TAKING THE FIRST STEPS TOWARDS A STANDARD FOR REPORTING ON PHYLOGENIES: MINIMAL INFORMATION ABOUT A PHYLOGENETIC ANALYLSIS (MIAPA)

Authors: LEEBENS-MACK, JIM - PENN STATE UNIV; VISION, TODD - UNIV OF NORTH CAROLINA; BRENNER, ERIC - UNIV OF NORTH CAROLINA; BOWERS, JOHN - UNIV OF GEORGIA; Cannon, Steven; CLEMENT, MARK - BRIGHAM YOUNG UNIV; CUNNINGHAM, CLIFFORD - DUKE UNIV; DEPAMPHILIS, CLAUDE - PENN STATE UNIV; DESALLE, ROB - AMER MUSEUM NATURAL HISTO; DOYLE, JEFF - CORNELL UNIV; EISEN, JONATHAN - INST GENOMIC RESEARCH; GU, XUN - IOWA STATE UNIV; HARSHMAN, JOHN - FIELD MUSEUM NATURAL HIST; KELLOGG, ELIZABETH - UNIV OF MO; KOONIN, EUGENE - NATL INST HEALTH; PHILIPPE, HERVE - CAN INST ADV RESEARCH; PIRES, J CHRIS - UNIV OF MO; QIU, YIN-LONG - UNIV OF MICHIGAN; RHEE, SEUNG - CARNEGIE INSTITUTION; SJOLANDER, KIMMEN - UNIV OF CA; SOLTIS, DOUGLAS - UNIV OF FLORIDA; STEVENS, PETER - UNIV OF MO; STEVENSON, DENNIS - NY BOTANICAL GARDEN; WARNOW, TANDY - UNIV OF TEXAS; ZMASEK, CHRISTIAN - GENOMICS INST NOVARTIS; SOLTIS, PAMELA - UNIV OF FLORIDA

Submitted to: OMICS: A Journal of Integrative Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/13/2006
Publication Date: 6/1/2006
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.