv: the bee species matrix. Species names are in the f...