Data from: RAD-seq data reveal a cryptic Viburnum species on the North American Coastal Plain

Spriggs EL, Eaton DAR, Sweeney PW, Schlutius C, Edwards EJ, Donoghue MJ

Date Published: December 4, 2018

DOI: https://doi.org/10.5061/dryad.m1vc0

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Sequence_data_min10
Downloaded 2 times
Description All ipyrad outfiles for the entire V. nudum complex + outgroups with all loci shared across at least 10 individuals
Download nudum-c88-d6-min10_outfiles.zip (256.3 Mb)
Details View File Details
Title Sequence_data_min20
Downloaded 1 time
Description All ipyrad outfiles for the entire V. nudum complex + outgroups with all loci shared across at least 20 individuals
Download nudum-c88-d6-min20_outfiles.zip (216.0 Mb)
Details View File Details
Title Sequence_data_files_min40
Downloaded 1 time
Description All ipyrad outfiles for the entire V. nudum complex + outgroups with all loci shared across at least 40 individuals
Download nudum-c88-d6-min40_outfiles.zip (111.3 Mb)
Details View File Details
Title morphological_trait_data
Downloaded 1 time
Description Table with all measured morphological traits.
Download morphological_trait_data2.txt (14.94 Kb)
Details View File Details
Title Figure S1. Heatmap of Shared Data Across All Pairs of Individuals
Downloaded 1 time
Description Figure S1. Heatmap of shared data across all pairs of individuals shows no systematic biases in missing data. Darker blues indicated more shared loci while lighter blues indicate fewer. Individuals are arranged phylogenetically, and the total number of loci per individual is displayed along the top of the chart as a bar graph.
Download S1_heatmap_min40.pdf (649.7 Kb)
Details View File Details
Title Figure S2. Results of Hierarchical STRUCTURE Analysis
Downloaded 1 time
Description Figure S2. Hierarchical STRUCTURE analysis identified clusters within each of the three major lineages. Colors indicate posterior probability of assignment of each individual to a particular cluster based on the combination of 10 replicate runs. The number of clusters (K) for each analysis is displayed at the top of each bar graph.
Download S2_structure.pdf (376.6 Kb)
Details View File Details
Title Figure S3. Phylogenetic Results
Downloaded 1 time
Description Figure S3. Similar phylogenetic trees were inferred across datasets and analysis methods. a) IQ-TREE min10 data set, b) IQ-TREE min20 data set, c) IQ-TREE min50 data set, d) RAxML min10 data set, e) RAxML min20 data set, f) RAxML min40 dataset, g) RAxML min50 data set, h) tetrad min10 data set, i) tetrad min20 data set j) tetrad min40 data set, k) tetrad min50 data set.
Download S3_phylogenetic_results.pdf (860.1 Kb)
Details View File Details
Title Figure S4. Phylogenetic Network Inferred with SplitsTree
Downloaded 1 time
Description Figure S4. Phylogenetic network inferred with SplitsTree4 (Hudson and Bryant 2006) showing relationships for all individuals in the V. nudum complex based on the min40 dataset.
Download S4_splitstree.pdf (354.3 Kb)
Details View File Details
Title Figure S5. D-Statistic Tests of Introgression
Downloaded 1 time
Description Figure S5. D-statistic tests find no evidence of introgression between the red and blue clades. A-F) Phylogeny displays the taxa for each test with the grey arrows indicating potential introgression. The graph to the right of each tree shows a histogram of z-scores for 100 replicate tests with different individuals sampled for each non-focal taxon. Higher Z-scores (lower p-values) are located on the right of each graph. Grey dotted line is at p=.01, black dotted line is at p=.01 with a bonferroni correction for 100 tests.
Download S5_D_statistic.pdf (372.7 Kb)
Details View File Details
Title Figure S6. Pairwise Geographic and Genetic Distances Between Individuals Within Each Species
Downloaded 1 time
Description Figure S6. Pairwise geographic and genetic distances between individuals within each species. A) V. cassinoides b) V. nitidum c) V. nudum. Line representing the correlation of genetic and geographic distances is plotted for V. cassinoides.
Download S6_IBD_species_separate.pdf (355.1 Kb)
Details View File Details
Title Figure S7. County Range Maps.
Downloaded 1 time
Description Figure S7. United States county maps colored to reflect the occurrence patterns of each of the three species: a) V. cassinoides b) V. nitidum c) V. nudum. Species occurrences were determined by visual inspection of herbarium specimens and georeferenced to county. d) all three species are shown together with V. cassinoides in blue, V. nitidum in red, and V. nudum in green. Counties with more than one species are black.
Download S7_county_range_maps.pdf (3.173 Mb)
Details View File Details
Title Figure S8. Species Distribution Models with Six Predictor Variables
Downloaded 1 time
Description Figure S8. Species distribution models using Maxent with six predictor variables downloaded from Worldclim (http://www.worldclim.org) at a 2.5 arc-minute resolution (mean annual temperature, annual precipitation, and precipitation seasonality, mean temperature of the wettest quarter, mean diurnal temperature, and precipitation of the wettest quarter) to infer the current (a,c,e) and LGM (b,d,f) distributions of each species Occurrence data for each species is plotted as points on the current distribution map. Relative probability of occurrence at each grid cell is indicated by shading.
Download S8_SDM_6var.pdf (1.779 Mb)
Details View File Details
Title Table S1. RAD Coverage and Sampling
Description Table S1. For each individual the number of raw reads, filtered reads, and loci in each of the four datasets is displayed.
Download TableS1.pdf (28.31 Kb)
Details View File Details
Title Table S2. List of Specimens Used for Range Maps
Description Table S2. List of specimens that were examined and included in the range maps.
Download tableS2.pdf (91.63 Kb)
Details View File Details
Title Sequence_data_files_min50
Downloaded 1 time
Description All ipyrad outfiles for the entire V. nudum complex + outgroups with all loci shared across at least 50 individuals
Download nudum-c88-d6-min50_outfiles.zip (30.86 Mb)
Details View File Details
Title Script to calculate genetic distances
Downloaded 1 time
Description Python script that can be used to calculate pairwise genetic distances between individuals. The input is an ipyrad .loci file and the output is a table that lists the number of loci shared between two individuals, the number of sites that match between them, and the total number of sites they share.
Download Calculate genetic distances.ipynb (15.83 Kb)
Details View File Details

When using this data, please cite the original publication:

Spriggs EL, Eaton DAR, Sweeney PW, Schlutius C, Edwards EJ, Donoghue MJ (2018) RAD-seq data reveal a cryptic Viburnum species on the North American Coastal Plain. Systematic Biology, online in advance of print. https://doi.org/10.1093/sysbio/syy084

Additionally, please cite the Dryad data package:

Spriggs EL, Eaton DAR, Sweeney PW, Schlutius C, Edwards EJ, Donoghue MJ (2018) Data from: RAD-seq data reveal a cryptic Viburnum species on the North American Coastal Plain. Dryad Digital Repository. https://doi.org/10.5061/dryad.m1vc0
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: