A Nuclear Ribosomal DNA Phylogeny of Acer Inferred with Maximum Likelihood, Splits Graphs, and Motif Analysis of 606 Sequences

Abstract

Abstract:The multi-copy internal transcribed spacer (ITS) region of nuclear ribosomal DNA is widely used to infer phylogenetic relationships among closely related taxa. Here we use maximum likelihood (ML) and splits graph analyses to extract phylogenetic information from ~ 600 mostly cloned ITS sequences, representing 81 species and subspecies of Acer, and both species of its sister Dipteronia. Additional analyses compared sequence motifs in Acer and several hundred Anacardiaceae, Burseraceae, Meliaceae, Rutaceae, and Sapindaceae ITS sequences in GenBank. We also assessed the effects of using smaller data sets of consensus sequences with ambiguity coding (accounting for within-species variation) instead of the full (partly redundant) original sequences. Neighbor-nets and bipartition networks were used to visualize confl ict among character state patterns. Species clusters observed in the trees and networks largely agree with morphology-based classifi cations; of de Jong's (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. Most nodes had higher bootstrap support with matrices of 105 or 40 consensus sequences than with the original matrix. Within-taxon ITS divergence did not differ between diploid and polyploid Acer, and there was little evidence of differentiated parental ITS haplotypes, suggesting that concerted evolution in Acer acts rapidly.

Evolution of pollen morphology in Loranthaceae

“…To test for potential sampling or missing data bias – a number of Loranthaceae genera are only incompletely known for the five gene regions (File S3) – a gene-jackknifing procedure was applied, using a restricted data set with no missing gene region (full results included in the OSM; summarised in File S1). Incompatible splits patterns in the bootstrap samples were investigated using bipartition (bootstrap support) networks, a special form of consensus networks (Holland & Moulton 2003; Grimm et al 2006). …”

RAxML-Cell: Parallel Phylogenetic Tree Inference on the Cell Broadband Engine

“…Some of the largest published ML-based biological analyses to date have been conducted with RAxML [13,18,19,22]. The program is also part of the greengenes project [8] (greengenes.lbl.gov) as well as the CIPRES (CyberInfrastructure for Phylogenetic RESearch, www.phylo.org) project.…”

“…In order to conduct a "publishable" tree reconstruction a certain number (typically 20-200) of distinct inferences (tree searches) on the original alignment as well as a large number (typically 100-1,000) of bootstrap analyses have to be conducted (see [13] for an example of a real-world analysis with RAxML). Thus, if the dataset is not extremely large, this represents the most reasonable approach to exploit HPC platforms from a user's perspective.…”

Phylogenetic Evaluation of Series Delimitations in Section Palmata (Acer, Aceroideae, Sapindaceae) Based on Sequences of Nuclear and Chloroplast Genes

“…Previous phylogenetic analyses, however, have included only 5-13 species (Ackerly and Donoghue 1998;Hasebe et al 1998;Suh et al 2000;Pfosser et al 2002;Tian et al 2002;Grimm et al 2006;Li et al 2006;Renner et al 2007Renner et al , 2008. Therefore, the objective of this study was to evaluate series delimitations of section Palmata by increasing species sampling and using DNA sequence data from both nuclear and chloroplast genomes.…”

“…The genus has been divided into sections with some sections being further divided into series (Pax 1902;Pojarkova 1933;Momotani 1962;Fang 1966;Ogata 1967;Xu 1996;de Jong 2004). Recent molecular phylogenetic studies of Acer recognize 16-22 sections including section Palmata (Ackerly and Donoghue 1998;Hasebe et al 1998;Suh et al 2000;Pfosser et al 2002;Tian et al 2002;Grimm et al 2006;Li et al 2006;Renner et al 2007Renner et al , 2008. As currently circumscribed (de Jong 2004;Xu et al 2008), section Palmata includes species from traditional sections Integrifolia, Microcarpa, and Palmata (Pojarkova 1933;Ogata 1967;Xu 1996; Table 1).…”