Subtropical coral-reef associated sedimentary facies characterized by molluscs (Northern Bay of Safaga, Red Sea, Egypt)

Summary The shallow marine subtropical Northern Bay of Safaga is composed of a complex pattern of sedimentary facies that are generally rich in molluscs. Thirteen divertaken bulk-samples from various sites (reef slopes, sand between coral patches, muddy sand, mud, sandy seagrass, muddy seagrass, mangrove channel) at water depths ranging from shallow subtidal to 40m were investigated with regard to their mollusc fauna >1mm, which was separated into fragments and whole individuals. Fragments make up more than 88% of the total mollusc remains of the samples, and their proportions correspond to characteristics of the sedimentary facies. The whole individuals were differentiated into 622 taxa. The most common taxon,Rissoina cerithiiformis, represented more than 5% of the total mollusc content in the samples. The main part of the fauna consists of micromolluscs, including both small adults and juveniles. Based on the results of cluster-, correspondence-, and factor analyses the fauna was grouped into several associations, each characterizing a sedimentary facies: (1) “Rhinoclavis sordidula—Corbula erythraeensis-Pseudominolia nedyma association” characterizes mud. (2) “Microcirce sp.—Leptomyaria sp. association” characterizes muddy sand. (3)”Smaragdia spp.-Perrinia stellata—Anachis exilis—assemblage” characterizes sandy seagrass. (4) “Crenella striatissima—Rastafaria calypso—Cardiates-assemblage” characterizes muddy seagrass. (5) “Glycymeris spp.-Parvicardium sueziensis-Diala spp.-assemblage” characterizes sand between coral patches. (6) “Rissoina spp.-Triphoridae —Ostreoidea-assemblage” characterizes reef slopes. (7) “Potamides conicus—Siphonaria sp. 2—assemblage” characterizes the mangrove. The seagrass fauna is related to those of sand between coral patches and reef slopes with respect to gastropod assemblages, numbers of taxa and diversity indices, and to the muddy sand fauna on the basis of bivalve assemblages and feeding strategies of bivalves. The mangrove assemblage is related to those of sand between coral patches and the reef slope with respect to taxonomic composition and feeding strategies of bivalves, but has a strong relationship to those of the fine-grained sediments when considering diversity indices. Reef slope assemblages are closely related to that of sand between coral patches in all respects, except life habits of bivalves, which distincly separates the reef slope facies from all others.     

Responses of mobile epifauna to small-scale seagrass patchiness: is fragmentation important?

Habitat fragmentation is a process involving splitting of continuous habitats into smaller, and more isolated habitat patches. To assess the effects of small-scale habitat patchiness and isolation without the confounding effect of habitat loss on benthic macrofauna, two field experiments were conducted in the Archipelago Sea, SW Finland. Using artificial seagrass units (ASUs) we contrasted continuous patches (“C”) with fragmented patches (“F”) of the same combined area as the continuous patches. The fragmentation treatment involved two isolation distances (0.5 and 3.0 m) between the ASUs (“F 0.5”) and (“F 3.0”). This design was repeated in two consecutive experiments where the patch area was 0.25 and 0.0625 m², respectively. Mobile epifauna were allowed to colonize patches for 12 days in both experiments. In both experiments, the total epifaunal density was significantly higher in the “F 0.5” treatment than in the “C” treatment, and the three dominant taxa showed positive or neutral responses to the habitat configuration. No fragmentation effect on the number of species was detected in either of the experiments, but fragmentation had a negative effect on the epifaunal diversity (Shannon’s H′) in the experiment with the largest patch area. Epifaunal diversity was significantly lower in “F 3.0” treatment than in “C” or “F 0.5” treatments in the first experiment, indicating stronger effect of isolation instead of fragmentation per se. Edge effects were indirectly tested by comparing epifaunal densities with patch edge:area ratios. The results suggest that edge effects may have a more important role than patch size for the total densities of epifaunal taxa, and that small, isolated patches have equal or higher habitat value compared to larger fragments.     

Recruitment patterns in Antarctic Peninsula shelf sediments: evidence of decoupling from seasonal phytodetritus pulses

Summer phytoplankton blooms on the West Antarctic Peninsula (WAP) shelf result in episodic deposition of labile food material for benthic detritivores. This summer deposition is thought to enhance benthic recruitment of macro- and megafauna. To explore seasonality in benthic recruitment, juvenile invertebrates (>100 μm) were collected in a seasonal time series at three stations on the WAP continental shelf. 4,098 juveniles were collected (average densities 2,000–7,000 m⁻²), with polychaetes dominant (2,581 individuals). The majority of polychaetes showed evidence of enhanced recruitment prior to the summer bloom, although patterns varied across stations. Additional taxa showed recruitment peaks in summer, but again, patterns varied among stations. Based on observed patterns, polychaete taxa are classified as “seasonal”, “marginally seasonal”, and “non-seasonal” recruiters, with the latter two patterns predominating. The year-round presence of small juveniles in most taxa suggests that recruitment occurs continuously, with periodic enhancement. Year-round recruitment is consistent with the presence of a persistent “food bank” of labile organic material in WAP shelf sediments, allowing recruitment to be largely decoupled from seasonal bloom dynamics.     

Macroevolution via secondary endosymbiosis: a Neo-Goldschmidtian view of unicellular hopeful monsters and Darwin’s primordial intermediate form

Seventy-five years ago, the geneticist Richard Goldschmidt hypothesized that single mutations affecting development could result in major phenotypic changes in a single generation to produce unique organisms within animal populations that he called “hopeful monsters”. Three decades ago, Sarah P. Gibbs proposed that photosynthetic unicellular micro-organisms like euglenoids and dinoflagellates are the products of a process now called “secondary endosymbiosis” (i.e., the evolution of a chloroplast surrounded by three or four membranes resulting from the incorporation of a eukaryotic alga by a eukaryotic heterotrophic host cell). In this article, we explore the evidence for Goldschmidt’s “hopeful monster” concept and expand the scope of this theory to include the macroevolutionary emergence of organisms like Euglena and Chlorarachnion from secondary endosymbiotic events. We argue that a Neo-Goldschmidtian perspective leads to the conclusion that cell chimeras such as euglenids and dinoflagellates, which are important groups of phytoplankton in freshwater and marine ecosystems, should be interpreted as “successful monsters”. In addition, we argue that Charles Darwin had euglenoids (infusoria) in mind when he speculated on the “primordial intermediate form”, although his Proto-Euglena-hypothesis for the origin of the last common ancestor of all forms of life is no longer acceptable.     

Hydro-morphologically related variance in benthic drift and its importance for numerical habitat modelling

Numerical fish-habitat modelling on various scales is considered to be state of the art in river management. However, most of the concepts applied use steady-state hydraulic parameters such as flow velocity and water depth. Herein we present analysis and discussion of the possibility of including a drift-feeding parameter (SI_F) into habitat evaluations based on multiplying suitability indices. “Sources” and “sinks” of benthic drift were identified according to both the zero-crossing and hydraulic-threshold methods in an alpine gravel-bed river. Minor differences could be determined between the two methods in a well-developed riffle–pool section. Macroinvertebrates, used for simulating benthic drift, were collected by multi-habitat sampling and appraised according to their critical threshold (τ _cr) for motion on the bed surface and sinking velocity (v _s). The findings of the calculation of drift rates using one- (1D) and two-dimensional (2D) hydrodynamic numerical models highlight a specification of best feeding position for drift-feeding fish (i.e. brown trout, grayling) considering the SI_F parameter. Riffle–pool sequences are characteristic of pristine alpine streams; our findings underline their importance as production (riffles) and consumption areas (pools) in terms of holistic river function. Moreover, the results indicate that (artificial) lateral obstruction (e.g. dams) may lead to a reduced transport rate of benthic organisms due to low bottom shear stress (<0.25 N m⁻²). Thus, deposition of drifting macroinvertebrates occurs in backwaters, with downstream impacts on benthic and fish communities.     

Mating behavior of the rock catfish, Silurus lithophilus

The mating behavior of the rock catfish Silurus lithophilus (Siluriformes: Siluridae), a species endemic to the Lake Biwa system, was observed from May to July in 1989–1994 along the rocky shore of the lake's outlet, the Seta River. The mating behavior of S. lithophilus involved a certain behavioral sequence: “chasing,”“clinging,” and “enfolding” while “squeezing” by the male; and “circling” by the spawned pair. The mating behavior of this species was basically similar to that of S. biwaensis, but greatly different from that of S. asotus, which spawns in running water (in ditches). The mating behavior of S. lithophilus (and S. biwaensis) might have developed as an adaptation to lentic environments such as the shores of the large river or the lake. Received: October 25, 2000 / Revised: February 25, 2001 / Accepted: March 8, 2001     

Horizontal gradient in fish assemblage structures in and around a seagrass habitat: some implications for seagrass habitat conservation

Horizontal gradients in fish assemblage structures in and around a seagrass habitat were evaluated by visual observations. The assemblage structures clearly differed between open microhabitats lacking seagrass, i.e., nearby sand and the area adjoining the outer margin of the seagrass bed (referred to as “outer gap”), and microhabitats with seagrass within the overall seagrass bed, although not differing among the latter microhabitats, including both edge and core portions. Such open microhabitats were found to be not always inferior, but nearly equal to or even sometimes greatly superior in fish species’ diversity and/or abundance to the microhabitats with seagrass. In particular, the outer gap was always ranked first in total species’ number and had outstanding abundance in spring. Similar open microhabitats adjoining seagrass walls facing the sand patch within the seagrass bed (referred to as “inner gap”) in spring were also characterized by higher fish species and individual numbers. The 11 most abundant fishes showed four discrete distribution patterns (three recognized herein and one implied by precedent studies), such contributing to a horizontal gradient in the fish assemblage structure. While no fishes showed a preference for the edge or core of the seagrass bed, group-forming juveniles of several species favored gap microhabitats, suggesting that, in addition to the traditionally recognized edge and core microhabitats, the concept of gap microhabitats should be included in seagrass conservation ecology.     

Structure and diversity of shallow soft-bottom benthic macrofauna in the Gulf of Lions (NW Mediterranean)

Samples of soft-sediment macrobenthos from 92 sites between 10 and 50 m depth were used to assess (1) the main soft-bottom macrofauna communities in the Gulf of Lions, (2) the different components of the diversity of benthic macrofauna in this area, and (3) the relevance of the use of major taxonomic groups as surrogates for the analysis of the structure and diversity of total macrofauna. Three main communities were identified by cluster analysis and associated procedures. These communities corresponded well to the assemblages recently identified on the basis of polychaete composition. The α-diversity indices were in accordance with those reported for similar communities in the Mediterranean. Conversely, the β-diversity value was higher than the few other data available in the literature for marine soft-bottom macrofauna. The total number of species in the studied area estimated by the “total species accumulation curve” (TS) method was 2,319, which was only 10% higher than the number obtained by extrapolation of the species–area curve. The similarity matrix based on polychaetes correlated best with the one based on total macrofauna. Polychaetes and crustaceans were also the best surrogates of total macrofauna when assessing α-diversity (except in the case of Δ*). Conversely, molluscs were the best surrogates of total macrofauna β-diversity. Our results show that the choice of an optimal surrogate for total benthic macrofauna depends on the characteristic of the benthic macrofauna to be studied. Moreover, this choice is also dependent on the environment to be studied.     

Linking limitation to species composition: importance of inter- and intra-specific variation in grazing resistance

Short-term responses of producers highlight that key nutrients (e.g., N, P)—or combinations of these nutrients—limit primary production in aquatic and terrestrial ecosystems. These discoveries continue to provide highly valuable insights, but it remains important to ask whether nutrients always predominantly limit producers despite wide variation in nutrient supply and herbivory among systems. After all, predictions from simple food chain models (derived here) readily predict that limitation by grazers can exceed that by nutrients, given sufficient enrichment. However, shifts in composition of producers and/or increasing dominance of invulnerable stages of a producer can, in theory, reduce grazer limitation and retain primacy of nutrient limitation along nutrient supply gradients. We observed both mechanisms (inter- and intra-species variation in vulnerability to herbivory) working in a two-part mesocosm experiment. We incubated diverse benthic algal assemblages for several months either in the presence or absence of benthic macro-grazers in mesocosms that spread a broad range of nutrient supply. We then conducted short-term assays of nutrient and grazer limitation on these communities. In the “historically grazed” assemblages, we found shifts from more edible, better competitors to more resistant producers over enrichment gradients (as anticipated by the food web model built with a tradeoff in resistance vs. competitive abilities). However, contrary to our expectations, “historically ungrazed” assemblages became dominated by producers with vulnerable juvenile forms but inedible adult forms (long filaments). Consequently, we observed higher resource limitation rather than grazer limitation over this nutrient supply gradient in both “historically grazed” (expected) and “historically ungrazed” (not initially expected). Thus, via multiple, general mechanisms involving resistance to grazing (changes in species composition or variation in stage-structured vulnerability), producer assemblages should remain more strongly or as strongly limited by nutrients than grazers, even over large enrichment gradients. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Quantum Information Processing in the Wall of Cytoskeletal Microtubules

Microtubules (MT) are composed of 13 protofilaments, each of which is a series of two-state tubulin dimers. In the MT wall, these dimers can be pictured as “lattice” sites similar to crystal lattices. Based on the pseudo-spin model, two different location states of the mobile electron in each dimer are proposed. Accordingly, the MT wall is described as an anisotropic two-dimensional (2D) pseudo-spin system considering a periodic triangular “lattice”. Because three different “spin-spin” interactions in each cell exist periodically in the whole MT wall, the system may be shown to be an array of three types of two-pseudo-spin-state dimers. For the above-mentioned condition, the processing of quantum information is presented by using the scheme developed by Lloyd.     

Mayfly production in a New Zealand glacial stream and the potential effect of climate change

In contrast to the northern hemisphere where species of Chironomidae are usually the dominant benthic invertebrates in the coldest upper reaches of glacial streams, mayflies (Deleatidium spp.: Leptophlebiidae) predominate in equivalent conditions in New Zealand. We examined the life histories and annual production of Deleatidium spp. at two sites on the Matukituki River (South Island, New Zealand) and at three sites in its glacier-fed tributary, Rob Roy Stream. Mean annual water temperature at the five sites ranged from 2.1 to 7.0°C. Monthly sampling showed that mayfly populations were poorly synchronised at all sites but were probably univoltine. The large Deleatidium cornutum was the dominant mayfly species found at the upper sites (Sites 1 and 2) on Rob Roy Stream, whereas above the confluence with Matukituki River (Site 3) it co-existed with a complex of smaller species we refer to as D. “angustum”. Deleatidium “angustum” also dominated at the Matukituki sites. Deleatidium production calculated for the five sites, assuming an 11-month nymphal life, ranged from 0.48 g dry weight/m²/year (Site 1) to 3.07 g dry weight/m²/year (Site 3). The values for D. cornutum at Sites 2 and 3 are high for a species of Deleatidium and reflect its large size. This species appears to be strongly adapted for growth at low temperatures. Climate change scenarios for New Zealand predict the gradual and ultimate loss of small South Island glaciers and a consequent warming of streams as runoff from rainfall and snow melt becomes more dominant in spring. As a result, suitable habitats will be lost for cold-water specialists such as D. cornutum, and they are likely to suffer reductions in their distributional range and local extinction. In contrast, species such as those in the D. “angustum” complex may extend their ranges into streams formerly dominated by glacial meltwater. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Handling editor: S. Stendera     

Impacts of dugong foraging on benthic animal communities in a Thailand seagrass bed

We studied the community structure and abundance of benthic animals in intertidal seagrass beds in Thailand, where dugongs (Dugong dugon) feed on the seagrass Halophila ovalis. Our objective was to examine whether the benthic community was affected by the foraging activity of the dugongs, which can cause disturbance to the sediment. We collected a total of 4156 benthic animals from three study sites and classified them into 77 different taxa. A lucinid bivalve, Pillucina sp., was the most abundant taxa (approximately 80% of individuals). Taxa richness of the benthic animals was higher in intact H.ovalis vegetation compared to dugong trails at all sites. In general, the densities of five functional groups (classified by position on/in the sediment and motility) and five dominant taxa were higher in intact seagrass vegetation compared to dugong trails, although the magnitude of this difference varied among functional groups and taxa. Densities were at least threefold higher in the seagrass vegetation than in the dugong trails for epifauna and shallow infauna, but were at most twofold higher for deep infauna. Taxa richness and abundance of the benthic animals in the dugong trails were similar between the day following, and 7–9days after, the creation of the trails. Thus, delayed and/or indirect effects of dugong herbivory on benthic communities were not detected in this study. These findings demonstrate that the foraging activity of dugongs in seagrass can have considerable impacts on the abundance and diversity of benthic organisms, although this effect varies among benthic animals with different lifestyles.     

Inventory, differentiation, and proportional diversity: a consistent terminology for quantifying species diversity

Almost half a century after Whittaker (Ecol Monogr 30:279–338, 1960) proposed his influential diversity concept, it is time for a critical reappraisal. Although the terms alpha, beta and gamma diversity introduced by Whittaker have become general textbook knowledge, the concept suffers from several drawbacks. First, alpha and gamma diversity share the same characteristics and are differentiated only by the scale at which they are applied. However, as scale is relative––depending on the organism(s) or ecosystems investigated––this is not a meaningful ecological criterion. Alpha and gamma diversity can instead be grouped together under the term “inventory diversity.” Out of the three levels proposed by Whittaker, beta diversity is the one which receives the most contradictory comments regarding its usefulness (“key concept” vs. “abstruse concept”). Obviously beta diversity means different things to different people. Apart from the large variety of methods used to investigate it, the main reason for this may be different underlying data characteristics. A literature review reveals that the multitude of measures used to assess beta diversity can be sorted into two conceptually different groups. The first group directly takes species distinction into account and compares the similarity of sites (similarity indices, slope of the distance decay relationship, length of the ordination axis, and sum of squares of a species matrix). The second group relates species richness (or other summary diversity measures) of two (or more) different scales to each other (additive and multiplicative partitioning). Due to that important distinction, we suggest that beta diversity should be split into two levels, “differentiation diversity” (first group) and “proportional diversity” (second group). Thus, we propose to use the terms “inventory diversity” for within-sample diversity, “differentiation diversity” for compositional similarity between samples, and “proportional diversity” for the comparison of inventory diversity across spatial and temporal scales. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Amphipod (Gammarus minus) responses to predators and predator impact on amphipod density

Recent theoretical work suggests that predator impact on local prey density will be the result of interactions between prey emigration responses to predators and predator consumption of prey. Whether prey increase or decrease their movement rates in response to predators will greatly influence the impact that predators have on prey density. In stream systems the type of predator, benthic versus water-column, is expected to influence whether prey increase or decrease their movement rates. Experiments were conducted to examine the response of amphipods (Gammarus minus) to benthic and water-column predators and to examine the interplay between amphipod response to predators and predator consumption of prey in determining prey density. Amphipods did not respond to nor were they consumed by the benthic predator. Thus, this predator had no impact on amphipod density. In contrast, amphipods did respond to two species of water-column predators (the predatory fish bluegills, Lepomis macrochirus, and striped shiners, Luxilus chrysocephalus) by decreasing their activity rates. This response led to similar positive effects on amphipod density at night by both species of predatory fish. However, striped shiners did not consume many amphipods, suggesting their impact on the whole amphipod “population” was zero. In contrast, bluegills consumed a significant number of amphipods, and thus had a negative impact on the amphipod “population”. These results lend support to theoretical work which suggests that prey behavioral responses to predators can mask the true impact that predators have on prey populations when experiments are conducted at small scales. Received: 21 March 1997 / Accepted: 15 December 1997     

An integrated strategy for the process development of a recombinant antibody-cytokine fusion protein expressed in BHK cells

Recombinant fusion proteins offer important new therapeutic approaches for the future. This report describes the use of three different genetic strategies (i.e. “mono-”, “bi-” and “tri-cistronic” vectors) to achieve stable secretion from BHK cells of a glycosylated antibody-cytokine fusion protein designed for use in anti-tumour therapy. It describes selection of a robust and effective production cell line based on stability of secretion of the product, quality of mRNA and protein products and performance in in vitro bioassays for potency. The data obtained at this stage were utilised in the selection of a suitable candidate production cell line. The relative productivity and general performance of the cells in stirred tank and fixed bed culture systems indicated that a variety of cell culture technologies provided robust tools for production of a highly selected cell clone. Consistency of the product glycosylation was determined by analysis of released oligosaccharides using matrix-assisted laser desorption ionisation – time of flight mass spectrometry and high-performance anion exchange chromatography. These investigations showed consistent expression of three glycoforms of the fusion protein which varied in their relative proportions in different culture systems and at different time points in a fixed bed reactor with continuous perfusion. In conclusion, this study dealt with a range of important scientific and technical issues which are essential for regulatory approval and commercial success of a recombinant protein and elucidates some useful markers for process development for similar recombinant biologicals. Received: 25 March 1999 / Accepted: 23 April 1999     

Enhancement of juvenile Caribbean spiny lobsters: an evaluation of changes in multiple response variables with the addition of large artificial shelters

Shortage of natural crevice shelters may produce population bottlenecks in juvenile Caribbean spiny lobsters (Panulirus argus), a socially gregarious species. We conducted a field experiment to test enhancement of a local population of juvenile P. argus with the addition of artificial shelters (“casitas”) that mimic large crevices (1.1 m² in surface area and 3.8 cm in height). Changes in density and biomass of juvenile lobsters 15–50 mm carapace length (CL) were assessed with a multiple before-after control-impact (MBACI) analysis. Separate analyses were also conducted on small (15–35 mm CL) and large (35.1–50 mm CL) juveniles to assess size-related effects. First, we carried out 13 lobster surveys on nine fixed 1-ha sites over a shallow reef lagoon (“before” period). Then, we deployed ten casitas in each of five sites and left four sites as controls, and conducted 22 further surveys (“after” period). Deployment of casitas resulted in a sixfold increase in juvenile density (76% contributed by small and 24% by large juveniles) and a sevenfold increase in biomass (40 and 60%, respectively). Capture–recapture results revealed that enhancement was achieved not by promoting individual growth but by increasing survival, persistence, and foraging ranges of small and large juveniles. Casitas both mitigated shortage of natural shelter and increased sociality, allowing for cohabitation of smaller, more vulnerable juveniles with larger conspecifics that have greater defensive abilities. Casitas may help enhance local populations of juvenile P. argus in Caribbean seagrass habitats, typically poor in natural crevice shelters. The use of MBACI and the simultaneous assessment of multiple interrelated response variables may be a powerful analytical approach to test shelter limitation in other species and to examine the function of structural habitat in other systems.     

Assessment of the Neva Estuary ecosystem state on the basis of structural characteristics of benthic animal communities in 1994–2005

In the years 1994–2005, the values of the integrated index IP’ at some stations of the Neva Bay changed from 38.1 to 81.9%, water quality changed from class 3 to class 5, and the states of some areas of the ecosystem that were evaluated as “tense” went to “catastrophic.” The integrated mean assessment of water quality according to the IP’ index over the entire Neva Bay throughout 12 years (1994–2005) remained relatively stable, waters were assessed as “polluted” (fourth class), and the state of the ecosystem was considered “critical.” The state of the eastern part of the Gulf of Finland in 1994–2005 was less favorable. The species diversity of zoobenthos in the resort zone of the eastern part of the Gulf of Finland is considerably lower than in the Neva Bay. Waters of the resort zone of the eastern part of the Gulf of Finland in 1994–2005 were assessed as one class lower than in the Neva Bay, i.e., as “polluted-dirty” (fourth-fifth class), and the state of the ecosystem was assessed as being in a “crisis.” In the resort zone, there was a decline in species diversity and abundance and biomass of benthic animals; i.e., all characteristics of the degradation of benthic animal communities were observed.     

Effects of the “Amoco Cadiz ” oil spill on an eelgrass community at roscoff (france) with special reference to the mobile benthic fauna

In October 1977 an investigation was initiated of the qualitative and quantitative composition of the fauna of the eelgrass (Zostera marina) beds at Roscoff. Samples were taken in 2 seagrass beds at different tidal levels in order to follow numerical changes in the course of the year. In March 1978 the area of study was struck by the oil slick of the tanker “Amoco Cadiz ”. For this reason sampling has been continued at the same frequency. The tabulated results show clearly that the oil slick had a profound but selective influence on the various animal groups; some of them disappeared while others were apparently unaffected. Rapid recovery of some species has taken place, but re-establishment of other species, particularly the filter feeders has not been observed. The very diverse amphipod fauna has disappeared, and has been replaced by a population ofPherusa fucicola andGammarus locusta; the latter was absent in the year before the oil disaster took place.     

Models on prebiotic polymer competition: A deterministic approach

Two simple models are proposed and analysed, in which it is shown that the formation of a new polymer, resulting from an “error” in the template action mechanism of production of an old polymer, may compromise the stability of the initial system under specific conditions, in the context of prebiotic evolution. Autocatalysis is shown to be a “selective advantage”, enabling the “mutant” to dominate in concentration and even replace the initial polymer. The addition of a third molecule playing the role of a catalyst causes hysteresis effects.     

Shifting ditypic site analysis: Heuristics for expanding the phylogenetic range of nucleotide sequences in Sankoff analyses

Summary We describe and illustrate a simple heuristic approach to the Sankoff methods for construction of parsimonious evolutionary trees from nucleotide sequence data. The procedure is intended to permit more valid inferences, particularly from relatively short sequences, concerning relationships among taxa separated for long time intervals. The procedure is based on the freat variability of evolutionary plasticity among sites in the molecules and removes from consideration the more highly variable sites. Editing is accomplished after classifying sites in carefully aligned arrays of sequences. Only “ditypic sites,” i.e., sites observed in only two evolutionary states within the array, are used in making phylogenetic inferences. This strategy makes possible the construction of good approximations to the most parsimonious Steiner strees, by means of efficient programs that require “dense species arrays,” i.e., species sets that differ from each other by relatively small numbers of differences in conservative sites. The technique is illustrated with 5S and 5.8S rRNA sequence data from published catalogs.