Specimens at the Center: An Informatics Workflow and Toolkit for Specimen-level analysis of Public DNA database data
文献类型：期刊论文
| 作者 | Pham, Kasey K.; Hahn, Marlene; Lueders, Kate; Brown, Bethany H.; Bruederle, Leo P.; Bruhl, Jeremy J.; Chung, Kyong-Sook; Derieg, Nathan J.; Escudero, Marcial5; Ford, Bruce A. |
| 刊名 | SYSTEMATIC BOTANY
 |
| 出版日期 | 2016 |
| 卷号 | 41期号:3页码:529-539 |
| 关键词 | Carex Cyperaceae phylogenetic workflow specimen-level data supermatrix taxon disparity index (TDI) |
| ISSN号 | 0363-6445 |
| DOI | 10.1600/036364416X692505 |
| 文献子类 | Article; Proceedings Paper |
| 英文摘要 | 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. |
| 学科主题 | Plant Sciences ; Evolutionary Biology |
| 出版地 | LARAMIE |
| 电子版国际标准刊号 | 1548-2324 |
| 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) |
| 语种 | 英语 |
| WOS记录号 | WOS:000385643400005 |
| 出版者 | AMER SOC PLANT TAXONOMISTS |
| 源URL | [http://ir.ibcas.ac.cn/handle/2S10CLM1/24969]  |
| 专题 | 植物研究所_系统与进化植物学研究中心_系统与进化植物学研究中心_学位论文 |
| 作者单位 | 1.Simpson, David A.] Royal Bot Gardens, Richmond TW9 3AB, Surrey, England 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 |
| 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. |
入库方式： OAI收割
来源：植物研究所
浏览0
下载0
收藏0
其他版本
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。