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United States Department of Agriculture

Agricultural Research Service

Title: Taking the First Steps Towards a Standard for Reporting on Phylogenies: Minimal Information About a Phylogenetic Analylsis (Miapa)

item Leebens-Mack, Jim - PENN STATE UNIV
item Vision, Todd - UNIV OF NORTH CAROLINA
item Brenner, Eric - UNIV OF NORTH CAROLINA
item Bowers, John - UNIV OF GEORGIA
item Cannon, Steven
item Clement, Mark - BRIGHAM YOUNG UNIV
item Cunningham, Clifford - DUKE UNIV
item Depamphilis, Claude - PENN STATE UNIV
item Doyle, Jeff - CORNELL UNIV
item Eisen, Jonathan - INST GENOMIC RESEARCH
item Gu, Xun - IOWA STATE UNIV
item Kellogg, Elizabeth - UNIV OF MO
item Koonin, Eugene - NATL INST HEALTH
item Philippe, Herve - CAN INST ADV RESEARCH
item Pires, J Chris - UNIV OF MO
item Qiu, Yin-Long - UNIV OF MICHIGAN
item Sjolander, Kimmen - UNIV OF CA
item Soltis, Douglas - UNIV OF FLORIDA
item Stevens, Peter - UNIV OF MO
item Stevenson, Dennis - NY BOTANICAL GARDEN
item Warnow, Tandy - UNIV OF TEXAS
item Zmasek, Christian - GENOMICS INST NOVARTIS
item Soltis, Pamela - UNIV OF FLORIDA

Submitted to: OMICS: A Journal of Integrative Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 13, 2006
Publication Date: June 1, 2006
Citation: Leebens-Mack, J., Vision, T., Brenner, E., Bowers, J.E., Cannon, S.B., Clement, M.J., Cunningham, C.W., Depamphilis, C., Desalle, R., Doyle, J.J., Eisen, J.A., Gu, X., Harshman, J., Kellogg, E., Koonin, E.V., Philippe, H., Pires, J., Qiu, Y., Rhee, S.Y., Sjolander, K., Soltis, D.E., Stevens, P., Stevenson, D.W., Warnow, T., Zmasek, C., Soltis, P.S. 2006. Taking the first steps towards a standard for reporting on phylogenies: minimal information about a phylogenetic analylsis (miapa). OMICS: A Journal of Integrative Biology. 10(20):231-237.

Interpretive Summary: Comparisons of the hereditary code (the DNA) within and between species tells us much about evolutionary relationships. These types of studies are important in most fields of biological and genetic study. These relationships are usually depicted as tree-like structures called "phylogenies" that show nested evolutionary patterns among gene sequences within and between organisms. With use of these methods in more biological fields and with ever larger amounts of data, it is becoming increasingly critical to establish minimal common reporting standards for describing these methods. The authors propose the development of reporting standards for describing evolutionary relationships among gene sequences. A model for this proposal is provided by the development of the Minimum Information About a Microarray Experiment (MIAME) standard, which has been very important in functional biology, allowing experimenters to better compare among large data sets, conduct meta-analyses and confirm previous experiments. Such standards will be important in several fields, including in work describing the evolution of agronomically valuable traits.

Technical Abstract: In the eight years since phylogenomics was introduced as the intersection of genomics and phylogenetics, the field has provided fundamental insights into gene function, genome history and organismal relationships. The utility of phylogenomics is growing with the increase in the number and diversity of taxa for which whole genome and large transcriptome sequence sets are being generated. We assert that the synergy between genomic and phylogenetic perspectives in comparative biology would be enhanced by the development and refinement of minimal reporting standards for phylogenetic analyses. Encouraged by the development of the Minimum Information About a Microarray Experiment (MIAME) standard, we propose a similar roadmap for the development of a Minimal Information About a Phylogenetic Analysis (MIAPA) standard. Key in the successful development and implementation of such a standard will be broad participation by developers of phylogenetic analysis software, phylogenetic databases, and journal editors.

Last Modified: 4/18/2015
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