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

Medlin, LK; Desdevies, Y. 2016 Phylogeny of ‘araphid’ diatoms inferred from SSU and LSU rDNA, rbcL and psbA sequences. Vie et Milieu, 66 (2). 129-154.

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Abstract/Summary

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

Item Type: Publication - Article
Additional Keywords: ARAPHID DIATOMS DIVERGENCE TIME ESTIMATION LSU PINNATE PHYLOGENY PSBA RBCL SSU SUPERTREE
Subjects: Botany
Divisions: Marine Biological Association of the UK > Other (MBA)
Depositing User: Dr Linda Medlin
Date made live: 20 Feb 2017 15:15
Last Modified: 06 Jun 2017 16:17
URI: http://plymsea.ac.uk/id/eprint/7314

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