Data from: A chloroplast tree for Viburnum (Adoxaceae) and its implications for phylogenetic classification and character evolution

Clement WC, Arakaki M, Sweeney PW, Edwards EJ, Donoghue MJ

Date Published: June 13, 2014

DOI: http://dx.doi.org/10.5061/dryad.hh12b

 

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Title Viburnum 10 gene region Data Set
Downloaded 8 times
Description This 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.
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Title Viburnum Plastid Coding Regions Data File
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Description This 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-KJ795038
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Title Viburnum Plastid Non-coding Gene Region Data
Downloaded 4 times
Description The 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-KJ796399
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Title Viburnum Plastid Coding and Non-coding Gene Regions Data File
Downloaded 20 times
Description This 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.
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Title Viburnum Phylogeny reconstructed from Plastid Coding Data
Downloaded 3 times
Description Bayesian 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.
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Title Viburnum Phylogeny reconstructed from Plastid Noncoding Phylogeny
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Description Bayesian 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.
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Title Viburnum Phylogeny reconstructed from Plastid Coding and Non-coding Gene Regions
Downloaded 2 times
Description Bayesian 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.
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Title Viburnum Phylogeny reconstructed from 10-gene region Data Set
Downloaded 7 times
Description Bayesian 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.
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Title Viburnum Plastid and ITS Data
Downloaded 5 times
Description This 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.
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Title Viburnum Phylogeny reconstructed from the Plastid and ITS data sets
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Description Bayesian 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.
Download PlastidITS.tre (70.42 Kb)
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When using this data, please cite the original publication:

Clement WC, Arakaki M, Sweeney PW, Edwards EJ, Donoghue MJ (2014) A chloroplast tree for Viburnum (Adoxaceae) and its implications for phylogenetic classification and character evolution. American Journal of Botany 101(6): 1029-1049. http://dx.doi.org/10.3732/ajb.1400015

Additionally, please cite the Dryad data package:

Clement WC, Arakaki M, Sweeney PW, Edwards EJ, Donoghue MJ (2014) Data from: A chloroplast tree for Viburnum (Adoxaceae) and its implications for phylogenetic classification and character evolution. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.hh12b
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