"Alternative vegetation configurations and assembly patterns on the dried Aral Sea bed", to Journal of Vegetation Science (9076650).
Abstract
# README **Title:** Data, metadata, and analysis scripts for: "Alternative vegetation configurations and assembly patterns on the dried Aral Sea bed" **Authors:**Azamat Sultamuratov¹, Bekhzod Adilov¹, Khabibullo Shomurodov², Tashkhanim Rakhimova¹, Farrukh Polvonov¹, Nodira Rakhimova¹, Allabek Mirzambetov¹, Jasur Sadinov¹, Shakhnoza Saribaeva¹, Miyassar Karlibayeva¹, Gulnora Begjanova³ **Affiliations:**¹ Laboratory of Geobotany, Institute of Botany, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan² Laboratory of Conservation and Ecology of Plants, Institute of Botany, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan³ Department of Biology, Karakalpak State University, Nukus, Uzbekistan **Corresponding authors:**- Azamat Sultamuratov (as.azamatsultamuratov@gmail.com; ORCID: 0009-0002-6923-7826)- Bekhzod Adilov (bekhzod.adilov82@gmail.com; ORCID: 0000-0001-7642-7789) **Related manuscript:**Sultamuratov, A., Adilov, B., Shomurodov, K., Rakhimova, T., Polvonov, F., Rakhimova, N., Mirzambetov, A., Sadinov, J., Saribaeva, S., Karlibayeva, M., & Begjanova, G. (2026). Alternative vegetation configurations and assembly patterns on the dried Aral Sea bed. *Journal of Vegetation Science*. **Archive DOI:** https://doi.org/10.5281/zenodo.23460037**GIVD Database ID:** AS-UZ-001 --- ## OverviewThis archive contains the processed vegetation-plot dataset, associated plot and species metadata, and modular R helper scripts used in the analyses for the study *"Alternative vegetation configurations and assembly patterns on the dried Aral Sea bed"*. The archived materials support input validation, data preprocessing, vegetation classification (modified TWINSPAN), multivariate statistical testing, diagnostic species identification, ordination, richness and cover analyses, historical ecological-type (Uzgiprozem) interpretation, and phylogenetic analyses. --- ## Archive Contents ### A. Data and Metadata Files (`meta_data/`) 1. **`df_data.csv`** — Processed vegetation plot × species dataset used as the main analytical matrix. - Rows represent vegetation plots (relevés) and columns represent species codes (or plot-species records). - Species values in the matrix are given as cover values. Zero indicates absence of a species in a plot. 2. **`df_com.csv`** — Plot-level and community metadata table. - Links unique plot identifiers to survey dates, community attributes, and interpreted historical ecological types (`Eco_typ`). - **Ecological-type abbreviations:** - `Ga` = halophyte - `Gp` = gypsophyte - `Po` = potamophyte - `Ps` = psammophyte - `GaGp` = halo-gypsophyte - `GaPo` = halo-potamophyte - `GaPs` = halo-psammophyte - `GpPs` = gypso-psammophyte - `PoGa` = potamo-halophyte - `PoPs` = potamo-psammophyte - `PsGa` = psammo-halophyte - `PsGp` = psammo-gypsophyte - `PsPo` = psammo-potamophyte - `GaGpPs` = halo-gypso-psammophyte - `GaPsPo` = halo-psammo-potamophyte - `PoGpGa` = potamo-gypso-halophyte - `PoPsGa` = potamo-psammo-halophyte 3. **`df_species.csv`** — Primary species metadata and taxonomic reference table. - Links species codes (`s_code`) used in the vegetation matrix to full scientific names (`sp_name`), life-form categories (`life_form`), and auxiliary taxonomic names used to improve species matching in phylogenetic workflows. - **Life-form categories:** - `An` = annuals - `Pr` = perennials - `Sr` = shrubs - `Ss` = subshrubs 4. **`schema.ini`** — Schema configuration file specifying column data formatting (e.g., text/date parsing for `df_com.csv`). #### Relationships Among Files- Plot identifiers in `df_data.csv` correspond to plot records in `df_com.csv`.- Species codes in `df_data.csv` correspond to taxonomic records in `df_species.csv`. --- ### B. R Analysis Scripts (`scripts/`) This archive includes 11 modular R scripts and a comprehensive PDF documentation file used to preprocess the data, perform the statistical and phylogenetic analyses, and generate derived outputs: 1. **`00_load_helpers.R`** — Initializes the R environment, loads required packages, sets global parameters, and sources the modular helper scripts.2. **`00_validate_inputs.R`** — Validates the structure and integrity of input data files (`df_data.csv`, `df_com.csv`, `df_species.csv`), checking plot IDs, species codes, and data completeness.3. **`01_data_preparation_helpers.R`** — Cleans and formats plot and species tables, assigns life-form subsets (full dataset, annuals, perennials, woody species), and prepares analytical matrices.4. **`02_filtering_transformation_helpers.R`** — Removes empty plots and species, applies species-occurrence frequency filtering (evaluating thresholds of 3, 4, and 5, retaining frequency ≥ 4 for main analyses), and exports raw and square-root transformed matrices.5. **`03_twinspan_screening_helpers.R`** — Executes modified TWINSPAN classification, evaluates partition levels (*k* = 5–8) using indicator species counts, minimum cluster size, and silhouette width, defines the retained six-group classification, and generates hierarchy diagrams and text reports.6. **`04_multivariate_tests_helpers.R`** — Calculates within-group Sørensen similarity, beta-diversity partitioning, compositional separation, multivariate dispersion, and resampling reproducibility across vegetation groups and growth-form subsets.7. **`05_diagnostic_species_helpers.R`** — Computes species constancy, fidelity, and cover summaries across clusters to identify diagnostic, constant, and dominant species, and constructs synoptic tables.8. **`06_ordination_helpers.R`** — Performs 3D Non-metric Multidimensional Scaling (NMDS) with projected ellipses, growth-form-specific Detrended Correspondence Analysis (DCA), and Correspondence Analysis (CA) linking vegetation groups to historical ecological types.9. **`07_richness_cover_helpers.R`** — Calculates plot-level species richness and vegetation cover across total vegetation and growth-form groups, performs one-way ANOVA across clusters, and exports summary tables and boxplots.10. **`08_uzgiprozem_helpers.R`** — Processes and summarizes historical ecological-type classifications (Uzgiprozem framework) across the six vegetation groups.11. **`09_phylogeny_helpers.R`** — Performs taxonomic matching, phylogenetic tree construction, Faith’s Phylogenetic Diversity (PD), SES.MPD, phylogenetically ordered occurrence heatmaps, and tanglegram comparisons with the modified TWINSPAN hierarchy.12. **`Metadata_Scripts.pdf`** — Detailed documentation of the analytical workflow, script functions, and input/output specifications. --- ## Access ConditionsMetadata describing the vegetation-plot database are registered in GIVD (ID: AS-UZ-001). The scripts and shareable metadata in this archive are publicly available under a Creative Commons Attribution 4.0 International (CC BY 4.0) license at https://doi.org/10.5281/zenodo.23460037. Access to raw plot-level relevé data remains subject to GIVD/sPlot database governance and applicable third-party restrictions.
