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J. Patrick Kociolek - One of the best experts on this subject based on the ideXlab platform.
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Re-examination of Mereschkowsky’s genus TetrAmphora (Bacillariophyta) and its separation from Amphora
Diatom Research, 2016Co-Authors: Joshua G. Stepanek, J. Patrick KociolekAbstract:The raphid diatom genus Amphora has been subject to considerable revision over the previous 30 years, with many species transferred to newly created or existing genera. Despite these efforts, recent work has demonstrated that taxa presently assigned to the genus continue to be non-monophyletic and further revision is required. This investigation re-examines Mereschkowsky’s genus TetrAmphora, which he described as including all Amphora species with four chloroplasts, arranged in pairs linked by large pyrenoids. Although largely ignored over the last 100 years, recent work has shown that taxa aligning with TetrAmphora are monophyletic and distinct from Amphora sensu stricto. Nine species belonging to TetrAmphora are illustrated and described, based on light and scanning electron microscope observations, as well as a preliminary molecular phylogeny for the group. From these observations, we designate Mereschkowsky’s T. ostrearia as the generitype of TetrAmphora, recognize T. lineolata, and transfer the Ampho...
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Description and phylogenetic position of Amphora aliformis (Bacillariophyta), a new species from Tokyo Bay
Phycologia, 2015Co-Authors: Joshua G. Stepanek, Shigeki Mayama, J. Patrick KociolekAbstract:The genus Amphora is a large and widely distributed group of raphid diatoms, frequently found in fresh, brackish, and salt water environments from around the world. Presented here is the description and phylogenetic position of Amphora aliformis, a new species collected from the Banzu Flats, Tokyo Bay, Japan. This species has a unique morphology, with features seldom or never before observed within the genus Amphora, such as a dorsal marginal wing and ventral apical pores, as well as a unique phylogenetic position as an early diverging lineage within the genus. As with many large and diverse groups of diatoms, new evidence has called into question the validity of the long standing classification system for the genus Amphora. Within the previous system, A. aliformis would be prescribed to the subgenus DiplAmphora based on morphological valve features. However, molecular phylogenetic analysis demonstrates that DiplAmphora is not monophyletic and furthers evidence that Amphora classification is in need of revision. Included here is a description of A. aliformis based on light microscope, scanning electron microscope, and molecular phylogenetic data, as well as a re-examination and discussion of the current state of Amphora classification.
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Molecular Phylogeny of Amphora sensu lato (Bacillariophyta): An Investigation into the Monophyly and Classification of the Amphoroid Diatoms
Protist, 2014Co-Authors: Joshua G. Stepanek, J. Patrick KociolekAbstract: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.
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Several new species of Amphora and HalAmphora from the western USA
Diatom Research, 2013Co-Authors: Joshua G. Stepanek, J. Patrick KociolekAbstract:Amphora Ehrenberg ex Kützing sensu lato incorporates a large and diverse group of diatoms. Although having its greatest taxonomic diversity in marine environments, inland waters of the USA appear to hold a large amount of undescribed taxa diversity requiring thorough taxonomic investigation. Presented here are descriptions and illustrations of seven new species collected from inland waters of the western USA, based on light and scanning electron microscope observations. Species described include A. copulatoides, A. manifesta and A. waldeniana from the genus Amphora subgenus Amphora and H. coloradiana, H. latecostata, H. punctata and H. subtilis from the genus HalAmphora (Cleve) Levkov. This work represents the first steps in a larger taxonomic and systematic investigation into Amphora sensu lato from inland waters of the USA
Joshua G. Stepanek - One of the best experts on this subject based on the ideXlab platform.
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re examination of mereschkowsky s genus tetrAmphora bacillariophyta and its separation from Amphora
Diatom Research, 2016Co-Authors: Joshua G. Stepanek, Patrick J KociolekAbstract:The raphid diatom genus Amphora has been subject to considerable revision over the previous 30 years, with many species transferred to newly created or existing genera. Despite these efforts, recent work has demonstrated that taxa presently assigned to the genus continue to be non-monophyletic and further revision is required. This investigation re-examines Mereschkowsky’s genus TetrAmphora, which he described as including all Amphora species with four chloroplasts, arranged in pairs linked by large pyrenoids. Although largely ignored over the last 100 years, recent work has shown that taxa aligning with TetrAmphora are monophyletic and distinct from Amphora sensu stricto. Nine species belonging to TetrAmphora are illustrated and described, based on light and scanning electron microscope observations, as well as a preliminary molecular phylogeny for the group. From these observations, we designate Mereschkowsky’s T. ostrearia as the generitype of TetrAmphora, recognize T. lineolata, and transfer the Ampho...
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Re-examination of Mereschkowsky’s genus TetrAmphora (Bacillariophyta) and its separation from Amphora
Diatom Research, 2016Co-Authors: Joshua G. Stepanek, J. Patrick KociolekAbstract:The raphid diatom genus Amphora has been subject to considerable revision over the previous 30 years, with many species transferred to newly created or existing genera. Despite these efforts, recent work has demonstrated that taxa presently assigned to the genus continue to be non-monophyletic and further revision is required. This investigation re-examines Mereschkowsky’s genus TetrAmphora, which he described as including all Amphora species with four chloroplasts, arranged in pairs linked by large pyrenoids. Although largely ignored over the last 100 years, recent work has shown that taxa aligning with TetrAmphora are monophyletic and distinct from Amphora sensu stricto. Nine species belonging to TetrAmphora are illustrated and described, based on light and scanning electron microscope observations, as well as a preliminary molecular phylogeny for the group. From these observations, we designate Mereschkowsky’s T. ostrearia as the generitype of TetrAmphora, recognize T. lineolata, and transfer the Ampho...
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Description and phylogenetic position of Amphora aliformis (Bacillariophyta), a new species from Tokyo Bay
Phycologia, 2015Co-Authors: Joshua G. Stepanek, Shigeki Mayama, J. Patrick KociolekAbstract:The genus Amphora is a large and widely distributed group of raphid diatoms, frequently found in fresh, brackish, and salt water environments from around the world. Presented here is the description and phylogenetic position of Amphora aliformis, a new species collected from the Banzu Flats, Tokyo Bay, Japan. This species has a unique morphology, with features seldom or never before observed within the genus Amphora, such as a dorsal marginal wing and ventral apical pores, as well as a unique phylogenetic position as an early diverging lineage within the genus. As with many large and diverse groups of diatoms, new evidence has called into question the validity of the long standing classification system for the genus Amphora. Within the previous system, A. aliformis would be prescribed to the subgenus DiplAmphora based on morphological valve features. However, molecular phylogenetic analysis demonstrates that DiplAmphora is not monophyletic and furthers evidence that Amphora classification is in need of revision. Included here is a description of A. aliformis based on light microscope, scanning electron microscope, and molecular phylogenetic data, as well as a re-examination and discussion of the current state of Amphora classification.
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Molecular Phylogeny of Amphora sensu lato (Bacillariophyta): An Investigation into the Monophyly and Classification of the Amphoroid Diatoms
Protist, 2014Co-Authors: Joshua G. Stepanek, J. Patrick KociolekAbstract: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.
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Several new species of Amphora and HalAmphora from the western USA
Diatom Research, 2013Co-Authors: Joshua G. Stepanek, J. Patrick KociolekAbstract:Amphora Ehrenberg ex Kützing sensu lato incorporates a large and diverse group of diatoms. Although having its greatest taxonomic diversity in marine environments, inland waters of the USA appear to hold a large amount of undescribed taxa diversity requiring thorough taxonomic investigation. Presented here are descriptions and illustrations of seven new species collected from inland waters of the western USA, based on light and scanning electron microscope observations. Species described include A. copulatoides, A. manifesta and A. waldeniana from the genus Amphora subgenus Amphora and H. coloradiana, H. latecostata, H. punctata and H. subtilis from the genus HalAmphora (Cleve) Levkov. This work represents the first steps in a larger taxonomic and systematic investigation into Amphora sensu lato from inland waters of the USA
David G. Mann - One of the best experts on this subject based on the ideXlab platform.
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Morphology and life history of Amphora commutata (Bacillariophyta) I: the vegetative cell and phylogenetic position
Phycologia, 2013Co-Authors: Shinya Sato, Nagumo Tamotsu, David G. MannAbstract:Amphoroid diatoms are recognized in the light microscope by their strongly dorsiventral frustules; their raphe system lies close to the ventral margin of the valve, and their girdle is much wider on the dorsal side. Historically, these diatoms were classified into the genus Amphora, although heterogeneity has long been pointed out based mainly on frustule fine structure, chloroplast arrangement, and molecular phylogeny. In this study detailed observations were undertaken on the frustule of an amphoroid species Amphora commutata. Distinct features of this species were the hyaline ventral side of the valve and hitherto unknown apical pores. The ontogeny of the valve and girdle bands was also reported. A molecular phylogenetic analysis of Amphora species, including representatives of the subgenera Amphora, OxyAmphora and DiplAmphora, was performed, based on nuclear encoded small subunit (SSU) rDNA. The best tree showed paraphyly of amphoroid diatoms and also suggested that the subgenus DiplAmphora, which inc...
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Mating system, auxosporulation, species taxonomy and evidence for homoploid evolution in Amphora (Bacillariophyta)
Phycologia, 2010Co-Authors: David G. Mann, Aloisie PoulíčkováAbstract:Abstract Mann D.G. and PoulIckova A. 2010. Mating system, auxosporulation, species taxonomy and evidence for homoploid evolution in Amphora (Bacillariophyta). Phycologia 49: 183–201. DOI: 10.2216/09-08.1 Cytological characteristics of the mitotic cycle, sexual reproduction and auxospore formation are described for three members of the type group of Amphora: A. ovalis, A. copulata and A. minutissima. All have a single lobed ventral chloroplast, nuclei with granular heterochromatin and a single nucleolus (unusually large in A. ovalis). Amphora copulata is heterothallic, with two mating types that do not differ in gamete behaviour. All three species reproduce allogamously via fusion of two rearranged gametes per gametangium to produce elongate zygotes enclosed within the volume delimited by the gametangial thecae. Pairing is strictly via the ventral sides of the cells, with tight apposition of the cells, and expansion of the auxospores is strictly perpendicular to the gametangium long axes. Comparisons are m...
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The systematics of Seminavis (Bacillariophyta): the lost identities of Amphora angusta, A. ventricosa and A. macilenta
European Journal of Phycology, 2002Co-Authors: Daniel B. Danielidis, David G. MannAbstract:Amphora angusta Gregory, Amphora ventricosa Gregory and Amphora macilenta Gregory have been misunderstood for the last 140 years. Gregory described these species from sublittoral sediments off the west coast of Scotland. Although the illustrations were excellent for their time (1857), it is impossible to be confident of identification using Gregory's paper, and subsequent authors have created such confusion that records of these taxa must be regarded as untrustworthy unless backed by photographic evidence. In this paper, the first to describe in detail the recently established genus Seminavis, we show that A. angusta is in fact a species of Amphora Ehrenberg, whereas A. ventricosa sensu Gregory represents two independent species of the genus Seminavis D. G. Mann, namely Seminavis ventricosa (Gregory) Garcia-Baptista (non S. ventricosa sensu Garcia-Baptista 1993) and Seminavis arranensis Danielidis & D. G. Mann, sp. nov. The form usually known as A. ventricosa is neither of these and requires a new name, S...
Vincent Serneels - One of the best experts on this subject based on the ideXlab platform.
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assessment of the Amphora spectrum in a rural late la tene settlement at reinach nord basel region switzerland
Journal of Archaeological Science: Reports, 2017Co-Authors: G Thierrinmichael, D Tretola C Martinez, Vincent SerneelsAbstract:Abstract The relatively high quantity of Amphorae among the ceramic material discovered in Late La Tene structures at Reinach-Nord appears quite unusual at a rural settlement of this period in NE Switzerland and warranted further investigation. How does the Amphora spectrum compare to the one of earlier or later sites in the region? On earlier settlements in the area between Lyon, the Upper Rhine Valley and NE Switzerland, we find Italic wine Amphorae from mainly the same few provenances in Etruria (Albinia, Cosa), Northern Campania (Falerne/Mondragone) and Pompeii. On later sites in the same region (especially the Roman colonial towns of Lyon, Augst and Avenches), wine is only one of many commodities imported in Amphorae and those of Italic provenance become rare. Macroscopic classification of the Amphora fabrics, petrographic and chemical analyses by XRF-WDS of 35 samples representative of fabric groups and the comparison with a large database (> 500 analyses from kiln sites, > 500 analyses from consumer sites) reveal basically the typical spectrum known for the region with slight differences to earlier as well as to later sites. These are, in comparison to earlier sites: - a smaller proportion originating from important production sites in Etruria and Northern Campania, no representation of the Pompeii region; - some ascertained imports from Southern Latium; - presence of a non-Italic fabric indicative of Spanish origin (Tarraconnensis). In contrast to later sites, Reinach still shows almost exclusively wine Amphorae mainly of Italic origin and a smaller number of different provenances, comparable to the diversity met on the earlier sites (10–15 groups).
G Thierrinmichael - One of the best experts on this subject based on the ideXlab platform.
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assessment of the Amphora spectrum in a rural late la tene settlement at reinach nord basel region switzerland
Journal of Archaeological Science: Reports, 2017Co-Authors: G Thierrinmichael, D Tretola C Martinez, Vincent SerneelsAbstract:Abstract The relatively high quantity of Amphorae among the ceramic material discovered in Late La Tene structures at Reinach-Nord appears quite unusual at a rural settlement of this period in NE Switzerland and warranted further investigation. How does the Amphora spectrum compare to the one of earlier or later sites in the region? On earlier settlements in the area between Lyon, the Upper Rhine Valley and NE Switzerland, we find Italic wine Amphorae from mainly the same few provenances in Etruria (Albinia, Cosa), Northern Campania (Falerne/Mondragone) and Pompeii. On later sites in the same region (especially the Roman colonial towns of Lyon, Augst and Avenches), wine is only one of many commodities imported in Amphorae and those of Italic provenance become rare. Macroscopic classification of the Amphora fabrics, petrographic and chemical analyses by XRF-WDS of 35 samples representative of fabric groups and the comparison with a large database (> 500 analyses from kiln sites, > 500 analyses from consumer sites) reveal basically the typical spectrum known for the region with slight differences to earlier as well as to later sites. These are, in comparison to earlier sites: - a smaller proportion originating from important production sites in Etruria and Northern Campania, no representation of the Pompeii region; - some ascertained imports from Southern Latium; - presence of a non-Italic fabric indicative of Spanish origin (Tarraconnensis). In contrast to later sites, Reinach still shows almost exclusively wine Amphorae mainly of Italic origin and a smaller number of different provenances, comparable to the diversity met on the earlier sites (10–15 groups).