Data from: The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach

Sun K, Meiklejohn KA, Faircloth BC, Glenn TC, Braun EL, Kimball RT

Date Published: June 26, 2014

DOI: http://dx.doi.org/10.5061/dryad.66942

 

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Title Trees_UCE_15sp_RAxML
Downloaded 21 times
Description Trees estimated from UCEs for all 15 species using RAxML. Results from both unpartitioned and partitioned by GC analyses are included.
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Title Trees_UCE_13sp_RAxML
Downloaded 13 times
Description Trees estimated from UCEs of 13 species using RAxML. Results of both unpartitioned and partitioned by GC analyses are included.
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Title Trees_MT_MrBayes_pavonine
Downloaded 15 times
Description Trees estimated in MrBayes using the mitochondrial matrix (ND2, CYB, and 12S) from 233 galliforms.
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Title Trees_MT_RAxML_pavonine
Downloaded 11 times
Description Trees estimated in RAxML from the mitochondrial matrix (ND2, CYB, and 12S) for 233 galliforms.
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Title Trees_MTandUCE_pavonine
Downloaded 18 times
Description Most likely tree estimated tree using the combined mitochondrial plus UCE data. There are two trees. First is the one with original estimated branch lengths. Second is the same tree with branch lengths re-estimated using mitochondrial data.
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Title Tree_UCE_SMRT-ML.bootcons
Downloaded 16 times
Description Tree estimated using the SMRT-ML method.
Download UCE_SMRT-ML.bootcons.tre (358 bytes)
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Title Trees_UCE_MrBayes_pavonine
Downloaded 17 times
Description Trees estimated using MrBayes from the UCE data (all 15 species).
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Title Alignment_Sun_MtUCE_alignment
Downloaded 17 times
Description Alignment of the combined mitochondrial (CYB, ND2, 12S) and UCE data for 233 species of galliforms.
Download Sun_MtUCE_alignment.nex (188.0 Mb)
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Title Alignment_Sun_1966_UCEs
Downloaded 46 times
Description Alignments of all of the 1966 UCEs included in the study.
Download Sun_1966_UCEs.zip (2.589 Mb)
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Title Alignment_Sun_Mt
Downloaded 42 times
Description Alignment of the mitochondrial data (CYB, ND2, 12S) from 233 galliform species.
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Title TraitMatrix_Ocelli
Downloaded 12 times
Description Presence/Absence of ocelli for the 233 taxa included in the mitochondrial matrix (all of the 15 species sampled for UCEs are included in that 233).
Download TraitMatrix_Ocelli.nex (14.91 Kb)
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Title Script_SMRTrax
Downloaded 20 times
Description Perl script for the SMRT-ML analysis.
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When using this data, please cite the original publication:

Sun K, Meiklejohn KA, Faircloth BC, Glenn TC, Braun EL, Kimball RT (2014) The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach. Proceedings of the Royal Society B 281(1790): 20140823. http://dx.doi.org/10.1098/rspb.2014.0823

Additionally, please cite the Dryad data package:

Sun K, Meiklejohn KA, Faircloth BC, Glenn TC, Braun EL, Kimball RT (2014) Data from: The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.66942
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