Growth of a root system described as diffusion. II. Numerical model and application

In simulation models for water movement and nutrient transport, uptake of water and nutrients by roots forms an essential part. As roots are spatially distributed, prediction of root growth and root distribution is crucial for modelling water and nutrient uptake. In a preceding paper, De Willigen et al. (2002; Plant and Soil 240, 225–234) presented an analytical solution for describing root length density distribution as a diffusion-type process. In the current paper, we present a numerical model that does the same, but which is more flexible with respect to where root input can occur. We show that the diffusion-type root growth model can describe well observed rooting patterns. We used rooting patterns for different types of crops: maize, gladiolus, eastern white cedar, and tomato. For maize, we used data for two different types of fertiliser application: broadcast and row application. In case of row application, roots extend more vertically than horizontally with respect to the broadcast application situation. This is reflected in a larger ratio of diffusion coefficients in vertical versus horizontal direction. For tomato, we considered tomatoes grown on an artificial rooting medium, i.e. rockwool. We have shown that, in principle, the model can be extended by including reduction functions on the diffusion coefficient in order to account for environmental conditions.     

The Regeneration of a Highly Disturbed Ecosystem: A Mined Peatland in Southern Québec

We studied the natural regeneration of an ombrotrophic peatland (Cacouna bog) located in southern Québec that was disturbed by peat mining and other anthropogenic activities over a 200-year period. Using an extensive collection of historical documents, as well as dendrochronological data, we reconstructed the history of the peatland. We also sampled vegetation and environmental variables, and integrated the data in a geographic information system. More than 60% of the total area of the bog was mined between 1942 and 1975, and 98 km of ditches were dug to drain the site. The peatland lost 34% of its initial peat volume between 1946 and 1998. Although the bog was severely disturbed, the spontaneous revegetation of the site by vascular plants was successful (90%–100% cover). However, only 10% of the total mined area has been recolonized by Sphagnum species, mainly because drainage ditches are still operational and contribute to drying out the bog. Water table level, peat deposit thickness, and pH are abiotic factors strongly influencing the vegetation composition in the bog. Spatial and historical factors are also important components in this study since they explain, either alone or in interaction with abiotic factors, 44% of the variation of the species data. The intensity of mining activities and the pattern of abandonment of mined sectors strongly influenced abiotic factors, which in turn affected the revegetation process. Even if the Sphagnum cover of the bog is low, the rapid “recovery” of the vegetation cover in the peatland indicates that after the reestablishment of an appropriate hydrological regime, a highly disturbed peatland has a considerable potential for regeneration. Received 24 April 2001; accepted 30 October 2001.     

Demography and genome divergence of lake and stream populations of an East African cichlid fish

Disentangling the processes and mechanisms underlying adaptive diversification is facilitated by the comparative study of replicate population pairs that have diverged along a similar environmental gradient. Such a setting is realized in a cichlid fish from southern Lake Tanganyika, Astatotilapia burtoni, which occurs within the lake proper as well as in various affluent rivers. Previously, we demonstrated that independent lake and stream populations show similar adaptations to the two habitat regimes. However, little is known about the evolutionary and demographic history of the A. burtoni populations in question and the patterns of genome divergence among them. Here, we apply restriction site‐associated DNA sequencing (RADseq) to examine the evolutionary history, the population structure and genomic differentiation of lake and stream populations in A. burtoni. A phylogenetic reconstruction based on genome‐wide molecular data largely resolved the evolutionary relationships among populations, allowing us to re‐evaluate the independence of replicate lake–stream population clusters. Further, we detected a strong pattern of isolation by distance, with baseline genomic divergence increasing with geographic distance and decreasing with the level of gene flow between lake and stream populations. Genome divergence patterns were heterogeneous and inconsistent among lake‐stream population clusters, which is explained by differences in divergence times, levels of gene flow and local selection regimes. In line with the latter, we only detected consistent outlier loci when the most divergent lake–stream population pair was excluded. Several of the thus identified candidate genes have inferred functions in immune and neuronal systems and show differences in gene expression between lake and stream populations.     

Species richness coincidence: conservation strategies based on predictive modelling

The present-day geographic distribution of individual species of five taxonomic groups (plants, dragonflies, butterflies, herpetofauna and breeding birds) is relatively well-known on a small scale (5 × 5 km squares) in Flanders (north Belgium). These data allow identification of areas with a high diversity within each of the species groups. However, differences in mapping intensity and coverage hamper straightforward comparisons of species-rich areas among the taxonomic groups. To overcome this problem, we modelled the species richness of each taxonomic group separately using various environmental characteristics as predictor variables (area of different land use types, biotope diversity, topographic and climatic features). We applied forward stepwise multiple regression to build the models, using a subset of well-surveyed squares. A separate set of equally well-surveyed squares was used to test the predictions of the models. The coincidence of geographic areas with high predicted species richness was remarkably high among the four faunal groups, but much lower between plants and each of the four faunal groups. Thus, the four investigated faunal groups can be used as relatively good indicator taxa for one another in Flanders, at least for their within-group species diversity. A mean predicted species diversity per mapping square was also estimated by averaging the standardised predicted species richness over the five taxonomic groups, to locate the regions that were predicted as being the most species-rich for all five investigated taxonomic groups together. Finally, the applicability of predictive modelling in nature conservation policy both in Flanders and in other regions is discussed.     

Mutations in the<Emphasis Type="Italic"> HLA</Emphasis> class II genes leading to loss of expression of HLA-DR and HLA-DQ in diffuse large B-cell lymphoma

Loss of expression of human leukocyte antigen (HLA) class II molecules on tumor cells affects the onset and modulation of the immune response through lack of activation of CD4+ T lymphocytes. Previously, we showed that the frequent loss of expression of HLA class II in diffuse large B-cell lymphoma (DLBCL) of the testis and the central nervous system (CNS) is mainly due to homozygous deletions in the HLA region on chromosome band 6p21.3. A minority of cases showed hemizygous deletions or mitotic recombination, implying that mutation of the remaining copy of the class II genes might be involved. Here, we studied three DLBCLs with loss of HLA-DQ expression for mutations in the DQB1 and DQA1 genes and three tumors with loss of HLA-DR expression for mutations in the DRB1 and DRA genes. In one case, a point mutation in exon 2 of the DQB1 gene, leading to the formation of a stop codon, was detected at position 47. In a second case, a stop codon was found at position 11 due to a deletion of 19 bp in exon 1 of the DRA gene. No mutations were found in the promoter sequences of the DRA, DQA1 and DQB1 genes. We conclude that both homozygous deletions and hemizygous deletions or mitotic recombination with mutations of the remaining allele may lead to loss of expression of the HLA class II genes, which is comparable to the mechanisms affecting HLA class I expression in solid cancers.