La Mar fungus-gnat diversity: data and analysis archive for "Rich but compressed: a diversity paradox in Andean–Amazonian fungus gnats across a coffee land-use gradient"

This archive contains the data, R analysis code, source tables and generated figures underlying the manuscript "Rich but compressed: a diversity paradox in Andean–Amazonian fungus gnats across a coffee land-use gradient" (target journal: Insect Conservation and Diversity). Malaise-trap sampling across three habitats — forest remnant, shaded coffee and sun-exposed monoculture coffee — in La Mar province (Ayacucho, Peru) over 26 fortnightly periods (2022–2023) yielded COI-barcoded Sciaroidea (fungus gnats) delimited into molecular operational taxonomic units (MOTUs). This cleaned re-analysis retained 2,685 sequences in 361 MOTUs across 78 habitat–period assemblages. The archive includes: original source data (aligned clustering FASTA, specimen/morphology workbook, collecting-event metadata); the cleaned analysis-ready specimen table; derived convenience matrices (MOTU abundance matrix, taxonomic assignments, taxonomic-distance inputs, habitat-period metadata, trap effort); modular R scripts (01–18) with a single run-all driver; all generated tables and figures (main Fig 1–5, supplementary Fig S1–S6, diagnostic figures); R session information; SHA-256 checksums; and specimen/sequence/voucher crosswalks. COI barcode sequences are deposited in GenBank under accession numbers PZ614493–PZ617177 (submission SUB16297165). Voucher specimens are held at National Museums Scotland pending taxonomic description, with primary material to be deposited at UNMSM, Lima. See README.md for folder structure and manifest_sha256.txt for file-level checksums.