Data from: Cryptic diversity and discordance in single-locus species delimitation methods within horned lizards (Phrynosomatidae: Phrynosoma)

Blair C, Bryson Jr. RW

Date Published: January 31, 2017

DOI: http://dx.doi.org/10.5061/dryad.r7989

 

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Title Phrynos_ND4_220_OGs
Downloaded 13 times
Description Multiple sequence alignment of unique ND4 haplotypes (220).
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Title Phrynos_ND4_Unique_Haplotypes_ABGD
Downloaded 8 times
Description Multiple sequence alignment for ABGD analysis of unique haplotypes with singletons removed.
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Title Phrynos_ND4_EvenSampling_149
Downloaded 5 times
Description Multiple sequence alignment of 149 ND4 haplotypes (even sampling) after pruning P. platyrhinos sequences.
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Title Phrynos_ND4_EvenSampling_ABGD
Downloaded 5 times
Description Multiple sequence alignment for ABGD analysis on the evenly sampled data set with singletons removed.
Download Phrynos_ND4_GMYC_OGs_fixed_EvenSampling_ABGD.fasta (130.6 Kb)
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Title Phrynosoma_ND4_all_OGs
Downloaded 6 times
Description Multiple sequence alignment of all ND4 sequences (368) including duplicate haplotypes.
Download Phrynosoma_ND4_all_OGs.fasta (334.2 Kb)
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Title Phrynosoma_ND4_363_ABGD
Downloaded 9 times
Description Multiple sequence alignment of 363 ND4 haplotypes (including duplicates) with singletons removed.
Download Phrynosoma_ND4_363_ABGD.fasta (329.7 Kb)
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Title RAxML_bestTree_220
Downloaded 8 times
Description ML tree from RAxML analysis of 220 haplotypes.
Download RAxML_bestTree_fixed.Phrynos_mPTP (17.86 Kb)
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Title RAxML_bipartitions_220
Downloaded 8 times
Description ML tree from RaxML analysis of 220 haplotypes with bootstrap support on nodes.
Download RAxML_bipartitions_fixed.Phrynos_mPTP (18.27 Kb)
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Title RAxML_bestTree_149
Downloaded 9 times
Description ML tree from RaxML analysis of 149 haplotypes on the evenly sampled data set.
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Title RAxML_bipartitions_149
Downloaded 5 times
Description ML tree from RAxML analysis of 149 haplotypes on the evenly sampled data set. Nodes are annotated with bootstrap proportions.
Download RAxML_bipartitions.Phrynos_fixed_EvenSampling_PTP (12.41 Kb)
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Title MCCTree_CAHeights_220
Downloaded 5 times
Description BEAST MCC tree based on 220 unique haplotypes. Node heights annotated using common ancestor heights.
Download MCCTree_CAHeights_220.tre (180.8 Kb)
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Title Phrynos_BEAST_GMYC_fixed_MeanHeights_220
Downloaded 6 times
Description BEAST MCC tree based on 220 unique haplotypes. Node heights annotated using mean heights.
Download Phrynos_BEAST_GMYC_fixed_MeanHeights_220.tre (180.8 Kb)
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Title Phrynos_BEAST_MCC_fixed_220_MedianHeights
Downloaded 12 times
Description BEAST MCC tree based on 220 unique haplotypes. Node heights annotated using median heights.
Download Phrynos_BEAST_MCC_fixed_220_MedianHeights.tre (180.8 Kb)
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Title Phrynos_GMYC_fixed_EvenSampling_MCC
Downloaded 5 times
Description BEAST MCC tree based on 149 unique haplotypes with even sampling. Node heights annotated using mean heights.
Download Phrynos_GMYC_fixed_EvenSampling_MCC.tre (121.1 Kb)
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Title Phrynos_BEAST_368_CaHeights
Downloaded 4 times
Description BEAST MCC tree based on 368 haplotypes (including duplicates). Node heights annotated using common ancestor heights.
Download Phrynos_BEAST_368_CaHeights.tre (307.7 Kb)
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Title Phrynos_BEAST_368_MeanHeights
Downloaded 5 times
Description BEAST MCC tree based on 368 haplotypes (including duplicates). Node heights annotated using mean heights.
Download Phrynos_BEAST_368_MeanHeights.tre (307.7 Kb)
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Title Phrynos_BEAST_368_MedianHeights
Downloaded 5 times
Description BEAST MCC tree based on 368 haplotypes (including duplicates). Node heights annotated using median heights.
Download Phrynos_BEAST_368_MedianHeights.tre (307.8 Kb)
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Title RAxML_bestTree_368
Downloaded 6 times
Description ML tree from RAxML analysis of 368 sequences (including duplicates).
Download RAxML_bestTree.Phrynos_368_RAxML (30.58 Kb)
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Title RAxML_bipartitions_368
Downloaded 7 times
Description ML tree from RAxML analysis of 368 sequences (including duplicates). Nodes annotated with bootstrap proportions.
Download RAxML_bipartitions.Phrynos_368_RAxML (31.19 Kb)
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When using this data, please cite the original publication:

Blair C, Bryson Jr. RW (2017) Cryptic diversity and discordance in single-locus species delimitation methods within horned lizards (Phrynosomatidae: Phrynosoma). Molecular Ecology Resources, online in advance of print. http://dx.doi.org/10.1111/1755-0998.12658

Additionally, please cite the Dryad data package:

Blair C, Bryson Jr. RW (2017) Data from: Cryptic diversity and discordance in single-locus species delimitation methods within horned lizards (Phrynosomatidae: Phrynosoma). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.r7989
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