Systematics Section / ASPT
Steele, Roxi , Guisinger-Bellian, Mary M. , Jansen, Robert K. , Linder, Randal .
Identifying Useful Low-copy Nuclear Markers for Examining Phylogenetic Relationships within Angiosperms.
Molecular systematics has progressed to the point where it is now expected that multiple independent markers are used in phylogenetic studies. Higher levels of confidence are obtained from phylogenies inferred from a consensus of organellar and nuclear markers. The availability of numerous universal primers has eased the burden of finding informative markers in the chloroplast genome, but the identification of useful nuclear regions is not yet a straightforward process. Because concerted evolution is not always as repeatable as once believed, nuclear genes with high numbers of copies (such as ITS) may not be useful in some groups. As a result, a preliminary search for low-copy nuclear regions is now a fundamental step prior to a comprehensive systematic study. Besides providing a high level of sequence variation that cannot typically be found in chloroplast sequences, low-copy nuclear regions provide the potential to accumulate datasets from multiple unlinked loci and have biparental inheritance. In the present study, we investigated 75 low-copy nuclear genes for phylogenetic utility in two unrelated lineages of rosids, an interspecific study of Psiguria (Cucurbitaceae) and an intergeneric study within Geraniaceae. For regions that were successfully amplified, those that showed single bands on gels were cloned to determine the number of copies in the genome and assess their phylogenetic utility. Three different outcomes were obtained: 1) a single copy was found and variation is phylogenetically informative, so direct sequences can be used in phylogenetic analyses, 2) multiple but distinct copies were found; therefore, a combination of cloning and development of copy-specific primers enable the identification of orthologous copies, or 3) multiple similar copies were found and the marker was abandoned because confirmation of orthology would be difficult. Our results have the potential to provide useful information for phylogenetic investigations at various taxonomic levels among other rosids and angiosperms.
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1 - University of Texas Austin, Plant Biology Graduate Program, 1 University Station A6720, Austin, Texas, 78712, USA
2 - University of Texas Austin, Section of Integrative Biology, 1 University Station, A6700, Austin, Texas, 78712-7640, USA
Low-copy Nuclear Markers
Presentation Type: Oral Paper:Papers for Sections
Location: Continental C/Hilton
Date: Tuesday, July 10th, 2007
Time: 8:30 AM