title: Molecular phylogeny of Amphora sensu lato (Bacillariophyta): an investigation into the monophyly and classification of the amphoroid diatoms.
abstract: Amphora sensu lato encompasses a large group of raphid diatoms, diverse in both form and ecology. The defining feature of this group has been an extreme asymmetry of the valve mantle and girdle bands, bringing both faces of the cell onto a single plane. Although this 'amphoroid' structure has long been the diagnostic feature and thus considered 'conservative' for the group, many have argued that the diversity of forms presently assigned to Amphora likely does not represent a monophyletic group. With the exception of several taxonomic transfers and the recent elevation of Halamphora to the level of genus, much of Amphora classification has remained unchanged for over 100 years. This study presents a phylogenetic analysis of Amphora s.l. based on a concatenated molecular alignment including the nuclear marker SSU rDNA and the chloroplast markers rbcL and psbC. These results are discussed within the framework of the current classification system of Amphora and Halamphora and lay the groundwork for a taxonomic revision of the group based on monophyly. The results of this analysis demonstrate that the genus Amphora is polyphyletic and that lineages assigned to the genus are distributed widely across the raphid diatom tree of life. The feature of amphoroid symmetry appears to have evolved independently several times. We discuss the nature of conservative characters in the raphid diatoms and their usefulness as a guide to phylogenetic relationships.
authors.affiliation: Department of Ecology and Evolutionary Biology and, Museum of Natural History, University of Colorado, Boulder, CO 80309, USA. Electronic address: joshua.stepanek@colorado.edu.
authors.forename: Joshua G
authors.initials: JG
authors.lastname: Stepanek
authors.affiliation: Department of Ecology and Evolutionary Biology and, Museum of Natural History, University of Colorado, Boulder, CO 80309, USA.
authors.forename: J Patrick
authors.initials: JP
authors.lastname: Kociolek
mesh_terms: D020418:Algal Proteins / Q000235:genetics; D016000:Cluster Analysis; D048028:DNA, Algal / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D017377:Diatoms / Q000145:classification* / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D012273:Ribulose-Bisphosphate Carboxylase / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D020418:Algal Proteins; D048028:DNA, Algal; D004275:DNA, Ribosomal; D012337:RNA, Ribosomal, 18S; C101625:RbcL protein, plastid; D012273:Ribulose-Bisphosphate Carboxylase
keywords: Amphora; Halamphora; SSU; phylogeny; psbC.; rbcL