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Variation in successional dynamics shape biodiversity patterns over a tropical-temperate latitudinal gradient

Cite this dataset

Bracewell, Sally; Johnston, Emma; Clark, Graeme (2024). Variation in successional dynamics shape biodiversity patterns over a tropical-temperate latitudinal gradient [Dataset]. Dryad. https://doi.org/10.5061/dryad.1rn8pk117

Abstract

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.

README: Successional dynamics vary over a tropical-temperate latitudinal gradient

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

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

Funding

Australian Research Council

UNSW Sydney