Decomposing niche components reveals simultaneous effects of opposite deterministic processes structuring alpine small mammal assembly

Our knowledge of community assembly dynamics under multiple stressors is limited because of opposite niche-based processes, i.e., limiting similarity and habitat filtering could simultaneously occur, masking the overall patterns. Alpine biomes provide the ideal systems to explore the influences of co-occurrence processes as these communities usually face multiple stresses such as resources limitation and habitat constraints. However, the assembly processes of mammals in alpine areas have hardly been exclusively studied. Here, we aimed to address how different processes structured small mammal communities at the tree line transition zone, which represents one of the most distinct vegetation boundaries separating alpine from montane habitats. We compiled a regional dataset including species list, phylogeny, and functional traits from field collections across 18 mountains of southwest China and complemented them with published data sources. The traits were decomposed into different niche c..., 2.1 Study area and field sampling
The study region is located in the southwest mountains of China, a global biodiversity hotspot (Mittermeier et al. 2011), and covers the Three Parallel Rivers of Yunnan Protected Areas (Fig 1). Four north-south trending mountain ranges dominate the region's topography (from west to east, Gaoligong, Nushan, Yunling, and Shaluli). Eighteen prominent mountains (or sky-islands) were selected as study sites to adequately represent the study region's extent (Appendix 1). The tree line in the region represents one of the most distinct vegetation boundaries separating alpine from montane habitats (Körner 2013; Testolin et al. 2020). Across the study region, the alpine tree line is located between ca. 3 800 – 4200 meters above mean sea level (m a.s.l.), and generally rises from south to north but varies between sites due to several abiotic or anthropogenic influences (Wang et al. 2013). The alpine habitats in the region experience a moderate decline in annual pr..., All statistical analyses and result illustrations were processed in the R 4.1.0 environment.
Initial data and R code were provided.
The uploaded files include:
1. overall_trait.R: R code to calculate observed phylogenetic and overall trait functional diversity indices, null models, and plots.
2. morpho_trait.R: R code to calculate observed morphological trait functional diversity indices, null models, and plots.
3. die_trait.R: R code to calculate observed resource acquisition trait functional diversity indices, null models, and plots.
4. habit_trait.R: R code to calculate observed habitat affinity trait functional diversity indices, null models, and plots.
5. lme.R: R code to calculate correlation coefficients between diversity metrics and generating linear mixed-effects models.
6. pool.sp.csv: species by site matrix of the regional species pool
7. pooltree: netwick file of the phylogenetic tree used to calculate phylogenetic diversity and tests phylogenetic signals.
8. reduced_traits....