Implications of shifts in coffee production on tree species richness, composition and structure on small farms around Mount Kenya

Small coffee farms around Mount Kenya in Kenya contain many planted and remnant tree species but little is known in the region about the relationship between trees on farms and the methods and dynamics of coffee production. Shifts in production may alter tree diversity and potentially impact on future biodiversity conservation efforts by affecting niches available for indigenous trees on farms. Here, knowledge was gathered on how changes in coffee production on 180 small farms around Mount Kenya may affect tree diversity, categorizing farms according to coffee yield levels over a period of five years as increasing, decreasing or stable production. Tree species richness, abundance and composition were analyzed using species accumulation curves, Rènyi diversity profiles, rank abundance and ecological distance ordinations, and the effects of coffee production examined using quasi-Poisson generalized linear regressions. Species richness were positively correlated with tree basal area but negatively related to coffee, banana and maize yields value. A difference in average tree species richness, abundance and basal area on increasing farms was observed compared to the decreasing and stable farms, even though formal tests on richness and densities differences were inconclusive. These dynamics do not significantly influence vegetation structure but seem to have a bearing on species composition on farms of different coffee production. The overall low abundance (23 % of trees) but high richness (78 % of species) of indigenous trees on coffee farms could change markedly if the dynamics observed in the current study persist, indicating the need for the development of intensified multi-species cropping systems.     

What is the relevance of smallholders’ agroforestry systems for conserving tropical tree species and genetic diversity in circa situm, in situ and ex situ settings? A review

Smallholders’ agroforests may be valuable for conserving tropical trees through three main mechanisms. First, trees planted and/or retained by farmers in agricultural landscapes where wild stands were once found may be circa situm reservoirs of biodiversity. Second, farmland trees may support conservation in situ by providing an alternative source of product to reduce extraction from forest, and by acting as ‘corridors’ or ‘stepping stones’ that connect fragmented wild stands. Third, the additional value that planting assigns to trees may result in greater interest in including them in seed collections, field trials and field ‘genebanks’ that support ex situ conservation. Here, we critically review the evidence for these mechanisms, and highlight areas for research and for intervention so that agroforestry practices can better support conservation in each setting, with an emphasis on often neglected genetic-level considerations. Based on current global challenges to diversity, conservation will need to rely increasingly on a smallholder-farm circa situm approach, but concerns on long-term effectiveness need to be properly quantified and addressed. Connectivity between widely dispersed, low density trees in agricultural landscapes is an important factor determining the success of the circa situm approach, while improving farmers’ access to a diversity of tree germplasm that they are interested in planting is required. The circumstances in which agroforestry plantings can support in situ conservation need to be better defined, and research on the stability of active tree seed collections (how long are species and populations retained in them?) as ex situ reservoirs of biodiversity is needed.     

Founder mutations in the Netherlands: geographical distribution of the most prevalent mutations in the low-density lipoprotein receptor and apolipoprotein B genes

Background

In the Netherlands, a screening programme was set up in 1994 in order to identify all patients with familial hypercholesterolaemia (FH). After 15 years of screening, we evaluated the geographical distribution, possible founder effects and clinical phenotype of the 12 most prevalent FH gene mutations.

Methods

Patients who carried one of the 12 most prevalent mutations, index cases and those identified between 1994 and 2009 through the screening programme and whose postal code was known were included in the study. Low-density lipoprotein cholesterol (LDL-C) levels at the time of screening were retrieved. The prevalence of identified FH patients in each postal code area was calculated and visualised in different maps.

Results

A total of 10,889 patients were included in the study. Mean untreated LDL-C levels ranged from 4.4 to 6.4 mmol/l. For almost all mutations, a region of high prevalence could be observed. In total, 51 homozygous patients were identified in the Netherlands, of which 13 true homozygous for one of the 12 most prevalent mutations. The majority of them were living in high-prevalence areas for that specific mutation.

Conclusions

Phenotypes with regard to LDL-C levels varied between the 12 most prevalent FH mutations. For most of these mutations, a founder effect was observed. Our observations can have implications with regard to the efficiency of molecular screening and physician’s perception of FH and to the understanding of the prevalence and distribution of homozygous patients in the Netherlands.     

Species accumulation within land use and tree diameter categories in Burkina Faso,Mali, Niger and Senegal

Although farmers have managed west African parkland savanna systems for 1,000 of years, concerns have been raised about the sustainability of these agro-ecosystems due to human population growth, shortening of fallow periods, droughts, desertification and new orientations towards cash generation away from subsistence farming. We conducted a tree diversity survey in 16 villages from Burkina Faso, Mali, Niger and Senegal, recording total species composition for 300 quadrats (mainly 50 × 20 m²) that were randomly sampled from the main landuse categories of parklands of village fields (VF), bush fields (BF), sylvopastoral zone (SP) and forest reserves (FR). About 110 tree species were encountered, including 100 indigenous species. The results from balanced species accumulation curves (based on randomized subsampling of the same number of quadrats from each village) showed that the accumulated number of species was smallest in VF, largest in FR and almost equal in BF and SP, whereas classical (unbalanced) species accumulation curves yielded different results. Although there was a significant within-village reduction in species richness with increasing diameter class [averaging 8.5–13.1 more species in the smallest (<5 cm) compared to the largest diameter class (>80 cm)] for the different landuse categories, new species were also encountered in larger diameter classes (2.7–7.2 species). The evidence for tree regeneration problems (including problems in FR) suggest that farmer-managed tree regeneration should be further explored and that advances in domestication and marketing of indigenous tree species may be crucial to tree conservation in parkland systems.     

Tree Diversity in Western Kenya: Using Profiles to Characterise Richness and Evenness

Species diversity is a function of the number of species and the evenness in the abundance of the component species. We calculated diversity and evenness profiles, which allowed comparing the diversity and evenness of communities. We applied the methodology to investigate differences in diversity among the main functions of trees on western Kenyan farms. Many use-groups (all trees and species that provide a specific use) could not be ranked in diversity or evenness. No use-group had perfectly even distributions. Evenness could especially be enhanced for construction materials, fruit, ornamental, firewood, timber and medicine, which included some of the most species-rich groups of the investigated landscape. When considering only the evenness in the distribution of the dominant species, timber, medicine, fruit and beverage ranked lowest (> 60% of trees belonged to the dominant species of these groups). These are also use-groups that are mainly grown by farmers to provide cash through sales. Since not all communities can be ranked in diversity, studies that attempt to order communities in diversity should not base the ordering on a single index, or even a combination of several indices, but use techniques developed for diversity ordering such as the Rényi diversity profile. The rarefaction of diversity profiles described in this article could be used in studies that compare results from surveys with different sample sizes.     

Bilayer edge and curvature effects on partitioning of lipids by tail length: atomistic simulations

The partitioning of lipids among different microenvironments in a bilayer is of considerable relevance to characterization of composition variations in biomembranes. Atomistic simulation has been ill-suited to model equilibrated lipid mixtures because the time required for diffusive exchange of lipids among microenvironments exceeds typical submicrosecond molecular dynamics trajectories. A method to facilitate local composition fluctuations, using Monte Carlo mutations to change lipid structures within the semigrand-canonical ensemble (at a fixed difference in component chemical potentials, Δμ), was recently implemented to address this challenge. This technique was applied here to mixtures of dimyristoylphosphatidylcholine and a shorter-tail lipid, either symmetric (didecanoylphosphatidylcholine (DDPC)) or asymmetric (hexanoyl-myristoylphosphatidylcholine), arranged in two types of structure: bilayer ribbons and buckled bilayers. In ribbons, the shorter-tail component showed a clear enrichment at the highly curved rim, more so for hexanoyl-myristoylphosphatidylcholine than for DDPC. Results on buckled bilayers were variable. Overall, the DDPC content of buckled bilayers tended to exceed by several percent the DDPC content of flat ones simulated at the same Δμ, but only for mixtures with low overall DDPC content. Within the buckled bilayer structure, no correlation could be resolved between the sign or magnitude of the local curvature of a leaflet and the mean local lipid composition. Results are discussed in terms of packing constraints, surface area/volume ratios, and curvature elasticity.     

Absolute versus per unit body length speed of prey as an estimator of vulnerability to predation

To study whether absolute (m/s) or relative (body lengths/s) speed should be used to compare the vulnerability of differently sized animals, we developed a simple computer simulation. Human 'predators' were asked to 'catch' (mouse-click) prey of different sizes, moving at different speeds across a computer screen. Using the simulation, a prey's chances of escaping predation depended on its speed (faster prey were more difficult to catch than slower prey of the same body size), but also on its size (larger prey were easier to catch than smaller prey at the same speed). Catching time, the time needed to catch a prey, also depended on both prey speed and prey size. Relative prey speed (body lengths/s or body surface/s) was a better predictor of catching time than was absolute prey speed (m/s). Our experiment demonstrates that, in contrast to earlier assertions, per unit body length speed of prey may be more 'ecologically relevant' than absolute speed. Copyright 1998 The Association for the Study of Animal Behaviour.     

Isolation and mapping of the rabbit DM genes

 Proper peptide presentation by major histocompatibility complex (MHC)-encoded class II antigens is dependent on the products of the MHC DM loci. We identified the rabbit orthologues (RLA-DMA and -DMB) of human HLA-DMA and -DMB and found that they have 76.9% and 78.8% identity with HLA-DMA and -DMB, respectively. Like classical class II MHC genes, RLA-DM genes are more closely related to human HLA-DM genes than to mouse H2-DM. Among the DM family, there is a high degree of variability at the amino terminus of the DMa chains, and length variability in the cytoplasmic tails of both DMα and DMβ. The rabbit DM genes are coexpressed with class II genes in lymphoid tissues, as are the DM genes of other mammals. The RLA-DM locus maps to the class II region of the rabbit MHC, and is flanked by the DP and DOB loci. Despite having some similarities to class II genes of bony fishes, the DM family represents a separate branch of the MHC class II family. Received: 30 May 1998 / Revised: 28 July 1998     

Investigations into the polymorphism of rat tail tendon fibrils using atomic force microscopy

Collagen type I displays a typical banding periodicity of 67 nm when visualized by atomic force or transmission electron microscopy imaging. We have investigated collagen fibers extracted from rat tail tendons using atomic force microscopy, under different ionic and pH conditions. The majority of the fibers reproduce the typical wavy structure with 67 nm spacing and a height difference between the peak and the grooves of at least 5 nm. However, we were also able to individuate two other banding patterns with 23+/-2 nm and 210+/-15 nm periodicities. The small pattern showed height differences of about 2 nm, whereas the large pattern seems to be a superposition of the 67 nm periodicity showing height differences of about 20 nm. Furthermore, we could show that at pH values of 3 and below the fibril structure gets dissolved whereas high concentrations of NaCl and CaCl(2) could prevent this effect.