Phylogeny of ‘araphid’ diatoms inferred from SSU and LSU rDNA, rbcL and psbA sequences

摘要

Phylogenies of the diatoms have largely been inferred from SSU rDNA udBecause previously published SSU rDNA topologies of araphid pennate uda supertree was constructed in order to summarize those trees and used to udanalyses where problems arose. As previously seen with the SSU trees, uddivided into two clades: basal and core araphids. The basal clade is sister to a udother araphids (core) and the raphid diatoms. Several subclades recovered in udnot correspond to current taxonomy in the diatoms but were supported by udmorphological characters. A phylogeny of diatoms was then estimated using udSSU and LSU rDNA, rbcL and psbA (total 4352 bp) with 42 diatom species udproblems in the supertree. Two rooting strategies were explored: 1) one udclosest outgroup of the diatoms and, 2) one bolidomonad and more distantly udoutgroups. Two different strategies were employed to analyze the four gene udboth Maximum Likelihood (ML) and Baysian Inference (BI) methods. In the first udvariable regions of the LSU rDNA and the third codon position of rbcL were ud(A+G) and Y (T+C) because of substitution saturation detected at these udIn the second, these regions were not recoded. Tree topologies of pennates udin all analyses. Pennates were divided into three major clades, basal araphid, udraphid diatoms, as shown in the supertree. The four gene trees displayed udhad stronger bootstrap within the subclades than those of the SSU supertree. udtime of the pennates with a Bayesian estimation was estimated, allowing for udfrom the fossil record and varying rates of molecular evolution of different udthe phylogenetic tree. The radiation of pennates into three major clades took udperiod of geological time before their first appearance in the fossil record and udproposed by other clocks using single genes.