DOI: 10.5061/dryad.5b5r1
title: Data from: Origins of the endemic scaly tree ferns on the Galápagos and Cocos Islands

description: Premise of research. Successful long-distance dispersal is rarely observed
 in scaly tree ferns (Cyatheaceae). Nevertheless, recent molecular evidence
 has suggested that the four endemic scaly tree ferns on the Galápagos
 Archipelago (Cyathea weatherbyana) and Cocos Island (Cyathea alfonsiana,
 Cyathea nesiotica, and Cyathea notabilis), two oceanic island groups west
 of Central and northern South America, probably each originated from
 different mainland America ancestors. However, the phylogenetic
 relationships inferred among these endemics and their mainland relatives
 have been unclear. This study is aimed at better resolving the
 relationships and tracing the origins of these island
 endemics.Methodology. Five plastid regions from 35 Cyathea species were
 analyzed to reconstruct phylogenetic relationships using parsimony,
 likelihood, and Bayesian approaches. We also estimated divergence times of
 these species, and our chronogram was used to reconstruct their
 biogeographical range history.Pivotal results. Our well-resolved
 phylogenetic tree of Cyathea, which is in agreement with previous studies,
 shows that when the four Galápagos and Cocos endemics are included, they
 each belong to separate subclades. Our biogeographical study suggests that
 the four endemics originated from independent colonization events from
 mainland America and that there was no dispersal of Cyathea between the
 island groups. We reveal more detailed relationships among the endemics
 and their respective close mainland relatives; some of these relationships
 differ from previous studies. Our findings are corroborated by new
 morphological data from ongoing stem anatomy studies.Conclusions. The four
 scaly tree ferns endemic to the Galápagos and Cocos Islands each did
 indeed originate as independent colonization events from separate sources
 in mainland America, and their closest relatives are identified here.
description: ReadMeA list of all files in
 this packageCyathea_alignmentAlignment of the combined dataset of five plastid regions: rbcL, rbcL-accD, rbcL-atpB, trnG-R, and trnL-F.Cyathea_ML_garliThe best maximum likelihood tree inferred from "Cyathea_alignment.nexus", using Garli with genthreshfortopoterm set to 1,000,000.Cyathea_MLBS_garliThe maximum likelihood bootstrapping trees (1000 replicates) inferred from "Cyathea_alignment.nexus", using Garli with genthreshfortopoterm set to 20,000.Cyathea_MPBS_con_PAUP*The maximum parsimony bootstrapping tree (50% majority consensus of 10000 replicates) inferred from "Cyathea_alignment.nexus", using PAUP*.Cyathea_BI_con_MrBayesThe 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.Cyathea_BI_chronogram_BEASTThe 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.Cyathea_biogeography_lagrangeThe 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.Cyathea_vouchersThe 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.