The bioeroded megasurface of Oura (Algarve,south Portugal): implications for the Neogene stratigraphy and tectonic evolution of southwest Iberia

The use of rocky palaeoshore bioerosion analysis as a tool to solve stratigraphic and tectonic issues is beginning to bear fruits. The occurrence of an extensive intra-Miocene marine abrasion platform in southern Portugal at Oura (Albufeira) has been identified on the basis of bioerosion trace fossils analysis. The observed ichnodiversity is rather low, with bivalve boring Gastrochaenolites being dominant. Nevertheless, the ichnoassemblage may be assigned to the Entobia ichnofacies. The palaeoichnological study of the Oura hardground confirmed the existence of an important intra-Miocene stratigraphic gap (ca. 3 Ma hiatus), represented by a razor-sharp erosional contact that separates the two main Neogene units in the Algarvian region: the lower carbonate sequence of Lagos–Portimão Formation (Langhian/Serravallian) and the upper siliciclastic sequence of the Cacela Formation (Upper Tortonian).     

The problem of characters susceptible to parallel evolution in phylogenetic analysis: a reply to Marquès and Gnaspini (2001) with emphasis on cave life phenotypic evolution

Marquès and Gnaspini [Cladistics 17 (2001) 371–381] analyzed the problem of the phylogenetic treatment of characters submitted to parallel evolution. Their proposal aimed at preserving the potential phylogenetic significance of supposedly homoplastic characters and considering them for phylogeny reconstruction. As an example, they used the troglobiomorphic features of animals restricted to caves; according to their preliminary hypothesis of homoplasy, troglobitic animals would exhibit a particular phenotype, referred to as troglobiomorphic, which they would acquire under similar selective pressures from the subterranean environment. We examined Marquès and Gnaspini's approach not from the point of view of its technical flaws, but from the point of view of the authors’ basic assertions on the treatment of troglobiomorphic characters and more generally the inclusion/exclusion/transformation of characters prior to phylogenetic analysis. In the present paper, we argue that this approach is invalidated by the repeated use of ad hoc hypotheses, which are supported neither by an existing phylogenetic pattern nor by available data. We consequently contest the adequateness of this approach with a cladistic analysis of historical questions.     

Molecular phylogeny of telenomine egg parasitoids (Hymenoptera: Platygastridae s.l.: Telenominae): evolution of host shifts and implications for classification

Parasitoid wasps of the subfamily Telenominae (Hymenoptera: Platygastroidea, Platygastridae) develop as immatures within the eggs of other insects (Lepidoptera, Hemiptera, Diptera and Neuroptera). Rearing records indicate that individual species are restricted to attack hosts within only one of these four main groups. We conducted a phylogenetic analysis of the group using sequence data from multiple genes (18S, 28S, COI, EF‐1α) to assess the pattern of shifts among host groups and to test the monophyly of and relationships among genera and species‐groups. Telenominae sensu Masner—that is, including only the nominate tribe Telenomini—is not monophyletic. Representatives of the Psix group of genera (Psix Kozlov & Lê and Paratelenomus Dodd) form a monophyletic group that is sister to Gryon Haliday (Scelioninae: Gryonini) and are excluded from the subfamily. The remaining telenomines are monophyletic. The genus Phanuromyia Dodd and the crassiclava group of Telenomus Haliday, both recorded as parasitoids of planthopper eggs (Hemiptera: Auchenorrhyncha, Fulgoroidea), form a monophyletic group that is sister to all other telenomines exclusive of the Psix group. Twenty‐nine species of the crassiclava and aradi groups of Telenomus are transferred to Phanuromyia as new combinations. Basal elements of the remaining species are all in groups reared from the eggs of true bugs (Heteroptera), primarily the stink bugs (Pentatomoidea) and seed bugs (Lygaeoidea). A shift to parasitism of lepidopteran eggs evolved within a single clade, occurring either one or two times. From this clade a small group of species, the Telenomus tabanivorus group, subsequently shifted to parasitism of egg masses of true flies (Tabanidae and Stratiomyiidae). Aholcus Kieffer and Platytelenomus Dodd both belong to the clade of lepidopteran parasitoids and are considered as junior synonyms of Telenomus (new synonymy for Aholcus). The monophyletic status of the two core genera, Telenomus and Trissolcus could not be resolved using these data. The phylogenetic pattern of host shifts suggests comparisons among taxa that may be fruitful in elucidating mechanisms by which parasitoids locate their hosts, the proximate factors that determine the host range, and the changes in these factors that influence host changes.     

The Lake Superior varve stratigraphy and implications for eastern Lake Agassiz outflow from 10,700 to 8900 cal ybp (9.5-8.0 C ka)

Glaciolacustrine rhythmites within sediment cores from Lake Superior record the regional recession of the Laurentide Ice Sheet (LIS) from 10,700 to 8900 cal ybp [ca. 9.5-8.0 ¹⁴C ka]. LIS retreat from Superior opened eastern Lake Agassiz outlets so that the rhythmites reflect the combined impacts of sediment-laden meltwater and Lake Agassiz discharge. Multiple rhythmite stratigraphies, a time series analysis of the thickness measurements, and high-resolution inorganic carbonate data demonstrate that this is an annual record (varved). The varve thickness records primarily document regional ice margin dynamics; correlative thick varve sequences at 9100 cal ybp [∼ 8.1 ¹⁴C ka] and 10,400-10,200 cal ybp [∼ 9.2-9.0 ¹⁴C ka] record two periods of enhanced glaciofluvial discharge, most likely moraine formation (the Nakina and Nipigon). General varve cessation is associated with the circumvention of Lake Agassiz and glacial meltwater into Lake Ojibway at 9040 cal ybp [∼ 8.1 ¹⁴C ka], although adjacent to the inlets from Lake Nipigon, rhythmic sedimentation persisted for 200 years.Positively identifying Lake Agassiz catastrophic discharge events remains speculative but seems feasible. Following retreat of Marquette ice that had re-advanced to fill the basin, the initial influx of Lake Agassiz water is expected at around 10,600 cal ybp [∼ 9.4 ¹⁴C ka], but at this time, most of northeastern Lake Superior was covered by ice. Three sets of thick-thin varves in western Lake Superior perhaps record influxes of Lake Agassiz at around 10,630, 10,600, and 10,570 cal ybp [∼ 9.4 ¹⁴C ka]. Varve formation in Superior coincides with high lake levels in Lake Huron, suggesting that high lake levels in Huron correspond to periods of high Agassiz and/or meltwater flow into Lake Superior.     

Expansion of bloom-forming Dolichospermum lemmermannii (Nostocales,Cyanobacteria) to the deep lakes south of the Alps: Colonization patterns,driving forces and implications for water use

Since the beginning of the 1990s, the largest lakes south of the Alps (Garda, Iseo, Como and Maggiore) showed a progressive colonization of Dolichospermum lemmermannii (Cyanobacteria). The appearance of surface blooms of this species raised serious concerns because of the impacts on the tourist economy and the potential toxigenic effects. Nevertheless, no detailed investigations were done to clarify the taxonomic position, ecology and toxicity of this species. In this work, phylogenetic analyses based on the 16S rRNA and rpoB genes demonstrated how the strains isolated from the Italian lakes were clustered together with other D. lemmermannii strains isolated in Northern Europe. The expansion of this species in the southern subalpine lakes contrasted with the prevailing south to north dispersion paths typical of other Nostocales (e.g. Cylindrospermopsis and Aphanizomenon). Conversely, the spread was consistent with the geographical areal of this cyanobacterium, which appears circumscribed between the 40th parallel and the Arctic Circle. This aspect highlights the ecological heterogeneity that characterizes the order Nostocales. In Lake Garda, D. lemmermannii always developed in the warmest months (>15 °C) with low abundances (generally <200 cell mL⁻¹). Nevertheless, owing to its ability to form surface water blooms, this species is considered as one of the most nuisance algae in the subalpine lake district. From the other side, different strains isolated from these large lakes tested negative for the biosynthesis of microcystins, anatoxin-a, nodularins and cylindrospermopsins, and for the presence of mcyE and anaC genes of the microcystins and anatoxin-a gene clusters.     

The evolution of Cayaponia (Cucurbitaceae): Repeated shifts from bat to bee pollination and long-distance dispersal to Africa 2-5 million years ago

? Premise of the study: The Cucurbitaceae genus Cayaponia comprises ～60 species that occur from Uruguay to the southern United States and the Caribbean; C. africana occurs in West Africa and on Madagascar. Pollination is by bees or bats, raising the question of the evolutionary direction and frequency of pollinator shifts. Studies that investigated such shifts in other clades have suggested that bat pollination might be an evolutionary end point. ? Methods: Plastid and nuclear DNA sequences were obtained for 50 accessions representing 30 species of Cayaponia and close relatives, and analyses were carried out to test monophyly, infer divergence times, and reconstruct ancestral states for habitat preferences and pollination modes. ? Key results: The phylogeny shows that Cayaponia is monophyletic as long as Selysia (a genus with four species from Central and South America) is included. The required nomenclatural transfers are made in this paper. African and Madagascan accessions of C. africana form a clade that is part of a polytomy with Caribbean and South American species, and the inferred divergence time of 2-5 Ma implies a transoceanic dispersal event from the New World to Africa. The ancestral state reconstructions suggest that Cayaponia originated in tropical forests from where open savannas were reached several times and that bee pollination arose from bat pollination, roughly concomitant with the shifts from forests to savanna habitats. ? Conclusions: Cayaponia provides the first example of evolutionary transitions from bat to bee pollination as well as another instance of transoceanic dispersal from the New World to Africa.     

A chimeric ubiquitin conjugating enzyme that combines the cell cycle properties of CDC34 (UBC3) and the DNA repair properties of RAD6 (UBC2): implications for the structure, function and evolution of the E2s.

The CDC34 (UBC3) protein from Saccharomyces cerevisiae has a 125 residue tail that contains a polyacidic region flanked on either side by sequences of mixed composition. We show that although a catalytic domain is essential for CDC34 activity, a major cell cycle determinant of this enzyme is found within a 74 residue segment of the tail that does not include the polyacidic stretch or downstream sequences. Transposition of the CDC34 tail onto the catalytic domain of a functionally unrelated E2 such as RAD6 (UBC2) results in a chimeric E2 that combines RAD6 and CDC34 activities within the same polypeptide. In addition to the tail, the cell cycle function exhibited by the chimera and CDC34 is probably dependent on a conserved region of the catalytic domain that is shared by both RAD6 and CDC34. Despite this similarity, the CDC34 catalytic domain cannot substitute for the DNA repair and growth functions of the RAD6 catalytic domain, indicating that although these domains are structurally related, sufficient differences exist to maintain their functional individuality. Expression of the CDC34 catalytic domain and tail as separate polypeptides are capable of only partial function; thus, while the tail displays autonomous structural characteristics, there is considerable advantage gained when both domains coexist within the same polypeptide. The ability of these and other derivatives to restore partial function to a cdc34 temperature-sensitive mutant but not to a disruption mutant suggests that interaction between two CDC34 polypeptides is a requirement of CDC34 activity. Based on this idea we propose a model that accounts for the initiating steps leading to multi-ubiquitin chain synthesis.(ABSTRACT TRUNCATED AT 250 WORDS)     

The structure and dynamics of the U4/U6 snRNP: implications for pre-mRNA splicing and use as a model system to investigate the RNA-mediated effects of (5F)Ura

Pre-mRNA splicing is one of the most complex and intricate processes in eukaryotic cell biology. Over the past decade, my laboratory has been interested in determining the structures of RNA components of the spliceosome, and in investigating how the structure, stability and dynamics of these RNA components are perturbed by nucleoside analog substitution. In particular, we have investigated the U4/U6 snRNA complex as a model system for understanding the biophysical basis for the RNA-mediated effects of the widely-used anticancer drug 5-fluorouracil ((5F)Ura). In this review, our studies that have provided novel information concerning the structure of U4 snRNA and its interactions with U6 snRNA and the Sm (or common) snRNA binding proteins are summarized. These studies have also quantified the structural and thermodynamic consequences of (5F)Ura in this model system. Our work to date provides the foundation on which future studies investigating the biophysical basis for spliceosomal assembly and for clarifying the mechanisms of anticancer drugs targeted at nucleic acid-mediated processes will be developed.     

Length-dependent degradation of single-stranded 3' ends by the Werner syndrome protein (WRN): implications for spatial orientation and coordinated 3' to 5' movement of its ATPase/helicase and exonuclease domains

Background  

The cancer-prone and accelerated aging disease Werner syndrome is caused by loss of function of the WRN gene product that possesses ATPase, 3' to 5' helicase and 3' to 5' exonuclease activities. Although WRN has been most prominently suggested to function in telomere maintenance, resolution of replication blockage and/or recombinational repair, its exact role in DNA metabolism remains unclear. WRN is the only human RecQ family member to possess both helicase and exonuclease activity, but the mechanistic relationship between these activities is unknown. In this study, model single-stranded and 3' overhang DNA substrates of varying length and structure were used to examine potential coordination between the ATPase/helicase and exonuclease activities of WRN.