The Effect of Branch Length Variation on the Selection of Models of Molecular Evolution

Models of sequence evolution play an important role in molecular evolutionary studies. The use of inappropriate models of evolution may bias the results of the analysis and lead to erroneous conclusions. Several procedures for selecting the best-fit model of evolution for the data at hand have been proposed, like the likelihood ratio test (LRT) and the Akaike (AIC) and Bayesian (BIC) information criteria. The relative performance of these model-selecting algorithms has not yet been studied under a range of different model trees. In this study, the influence of branch length variation upon model selection is characterized. This is done by simulating sequence alignments under a known model of nucleotide substitution, and recording how often this true model is recovered by different model-fitting strategies. Results of this study agree with previous simulations and suggest that model selection is reasonably accurate. However, different model selection methods showed distinct levels of accuracy. Some LRT approaches showed better performance than the AIC or BIC information criteria. Within the LRTs, model selection is affected by the complexity of the initial model selected for the comparisons, and only slightly by the order in which different parameters are added to the model. A specific hierarchy of LRTs, which starts from a simple model of evolution, performed overall better than other possible LRT hierarchies, or than the AIC or BIC. Received: 2 October 2000 / Accepted: 4 January 2001     

Foramanifera and biostratigraphy of the Valdeteja Formation stratotype (Carboniferous, Cantabrian Zone, NW Spain)

Summary The Valdeteja Formation is a lithostratigraphic unit of essentially Bashkirian age widely distributed through the Cantabrian Zone (Iberian Massif, NW Spain). It consists mainly of limestones with subordinate limestone breccias and some marly intercalations, deposited in shallow carbonate platforms and in the adjacent slope and basin settings (see Eichmüller, 1985). Its considerable thickness, rather continuous stratigraphic record and large lateral extent in the Cantabrian Zone have attracted the attention of geologists who have carried out a number of studies dealing with the palaeontological content, sedimentology, and palaeogeography of this formation. In spite of these diverse investigation, the precise age of the Valdeteja Formation, particularly the age of several fossiliferous beds defined at its stratotype, as well as the age of the top of the formation, remain obscure. This paper studies the foraminifera (mainly fusulinoideans) yielded by several beds throughout the type-section. The biostratigraphic information provided by these faunas allows us to establish the age of the mentioned beds in terms of the Russian stratigraphic scale. It confirms an early Moscovian age for the top of the type section, a matter of discussion for a very long time. Moreover, this research may have general interest in Carboniferous stratigraphy since it provides data on the fusulinoidean assemblages existing in western Europe during Bashkirian time, an interval containing a rather poor fossil record in this part of Eurasia.     

Selection of the conodont Idiognathodus simulator (Ellison) as the event marker for the base of the global Gzhelian Stage (Upper Pennsylvanian, Carboniferous)

Studies carried out for more than 10 years by the Task Group to establish GSSPs at the base of the Moscovian–Kasimovian and Kasimovian–Gzhelian boundaries have resulted in the proposal that the level at which the conodont species Idiognathodus simulator (Ellison, 1941) first appears be selected to mark the base of the Gzhelian Stage. This expands this eastern European chronostratigraphic unit to a global scale.I. simulator (sensu Barrick et al., 2008) has been identified so far in Midcontinent and eastern North America, the Moscow and Donets basins and southern Urals of eastern Europe, and in south-central China. Correlation of this level based on this species and other conodont species can be reinforced in some areas by ammonoid and fusulinid data.     

LXR/ApoE Activation Restricts Innate Immune Suppression in Cancer

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Effect of elevated CO2 on growth and crassulacean-acid-metabolism activity of Kalanchoë pinnata under tropical conditions

 Kalancho? pinnata (Lam.) Pers. (Crassulaceae), a succulent-leaved crassulacean-acid-metabolism plant, was grown in open-top chambers at ambient and elevated (two times ambient) CO₂ concentrations under natural conditions at the Smithsonian Tropical Research Institute, Republic of Panama. Nocturnal increase in titratable acidity and nocturnal carbon gain were linearly related, increased with leaf age, and were unaffected by CO₂ treatments. However, under elevated CO₂, dry matter accumulation increased by 42–51%. Thus, the increased growth at elevated CO₂ was attributable entirely to increased net CO₂ uptake during daytime in the light. Malic acid was the major organic acid accumulated overnight. Nocturnal malate accumulation exceeded nocturnal citrate accumulation by six-to eightfold at both CO₂ concentrations. Basal (predawn) starch levels were higher in leaves of plants grown at elevated CO₂ but diurnal fluctuations of starch were of similar magnitude under both ambient and elevated CO₂. In both treatments, nocturnal starch degradation accounted for between 78 and 89% of the nocturnal accumulation of malate and citrate. Glucose, fructose, and sucrose were not found to exhibit marked day-night fluctuations. Received: 4 March 1996 / Accepted: 25 May 1996     

Evolutionary history of Trachylepis skinks in the Seychelles islands: introgressive hybridization,morphological evolution and geographic structure

The Seychelles is a remarkably interesting archipelago for evolutionary studies, but only recently have molecular markers been used to explore its biogeographic patterns. Here we used morphological and molecular data to examine diversity and phylogenetic relationships of two endemic skink sister‐species from this archipelago: Trachylepis sechellensis and Trachylepis wrightii. Mitochondrial DNA genealogy rendered a monophyletic T. wrightii nested within a paraphyletic T. sechellensis, whereas nuclear DNA sequences from five unlinked markers reflected the accepted taxonomy. Hybridization and massive mtDNA introgression leading to the complete replacement of the native mtDNA lineage of T. sechellensis in some of the islands were invoked to explain this result, and morphological variation also seemed to reflect this pattern of reticulation. A Mio‐Pliocene divergence between both species is suggested. Multilocus molecular data were used to uncover biogeographic patterns within the archipelago, which reflected shared patterns with other co‐distributed lizard taxa; specifically a north–south marked structure, a close relationship between populations from Fregate and the southern islands, and a detectable isolation within the southern group, between Mahé, and Silhouette and North Islands. Gene flow from these latter islands towards the northern group was also suggested. These results add to the growing body of evidence of the influence of geographic distance and sea‐level oscillations in shaping the genetic structure of Seychellois taxa and of the existence of common biogeographic patterns across the archipelago.     

Production of Bacillus thuringiensis subsp. medellin by batch and fed-batch culture

Bacillus thuringiensis subsp. medellin was grown until sporulation in a 1.1 l fermenter in batch and intermittent fed-batch culture. At optimum conditions 25 g dry cells l–1 and 9×108 spores ml–1 were produced. Toxicity of the final biomass showed a half lethal concentration on third instar Culex quinquefasciatus larvae of 295 ng ml–1.