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

Gary W. Saunders,Tanya E. Moore 한국조류학회I 2013 ALGAE Vol.28 No.1

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.

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

Saunders, Gary W.,Moore, Tanya E. The Korean Society of Phycology 2013 ALGAE Vol.28 No.1

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.

First report of Halopeltis (Rhodophyta, Rhodymeniaceae) from the non-tropical Northern Hemisphere: H. adnata (Okamura) comb. nov. from Korea, and H. pellucida sp. nov. and H. willisii sp. nov. from the North Atlantic

Craig W. Schneider,D. Wilson Freshwater2,Gary W. Saunders 한국조류학회I 2012 ALGAE Vol.27 No.2

Using genetic sequencing (COI-5P, LSU, rbcL) to elucidate their phylogenetic positions and then morphological characters to distinguish each from existing species, three procumbent species, including two novel species, from warm temperate Northern Hemisphere waters are added to the recently resurrected genus Halopeltis J. Agardh: H. adnata (Okamura) comb. nov. from Korea, H. pellucida sp. nov. from Bermuda and H. willisii sp. nov. from North Carolina, USA. Prior to these reports, the genus was confined to the Southern Hemisphere and tropical equatorial waters of the Northern Hemisphere although the latter records lack molecular confirmation. These three additional species join the six known species presently residing in Halopeltis.

First report of Halopeltis (Rhodophyta, Rhodymeniaceae) from the non-tropical Northern Hemisphere: H. adnata (Okamura) comb. nov. from Korea, and H. pellucida sp. nov. and H. willisii sp. nov. from the North Atlantic

Schneider, Craig W.,Freshwater, D. Wilson,Saunders, Gary W. The Korean Society of Phycology 2012 ALGAE Vol.27 No.2

Using genetic sequencing (COI-5P, LSU, $rbc$L) to elucidate their phylogenetic positions and then morphological characters to distinguish each from existing species, three procumbent species, including two novel species, from warm temperate Northern Hemisphere waters are added to the recently resurrected genus $Halopeltis$ J. Agardh: $H.$ $adnata$ (Okamura) comb. nov. from Korea, $H.$ $pellucida$ sp. nov. from Bermuda and $H.$ $willisii$ sp. nov. from North Carolina, USA. Prior to these reports, the genus was confined to the Southern Hemisphere and tropical equatorial waters of the Northern Hemisphere although the latter records lack molecular confirmation. These three additional species join the six known species presently residing in $Halopeltis$.

Taxonomic assessment of North American species of the genera Cumathamnion, Delesseria, Membranoptera and Pantoneura (Delesseriaceae, Rhodophyta) using molecular data

Wynne, Michael J.,Saunders, Gary W. The Korean Society of Phycology 2012 ALGAE Vol.27 No.3

Evidence from molecular data supports the close taxonomic relationship of the two North Pacific species Delesseria decipiens and D. serrulata with Cumathamnion, up to now a monotypic genus known only from northern California, rather than with D. sanguinea, the type of the genus Delesseria and known only from the northeastern North Atlantic. The transfers of D. decipiens and D. serrulata into Cumathamnion are effected. Molecular data also reveal that what has passed as Membranoptera alata in the northwestern North Atlantic is distinct at the species level from northeastern North Atlantic (European) material; M. alata has a type locality in England. Multiple collections of Membranoptera and Pantoneura fabriciana on the North American coast of the North Atlantic prove to be identical for the three markers that have been sequenced, and the name Membranoptera fabriciana (Lyngbye) comb. nov. is proposed for them. Many collections of Membranoptera from the northeastern North Pacific (predominantly British Columbia), although representing the morphologies of several species that have been previously recognized, are genetically assignable to a single group for which the oldest name applicable is M. platyphylla.

Taxonomic assessment of North American species of the genera Cumathamnion, Delesseria, Membranoptera and Pantoneura (Delesseriaceae, Rhodophyta) using molecular data

Michael J. Wynne,Gary W. Saunders 한국조류학회I 2012 ALGAE Vol.27 No.3

Evidence from molecular data supports the close taxonomic relationship of the two North Pacific species Delesseria decipiens and D. serrulata with Cumathamnion, up to now a monotypic genus known only from northern California,rather than with D. sanguinea, the type of the genus Delesseria and known only from the northeastern North Atlantic. The transfers of D. decipiens and D. serrulata into Cumathamnion are effected. Molecular data also reveal that what has passed as Membranoptera alata in the northwestern North Atlantic is distinct at the species level from northeastern North Atlantic (European) material; M. alata has a type locality in England. Multiple collections of Membranoptera and Pantoneura fabriciana on the North American coast of the North Atlantic prove to be identical for the three markers that have been sequenced, and the name Membranoptera fabriciana (Lyngbye) comb. nov. is proposed for them. Many collections of Membranoptera from the northeastern North Pacific (predominantly British Columbia), although representing the morphologies of several species that have been previously recognized, are genetically assignable to a single group for which the oldest name applicable is M. platyphylla.

The phylogeographic history of amphitropical Callophyllis variegata (Florideophyceae, Rhodophyta) in the Pacific Ocean

Bringloe, Trevor T.,Macaya, Erasmo C.,Saunders, Gary W. The Korean Society of Phycology 2019 ALGAE Vol.34 No.2

Chilean species of marine macroalgae with amphitropical distributions oftentimes result from introductions out of the Northern Hemisphere. This possibility was investigated using haplotype data in an amphitropical red macroalgae present in Chile, Callophyllis variegata. Published sequence records from Canada and the United States were supplemented with new collections from Chile (April 2014-November 2015). Specimens of C. variegata were amplified for the 5′ end of the cytochrome c oxidase subunit I gene (COI-5P) and the full length nuclear internal transcribed spacer region. Haplotype networks and biogeographic distributions were used to infer whether C. variegata was introduced between hemispheres, and several population parameters were estimated using IMa2 analyses. C. variegata displayed a natural amphitropical distribution, with an isolation time of approximately 938 ka between hemispheres. It is hypothesized that contemporary populations of C. variegata were established from a refugial population during the late Pleistocene, and may have crossed the tropics via rafting on buoyant species of kelp or along deep-water refugia coincident with global cooling, representing a rare case of a non-human mediated amphitropical distribution.

The phylogeographic history of amphitropical Callophyllis variegata (Florideophyceae, Rhodophyta) in the Pacific Ocean

Trevor T. Bringloe,Erasmo C. Macaya,Gary W. Saunders 한국조류학회I 2019 ALGAE Vol.34 No.2

Chilean species of marine macroalgae with amphitropical distributions oftentimes result from introductions out ofthe Northern Hemisphere. This possibility was investigated using haplotype data in an amphitropical red macroalgaepresent in Chile, Callophyllis variegata. Published sequence records from Canada and the United States were supplementedwith new collections from Chile (April 2014-November 2015). Specimens of C. variegata were amplified for the 5′end of the cytochrome c oxidase subunit I gene (COI-5P) and the full length nuclear internal transcribed spacer region. Haplotype networks and biogeographic distributions were used to infer whether C. variegata was introduced betweenhemispheres, and several population parameters were estimated using IMa2 analyses. C. variegata displayed a naturalamphitropical distribution, with an isolation time of approximately 938 ka between hemispheres. It is hypothesized thatcontemporary populations of C. variegata were established from a refugial population during the late Pleistocene, andmay have crossed the tropics via rafting on buoyant species of kelp or along deep-water refugia coincident with globalcooling, representing a rare case of a non-human mediated amphitropical distribution.

PHYLOGENETIC RELATIONSHIPS AMONG LINEAGES OF THE CERAMIACEAE (CERAMIALES, RHODOPHYTA) BASED ON NUCLEAR SMALL SUBUNIT rDNA SEQUENCE DATA¹

Choi, Han-Gu,Kraft, Gerald T.,Kim, Hyung-Seop,Guiry, Michael D.,Saunders, Gary W. Blackwell Publishing Ltd 2008 Journal of phycology Vol.44 No.4

<P>Phylogenetic relationships among 69 species of the Ceramiales (51 Ceramiaceae, six Dasyaceae, seven Delesseriaceae, and five Rhodomelaceae) were determined based on nuclear SSU rDNA sequence data. We resolved five strongly supported but divergent lineages among the included Ceramiaceae: (i) the genus <I>Inkyuleea</I>, which weakly joins other orders of the Rhodymeniophycidae rather than the Ceramiales in our analyses; (ii) the tribe Spyridieae, which is sister to the remainder of the included ceramialean taxa; (iii) the subfamily Ceramioideae, weakly including the tribe Warrenieae; (iv) the subfamily Callithamnioideae; and (v) the subfamily Compsothamnioideae, which emerges as sister to the Dasyaceae/Delesseriaceae/Rhodomelaceae complex, thus rendering the Ceramiaceae sensu lato unequivocally paraphyletic, as has been argued separately on anatomical grounds by Kylin and Hommersand. Our data support a restricted concept of the Ceramiaceae that includes only one of the five lineages (Ceramioideae) that we have resolved. In addition to failing to ally with the Ceramiales in our molecular analyses, species of <I>Inkyuleea</I> differ substantially from other Ceramiaceae sensu lato in details of pre- and postfertilization development. The genus <I>Inkyuleea</I> is here assigned to the Inkyuleeaceae fam. nov., which we provisionally retain in the Ceramiales. Species of <I>Spyridia</I> also differ from the remaining Ceramiaceae in their postfertilization development, and, in light of our molecular data, the genus <I>Spyridia</I> is assigned to the Spyridiaceae. The Callithamnioideae is strongly monophyletic (100% in all analyses), which, in combination with key anatomical differences, supports elevation to family status for this lineage as the Callithamniaceae. Similarly, the Compsothamnioideae is solidly monophyletic in our molecular trees and has a unique suite of defining anatomical characters that supports family status for a complex that we consider to include the tribes Compsothamnieae, Dasyphileae, Griffithsieae, Monosporeae, Ptiloteae, Spermothamnieae, Sphondylothamnieae, Spongoclonieae, and Wrangelieae, for which the reinstated family name Wrangeliaceae is available.</P>

Intensive land-based production of red and green macroalgae for human consumption in the Pacific Northwest: an evaluation of seasonal growth, yield, nutritional composition, and contaminant levels

Bradley A. Gadberry,John Colt,Desmond Maynard,Diane C. Boratyn,Ken Webb,Ronald B. Johnson,Gary W. Saunders,Richard H. Boyer 한국조류학회I 2018 ALGAE Vol.33 No.1

Turkish towel (Chondracanthus exasperatus), Pacific dulse (Palmaria mollis, also known as Red ribbon seaweed), and sea lettuce (Ulva spp.) were cultivated in a land-based intensive culture system at the Manchester Research Station, USA from August 2013 to September 2014. Macroalgae were grown in tumble-aerated tanks, harvested bimonthly for seasonal growth calculations, and analyzed for protein, lipid, ash, and amino acid content. Growth rate of all three species exhibited a similar pattern, with the highest specific growth rates occurring during the summer months (Turkish towel: 7.8%, Pacific dulse: 8.2%, and sea lettuce: 6.2%). Growth of all three species was lowest around winter solstice; with negative growth only observed in sea lettuce. On a dry weight basis significant differences in protein content existed between the three species with highest values for sea lettuce (29.5 ± 1.4%). Lipid content varied between species (0.95-2.78%) with significantly higher lipid observed in sea lettuce (0.58-4.82%). No significant differences were detected on a seasonal basis among each species. Essential amino acids accounted for 43 ± 0.9 to 47 ± 1.2% of total amino acids with Turkish towel having the highest value. Turkish towel had a significantly higher taurine level (0.82 ± 0.27) than the other macroalgae. The levels of persistent organic pollutants and heavy metals were low. The estimated annual product of the three species ranged from 50- to 70-mt dry weight ha-1 y-1, significantly higher than conventional crops. Land-based culture of these species can produce year-round harvest, consistent product quality, and low contaminant levels.