Data and Code for: Topographic connectivity is associated with millennial-scale lags in Holocene plant community assembly on the eastern Tibetan Plateau

Here, we provide the processed data and analysis code associated with the manuscript “Topographic connectivity is associated with millennial-scale lags in Holocene plant community assembly on the eastern Tibetan Plateau.” The repository contains harmonised downstream datasets and scripts used for statistical analyses, figure generation, and supplementary robustness tests based on sedimentary ancient DNA (sedaDNA) records from five alpine lakes on the eastern Tibetan Plateau: Dangzi Co, Donggi Cona, Naleng Co, Ximen Co, and Zhagaer Co. The raw next-generation sequencing (NGS) data are archived in the European Nucleotide Archive (ENA) under the following accession numbers: PRJEB98248 (Dangzi Co), PRJEB77355 (Donggi Cona), PRJNA596631 (Naleng Co), PRJEB72448 (Ximen Co), and PRJEB98242 (Zhagaer Co). This Zenodo record provides the processed datasets used for downstream analyses, including the customised eastern Tibetan Plateau plant reference database, filtered read tables, rarefied read tables, growth-form trait tables, and source data for the main figures. The accompanying R scripts document the analytical workflow used in the manuscript. These include scripts for generating time slices, rarefaction-based standardisation, spatial zeta diversity analysis, functional-group analyses, forward and reverse fixed-point origin (FPO) zeta analyses, residual-based connectivity analysis, zeta-order robustness analysis, and leave-one-out sensitivity analysis.