Landscape-scale responses of freshwater biodiversity to connectivity and stressors

Aim
There is compelling evidence that drivers and patterns of biodiversity and ecosystem functioning vary across multiple spatial scales, from global to regional, landscape and patch. However, macroecological processes impacting freshwater biodiversity are poorly understood compared to marine and terrestrial ecosystems. Despite step changes in data availability, we have a fragmented view beyond the local-scale of how hydrological and landscape connectivity interact with ecosystem stressors to shape freshwater biodiversity and functioning. While macroecological patterns can vary substantially among taxonomic groups, previous studies have focussed on individual habitat types, sites, or taxonomic groups within landscapes, hindering direct comparisons. We present a cross-landscape, multi-species analysis of the interactive effects of landscape and hydrological connectivity and stressors on standing freshwater quality and the diversity of several major freshwater taxonomic groups.
Location
G..., Data collation and quality assurance
Chlorophyll-a concentration
Chlorophyll-a (μg/l) data are available for 518 water bodies between 2005 and 2014 across Scotland and England. These data were provided by the Scottish Environment Protection Agency (for Scotland) and the Environment Agency (for England). Data are available for 333 lakes and 185 reservoirs. We calculated the mean chlorophyll-a concentration over the time period, for each location. We removed data for water bodies that did not have associated connectivity and stressor metrics, and we removed reservoirs, resulting in a dataset of chlorophyll-a concentrations for 287 water bodies.
Macrophytes
Data are available for 2607 water bodies in Scotland, England and Wales, for the species described in Table 4.2 of Willby, Pitt and Phillips (2012). Data come from publicly available primary datasets generated from macrophyte surveys undertaken by or on behalf of UK environment and conservation organisations and were collated by th..., , # Landscape-scale responses of freshwater biodiversity to connectivity and stressors

[https://doi.org/10.5061/dryad.bcc2fqzn8](https://doi.org/10.5061/dryad.bcc2fqzn8)

This repository contains data and code related to the paper “Landscape-scale responses of freshwater biodiversity to connectivity and stressors” submitted to Global Ecology and Biogeography.

## Description of the data and file structure

The folder contains the following files:

* **beetles_1.Rmd** (for beetles analysis)
* **molluscs_1.Rmd** (for molluscs analysis)
* **odonata_1.Rmd** (for odonata analysis)
* **macrophytes_1.Rmd** (for macrophytes analysis)
* **chl_1.Rmd** (for chlorophyll analysis)
* **fish_1.Rmd** (for fish analysis)
* **birds_1.Rmd** (for birds analysis)

and similarly named .html files containing output of these R markdown scripts.

The following files create additional output (specifically, the figures within the associated paper's main text and Supporting Information):

* **gam_plots_all_response...,