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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.)

The tropical to warm-temperate marine brown macroalgal genus Lobophora (Dictyotales, Phaeophyceae) recently drew attention because of its striking regional diversity. In this study we reassess Lobophora global species diversity, and species distributions, and explore how historical factors have shaped current diversity patterns. We applied a series of algorithmic species delineation techniques on a global mitochondrial cox3 dataset of 598 specimens, resulting in an estimation of 98-121 species. This diversity by far exceeds traditional diversity estimates based on morphological data. A multi-locus time-calibrated species phylogeny using a relaxed molecular clock, along with DNA-confirmed species distribution data was used to analyse ancestral area distributions, dispersal-vicariance-founder events, and temporal patterns of diversification under different biogeographical models. The origin of Lobophora was estimated in the Upper Cretaceous (-75 to -60 MY), followed by gradual diversification until present. While most speciation events were inferred within marine realms, founder events also played a non-negligible role in Lobophora diversification. The Central Indo-Pacific showed the highest species diversity as a result of higher speciation events in this region. Most Lobophora species have small ranges limited to marine realms. Lobophora probably originated in the Tethys Sea and dispersed repeatedly in the Atlantic (including the Gulf of Mexico) and Pacific Oceans. The formation of the major historical marine barriers (Terminal Tethyan event, Isthmus of Panama, Benguela upwelling) did not act as important vicariance events. Long-distance dispersal presumably represented an important mode of speciation over evolutionary time-scales. The limited geographical ranges of most Lobophora species, however, vouch for the rarity of such events., (Copyright © 2017 Elsevier Inc. All rights reserved.)

The green plants (Viridiplantae) are an ancient group of eukaryotes comprising two main clades: the Chlorophyta, which includes a wide diversity of green algae, and the Streptophyta, which consists of freshwater green algae and the land plants. The early-diverging lineages of the Viridiplantae comprise unicellular algae, and multicellularity has evolved independently in the two clades. Recent molecular data have revealed an unrecognized early-diverging lineage of green plants, the Palmophyllales, with a unique form of multicellularity, and typically found in deep water. The phylogenetic position of this enigmatic group, however, remained uncertain. Here we elucidate the evolutionary affinity of the Palmophyllales using chloroplast genomic, and nuclear rDNA data. Phylogenetic analyses firmly place the palmophyllalean Verdigellas peltata along with species of Prasinococcales (prasinophyte clade VI) in the deepest-branching clade of the Chlorophyta. The small, compact and intronless chloroplast genome (cpDNA) of V. peltata shows striking similarities in gene content and organization with the cpDNAs of Prasinococcales and the streptophyte Mesostigma viride, indicating that cpDNA architecture has been extremely well conserved in these deep-branching lineages of green plants. The phylogenetic distinctness of the Palmophyllales-Prasinococcales clade, characterized by unique ultrastructural features, warrants recognition of a new class of green plants, Palmophyllophyceae class. nov.

New empirical and quantitative data in the study of calcium carbonate biomineralization and an expanded coralline psbA framework for phylomineralogy are provided for crustose coralline red algae. Scanning electron microscopy (SEM) and energy dispersive spectrometry (SEM-EDS) pinpointed the exact location of calcium carbonate crystals within overgrown reproductive conceptacles in rhodolith-forming Lithothamnion species from the Gulf of Mexico and Pacific Panama. SEM-EDS and X-ray diffraction (XRD) analysis confirmed the elemental composition of these calcium carbonate crystals to be aragonite. After spore release, reproductive conceptacles apparently became overgrown by new vegetative growth, a strategy that may aid in sealing the empty conceptacle chamber, hence influencing the chemistry of the microenvironment and in turn promoting aragonite crystal growth. The possible relevance of various types of calcium carbonate polymorphs present in the complex internal structure and skeleton of crustose corallines is discussed. This is the first study to link SEM, SEM-EDS, XRD, Microtomography and X-ray microscopy data of aragonite infill in coralline algae with phylomineralogy. The study contributes to the growing body of literature characterizing and speculating about how the relative abundances of carbonate biominerals in corallines may vary in response to changes in atmospheric pCO2 , ocean acidification, and global warming., (© 2016 Phycological Society of America.)

The Florideophyceae is the most abundant and taxonomically diverse class of red algae (Rhodophyta). However, many aspects of the systematics and divergence times of the group remain unresolved. Using a seven-gene concatenated dataset (nuclear EF2, LSU and SSU rRNAs, mitochondrial cox1, and plastid rbcL, psaA and psbA genes), we generated a robust phylogeny of red algae to provide an evolutionary timeline for florideophyte diversification. Our relaxed molecular clock analysis suggests that the Florideophyceae diverged approximately 943 (817-1,049) million years ago (Ma). The major divergences in this class involved the emergence of Hildenbrandiophycidae [ca. 781 (681-879) Ma], Nemaliophycidae [ca. 661 (597-736) Ma], Corallinophycidae [ca. 579 (543-617) Ma], and the split of Ahnfeltiophycidae and Rhodymeniophycidae [ca. 508 (442-580) Ma]. Within these clades, extant diversity reflects largely Phanerozoic diversification. Divergences within Florideophyceae were accompanied by evolutionary changes in the carposporophyte stage, leading to a successful strategy for maximizing spore production from each fertilization event. Our research provides robust estimates for the divergence times of major lineages within the Florideophyceae. This timeline was used to interpret the emergence of key morphological innovations that characterize these multicellular red algae.

A phylogeny for the Rhodophyta has been inferred by parsimony analysis of plastid rbcL sequences representing 81 species, 68 genera, 38 families, and 17 orders of red algae; rbcL encodes the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase. Levels of sequence divergence among species, genera, and families are high in red algae, typically much greater than those reported for flowering plants. The Rhodophyta traditionally consists of one class, Rhodophyceae, and two subclasses, Bangiophycidae and Florideophycidae. The Bangiophycidae with three orders (Porphyridiales, Compsopogonales, and Bangiales) appears to be polyphyletic, and the Florideophycidae with 17 orders is monophyletic in this study. The current classification of the Florideophycidae based on ultrastructure of pit connections is supported. With the exception of the Rhodogorgonales, which appears to be misplaced, orders with one or two pit-plug cap layers (Hildenbrandiales, Corallinales, Acrochaetiales, Palmanales, Batrachospermales, and Nemaliales) terminate long branches of basal position within Florideophycidae in the most parsimonious rbcL tree. Orders that lack typical cap layers but possess a cap membrane are resolved as a monophyletic clade sister to the Ahnfeltiales. The large order Gigartinales, which is distributed among five rbcL clades, is polyphyletic. Families that possess typical carrageenan in their cell walls are resolved as a terminal clade containing two family complexes centered around the Solieriaceae and Gigartinaceae.

A systematic reassessment of the sole representative of the South African genus Phyllymenia, P. belangeri , indicates a lack of clear-cut diagnostic characters to separate it from Grateloupia . The morphology of the auxiliary cell ampullae, widely regarded as a key generic character in the Halymeniaceae, is almost identical in both genera. The autapomorphic character that has traditionally separated Phyllymenia from Grateloupia is the formation of pronounced lateral cytoplasmic protuberances on inner cortical cells. However, the establishment of protuberances is correlated with the presence of large intercellular spaces between neighbouring cortical cell files, coupled with narrow intercalary cortical cells. Thus, in order to establish secondary pit connections to more distant neighbouring cells, cortical cell protuberances may have become more prominent in P. belangeri than in species of Grateloupia with smaller intercellular spaces. Phylogenetic analyses of chloroplast-encoded rbc L sequences for a dataset including four representatives of P. belangeri and 32 other species, currently placed in Grateloupia or Prionitis , resolve (with high support) P. belangeri as a sister taxon of G. longifolia from South Africa. Based on morphological and molecular evidence, it is therefore proposed that Phyllymenia be reduced to a synonym of Grateloupia . [ABSTRACT FROM AUTHOR]

Red algae are exceptional for the great diversity in reproductive morphology and for their complex life histories. In particular, the family Phyllophoraceae, consisting of ∼100 species worldwide, stands out in exhibiting a wide spectrum of unique life history types that makes it unusually interesting for assessing the phylogenetic importance of reproductive traits relative to classification criteria. Type of life history and position of the reproductive structures on the plant body have traditionally formed the basis for separating eleven genera in the Phyllophoraceae; however, phylogenetic analyses inferred from three sets of DNA sequences [chloroplast-encoded rbcL, nuclear large-subunit ribosomal RNA gene (LSU), and internal transcribed spacer regions (ITS) of nuclear ribosomal DNA], instead indicate a lack of correlation between type of life history and phylogenetic relationships among the established taxa. This lack of correlation dramatically challenges all of the traditional taxonomy. The study will answer the question which morphological features and which aspects of life history evolution can be used as meaningful indicators of phylogenetic relationships in the Phyllophoraceae. The results are addressed in light of global biogeographic hypotheses for the family. [ABSTRACT FROM AUTHOR]

Hovencamp (1997) recommends that geographical information can be extracted from cladistic analyses of phylogenetic data in which the Earth's history is resolved in terms of vicariance events that established barriers to migration. Nodes in a cladogram that specify two sister groups which do not overlap in their distributions are taken as evidence for a vicariance event and the sequential order of cladogram nodes leads to a procedure whereby the sequence of vicariance events can be reconstructed. For red algae, two such events are the persistence of the northward extension of the eastern end of Gondwanaland across a cool to warm temperature gradient with the formation of present-day Australasia, and the opening of the Tethyan Ocean followed by closure of the Tethyan Seaway between Africa and Eurasia. Phylogenetic hypotheses related to the first of these events are seen among genera belonging to the Bonnemaisoniaceae, Gracilariaceae, Kallymeniaceae, Gigartinaceae, and Delesseriaceae. A Tethyan origin and distribution is exemplified in part by families that comprise the Solieriaceae complex. Orders such as the Rhodymeniales, Halymeniales and the families Ceramiaceae and Rhodomelaceae contain taxa that fall partly into the first and partly into the second category. Phylogenies are constructed from rbcL sequence data and compared to the morphological evidence. The biogeographical speculations resulting from these observations are preliminary in nature and can only be confirmed or refuted with addtional data and more refined analytical techniques. [ABSTRACT FROM AUTHOR]

The current system of classification of the Delesseriaceae rests largely on Kylin's treatment which encompass the subfamilies Delesserioideae with five ‘Groups’ and Nitophylloideae with six ‘Groups’. In this study we test the Kylin system based on phylogenetic analyses inferred from two molecular data sets and morphological evidence. A total of 145 delesseriacean taxa worldwide were sequenced for chloroplast-encoded rbcL, and 82 taxa for the nuclear-encoded large subunit ribosomal RNA gene (LSU). Three large clades are identified in the combined data sets, one of which corresponds to the Delesserioideae, one to a narrowly circumscribed Nitophylloideae, and the third to a new subfamily comprising the remainder of the Nitophylloideae sensu Kylin. Belonging to the Delesserioideae are an expanded Hemineura group that includes Hemineura, Patulophycus, Marionella, Laingia, Botryocarpa and possibly Pseudophycodrys, a Caloglossa group, a Hypoglossum group that includes Hypoglossum, Branchioglossum, Bartoniella, Zellera, Phitymorphora, and Chauviniella, a Delesseria group with Delesseria, Membranoptera and possibly Grinnellia (but not Apoglossum) and most southern hemisphere species of Delesseria which are properly placed in Paraglossum J. Agardh 1898. The revised Nitophylloideae contains Nitophyllum, Valeriemaya, Polyneuropsis, Calonitophyllum and also Martensia and Opephyllum. The unnamed subfamily includes the Phycodrys group with Phycodrys and Polyneura, the Cryptopleura group with species placed in Cryptopleura, Hymenena, Acrosorium and Botryoglossum, the Myriogrammeae with Myriogramme and Haraldiophyllum, and the Schizoserideae with Schizoseris, Neuroglossum, Drachiella, Abroteia, and South American species of Platyclinia. This research promotes the correlation of molecular and morphological phylogenies with biogeographic hypotheses for the family. [ABSTRACT FROM AUTHOR]

The taxonomic and evolutionary relationships between Porphyra of the boreal North Pacific (NP) and North Atlantic (NA) are being examined using near full length sequences of rbcL and the rbcL rbcS spacer (∼1420 bp). Phylogenetic analysis openface> 20 recognized species produced clusters containing both NP and NA species: Porphyra carolinenesis (NA) and Porphyra perforata (NP); Porphyra. leucosticta (NA) and Porphyra fucicola (NP); Porphyra‘ amplissima’ (NA) and Porphyra cuneiformis (NP); Porphyra‘ umbilicalis’ (NA) and Porphyra mumfordii (NP). A cluster of NP species including Porphyra abbottae, Porphyra kurogii, Porphyra pseudolinearis, and Porphyra pseudolanceolata formed a sister clade to P. fucicola (NP), P. leucosticta (NA) and several cryptic NA taxa. These results demonstrate that a number of “independent” migrations occurred between the North Pacific and Northern Atlantic. Furthermore these results confirm the hypothesis, based on similarities in morphology, isozymes, and karyotype, of Lindstrom & Cole (1992), that several sibling species pairs exist for Porphyra of the boreal North Pacific (NP) and North Atlantic (NA). [ABSTRACT FROM AUTHOR]