Appendix A. Location of field sites in Strangford Lough, Northern Ireland.

Location of field sites in Strangford Lough, Northern Ireland

Appendix B. Artificial stabilization treatments showing maerl tied to plastic mesh.

Artificial stabilization treatments showing maerl tied to plastic mesh

Advancing the taxonomy of economically important red seaweeds (Rhodophyta)

<p>The cultivation of red seaweeds for food (nori), agar and carrageenans is the basis of a valuable industry. However, taxonomic knowledge of these cultivated seaweeds and their wild relatives has not kept pace with advances in molecular systematics despite the fundamental importance of being able to identify commercially important species and strains, discover cryptic and endemic taxa and recognize non-native species with potentially damaging diseases and epiphytes. This review focuses on molecular taxonomic advances in the cultivated red algae with the highest commercial value globally: <i>Eucheuma</i> and <i>Kappaphycus, Porphyra sensu lato</i> and <i>Gracilaria</i>. All three groups are similarly taxonomically challenging: speciose, morphologically plastic, with poorly resolved species boundaries. <i>Eucheuma</i> and <i>Kappaphycus</i> are frequently misidentified and the molecular markers <i>cox</i>2-3 spacer, <i>cox</i>1 and RuBisCO spacer have helped in understanding phylogenetic relationships and identifying new species and haplotypes. In <i>Porphyra sensu lato</i> (Bangiales) species identification and phylogenetic relationships were highly problematic until a taxonomic revision based on a two-gene phylogeny (18S and <i>rbc</i>L) resulted in nine genera of bladed species. <i>Pyropia</i>, with at least 89 species, three in nori cultivation, has potential for new commercial evaluation. In <i>Gracilaria sensu lato</i>, earlier efforts to resolve species-level taxonomy and generic descriptions were superseded by application of molecular tools, including DNA sequences of the RuBisCO spacer, <i>rbc</i>L gene, 18S and the ITS region. Studies of these cultivated red algal genera highlight the need for a robust taxonomy, a more standardized approach to the molecular markers used and a comprehensive dataset for each representative species. Current work on DNA-based species delimitation, the emergence of high throughput sequencing, multi-gene phylogenies, publication of whole genomes (e.g. <i>Porphyra umbilicalis</i>) and genomes in the pipeline (e.g. <i>Gracilaria</i>) are increasingly improving our understanding of phylogenomic relationships and species relationships. This knowledge, in turn, can then be applied to improving red seaweed aquaculture.</p

The genera <i>Melanothamnus</i> Bornet & Falkenberg and <i>Vertebrata</i> S.F. Gray constitute well-defined clades of the red algal tribe Polysiphonieae (Rhodomelaceae, Ceramiales)

<p><i>Polysiphonia</i> is the largest genus of red algae, and several schemes subdividing it into smaller taxa have been proposed since its original description. Most of these proposals were not generally accepted, and currently the tribe Polysiphonieae consists of the large genus <i>Polysiphonia</i> (190 species), the segregate genus <i>Neosiphonia</i> (43 species) and 13 smaller genera (< 10 species each). In this paper, phylogenetic relationships of the tribe Polysiphonieae are analysed, with particular emphasis on the genera <i>Carradoriella, Fernandosiphonia, Melanothamnus, Neosiphonia, Polysiphonia sensu stricto</i>, <i>Streblocladia</i> and <i>Vertebrata</i>. We evaluated the consistency of 14 selected morphological characters in the identified clades. Based on molecular phylogenetic (<i>rbc</i>L and 18S genes) and morphological evidence, two speciose genera are recognized: <i>Vertebrata</i> (including the type species of the genera <i>Ctenosiphonia, Enelittosiphonia, Boergeseniella</i> and <i>Brongniartella</i>) and <i>Melanothamnus</i> (including the type species of the genera <i>Fernandosiphonia</i> and <i>Neosiphonia</i>). Both genera are distinguished from other members of the Polysiphonieae by synapomorphic characters, the emergence of which could have provided evolutionarily selective advantages for these two lineages. In <i>Vertebrata</i> trichoblast cells are multinucleate, possibly associated with the development of extraordinarily long photoprotective trichoblasts. <i>Melanothamnus</i> has 3-celled carpogonial branches and plastids lying exclusively on radial walls of the pericentral cells, which similarly may improve resistance to damage caused by excessive light. Other relevant characters that are constant in each genus are also shared with other clades. The evolutionary origin of the genera <i>Melanothamnus</i> and <i>Vertebrata</i> is estimated as 75.7–95.78 and 90.7–138.66 Ma, respectively. Despite arising in the Cretaceous, before the closure of the Tethys Seaway, <i>Melanothamnus</i> is a predominantly Indo-Pacific genus and its near-absence from the north-eastern Atlantic is enigmatic. The nomenclatural implications of this work are that 46 species are here transferred to <i>Melanothamnus</i>, six species are transferred to <i>Vertebrata</i>, and 13 names are resurrected for <i>Vertebrata</i>.</p