DOI: 10.5061/dryad.6ph57
title: Data from: Herbarium specimens reveal a historical shift in phylogeographic structure of common ragweed during native range disturbance

description: Invasive plants provide ample opportunity to study evolutionary shifts
 that occur after introduction to novel environments. However, although
 genetic characters pre-dating introduction can be important determinants
 of later success, large-scale investigations of historical genetic
 structure have not been feasible. Common ragweed (Ambrosia artemisiifolia
 L.) is an invasive weed native to North America that is known for its
 allergenic pollen. Palynological records from sediment cores indicate that
 this species was uncommon before European colonization of North America,
 and ragweed populations expanded rapidly as settlers deforested the
 landscape on a massive scale, later becoming an aggressive invasive with
 populations established globally. Toward a direct comparison of genetic
 structure now and during intense anthropogenic disturbance of the late
 19th century, we sampled 45 natural populations of common ragweed across
 its native range as well as historical herbarium specimens collected up to
 140 years ago. Bayesian clustering analyses of 453 modern and 473
 historical samples genotyped at three chloroplast spacer regions and six
 nuclear microsatellite loci reveal that historical ragweed’s
 spatial-genetic structure mirrors both the paleo-record of Ambrosia pollen
 deposition and the historical pattern of agricultural density across the
 landscape. Furthermore, for unknown reasons this spatial-genetic pattern
 has changed substantially in the intervening years. Following on previous
 work relating morphology and and genetic expression between plants
 collected from eastern North America and Western Europe, we speculate that
 the cluster associated with humans’ rapid transformation of the landscape
 is a likely source of these aggressive invasive populations.
description: FASTA alignment of
 concatenated haplotype sequencesFASTA file containing a
 multiple sequence alignment of all unique haplotype sequences
 (post-concatenation) used in analyses in this study. Sequences are labeled
 "XXYYZZ", where XX is the psbA-trnH haplotype sequence ID as
 defined on GENBANK, YY is the atpF-atpH haplotype sequence ID as defined
 on GENBANK, and ZZ is the psbK-psbI haplotype sequence ID as defined on
 GENBANK. For each accession, the individual haplotype sequences are
 concatenated in the same order as the labels.MLST_output_08-Nov-2012.fastaNewick tree file relating four temporal clusters defined by GENELANDBootstrap support values are indicated as percentage of 100 replicates. Four clusters (branch tips) are included: HISTORICAL WEST, HISTORICAL NORTHEAST, MODERN WEST, and MODERN NORTHEAST.hist_modern_GENELAND_clusters_genepop.txt.populations.NJBS100.for_dryad.phy.newTESS input file for spatial-genetic analysis of historical samplespopulations_historical.TESS.noBermuda.win.txtTESS input file for spatial-genetic analysis of modern samplespopulations_modern.TESS.win.txtGENEPOP input file with populations defined as historical and modern clusters inferred by GENELANDhist_modern_GENELAND_clusters_genepop.txtGENEPOP input file with modern populations dataGENEPOP_input_modern_pops_updatedGENELAND genotype input file for modern samplesmodern_noEls_genotypes.txtGENELAND coordinate input file for modern samplesmodern_noEls_coordinates.txtGENELAND sample ID input file for modern samplesmodern_noEls_IDs.txtGENELAND genotype input file for historical sampleshistorical_genotypes.txtGENELAND coordinates input file for historical sampleshistorical_coordinates.txtGENELAND IDs input file for historical sampleshistorical_IDs.txtSTRUCTURE input file for modern populationspopulations_modern.structure.txtSTRUCTURE input file for historical populations (with GENELAND-inferred cluster definitions included)GLclusters_hist.structure.txtStudy sample information (provenance, haplotypes, genotypes)2019-02-21 sample info table for dryad.xlsx