摘要 : The sequence of the plastid genome of Amborella trichopoda,the putative sister to all other extant angiosperms, was recentlyreported (Molecular Biology and Evolution 20: 1499–1505).Goremykin et ... 展开 The sequence of the plastid genome of Amborella trichopoda,the putative sister to all other extant angiosperms, was recentlyreported (Molecular Biology and Evolution 20: 1499–1505).Goremykin et al. used sequence data for 61 plastid genes fromAmborella and 12 other embryophytes in phylogenetic analysesand concluded that Amborella is not the sister to the remainingflowering plants; the monocots instead occupy this position.The authors attributed their results, which differ substantiallyfrom all recent phylogenetic analyses of angiosperms, to theincreased character sampling (30 017 nucleotides in their alignedmatrix) in their analysis relative to published studies thatincluded fewer genes but more taxa. We hypothesized that thedifference in topology is not due to limited character samplingin previous studies but to limited taxon sampling in the analysisby Goremykin et al. To test this, we conducted a series of phylogeneticanalyses using a three-gene, 12 (or more)-taxon data set toevaluate the topological effects of (i) including three vs.61 genes for (nearly) the same set of taxa, (ii) analyzing differentcodon positions, (iii) substituting representatives of otherbasal lineages for Amborella, (iv) replacing the grasses usedto represent the monocots with other monocots, selected eitherfor their phylogenetic position or randomly, and (v) addingother basal taxa—Nymphaea, Austrobaileya, magnoliids,and monocots—to the 12-taxon data set. Our results demonstratethat the "monocots basal" topology obtained by Goremykin etal. is not due to increased character sampling of the plastidgenome; their topology was obtained using only two plastid genesor two plastid genes and one nuclear gene. This topology wasalso retained when either Nymphaea or Austrobaileya was substitutedfor Amborella, demonstrating that any of the three basal lineageswill attach to Calycanthus for lack of any other close branch.Furthermore, the "monocots basal" topology is not robust tochanges in sampling of monocots. Simply adding Oncidium, forexample, places Amborella sister to the other angiosperms. Thus,limited taxon sampling, focusing on organisms with completegenome sequences, can lead to artifactual results. 收起