Molecular systematics of Crassiphycus and Hydropuntia (Gracilariales, Rhodophyta) with the description of poorly known taxa in the Western Atlantic Ocean

References

• Abbott, I.A., Zhang, J. & Xia, B. (1991). Gracilaria mixta sp. nov. and other western Pacific species of the genus (Rhodophyta, Gracilariaceae). Pacific Science, 45: 12–27.
   Google Scholar
• Agardh, J.G. (1852). Species Genera et Ordines Algarum … Vol. 2, pt. 3, fasc. 1, 701–786. Lund.
   Google Scholar
• Aguirre, J., Riding, R. & Braga, J.C. (2000). Late Cretaceous incident light reduction: evidence from benthic algae. Lethaia, 33: 205–213.
   Web of Science ®Google Scholar
• Ardito, S.M., Sentíes, A. & Dreckmann, K.M. (2014). Caracterización morfoanatómica de Hydropuntia usneoides (Gracilariaceae, Rhodophyta) para la costa venezolana. Interciencia, 39: 49–53.
   Google Scholar
• Ayres‐Ostrock, L.M., Valero, M., Mauger, S., Oliveira, M.C., Plastino, E.M., Guillemin, M.L. & Destombe, C. (2019). Dual influence of terrestrial and marine historical processes on the phylogeography of the Brazilian intertidal red alga Gracilaria caudata. Journal of Phycology, 55: 1096–1114.
   PubMed Web of Science ®Google Scholar
• Bellorin, A.M., Oliveira, M.C. & Oliveira, E.C. (2002). Phylogeny and systematics of the marine algal family Gracilariaceae (Gracilariales, Rhodophyta) based on small subunit rDNA and ITS sequences of Atlantic and Pacific species. Journal of Phycology, 38: 551–563.
   Web of Science ®Google Scholar
• Bird, C.J., Oliveira, E.C. & McLachlan, J. (1986). Gracilaria cornea, the correct name for the western Atlantic alga hitherto known as G. debilis (Rhodophyta, Gigartinales). Canadian Journal of Botany, 64: 2045–2051.
   Google Scholar
• Børgesen, F. (1920). The Marine Algae of the Danish West Indies, Pt. 3. Rhodophyceae (6) with addenda to the Chlorophyceae, Phaeophyceae and Rhodophyceae. Dansk Botanisk Arkiv, 4: 14–35.
   Google Scholar
• Bouckaert, R., Vaughan, T.G., Barido-Sottani, J., Duchêne, S., Fourment, M., Gavryushkina, A., Heled, J., Jones, G., Kühnert, D., De Maio, N., Matschiner, M., Mendes, F.K., Müller, N.F., Ogilvie, H.A., du Plessis, L., Popinga, A., Rambaut, A., Rasmussen, D., Siveroni, I., Suchard, M.A., Wu, C.-H., Xie, D., Zhang, C., Stadler, T. & Drummond, A.J. (2019). BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLOS Computational Biology 15: e1006650.
   PubMed Web of Science ®Google Scholar
• Carvalho-Filho, A., Santos, S. & Sampaio, I. (2010). Macrodon atricauda (Günther, 1880) (Perciformes: Sciaenidae), a valid species from the southwestern Atlantic, with comments on its conservation. Zootaxa, 2519: 48–58.
   Google Scholar
• Chang, C.F. & Xia, B.-M. (1963). Polycavernosa, a new genus of the Gracilariaceae. Studia Marina Sinica, 3: 120–126.
   Google Scholar
• Darriba, D., Taboada, G.L., Doallo, R. & Posada, D. (2012). jModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9: 772, https://doi.org/10.1038/nmeth.2109.
   PubMed Web of Science ®Google Scholar
• Du, Q., Bi, G., Mao, Y. & Sui, Z. (2016). The complete chloroplast genome of Gracilariopsis lemaneiformis (Rhodophyta) gives new insight into the evolution of family Gracilariaceae. Journal of Phycology, 52: 441–450.
   PubMed Web of Science ®Google Scholar
• Duchêne, S., Lanfear, R. & Ho, S.Y. (2014). The impact of calibration and clock-model choice on molecular estimates of divergence times. Molecular Phylogenetics and Evolution, 78: 277–289.
   PubMed Web of Science ®Google Scholar
• Floeter, S.R., Guimarães, R.Z., Rocha, L.A., Ferreira, C.E., Rangel, C.A. & Gasparini, J.L. (2001). Geographic variation in reef‐fish assemblages along the Brazilian coast. Global Ecology and Biogeography 10: 423–431.
   Web of Science ®Google Scholar
• Fox, M. (1957). A first list of marine algae from Nigeria. Botanical Journal of the Linnean Society, 55: 615–631.
   Google Scholar
• Fredericq, S. & Hommersand, M.H. (1989). Proposal of the Gracilariales, ord. nov. (Rhodophyta) based on an analysis of the reproductive development of Gracilaria verrucosa. Journal of Phycology, 25: 213–227.
   Web of Science ®Google Scholar
• Fredericq, S. & Hommersand, M.H. (1990). Diagnoses and key to the genera of the Gracilariaceae (Gracilariales, Rhodophyta). Hydrobiologia, 204/205: 173–178.
   Web of Science ®Google Scholar
• Fredericq, S. & Norris, J.N. (1985). Morphological studies on some tropical species of Gracilaria Grev. (Gracilariaceae, Rhodophyta): taxonomic concepts based on reproductive morphology. In Taxonomy of Economic Seaweeds, Vol. I. (Abbott, I.A. & Norris, J.N., editors), 137–155. California Sea Grant College Program, Univ. Calif. La Jolla.
   Google Scholar
• Freshwater, D.W. & Rueness, J. (1994). Phylogenetic relationships of some European Gelidium (Gelidiales, Rhodophyta) species based on rbcL nucleotide sequence analysis. Phycologia, 33: 187–94.
   Web of Science ®Google Scholar
• Greville, R.K. (1830). Algae Britannicae, or descriptions of the marine and other inarticulated plants of the British Islands, belonging to the order Algae; with plates illustrative of the genera. Edinburgh: MacLachlan & Stewart; Baldwin & Cradock, [iii]+lxxxviii+218 pp., XIX pls.
   Google Scholar
• Guimarães, M., Plastino, E.M. & Destombe, C. (2003). Green mutant frequency in natural populations of Gracilaria domingensis (Gracilariales, Rhodophyta) from Brazil. European Journal of Phycology, 38: 165–169.
   Web of Science ®Google Scholar
• Guiry, M.D., Norris, J.N., Fredericq, S. & Gurgel, C.F.D. (2018). Crassiphycus Guiry, Gurgel, J.N.Norris & Fredericq, gen. nov., a replacement name for Crassa Gurgel, J.N.Norris & Fredericq, nom. inval. (Gracilariaceae, Rhodophyta), with some additional nomenclatural notes. Notulae Algarum, 82: 1–4.
   Google Scholar
• Gurgel, C.F.D. (2017). Gracilariales. In Syllabus of Plant Families (2/2) Rhodobionta (A. Engler’s Syllabus der Pflanzenfamilien series) (Frey, W., editor). Borntraeger-Cramer Publisher, Stuttgart.
   Google Scholar
• Gurgel, C.F.D. & Fredericq, S. (2004). Systematics of the Gracilariaceae (Gracilariales, Rhodophyta): a critical assessment based on rbcL sequence analysis. Journal of Phycology, 40: 138–159.
   Web of Science ®Google Scholar
• Gurgel, C.F.D., Fredericq, S. & Norris, J.N. (2004). Phylogeography of Gracilaria tikvahiae (Gracilariaceae, Rhodophyta): a study of genetic discontinuity in a continuously distributed species based on molecular evidence. Journal of Phycology, 40: 748–758.
   Web of Science ®Google Scholar
• Gurgel, C.F.D., Fredericq, S., Norris, J.N. & Yoneshigue-Valentin, Y. (2008). Two new flat species of Gracilaria (Gracilariales, Rhodophyta) from Brazil: G. abyssalis sp. nov. and G. brasiliensis sp. nov. Phycologia, 47: 249–264.
   Web of Science ®Google Scholar
• Gurgel, C.F.D., Norris, J.N., Schmidt, W.E., Le, H.N. & Fredericq, S. (2018). Systematics of the Gracilariales (Rhodophyta) including new subfamilies, tribes, subgenera and two new genera, Agarophyton gen. nov. and Crassa gen. nov. Phytotaxa, 374: 1–23.
   Web of Science ®Google Scholar
• Heled, J. & Drummond, A.J. (2011). Calibrated tree priors for relaxed phylogenetics and divergence time estimation. Systematic Biology, 61: 138–149.
   PubMed Web of Science ®Google Scholar
• Hommersand, M.H. (1990). Biogeography of the marine red algae of the North Atlantic Ocean. In Evolutionary Biogeography of the Marine Algae of the North Atlantic, 349–410. Springer, Berlin.
   Google Scholar
• Iha, C., Grassa, C.J., Lyra, G.M., Davis, C.C., Verbruggen, H. & Oliveira, M.C. (2018). Organellar genomics: a useful tool to study the evolutionary relationships and molecular evolution in Gracilariaceae (Rhodophyta). Journal of Phycology, 54: 775–787.
   PubMed Web of Science ®Google Scholar
• Jablonski, D. & Raup, D.M. (1995). Selectivity of end-Cretaceous marine bivalve extinctions. Science, 268: 389–391.
   PubMed Web of Science ®Google Scholar
• Kim, M.S., Yang, E.C. & Boo, S.M. (2006). Taxonomy and phylogeny of flattened species of Gracilaria (Gracilariaceae, Rhodophyta) from Korea based on morphology and protein-coding plastid rbcL and psbA sequences. Phycologia, 45: 520–528.
   Web of Science ®Google Scholar
• Kylin, H. (1956). Die Gattungen der Rhodophyceen. C.W.K. Gleerups, Lund, XV+673 pp.
   Google Scholar
• Lawson, G.W. & John, D.M. (1982). The marine algae and coastal environment of tropical West Africa. Nova Hedwigia, 70: 1–455.
   Google Scholar
• Leliaert, F., Payo, D.A., Gurgel, C.F.D., Schils, T., Draisma, S.G., Saunders, G.W., (…) & Le Gall, L. (2018). Patterns and drivers of species diversity in the Indo‐Pacific red seaweed Portieria. Journal of Biogeography, 45: 2299–2313.
   Web of Science ®Google Scholar
• Lin, S.M., Fredericq, S. & Hommersand, M.H. (2001). Systematics of the Delesseriaceae (Ceramiales, Rhodophyta) based on LSU rDNA and rbcL sequences, including the Phycodroideae, subfam. nov. Journal of Phycology, 37: 881–899.
   Web of Science ®Google Scholar
• Lyra, G.M., Costa, E.S., De Jesus, P.B., De Matos, J.C.G., Caires, T.A., Oliveira, M.C., Oliveira, E.C., Xi, Z., Nunes, J.M.C & Davis, C.C. (2015). Phylogeny of Gracilariaceae (Rhodophyta): evidence from plastid and mitochondrial nucleotide sequences. Journal of Phycology, 51: 356–366.
   PubMed Web of Science ®Google Scholar
• Lyra, G.M., Gurgel, C.F.D., Costa, E.S., Jesus, P.B., Oliveira, M.C., Oliveira, E.C., Davis, C.C. & Nunes, J.M.C. (2016). Delimitating cryptic species in the Gracilaria domingensis complex (Gracilariaceae, Rhodophyta) using morphological and molecular data. Journal of Phycology, 52: 997–1017.
   PubMed Web of Science ®Google Scholar
• Miller, M.A., Pfeiffer, W. & Schwartz, T. (2010). Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In Proceedings of the Gateway Computing Environments Workshop (GCE), 1–8. 14 Nov. 2010, New Orleans, LA.
   Google Scholar
• Montagne, C. (1842). Prodromus generum specierumque phycearum novarum …, [1]–16. Gide, Paris.
   Google Scholar
• Nan, F., Feng, J., Lv, J., Liu, Q., Fang, K., Gong, C. & Xie, S. (2017). Origin and evolutionary history of freshwater Rhodophyta: further insights based on phylogenomic evidence. Scientific Reports, 7: 1–12.
   PubMed Web of Science ®Google Scholar
• Ng, P.-K. (2019). Molecular data complement morphological observations in the systematics of Gracilariaceae. In Taxonomy of Southeastern Asian Seaweeds (Phang, S.-M., Song, S.-L. & Lim, P.-E., editors), Institute of Ocean & Earth Sciences, University of Malaya, Monograph Series, 17: 93–113.
   Google Scholar
• Ng, P.-K., Lin, S.-M., Lim, P.-E., Hurtado, A.Q., Phang, S.-M., Yow, Y.-Y. & Sun, Z. (2017). Genetic and morphological analyses of Gracilaria firma and G. changii (Gracilariaceae, Rhodophyta), the commercially important agarophytes in western Pacific. PLoS ONE, 12: e0182176.
   PubMed Web of Science ®Google Scholar
• Núñez-Resendiz, M.L., Dreckmann, K.M., Sentíes, A., Díaz-Larrea, J. & Zuccarello, G.C. (2015). Genetically recognizable but not morphologically: the cryptic nature of Hydropuntia cornea and H. usneoides (Gracilariales, Rhodophyta) in the Yucatan Peninsula. Phycologia, 54: 407–416.
   Web of Science ®Google Scholar
• Núñez-Resendiz, M.L., Zuccarello, G.C., Dreckmann, K.M., & Sentíes, A. (2017). Phylogeography of Hydropuntia cornea/Hydropuntia usneoides complex (Gracilariales, Rhodophyta) in the Yucatan Peninsula. Phycologia, 56: 14–20.
   Web of Science ®Google Scholar
• Paiva, P.C., Mutaquilha, B.F., Coutinho, M.C.L. & Santos, C.S. (2019). Comparative phylogeography of two coastal species of Perinereis Kinberg, 1865 (Annelida, Polychaeta) in the South Atlantic. Marine Biodiversity, 49: 1537–1551.
   Web of Science ®Google Scholar
• Pepato, A.R., Vidigal, T.H. & Klimov, P.B. (2019). Evaluating the boundaries of marine biogeographic regions of the Southwestern Atlantic using halacarid mites (Halacaridae), meiobenthic organisms with a low dispersal potential. Ecology and Evolution, 9: 13359–13374.
   PubMed Web of Science ®Google Scholar
• Plastino, E.M. & Oliveira, E.C. (1997). Gracilaria caudata J. Agardh (Gracilariales, Rhodophyta) restoring an old name for a common western Atlantic alga. Phycologia, 36: 225–232.
   Web of Science ®Google Scholar
• Rambaut, A. (2012). FigTree v1.4.2: Tree figure drawing tool. http://tree.bio.ed.ac.uk/software/figtree/; searched on 21 June 2019.
   Google Scholar
• Rambaut, A. & Drummond, A.J. (2014). TreeAnnotator v2. 1.2. Edinburgh: University of Edinburgh, Institute of Evolutionary Biology.
   Google Scholar
• Rambaut, A., Drummond, A.J., Xie, D., Baele, G. & Suchard, M.A. (2018). Posterior summarisation in Bayesian phylogenetics using Tracer 1.7. Systematic Biology, 67: 901–904.
   PubMed Web of Science ®Google Scholar
• Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D.L., Darling, A., Höhna, S., Larget, B., Liu, L., Surchard, M.A. & Huelsenbeck, J.P. (2012). MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61: 539–542.
   PubMed Web of Science ®Google Scholar
• Santos, S., Hrbek, T., Farias, I. P., Schneider, H. & Sampaio, I. (2006). Population genetic structuring of the king weakfish, Macrodon ancylodon (Sciaenidae), in Atlantic coastal waters of South America: deep genetic divergence without morphological change. Molecular Ecology, 15: 4361–4373.
   PubMed Web of Science ®Google Scholar
• Schramm, A. & Mazé, H. (1865). Essai de classification des algues de la Guadeloupe. [Ed.1a]. [iii]+52 pp. Basse-Terré, Guadeloupe: Imprimerie du Gouvernement.
   Google Scholar
• Silva, P.C., Basson, P.W. & Moe, R.L. (1996). Catalogue of the Marine Algae of the Indian Ocean. University of California Publications in Botany, 79: 1–1259.
   Google Scholar
• Skelton, P.W., Spicer, R.A., Kelley, S.P. & Gilmour, I. (2003). The Cretaceous World. Cambridge University Press, Cambridge.
   Google Scholar
• Soares, L.P., Gurgel, C.F.D. & Fujii, M.T. (2015). Taxonomic reassessment of Gracilaria cearensis (Rhodophyta, Gracilariales), a poorly defined yet common flattened species based on morphological and molecular analysis including topotype collections. Phytotaxa, 201: 241–255.
   Web of Science ®Google Scholar
• Steentoft, M. (1967). A revision of the marine algae of São Tomé and Príncipe (Gulf of Guinea). Journal of the Linnean Society of London, Botany, 60: 99–146.
   Google Scholar
• Taylor, W.R. (1960). Marine Algae of the Eastern Tropical and Subtropical Coasts of the Americas. University of Michigan Press, Ann Arbor.
   Google Scholar
• Thiers, B. (2020). Index Herbariorum: A Global Directory of Public Herbaria and Associated Staff. New York Botanical Garden’s Virtual Herbarium. http://sweetgum.nybg.org/ih/[continuously updated].
   Google Scholar
• Tsuda, R.T. & Abbott, I.A. (1985). Collecting, handling, preservation, and logistics. In Handbook of Phycological Methods, Vol. IV, Ecological Field Methods: Macroalgae (Littler, M.M. & Littler, D.S., editors), 67–86. Cambridge University Press, Cambridge.
   Google Scholar
• Vilchis, M.I., Neustupa, J., Dreckmann, K., Quintanar, A. & Sentíes, A. (2019). Discrimination of the species of the Crassiphycus corneus/C. usneoides complex (Gracilariaceae, Rhodophyta) through geometric morphometric analysis. Nova Hedwigia, 109: 291–301.
   Web of Science ®Google Scholar
• Wynne, M.J. (1989). The re-instatement of Hydropuntia Montagne (Gracilariaceae, Rhodophyta). Taxon, 38: 476–479.
   Web of Science ®Google Scholar
• Wynne, M.J. (2017). A checklist of the benthic marine algae of the tropical and subtropical western Atlantic: fourth revision. Nova Hedwigia Beihefte, 145: 1–202.
   Google Scholar
• Yamamoto, H. (1984). An evaluation of some vegetative features and some interesting problems in Japanese populations of Gracilaria. Hydrobiologia, 116/117: 51–54.
   Google Scholar
• Yang, E.C., Kim, M.S., Geraldino, P.J.L., Sahoo, D., Shin, J.A. & Boo, S.M. (2008). Mitochondrial cox1 and plastid rbcL genes of Gracilaria vermiculophylla (Gracilariaceae, Rhodophyta). Journal of Applied Phycology, 20: 161–168.
   Web of Science ®Google Scholar
• Yang, E.C., Boo, S.M., Bhattacharya, D., Saunders, G.W., Knoll, A.H., Fredericq, S., Graf, L., & Yoon, H.S. (2016). Divergence time estimates and the evolution of major lineages in the florideophyte red algae. Scientific Reports, 6: 1–11.
   Google Scholar