This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional ''kingdoms.'' The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles.

/pdf/the-new-higher-level-classification-of-eukaryotes-with-12im7rq9o7.pdf

The new higher level classification of eukaryotes with emphasis on the taxonomy of protists

Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences

Over the past two decades, molecular phylogenetic data have allowed evaluations of hypotheses on the evolution of green algae based on vegetative morphological and ultrastructural characters. Higher taxa are now generally recognized on the basis of ultrastructural characters. Molecular analyses have mostly employed primarily nuclear small subunit rDNA (18S) and plastid rbcL data, as well as data on intron gain, complete genome sequencing, and mitochondrial sequences. Molecular-based revisions of classification at nearly all levels have occurred, from dismemberment of long-established genera and families into multiple classes, to the circumscription of two major lineages within the green algae. One lineage, the chlorophyte algae or Chlorophyta sensu stricto, comprises most of what are commonly called green algae and includes most members of the grade of putatively ancestral scaly flagellates in Prasinophyceae plus members of Ulvophyceae, Trebouxiophyceae, and Chlorophyceae. The other lineage (charophyte algae and embryophyte land plants), comprises at least five monophyletic groups of green algae, plus embryophytes. A recent multigene analysis corroborates a close relationship between Mesostigma (formerly in the Prasinophyceae) and the charophyte algae, although sequence data of the Mesostigma mitochondrial genome analysis places the genus as sister to charophyte and chlorophyte algae. These studies also support Charales as sister to land plants. The reorganization of taxa stimulated by molecular analyses is expected to continue as more data accumulate and new taxa and habitats are sampled. Twenty years ago, a relatively slim volume with chapters by leading chlorophycologists celebrated the systematics of green algae (Irvine and John, 1984), a field that was undergoing rapid and fascinating changes, both in content and theory. ‘‘The present period may be termed the ‘Age of Ultrastructure’ in green algal systematics,’’ wrote Frank Round (1984, p. 7) in the introductory chapter, which summarized the history and state of the art. Round (1984) argued that light microscopy had laid the foundation in the preceding two centuries, but that the foundation was largely descriptive—alpha taxonomy in the most restricted sense. Ultrastructure, he asserted, had enlarged and presumably would continue to expand our horizons to unify systematics of green algae and overcome the fragmented alpha taxonomy that had dominated the field. Little did Round know that this golden age of green algal systematics was about to go platinum. Molecular systematics, in concert with a rigorous theoretical approach to data analysis and hypothesis testing (Theriot, 1992; Swofford et al., 1996), would at first complement and then transform the age of ultrastructure and usher in the ‘‘Age of Molecules.’’ In this article, we review the major advances in green algal systematics in the past 20 years, with a focus on well-supported, monophyletic taxa and the larger picture of phylogeny and evolution of green algae. We will review the types of data that have fueled these advances. As will become obvious, this perspective entails discussion of some embryophytes as well as their closest green algal relatives. In addition, we will point

/pdf/green-algae-and-the-origin-of-land-plants-2q6795w3qm.pdf

Green algae and the origin of land plants

Marine macroalgae, especially the Rhodophyta, can be notoriously difficult to identify owing to their relatively simple morphology and anatomy, convergence, rampant phenotypic plasticity, and alternation of heteromorphic generations. It is thus not surprising that algal systematists have come to rely heavily on genetic tools for molecular assisted alpha taxonomy. Unfortunately the number of suitable marker systems in the three available genomes is enormous and, although most workers have settled on one of three or four models, the lack of an accepted standard hinders the comparison of results between laboratories. The advantages of a standard system are obvious for practical purposes of species discovery and identification; as well, compliance with a universal marker, such as cox1 being developed under the label ‘DNA barcode’, would allow algal systematists to benefit from the rapidly emerging technologies. Novel primers were developed for red algae to PCR amplify and sequence the 5′ cox1 ‘barcode’ region and were used to assess three known species-complex questions: (i) Mazzaella species in the Northeast Pacific; (ii) species of the genera Dilsea and Neodilsea in the Northeast Pacific; and (iii) Asteromenia peltata from three oceans. These models were selected because they have all caused confusion with regards to species number, distribution, and identification in the field, and because they have all been studied with molecular tools. In all cases the DNA barcode resolved accurately and unequivocally species identities and, with the enhanced sampling here, turned up a variety of novel observations in need of further taxonomic investigation.

/pdf/applying-dna-barcoding-to-red-macroalgae-a-preliminary-4b0nx1y6wu.pdf

Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications

Multicellular filaments from the ca. 1200-Ma Hunting Formation (Somerset Island, arctic Canada) are identified as bangiacean red algae on the basis of diagnostic cell-division patterns. As the oldest taxonomically resolved eukaryote on record Bangiomorpha pubescens n. gen. n. sp. provides a key datum point for constraining protistan phylogeny. Combined with an increasingly resolved record of other Proterozoic eukaryotes, these fossils mark the onset of a major protistan radiation near the Mesoproterozoic/Neoproterozoic boundary.Differential spore/gamete formation shows Bangiomorpha pubescens to have been sexually reproducing, the oldest reported occurrence in the fossil record. Sex was critical for the subsequent success of eukaryotes, not so much for the advantages of genetic recombination, but because it allowed for complex multicellularity. The selective advantages of complex multicellularity are considered sufficient for it to have arisen immediately following the appearance of sexual reproduction. As such, the most reliable proxy for the first appearance of sex will be the first stratigraphic occurrence of complex multicellularity.Bangiomorpha pubescens is the first occurrence of complex multicellularity in the fossil record. A differentiated basal holdfast structure allowed for positive substrate attachment and thus the selective advantages of vertical orientation; i.e., an early example of ecological tiering. More generally, eukaryotic multicellularity is the innovation that established organismal morphology as a significant factor in the evolutionary process. As complex eukaryotes modified, and created entirely novel, environments, their inherent capacity for reciprocal morphological adaptation, gave rise to the “biological environment” of directional evolution and “progress.” The evolution of sex, as a proximal cause of complex multicellularity, may thus account for the Mesoproterozoic/Neoproterozoic radiation of eukaryotes.

Bangiomorpha pubescens n. gen., n. sp.: implications for the evolution of sex, multicellularity, and the Mesoproterozoic/Neoproterozoic radiation of eukaryotes

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.

https://www.pnas.org/content/pnas/91/15/7281.full.pdf

A gene phylogeny of the red algae (Rhodophyta) based on plastid rbcL

The present classification of the Delesseriaceae retains the essential features of Kylin's system, which recognizes two subfamilies Delesserioideae and Nitophylloideae and a series of “groups” or tribes. In this study we test the Kylin system based on phylogenetic parsimony and distance analyses inferred from two molecular data sets and morphological evidence. A set of 72 delesseriacean and 7 additional taxa in the order Ceramiales was sequenced in the large subunit rDNA and rbcL analyses. Three large clades were identified in both the separate and combined data sets, one of which corresponds to the Delesserioideae, one to a narrowly circumscribed Nitophylloideae, and one to the Phycodryoideae, subfam. nov., comprising the remainder of the Nitophylloideae sensu Kylin. Two additional trees inferred from rbcL sequences are included to provide broader coverage of relationships among some Delesserioideae and Phycodryoideae. Belonging to the Delesserioideae are the Caloglosseae with Caloglossa; an expanded Hemineureae that includes Hemineura, Patulophycus, Marionella, Laingia, Botryocarpa, and Pseudophycodrys; the Delesserieae with Delesseria and Membranoptera; the Apoglosseae with Apoglossum and a group of southern hemisphere species presently placed in Delesseria that belong in Paraglossum; the Hypoglosseae with Hypoglossum, Branchioglossum, Zellera, and Bartoniella; and the Grinnellieae with Grinnellia. The revised Nitophylloideae contains the Nitophylleae with Nitophyllum, Valeriemaya, Polyneuropsis, and Calonitophyllum and the Martensieae with Opephyllum and Martensia. A new subfamily, Phycodryoideae, is proposed to include the Phycodryeae with Phycodrys, Polyneura, Nienburgia, Cladodonta, Heterodoxia, and Womersleya; the Cryptopleureae with Cryptopleura, Hymenena, Acrosorium, and Botryoglossum; the Myriogrammeae with Myriogramme and Haraldiophyllum; and the Schizoserideae with Schizoseris, Neuroglossum, Drachiella, Abroteia, and species from South America placed in Platyclinia. This research promotes the correlation of molecular and morphological phylogenies.

http://suzannefredericqseaweedslab.com/delessejphycol200.pdf

SYSTEMATICS OF THE DELESSERIACEAE (CERAMIALES, RHODOPHYTA) BASED ON LARGE SUBUNIT rDNA AND rbcL SEQUENCES, INCLUDING THE PHYCODRYOIDEAE, SUBFAM. NOV.

Seaweeds of the British Isles. Volume 1 Rhodophyta, Part 3A Ceramiales.

The wondrously diverse eukaryotes that constitute the red algae have been the focus of numerous recent molecular surveys and remain a rich source of undescribed and little known species for the traditional taxonomist. Molecular studies place the red algae in the kingdom Plantae; however, supraordinal classification has been largely confined to debate on subclass vs. class level status for the two recognized subgroups, one of which is widely acknowledged as paraphyletic. This narrow focus has generally masked the extent to which red algal classification needs modification. We provide a comprehensive review of the literature pertaining to the antiquity, diversity, and systematics of the red algae and propose a contemporary classification based on recent and traditional evidence.

Assessing red algal supraordinal diversity and taxonomy in the context of contemporary systematic data

Molecular data obtained by a procedure for extracting PCR-amplifiable nuclear and chloroplast DNA from old and formalin-fixed red algal herbarium specimens were used to elucidate problems in the systematics of Pacific Gigartinaceae. Correspondence between nucleotide sequences of the internal transcribed spacer 1 region or the RUBISCO spacer from type specimens and modern collections supports the following conclusions. (1) The type of Fucus cordatus Turner, now Iridaea cordata (Turner) Bory, came from the southern hemisphere (probably from Isla de los Estados, Argentina) rather than from Banks Island, B.C., Canada. (2) The type of Iridaea heterocarpa P. et R. [ Mazzaella heterocarpa (P. et R.) Fred.] represents the tetrasporangial phase of a species of Chondrus , possibly C. crispus Stackh. (3) The types of Iridaea lilacina P. et R., I. phyllocarpa P. et R., and Iridophycus furcatum S. et G. represent a single species from Alaska, Mazzaella phyllocarpa (P. et R.) Perest., currently but incorrectly called M. heterocarpa. (4) The type of Iridophycus oregonum Doty represents the tetrasporangial phase of the species from southern Alaska to southern California known incorrectly as M. heterocarpa . (5) Mazzaella splendens (S. et G.) Fred. is more closely related to M. linearis (S. et G.) Fred. than it is to M. flaccida (S. et G.) Fred. (6) Iridophycus coriaceum S. et G. is conspecific with M. splendens , whereas Rhodoglossum coriaceum E.Y. Dawson is an independent species: Mazzaella coriacea (E.Y. Dawson) Hughey. (7) Iridaea cornucopiae P. et R. is conspecific with Mazzaella laminarioides (Bory) Fred., and the type probably came from Chile rather than from the North Pacific. (8) Plants attributed to Iridaea cornucopiae in Pacific North America are referable to Mazzaella parksii (S. et G.) comb. nov. (9) Rhodoglossum parvum G. M. Smith et Hollenb. is an independent species: Mazzaella parva (G. M. Smith et Hollenb.) comb. nov. (10) Grateloupia squarrulosa S. et G., Grateloupia johnstonii S. et G., and Gigartina pectinata E.Y. Dawson represent a single species: Chondracanthus squarrulosus (S. et G.) comb. nov.

Max H. Hommersand

Papers

A gene phylogeny of the red algae (Rhodophyta) based on plastid rbcL

SYSTEMATICS OF THE DELESSERIACEAE (CERAMIALES, RHODOPHYTA) BASED ON LARGE SUBUNIT rDNA AND rbcL SEQUENCES, INCLUDING THE PHYCODRYOIDEAE, SUBFAM. NOV.

Seaweeds of the British Isles. Volume 1 Rhodophyta, Part 3A Ceramiales.

Assessing red algal supraordinal diversity and taxonomy in the context of contemporary systematic data

Solving taxonomic and nomenclatural problems in pacific gigartinaceae (rhodophyta) using dna from type material