Hilary A. McManus

The revised classification of eukaryotes.

This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re‐introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under‐sampled areas and from environmental genomic information.

MOLECULAR PHYLOGENETIC RELATIONSHIPS IN THE FRESHWATER FAMILY HYDRODICTYACEAE (SPHAEROPLEALES, CHLOROPHYCEAE), WITH AN EMPHASIS ON PEDIASTRUM DUPLEX1

The freshwater green algal family Hydrodictyaceae (Sphaeropleales, Chlorophyta) has traditionally consisted of four coenobial genera, Pediastrum Meyen 1829, Hydrodictyon Roth 1797, Sorastrum Kützing 1845, and Euastropsis Lagerheim1894. Two recent molecular phylogenetic studies demonstrated the need for reevaluation of the generic and species boundaries in this morphology‐rich family. This study expands the previous work to include phylogenetic analyses of 103 ingroup isolates representing North America, Europe, and Australia, with an emphasis on the common and geographically widespread species Pediastrum duplex. Nucleotide sequence data were collected from the nuclear LSU (26S rDNA) and the chloroplast RUBISCO LSU (rbcL) genes, totaling >3,000 aligned characters. The 26S and rbcL data sets were analyzed using maximum‐likelihood (ML) and Bayesian phylogenetic methods. In addition, SEM was used to examine the wall morphology of a majority of the isolates. The results supported previous indications that the P. duplex Meyen 1829 morphotype is nonmonophyletic and resolved some previously ambiguous relationships recovered in earlier phylogenetic estimations using fewer isolates. These new data allowed testing of the recent taxonomic revisions of the family that split Pediastrum into five genera. Some of the previous revisions by Buchheim et al. (2005) were well supported (erection of Stauridium and Monactinus), while others were not (Pediastrum, Pseudopediastrum, Parapediastrum).

Molecular phylogenetics, morphological variation and colony-form evolution in the family Hydrodictyaceae (Sphaeropleales, Chlorophyta)

H.A. McManus and L.A. Lewis. 2005. Molecular phylogenetics, morphological variation and colony-form evolution in the family Hydrodictyaceae (Sphaeropleales, Chlorophyta). Phycologia 44: 582–595. A phylogenetic analysis of 26S and internal transcribed spacer–2 ribosomal DNA (rDNA) data from members of the freshwater green algal family Hydrodictyaceae, including multiple taxa from both culture collections and new isolates, sets the stage to explore morphological variation and patterns of colony-form evolution within the family. These analyses particularly focus on Pediastrum boryanum, P. tetras, P. duplex, Hydrodictyon and Sorastrum. The genera Hydrodictyon and Sorastrum are derived from within Pediastrum in the individual and combined analyses, indicating a pattern of colony-form evolution within the family from two-dimensionality to three-dimensionality. In some cases the gene topologies reveal discrepancies in the morphological characters used to delimit species, varieties and forms within Pediastrum. Some isolates, such as those of H. reticulatum, exhibited little or no genetic variation between different geographic localities. Additional data and taxa are needed to better resolve and support these relationships, but the present results illustrate that some taxonomic revisions will be necessary.

Evolution of the life cycle in land plants

Abstract  All sexually reproducing eukaryotes have a life cycle consisting of a haploid and a diploid phase, marked by meiosis and syngamy (fertilization). Each phase is adapted to certain environmental conditions. In land plants, the recently reconstructed phylogeny indicates that the life cycle has evolved from a condition with a dominant free‐living haploid gametophyte to one with a dominant free‐living diploid sporophyte. The latter condition allows plants to produce more genotypic diversity by harnessing the diversity‐generating power of meiosis and fertilization, and is selectively favored as more solar energy is fixed and fed into the biosystem on earth and the environment becomes more heterogeneous entropically. Liverworts occupy an important position for understanding the origin of the diploid generation in the life cycle of land plants. Hornworts and lycophytes represent critical extant transitional groups in the change from the gametophyte to the sporophyte as the independent free‐living generation. Seed plants, with the most elaborate sporophyte and the most reduced gametophyte (except the megagametophyte in many gymnosperms), have the best developed sexual reproduction system that can be matched only by mammals among eukaryotes: an ancient and stable sex determination mechanism (heterospory) that enhances outcrossing, a highly bimodal and skewed distribution of sperm and egg numbers, a male‐driven mutation system, female specialization in mutation selection and nourishment of the offspring, and well developed internal fertilization. The study of evolution of the land plant life cycle requires a multidisciplinary approach that considers morphology, development, genetics, phylogeny, ecology, and evolution in an integrated fashion, and will deepen our understanding of plant evolution.

DISTINGUISHING MULTIPLE LINEAGES OF PEDIASTRUM DUPLEX WITH MORPHOMETRICS AND A PROPOSAL FOR LACUNASTRUM GEN. NOV 1

Accurately defining species boundaries in the green algae (Chlorophyta) is integral for studies of biodiversity and conservation, water‐quality assessments, and the use of particular species as paleoindicators. Recent molecular phylogenetic and SEM analyses of the family Hydrodictyaceae (Chlorophyta) resolved three phylogenetic lineages of isolates with the Pediastrum duplex Meyen 1829 phenotype. The present study employed analyses of cell shape and cell wall ultrastructure to determine if the three lineages possessing the P. duplex morphotype were distinguishable. Only one of the groups, containing isolates with the P. duplex var. gracillimum West et G. S. West phenotype, was shown to be morphologically distinct from the other two P. duplex groups. The erection of a new genus, Lacunastrum, is proposed to recognize this group as a separate taxon.

Invasion of protein coding genes by green algal ribosomal group I introns.

The spread of group I introns depends on their association with intron-encoded homing endonucleases. Introns that encode functional homing endonuclease genes (HEGs) are highly invasive, whereas introns that only encode the group I ribozyme responsible for self-splicing are generally stably inherited (i.e., vertical inheritance). A number of recent case studies have provided new knowledge on the evolution of group I introns, however, there are still large gaps in understanding of their distribution on the tree of life, and how they have spread into new hosts and genic sites. During a larger phylogenetic survey of chlorophyceaen green algae, we found that 23 isolates contain at least one group I intron in the rbcL chloroplast gene. Structural analyses show that the introns belong to one of two intron lineages, group IA2 intron-HEG (GIY-YIG family) elements inserted after position 462 in the rbcL gene, and group IA1 introns inserted after position 699. The latter intron type sometimes encodes HNH homing endonucleases. The distribution of introns was analyzed on an exon phylogeny and patterns were recovered that are consistent with vertical inheritance and possible horizontal transfer. The rbcL 462 introns are thus far reported only within the Volvocales, Hydrodictyaceae and Bracteacoccus, and closely related isolates of algae differ in the presence of rbcL introns. Phylogenetic analysis of the intron conserved regions indicates that the rbcL699 and rbcL462 introns have distinct evolutionary origins. The rbcL699 introns were likely derived from ribosomal RNA L2449 introns, whereas the rbcL462 introns form a close relationship with psbA introns.

Plastomes of the green algae Hydrodictyon reticulatum and Pediastrum duplex (Sphaeropleales, Chlorophyceae)

Background Comparative studies of chloroplast genomes (plastomes) across the Chlorophyceae are revealing dynamic patterns of size variation, gene content, and genome rearrangements. Phylogenomic analyses are improving resolution of relationships, and uncovering novel lineages as new plastomes continue to be characterized. To gain further insight into the evolution of the chlorophyte plastome and increase the number of representative plastomes for the Sphaeropleales, this study presents two fully sequenced plastomes from the green algal family Hydrodictyaceae (Sphaeropleales, Chlorophyceae), one from Hydrodictyon reticulatum and the other from Pediastrum duplex. Methods Genomic DNA from Hydrodictyon reticulatum and Pediastrum duplex was subjected to Illumina paired-end sequencing and the complete plastomes were assembled for each. Plastome size and gene content were characterized and compared with other plastomes from the Sphaeropleales. Homology searches using BLASTX were used to characterize introns and open reading frames (orfs) ≥ 300 bp. A phylogenetic analysis of gene order across the Sphaeropleales was performed. Results The plastome of Hydrodictyon reticulatum is 225,641 bp and Pediastrum duplex is 232,554 bp. The plastome structure and gene order of H. reticulatum and P. duplex are more similar to each other than to other members of the Sphaeropleales. Numerous unique open reading frames are found in both plastomes and the plastome of P. duplex contains putative viral protein genes, not found in other Sphaeropleales plastomes. Gene order analyses support the monophyly of the Hydrodictyaceae and their sister relationship to the Neochloridaceae. Discussion The complete plastomes of Hydrodictyon reticulatum and Pediastrum duplex, representing the largest of the Sphaeropleales sequenced thus far, once again highlight the variability in size, architecture, gene order and content across the Chlorophyceae. Novel intron insertion sites and unique orfs indicate recent, independent invasions into each plastome, a hypothesis testable with an expanded plastome investigation within the Hydrodictyaceae.

Organellar phylogenomics inform systematics in the green algal family Hydrodictyaceae (Chlorophyceae) and provide clues to the complex evolutionary history of plastid genomes in the green algal tree of life

PREMISE OF THE STUDY Phylogenomic analyses across the green algae are resolving relationships at the class, order, and family levels and highlighting dynamic patterns of evolution in organellar genomes. Here we present a within-family phylogenomic study to resolve genera and species relationships in the family Hydrodictyaceae (Chlorophyceae), for which poor resolution in previous phylogenetic studies, along with divergent morphological traits, have precluded taxonomic revisions. METHODS Complete plastome sequences and mitochondrial protein-coding gene sequences were acquired from representatives of the Hydrodictyaceae using next-generation sequencing methods. Plastomes were characterized, and gene order and content were compared with plastomes spanning the Sphaeropleales. Single-gene and concatenated-gene phylogenetic analyses of plastid and mitochondrial genes were performed. KEY RESULTS The Hydrodictyaceae contain the largest sphaeroplealean plastomes thus far fully sequenced. Conservation of plastome gene order within Hydrodictyaceae is striking compared with more dynamic patterns revealed across Sphaeropleales. Phylogenetic analyses resolve Hydrodictyon sister to a monophyletic Pediastrum, though the morphologically distinct P. angulosum and P. duplex continue to be polyphyletic. Analyses of plastid data supported the neochloridacean genus Chlorotetraëdron as sister to Hydrodictyaceae, while conflicting signal was found in the mitochondrial data. CONCLUSIONS A phylogenomic approach resolved within-family relationships not obtainable with previous phylogenetic analyses. Denser taxon sampling across Sphaeropleales is necessary to capture patterns in plastome evolution, and further taxa and studies are needed to fully resolve the sister lineage to Hydrodictyaceae and polyphyly of Pediastrum angulosum and P. duplex.

Testing the boundaries of the green algal species Pediastrum alternans (Chlorophyceae) using conventional, geometric morphometric and phylogenetic methods

Abstract: This article focuses on a detailed morphological and molecular analysis of the microscopic green alga Pediastrum alternans as it exhibits ambiguous morphology, questionable phylogenetic position and scattered distribution. The species, originally described from lakes close to the Baltic Sea in Denmark, was recently renamed Pseudopediastrum alternans based on rDNA sequencing of one culture from Namibia. In the present study, the African culture was morphologically and genetically compared with a culture identified as Ps. alternans from a coastal lake from northern Poland and a culture of Ps. boryanum var. longicorne from southern Poland. Conventional measurements, statistical and geometric morphometric analyses of the number of cells in coenobia, cell shape and size and wall ornamentation showed significant differences in the morphology of the three cultures. The analyses supported the phylogenetic distinction of the cultures based on rDNA and chloroplast DNA sequencing. Cultures of Pseudopediastrum alternans from Africa and Poland were not monophyletic. The African culture was moderately supported in a clade that could potentially represent a new species of Pseudopediastrum; whereas, the Polish culture formed a distinct lineage that was sister to some Ps. boryanum strains. The third culture, identified as Ps. boryanum var. longicorne, was nested within Ps. boryanum, as expected based on its morphology. Additional morphological comparison between the cultures and the iconotype showed that the Polish culture fits the description of Ps. alternans; whereas, the African one is so different from the iconotype that it cannot be called Ps. alternans. Analysis of plasticity of the Polish culture showed that its morphology is rather stable under varying nutrient and salinity conditions, and the culture cannot be misidentified as other Pseudopediastrum species.

Novel green algal isolates from the Egyptian hyper-arid desert oases: a polyphasic approach with a description of Pharao desertorum gen. et sp. nov. (Chlorophyceae, Chlorophyta)

The biodiversity of terrestrial algae is still grossly understudied, and African deserts in particular are barely touched in this respect. Here, four coccoid green algae from oases in the Western Desert of Egypt were characterized using a combination of morphotaxonomic, ecological and 18S rDNA data, with additional carotenoid and lipid analyses for two of the strains. Three strains were identified as affiliated with known taxa: Mychonastes sp., Asterarcys sp. (first report of this genus from a desert soil), and Stichococcus cf. deasonii. The fourth strain is proposed to represent a new cryptic genus Pharao gen. nov., with the type species P. desertorum sp. nov. The new taxon is sister to the clade of uncharacterized North American desert strains of Radiococcaceae (Chlorophyceae, Chlorophyta). The pigment profile of P. desertorum gen. et sp. nov. revealed carotenoids and chlorophylls typical of green algae. Bioorganic analysis showed a complex lipidome based on phospho‐ (PC), galacto‐ (MGDG and DGDG), betaine‐ (DGTS), and sulfoquinovosyl‐ (SQDG) membrane lipids, besides significant amounts of storage neutral lipids such as diacyl‐ (DAG) and triacylglycerols (TAG). The presence of saturated alkyl chains within all the membrane lipid classes in P. desertorum and Asterarcys sp. appears to reflect the need to maintain membrane fluidity and viscosity. In summary, African deserts likely still harbor new taxa to be described, and lipidomic analyses of such taxa may provide clues about their ability to survive in the extremely harsh desert habitats.