Codon usage in the vertebrate hemoglobins and its implications

A study of codon usage in vertebrate hemoglobins revealed an evolutionary trend toward elevated numbers of CpG codon boundary pairs in mammalian hemoglobin alpha genes. Selection for CpG codon boundaries countering the generally observed CpG suppression is strongly suggested by these data. These observations parallel recently published experimental results that indicate that constitutive expression of the human alpha-globin gene appears to be determined by regulatory information encoded within the structural gene. The possibility is raised that, in the absence of selection, CpG decay can be used to date the evolutionary origin of a mammalian alpha pseudogene from its active alpha gene.      

Evolution of crystallins: expression of lens-specific proteins in the blind mammals mole (Talpa europaea) and mole rat (Spalax ehrenbergi)

The mole (Talpa europaea; Insectivora) and the mole rat (Spalax ehrenbergi; Rodentia) both have degenerated eyes as a convergent adaptation to subterranean life. The rudimentary eye lenses of these blind mammals no longer function in a visual process. The crystallin genes, which display a lens-specific expression pattern, were studied in these blind mammals and in related species with normal eyes by hybridizing their genomic DNAs with probes obtained from cDNA clones for alpha A-, alpha B-, and beta Bp-crystallins from calf and gamma 3- crystallin from the rat. For all crystallin genes examined, the hybridization signals of mole and mole rat genomic DNA were comparable, respectively, with those of shrew and of rat and mouse, normal-vision representatives of the orders Insectivora and Rodentia. The expression of the crystallins at the protein level was tested by using antiserum specific for alpha-crystallin in immunofluorescence reactions on lens sections of mole and mole rat eyes and by using antisera against the beta- and gamma-crystallins on sections of the mole eye. All antisera gave positive fluorescence reactions exclusively with lens tissue of these blind mammals, indicating that the crystallins are still normally expressed despite the fact that these lenses have had no function in a visual process in these mammals for at least many million years. These findings apparently imply that some unknown selective advantage has conserved the crystallin genes and their expression after the loss of normal function of the lenses.      

The evolutionary history of the amylase multigene family in Drosophila pseudoobscura

In Drosophila pseudoobscura, the amylase (Amy) multigene family is contained within a series of inversions, or gene arrangements, on the third chromosome. The Standard (ST), Santa Cruz (SC), and Tree Line (TL) inversions are central to the phylogeny of arrangements, and have clusters of other arrangements derived from them. The gene arrangements belonging to each of these three clusters have a characteristic number of Amy genes, ranging from three in ST to two in SC to one in TL. This distribution pattern can reflect a history of either duplications or deletions, although the data available in the past did not permit a decision between these alternatives. We provide unambiguous evidence that three Amy genes were present before the divergence of the ST, SC, and TL arrangements. Thus, the current status of the Amy multigene family is the result of deletions in the TL and SC arrangements, which created three new pseudogenes: TL Amy2-psi, TL Amy3-psi, and SC Amy3- psi. Analysis of pseudogene sequences revealed that, in the SC and ST arrangements, pseudogene evolution has been retarded, most likely due to the homogenization effect of gene conversion. Finally, by determining the original copy number, we have reconstructed the evolutionary history of the Amy multigene family and linked it with the evolution of the central gene arrangements.      

Enhancing the structural diversity between forest patches—A concept and real-world experiment to study biodiversity,multifunctionality and forest resilience across spatial scales

Intensification of land use by humans has led to a homogenization of landscapes and decreasing resilience of ecosystems globally due to a loss of biodiversity, including the majority of forests. Biodiversity–ecosystem functioning (BEF) research has provided compelling evidence for a positive effect of biodiversity on ecosystem functions and services at the local (α-diversity) scale, but we largely lack empirical evidence on how the loss of between-patch β-diversity affects biodiversity and multifunctionality at the landscape scale (γ-diversity). Here, we present a novel concept and experimental framework for elucidating BEF patterns at α-, β-, and γ-scales in real landscapes at a forest management-relevant scale. We examine this framework using 22 temperate broadleaf production forests, dominated by Fagus sylvatica. In 11 of these forests, we manipulated the structure between forest patches by increasing variation in canopy cover and deadwood. We hypothesized that an increase in landscape heterogeneity would enhance the β-diversity of different trophic levels, as well as the β-functionality of various ecosystem functions. We will develop a new statistical framework for BEF studies extending across scales and incorporating biodiversity measures from taxonomic to functional to phylogenetic diversity using Hill numbers. We will further expand the Hill number concept to multifunctionality allowing the decomposition of γ-multifunctionality into α- and β-components. Combining this analytic framework with our experimental data will allow us to test how an increase in between patch heterogeneity affects biodiversity and multifunctionality across spatial scales and trophic levels to help inform and improve forest resilience under climate change. Such an integrative concept for biodiversity and functionality, including spatial scales and multiple aspects of diversity and multifunctionality as well as physical and environmental structure in forests, will go far beyond the current widely applied approach in forestry to increase resilience of future forests through the manipulation of tree species composition.     

Evidence for gene conversion in the amylase multigene family of Drosophila pseudoobscura

The alpha-amylase (Amy) multigene family in Drosophila pseudoobscura is located on the third chromosome, which is polymorphic for more than 40 inverted gene arrangements. The number of copies in this family ranges from one to three, depending on the arrangement in question. A previous study of the three Amy genes from the Standard (ST) arrangement suggested either that duplicated copies (Amy2 and Amy3) are functionally constrained or that they are undergoing gene conversion with Amy1. In order to elucidate further the pattern of molecular evolution in this family, we cloned and sequenced four additional Amy genes, two from the Santa Cruz (SC) and two from the Chiricahua (CH) gene arrangement. Of the two alternatives, only the hypothesis of gene conversion is supported by the sequence analysis. The homogenization effect of gene conversion has been strongest in SC, whose copies differ by only two nucleotides, less noticeable in ST, and negligible in the CH. Furthermore, the action of gene conversion is apparently localized, occurring only in the coding region. Interestingly, these results concur with the findings of other workers for the duplicated Amy genes in the Drosophila melanogaster group. Thus, the occurrence of gene conversion in the Amy multigene family seems to be a common feature in the Drosophila species studied so far.      

Immortalization of murine B cells in vitro with oncogene-containing retroviral vectors.

A large panel of oncogene-containing retroviral vectors has been constructed and used to infect activated murine splenic B cells to determine whether particular oncogenes are capable of directly mediating B cell immortalization. Mature B cell lines have been consistently established with some of these retroviral vectors. These B cell lines arose at a low frequency, indicating that more genetic events were required in addition to infection with the retroviral vector for immortalization to occur. All such lines were LPS-dependent and non-tumorigenic. All lines secrete IgG and express surface IgG, but not IgD or IgM. In addition, they are CD11b+ and CD23-. These cells may be derived from the CD5 "lineage" or a related B cell subset and appear to be more susceptible to immortalization than conventional B cells.     

Community mean traits as additional indicators to monitor effects of land-use intensity on grassland plant diversity

Semi-natural grasslands, biodiversity hotspots in Central-Europe, suffer from the cessation of traditional land-use. Amount and intensity of these changes challenge current monitoring frameworks typically based on classic indicators such as selected target species or diversity indices. Indicators based on plant functional traits provide an interesting extension since they reflect ecological strategies at individual and ecological processes at community levels. They typically show convergent responses to gradients of land-use intensity over scales and regions, are more directly related to environmental drivers than diversity components themselves and enable detecting directional changes in whole community dynamics. However, probably due to their labor- and cost intensive assessment in the field, they have been rarely applied as indicators so far.Here we suggest overcoming these limitations by calculating indicators with plant traits derived from online accessible databases. Aiming to provide a minimal trait set to monitor effects of land-use intensification on plant diversity we investigated relationships between 12 community mean traits, 2 diversity indices and 6 predictors of land-use intensity within grassland communities of 3 different regions in Germany (part of the German ‘Biodiversity Exploratory’ research network). By standardization of traits and diversity measures, use of null models and linear mixed models we confirmed (i) strong links between functional community composition and plant diversity, (ii) that traits are closely related to land-use intensity, and (iii) that functional indicators are equally, or even more sensitive to land-use intensity than traditional diversity indices. The deduced trait set consisted of 5 traits, i.e., specific leaf area (SLA), leaf dry matter content (LDMC), seed release height, leaf distribution, and onset of flowering. These database derived traits enable the early detection of changes in community structure indicative for future diversity loss. As an addition to current monitoring measures they allow to better link environmental drivers to processes controlling community dynamics.     

A CONCEPTUAL MODEL OF A SILTATION SYSTEM IN SHALLOW LAKES WITH LITTORAL VEGETATION

SUMMARY

In shallow lakes a siltation system develops when wind driven water turbulence erodes the lake floor, silt is resuspended and transported by means of waterdrift into the littoral vegetation. Here, due to the resistance of the vegetation, the turbulence is reduced and the silt deposited. Through this mechanism, the prevailing winds have a major rôle in the erosion and siltation pattern, lake morphology, vegetation pattern and in the mixing of water and nutrients from the open water and the reedswamp and vice versa. The model explains the uneven distribution of vegetation at the lakes Neusiedlersee (Austria) and Chilwa (Malawi) satisfactorily, if one assumes a positive correlation between siltation and reedswamp growth and spread.     

Causes of variation in mineral soil C content and turnover in differently managed beech dominated forests

Background and aims

Forest soils are important carbon stores and considered as net CO₂ sinks over decadal to centennial time scales. Intensive forest management is thought to reduce the carbon sequestration potential of forest soils. Here we study the effects of decades of forest management (as unmanaged forest, forest under selection cutting, forest under age class management) on the turnover of mineral associated soil organic matter (MOM) in German beech (Fagus sylvatica L.) dominated forests.

Methods

Radiocarbon contents were determined by accelerator mass spectrometry (AMS) in 79 Ah horizon MOM fractions of Cambisols (n?=?13), Luvisols (n?=?51) and Stagnosols (n?=?15). Mean residence times (MRTs) for soil organic carbon (SOC) were estimated with a 2-pool model using the litter input derived from a forest inventory.

Results

MOM fractions from Ah horizons contained 64?±?8.8 % of the bulk SOC. The radiocarbon content of MOM fractions in Ah horizons, expressed as Δ¹⁴C, ranged between ?2.8?‰ and 114?‰ for the three soil groups. Almost all samples contained a detectable proportion of ‘bomb’ carbon fixed from the atmosphere since 1963. Under the assumption that depending on the soil texture between 19 % and 24 % of the SOC from the labile pool is transferred to the stable SOC pool, the corresponding MRTs ranged between 72 and 723 years, with a median of 164 years.

Conclusions

Our results indicate that the MOM fraction of Ah horizons from beech forests contained a high proportion of young carbon, but we did not find a significant decadal effect of forest management on the radiocarbon signature and related turnover times. Instead, both variables were controlled by clay contents and associated SOC concentrations (p?<?0.01). This underlines the importance of pedogenic properties for SOC turnover in the MOM fraction.     

A comparison of the strength of biodiversity effects across multiple functions

In order to predict which ecosystem functions are most at risk from biodiversity loss, meta-analyses have generalised results from biodiversity experiments over different sites and ecosystem types. In contrast, comparing the strength of biodiversity effects across a large number of ecosystem processes measured in a single experiment permits more direct comparisons. Here, we present an analysis of 418 separate measures of 38 ecosystem processes. Overall, 45 % of processes were significantly affected by plant species richness, suggesting that, while diversity affects a large number of processes not all respond to biodiversity. We therefore compared the strength of plant diversity effects between different categories of ecosystem processes, grouping processes according to the year of measurement, their biogeochemical cycle, trophic level and compartment (above- or belowground) and according to whether they were measures of biodiversity or other ecosystem processes, biotic or abiotic and static or dynamic. Overall, and for several individual processes, we found that biodiversity effects became stronger over time. Measures of the carbon cycle were also affected more strongly by plant species richness than were the measures associated with the nitrogen cycle. Further, we found greater plant species richness effects on measures of biodiversity than on other processes. The differential effects of plant diversity on the various types of ecosystem processes indicate that future research and political effort should shift from a general debate about whether biodiversity loss impairs ecosystem functions to focussing on the specific functions of interest and ways to preserve them individually or in combination.