DOI: 10.5061/dryad.f32p4
title: Data from: Genomic reconstruction of 100 000-year grassland history in a forested country: population dynamics of specialist forbs

description: Grassland ecosystems worldwide have been extensively converted to other
 land uses and are globally imperiled. Because many grasslands have been
 maintained by human activities, understanding their origin and history is
 fundamentally important to better contemporary management. However,
 existing methods to reconstruct past vegetation can produce contrasting
 views on grassland history. Here, we inferred demographic histories of 40
 populations of four grassland forb species throughout Japan using
 high-resolution genome sequences and model-flexible demographic simulation
 based on the site frequency spectrum. Although two species showed a slight
 decline in population size between 100 000–10 000 years ago, our results
 suggest that population sizes of studied species have been maintained
 within the range of 0.5–2.0 times the most recent estimates for at least
 100 000 years across Japan. Our results suggest that greater than 90%
 declines in Japanese grasslands and subsequent losses of grassland species
 in the last 100 years are geologically and biologically important and will
 have substantial consequences for Japanese biota and culture. People have
 had critical roles in maintaining disturbance-dependent grassland
 ecosystems and biota in this warm and wet forested country. In these
 contexts, disturbances associated with forest harvesting and traditional
 extensive farming have the potential to maintain grassland ecosystems and
 can provide important opportunities to reconcile resource production and
 conservation of grassland biodiversity.
description: RAD-seq raw reads
 Sanguisorba_site4Sanguisorba_site4.zipRAD-seq raw reads Sanguisorba_site1-2Sanguisorba_site1-2.zipRAD-seq raw reads Sanguisorba_site1-1Sanguisorba_site1-1.zipRAD-seq raw reads Sanguisorba_site9-1Sanguisorba_site9-1.zipRAD-seq raw reads Sanguisorba_site9-2Sanguisorba_site9-2.zipRAD-seq raw reads Sanguisorba_site11-1Sanguisorba_site11-1.zipRAD-seq raw reads Sanguisorba_site11-2Sanguisorba_site11-2.zipRAD-seq raw reads Sanguisorba_site12-2Sanguisorba_site12-2.zipRAD-seq raw reads Sanguisorba_site12-1Sanguisorba_site12-1.zipRAD-seq raw reads Sanguisorba_site15-1Sanguisorba_site15-1.zipRAD-seq raw reads Sanguisorba_site15-2Sanguisorba_site15-2.zipRAD-seq raw reads Sanguisorba_site15-3Sanguisorba_site15-3.zipRAD-seq raw reads Sanguisorba_site16-2Sanguisorba_site16-2.zipRAD-seq raw reads Sanguisorba_site16-1Sanguisorba_site16-1.zipRAD-seq raw reads Sanguisorba_site15-4Sanguisorba_site15-4.zipRAD-seq raw reads Sanguisorba_site16-3Sanguisorba_site16-3.zipRAD-seq raw reads Sanguisorba_site22-1Sanguisorba_site22-1.zipRAD-seq raw reads Sanguisorba_site22-3Sanguisorba_site22-3.zipRAD-seq raw reads Sanguisorba_site22-2Sanguisorba_site22-2.zipRAD-seq raw reads Sanguisorba_site23-1Sanguisorba_site23-1.zipRAD-seq raw reads Sanguisorba_site23-2Sanguisorba_site23-2.zipRAD-seq raw reads Sanguisorba_site23-3Sanguisorba_site23-3.zipRAD-seq raw reads Sanguisorba_site25-1Sanguisorba_site25-1.zipRAD-seq raw reads Sanguisorba_site25-2Sanguisorba_site25-2.zipRAD-seq raw reads Dianthus_site2-1RAD-seq raw reads Dianthus_site5-1RAD-seq raw reads Dianthus_site5-2RAD-seq raw reads Dianthus_site8-1RAD-seq raw reads Dianthus_site9-1RAD-seq raw reads Dianthus_site12-1RAD-seq raw reads Dianthus_site15-1RAD-seq raw reads Dianthus_site19-1RAD-seq raw reads Dianthus_site21-1RAD-seq raw reads Dianthus_site23-1RAD-seq raw reads Dianthus_site24-1RAD-seq raw reads Swertia_site3-1RAD-seq raw reads Swertia_site3-2RAD-seq raw reads Swertia_site3-3RAD-seq raw reads Swertia_site6-1RAD-seq raw reads Swertia_site6-2RAD-seq raw reads Swertia_site9-1RAD-seq raw reads Swertia_site9-2RAD-seq raw reads Swertia_site9-3RAD-seq raw reads Swertia_site10-1RAD-seq raw reads Swertia_site10-2RAD-seq raw reads Swertia_site10-3RAD-seq raw reads Swertia_site13-1RAD-seq raw reads Swertia_site13-2RAD-seq raw reads Swertia_site13-3RAD-seq raw reads Swertia_site14-1RAD-seq raw reads Swertia_site14-2RAD-seq raw reads Swertia_site14-3RAD-seq raw reads Swertia_site18-1RAD-seq raw reads Swertia_site18-2RAD-seq raw reads Swertia_site18-3RAD-seq raw reads Swertia_site21-1RAD-seq raw reads Swertia_site21-2RAD-seq raw reads Swertia_site21-3RAD-seq raw reads Swertia_site23-2RAD-seq raw reads Swertia_site23-1RAD-seq raw reads Swertia_site24-1RAD-seq raw reads Swertia_site24-2RAD-seq raw reads Swertia_site23-3-1SjaRAD3_IPd012_ctgggccg-1.fastq.zip needs to be combined with SjaRAD3_IPd012_ctgggccg-2.fastq.zipSjaRAD3_IPd012_ctgggccg-1.fastq.zipRAD-seq raw reads Swertia_site23-3-2SjaRAD3_IPd012_ctgggccg-2.fastq needs to be combined with SjaRAD3_IPd012_ctgggccg-1.fastqSjaRAD3_IPd012_ctgggccg-2.fastq.zipRAD-seq raw reads Patrinia_site3-1RAD-seq raw reads Patrinia_site3-2RAD-seq raw reads Patrinia_site6-1RAD-seq raw reads Patrinia_site6-2RAD-seq raw reads Patrinia_site7-1RAD-seq raw reads Patrinia_site7-2RAD-seq raw reads Patrinia_site7-3RAD-seq raw reads Patrinia_site9-1RAD-seq raw reads Patrinia_site9-2RAD-seq raw reads Patrinia_site11-1RAD-seq raw reads Patrinia_site11-2RAD-seq raw reads Patrinia_site11-3RAD-seq raw reads Patrinia_site15-1RAD-seq raw reads Patrinia_site15-2RAD-seq raw reads Patrinia_site15-3RAD-seq raw reads Patrinia_site17-1RAD-seq raw reads Patrinia_site17-2RAD-seq raw reads Patrinia_site17-3RAD-seq raw reads Patrinia_site20-1RAD-seq raw reads Patrinia_site20-2RAD-seq raw reads Patrinia_site20-3RAD-seq raw reads Patrinia_site23-1RAD-seq raw reads Patrinia_site23-2RAD-seq raw reads Patrinia_site25-1RAD-seq raw reads Patrinia_site25-2