DOI: 10.5061/dryad.kd51c5bch
title: Sequencing data for: Chronosequence of invasion reveals minimal losses of population genomic diversity, niche expansion, and trait divergence in the polyploid, leafy spurge

description: Rapid evolution may play an important role in the range expansion of
 invasive species and modify forecasts of invasion, which are the backbone
 of land management strategies. However, losses of genetic variation
 associated with colonization bottlenecks may constrain trait and niche
 divergence at leading range edges, thereby impacting management decisions
 that anticipate future range expansion. The spatial and temporal scales
 over which adaptation contributes to invasion dynamics remain unresolved.
 We leveraged detailed records of the ~130-year invasion history of the
 invasive polyploid plant, leafy spurge (Euphorbia virgata), across ~500km
 in Minnesota, U.S.A. We examined the consequences of range expansion for
 population genomic diversity, niche breadth, and the evolution of
 germination behavior. Using genotyping-by-sequencing, we found some
 population structure in the range core, where introduction occurred, but
 panmixia among all other populations. Range expansion was accompanied by
 only modest losses in sequence diversity, with small, isolated populations
 at the leading edge harboring similar levels of diversity to those in the
 range core. The climatic niche expanded during most of the range
 expansion, and the niche of the range core was largely non-overlapping
 with the invasion front. Ecological niche models indicated that mean
 temperature of the warmest quarter was the strongest determinant of
 habitat suitability and that populations at the leading edge had the
 lowest habitat suitability. Guided by these findings, we tested
 for rapid evolution in germination behavior over the time course
 of range expansion using a common garden experiment and temperature
 manipulations. Germination behavior diverged from early to late phases of
 the invasion, with populations from later phases having higher dormancy at
 lower temperatures. Our results suggest that trait evolution may have
 contributed to niche expansion during invasion and that distribution
 models, which inform future management planning, may underestimate
 invasion potential without accounting for evolution.
description: Sampling and sequencing In 2019, we
 collected leaf tissue from six individuals in each of 14 populations
 distributed evenly across Minnesota (hereafter: population samples). In
 addition, we collected tissue from one individual in each of 157
 populations distributed relatively evenly across Minnesota, eastern South
 Dakota, eastern North Dakota, and western Wisconsin (hereafter: landscape
 samples). We sampled tissue from individuals that were at least five
 meters apart to minimize collecting from the same genet and placed tissues
 immediately in silica for preservation until DNA extraction.
 We extracted DNA using QIAGEN DNeasy Plant Mini Kits (QIAGEN
 Inc.). Dual-indexed GBS (genotyping-by-sequencing) libraries were created
 using the BamHI + NsiI enzyme combination. All libraries were pooled and
 sequenced on an Illumina NovaSeq System (Illumina Inc., San Diego, CA,
 USA) with 1x100-bp sequencing. Once sequenced, the reads were
 demultiplexed and balanced with a mean quality score ≥ Q30 for all
 libraries. We filtered low-quality bases using Trimmomatic (Bolger et al.
 2014) and used Stacks v.2.5.9 (Rochette et al. 2019) to build loci de novo
 (i.e., without aligning reads to a reference genome). Overall, we obtained
 510 million reads across the 241 samples (599,386 – 3,376,078 of raw reads
 per individual). Mean read depth per locus ranged from 14x to
 26x.
description: FASTQ format is a text-based format for storing both a biological
 sequence (usually nucleotide sequence) and its corresponding quality
 scores. FASTQ files may be opened with any standard text-based file editor
 (e.g., Notepad).
description: # Genomic sequencing Data For Manuscript: Chronosequence of invasion
 reveals minimal losses of population genomic diversity, niche expansion,
 and trait divergence in the polyploid, leafy spurge Supporting genomic
 sequencing data for manuscript: Chronosequence of invasion reveals minimal
 losses of population genomic diversity, niche expansion, and trait
 divergence in the polyploid, leafy spurge Thomas A. Lake, Ryan D. Briscoe
 Runquist, Lex E. Flagel, David A. Moeller bioRxiv 2023.04.04.535556; doi:
 https://doi.org/10.1101/2023.04.04.535556 In 2019, the authors collected
 leafy spurge (*Euphorbia* *virgata*) leaf tissue from six individuals in
 each of 14 populations in Minnesota (hereafter: population samples). In
 addition, the authors collected tissue from one individual in each of 157
 populations throughout Minnesota, northern Iowa, eastern South Dakota,
 eastern North Dakota, and western Wisconsin (hereafter: landscape
 samples). The authors extracted DNA using QIAGEN DNeasy Plant Mini Kits
 (QIAGEN Inc.). Dual-indexed GBS (genotyping-by-sequencing) libraries were
 created using the BamHI + NsiI enzyme combination. All libraries were
 pooled and sequenced on an Illumina NovaSeq System (Illumina Inc., San
 Diego, CA, USA) with 1x100-bp sequencing. Once sequenced, the reads were
 demultiplexed and balanced with a mean quality score ≥ Q30 for all
 libraries. The following 241 .fastq.gz files contain the DNA sequencing
 contents output from the Illumina NovaSeq System. ## Description of the
 Data and file structure The .fastq.gz files contain sequencing data output
 from the Illumina NovaSeq System. These are text files and can be opened
 and manipulated with any text editor. The files are named with the sample
 name and sample number. Example: ANO001-0\_S616\_R1\_001.fastq.gz
 ANO001-0—The sample name. This corresponds to the geographic location of
 the sample, abbreviated by either Minnesota counties (e.g., ANO; Anoka
 County) or State (e.g., ND; North Dakota, SD for South Dakota, WIS for
 Wisconsin, and IOWA for Iowa). S616—The sample number identifier. This
 corresponds to the order the samples were sequenced. R1—The read. In this
 example, R1 means Read 1. 001—The last segment is always 001. fastq.gz—The
 file is a .fastq file and is compressed with gzip to reduce file size. The
 sample names also correspond to Table S1 in the manuscript. Table S1.
 Population name, geographic location, and number of individuals sampled
 per population, totaling 14 population samples and 157 landscape samples
 of leafy spurge. Population samples are indicated in bold. Population
 Latitude Longitude Number of Individuals Sampled ANO001 45.28849 -93.12503
 6 ANO002 45.20712 -93.29607 1 In the case of the ANO001 population, six
 .fastq.gz files correspond to the six individual sampled (population
 samples). ANO001-0\_S616\_R1\_001.fastq.gz
 ANO001-1\_S756\_R1\_001.fastq.gz ANO001-2\_S689\_R1\_001.fastq.gz
 ANO001-3\_S700\_R1\_001.fastq.gz ANO001-4\_S712\_R1\_001.fastq.gz
 ANO001-5\_S724\_R1\_001.fastq.gz ## Sharing/access Information This work
 is licensed under a CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
 license.