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Objective: The body of DNA sequence data lacking taxonomically informative sequence headers is rapidly growing in user and public databases (e.g. sequences lacking identification and contaminants). In the context of systematics studies, sorting such sequence data for taxonomic curation and/or molecular diversity characterization (e.g. crypticism) often requires the building of exploratory phylogenetic trees with reference taxa. The subsequent step of segregating DNA sequences of interest based on observed topological relationships can represent a challenging task, especially for large datasets., Results: We have written TREE2FASTA, a Perl script that enables and expedites the sorting of FASTA-formatted sequence data from exploratory phylogenetic trees. TREE2FASTA takes advantage of the interactive, rapid point-and-click color selection and/or annotations of tree leaves in the popular Java tree-viewer FigTree to segregate groups of FASTA sequences of interest to separate files. TREE2FASTA allows for both simple and nested segregation designs to facilitate the simultaneous preparation of multiple data sets that may overlap in sequence content.

Interspecific systematics in the red algal order Sporolithales remains problematic. To re-evaluate its species, DNA analyses were performed on historical type material and recently collected specimens assigned to the two genera Sporolithon and Heydrichia. Partial rbcL sequences from the lectotype specimens of Sporolithon ptychoides (the generitype species) and Sporolithon molle, both from El Tor, Egypt, are exact matches to field-collected topotype specimens. Sporolithon crassum and Sporolithon erythraeum also have the same type locality; material of the former appears to no longer exist, and we were unable to PCR amplify DNA from the latter. A new species, Sporolithon eltorensis, is described from the same type locality. We have not found any morpho-anatomical characters that distinguish these three species. No sequenced specimens reported as S. ptychoides from other parts of the world represent this species, and likely reports of S. ptychoides and S. molle based on morpho-anatomy are incorrect. A partial rbcL sequence from the holotype of Sporolithon dimotum indicates it is not a synonym of S. ptychoides, and data from the holotype of S. episporum confirm its specific recognition. DNA sequences from topotype material of Heydrichia woelkerlingii, the generitype species, and isotype material of Heydrichia cerasina confirm that these are distinct species; the taxon reported to be H. woelkerlingii from New Zealand is likely an undescribed species. Type specimens of all other Sporolithon and Heydrichia species need to be sequenced to confirm that they are distinct species; morpho-anatomical studies have proved inadequate for this task., (© 2017 Phycological Society of America.)

Background: The Hawaiian red algal flora is diverse, isolated, and well studied from a morphological and anatomical perspective, making it an excellent candidate for assessment using a combination of traditional taxonomic and molecular approaches. Acquiring and making these biodiversity data freely available in a timely manner ensures that other researchers can incorporate these baseline findings into phylogeographic studies of Hawaiian red algae or red algae found in other locations., Results: A total of 1,946 accessions are represented in the collections from 305 different geographical locations in the Hawaiian archipelago. These accessions represent 24 orders, 49 families, 152 genera and 252 species/subspecific taxa of red algae. One order of red algae (the Rhodachlyales) was recognized in Hawaii for the first time and 196 new island distributional records were determined from the survey collections. One family and four genera are reported for the first time from Hawaii, and multiple species descriptions are in progress for newly discovered taxa. A total of 2,418 sequences were generated for Hawaiian red algae in the course of this study--915 for the nuclear LSU marker, 864 for the plastidial UPA marker, and 639 for the mitochondrial COI marker. These baseline molecular data are presented as neighbor-joining trees to illustrate degrees of divergence within and among taxa. The LSU marker was typically most conserved, followed by UPA and COI. Phylogenetic analysis of a set of concatenated LSU, UPA and COI sequences recovered a tree that broadly resembled the current understanding of florideophyte red algal relationships, but bootstrap support was largely absent above the ordinal level. Phylogeographic trends are reported here for some common taxa within the Hawaiian Islands and include examples of those with, as well as without, intraspecific variation., Conclusions: The UPA and COI markers were determined to be the most useful of the three and are recommended for inclusion in future algal biodiversity surveys. Molecular data for the survey provide the most extensive assessment of Hawaiian red algal diversity and, in combination with the morphological/anatomical and distributional data collected as part of the project, provide a solid baseline data set for future studies of the flora. The data are freely available via the Hawaiian Algal Database (HADB), which was designed and constructed to accommodate the results of the project. We present the first DNA sequence reference collection for a tropical Pacific seaweed flora, whose value extends beyond Hawaii since many Hawaiian taxa are shared with other tropical areas.

The siphonous green algae are an assemblage of seaweeds that consist of a single giant cell. They comprise two sister orders, the Bryopsidales and Dasycladales. We infer the phylogenetic relationships among the siphonous green algae based on a five-locus data matrix and analyze temporal aspects of their diversification using relaxed molecular clock methods calibrated with the fossil record. The multi-locus approach resolves much of the previous phylogenetic uncertainty, but the radiation of families belonging to the core Halimedineae remains unresolved. In the Bryopsidales, three main clades were inferred, two of which correspond to previously described suborders (Bryopsidineae and Halimedineae) and a third lineage that contains only the limestone-boring genus Ostreobium. Relaxed molecular clock models indicate a Neoproterozoic origin of the siphonous green algae and a Paleozoic diversification of the orders into their families. The inferred node ages are used to resolve conflicting hypotheses about species ages in the tropical marine alga Halimeda.

The gelatinous, calciferous red alga Renouxia antillana was described in 1995 based on material from Guadeloupe, French West Indies, and accommodated in a new family and order (Rhodogorgonaceae, Rhodogorgonales) along with the genus Rhodogorgon from Belize and Caribbean Panama. For more than 20 years, Renouxia has remained monotypic, with rare reports in the Caribbean and the Indo-Pacific (from Réunion Island to French Polynesia). DNA-based analyses of recently collected Renouxia specimens from Egypt showed that they are not conspecific with the Caribbean R. antillana and are described as R. marerubra sp. nov. Uncorrected p-distances between the Red Sea specimens and the generitype were 8.0% for COI, 6.5-7.3% for rbcL and 3.1% for UPA. Morphological and anatomical features are also presented for the newly described species and compared to its congener, with the first documented report of monoecism in the Rhodogorgonales. Besides the new record of Renouxia from the Red Sea, the geographic distribution of the genus is here extended with additional records from Sri Lanka, Indonesia, as well as the islands of Guam and Kosrae in the Western Pacific. The UPA phylogeny suggests that these new distribution records may also represent undescribed species, with representatives in two distinct genetic groups. [ABSTRACT FROM AUTHOR]

When placed in marine laboratory microcosm tanks, Syringoderma floridana (Syringodermataceae, Syringodermatales) described from Atlantic Florida, grew from the surface of bare rhodoliths collected from 55 to 85 m depth in the northwestern Gulf of Mexico following the 2010 Deepwater Horizon oil spill. A partial nuclear 28S large subunit rDNA sequence of S. floridana epitype specimens from Jupiter, Palm Beach County, Florida, confirmed the molecular identity of this species, which had been reported from Atlantic Florida waters. Among the five species currently recognized in the genus Syringoderma, S. floridana is the only known subtropical species. The range of the species is here extended from Atlantic Florida to the northwestern, southeastern, and northeastern Gulf of Mexico. The taxonomic validity of the monospecific Microzonia, the only other genus in the Syringodermatales, was reassessed on the basis of publicly available sequence data (chloroplast-encoded rbcL and psaA, and nuclear 28S) and described morphological features. In all molecular analyses, Microzonia velutina is nested within specimens of Syringoderma. Microzonia has nomenclatural priority over Syringoderma; thus, the latter is reduced to synonymy under Microzonia. New nomenclatural combinations are proposed. [ABSTRACT FROM AUTHOR]

The tropical alga previously recognized as Gibsmithia hawaiiensis (Dumontiaceae, Rhodophyta) was recently suggested to represent a complex of species distributed throughout the Indo-Pacific Ocean and characterized by a peculiar combination of hairy (pilose) gelatinous lobes growing on cartilaginous stalks. Phylogenetic reconstructions based on three genetic markers are presented here with the inclusion of new samples. Further diversity is reported within the complex, with nine lineages spread in four major phylogenetic groups. The threshold between intra- and interspecific relationships was assessed by species delimitation methods, which indicate the existence of 8-10 putative species in the complex. Two species belonging to the G. hawaiiensis complex are described here: Gibsmithia malayensis sp. nov. from the Coral Triangle and Gibsmithia indopacifica sp. nov., widely distributed in the Central and Eastern Indo-Pacific. Morphological differences in the vegetative and reproductive structures of the newly described species are provided and compared to the previously described species of the complex. Additional lineages represent putative species, which await further investigation to clarify their taxonomic status. Gibsmithia hawaiiensis sensu stricto is confirmed to be endemic to the Hawaiian Islands, and Gibsmithia eilatensis is apparently confined to the Red Sea, with an expanded distribution in the region. New records of the G. hawaiiensis complex are reported from Egypt, Saudi Arabia, Indonesia, Philippines, and the Federated States of Micronesia, indicating that the complex is more broadly distributed than previously considered. The isolated position of Gibsmithia within the Dumontiaceae is corroborated by molecular data. [ABSTRACT FROM AUTHOR]

The siphonous green algal family Caulerpaceae includes the monotypic genus Caulerpella and the species-rich genus Caulerpa. A molecular phylogeny was inferred from chloroplast tufA and rbcL DNA sequences analyzed together with a five marker dataset of non-caulerpacean siphonous green algae. Six Caulerpaceae lineages were revealed, but relationships between them remained largely unresolved. A Caulerpella clade representing multiple cryptic species was nested within the genus Caulerpa. Therefore, that genus is subsumed and Caulerpa ambigua Okamura is reinstated. Caulerpa subgenus status is proposed for the six lineages substantiated by morphological characters, viz., three monotypic subgenera Cliftonii, Hedleyi, and Caulerpella, subgenus Araucarioideae exhibiting stolons covered with scale-like appendages, subgenus Charoideae characterized by a verticillate branching mode, and subgenus Caulerpa for a clade regarded as the Caulerpa core clade. The latter subgenus is subdivided in two sections, i.e., Sedoideae for species with pyrenoids and a species-rich section Caulerpa. A single section with the same name is proposed for each of the other five subgenera. In addition, species status is proposed for Caulerpa filicoides var. andamanensis (W.R. Taylor). All Caulerpa species without sequence data were examined (or data were taken from species descriptions) and classified in the new classification scheme. A temporal framework of Caulerpa diversification is provided by calibrating the phylogeny in geological time. The chronogram suggests that Caulerpa diversified into subgenera and sections after the Triassic- Jurassic mass extinction and that infra-section species radiation happened after the Cretaceous- Tertiary mass extinction. [ABSTRACT FROM AUTHOR]

A total of 290 florideophyte samples from the Hawaiian Rhodophyta Biodiversity Survey, spanning 17 orders of red algae, were sequenced for the mitochondrial COI DNA barcode, partial nuclear LSU rRNA gene, and plastid UPA rRNA marker. COI was A-T rich (>60% overall) in comparison to the two rRNA markers, and was also the least conserved, with the third codon position showing the most substitution. Saturation was reached at F84 distances of approximately 0.11 for COI and 0.30 for LSU, but not at all for UPA, and some differences were found when orders or groups of families were individually examined. Rates of sequencing success for the three markers ranged from 46.8% for COI to 64.7% for UPA and 79.6% for LSU, indicating substantial differences in ease of data acquisition. Concatenation of marker sequences starting with the least saturated marker (UPA), and adding in order of degree of saturation (UPA+LSU, followed by UPA+LSU+COI) resulted in a strong increase in bootstrap support with neighbor-joining analysis, indicating that some phylogenetic utility can be gained from barcode-like sequences that are obtained for biodiversity surveys. [ABSTRACT FROM AUTHOR]

The genus Pseudochlorodesmis (Bryopsidales) is composed of diminutive siphons of extreme morphological simplicity. The discovery of Pseudochlorodesmis-like juveniles in more complex Bryopsidales (e.g., the Halimeda microthallus stage) jeopardized the recognition of this genus. Confronted with this uncertainty, taxonomists transferred many simple siphons into a new genus, Siphonogramen. In this study, we used a multimarker approach to clarify the phylogenetic and taxonomic affinities of the Pseudochlorodesmis-Siphonogramen (PS) complex within the more morphologically complex bryopsidalean taxa. Our analyses reveal a new layer of diversity largely distinct from the lineages containing the structurally complex genera. The PS complex shows profound cryptic diversity exceeding the family level. We discuss a potential link between thallus complexity and the prevalence and profundity of cryptic diversity. For taxonomic simplicity and as a first step toward clarifying the taxonomy of these simple siphons, we propose to maintain Pseudochlorodesmis as a form genus and subsume Siphonogramen and Botryodesmis therein. [ABSTRACT FROM AUTHOR]