Specimens at the Center: An Informatics Workflow and Toolkit for Specimen-level analysis of Public DNA database data

doi:10.1600/036364416X692505

	Specimens at the Center: An Informatics Workflow and Toolkit for Specimen-level analysis of Public DNA database data
	Pham, Kasey K.; Hahn, Marlene ; Lueders, Kate ; Brown, Bethany H.; Bruederle, Leo P.; Bruhl, Jeremy J.; Chung, Kyong-Sook ; Derieg, Nathan J.; Escudero, Marcial 5; Ford, Bruce A.; Gebauer, Sebastian ; Gehrke, Berit 8; Hoffmann, Matthias H.; Hoshino, Takuji 9; Jimenez-Mejias, Pedro ; Jung, Jongduk 11; Kim, Sangtae 12; Luceno, Modesto ; Maguilla, Enrique ; Martin-Bravo, Santiago ; Naczi, Robert F. C.; Reznicek, Anton A.; Roalson, Eric H.; Simpson, David A.; Starr, Julian R.; Villaverde, Tamara 13; Waterway, Marcia J.; Wilson, Karen L.; Yano, Okihito 20,25; Zhang, Shuren21 ; Hipp, Andrew L.
	2016
发表期刊	SYSTEMATIC BOTANY
ISSN	0363-6445
卷号	41 期号:3 页码:529-539
摘要	Major public DNA databases - NCBI GenBank, the DNA DataBank of Japan (DDBJ), and the European Molecular Biology Laboratory (EMBL) - are invaluable biodiversity libraries. Systematists and other biodiversity scientists commonly mine these databases for sequence data to use in phylogenetic studies, but such studies generally use only the taxonomic identity of the sequenced tissue, not the specimen identity. Thus studies that use DNA supermatrices to construct phylogenetic trees with species at the tips typically do not take advantage of the fact that for many individuals in the public DNA databases, several DNA regions have been sampled; and for many species, two or more individuals have been sampled. Thus these studies typically do not make full use of the multigene datasets in public DNA databases to test species coherence and select optimal sequences to represent a species. In this study, we introduce a set of tools developed in the R programming language to construct individual-based trees from NCBI GenBank data and present a set of trees for the genus Carex (Cyperaceae) constructed using these methods. For the more than 770 species for which we found sequence data, our approach recovered an average of 1.85 gene regions per specimen, up to seven for some specimens, and more than 450 species represented by two or more specimens. Depending on the subset of genes analyzed, we found up to 42% of species monophyletic. We introduce a simple tree statistic-the Taxonomic Disparity Index (TDI)-to assist in curating specimen-level datasets and provide code for selecting maximally informative (or, conversely, minimally misleading) sequences as species exemplars. While tailored to the Carex dataset, the approach and code presented in this paper can readily be generalized to constructing individual-level trees from large amounts of data for any species group.
关键词	Carex Cyperaceae phylogenetic workflow specimen-level data supermatrix taxon disparity index (TDI)
学科领域	Plant Sciences ; Evolutionary Biology
DOI	10.1600/036364416X692505
收录类别	SCI
语种	英语
WOS关键词	MULTIPLE SEQUENCE ALIGNMENT ; SUBGENUS VIGNEA CYPERACEAE ; PHYLOGENETIC-RELATIONSHIPS ; CAREX CYPERACEAE ; TRIBE CARICEAE ; SEDGES CAREX ; EVOLUTION ; NRDNA ; LINEAGES ; DIVERSIFICATION
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED) ; Conference Proceedings Citation Index - Science (CPCI-S)
WOS记录号	WOS:000385643400005
出版者	AMER SOC PLANT TAXONOMISTS
文献子类	Article; Proceedings Paper
出版地	LARAMIE
EISSN	1548-2324
作者邮箱	kase.khanh.pham@gmail.com ; ahipp@mortonarb.org
作品OA属性	Green Published
引用统计	被引频次：7[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/24969
专题	系统与进化植物学国家重点实验室
作者单位	1.[Pham, Kasey K.; Hahn, Marlene; Lueders, Kate; Brown, Bethany H.; Hipp, Andrew L.] Morton Arboretum, Lisle, IL 60532 USA 2.Pham, Kasey K.] Michigan State Univ, E Lansing, MI 48824 USA 3.Bruederle, Leo P.; Derieg, Nathan J.] Univ Colorado Denver, Denver, CO 80217 USA 4.Bruhl, Jeremy J.] Univ New England, Armidale, NSW 2351, Australia 5.Jungwon Univ, Chungbuk 367805, South Korea 6.Univ Seville, Dept Plant Biol & Ecol, Seville 41004, Spain 7.Ford, Bruce A.] Univ Manitoba, Winnipeg, MB R3T 2N2, Canada 8.Gebauer, Sebastian; Hoffmann, Matthias H.] Univ Halle Wittenberg, D-06108 Halle, Saale, Germany 9.Johannes Gutenberg Univ Mainz, D-44122 Mainz, Germany 10.Okayama Univ Sci, Okayama 7000005, Japan 11.Jimenez-Mejias, Pedro; Roalson, Eric H.] Washington State Univ, Pullman, WA 99164 USA 12.Ajou Univ, Suwon 16499, South Korea 13.Sungshin Womens Univ, Seoul 136742, South Korea 14.Univ Pablo de Olavide, Seville 41004, Spain 15.Naczi, Robert F. C.] New York Bot Garden, Bronx, NY 10458 USA 16.Reznicek, Anton A.] Univ Michigan, Ann Arbor, MI 48109 USA 17.Simpson, David A.] Royal Bot Gardens, Richmond TW9 3AB, Surrey, England 18.Starr, Julian R.] Univ Ottawa, Ottawa, ON K1N 6N5, Canada 19.Waterway, Marcia J.] McGill Univ, Macdonald Campus, Ste Anne De Bellevue, PQ H9X 3V9, Canada 20.Wilson, Karen L.] Royal Bot Garden Sydney, Sydney, NSW 2000, Australia 21.Univ Tokyo, Univ Museum, Tokyo 1130033, Japan 22.Chinese Acad Sci, Beijing Inst Bot, Beijing 100093, Peoples R China 23.Hipp, Andrew L.] Field Museum, Chicago, IL 60605 USA 24.Brown, Bethany H.] Ball Hort Co, West Chicago, IL 60185 USA 25.Derieg, Nathan J.] Univ Calif Santa Barbara, Santa Barbara, CA 93106 USA 26.12 Okayama Univ Sci, Okayama, Okayama, Japan
推荐引用方式 GB/T 7714	Pham, Kasey K.,Hahn, Marlene,Lueders, Kate,et al. Specimens at the Center: An Informatics Workflow and Toolkit for Specimen-level analysis of Public DNA database data[J]. SYSTEMATIC BOTANY,2016,41(3):529-539.
APA	Pham, Kasey K..,Hahn, Marlene.,Lueders, Kate.,Brown, Bethany H..,Bruederle, Leo P..,...&Hipp, Andrew L..(2016).Specimens at the Center: An Informatics Workflow and Toolkit for Specimen-level analysis of Public DNA database data.SYSTEMATIC BOTANY,41(3),529-539.
MLA	Pham, Kasey K.,et al."Specimens at the Center: An Informatics Workflow and Toolkit for Specimen-level analysis of Public DNA database data".SYSTEMATIC BOTANY 41.3(2016):529-539.

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