Data from: Impacts of inference method and dataset filtering on phylogenomic resolution in a rapid radiation of ground squirrels (Xerinae: Marmotini)

McLean BS, Bell KC, Allen JM, Helgen KM, Cook JA

Date Published: October 9, 2018

DOI: https://doi.org/10.5061/dryad.t358vv1.2

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Title README
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Title Supplementary Appendix S1
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Description .csv file containing taxonomic identities, institutional IDs, collection year, and number of UCE contigs assembled for all samples sequenced in this study data fields are synonymized with standard Darwin Core terms (https://github.com/tdwg/dwc) where possible
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Title Supplementary Fig. S1
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Description Barplots displaying changes across empirically filtered (‘Information-Filtered’) and randomly selected (‘Randomly Selected 1-5’) datasets in 3 different metrics; a) total numbers of sites analyzed, b) total numbers of variable sites analyzed, and c) total numbers of parsimony-informative sites analyzed. The grey box at far left represents the baseline UCE dataset. Boxes of the same color contain identical numbers of loci. Cumulatively, the plots show that changes in our metric of information content (proportion of variable sites) due to changes in absolute numbers of variable sites (i.e., panel b) and not change in locus length or other properties.
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Title Supplementary Fig. S2
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Description Relationships of UCE variability (proportion of variable sites per locus (i.e., our metric)) with alternative metrics of information content: a) the proportion of parsimony sites per locus, b) the mean bootstrap support found in corresponding gene trees, and c) the proportion of gene tree nodes resolved with >70% bootstrap support.
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Title Supplementary Fig. S3
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Description Pairwise changes in Robinson-Foulds distances among 4 inference methods across the filtering regimes employed in this study. Base = the original baseline UCE dataset.
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Title UCE alignments - baseline dataset
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Description Trimmed UCE alignments in fasta format. This is the “baseline” dataset as described in the text. These same data are available on GenBank.
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Title raxml_empirical_trees
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Description RAxML trees from empirically filtered datasets with support values from 100 bootstrap replicates and rooted on Aplodontia rufa. Trees are named with the filtering level used (e.g., 5var = at least 5 percent variable sites per locus) followed by the number of resulting UCE loci in each dataset
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Title astral_empirical_trees
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Description ASTRAL species trees from empirically filtered datasets with support values from 100 bootstrap replicates and rooted on Aplodontia rufa. Trees are named with the filtering level used (e.g., 5var = at least 5 percent variable sites per locus) followed by the number of resulting UCE loci in each dataset
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Title njst_empirical_trees
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Description NJst species trees from empirically filtered datasets labeled with support values from 100 bootstrap replicates and rooted on Aplodontia rufa. Trees are named with the filtering level used (e.g., 5var = at least 5 percent variable sites per locus) followed by the number of resulting UCE loci in each dataset
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Title svdquartets_empirical_trees
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Description SVDQuartets species trees from empirically filtered datasets with support values from 100 bootstrap replicates and rooted on Aplodontia rufa. Trees are named with the filtering level used (e.g., 5var = at least 5 percent variable sites per locus) followed by the number of resulting UCE loci in each dataset
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When using this data, please cite the original publication:

McLean BS, Bell KC, Allen JM, Helgen KM, Cook JA (2018) Impacts of inference method and dataset filtering on phylogenomic resolution in a rapid radiation of ground squirrels (Xerinae: Marmotini). Systematic Biology, online in advance of print. https://doi.org/10.1093/sysbio/syy064

Additionally, please cite the Dryad data package:

McLean BS, Bell KC, Allen JM, Helgen KM, Cook JA (2018) Data from: Impacts of inference method and dataset filtering on phylogenomic resolution in a rapid radiation of ground squirrels (Xerinae: Marmotini). Dryad Digital Repository. https://doi.org/10.5061/dryad.t358vv1.2
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