Risk ratio as parameter for the genetic characterization of complex binary traits in cattle. A simulation study under various genetic models using halfsib families

The risk ratio (λ_R) is defined as ‘the recurrence risk for a relative of an affected individual divided by the prevalence in the general population’ and is considered as the most important parameter when designing mapping experiments for diseases in humans. In this paper, the risk ratio was introduced as a parameter to genetically characterize complex binary traits such as mastitis in cattle. Simulations were applied to evaluate the properties of λ_R under different genetic models (monogenic, digenic, polygenic and mixed models) and in dependency of their parameters for a design consisting of unbalanced halfsib families typically found in dairy cattle. Population prevalences of the simulated data ranged from 5 to 40% and λ_R was estimated on a phenotypic level. In the discrete loci models complexity of the traits was introduced through different levels of penetrance and the proportions of phenocopies within each genetic background. The risk ratio and the power to reject the null hypothesis of independent halfsibs (λ_R=1) were influenced by the prevalence in all genetic models chosen. Absolute values for λ_R were higher for lower prevalences, for example, λ_R=2.77 and 1.62 for a pure monogenic recessive model with 5 and 20% prevalence, respectively, whereas the power decreases in the case of lower prevalences. For all the prevalences investigated, higher risk ratios were found for discrete loci models compared with the polygenic models, with higher values for the monogenic relative to the digenic models in general. For the mixed models, λ_R was intermediate between the polygenic and discrete loci models. Genes with dominant relative to recessive inheritance for susceptibility caused higher risk ratios in monogenic and mixed models, for example, λ_R=5.16 and 2.77 for a pure monogenic model with 5% prevalence. In the discrete loci models, λ_R decreased with lower penetrance and a higher proportion of phenocopies. Risk ratios increased with the heritability in the polygenic and in addition with the effect of the major gene in mixed models. Consistent patterns of risk ratios were observed under the analysed genetic models and parameters, which indicate that the risk ratio is a parameter well suited to genetically characterize binary traits in unbalanced halfsib families.     

Policy impacts on regulating ecosystem services: looking at the implications of 60 years of landscape change on soil erosion prevention in a Mediterranean silvo-pastoral system

Context

Policy decisions form a major driver of land use change, with important implications for socially and environmentally susceptible regions. It is well known that there can be major unintended consequences, especially where policies are not tailored to regionally specific contexts.

Objectives

In this paper we assess the implications of 60 years of agricultural policies on soil erosion prevention (SEP) by vegetation, an essential regulating ecosystem service in Mediterranean Europe.

Methods

To assess these implications we produced and analysed a time series of land cover/use and environmental conditions datasets (from 1951 to 2012) in relation to changing agricultural policies for a specific region in the southern Portugal. A set of indicators related to SEP allowed us to identify that land use intensification as increased soil erosion in the last 60 years.

Results

Particularly in the last 35 years, as a consequence of headage payments for cattle, the agricultural policy had a significant effect in the density and renewal of the tree cover, resulting in drastic effects for the provision of the SEP service. These are more significant after 1986, coinciding with the implementation of several Common Agricultural Policy instruments focused on increasing the modernization and productivity capacity of farm systems.

Conclusions

The results show some unintended effects of agricultural policy mechanisms on ecosystem service provision and highlight the need for context-based policies, tailored to the environmental constrains and potentials of each region.

     

Considering the preferences for nitrogen forms by invasive plants: a case study from a hydroponic culture experiment

Although preference for NH₄⁺, NO₃^? or a combination of the two often differs among species, we know little about the responses of invasive plants to different inorganic N forms. Furthermore, many studies have suggested that an increase in N availability may facilitate further invasions. However, most of these studies predicted the positive feedback without considering the preference for N forms of invasive plants. Therefore, we cultivated four common invasive species (Mikania micrantha, Ipomoea cairica, Wedelia trilobata and Bidens pilosa) in South China with hydroponic media containing different forms of N (i.e. NO₃^?, NH₄NO₃ and NH₄⁺) at equimolar concentrations. Our results showed that the N forms significantly affected the growth, biomass allocation and physiological traits of the plants. All four invasive plants supplied with NO₃^? alone had better performance and greater allocation to root biomass than did plants that were supplied with NH₄⁺ alone. Moreover, the photosynthetic rate, pigment content and photosystem II activity of plants supplied with NO₃^? or NH₄NO₃ were significantly higher than those of plants supplied with NH₄⁺alone. The results suggested that all four invasive plants preferred NO₃^? rather than NH₄⁺, and changes in NO₃^? played an important role in furthering the invasions of these plants than did changes in NH₄⁺. Our results implied that decreasing NO₃^? may be a useful tool for controlling and managing invasive plants preferring NO₃^?. In addition, this study highlighted the importance of considering plant N form preference to better understand plant invasions.