DOI: 10.5061/dryad.rc1jr0v
title: Data from: Population history provides foundational knowledge for utilizing and developing native plant restoration materials

description: A species’ population structure and history are critical pieces of
 information that can help guide the use of available native plant
 materials in restoration treatments and decide what new native plant
 materials should be developed to meet future restoration needs. In the
 western United States, Pseudoroegneria spicata (bluebunch wheatgrass;
 Poaceae) is an important component of grassland and shrubland plant
 communities and commonly used for restoration due to its drought
 resistance and competitiveness with exotic weeds. We used next-generation
 sequencing data to investigate the processes that shaped P. spicata’s
 geographic pattern of genetic variation across the Intermountain West.
 Pseudoroegneria spicata’s genetic diversity is partitioned into
 populations that likely differentiated since the Last Glacial Maximum.
 Adjacent populations display varying magnitudes of historical gene flow,
 with migration rates ranging from multiple migrants per generation to
 multiple generations per migrant. When considering the commercial
 germplasm sources available for restoration, genetic identities remain
 representative of the wildland localities from which germplasm sources
 were originally developed, and they maintain high levels of heterozygosity
 and nucleotide diversity. However, the commercial germplasm sources
 represent a small fraction of the overall genetic diversity of P. spicata
 in the Intermountain West. Given the low migration rates and long
 divergence times between some pairs of P. spicata populations, using
 commercial germplasm sources could facilitate undesirable restoration
 outcomes when used in certain geographic areas, even if the environment in
 which the commercial materials thrive is similar to that of the
 restoration site. As such, population structure and history can be used to
 provide guidance on what geographic areas may need additional native plant
 materials so that restoration efforts support species and community
 resilience and improve outcomes.
description: Phylip_fileThis is a variable phylip file created by the populations program in Stacks 1.46. We used a population map that included only samples used in modeling (see Supplemental Table S1). The 4 populations in the phylip file are defined as follows: 1 - WAS; 2 - EGB; 3 - P/W; 4 - WGB. See figures and text for population descriptions.pssp_modeling_groups.phylippssp_polySTRUCTURE-formatted file used to investigate variation between diploids and tetraploids using PCA (in adegenet). The file contains 959 individuals and 8945 unlinked loci (i.e., only 1 locus per stack is recorded in this file). The first column contains sampling locality names combined with an ID number (unique per individual). There are 2 rows per individuals - each records 1 allele. The second column is records a populations identifier - right now all diploids are recorded as "1" and all allotetraploids are recorded as "2". The subsequent columns contain the loci. Missing data is recorded as "-9". See Supplemental Table S1 for more information.pssp_diploidSTRUCTURE-formatted file containing 834 P. spicata diploid individuals (wildland collections + commercial germplasm sources). This file was used in PCA (utilizing adegenet in R) and in STRUCTURE and sPCA analyses (not including the commercial germplasm sources). The file 3040 unlinked loci (i.e., only 1 locus per stack is recorded). The first column contains sampling locality names combined with an ID number (unique per individual). There are 2 rows per individuals - each records 1 allele. The second column is records a populations identifier - right now numbers reflect regional population identity, with commercial germplasm sources = "0". The subsequent columns contain the loci. Missing data is recorded as "-9". See Supplemental Table S1 for more information.psspVariant Call Format (vcf) file created by the populations program in Stacks v1.46. File contains 113,310 loci (in rows) from 834 diploid P. spicata individuals (in columns). Individuals are named with a sampling locality name and unique identifier (i.e., number).