Cystoseira sensu lato (s.l.) – encompassing the genera Cystoseira sensu stricto (s.s.), Ericaria and Gongolaria – is a diverse group of forest-forming brown macroalgae endemic to the warm-temperate North-east Atlantic. These algae have immense biogeographic and ecological significance and have been experiencing recent regional declines. Most Cystoseira s.l. display important morphological plasticity and can be confused with similar species. Therefore, species boundaries, geographic ranges and phylogenetic affinities remain imprecise for most. In the face of persistent taxonomic difficulties, several authors underlined the necessity for new molecular-based approaches, but studies so far lacked representativity, resolution and standardization. To fill in these gaps, in this study we sequenced a comprehensive collection of Cystoseira s.l. spanning its entire North-east Atlantic range for a ~1200 bp cox1 barcode, and sequenced selected individuals representing major genetic entities for a few additional plastid markers. Phylogeographic, phylogenetic and species delimitation methods revealed 27 Molecular Operational Taxonomic Units, including unaccounted cryptic diversity, and elucidated with unprecedented resolution species compositions and phylogenetic relationships within each genus. Some entities within the lineages Cystoseira compressa/humilis, Ericaria brachycarpa/crinita, E. selaginoides and tophulose Gongolaria, as well as among free-living algae, conflicted with a priori taxonomic assignments, and required the redefinition, reinstatement and recognition of new taxa. For some, diagnostic mutations and biogeography were more useful for species identifications than morphological characters or conventional barcoding gaps. A few species showed narrow geographic ranges and others were the sole representatives of their respective lineages. Several sister-species showed Atlantic vs Mediterranean complementary ranges. Phylogenetic signal of cox1 was nevertheless insufficient to confidently determine patterns of lineage splitting in several lineages and species complexes and did not improve significantly with additional plastid markers. We discuss novel systematics and biogeography insights considering the advantages and shortcomings of the barcoding approach employed, and how this comprehensive baseline study can be expanded to address multiple questions still left unanswered. HIGHLIGHTS

The macroalgal flora of Graciosa (central group of Azores archipelago) is poorly known, with only 116 species recorded so far (authors personal data). The published information reflects occasional collections from sporadic field visits to the Island. To overcome this, a thorough investigation under the Expedition “GRACIOSA/2004”, the Campaigns “PADEL/2006”, “MACROBIOLMOL/2014” and “PIMA-BALA/2017” involving sample collecting and presence data recording, was undertaken over an area of 19 km² encompassing littoral and sublittoral levels down to about 40 m around the Island. This paper lists the taxonomic records and provides information on species ecology and occurrence around the Island improving the knowledge of the Azorean macroalgal flora at both local and regional scales. A total of 1692 specimens belonging to 250 taxa of macroalgae (and including 55 taxa identified only at the genus level) are registered, comprising 166 Rhodophyta, 36 Chlorophyta and 48 Ochrophyta (Phaeophyceae). From these, 195 are identified to the species level (126 Rhodophyta, 31 Chlorophyta and 38 Ochrophyta) and comprise 156 native, 20 of uncertain origin and 14 introductions to the Island. Predaea feldmannii subsp. azorica Gabriel is an Azorean endemic, whereas Codium elisabethiae O.C. Schmidt, Botryocladia macaronesica Afonso-Carrillo, Sobrino, Tittley & Neto, Phyllophora gelidioides P.Crouan & H.Crouan ex Karsakoff and Laurencia viridis Gil-Rodríguez & Haroun represent Macaronesian endemics. Seventy-nine species are newly recorded to the algal flora of the Island.

The macroalgal flora of the Island of São Miguel (eastern group of the Azores Archipelago) has attracted the interest of many researchers in the past, the first publications going back to the nineteenth century. Initial studies were mainly taxonomic, resulting in the publication of a checklist of the Azorean benthic marine algae. Later, the establishment of the University of the Azores on the Island permitted the logistic conditions to develop both temporal studies and long-term research and this resulted in a significant increase on research directed at the benthic marine algae and littoral communities of the Island and consequent publications. Prior to the present paper, the known macroalgal flora of São Miguel Island comprised around 260 species. Despite this richness, a significant amount of the research was never made public, notably Masters and PhD theses encompassing information regarding presence data recorded at littoral and sublittoral levels down to a depth of approximately 40 m around the Island and the many collections made, which resulted in vouchers deposited in the AZB Herbarium Ruy Telles Palhinha and the LSM- Molecular Systematics Laboratory at the Faculty of Sciences and Technology of the University of the Azores. The present publication lists the macroalgal taxonomic records, together with information on their ecology and occurrence around São Miguel Island, improving the knowledge of the Azorean macroalgal flora at local and regional scales. A total of 12,781 specimens (including some identified only to genus) belonging to 431 taxa of macroalgae are registered, comprising 284 Rhodophyta, 59 Chlorophyta and 88 Ochrophyta (Phaeophyceae). Of these, 323 were identified to species level (212 Rhodophyta, 48 Chlorophyta and 63 Ochrophyta), of which 61 are new records for the Island (42 Rhodophyta, 9 Chlorophyta and 10 Ochrophyta), one an Azorean endemic (Predaea feldmannii subsp. azorica Gabriel), five are Macaronesian endemisms (the red algae Botryocladia macaronesica Afonso-Carrillo, Sobrino, Tittley & Neto, Laurencia viridis Gil-Rodríguez & Haroun, Millerella tinerfensis (Seoane-Camba) S.M.Boo & J.M.Rico, Phyllophora gelidioides P.Crouan & H.Crouan ex Karsakoff and the green alga Codium elisabethiae O.C.Schmidt), 19 are introduced species (15 Rhodophyta, two Chlorophyta and two Ochrophyta) and 32 are of uncertain status (21 Rhodophyta, five Chlorophyta and six Ochrophyta).

The algal flora of the Island of Santa Maria (eastern group of the Azores archipelago) has attracted interest of researchers on past occasions (Drouët 1866, Agardh 1870, Trelease 1897, Schmidt 1931, Ardré et al. 1974, Fralick and Hehre 1990, Neto et al. 1991, Morton and Britton 2000, Amen et al. 2005, Wallenstein and Neto 2006, Tittley et al. 2009, Wallenstein et al. 2009a, Wallenstein et al. 2010, Botelho et al. 2010, Torres et al. 2010, León-Cisneros et al. 2011, Martins et al. 2014, Micael et al. 2014, Rebelo et al. 2014, Ávila et al. 2015, Ávila et al. 2016, Machín-Sánchez et al. 2016, Uchman et al. 2016, Johnson et al. 2017, Parente et al. 2018). Nevertheless, the Island macroalgal flora is not well-known as published information reflects limited collections obtained in short-term visits by scientists. To overcome this, a thorough investigation, encompassing collections and presence data recording, was undertaken at both the littoral and sublittoral levels down to a depth of approximately 40 m, covering an area of approximately 64 km². The resultant taxonomic records are listed in the present paper which also provides information on species ecology and occurrence around the Island, improving, thereby, the knowledge of the Azorean macroalgal flora at both local and regional scales. A total of 2329 specimens (including some taxa identified only to genus level) belonging to 261 taxa of macroalgae are registered, comprising 152 Rhodophyta, 43 Chlorophyta and 66 Ochrophyta (Phaeophyceae). Of these, 174 were identified to species level (102 Rhodophyta, 29 Chlorophyta and 43 Ochrophyta), encompassing 52 new records for the Island (30 Rhodophyta, 9 Chlorophyta and 13 Ochrophyta), 2 Macaronesian endemics (Laurencia viridis Gil-Rodríguez & Haroun; and Millerella tinerfensis (Seoane-Camba) S.M.Boo & J.M.Rico), 10 introduced (the Rhodophyta Acrothamnion preissii (Sonder) E.M.Wollaston, Antithamnion hubbsii E.Y.Dawson, Asparagopsis armata Harvey, Bonnemaisonia hamifera Hariot, Melanothamnus harveyi (Bailey) Díaz-Tapia & Maggs, Scinaia acuta M.J.Wynne and Symphyocladia marchantioides (Harvey) Falkenberg; the Chlorophyta Codium fragile subsp. fragile (Suringar) Hariot; and the Ochrophyta Hydroclathrus tilesii (Endlicher) Santiañez & M.J.Wynne, and Papenfussiella kuromo (Yendo) Inagaki) and 18 species of uncertain status (11 Rhodophyta, 3 Chlorophyta and 4 Ochrophyta).

The algal flora of the western group of the Azores archipelago (Islands of Flores and Corvo) has attracted the interest of many researchers on numerous past occasions (such as Drouet 1866, Trelease 1897, Gain 1914, Schmidt 1929, Schmidt 1931, Azevedo et al. 1990, Fralick and Hehre 1990, Neto and Azevedo 1990, Neto and Baldwin 1990, Neto 1996, Neto 1997, Neto 1999, Tittley and Neto 1996, Tittley and Neto 2000, Tittley and Neto 2005, Tittley and Neto 2006, Azevedo 1998, Azevedo 1999, Tittley et al. 1998, Dionísio et al. 2008, Neto et al. 2008). Despite this interest, the macroalgal flora of the Islands cannot be described as well-known with the published information reflecting limited collections preformed in short-term visits by scientists. To overcome this, a thorough investigation, encompassing collections and presence data recording, has been undertaken for both the littoral and sublittoral regions, down to a depth of approximately 40 m, covering a relatively large area on both Islands (approximately 143 km² for Flores and 17 km² for Corvo). This paper lists the resultant taxonomic records and provides information on species ecology and occurrence around both these Islands, thereby improving the knowledge of the Azorean macroalgal flora at both local and regional scales. For the Island of Flores, a total of 1687 specimens (including some taxa identified only to genus level) belonging to 196 taxa of macroalgae are registered, comprising 120 Rhodophyta, 35 Chlorophyta and 41 Ochrophyta (Phaeophyceae). Of these taxa, 128 were identified to species level (80 Rhodophyta, 22 Chlorophyta and 26 Ochrophyta), encompassing 37 new records for the Island (20 Rhodophyta, 6 Chlorophyta and 11 Ochrophyta); two Macaronesian endemics (Laurencia viridis Gil-Rodríguez & Haroun and Millerella tinerfensis (Seoane-Camba) S.M.Boo & J.M.Rico); six introduced (the Rhodophyta Asparagopsis armata Harvey, Neoizziella divaricata (C.K.Tseng) S.-M.Lin, S.-Y.Yang & Huisman and Symphyocladia marchantioides (Harvey) Falkenberg; the Chlorophyta Codium fragile subsp. fragile (Suringar) Hariot; and the Ochrophyta Hydroclathrus tilesii (Endlicher) Santiañez & M.J.Wynne and Papenfussiella kuromo (Yendo) Inagaki); and 14 species of uncertain status (10 Rhodophyta, two Chlorophyta and two Ochrophyta). For the Island of Corvo, a total of 390 specimens distributed in 56 taxa of macroalgae are registered, comprising 30 Rhodophyta, nine Chlorophyta and 17 Ochrophyta (Phaeophyceae). Whilst a number of taxa were identified only to the genus level, 43 were identified to species level (22 Rhodophyta, eight Chlorophyta and 13 Ochrophyta), comprising 22 new records for the Island (nine Rhodophyta, four Chlorophyta and nine Ochrophyta), two introduced species (the Rhodophyta Asparagopsis armata and the Chlorophyta Codium fragile subsp. fragile and seven species of uncertain status (five Rhodophyta and two Ochrophyta).