From famine to feast? Selecting nuclear DNA sequence loci for plant species-level phylogeny reconstruction
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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Tài liệu tham khảo
Brown G.R, 2001, Anchored reference loci in loblolly pine (Pinus taeda L.) for integrating pine genomics, Genetics, 159, 799, 10.1093/genetics/159.2.799
Chandappa L. H. Feltus F. A. Singh H. P. & Paterson A. H. 2005 Conserved PCR primers from rice–banana and rice–onion alignments. XIII Plant–Animal Genome Conf. Abstract San Diego USA.
p. 576 Eds. Cracraft J& Donoghue M.J. 2004 New York:Oxford University Press.
Donoghue M.J, 2004, Assembling the Tree of Life, 1
Doyle J.J, 2003, Chloroplast expressed glutamine synthetase in Glycine and related Leguminosae: phylogeny, gene duplication and ancient polyploidy, Syst. Bot, 28, 567
Lukens L, 2003, Comparison of a Brassica oleracea genetic map with the genome of Arabidopsis thaliana, Genetics, 146, 359, 10.1093/genetics/164.1.359
Moore W.S, 1995, Inferring phylogenies from mtDNA variation: mitochondrial-gene versus nuclear-gene trees, Evolution, 49, 718
Nesbitt T.C, 2002, Comparative sequencing in the genus Lycopersicon: implications for the evolution of fruit size in the domestication of cultivated tomatoes, Genetics, 162, 365, 10.1093/genetics/162.1.365
Padolina J, 2004, Identification of broadly applicable nuclear DNA regions for phylogenetic reconstruction in angiosperms, Bot. Soc. Am, 2004, 528
Pamilo P, 1988, Relationships between gene trees and species trees, Mol. Biol. Evol, 5, 568
Scherson R. Choi H.-K. Cook D. & Sanderson M. J. In press. Phylogenetics of New World Astragalus : the utility of genomics technology in reconstructing phylogenies at low taxonomic levels. Brittonia .
Syring J. V. Willyard A. Cronn R. C. & Liston A. In press. Evolutionary relationships among Pinus (Pinaceae) subsections inferred from multiple low-copy nuclear loci. Am. J. Bot .
Thießen G, 2002, Developmental genetics and plant evolution, 173
Wendel J.F, 1998, Molecular systematics of plants II. DNA sequencing, 265, 10.1007/978-1-4615-5419-6_10
Wolfe A.D, 1998, Molecular systematics of plants II. DNA sequencing, 43, 10.1007/978-1-4615-5419-6_2
Wortley A. H. & Scotland R.W. 2005 Determining the potential utility of datasets for phylogeny reconstruction. Taxon . In press.