DOI: 10.5061/dryad.hh12b
title: Data from: A chloroplast tree for Viburnum (Adoxaceae) and its implications for phylogenetic classification and character evolution

description: Premise of the study: Despite recent progress, significant uncertainties
 remain concerning relationships among early-branching lineages within
 Viburnum (Adoxaceae). This has prohibited a new classification, and has
 hindered studies of character evolution and the increasing use of Viburnum
 in addressing a wide range of ecological and evolutionary questions. We
 hoped to resolve these issues by sequencing whole plastid genomes for
 representative species and combining these with molecular data previously
 obtained from an expanded taxon sample. Methods: We performed paired-end
 Illumina sequencing of plastid genomes of 22 Viburnum species, and
 combined these data with a 10-gene dataset to infer phylogenetic
 relationships for 113 species. We used the results to devise a
 comprehensive phylogenetic classification and to analyze the evolution of
 eight morphological characters that vary among early-branching lineages.
 Key results: With greatly increased levels of confidence in most of the
 early branches, we propose a phylogenetic classification of Viburnum,
 providing formal phylogenetic definitions for 30 clades, including 13 with
 ICN names, eight with previously proposed informal names, and nine newly
 proposed names for major branches. Our parsimony reconstructions of bud
 structure, leaf margins, inflorescence form, ruminate endosperm,
 extrafloral nectaries, glandular trichomes, palisade anatomy, and pollen
 exine showed varying levels of homoplasy, but collectively provided
 morphological support for some, though not all, of the major clades.
 Conclusions: Our study demonstrates the value of next generation plastid
 sequencing, the ease of creating a formal phylogenetic classification, and
 the utility of such a system in describing patterns of character
 evolution.
description: Viburnum 10 gene region
 Data SetThis nexus file contains
 9,795 bp representing the nine chloroplast (matK, ndhF, rbcL, petB-petD,
 trnH-psbA, rpl32-trnL, trnC-ycf6, trnK, trnS-trnG) and one nuclear
 ribosomal (internal transcribed spacer region, ITS) gene regions sampled
 for 113 taxa. This data file was used to generate the results from
 Appendix S4. Gene regions are concatenated in this file, but are annotated
 with character sets at the end of the file.SangerData.nexViburnum Plastid Coding Regions Data FileThis nexus file contains 52,758 bp representing the 72 chloroplast gene regions sampled for 22 taxa. This data file was used to generate the results shown in Appendix S2. Gene regions are concatenated in this file, but are annotated with character sets at the end of the file. Those gene regions greater than 200 bp are also available on Genbank. The order of species for Genbank accession numbers is as follows: V. acerifolium, V. amplificatum, V. carlesii, V. cassinoides, V. clemensiae, V. cylindricum, V. dentatum, V. dilatatum, V. erubescens, V. grandiflorum, V. lantanoides, V. lentago, V. lutescens, V. molle, V. opulus, V. plicatum, V. punctatum, V. sieboldii, V. taiwanianum, V. tinus, V. triphyllum, V. vernicosum. Gene regions marked with an asterisk (*) indicate missing data for V. vernicosum. atpA: KJ796313-KJ796334 atpB: KJ795390-KJ795411 atpE: KJ795676-KJ795697 atpF: KJ795061-KJ795082 atpH: KJ795500-KJ795521 atpI: KJ795941-KJ795962 ccsA: KJ795875-KJ795896 cemA: KJ795761-KJ795782 infA: KJ796248-KJ796269 ndhA*: KJ794820-KJ794840 ndhA: KJ796335-KJ796355 ndhC: KJ796028-KJ796049 ndhD: KJ795588-KJ795609 ndhE*: KJ796007-KJ796027 ndhG*: KJ795281-KJ795301 ndhH*: KJ796292-KJ796312 ndhI*: KJ795719-KJ795739 ndhJ: KJ795324-KJ795345 petA: KJ795544-KJ795565 petB: KJ795193-KJ795214 petD: KJ795171-KJ795192 psaA: KJ796270-KJ796291 psaB: KJ795083-KJ795104 psaC: KJ795740-KJ795760 psbA: KJ795522-KJ795543 psbB: KJ794885-KJ794906 psbC*: KJ795368-KJ795389 psbD: KJ796160-KJ796181 psbE: KJ796204-KJ796255 psbH: KJ795105-KJ795126 rpl2: KJ795654-KJ795675 rpl14: KJ795259-KJ795280 rpl16: KJ795897-KJ795918 rpl20: KJ794951-KJ794972 rpl22: KJ794907-KJ794928 rpl23: KJ795237-KJ795258 rpl33: KJ795434-KJ795455 rpoA: KJ795215-KJ795236 rpoB: KJ796226-KJ796247 rpoC1: KJ795149-KJ795170 rpoC1: KJ795985-KJ796006 rpoC2: KJ796116-KJ796137 rps2: KJ796050-KJ796071 rps3: KJ795963-KJ795984 rps4: KJ794841-KJ794862 rps8: KJ795412-KJ795433 rps11: KJ795853-KJ795874 rps14: KJ795456-KJ795477 rps15*: KJ795698-KJ795718 rps16: KJ795478-KJ795499 rps18: KJ795610-KJ795631 rps19: KJ795809-KJ795830 ycf3: KJ795831-KJ795852 ycf4: KJ795017-KJ795038PlastidCodingData.nexusViburnum Plastid Non-coding Gene Region DataThe nexus file contains 16,819 bp of plastid non-coding data sampled for 22 species of Viburnum. The gene regions have been concatenated but have been annotated using charsets at the end of the file. These data were used to generate the trees associated with Appendix S3. Sequences greater than 200 base pairs have also been submitted to Genbank. The order of species for Genbank accession numbers is as follows: V. acerifolium, V. amplificatum, V. carlesii, V. cassinoides, V. clemensiae, V. cylindricum, V. dentatum, V. dilatatum, V. erubescens, V. grandiflorum, V. lantanoides, V. lentago, V. lutescens, V. molle, V. opulus, V. plicatum, V. punctatum, V. sieboldii, V. taiwanianum, V. tinus, V. triphyllum, V. vernicosum. atpB-rbcL: KJ796182-KJ796203 cemA-petA: KJ796138-KJ796159 ndhE-ndhG: KJ794973-KJ794994 psaI-ycf4: KJ794929-KJ794950 psbC-trnS(UGA): KJ795783-KJ795804 psbK-psbI: KJ794995-KJ795016 rpl16-rps3: KJ795346-KJ795367 rpl20-rps12: KJ795566-KJ795587 rps18-rpl20: KJ796072-KJ796093 trnF(GAA)-ndhJ: KJ795302-KJ795323 trnL(UAA)-trnF(GAA): KJ795039-KJ795030 trnL(UAA) intron: KJ796356-KJ796377 trnM(CAU)-atpE: KJ795632-KJ795653 trnP(GGG)-psaJ: KJ794863-KJ794884 trnQ(UUG)-psbK: KJ795919-KJ795940 trnS(GGA)-rps4: KJ796094-KJ796115 trnS(UGA)-lhbA: KJ795127-KJ795148 trnV(UAC) intron: KJ796378-KJ796399PlastidNonCodingData.nexusViburnum Plastid Coding and Non-coding Gene Regions Data FileThis nexus file contains 69,577 representing all gene regions assembled and analyzed from the plastid sequencing of 22 Viburnum taxa. The data are concatenated, and two partitions, coding and noncoding, are delineated using character sets at the end of the data file. For each gene region, please refer to the Viburnum Plastid Coding and Viburnum Plastid Non-coding gene region data files. Additionally, the data in this file were used to generate the trees associated with Fig. 1.PlastidCodingNonCoding.nexusViburnum Phylogeny reconstructed from Plastid Coding DataBayesian majority-rule consensus tree of chloroplast coding regions assembled from next-generation sequencing of Viburnum plastids. This tree is associated with the Viburnum Plastid Coding Gene Region data file, and is the tree used in Appendix S2.PlastidCoding.treViburnum Phylogeny reconstructed from Plastid Noncoding PhylogenyBayesian majority-rule consensus tree of chloroplast non-coding regions assembled fro, next-generation sequencing of Viburnum plastids. This tree is associated with the Viburnum Plastid Non-coding Gene Region data file, and is the tree used in Appendix S3.PlastidNoncoding.treViburnum Phylogeny reconstructed from Plastid Coding and Non-coding Gene RegionsBayesian majority-rule consensus tree of chloroplast coding and non-coding regions assembled from next-generation sequencing of Viburnum plastids. This tree is associated with the Viburnum Plastid Coding and Noncoding Gene Region data file, and is the tree used in Figure 1.PlastidCodingNonCoding.treViburnum Phylogeny reconstructed from 10-gene region Data SetBayesian majority-rule consensus tree of 113 Viburnum species sampled for nine chloroplast regions and the internal transcribed spacer region (ITS). This phylogeny was reconstructed from the Viburnum 10 gene data set and is in Appendix S4.SangerData.treViburnum Plastid and ITS DataThis nexus file contains 71,935 bp for 113 Viburnum species. It includes the nine chloroplast regions and ITS sampled for the 113 taxa as well as all gene regions assembled from plastid sequencing for 22 Viburnum taxa. The plastid coding, non-coding, and ITS partitions have been identified as character sets at the end of the file. Please refer to other data file submissions associated with this paper to retrieve individual gene regions. These data were used to generate the phylogenies associated with Figure 2.PlastidITSData.nexusViburnum Phylogeny reconstructed from the Plastid and ITS data setsBayesian majority-rule consensus tree of 113 species of Viburnum. Data generated from the whole plastid sequencing were combined with data from 10 gene regions previously sampled for Viburnum (Clement and Donoghue, 2011; Chatelet et al., 2013). This tree was generated from the Plastid and ITS data set, and it was used to reconstruct the phylogenies associated with Figure 2.PlastidITS.tre