Foraminifera may structure meiobenthic communities

The cosmopolitan benthic foraminiferan, Ammonia beccarii, is a fervent microfloral predator which often forms densely-populated 2–4 cm² aggregates in the field. Sediments within aggregate patches become extensively pelletized, mucus bound and depleted in microfloral food. On a West German Wattenmeer mudflat, copepodite and naupliar densities of a predominant harpacticoid copepod, Amphiascoides limicola, were significantly depressed in sediments containing>100 A. beccarii·3 cm^-2 suggesting a possible foraminiferal: copepod amensalism. Therefore, I cultured A. beccarii and A. limicola separately in sediment microcosms and then tested if A. limicola's seemingly negative reaction to sediments containing A. beccarii occurs under controlled conditions, how various life stages of A. limicola are affected, and what the repulsive mechanisms of A. beccarii may be. In natural field sediments seeded with a latin-square dispersion of sterile sediment patches containing 0 or 100 A. beccarii, mean A. limicola naupliar and copepodite densities were 2 to 6 times lower in Ammonia-rich patches than Ammonia-poor patches (i.e. patches containing <100 A. beccarii·3 cm^-2). Choice experiments directly testing potential A. beccarii inhibitory mechanisms were conducted with A. limicola copepodites: Cubic microcosms containing a latin-square patch dispersion of (1) sterile sediments (SS) seeded with 100 A. beccarii (low microflora), (2) SS bound with sterile mucus (0.0001%) (low microflora), (3) SS seeded with pelletized sediments (high microflora), and (4) SS seeded with mucus and pellets (high microflora), showed that copepodites colonized 12 & 3, but 1 & 4 were not significantly different. Mucus addition by itself, in the absence of pelletization and microflora, strongly facilitated colonization—as did addition of microfloral-rich pelletized sediments. Pelletization and mucousbinding combined, but with low microflora, were least attractive to A. limicola. Pelletization and mucous-binding combined, but with high microflora, were more attractive to A. limicola than its complement, but not significantly so. Thus A. beccarii's inhibition of A. limicola is probably not caused by sediment pelletization and simple mucous exudates but by local microfloral depletion within aggregate foraminiferal patches.Contribution No 774 of the Belle W. Baruch Institute for Marine Biology and Coastal Research     

Simple Models of Agglutinated Foraminifera Test Construction

ABSTRACT. The characteristic grain size distributions observed in the test walls of agglutinated foraminifera can be replicated by numerical simulations. the logistics employed by the model parallel those seen in foraminifera during culturing experiments of test construction. Both fractal and log-normal grain distributions are generated by a simple space-filling algorithm. However, to generate the specific grain distributions observed in foramimferan tests a strong preference for selecting larger grains from the available sediment must be effected. the exclusion of smaller grains, during selection, produces log-normal grain distributions similar to those previously observed. These and similar modelling techniques may provide valuable insights into the mechanisms of shell construction employed by protists.     

Palaeobiology and evolution of the earliest agglutinated Foraminifera: Platysolenites, Spirosolenites and related forms

Tubular agglutinated fossils of Platysolenites antiquissimus Eichwald, 1860, P. cooperi n.sp. and Spirosolenites spiralis Glaessner, 1979 are examined from selected lower Cambrian successions in Avalonia (England; Wales; Newfoundland) and Baltica (Russia and Estonia). Platysolenites cooperi n.sp. is shown to extend below the first appearance of P. antiquissimus in the Neoproterozoic-Cambrian boundary stratotype region, SE Newfoundland, and to occur at higher stratigraphic levels in Wales and Finnmark. Taphonomic, teleological and ultrastructural studies on well-preserved material are consistent with a similar grade of organization and mode of life for P. antiquissimus and the living astrorhizacean foraminiferid Bathysiphon. However, agglutinated proloculi are here described from both rectilinear P. antiquissimus and coiled S. spiralis, which suggests that neither were typical astrorhizaceans.     

Foraminifera in stratigraphy

Jenkins, D. G. & Murray, J. W. (ed.) 1989: Stratigraphical Atlas of Fossil Foraminifera. 2nd edition.     

The structure of protein evolution and the evolution of protein structure

The observed distribution of protein structures can give us important clues about the underlying evolutionary process, imposing important constraints on possible models. The availability of results from an increasing number of genome projects has made the development of these models an active area of research. Models explaining the observed distribution of structures have focused on the inherent functional capabilities and structural properties of different folds and on the evolutionary dynamics. Increasingly, these elements are being combined.     

Two species of Foraminifera of the genus Turrilina with different wall structure

Two species of the foraminiferal genus Turrilina Andreae, 1844, occurring in the Tertiary beds of Denmark and Holland, can be distinguished by their wall structure only. In consequence it is recommended that the wall structure as a systematic character may in this and similar cases be of specific value only.     

Floral structure and evolution in the Anacardiaceae

WANNAN, B. S. & QUINN, C. J, 1991. Floral structure and evolution in the Anacardiaceae. Carpel morphology and anatomy is investigated in 17 genera and carpellode morphology in 12 genera. There is an evolutionary sequence in the family from poorly differentiated, nearly apocarpous gynoecia towards syncarpous gynoecia with clearly defined stigmata, styles and ovaries. There has also been marked reduction culminating in pseudomonomery. The carpellodes of the male flowers appear more conservative, and provide evidence of affinities between genera with quite different fertile gynoecia. The characters have been polarized using Burseraceae as a sister group. Data from these sources, as well as from pericarp anatomy, wood anatomy and biflavonoid content indicate that the long standing intrafamilial classification into five tribes is artificial, and that the two small satellite families, Blepharocaryaceae and Julianiaceae should be included in the family. A large monophyletic group is recognized comprised of essentially four of the existing tribes (Anacardiëae, Dobineëae, Semecarpeae, Rhoëae), as well as the two satellite families. This group incorporates two subgroups of more closely allied genera. The remaining genera (mostly Spondiadeae) are very diverse, and for the present are placed in an artificial group characterised by a set of plesiomorphs. Relationships within this group must be resolved before a satisfactory taxonomy of the family can be achieved.     

A novel polyubiquitin structure in Cercozoa and Foraminifera: evidence for a new eukaryotic supergroup

Ubiquitin is a 76 amino acid protein with a remarkable degree of evolutionary conservation. Ubiquitin plays an essential role in a large number of eukaryotic cellular processes by targeting proteins for proteasome-mediated degradation. Most ubiquitin genes are found as head-to-tail polymers whose products are posttranslationally processed to ubiquitin monomers. We have characterized polyubuiquitin genes from the photosynthetic amoeboflagellate Chlorarachnion sp. CCMP 621 (also known as Bigelowiella natans) and found that they deviate from the canonical polyubiquitin structure in having an amino acid insertion at the junction between each monomer, suggesting that polyubiquitin processing in this organism is unique among eukaryotes. The gene structure indicates that processing likely cleaves monomers at the amino terminus of the insertion. We examined the phylogenetic distribution of the insertion by sequencing polyubiquitin genes from several other eukaryotic groups and found it to be confined to Cercozoa (including Chlorarachnion, Lotharella, Cercomonas, and Euglypha) and Foraminifera (including Reticulomyxa and Haynesina). This character strongly suggests that Cercozoa and Foraminifera are close relatives and form a new "supergroup" of eukaryotes.     

Chromatin structure and evolution in the human genome

Background  

Evolutionary rates are not constant across the human genome but genes in close proximity have been shown to experience similar levels of divergence and selection. The higher-order organisation of chromosomes has often been invoked to explain such phenomena but previously there has been insufficient data on chromosome structure to investigate this rigorously. Using the results of a recent genome-wide analysis of open and closed human chromatin structures we have investigated the global association between divergence, selection and chromatin structure for the first time.     

Size change in the phylogeny of Foraminifera

In the animal kingdom evolutionary size changes involved increasing, decreasing and stationary patterns. Planktic and benthic Foraminifera chiefly increased their size during evolution. This increase, however, did not always occur gradually, but could be interrupted by periods when the animals maintained or even decreased in size. The rate of the size increase is different for the various species examined, some benthic forms grew only 10% during the Oligocene-Pleistocene interval, while for others this figure was up to 96%. Some benthic species increased in size in certain areas, but not in others. It is not improbable that some phylogenetic trends of planktic Foraminifera representing, according to stratigraphers, the evolution of one species into another, represent in reality, from the biological point of view, specimens of the same species which changed their size and in addition some minor morphological traits which are encompassed by the normal span of intraspecific variability. A comprehensive understanding and explanation of the size change of Foraminifera needs much additional research. ▭ Foraminifera, size change.     

Introns and higher-order structure in the evolution of serpins

Summary The serpins are a large family of eukaryotic proteins, many but not all of whose members are proteinase inhibitors. Most members of this family show relatively low sequence identity, but crystal structures determined for 6 different serpins are closely similar. The intron positions of 11 serpins, and the intron sizes in 9 of these 11, have been determined. There is considerable diversity in number, position, and size of introns among these serpins, though subsets show clear similarity or identity. Dendrograms derived from comparisons of DNA and amino acid sequences and of intron positions for the 11 serpins differ from each other and from dendrograms previously derived from protein sequences. These dendrograms are difficult to reconcile exclusively with a loss of introns from a large primordial set during the evolution of the serpin family. The tertiary structure of the serpins does support the idea that this protein family arose from an early recombination event which fused the amino and carboxyl domains. The structure of the carboxyl domain also suggests that an insertion subsequent to the fusion event contributed two strands of -sheet, which complemented three -sheet strands of the amino domain, to complete -sheet A, which is the central secondary structure feature of the serpins. Few of the introns lie between regions of secondary or tertiary structure, and it seems more likely that many were acquired subsequent to the early events of serpin evolution and have undergone multiple insertions, deletions, and migrations since, subject to the constraint of the serpin structure.Abbreviations Api -1-proteinase inhibitor (human) - Aci -1-antichymotrypsin (human) - Agt angiotensinogen (rat) - Oah ovalbumin (chicken) - Gyh gene y (chicken) - At3 antithrombin 3 (human) - Pi1 plasminogen activator inhibitor 1—endothelial (human) - Pi2 plasminogen activator inhibitor 2—placental (human) - Cli Cl inhibitor (human) - Apl antiplasmin (human) - Bz4 Z protein (barley).     

SINEs, evolution and genome structure in the opossum

Short INterspersed Elements (SINEs) are non-autonomous retrotransposons, usually between 100 and 500 base pairs (bp) in length, which are ubiquitous components of eukaryotic genomes. Their activity, distribution, and evolution can be highly informative on genomic structure and evolutionary processes. To determine recent activity, we amplified more than one hundred SINE1 loci in a panel of 43 M. domestica individuals derived from five diverse geographic locations. The SINE1 family has expanded recently enough that many loci were polymorphic, and the SINE1 insertion-based genetic distances among populations reflected geographic distance. Genome-wide comparisons of SINE1 densities and GC content revealed that high SINE1 density is associated with high GC content in a few long and many short spans. Young SINE1s, whether fixed or polymorphic, showed an unbiased GC content preference for insertion, indicating that the GC preference accumulates over long time periods, possibly in periodic bursts. SINE1 evolution is thus broadly similar to human Alu evolution, although it has an independent origin. High GC content adjacent to SINE1s is strongly correlated with bias towards higher AT to GC substitutions and lower GC to AT substitutions. This is consistent with biased gene conversion, and also indicates that like chickens, but unlike eutherian mammals, GC content heterogeneity (isochore structure) is reinforced by substitution processes in the M. domestica genome. Nevertheless, both high and low GC content regions are apparently headed towards lower GC content equilibria, possibly due to a relative shift to lower recombination rates in the recent Monodelphis ancestral lineage. Like eutherians, metatherian (marsupial) mammals have evolved high CpG substitution rates, but this is apparently a convergence in process rather than a shared ancestral state.     

The Foraminifera of the Pitcairn Islands

Foraminifera were recovered from 18 samples collected in the Pitcairn Islands, 12 from Henderson Island (including the best and most comprehensive collections) and three each from Oeno Atoll and Pitcairn Island itself. Although both algae and sediment samples were collected, the living Foraminifera came, almost exclusively, from phytal (attached or clinging) habitats. Foraminifera in the sediment samples are mainly thanatocoenoses. The fauna is an exclusively calcareous, relatively low diversity assemblage, dominated by large soritids [Marginopora, Amphisorus, Sorites) and Amphistegina , all of which are ubiquitous throughout the tropical Pacific. These larger Foraminifera are usually accompanied by small miliolids in particular, as well as by small attached Foraminifera (discorbids and the like). Typical reefal Foraminifera are generally under-represented. So far, no endemic species have been found. Of more significance, perhaps, is the apparent absence of Calcarina , small rotaliids, elphidiids and agglutinating species, so common in the western Pacific islands. One sample of fossil Foraminifera was analysed, from a shelly sand (c. 30 m above present sea-level) on Henderson Island. Though, for the most part, like the Recent assemblages, this was characterized by Archaias , a soritid which was not found in any of the modern collections made by the 1991– 92 Expedition. This could either be a sampling artifact or refer to a real environmental change since the Pleistocene.     

Magmas gene structure and evolution

Magmas is a nuclear encoded protein found in the mitochondria of mammalian cells. It participates in granulocyte-macrophage-colony stimulating factor (GM-CSF) signaling in hematopoietic cells and has an essential role in invertebrate development. In order to characterize the protein structural features and gene evolution of Magmas, a dataset containing 61 Magmas homologs from 52 species distributed among animals, plants and fungi was analyzed. All Magmas members were found to possess three novel sequence motifs in addition to a conserved leader peptide. Phylogenetic tree and dN/dS rate ratios showed that Magmas was evolutionarily conserved. Analysis of Magmas gene organization demonstrated incremental intron acquisition in plants and vertebrates. Significant genetic diversity in Magmas was observed from kingdom specific amino acid signatures, the presence of predicted signal peptides that target the protein to other intracellular locations besides the mitochondria, and the detection of multiple isoforms in higher animals. These studies demonstrate that Magmas members constitute an important family of conserved proteins having multifunctional activities, and provide a basis for future experiments.     

Wall structure and evolution in cyclostomate Bryozoa

The Stenolaemata comprise both basically single-walled forms (Cyclostomata) and doublewalled forms (Trepostomata, Cystoporata and Cryptostomata) from their first appearance in the geological record. At the end of the Palaeozoic the main groups of apparently double-walled stenolaemates died out, and only the single-walled cyclostomates survived. During the Mesozoic, evolution within the Stenolaemata was apparently repeated by the further development of double-walled forms such as cerioporids, lichenoporids and cancelloids, from single-walled ancestors. These double-walled groups are all remarkable homeomorphs of the major Palaeozoic groups of Bryozoa. A monophyletic origin of the post-Palaeozoic Cyclostomata from Palaeozoic single-walled forms is thus suggested.