Data from: Geographic range size is predicted by plant mating system

Grossenbacher D, Briscoe Runquist R, Goldberg EE, Brandvain Y

Date Published: June 15, 2015

DOI: http://dx.doi.org/10.5061/dryad.hv117

 

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Title Geographic data organized by genus
Downloaded 29 times
Description For each genus in the study there are two types of files: 1) "orignal.gbif.genus" contains all known occurrence records for the species in our study as downloaded from the Global Biodiversity Information Facility (http://www.gbif.org) 2) "ft.clean.gbif.genus" contains the filtered and cleaned records used in downstream analyses (note that scripts to generate these cleaned files are in folder "get.clean.geo").
Download data geographic.zip (84.95 Mb)
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Title Mating system data organized by genus
Downloaded 28 times
Description For each genus in the study there is a unique file "genus.csv" that contains the following data columns: species names (species), mating system category (mate.sys), method used to assign mating system (method), source (ref), notes (notes), and availability of loci on genbank (rps, its, trn).
Download data mating system.zip (22.64 Kb)
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Title Phylogenetic data orangized by genus
Downloaded 30 times
Description For each genus, there are several files: original genbank download of its sequences (original.genbank.genus.fasta), aligned its sequences (genus.its.aligned.fa), BEAST xml file (genus.its.aligned.xml), BEAST output files (genus.its.aligned.log, genus.its.aligned.ops, genus.its.aligned.trees), subset of 9000 trees from the posterior (genus.its.final.tree), and consensus tree used only for data visualization (genus.its.consensus.tree).
Download data phylogenetic.zip (438.9 Mb)
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Title Correlated trait data table
Downloaded 16 times
Description This data table contains the following columns: species name (species), number of gametic chromosomes (X1N), qualitative ploidy assignment (ploidy.qual), notes on ploidy (ploidy.notes), source for ploidy (ploidy.source), qualitative life history assignment (life.history.qual), notes on life history (ann.per.notes), life history source (ann.per.source)
Download data.correlated.traits.csv (113.0 Kb)
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Title R scripts for filtering geographic data
Downloaded 65 times
Description For each genus there is a unique R script used to filter and clean the original geographic data downloaded from the Global Biodiversity Information Facility (http://www.gbif.org). These scripts filter GBIF data for quality by excluding records with coordinate accuracy < 100 km, coordinates failing to match the locality description, and taxonomic misidentifications (verified by the authors and taxonomic specialists of each clade). Species’ epithets were checked against the most recently published taxonomies and synonyms and spelling errors are corrected here. Finally, coordinates outside the native species range with published monographs and online databases that report native and invaded ranges (e.g. GRIN database, http:// www.ars-grin.gov/), are identified and excluded.
Download get.clean.geo.zip (71.17 Kb)
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Title R script for grabbing sister pairs across a sample of trees
Downloaded 33 times
Description This R script grabs all sister pairs from across a sample of trees,computes the average branch length (dist), computes the posterior probability (pp = proportion of sampled trees with a given sister pair), and grabs the mating system of the sister pair.
Download get.sisters.R (4.341 Kb)
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Title R script for calculating sister pair range size and co-occurrence
Downloaded 25 times
Description This R script takes a list of sister pairs (generated using script "get.sisters"), computes their geographic range sizes across varying spatial scales, and computes various metrics of co-occurrence used in American Journal of Botany paper "No association between plant mating system and geographic range overlap".
Download get.sisters.rangesize.cooccur.R (9.001 Kb)
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Title R script for range size stats and figures
Downloaded 28 times
Description This R script performs statistical analyses and generates figures used in Ecology Letters paper "Geographic range size is predicted by plant mating system".
Download get.stats.rangesize.R (26.48 Kb)
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Title R script for co-occurrence stats and figures
Downloaded 39 times
Description This R script performs statistical analyses and generates figures used in Ecology Letters paper American Journal of Botany paper "No association between plant mating system and geographic range overlap".
Download get.stats.cooccurrence.R (12.66 Kb)
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Title Data summary table of sister pairs
Downloaded 16 times
Description This data table contains summary information of sister pairs used in final analyses and for generating figures (see R scripts "get.stats.cooccurrence" and "get.stats.rangesize"), and includes the following columns: genus (genus); sister species A (sp.A); sister species B (sp.B); sister species A and B separated by underscore (ba); branch length (dist); posterior probability (pp); weighting factor using for data visualization (fig.weight); mating system classification of (sp.A.mate, sp.B.mate, mate.diff); range size of species A and B across 4 spatial resolutions (A.range.res1, B.range.res1, A.range.res0.5, B.range.res0.5, A.range.res0.1, B.range.res0.1, A.range.res0.05, B.range.res0.05); co-occurrence index across 4 spatial resolutions (overlap.min.res1, overlap.min.res0.5, overlap.min.res0.1, overlap.min.res0.05); latitudinal characteristics of species A and B (lat.mean.spA, lat.med.spA, lat.min.spA, lat.max.spA, lat.mean.spB,lat.med.spB, lat.min.spB, lat.max.spB); ploidy category for species A and B (ploidy.spA, ploidy.spB); life history category for species A and B (life.history.spA, life.history.spB)
Download sister.summary.table.csv (138.4 Kb)
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When using this data, please cite the original publication:

Grossenbacher D, Briscoe Runquist R, Goldberg EE, Brandvain Y (2015) Geographic range size is predicted by plant mating system. Ecology Letters 18(7): 706-713. http://dx.doi.org/10.1111/ele.12449

Additionally, please cite the Dryad data package:

Grossenbacher D, Briscoe Runquist R, Goldberg EE, Brandvain Y (2015) Data from: Geographic range size is predicted by plant mating system. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.hv117
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