Data from: The challenges of resolving a rapid, recent radiation: empirical and simulated phylogenomics of Philippine shrews

Giarla TC, Esselstyn JA

Date Published: May 12, 2015

DOI: http://dx.doi.org/10.5061/dryad.b7156

 

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 Online Appendix 1 - SNP Analysis Pipeline
Downloaded 154 times
Description Text file containing commands and software used to obtain SNPs from our UCE reads.
Download Online Appendix 1 - SNP Analysis Pipeline.txt (4.063 Kb)
Details View File Details
Title Online Appendix 2 - Locus Info
Downloaded 18 times
Description Excel file containing information on each UCE locus used in this study. This information includes: locus length, number of informative sites, number of SNPs, and best fitting model. There are two sheets: one listing all of the loci included in our final dataset (1,112 loci) and another listing only the loci that had phylogenetically informative sites (919 loci).
Download Online Appendix 2 - Locus Info.xlsx (136.5 Kb)
Details View File Details
Title Online Appendix 3 - BPP Results
Downloaded 13 times
Description Theta and tau estimates, and corresponding ESS values, from eight BP&P runs corresponding to eight subsets of the 919-locus dataset. These values were used to construct a species tree that was used as the "true" tree from which we simulated character data.
Download Online Appendix 3 - BPP Results.xlsx (55.44 Kb)
Details View File Details
Title Figure S1 Smilogram
Downloaded 31 times
Description Figure S1. Scatter plot of the frequency of variant bases relative to the position of those sites in their alignments
Download Figure S1 Smilogram.pdf (430.2 Kb)
Details View File Details
Title Figure S2 Concatenated Full MrBayes
Downloaded 26 times
Description Figure S2. Non-condensed trees from concatenated analyses. Condensed trees are shown in Fig. 3 in the main text. Numbers at nodes indicate Bayesian posterior probabilities.
Download Figure S2 Concatenated Full MrBayes.pdf (541.7 Kb)
Details View File Details
Title Figure S3 Empirical StarBEAST
Downloaded 40 times
Description Figure S3. All 19 empirical *BEAST subsets. Subsets 1–18 are based on random subsets of 50 loci each; subset 19 includes the remaining 19 loci not included in the other subsets. Numbers at nodes denote Bayesian PPs. Black circles at nodes indicate PPs ≥ 0.95.
Download Figure S3 Empirical StarBEAST.pdf (843.0 Kb)
Details View File Details
Title Figure S4 Sim-Matching StarBEAST
Downloaded 18 times
Description Figure S4. All 10 Sim-Matching *BEAST subsets. Each species tree is based on analysis of a different subset of 50 simulated loci. Numbers at nodes denote Bayesian PPs.
Download Figure S4 Sim-Matching StarBEAST.pdf (520.8 Kb)
Details View File Details
Title Figure S5 Sim-Multi-Individual StarBEAST
Downloaded 19 times
Description Figure S5. All 10 Sim-Multi-Individual *BEAST subsets. Each species tree is based on analysis of a different subset of 50 simulated loci. Numbers at nodes denote Bayesian PPs.
Download Figure S5 Sim-Multi-Individual StarBEAST.pdf (501.6 Kb)
Details View File Details
Title Figure S6 Sim-3x-Rate StarBEAST
Downloaded 51 times
Description Figure S6. All 10 Sim-3x-Rate *BEAST subsets. Each species tree is based on analysis of a different subset of 50 simulated loci. Numbers at nodes denote Bayesian PPs.
Download Figure S6 Sim-3x-Rate StarBEAST.pdf (496.9 Kb)
Details View File Details
Title 1112 Empirical UCE Nexus Files
Downloaded 17 times
Description All 1,112 UCE nexus alignments.
Download new-incomplete-50percent-all-species-padded.zip (1.111 Mb)
Details View File Details
Title 500 Sim-Matching simulated alignments
Downloaded 8 times
Description Fasta files for Sim-Matching simulation
Download 500-sim-matching-fasta-files.zip (373.5 Kb)
Details View File Details
Title 500 Sim-Multi-Individual simulated alignments
Downloaded 8 times
Description Fasta files for Sim-Multi-Individual simulation
Download 500-sim-multi-individual-fasta-files.zip (483.1 Kb)
Details View File Details
Title 500 Sim-3x-Rate simulated alignments
Downloaded 9 times
Description Fasta files for Sim-3x-Rate simulation
Download 500-sim-3x-rate-fasta-files.zip (407.0 Kb)
Details View File Details
Title SNP Data
Downloaded 16 times
Description Nexus file containing data for 1,170 SNPs genotyped for all 19 individuals.
Download SNP-data.nex (22.84 Kb)
Details View File Details
Title All 919 Empirical Gene Trees
Downloaded 7 times
Description All 919 PhyML gene trees inferred using CloudForest. After collapsing short branches into polytomies, these trees were used to infer the species tree topologies used in MulRF and ASTRAL.
Download genetrees.tre (851.9 Kb)
Details View File Details
Title All Empirical Bootstrap Gene Trees
Downloaded 6 times
Description 100 bootstrap replicates for 919 loci. Bootstrap replicates were made in CloudForest. Each of the 100 bootstrap sets were used to infer species trees. These pseudoreplicates were used to add nodal support metrics to empirical MulRF and ASTRAL trees.
Download 100-bootreps.tree.zip (9.888 Mb)
Details View File Details
Title Whole Mitochondrial Genomes and MrBayes Block
Downloaded 14 times
Description Nexus file containing sequences for 19 whole mitochondrial genomes and a MrBayes block with MrBayes settings.
Download MrBayes-WMG-Input.nex (297.2 Kb)
Details View File Details

When using this data, please cite the original publication:

Giarla TC, Esselstyn JA (2015) The challenges of resolving a rapid, recent radiation: empirical and simulated phylogenomics of Philippine shrews. Systematic Biology 64(5): 727-740. http://dx.doi.org/10.1093/sysbio/syv029

Additionally, please cite the Dryad data package:

Giarla TC, Esselstyn JA (2015) Data from: The challenges of resolving a rapid, recent radiation: empirical and simulated phylogenomics of Philippine shrews. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.b7156
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: