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ARS Home » Pacific West Area » Davis, California » Nat'l Clonal Germplasm Rep - Tree Fruit & Nut Crops & Grapes » Research » Publications at this Location » Publication #169046
Title: APPENDIX II. MOLECULAR ANALYSES: TYPES OF ANALYSIS AND DESCRIPTION OF APPROPRIATE DTA TO ADDRESS EVOLUTIONARY QUESTIONS

Author
item Aradhya, Mallikarjuna
item POTTER, DANIEL - UNIVERSITY OF CALIFORNIA
item Simon, Charles

Submitted to: Darwin's Harvest: New Approaches to the Origins, Evolution, and Conservation of Crops
Publication Type: Other
Publication Acceptance Date: 8/9/2004
Publication Date: 8/21/2004
Citation: Motley, T.J., Cross, H.B., Zerega, N.J.C., and Aradhya, M.K. 2005. Appendix II. Molecular Analysis. In: Motley, T.J., Zerega, N., and Cross H. (Eds), Darwin's Harvest: Origin, Evolution, and Conservation of Crop Plants. 370-379, Columbia University Press, New York.

Interpretive Summary: Two major approaches to analyses of molecular data have been described: (1) Genetic diversity at the intra- and interspecific levels; and (2) Phylogenetic systematics. In our opinion, these two approaches will cover a wide range of analyses techniques to address questions related to the assessment of genetic diversity, structure, and, conspecific and congeneric differentiation. We have attempted to list step-by-step analyses procedures including data treatment, hypothesis testing, various population genetic models, and statistical methods to analyze different types of molecular data. A number of multivariate statistical methods such as cluster analyses, data dimension reduction methods, minimum spanning trees used in the numerical taxonomic treatment of data have been considered. Phylogenetic analyses including character-based maximum parsimony and maximum likelihood methods and distance based minimum evolution methods have been listed.

Technical Abstract: The chapter contains various population genetic and phylogenetic methods that are available for analyzing molecular data. The population genetic methods address questions related to genetic structure and differentiation within and among species. Both univariate and multivariate techniques have been considered for comprehensive data exploration. Various phylogenetic methods for reconstruction of evolutionary relationships among taxa at the higher taxonomic levels have been included among the data analysis techniques.