@ARTICLE{TreeBASE2Ref15626, author = {Guido W Grimm and Susanne S Renner and Alexandros Stamatakis and Vera Hemleben}, title = {A nuclear ribosomal DNA phylogeny of Acer inferred with maximum likelihood, splits graphs, and motif analyses of 606 sequences}, year = {2006}, keywords = {}, doi = {}, url = {}, pmid = {}, journal = {Evolutionary Bioinformatics}, volume = {2}, number = {}, pages = {279--294}, abstract = {The internal transcribed spacer (ITS) region of nuclear ribosomal DNA is a biparentally inherited, multi-copy marker that is widely used to infer phylogenetic relationships among closely related taxa. In a strict sense, sequences in ITS data sets are not homologous unless one was to sequence tandem repeats at a specified position in the nucleolus organizer region. We use maximum likelihood (ML) and splits graphs analyses to extract phylogenetic information from 584 (mostly cloned) ITS sequences, representing 81 species and subspecies of Acer, plus both species of its sister genus Dipteronia. Analyses of motifs and clade-specific substitution biases compared Acer to several hundred ITS sequences of Sapindales from GenBank, representing Anacardiaceae, Burseraceae, Meliaceae, Rutaceae, and Sapindaceae. Taxon sampling within the genus involved multiple accessions of representatives from all morphological groups, including all known polyploid maple taxa. Because of the large size of the matrices, we used RAxML-VI-HPC for tree inference under the best-fit GTR+ model. Results obtained with the full 584-sequence matrix were compared with those from reduced matrices of consensus sequences that used ambiguity coding to account for within-species/subspecies variation. Neighbor-nets and bipartition networks were used to visualize conflict among character state patterns. Species clusters observed in the trees and networks agree well with morphology-based classifications; of de Jongs (1994) 16 sections, nine are supported in neighbor-net and bipartition networks, and ten by sequence motifs and the ML tree; of his 19 series, 14 are supported in networks, motifs, and the ML tree. Within-taxon ITS divergence did not differ between diploid and polyploid species or subspecies, and there was little evidence of differentiated parental ITS haplotypes, suggesting that concerted evolution in Acer acts rapidly.} }

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