Data from: Evolutionary dynamics of Rh2 opsins in birds demonstrate an episode of accelerated evolution in the New World warblers (Setophaga)

Bloch NI, Price TD, Chang BSW

Date Published: March 31, 2015

DOI: http://dx.doi.org/10.5061/dryad.b2m1n

 

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Title Time calibrated phylogeny of the New World warblers, Old World warblers and Bowerbirds used in this study.
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Description Phylogeny shown in Fig. 1. Branch lengths are proportional to time
Download Fig1_Newick (1.843 Kb)
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Title Variation in Rh2 non-synonymous rates of evolution (dN ) across species in the limited dataset
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Description Gene tree for Rh2 where branch lengths are scaled by dN rate (substitutions per codon) estimated along that branch by a free-ratio model as implemented in PAML
Download Fig4_RH2_dN_LimDataSet (895 bytes)
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Title Variation in Rh2 non-synonymous rates of evolution (dN ) across species in the main dataset
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Description Gene tree for Rh2 where branch lengths are scaled by dN rate (substitutions per codon) estimated along that branch by a free-ratio model as implemented in PAML
Download Fig4_RH2_dN_MainDataSet (703 bytes)
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Title RH2 nucleotide sequences
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Download RH2 nucleotide sequences.txt (29.01 Kb)
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Title RH1 nucleotide sequences
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Download RH1 nucleotide sequences.txt (27.43 Kb)
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Title RH2 amino acid aligment
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Description Alignment of RH2 amino acid sequences - corresponds to figure S1
Download RH2 amino acid aligment.txt (10.78 Kb)
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Title Variation in Rh1 non-synonymous rates of evolution (dN ) across Passerines
Downloaded 4 times
Description Branch lengths are scaled by dN rates. Branch lengths were estimated using a free ratio model as implemented in PAML, that estimates independent dN rates for each branch in the tree.
Download FigS4_RH1_dN (768 bytes)
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When using this data, please cite the original publication:

Bloch NI, Price TD, Chang BSW (2015) Evolutionary dynamics of Rh2 opsins in birds demonstrate an episode of accelerated evolution in the New World warblers (Setophaga). Molecular Ecology 24(10): 2449-2462. http://dx.doi.org/10.1111/mec.13180

Additionally, please cite the Dryad data package:

Bloch NI, Price TD, Chang BSW (2015) Data from: Evolutionary dynamics of Rh2 opsins in birds demonstrate an episode of accelerated evolution in the New World warblers (Setophaga). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.b2m1n
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