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The Tortoise and the Hare: Choosing between Noncoding Plastome and Nuclear Adh Sequences for Phylogeny Reconstruction in a Recently Diverged Plant Group

Randall L. Small, Julie A. Ryburn, Richard C. Cronn, Tosak Seelanan and Jonathan F. Wendel
American Journal of Botany
Vol. 85, No. 9 (Sep., 1998), pp. 1301-1315
Stable URL: http://www.jstor.org/stable/2446640
Page Count: 15
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The Tortoise and the Hare: Choosing between Noncoding Plastome and Nuclear Adh Sequences for Phylogeny Reconstruction in a Recently Diverged Plant Group
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Abstract

Phylogenetic resolution is often low within groups of recently diverged taxa due to a paucity of phylogenetically informative characters. We tested the relative utility of seven noncoding cpDNA regions and a pair of homoeologous nuclear genes for resolving recent divergences, using tetraploid cottons (Gossypium) as a model system. The five tetraploid species of Gossypium are a monophyletic assemblage derived from an allopolyploidization event that probably occurred within the last 0.5-2 million years. Previous analysis of cpDNA restriction site data provided only partial resolution within this clade despite a large number of enzymes employed We sequenced three cpDNA introns (rpll6, rpoC1, ndhA) and four cpDNA spacers (accD-psal, trnL-trnF, trnT-trnL, atpB-rbcL) for a total of over 7 kb of sequence per taxon, yet obtained only four informative nucleotide substitutions (0.05%) resulting in incomplete phylogenetic resolution. In addition, we sequenced a 1.65-kb region of a homoeologous pair of nuclear-encoded alcohol dehydrogenase (Adh) genes. In contrast with the cpDNA sequence data, the Adh homoeologues yielded 25 informative characters (0 76%) and provided a robust and completely resolved topology that is concordant with previous cladistic and phenetic analyses. The enhanced resolution obtained using the nuclear genes reflects an approximately three- to sixfold increase in nucleotide substitution rate relative to the plastome spacers and introns.

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