Extreme floristic turnover between coastal fog oases and Andean shrublands: lichen diversity and community assembly in southern Peru — dataset and analysis scripts

Published: 6 April 2026| Version 1 | DOI: 10.17632/7rydj6wd9n.1
Contributors:
JOSÉ ANTONIO VALERIANO ZAPANA,
,
,

Description

This repository contains the data and analysis scripts supporting the manuscript entitled “Extreme floristic turnover between coastal fog oases and Andean shrublands: lichen diversity and community assembly in southern Peru”. The study documents lichen diversity and community differentiation across coastal fog oases and Andean shrublands in the Moquegua region, southern Peru. The repository includes the species abundance matrix at the sampling-unit level, the taxonomic checklist, processed community matrices used in the main analyses, station-level metadata, and R scripts for data preparation, alpha diversity, beta diversity partitioning, functional composition, diagnostic species analysis, and final figure assembly. Sampling was conducted across eight sectors representing two contrasting ecosystem types: three coastal fog oasis sectors (Tacahuay, Huacaluna, and Amoquinto) and five Andean shrubland sectors (Altarani, Alto Coscore, Calientes, Charaque, and Tala). The full sampling design comprised 40 stations and 200 sampling units. Because no lichen species were recorded in Amoquinto under the standardized sampling protocol, this sector was retained in richness and detection summaries but excluded from species-composition analyses requiring non-empty community matrices. This repository was prepared specifically for the current manuscript submission and contains the analytical inputs and scripts corresponding to the results reported in this version of the study.

Files

Steps to reproduce

Field data were collected in southern Peru across eight sectors representing two ecosystem types: coastal fog oases (Tacahuay, Huacaluna, and Amoquinto) and Andean shrublands (Altarani, Alto Coscore, Calientes, Charaque, and Tala). The sampling design comprised 40 stations and 200 sampling units (five sampling units per station). Lichen abundance was recorded using a standardized Braun-Blanquet cover-abundance approach, and species were identified using morphological and chemical characters. To reproduce the analytical workflow, download all repository files into a single working directory and open R or RStudio (R v. 4.5.1 or later). The main input files are species_abundance_matrix.csv and taxonomic_checklist.csv. Run the scripts in the following order: 00_style_guide_jvs.R, 01_Setup_Data_JVS.R, 02_Alpha_Inventory_JVS.R, 03_Beta_Diversity_JVS.R, 04_Functional_Environmental_JVS.R, 05_Diagnostic_Species_JVS.R, and 06_Figures_Publication_JVS.R. The setup script performs data cleaning, quality control, incorporation of the Amoquinto zero-detection sector, and generation of processed community matrices and station-level metadata. Subsequent scripts reproduce the taxonomic inventory, sample completeness analyses, alpha diversity, beta diversity partitioning, PERMANOVA, PERMDISP, PCoA, LCBD, functional composition analyses, ecosystem- and sector-level diagnostic species analyses (IndVal.g), and final publication-ready figures. Output files are written automatically to the resultados directory. Amoquinto was sampled using the same standardized protocol as all other sectors, but no lichen species were recorded under this design. For this reason, Amoquinto was retained in richness and detection summaries but excluded from species-composition analyses that require non-empty community matrices.

Institutions

Categories

Ecology, Botany, Biological Classification, Biodiversity Indicator

Funders

  • “Variabilidad espacio-temporal de elementos traza, utilizando líquenes y tillandsias como bioindicadores de la calidad del aire en el ámbito del proyecto minero Anglo American Quellaveco, provincia de Mariscal Nieto, región Moquegua, 2021
    Grant ID: Resolución de Comisión Organizadora N° 428-2021-UNAM
  • Biodiversidad, índice de pureza atmosférica (IPA) y bioacumulación de metales (Pb, Cr, Cd, Cu, Ni, Zn) en los líquenes presentes en las lomas de Amoquinto, Huacaluna (Moquegua) y Tacahuay (Tacna), 2020 y 2021
    Grant ID: Resolución de Comisión Organizadora N° 0835-2019-UNAM

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