From famine to feast? Selecting nuclear DNA sequence loci for plant species-level phylogeny reconstruction

Philosophical Transactions of the Royal Society B: Biological Sciences - Tập 361 Số 1465 - Trang 211-225 - 2006
Colin E. Hughes1, Ruth J. Eastwood1, C. Donovan Bailey2
1Department of Plant Sciences, University of OxfordSouth Parks Road, Oxford OX1 3RB, UK
2Department of Biology, New Mexico State UniversityPO Box 3001 Department 3AF, Las Cruces, NM 88003-8001, USA

Tóm tắt

Phylogenetic analyses of DNA sequences have prompted spectacular progress in assembling the Tree of Life. However, progress in constructing phylogenies among closely related species, at least for plants, has been less encouraging. We show that for plants, the rapid accumulation of DNA characters at higher taxonomic levels has not been matched by conventional sequence loci at the species level, leaving a lack of well-resolved gene trees that is hindering investigations of many fundamental questions in plant evolutionary biology. The most popular approach to address this problem has been to use low-copy nuclear genes as a source of DNA sequence data. However, this has had limited success because levels of variation among nuclear intron sequences across groups of closely related species are extremely variable and generally lower than conventionally used loci, and because no universally useful low-copy nuclear DNA sequence loci have been developed. This suggests that solutions will, for the most part, be lineage-specific, prompting a move away from ‘universal’ gene thinking for species-level phylogenetics. The benefits and limitations of alternative approaches to locate more variable nuclear loci are discussed and the potential of anonymous non-genic nuclear loci is highlighted. Given the virtually unlimited number of loci that can be generated using these new approaches, it is clear that effective screening will be critical for efficient selection of the most informative loci. Strategies for screening are outlined.

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Philosophical Transactions of the Royal Society B: Biological Sciences

Tập 361 Số 1465

211-225

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