@ARTICLE{TreeBASE2Ref16908, author = {Sang-Hun Oh and Daniel Potter}, title = {Phylogenetic utility of the second intron of <i>LEAFY</i> in <i>Neillia</i> and <i>Stephanandra</i> (Rosaceae) and implications for the origin of <i>Stephanandra</i>.}, year = {2003}, keywords = {}, doi = {}, url = {}, pmid = {}, journal = {Molecular Phylogenetics and Evolution}, volume = {29}, number = {}, pages = {203--215}, abstract = {A homeotic gene, <i>LEAFY</i>, has been suggested to be a single-copy gene in diploid angiosperms. Nucleotide sequences of the second intron of this gene, along with those of several regions of the chloroplast genome (<i>trnL-trnF, trnD-trnY-trnE-trnT</i>, and <i>matK-trnK</i>) and nuclear ribosomal ITS, were obtained from the species of <i>Neillia</i> and <i>Stephanandra</i> to examine the phylogenetic utility of the intron and to elucidate the phylogenetic relationships among species of the two genera. PCR amplification of the second intron of <i>LEAFY</i> using universal degenerate primers produced PCR products in sufficient quantity for successful direct sequencing. The length of the intron ranged from 591 to 622 base pairs (bp) in <i>Neillia</i> and <i>Stephanandra</i>, except in <i>N. thibetica</i> (ca. 1370 bp), and sequence analysis of this region from multiple accessions revealed low levels of infraspecific variation. Comparison of the <i>LEAFY</i> data with ITS and cpDNA data demonstrated that the <i>LEAFY</i> intron was the most variable and useful for phylogenetic analysis at the species level, providing many more phylogenetically informative characters per 100 bp (7.4) than either ITS (3.2) or cpDNA (0.7). Phylogenetic analyses of <i>LEAFY</i> data using both maximum parsimony and likelihood methods generated well supported and highly resolved gene trees with few homoplasies (CI = 0.97). <i>Stephanandra</i> is monophyletic and is nested within <i>Neillia</i> in both <i>LEAFY</i> and cpDNA trees, while the relationship is poorly resolved by ITS data. <i>LEAFY</i> and cpDNA data, however, strongly conflicted with each other with respect to the position of <i>Stephanandra</i>: <i>LEAFY</i> trees placed <i>Stephanandra</i> as sister to the ((<i>N. affinis, N. gracilis</i>), <i>N. thyrsiflora</i>) clade whereas cpDNA data suggested <i>Stephanandra</i> is sister to <i>N. uekii</i>. Both gene trees, however, are nearly identical to each other when <i>Stephanandra</i> is excluded. A hybrid origin of <i>Stephanandra</i> is suggested as a plausible hypothesis to explain the incongruence between <i>LEAFY</i> and cpDNA data sets, though gene duplication/loss and lineage sorting events cannot be ruled out as possibilities.} }

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