Warming winters promote biodiversity through reduced mortality of a habitat-forming species in soft-sediment intertidal systems


Summary of the study: Habitat-forming species enhance biodiversity by providing shelter, substrate, and feeding grounds for many species. Climate-change effects on these species may have wide ranging impacts on local species richness and abundance. Higher winter temperatures in particular are an important driver of demographic parameters in temperate to polar environments. However, the extent of these effects on biodiversity remains unclear. We address this topic by studying the abundance of the tube-worm Lanice conchilega, a habitat-forming species that shows mass mortalities in intertidal areas after cold winters. Using 15 years of data collected throughout the intertidal Dutch Wadden Sea, we modeled population dynamics of L. conchilega relative to inundation and winter temperatures, and related its population growth to changes in species richness. Winter temperature was positively associated with L. conchilega's population growth, which in turn correlated with increased species richness. Specifically, for every 28-fold increase in L. conchilega population, one additional species was found per sample. We conclude that increases in winter temperature promote L. conchilega’s abundance and in turn species richness. The positive feedback between warmer winters and L. conchilega might represent a silver lining within the environmental and biodiversity crisis we are facing.

Code version: 1.0

Overview of content: 
data files: 
 - rt_drichnes_data.csv: data for the Lanice conchilega population growth (Rt) INLA models and for the change in species richness (delta richness) INLA models.
 - richness_data.csv: data for the richness analysis.
 - community_composition_data.csv: data for the PERMANOVA and the constrained analysis of proximities comparing species composition in samples with and without L. conchilega. 
Each file also has their own metadata file describing variables included in the dta set. 

code:
 - rt_temperature_analysis_spde10: files with this name include the code for the Lanice conchilega population growth (Rt) vs average winter temperature INLA models. There are two versions of this model: one with no temporal structure in the SPDE (rt_temperature_analysis_spde10_no-time.R) and one with a replicated temporal structure (rt_temperature_analysis_spde10_repl.R)
 - rt_freezing_analysis_spde10: files with this name include the code for the Lanice conchilega population growth (Rt) vs number of freezing days INLA models. There are two versions of this model: one with no temporal structure in the SPDE (rt_freezing_analysis_spde10_no-time.R) and one with a replicated temporal structure (rt_freezing_analysis_spde10_repl.R)
 - richness_analysis_spde10: files with this name include the code for the Richness vs L. conchilega abundance INLA models. There are three versions of this model: one with no temporal structure in the SPDE (richness_analysis_spde10_no-time.R), one with a replicated temporal structure (richness_analysis_spde10_repl.R), and one with an AR1 temporal structure (richness_analysis_spde10_ar1.R)
 - drichness_analysis_spde10: files with this name include the code for the delta Richness vs L. conchilega population growth INLA models. There are two versions of this model: one with no temporal structure in the SPDE (drichness_analysis_spde10_no-time.R) and one with a replicated temporal structure (drichness_analysis_spde10_repl.R)
 - community_composition_analysis: runs the PERMANOVA and the constrained analysis of proximities comparing species composition in samples with and without L. conchilega.