Data from: Origins of the endemic scaly tree ferns on the Galápagos and Cocos Islands

Kao T, Pryer KM, Turner MD, White RA, Korall P

Date Published: November 16, 2015

DOI: http://dx.doi.org/10.5061/dryad.5b5r1

 

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Title ReadMe
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Description A list of all files in this package
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Title Cyathea_alignment
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Description Alignment of the combined dataset of five plastid regions: rbcL, rbcL-accD, rbcL-atpB, trnG-R, and trnL-F.
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Title Cyathea_ML_garli
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Description The best maximum likelihood tree inferred from "Cyathea_alignment.nexus", using Garli with genthreshfortopoterm set to 1,000,000.
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Title Cyathea_MLBS_garli
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Description The maximum likelihood bootstrapping trees (1000 replicates) inferred from "Cyathea_alignment.nexus", using Garli with genthreshfortopoterm set to 20,000.
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Title Cyathea_MPBS_con_PAUP*
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Description The maximum parsimony bootstrapping tree (50% majority consensus of 10000 replicates) inferred from "Cyathea_alignment.nexus", using PAUP*.
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Title Cyathea_BI_con_MrBayes
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Description The Bayesian tree (50% majority consensus) inferred from "Cyathea_alignment.nexus", using MrBayes, the analysis was carried out with two independent MCMC runs of 1,000,000 generations, four chains each, and trees sampled every 1000 generations, first 25% of generations were discarded as burn-in.
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Title Cyathea_BI_chronogram_BEAST
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Description The chronogram inferred from "Cyathea_alignment.nexus", using BEAST. Three secondary calibration priors (see table 3 of the paper), a birth-death speciation prior, and the relaxed clock Log normal model were used. Three independent MCMC runs with 10,000,000 generation were carried out. The trees from the three runs were combined in LogCombiner with a 10% burn-in and summarized in TreeAnnotator.
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Title Cyathea_biogeography_lagrange
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Description The evolution of geographic range inferred from "Cyathea_BI_chronogram_BEAST.tre", using Lagrange. C: Cocos island; G: Galapagos; M: Mainland America; P: West Pacific. Disperse to Cocos island and Galapagos before the birth of Galapagos Archipelago (14.5 Ma) is prohibit.
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Title Cyathea_vouchers
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Description The voucher specimens, herbarium, geographical source of voucher, fern DNA database number (http://fernlab.biology.duke.edu), and GeneBank accession numbers for rbcL, rbcL-accD, rbcL-atpB, trnG-R, trnL-F.
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When using this data, please cite the original publication:

Kao T, Pryer KM, Turner MD, White RA, Korall P (2015) Origins of the endemic scaly tree ferns on the Galápagos and Cocos Islands. International Journal of Plant Sciences 176(9): 869-879. http://dx.doi.org/10.1086/683303

Additionally, please cite the Dryad data package:

Kao T, Pryer KM, Turner MD, White RA, Korall P (2015) Data from: Origins of the endemic scaly tree ferns on the Galápagos and Cocos Islands. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.5b5r1
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