A molecular investigation of the systematic relationships of Sirodotia species (Batrachospermales, Rhodophyta) in North America

Vis, Morgan L.; Sheath, Robert G.

doi:10.2216/i0031-8884-38-4-261.1

Cited by 36 publications

(37 citation statements)

References 8 publications

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“…9). We have also developed an M13 linked reverse primer (RUr), but typically find that our modification of Vis and Sheath's (1999) rbcL R' (rbcLrevNEW) works for most red algae (Fig. 9).…”

Section: Ribulose-15-bisphosphate Carboxylase Large Subunit (Rbcl ~mentioning

confidence: 99%

Refinements for the amplification and sequencing of red algal DNA barcode and RedToL phylogenetic markers: a summary of current primers, profiles and strategies

Saunders¹,

Moore²

2013

ALGAE

196

123

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This review provides a comprehensive summary of the PCR primers and profiles currently in use in our laboratory for red algal DNA barcoding and phylogenetic research. While work focuses on florideophyte taxa, many of the markers have been applied successfully to the Bangiales, as well as other lineages previously assigned to the Bangiophyceae sensu lato. All of the primers currently in use with their respective amplification profiles and strategies are provided, which can include full fragment, overlapping fragments and what might best be called "informed overlapping fragments", i.e., a fragment for a marker is amplified and sequenced for a taxon and those sequence data are then used to identify the best primers to amplify the remaining fragment(s) for that marker. We extend this strategy for the more variable markers with sequence from the external PCR primers used to "inform" the selection of internal sequencing primers. This summary will hopefully serve as a useful resource to systematists in the red algal community.Key Words: DNA barcode; Florideophyceae; molecular markers; phylogeny; polymerase chain reaction; primers; RedToL INTRODUCTIONThere can be little question that molecular techniques have radically altered the face of phycological research especially in the fields of biodiversity and systematics (Maggs et al. 2007). Whereas in the early years researchers focused strongly on two commonly used markers, viz., the plastid rbcL ) and the nuclear small subunit rDNA (Bird et al. 1992, Ragan et al. 1994, Saunders and Kraft 1994, a number of alternative markers have been developed for use with red algae from the population to the highest taxonomic levels (see Maggs et al. 2007, Table 6.1, for a list). Of particular importance in this regard have been the recent large-scale DNA barcoding (iBOL: http://ibol.org) (Saunders 2005) and Red Algal Tree of Life initiatives (RedToL: http://dblab.rutgers.edu/ redtol/) (Vis et al. 2010). Both of these projects target a broader and more comprehensive taxonomic sampling than previous initiatives, challenging researchers to develop more universal amplification strategies for markers (e.g., Saunders and McDevit 2012). Not even widely used markers such as the nuclear SSU and large subunit rDNA (Harper and Saunders 2001b) or the plastid rbcL ) have weathered these global initiatives without the need for refinement.In this review, we focus strictly on the primers, profiles and strategies for the PCR amplification of markers currently in use in our lab (for a review of current collection and DNA extraction protocols see Saunders and McDevit 2012). Being partners in both the DNA barcode and Red- Received February 5, 2013, Accepted February 26, 2013 *Corresponding Author E-mail: gws@unb.ca Tel: This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work i...

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“…9). We have also developed an M13 linked reverse primer (RUr), but typically find that our modification of Vis and Sheath's (1999) rbcL R' (rbcLrevNEW) works for most red algae (Fig. 9).…”

Section: Ribulose-15-bisphosphate Carboxylase Large Subunit (Rbcl ~mentioning

confidence: 99%

Refinements for the amplification and sequencing of red algal DNA barcode and RedToL phylogenetic markers: a summary of current primers, profiles and strategies

Saunders¹,

Moore²

2013

ALGAE

196

123

View full text Add to dashboard Cite

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“…Vis & Sheath (1999) analysed S. suecica, S. tenuissima and S. huillensis from a few sites in North America and determined S. tenuissima to be synonymous with S. suecica, but S. huillensis to be a distinct species. A study of the Batrachospermales in Australia revealed a single sample of S. suecica from that continent showed little sequence divergence from North American specimens, potentially suggesting it may be more readily dispersed than previously thought (Vis & Entwisle, 2000).…”

Section: Introductionmentioning

confidence: 99%

Circumscription of species in the genusSirodotia(Batrachospermales, Rhodophyta) based on molecular and morphological data

Lam

Entwisle

Eloranta³

et al. 2012

European Journal of Phycology

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Species level taxonomy and phylogeographical distribution patterns in the freshwater rhodophyte Sirodotia are resolved through phylogenetic inferences based on rbcL and cox2-3 sequence data. Previous studies focused on the taxonomy of specific Sirodotia species or the distributions across a limited geographical region. Our molecular phylogenies included samples attributable to five recognized Sirodotia species and include collections from Australia, Brazil, Costa Rica, Canada, Finland, Mexico, New Zealand, South Africa and the United States. Both rbcL and cox2-3 phylogenies inferred S. suecica, S. tenuissima and S. goebelii as a monophyletic group with little sequence divergence. This result supports the synonymy of S. tenuissima and S. goebelii with S. suecica (the species name with priority). Within this clade, samples collected from Australia and New Zealand formed a monophyletic group with no other discernible phylogeographical patterns within S. suecica. This result seems to be somewhat unusual in the Batrachospermales, as other species have shown greater genetic variation among geographically distant locations. As in previous studies, S. huillensis and S. delicatula were inferred as a separate species based on the rbcL phylogeny, supporting the current taxonomy. A specimen of S. aff. huillensis from South Africa, may represent a new species but further research is necessary before it can be designated as such.

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“…In very fast current, thalli are dense almost without distinct whorls, whereas in moderate current species occurs as 'typical' form. According to the mo lecular analyses, all these forms are ecotypes with very similar sequence data (Vis & shEath 1999;lam et al 2012). Typical features for Sirodotia suecica are car pogonium with hemispherical protuberance, and inde finite carposporophytes with carposporohyte filaments creeping along cortical filaments.…”

Section: Taxonomical Notesmentioning

confidence: 92%

Intensive study of freshwater red algae (Rhodophyta) in Finland

Eloranta¹,

Eloranta²,

Perämäki³

2016

Fottea

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Abstract:Freshwater red algae (Rhodophyta) were studied in Central Finland by examining 2224 rivers and brooks during the open water periods of the years 2012-2015 with supplementary sampling in S-and SWFinland, the W-coast rivers and Lapland. A total of 1957 records of algae were made. Approximately 56.2% of the studied locations had 1-6 taxa. The total taxa collected were 25, with 5 taxa new to Finland. While sampling, ecological variables were recorded and measured. The most common taxa were Batrachospermum gelatinosum (37.0%), Sheathia arcuata (10.7%), Audouinella hermannii (11.2%) and Sirodotia suecica (7.0%). Lemanea spp. (9.9%) occurred in larger rivers. Most records were from July and August, but some also in winter months. From the most rare taxa, Lemanea condensata was found in Lapland rivers, Batrachospermum vogesiacum in acid, dystrophic rivers in Central Finland, B. atrum in 7 eutrophic rivers, Kumanoa globospora in 6 rivers of Central Finland, Batrachospermum elegans in 6 and K. virgatodecaisneana in 5 harder-water rivers of SW-Finland.

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A molecular investigation of the systematic relationships of Sirodotia species (Batrachospermales, Rhodophyta) in North America

Cited by 36 publications

References 8 publications

Refinements for the amplification and sequencing of red algal DNA barcode and RedToL phylogenetic markers: a summary of current primers, profiles and strategies

Refinements for the amplification and sequencing of red algal DNA barcode and RedToL phylogenetic markers: a summary of current primers, profiles and strategies

Circumscription of species in the genusSirodotia(Batrachospermales, Rhodophyta) based on molecular and morphological data

Intensive study of freshwater red algae (Rhodophyta) in Finland

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