Molecular evolution of the MAGUK family in metazoan genomes

Background  

Development, differentiation and physiology of metazoans all depend on cell to cell communication and subsequent intracellular signal transduction. Often, these processes are orchestrated via sites of specialized cell-cell contact and involve receptors, adhesion molecules and scaffolding proteins. Several of these scaffolding proteins important for synaptic and cellular junctions belong to the large family of membrane-associated guanylate kinases (MAGUK). In order to elucidate the origin and the evolutionary history of the MAGUKs we investigated full-length cDNA, EST and genomic sequences of species in major phyla.     

Late Quaternary history of Hippophaë rhamnoides L. (Elaeagnaceae) inferred from chalcone synthase intron (Chsi) sequences and chloroplast DNA variation

Fossil pollen records indicate that Hippophaë rhamnoides (Sea Buckthorn) was widespread on late‐ and early postglacial raw soils throughout much of central and northern Europe, but that Early Holocene reforestation restricted populations to northern coastal habitats, or along mountain streams in the Alps, Pyrenees, and Carpathians. We used sequence variation at the nuclear chalcone synthase intron (Chsi), in conjunction with chloroplast DNA–restriction fragment length polymorphism data, to investigate the intraspecific phylogeny, phylogeographic structure, and expansion demographic history of this dioecious and wind‐pollinated shrub at its range‐wide scale in Europe and Asia Minor. Four major Chsi phylogroups of unresolved relationships were identified with estimated divergences ～172 000 years ago. Large‐scale phylogeographic structures of nuclear and cytoplasmic markers were congruent in identifying (i) southeastern Europe as the most likely source of colonization into central Europe and Scandinavia, and (ii) the area just north of the Alps as a contact zone between populations from the Alps and the east/central European‐Scandinavian lineage. Coalescence‐based analyses (i.e. nested clade analysis and mismatch distributions) of Chsi variation were able to detect at least four major episodes of population growth, all within about the last 40 000 years. In particular, these analyses identified a nearly synchronized timing of population expansions in various parts of the species’ range in central‐eastern Europe/Asia Minor, most likely correlating with the Younger Dryas Stadial (～13 000–11 600 years ago). It remains to be established whether the phylogeographic history of H. rhamnoides, and particularly its rapid response to the rapid environmental changes of the Younger Dryas cold snap, is unique to the species, or whether it is shared with other cold‐tolerant shrub (or grassland) species known from late‐glacial raw soils in Europe.     

The phylogeny and biogeography of Gentiana L. sect. Ciminalis (Adans.) Dumort.: A historical interpretation of distribution ranges in the European high mountains

Gentiana sect. Ciminalis consists of seven mostly ecologically or geographically vicariant and closely related species which are distributed throughout the South and Central European high mountains. The analysis of a RAPD data set and trn L-intron and ITS sequences resulted in slightly different phylogenetic hypotheses. In the preferred hypothesis the group consists of two completely resolved main lineages: 1) G. clusii and G. alpina. 2) G. dinarica, G. acaulis, G. ligustica, G. angustifolia and G. occidentalis. The most important conclusions we have drawn from this phylogenetic hypothesis and from the observed patterns of molecular variation are: 1) The calcifuge ecology of G. acaulis and G. alpina evolved independently from calcicole ancestors. 2) Among the calcicole taxa speciation proceeded from East to West in a simple vicariant pattern. 3) The application of a provisional molecular clock indicates that speciation events in sect. Ciminalis probably occurred in the Quaternary. 4) Differences in infraspecific genetic variation among the widespread species suggest that G. alpina probably experienced more recent dispersal or gene flow than G. clusii and G. acaulis. 5) The large number of mutations in the lineage leading to G. angustifolia, compared to the few mutations in the lineage leading to G. dinarica, may be a result of their different population histories. While the extant range of G. angustifolia was strongly affected by Quaternary climatic fluctuations, that of G. dinarica has had a more stable climatic history. 6) The low number of mutations and the basal position in one clade of the preferred cladogram leads to the conclusion that G. dinarica is the species most similar to the last common ancestor of sect. Ciminalis.     

Mitochondrial growth and division during the cell cycle in HeLa cells

The growth and division of mitochondria during the cell cycle was investigated by a morphometric analysis of electron micrographs of synchronized HeLa cells. The ratio of total outer membrane contour length to cytoplasmic area did not vary significantly during the cell cycle, implying a continuous growth of the mitochondrial outer membrane. The mean fraction of cytoplasmic area occupied by mitochondrial profiles was likewise found to remain constant, indicating that the increase in total mitochondrial volume per cell occurs continuously during interphase, in such a way that the mitochondrial complement occupies a constant fraction( approximately 10-11(percent)) of the volume of the cytoplasm. The mean area, outer membrane contour length, and axis ratio of the mitochondrial profiles also did not vary appreciably during the cell cycle; furthermore, the close similarity of the frequency distributions of these parameters for the six experimental time-points suggested a stable mitochondrial shape distribution. The constancy of both the mean mitochondrial profile area and the number of mitochondrial profiles per unit of cytoplasmic area was interpreted to indicate the continuous division of mitochondria at the level of the cell population. Furthermore, no evidence was found for the occurrence of synchronous mitochondrial growth and division within individual cells. Thus, it appears that, in HeLa cells, there is no fixed temporal relationship between the growth and division of mitochondria and the events of the cell cycle. A number of statistical methods were developed for the purpose of making numerical estimates of certain three-dimensional cellular and mitochondrial parameters. Mean cellular and cytoplasmic volumes were calculated for the six time-points; both exhibited a nonlinear, approx. twofold increase. A comparison of the axis ratio distributions of the mitochondrial profiles with theoretical distributions expected from random sectioning of bodies of various three-dimensional shapes allowed the derivation of an "average" mitochondrial shape. This, in turn, permitted calculations to be made which expressed the two-dimensional results in three-dimensional terms. Thus, the estimated values for the number of mitochondria per unit of cytoplasmic volume and for the mean mitochondrial volume were found to remain constant during the cell cycle, while the estimated number of mitochondria per cell increase approx. twofold in an essentially continuous manner.     

Quaternary diversification in European alpine plants: pattern and process

Molecular clock approaches applied previously to European alpine plants suggest that Primula sect. Auricula, Gentiana sect. Ciminalis and Soldanella diversified at the beginning of the Quaternary or well within this period, whereas Globularia had already started diversifying in the (Late-)Tertiary. In the first part of this paper we present evidence that, in contrast to Globularia and Soldanella, the branching patterns of the molecular internal transcribed spacer phylogenies of both Primula and Gentiana are incompatible with a constant-rates birth-death model. In both of these last two taxa, speciation probably decreased through Quaternary times, perhaps because of some niche-filling process and/or a decrease in specific range size. In the second part, we apply nonlinear regression analyses to the lineage-through-time plots of P. sect. Auricula to test a range of capacity-dependent models of diversification, and the effect of Quaternary climatic oscillations on diversification and extinction. At least for one major clade of sect. Auricula there is firm evidence that both diversification and extinction are a function of temperature. Intriguingly, temperature appears to be correlated positively with extinction, but negatively with diversification. This suggests that diversification did not take place, as previously assumed, in geographical isolation in high-altitude interglacial refugia, but rather at low altitudes in geographically isolated glacial refugia.