Jumping behavior in the oligotrich ciliates Strobilidium velox and Halteria grandinella,and its significance as a defense against rotifer predators

The jumping behavior of Strobilidium velox and Halteria grandinella was analyzed videographically. On average, undisturbed cells of these species jumped 1.7–3.6 and 8 times per minute and spent 0.8 and 1.0% of their time jumping, respectively. Both ciliate species initiated jumps after encounters with rotifer predators. S. velox jumped on contact with Asplanchna girodi, traveling a mean distance of 1.5 mm (33 body lengths) at a mean velocity of 7 mm/s (154 body lengths/s) at 17°C. H. grandinella jumped on contact or near contact with Synchaeta pectinata, traveling a mean distance of 0.37 mm (18 body lengths) at a mean velocity of 2.76 mm/s (131 body lengths/s) at 20°C. The maximum velocity recorded during these escape jumps was 16.07 mm/s for S. velox and 3.70 mm/s for H. grandinella. In S. velox, swimming velocity during jumps was not significantly correlated either with swimming velocity just before jumping (mean = 0.15 mm/s) or with distance traveled. In H. grandinella, jumping velocity and distance also were not significantly correlated. Jumping in S. velox and H. grandinella was calculated to require approximately 149% and 41 % of total metabolic rate, respectively. Jumping seemed to be an effective defense against rotifer predation. Only 3% of 93 S. velox cells contacted by A. girodi were captured, and only 12% of 92 H. grandinella cells contacted or closely approached by S. pectinata were captured; all other cells jumped away. A predation experiment showed that A. girodi was about twice as, and significantly more, likely to ingest Paramecium tetraurelia as S. velox in a mixture of equal numbers of these ciliates. The swimming velocity of S. velox during jumps is the highest one so far reported for an oligotrich, and equals the highest one reported for any ciliate (Mesodinium rubrum).     

Bermuda as an Evolutionary Life Raft for an Ancient Lineage of Endangered Lizards

Oceanic islands are well known for harboring diverse species assemblages and are frequently the basis of research on adaptive radiation and neoendemism. However, a commonly overlooked role of some islands is their function in preserving ancient lineages that have become extinct everywhere else (paleoendemism). The island archipelago of Bermuda is home to a single species of extant terrestrial vertebrate, the endemic skink Plestiodon (formerly Eumeces) longirostris. The presence of this species is surprising because Bermuda is an isolated, relatively young oceanic island approximately 1000 km from the eastern United States. Here, we apply Bayesian phylogenetic analyses using a relaxed molecular clock to demonstrate that the island of Bermuda, although no older than two million years, is home to the only extant representative of one of the earliest mainland North American Plestiodon lineages, which diverged from its closest living relatives 11.5 to 19.8 million years ago. This implies that, within a short geological time frame, mainland North American ancestors of P. longirostris colonized the recently emergent Bermuda and the entire lineage subsequently vanished from the mainland. Thus, our analyses reveal that Bermuda is an example of a “life raft” preserving millions of years of unique evolutionary history, now at the brink of extinction. Threats such as habitat destruction, littering, and non-native species have severely reduced the population size of this highly endangered lizard.     

Ultrastructural Study of an Endosymbiotic Alga and Its Host Ciliate Stentor niger

Stentor niger collected in the suburbs of Hiroshima contained in its cytoplasm several hundreds of endosymbiotic algae and innumerable brownish pigment granules. The body of the ciliate was dark due to a mixture of the green endosymbiotic algae and brown pigment granules. The algae belonged to the genus Chlorella; each was enclosed in a perialgal vacuole and dispersed uniformly in the host cytoplasm from the myoneme layer inward to the center of the ciliate. The cell wall and plasma membrane of the alga enclosed a nucleus, chloroplast, mitochondrion, Golgi complex, accumulation bodies, myelinated vesicles, and many ribosomes. The chloroplast occupied more than half of the volume of the alga and contained a conspicuous pyrenoid. Algal multiplication occurred by two successive divisions of an alga, leading to four autospores within a perialgal vacuole; the walls of the vacuole invaginated to separate the autospores each into its own vacuole. Three types of pigment granules were scattered uniformly throughout the cytoplasm of the ciliate. The ultrastructure of the membranellar region, somatic cortex, and macro- and micronucleus of the ciliate are also described.     

The Structure of the Herpes Simplex Virus DNA-Packaging Terminase pUL15 Nuclease Domain Suggests an Evolutionary Lineage among Eukaryotic and Prokaryotic Viruses

Herpes simplex virus 1 (HSV-1), the prototypic member of herpesviruses, employs a virally encoded molecular machine called terminase to package the viral double-stranded DNA (dsDNA) genome into a preformed protein shell. The terminase contains a large subunit that is thought to cleave concatemeric viral DNA during the packaging initiation and completion of each packaging cycle and supply energy to the packaging process via ATP hydrolysis. We have determined the X-ray structure of the C-terminal domain of the terminase large-subunit pUL15 (pUL15C) from HSV-1. The structure shows a fold resembling those of bacteriophage terminases, RNase H, integrases, DNA polymerases, and topoisomerases, with an active site clustered with acidic residues. Docking analysis reveals a DNA-binding surface surrounded by flexible loops, indicating considerable conformational changes upon DNA binding. In vitro assay shows that pUL15C possesses non-sequence-specific, Mg²⁺-dependent nuclease activity. These results suggest that pUL15 uses an RNase H-like, metal ion-mediated catalysis mechanism for cleavage of viral concatemeric DNA. The structure reveals extra structural elements in addition to the RNase H-like fold core and variations in local architecture of the nuclease active site, which are conserved in herpesvirus terminases and bear great similarity to the phage T4 gp17 but are distinct from podovirus and siphovirus orthologs and cellular RNase H, delineating a new evolutionary lineage among a large family of eukaryotic viruses and simple and complex prokaryotic viruses.     

Lineage Specificity of the Evolutionary Dynamics of the mtDNA D-Loop Region in Rodents

This paper reports an intraorder study on the D-loop-containing region of the mitochondrial DNA in rodents. A complete multialignment of this region is not feasible with the exception of some conserved regions. The comparative analysis of 25 complete rodent sequences from 23 species plus one lagomorph has revealed that only the central domain (CD), a conserved region of about 80 bp in the extended termination-associated sequences (ETAS) domain, adjacent to the CD, the ETAS1, and conserved sequence block (CSB) 1 blocks are present in all rodent species, whereas the presence of CSB2 and CSB3 is erratic within the order. We have also found a conserved region of 90 bp located between tRNAPro and ETAS1 present in fat dormouse, squirrel, guinea pig, and rabbit. Repeated sequences are present in both the ETAS and the CSB domain, but the repeats differ in length, copy number, and base composition in different species. The potential use of the D-loop for evolutionary studies has been investigated; the presence/absence of conserved blocks and/or repeated sequences cannot be used as a reliable phylogenetic marker, since in some cases they may be shared by distantly related organisms but not by close ones, while in other ones a relationship between tree topology and presence/absence of such motifs is observed. Better results can be obtained by the use of the CD, which, however, due to its reduced size, when used for tracing a phylogenetic tree, shows some nodes with low statistical support. Received: 26 February 2001 / Accepted: 6 June 2001     

Molecular Evolutionary Analyses of Nuclear-Encoded Small Subunit Ribosomal RNA Identify an Independent Rhizopod Lineage Containing the Euglyphina and the Chlorarachniophyta

The Rhizopoda comprise a diverse assemblage of protists which depend on lobose or filose pseudopodia for locomotion. The biochemical and morphological diversity of rhizopods has led to an uncertain taxonomy. Ribosomal RNA sequence comparisons offer a measure of evolutionary relatedness that is independent of morphology and has been used to demonstrate a polyphyletic origin of the Lobosea. We sequenced complete small subunit ribosomal RNA coding regions from the filose amoebae, Euglypha rotunda and Paulinella chromatophora (Euglyphina) to position these taxa in the eukaryote phylogeny. The neighbor-joining analyses show that E. rotunda and P. chromatophora share a monophyletic origin and are not closely related to any lobose amoebae in our analyses. Instead, the Euglyphina form a robust sister group to the Chlorarachniophyta. These results provide further evidence for the polyphyly of the Rhizopoda and support the creation of a new amoeboid lineage which includes the Euglyphina and the chlorarachniophyte algae; taxa with tubular mitochondrial cristae and filose or reticulate pseudopodia.     

Search for Clues to the Evolutionary Meaning of Ciliate Phylogeny*†

SYNOPSIS. Progress in ciliatology and in allied fields may demystify ciliate phylogenetics. Concentration on hymenostomes (mainly Tetrahymena and Paramecium) may have obscured directional features of ciliate physiology in phylogenetic problems. Therefore, means are suggested for “domesticating” the presumptively primitive, predominantly marine, sand-dwelling gymnostomes having nondividing diploid macronuclei. The prize quarry is the marine psammophile Stephanopogon whose homokaryotic condition may mark it as a living fossil. Eventual axenic cultivation of these “primitive” ciliates may be aided by use as food of easily grown photosynthetic prokaryotes, some isolated from the marine sulfuretum or adjacent aerobic muds and sands where “karyorelictid” ciliates flourish. We assume that: (a) the macronucleus evolved as a coordinator of chemical and physical signals, for efficient detection of food and toxins; (b) oral structures evolved meanwhile as sensors as well as mechanical food-gatherers. This conjunction enabled complexity of adaptive behavior and evolutionary success. Ciliate origins cannot be considered apart from origin(s) of phagotrophy and its underlying versatile heterotrophy. Because of the well developed heterotrophy in some photosynthetic prokaryotes (including several proposed as food organisms), they are viewed as alternatives to blue-green algae as forebears of eukaryotes. Nor can ciliate origins be considered apart from origin(s) of eukaryotes. A check of these assumptions—that Stephanopogon and gymnostomes with nondividing macronuclei are primitive—may be forthcoming from sequencing amino acids in certain key enzymes, given an adequate sampling of ciliates, flagellates (especially dinoflagellates and cryptomonads), lower fungi, and photosynthetic prokaryotes other than blue-green algae.     

The Rhinal Bone and Its Evolutionary Significance

Bjerring, H. C. (Section of Palaeozoology, Swedish Museum of Natural History, Stockholm, Sweden.) The rhinal bone and its evolutionary significance. Zool. Scripta 1 (5): 193–201, 1972.– On the basis of serially sectioned embryos of Amia calva, the ethmoidal region of the endocranium and certain adjacent exo-skeletal elements are analysed. The results include evidence of the existence of branchial moieties pertaining to the first or premandibular metamere. Each of these moieties comprises infrapharyngobranchial (the ethmobasal), suprapharyngobranchial (the orbitonasal lamina), and epibranchial (the palatoquadrate pterygoid process) endoskeletal components as well as horizontal infrapharyngeal (the vomer), ascending infrapharyngeal (the rhinal), and epal (the dermopalatines and ectopterygoid) dental plates. The anterior cerebral arteries may represent the efferent blood vessels of the first-metamere branchial moieties. A hypothesis on the origin of the nasal sacs is offered.      

Ultrastructure of the Peritrich Ciliate Ambiphrya ameiuri and Its Attachment to the Gills of the Catfish Ictalurus punctatus1

Ambiphrya ameiuri is an ectocommensal peritrich that attaches to the gills of warm-water fishes and filters bacteria from the water. The ultrastructure of this protozoon, its attachment to the fish gills, and its effect on the gill tissue were investigated by scanning and transmission electron microscopy. The peritrich attached to the gills by fibers extending from the scopula. A microtubular array, apparently a barren kinetosome, was present in each lobular projection, but no scopular cilia were observed. At low densities Ambiphrya had no apparent harmful effects on the fish; however, at high densities respiration may be impeded. Ultrastructural studies indicate that this organism receives no nourishment from the host tissue.     

A Somatic Kinetid Study of the Pycnotrichid Ciliate Vestibulongum corlissi N. G., N. Sp. (Class: Litostomatea), Symbiont in the Intestines of the Surgeonfish,Acanthurus xanthopterus1

ABSTRACT The ciliate Vestibulongum corlissi n. g., n. sp. was collected from the intestines of surgeonfish, Acanthurus xanthopterus, in the summer of 1986. In has been examined in the light microscope after protargol staining and by scanning and transmission electron microscopy. Its form is distinct from that of other pycnotrichid ciliates at the generic level. Somatic kinetids were examined; these demonstrate that its cytostome is posterior and that the kinetid structures and the presence of a second transverse microtubular ribbon confirm its placement in the class Litostomatea.     

Assessment of Species Diversity and Distribution of an Ancient Diatom Lineage Using a DNA Metabarcoding Approach

Background

Continuous efforts to estimate actual diversity and to trace the species distribution and ranges in the natural environments have gone in equal pace with advancements of the technologies in the study of microbial species diversity from microscopic observations to DNA-based barcoding. DNA metabarcoding based on Next Generation Sequencing (NGS) constitutes the latest advancement in these efforts. Here we use NGS data from different sites to investigate the geographic range of six species of the diatom family Leptocylindraceae and to identify possible new taxa within the family.

Methodology/Principal Findings

We analysed the V4 and V9 regions of the nuclear-encoded SSU rDNA gene region in the NGS database of the European ERA-Biodiversa project BioMarKs, collected in plankton and sediments at six coastal sites in European coastal waters, as well as environmental sequences from the NCBI database. All species known in the family Leptocylindraceae were detected in both datasets, but the much larger Illumina V9 dataset showed a higher species coverage at the various sites than the 454 V4 dataset. Sequences identical or similar to the references of Leptocylindrus aporus, L. convexus, L. danicus/hargravesii and Tenuicylindrus belgicus were found in the Mediterranean Sea, North Atlantic Ocean and Black Sea as well as at locations outside Europe. Instead, sequences identical or close to that of L. minimus were found in the North Atlantic Ocean and the Black Sea but not in the Mediterranean Sea, while sequences belonging to a yet undescribed taxon were encountered only in Oslo Fjord and Baffin Bay.

Conclusions/Significance

Identification of Leptocylindraceae species in NGS datasets has expanded our knowledge of the species biogeographic distribution and of the overall diversity of this diatom family. Individual species appear to be widespread, but not all of them are found everywhere. Despite the sequencing depth allowed by NGS and the wide geographic area covered by this study, the diversity of this ancient diatom family appears to be low, at least at the level of the marker used in this study.     

Evolutionary Correlation Between Linker Histones and Microtubular Structures

Histones of the H1 group (linker histones) are abundant components of chromatin in eukaryotes, occurring on average at one molecule per nucleosome. The recent reports on the lack of a clear phenotypic effect of knock-out mutations as well as overexpression of histone H1 genes in different organisms have seriously undermined the long-held view that linker histones are essential for the basic functions of eukaryotic cells. In an attempt to resolve the paradox of an abundant conserved protein without a clear function, we re-examined the molecular and phylogenetic data on linker histones to see if they could reveal any correlation between the features of H1 and the functional or morphological characteristics of cells or organisms. Because of an earlier demonstration that in sea urchin the chromatin-type histone H1 is also found in the flagellar microtubules (Multigner et al. 1992), we focused on the correlation between the features of H1 and those of microtubular structures. A phylogenetic tree based on multiple alignment of over 100 available H1 sequences suggests that the first divergence of the globular domain of H1 (GH1) resulted in branching into separate types characteristic for plants/Dictyostelium and for animals/ascomycetes, respectively. The GH1s of these two types differ by a short region (usually 5 amino acids) placed at a specific location within the C-terminal wing subdomain of GH1. Evolutionary analysis of the diversification of H1 mRNA into cell-cycle-dependent (polyA⁻) and independent (polyA⁺) forms showed a mosaic occurrence of these two forms in plants and animals, despite the fact that the H1 proteins of plants and animals belong to two well-distinguished groups. However, among organisms from both animal and plant kingdom, only those with H1 mRNA of a polyA⁻ type have flagellated gametes. This correlation as well as the demonstration that in Volvox carteri the accumulation of polyA⁻ mRNA of H1 occurs concurrently with the production of new flagella (Lindauer et al. 1993), suggests a direct link between polyA⁻ phenotype of histone H1 mRNA and flagellogenesis. Received: 25 May 2000 / Accepted: 5 February 2001     

Inverse Correlation Between an Organ's Cancer Rate and Its Evolutionary Antiquity

Human cancer rates vary dramatically across the range of internal organs in the body, but there is no single model to explain the variation and there is also no obvious overall pattern to it. Theories have been proposed to account for high rates in particularly cancer-prone organs, and they usually concentrate on the peculiar vulnerability of certain cells to mutation (e.g., lung cells'' direct exposure to airborne carcinogens). These explanations are valuable for understanding mechanisms of disease and also for cancer prevention, but they address neither the overall distribution of cancers nor the possibility that some states of differentiation may be intrinsically less stable than others to the effects of random mutation, a possibility predicted on purely theoretical grounds many years ago. This brief report describes an overall pattern to human organ-specific cancer incidence data and shows that organ-specific cancer rates correlate negatively with an organ''s evolutionary antiquity. Although the relationship may just be coincidental, it suggests the possibility that recently-evolved differentiation states may be intricnsically more vulnerable to neoplastic change. Extrapolation of the regression line to a cancer incidence of zero equates to a level of tissue organization typical of 660 Myr ago; the inferred beginning of neoplasia therefore coincides with the rise of complex multicellular animals.Key Words: cancer, neoplasia, evolution, differentiation, stability     

Cell Lineage of the Ilyanassa Embryo: Evolutionary Acceleration of Regional Differentiation during Early Development

Cell lineage studies in mollusk embryos have documented numerous variations on the lophotrochozoan theme of spiral cleavage. In the experimentally tractable embryo of the mud snail Ilyanassa, cell lineage has previously been described only up to the 29-cell stage. Here I provide a chronology of cell divisions in Ilyanassa to the stage of 84 cells (about 16 hours after first cleavage at 23°C), and show spatial arrangements of identified nuclei at stages ranging from 27 to 84 cells. During this period the spiral cleavage pattern gives way to a bilaterally symmetric, dorsoventrally polarized pattern of mitotic timing and geometry. At the same time, the mesentoblast cell 4d rapidly proliferates to form twelve cells lying deep to the dorsal ectoderm. The onset of epiboly coincides with a period of mitotic quiescence throughout the ectoderm. As in other gastropod embryos, cell cycle lengths vary widely and predictably according to cell identity, and many of the longest cell cycles occur in small daughters of highly asymmetric divisions. While Ilyanassa shares many features of embryonic cell lineage with two other caenogastropod genera, Crepidula and Bithynia, it is distinguished by a general tendency toward earlier and more pronounced diversification of cell division pattern along axes of later differential growth.     

Pharmacological Characterization of an Opioid Receptor in the Ciliate Tetrahymena

A pharmacological characterization has been performed of the opioid receptor involved in modulation of phagocytosis in the protozoan ciliate Tetrahymena. Studies on inhibition of phagocytosis by mammalian prototypic opioid agonists revealed that morphine and β-endorphin have the highest intrinsic activity, whereas all the other opioids tested can only be considered partial agonists. However, morphine (a mu-receptor agonist) is twice as potent as β-endorphin (a delta-receptor agonist). Furthermore, the sensitivity for the opioid antagonist naloxone, determined in the presence of morphine and β-endorphin, is very similar to the sensitivity exhibited by mammalian tissues rich in mu-opioid receptors. We suggest that the opioid receptor coupled to phagocytosis in Tetrahymena is mulike in some of its pharmacological characteristics and may serve as a model system for studies on opioid receptor function and evolution.     

Correlation Between Ka/Ks and Ks is Related to Substitution Model and Evolutionary Lineage

In 2005, Wyckoff and coworkers described a surprisingly strong correlation between Ka/Ks and Ks in several data sets using the LPB93 algorithm. This finding indicated the possibility of a paradigm shift in the way selection strength can be measured using the Ka/Ks ratio. We carried out a calculation of Ka and Ks using six different algorithms on three cross-species orthologous data sets and found a highly variable correlation among the algorithms and lineages. Algorithms based on the GY-HKY substitution model exhibit a weaker positive correlation or a stronger negative correlation than those based on the K2P and JC69 substitution model. Even if one algorithm shows a positive correlation between Ka/Ks and Ks in a warm-blooded lineage, it may show no correlation in a cold-blooded lineage. This algorithm-related and evolutionary lineage-related correlation indicates the need for great caution in drawing conclusions when using only one Ka and Ks algorithm in a genomewide analysis of selection strength. Our results indicated that currently used algorithms for Ka and Ks calculations are flawed and need improvements.     

The Early Origin of the Antarctic Marine Fauna and Its Evolutionary Implications

The extensive Late Cretaceous – Early Paleogene sedimentary succession of Seymour Island, N.E. Antarctic Peninsula offers an unparalleled opportunity to examine the evolutionary origins of a modern polar marine fauna. Some 38 modern Southern Ocean molluscan genera (26 gastropods and 12 bivalves), representing approximately 18% of the total modern benthic molluscan fauna, can now be traced back through at least part of this sequence. As noted elsewhere in the world, the balance of the molluscan fauna changes sharply across the Cretaceous – Paleogene (K/Pg) boundary, with gastropods subsequently becoming more diverse than bivalves. A major reason for this is a significant radiation of the Neogastropoda, which today forms one of the most diverse clades in the sea. Buccinoidea is the dominant neogastropod superfamily in both the Paleocene Sobral Formation (SF) (56% of neogastropod genera) and Early - Middle Eocene La Meseta Formation (LMF) (47%), with the Conoidea (25%) being prominent for the first time in the latter. This radiation of Neogastropoda is linked to a significant pulse of global warming that reached at least 65°S, and terminates abruptly in the upper LMF in an extinction event that most likely heralds the onset of global cooling. It is also possible that the marked Early Paleogene expansion of neogastropods in Antarctica is in part due to a global increase in rates of origination following the K/Pg mass extinction event. The radiation of this and other clades at ∼65°S indicates that Antarctica was not necessarily an evolutionary refugium, or sink, in the Early – Middle Eocene. Evolutionary source – sink dynamics may have been significantly different between the Paleogene greenhouse and Neogene icehouse worlds.