Data from: A hybrid phylogenetic–phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification

Leaché AD, Wagner P, Linkem CW, Böhme W, Papenfuss TJ, Chong RA, Lavin BR, Bauer AM, Nielsen SV, Greenbaum E, Rödel M, Schmitz A, LeBreton M, Ineich I, Chirio L, Ofori-Boateng C, Eniang EA, Baha El Din S, Lemmon AR, Burbrink FT

Date Published: July 1, 2014

DOI: http://dx.doi.org/10.5061/dryad.4kt16

 

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Title Sanger Sequence Data
Downloaded 16 times
Description Mitochondrial and nuclear loci in nexus format, with data partitioning.
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Title Sequence Capture Loci
Downloaded 24 times
Description Sequence capture loci (a.k.a. anchored phylogenomics data). The data are in Nexus format (partitioned).
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Title Hybrid Phylogeny
Downloaded 15 times
Description The final hybrid species tree for African Agama lizards (Newick format). The Sanger data (mtDNA and four nuclear genes) were used to estimate a time-calibrated species tree using *BEAST. This posterior distribution of species trees was then filtered using the anchored phylogenomics tree as a backbone constraint.
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Title Sequence Capture Gene Trees
Downloaded 14 times
Description Maximum likelihood (ML) trees for each sequence capture gene used for species tree analyses. ML analyses were run with RAxML.
Download SequenceCaptureGeneTrees.tre (353.9 Kb)
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When using this data, please cite the original publication:

Leaché AD, Wagner P, Linkem CW, Böhme W, Papenfuss TJ, Chong RA, Lavin BR, Bauer AM, Nielsen SV, Greenbaum E, Rödel M, Schmitz A, LeBreton M, Ineich I, Chirio L, Ofori-Boateng C, Eniang EA, Baha El Din S, Lemmon AR, Burbrink FT (2014) A hybrid phylogenetic–phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification. Molecular Phylogenetics and Evolution, online in advance of print. http://dx.doi.org/10.1016/j.ympev.2014.06.013

Additionally, please cite the Dryad data package:

Leaché AD, Wagner P, Linkem CW, Böhme W, Papenfuss TJ, Chong RA, Lavin BR, Bauer AM, Nielsen SV, Greenbaum E, Rödel M, Schmitz A, LeBreton M, Ineich I, Chirio L, Ofori-Boateng C, Eniang EA, Baha El Din S, Lemmon AR, Burbrink FT (2014) Data from: A hybrid phylogenetic–phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.4kt16
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