DOI: 10.5061/dryad.31zcrjdwq
title: Data from: Global spatiotemporal patterns of demographic fluctuations in terrestrial vertebrates during the Late Pleistocene

description: Demographic fluctuations are crucial for assessing species’ threat levels,
 yet their global spatiotemporal patterns and historical drivers remain
 unknown. Here, we used single whole-genome sequence data for 527 extant
 and widespread terrestrial vertebrates to investigate their demographic
 fluctuations during the Late Pleistocene. Effective population size (Ne)
 simulations indicated that all taxa experienced a population decline from
 the Last Interglacial to the Last Glacial Maximum (LGM). After the LGM,
 birds, and amphibians underwent population expansion, whereas mammals and
 reptiles’ populations declined. Regions with high Ne shifted from
 Neotropical to Afrotropical and to Palearctic, some overlapping with
 recognized glacial refugia and biodiversity hotspots. In addition,
 climate-related factors exerted long-term effects on Ne, while human
 disturbances might confine to specific regions around the
 Pleistocene-Holocene boundary. This study underscores the significance of
 quantifying vertebrate genetic vulnerability to guide biodiversity
 conservation in response to environmental changes.
description: # Data from: Global spatiotemporal patterns of demographic fluctuations
 for terrestrial vertebrates during the Late Pleistocene
 [https://doi.org/10.5061/dryad.31zcrjdwq](https://doi.org/10.5061/dryad.31zcrjdwq) ## Files and variables ### `The_genomic_information.csv` This file contains the names of each species and their Genbank accession IDs used in this study: * **Latin name**: The scientific name of each species * **Class**: The class of each species * **Order**: The order to which each species belongs * **Family**: The family classification for each species * **Accession ID**: The GenBank ID of the genome used for each species * **Project ID**: The project ID associated with each genome * **Sample ID**: The sample ID for each genome ### `01.Ne_cluster_analysis` This folder contains the effective population size (*Ne*) data, IUCN conservation status information, and taxonomic information for each species in this study. * **`species_raw_Ne.txt`**: This file contains the effective population size (Ne, in units of x10^4) data for terrestrial vertebrates during the Late Pleistocene, split by equidistant time points (log-transformed). * **`IUCN_red_list_status.csv`**: This file contains IUCN conservation status information for the species studied. * **`Vertebrate_taxonomy.csv`**: This file contains the taxonomic information of the species studied. ### `02.SES_Ne` This folder contains the grid files used in the study, mean normalized *Ne* values and species counts for each grid cell. * **`grid_shp`**: The grid files used in the study. * **`distribution_01`** (folder): This folder contains 0-1 matrices representing species distributions for different periods (10 ka - 120 ka), simulated using SDMs. * **`map_all_removeoutliner.RData`**: This file contains mean normalized Ne values and species counts for each grid cell. * **`PSMC_Ne_timesplit.csv`**: This file contains normalized Ne values corresponding to each period (10 ka - 120 ka). ### Code Folder (Zenodo) #### `01.Run_psmc_pipelines` This folder contains the workflow for SNP calling and PSMC analysis. #### `02.Ne_cluster_analysis.R` Script for performing the cluster analysis of *Ne*. #### `03.Standard_Effect_Size_of_Ne.R` Script for calculating an inverse range size-weighted *Ne*. ### External References The code used to establish the SDMs can be found in the following reference: * W. Thuiller, M. Guéguen, J. Renaud, D. N. Karger, N. E. Zimmermann, "Uncertainty in ensembles of global biodiversity scenarios," *Nature Communications*, 10, 1446 (2019). The code used for the spatial mixed-effects model (spaMM) analysis can be found in the following reference: * M. Huang, G. Huang, H. Fan, F. Wei, "Influence of Last Glacial Maximum legacies on functional diversity and community assembly of extant Chinese terrestrial vertebrates," *The Innovation*, 4 (2023). ## Software 1. R version 4.3.3 2. fastp version 0.23.2 3. BWA version 0.7.17 4. Picard version 2.21.6 5. PSMC version 0.6.5-r67 ### Required R packages 1. stringr version 4.2.3 2. dplyr version 1.0.10 3. tidyr version 4.2.3 4. foreach version 1.5.2 5. dtwclust version 5.5.12 6. dtw version 1.23.1 7. amap version 0.8.19 8. ggplot2 version 3.5.0 9. ggdendro version 0.1.23 10. ggpmisc version 4.2.3 11. ComplexHeatmap version 2.14.0 12. doParallel version 1.0.17 13. picante version 4.2.3 14. sf version 4.2.3