An approximate maximum likelihood approach, applied to phylogenetic trees.

A novel type of approximation scheme to the maximum likelihood (ML) approach is presented and discussed in the context of phylogenetic tree reconstruction from aligned DNA sequences. It is based on a parameterized approximation to the conditional distribution of hidden variables (related, e.g., to the sequences of unobserved branch point ancestors) given the observed data. A modified likelihood, based on the extended data, is then maximized with respect to the parameters of the model as well as to those involved in the approximation. With a suitable form of the approximation, the proposed method allows for simpler updating of the parameters, at the cost of an increased parameter count and a slight decrease in performance. The method is tested on phylogenetic tree reconstruction from artificially generated sequences, and its performance is compared to that of ML, showing that the approach is competitive for reasonably similar sequences. The method is also applied to real DNA sequences from primates, yielding a result consistent with those obtained by other standard algorithms.     

Late-flowering dune populations of Dactylorhiza incarnata (Orchidaceae): variation patterns and taxonomic inferences

Principal components analysis (PCA) was applied to summarize variation in 23 morphological characters scored from nine late-flowering dune populations of Dactylorhiza incarnata (Orchidaceae) in Wales, The Netherlands, and Denmark. The Dutch and Danish groups of populations were vaguely separated in a PCA conducted on populations, and a very broad overlap between them was found in a PCA conducted on individual specimens. On the other hand, a clear morphological distinction between the Welsh and continental groups of populations appeared from both PCAs. The probability of each character to distinguish correctly between the main groups of populations was estimated. Three characters were found to distinguish reliably (success ≥ 90 %) between the Welsh and continental groups of populations, while no character was found to distinguish reliably between the Dutch and Danish groups of populations. It is concluded that the Welsh and Dutch/Danish populations represent two distinct taxa distributed in the British Isles and in continental Northwestern Europe, respectively. The British taxon is recognized as D. incarnata subsp. coccinea and the continental one as D. incarnata subsp. lobelii (stat. nov.). Brief taxonomic accounts are provided.     

Three new species of Aiphanes (Palmae) with notes on the genus in Ecuador

Twelve species of the palm genus Aiphanes occur in Ecuador. The morphological variation in the genus is surveyed, and the distribution of the Ecuadorean species is discussed. A key to the species of Aiphanes in Ecuador is provided. Aiphanes chiribogensis, A. grandis , and A. verrucosa are described as new species, and illustrated. Aiphanes caryotifolia, A. eggersii, A. erinacea, A. fosteriorum, A. gela-tinosa, A. macroloba, A. schultzeana , and A. tricuspidata are characterized. One still unidentified species resembling A. tessmannii is discussed.     

Application dependency of lca methodology: Key variables and their mode of influencing the method

The reason to perform an LCA is essentially to use it in support of a decision. A decision gives rise to a change somewhere in society compared to a scenario in which this decision was not taken. The key requirement for the LCA in any application is therefore, that it shall reflect the environmental change caused by the decision. It is found, that the need to differentiate LCA methodology for the use in different applications is born by a few key characteristics of the decision to be supported. The first key characteristic is the environmental consequence of the decision, i.e. the nature and extent of the environmental change caused by the decision. When modelling the environmental change, its extent in time and space will differ between decision types, thus giving rise to different requirements, primarily for the scoping and inventory phases of the LCA. Furthermore, some decisions will imply trade-offs between different impact categories, while others will not, thus causing different requirements for the impact assessment. The second key characteristic is the social and economic consequence of the decision, the magnitude of which will influence the need for certainty, transparency and documentation. The third characteristic is the context in which the decision is taken, including the decision maker and interested parties, implicitly influencing the impact assessment and weighting.     

Precipitated Proteins Improve the Production of Carrot Somatic Embryos

Extracellular compounds isolated from embryogenic carrot cell suspension cultures increase, by 1.5 to 6-fold, end-stage embryo production when added back to carrot cultures initiating embryogenesis. The causative factors related to the enhancement of embryo production are most likely to be extracellular, high molecular weight proteins found in the embryo-free medium (EFM) after somatic embryos have been formed. The addition of heat-treated EFM to fresh cultures did not result in enhancing effects on the production of end-stage embryos. However, the addition of compounds precipitated from EFM, by high concentrations of salt, accelerated by four days the formation of comparable amounts of end-stage embryos and surpassed total end-stage embryo levels by a factor of 4-6, dependent on the precipitate dose. These results suggest that heat-labile polypeptide molecules may be responsible for growth factor-like effects during somatic embryogenesis.     

Identification of Two Human Rho GDP Dissociation Inhibitor Proteins Whose Overexpression Leads to Disruption of the Actin Cytoskeleton

Proteins (IEF's 1120, 8118, 8120) sharing similarity to the bovine Rho GDP dissociation inhibitor (GDI) have been identified in the human two-dimentional-gel database of keratinocyte proteins. Molecular cloning of the corresponding cDNAs showed that IEF 8118 is the human homolog of bovine GDI while IEF 8120 is a distinct although related protein. All available information indicates the IEF 1120 is a derivative of IEF 8120. The cDNAs coding for IEF's 8118 and 8120 were recombined into vaccinia virus and expressed in differentiated human keratinocytes and their effect on the actin cytoskeleton was assessed by immunofluorescence using TRITC-phalloidin. The results showed that overexpression of both GDI proteins leads to rounding up of the cells and loss of stress fibers and focal contact sites. In addition, the cell to cell adhesion belts gradually disappeared, an effect that was particularly pronounced in infected cells overexpressing IEF 8120. Taken together, the results imply that Rho GDI's play a role in modulating the activity of the Rho proteins as their overexpression mimics phenotypic changes associated with the inactivation of these proteins.     

Spatial variation in the evolutionary potential and constraints of basal metabolic rate and body mass in a wild bird

An organism's energy budget is strongly related to resource consumption, performance, and fitness. Hence, understanding the evolution of key energetic traits, such as basal metabolic rate (BMR), in natural populations is central for understanding life-history evolution and ecological processes. Here we used quantitative genetic analyses to study evolutionary potential of BMR in two insular populations of the house sparrow (Passer domesticus). We obtained measurements of BMR and body mass (M_b) from 911 house sparrows on the islands of Leka and Vega along the coast of Norway. These two populations were the source populations for translocations to create an additional third, admixed ‘common garden’ population in 2012. With the use of a novel genetic group animal model concomitant with a genetically determined pedigree, we differentiate genetic and environmental sources of variation, thereby providing insight into the effects of spatial population structure on evolutionary potential. We found that the evolutionary potential of BMR was similar in the two source populations, whereas the Vega population had a somewhat higher evolutionary potential of M_b than the Leka population. BMR was genetically correlated with M_b in both populations, and the conditional evolutionary potential of BMR (independent of body mass) was 41% (Leka) and 53% (Vega) lower than unconditional estimates. Overall, our results show that there is potential for BMR to evolve independently of M_b, but that selection on BMR and/or M_b may have different evolutionary consequences in different populations of the same species.