Data from: Herbarium specimens reveal a historical shift in phylogeographic structure of common ragweed during native range disturbance

 

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Title FASTA alignment of concatenated haplotype sequences
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Description FASTA 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.
Download MLST_output_08-Nov-2012.fasta (62.18 Kb)
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Title Newick tree file relating four temporal clusters defined by GENELAND
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Description Bootstrap support values are indicated as percentage of 100 replicates. Four clusters (branch tips) are included: HISTORICAL WEST, HISTORICAL NORTHEAST, MODERN WEST, and MODERN NORTHEAST.
Download hist_modern_GENELAND_clusters_genepop.txt...hy.new (130 bytes)
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Title TESS input file for spatial-genetic analysis of historical samples
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Download populations_historical.TESS.noBermuda.win.txt (32.56 Kb)
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Title TESS input file for spatial-genetic analysis of modern samples
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Download populations_modern.TESS.win.txt (31.79 Kb)
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Title GENEPOP input file with populations defined as historical and modern clusters inferred by GENELAND
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Download hist_modern_GENELAND_clusters_genepop.txt (53.86 Kb)
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Title GENEPOP input file with modern populations data
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Download GENEPOP_input_modern_pops_updated (25.61 Kb)
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Title GENELAND genotype input file for modern samples
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Download modern_noEls_genotypes.txt (21.11 Kb)
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Title GENELAND coordinate input file for modern samples
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Download modern_noEls_coordinates.txt (7.744 Kb)
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Title GENELAND sample ID input file for modern samples
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Download modern_noEls_IDs.txt (2.742 Kb)
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Title GENELAND genotype input file for historical samples
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Download historical_genotypes.txt (21.44 Kb)
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Title GENELAND coordinates input file for historical samples
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Download historical_coordinates.txt (7.918 Kb)
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Title GENELAND IDs input file for historical samples
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Download historical_IDs.txt (2.934 Kb)
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Title STRUCTURE input file for modern populations
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Download populations_modern.structure.txt (25.41 Kb)
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Title STRUCTURE input file for historical populations (with GENELAND-inferred cluster definitions included)
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Download GLclusters_hist.structure.txt (25.80 Kb)
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When using this data, please cite the original publication:

Martin MD, Zimmer EA, Olsen MT, Foote AD, Gilbert MTP, Brush GS (2014) Herbarium specimens reveal a historical shift in phylogeographic structure of common ragweed during native range disturbance. Molecular Ecology 23(7): 1701-1716. http://dx.doi.org/10.1111/mec.12675

Additionally, please cite the Dryad data package:

Martin MD, Zimmer EA, Olsen MT, Foote AD, Gilbert MTP, Brush GS (2014) Data from: Herbarium specimens reveal a historical shift in phylogeographic structure of common ragweed during native range disturbance. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.6ph57
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