DOI: 10.5061/dryad.1rn8pk117
title: Variation in successional dynamics shape biodiversity patterns over a tropical-temperate latitudinal gradient

description: Successional dynamics can vary due to a range of ecological and
 environmental factors, but our understanding of biogeographic variation in
 succession, and the processes contributing to community development across
 ecosystems, is limited. The pattern and rate of recruitment of dispersive
 propagules likely differs over large spatial scales and can be an
 important predictor of successional trajectory. Over a 20-degree
 tropical-temperate latitudinal gradient, we measured sessile invertebrates
 over 12 months of community development and successive 3-month recruitment
 windows to understand succession and how it is influenced by recruitment.
 Succession and recruitment patterns varied over latitude. In the tropics,
 fast temporal turnover, fluctuating abundances, and lack of successional
 progression suggest that the contribution of stochastic processes was
 high. As latitude increased, successional progression became more
 apparent, characterized by increasing species richness and community
 cover, and a shift to more competitive taxa over time. At temperate
 locations, species identities were similar between older communities and
 recruiting assemblages, however community composition became more variable
 across space over time. Such divergence suggests an important role of
 early colonisers and species interactions on community structure. These
 findings demonstrate differences in the processes contributing to
 community development and biodiversity patterns over latitude.
 Understanding such biogeographic variation in community dynamics and
 identifying the prevalence of different processes can provide insights
 into how communities assemble and persist in response to environmental
 variability.
description: # Successional dynamics vary over a tropical-temperate latitudinal
 gradient
 [https://doi.org/10.5061/dryad.1rn8pk117](https://doi.org/10.5061/dryad.1rn8pk117) This repository contains code and data to reproduce the results of the manuscript “Successional dynamics vary over a tropical-temperate latitudinal gradient”. Bracewell, S. A., Johnston, E. L., and Clark, G. F. The American Naturalist *Raw data files:* **Latitude.csv** - abundance census of species for each sampling tile, consisting of 49 data points per location. * Plate_ID: sample identifier * Rep: rep number or sample (1:8 per site) * Latitude: latitude of site * Site: site name * Site1: shortened site name * Month: number of months the sample was collected after deployment * Collection: calendar month sample was collected * Panel: panel number the sample was located on (one or two) * Point_number: identification point of organism on sample (1:49) * Taxa: taxa of identified organism * Species: species/morphospecies of identified organism **PresenceAbsence.csv** - presence absence data sheet of all species found on each tile. Site, Site1, Latitude, PlateID, Month, Rep, Panel as above. Remaining column headers are species/morphospecies ID’s. **PresenceAbsence_pc.csv** - percent cover incl. 0.1% nominal percent for those additional species found outside of the 49-point census. Column headers as above. **ozdata.csv** – longitudinal and latitudinal data for all of Australia required to produce map outline in fig.1. * long: longitude * lat: latitude * group: number identifier for each state * order: number identifier for each lat/long combo * state: Australian state * border: coastal or state borders **sites_lat_long.csv** - latitude and longitude of each site to recreate the map in fig.1. **Temp_data.csv** - temperature data to recreate temperature component for map in fig.1 and fig. A1. Site and Panel as above. * Month: calendar month temperature was logged * Day: day of the calendar month temperature was logged * Year: year temperature was logged * Time: time temperature was logged * Period: morning(am)/afternoon(pm) * Temperature: temperature that was logged (oC) **Rainfall_data.csv** - rainfall data to recreate rainfall component of fig. A1. Site, Day, Month, Year as above. * Rainfall_mm: amount of rainfall (mm) * Missing values indicate data that was not available. *R generated data required for analysis/figures:* **all_nulljacc_AmNat.csv** – Jaccard dissimilarity and null model simulations between all samples. * ss: site * P1: sample 1 * P2: sample 2 * jacc: Jaccard dissimilarity between sample 1 and sample 2 * nulljacc_dev: deviation between observed Jaccard and the mean of the null distribution as per Tucker et al. (2015) **all_nullbray_AmNat.csv** – Bray-Curtis dissimilarity and null model simulations between all samples. ss, P1, and P2 as above. * brayc: Bray-Curtis dissimilarity between sample 1 and sample 2 * nullbrayc: mean of randomisation between sample 1 and sample 2 * mean_null_diss: mean of randomisations for whole metacommunity (site) * null_dev: brayc - nullbrayc * mean_null_dev: brayc – mean_null_diss **Rarefied_beta_diversity_jacc.csv** - rarefied beta diversity using Jaccard dissimilarity used in Appendix B. Site, Month, and Latitude as above. * Samples: rep number * Rarefaction: mean of the values of the accumulation curves * IC_up: upper confidence interval * IC_low: lower confidence interval * NA indicates that no value was generated **Rarefied_beta_diversity_bray.csv** - rarefied beta diversity using Bray-Curtis dissimilarity used in Appendix B. Column variables as above. *Scripts/software:* All diversity calculations, statistical analyses, and figures were done using R program version 4.2.2. The following packages are required to run each script: * plyr * dplyr * vegan * tidyverse * lme4 * lmerTest * reshape2 * boot * broom.mixed * purrr * patchwork * RVAideMemoire * Scales **Latitude_succession_AmNat.R** – run first before ALPHA, BETA or APPENDIX scripts. Loads data files and contains code for data manipulation. **ALPHA_Latitude_succession_AmNat.R** - contains script for all alpha diversity analyses, including taxonomic group analyses, and recreate figs. 5, 6, and 7. **BETA_Latitude_succession_AmNat.R** - contains script for all beta diversity analyses, including null models, and recreate figs. 2, 3, and 4. **APPENDIX_Latitude_succession_AmNat.R** - contains script for analyses and recreation of figures in Appendix A and B. **PANullDevFctsOikos.R** - code taken from Tucker et al. 2015, functions required to run null models. **ExampleSimulationNullDevCalc.R** - code taken from Tucker et al. 2015, provides example simulations for null model calculations. **MetacommunityDynamicsFctsOikos.R** - code taken from Tucker et al. 2015, required to run example simulations in ExampleSimulationNullDevCalc.R. **rare_beta.R** **–** contains rare_beta function taken from Rarefy package required to run rarefied beta diversity analysis in Appendix B. *Additional files* **Example_plate_photos_and**_**CPCe files.zip** - examples of data collection from photos and associated CPCe files. *References* Tucker, C. M., L. G. Shoemaker, K. F. Davies, D. R. Nemergut, and B. A. Melbourne. 2015. Differentiating between niche and neutral assembly in metacommunities using null models of β-diversity. *Oikos* 125:778-789. [https://doi.org/10.1111/oik.02803](https://doi.org/10.1111/oik.02803) Thouverai, E., S. Pavoine, E. Tordoni, D. Rocchini, C. Ricotta, A. Chiarucci, and G. Bacaro. 2020. Rarefy: Rarefaction Methods. R package version 1.0. [https://CRAN.R-project.org/package=Rarefy](https://CRAN.R-project.org/package=Rarefy)