Invited review: Genomic selection for small ruminants in developed countries: how applicable for the rest of the world?

Improved management and use of estimated breeding values in breeding programmes, have resulted in rapid genetic progress for small ruminants (SR) in Europe and other developed countries. The development of single nucleotide polymorphisms chips opened opportunities for genomic selection (GS) in SR in these countries. Initially focused on production traits (growth and milk), GS has been extended to functional traits (reproductive performance, disease resistance and meat quality). The GS systems have been characterized by smaller reference populations compared with those of dairy cattle and consisting mostly of cross- or multi-breed populations. Molecular information has resulted in gains in accuracy of between 0.05 and 0.27 and proved useful in parentage verification and the identification of QTLs for economically important traits. Except for a few established breeds with some degree of infrastructure, the basic building blocks to support conventional breeding programmes in small holder systems are lacking in most developing countries. In these systems, molecular data could offer quick wins in undertaking parentage verification and genetic evaluations using G matrix, and determination of breed composition. The development of next-generation molecular tools has prompted investigations on genome-wide signatures of selection for mainly adaptive and reproduction traits in SR in developing countries. Here, the relevance of the developments and application of GS and other molecular tools in developed countries to developing countries context is examined. Worth noting is that in the latter, the application of GS in SR will not be a ‘one-size fits all’ scenario. For breeds with some degree of conventional genetic improvement, classical GS may be feasible. In small holder systems, where production is key, community-based breeding programmes can provide the framework to implement GS. However, in fragile growth systems, for example those found in marginal environments, innovative GS to maximize adaptive diversity will be required. A cost-benefit analysis should accompany any strategy of implementing GS in these systems.     

Into the world of steroids: A biochemical “keep in touch” in plants and animals

Evolution of steroids such as sex hormones and ecdysteroids occurred independently in the animal and plant kingdoms. Plants use phytoecdysteroids (PEs) to control defense interactions with some predators; furthermore, PEs can exert beneficial influence on many aspects of mammalian metabolism. Endocrine disrupting compounds such as the estrogen agonist bisphenol A (BPA) are widespread in the environment, posing a potential hormonal risk to animals and plants. Adverse BPA effects on reproductive development and function are coupled with other toxic effects. BPA bioremediation techniques could be developed by exploiting some tolerant plant species.Key words: androgens, endocrine disrupting compounds, bisphenol A, estrogens, hormone receptors, phytoecdysteroids     

Origin of the parasites of an invading species,the Australian cane toad (Bufo marinus): are the lungworms Australian or American?

Phylogeographical analyses that identify the geographical origin of parasites in invading species can clarify the parasites' potential for biological control of the invader and the risks posed by the parasite to native species. Our data on nuclear and mitochondrial genetic sequences show that the nematode lungworms (Rhabdias spp.) in invasive Australian populations of cane toads (Bufo marinus) are Rhabdias pseudosphaerocephala, a South American species. We did not find this lungworm species in any Australian frogs sympatric with cane toads, suggesting that the parasite does not attack Australian frogs and hence may offer potential as a biocontrol agent of the toad.     

Cyclic-AMP mediated drugs: differential or global reduction of eicosanoid synthesis in the isolated rat lung?

In this study the question was addressed whether cAMP mediated drugs induce a differential reduction of branches of the arachidonic acid metabolism rather than a global reduction of eicosanoid synthesis. The isolated lungs of actively sensitized rats were employed to study prostaglandin and leukotriene release in the presence and absence of the cAMP mediated drugs theophylline, milrinone, sulmazole, isobutyl-methylxanthine and salbutamol. The release of eicosanoids as measured by RIA was predominantly basal and continuous, with a mild antigen induced stimulation only for TXB(2) and the leukotrienes. All drugs reduced eicosanoid release globally. It is concluded that cAMP mediated drugs interfere with arachidonic acid metabolism at a site proximal to the branching into lipoxygenase and cyclo-oxygenase pathways.     

Invasion in a heterogeneous world: resistance,coexistence or hostile takeover?

We review and synthesize recent developments in the study of the invasion of communities in heterogeneous environments, considering both the invasibility of the community and impacts to the community. We consider both empirical and theoretical studies. For each of three major kinds of environmental heterogeneity (temporal, spatial and invader-driven), we find evidence that heterogeneity is critical to the invasibility of the community, the rate of spread, and the impacts on the community following invasion. We propose an environmental heterogeneity hypothesis of invasions, whereby heterogeneity both increases invasion success and reduces the impact to native species in the community, because it promotes invasion and coexistence mechanisms that are not possible in homogeneous environments. This hypothesis could help to explain recent findings that diversity is often increased as a result of biological invasions. It could also explain the scale dependence of the diversity–invasibility relationship. Despite the undoubted importance of heterogeneity to the invasion of communities, it has been studied remarkably little and new research is needed that simultaneously considers invasion, environmental heterogeneity and community characteristics. As a young field, there is an unrivalled opportunity for theoreticians and experimenters to work together to build a tractable theory informed by data.     

On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world?

This paper presents and discusses evidence suggesting how the diversity of domain folds in existence today might have evolved from peptide ancestors. We apply a structure similarity detection method to detect instances where localized regions of different protein folds contain highly similar sequences and structures. Results of performing an all-on-all comparison of known structures are described and compared with other recently published findings. The numerous instances of local sequence and structure similarities within different protein folds, together with evidence from proteins containing sequence and structure repeats, argues in favor of the evolution of modern single polypeptide domains from ancient short peptide ancestors (antecedent domain segments (ADSs)). In this model, ancient protein structures were formed by self-assembling aggregates of short polypeptides. Subsequently, and perhaps concomitantly with the evolution of higher fidelity DNA replication and repair systems, single polypeptide domains arose from the fusion of ADSs genes. Thus modern protein domains may have a polyphyletic origin.     

Telomere-Specialized Retroelements in Drosophila: Adaptive Symbionts of the Genome,Neutral, or in Conflict?

Linear chromosomes shorten in every round of replication. In Drosophila, telomere-specialized long interspersed retrotransposable elements (LINEs) belonging to the jockey clade offset this shortening by forming head-to-tail arrays at Drosophila telomere ends. As such, these telomeric LINEs have been considered adaptive symbionts of the genome, protecting it from premature decay, particularly as Drosophila lacks a conventional telomerase holoenzyme. However, as reviewed here, recent work reveals a high degree of variation and turnover in the telomere-specialized LINE lineages across Drosophila. There appears to be no absolute requirement for LINE activity to maintain telomeres in flies, hence the suggestion that the telomere-specialized LINEs may instead be neutral or in conflict with the host, rather than adaptive.     

A carboxysomal carbon-concentrating mechanism in the cyanelles of the 'coelacanth' of the algal world, Cyanophora paradoxa?

Cyanelles are the peculiar plastids of glaucocystophyte algae that retained a peptidoglycan wall from the ancestral cyanobacterial endosymbiont. All cyanobacteria and most algae possess an inorganic carbon-concentrating mechanism (CCM) that involves a microcompartment--carboxysomes in prokaryotes and pyrenoids in eukaryotes--harboring the bulk of cellular (plastidic) Rubisco. In the case of the living fossil, Cyanophora paradoxa, the existence of a CCM was a matter of debate. Microarray data revealing 142 CO(2)-responsive genes (induced or repressed through a shift from high to low CO(2) conditions), gas exchange measurements and measurements of photosynthetic affinity provided strong support for a CCM. We favor a recent hypothesis that glaucocystophyte cyanelles as the closest cousins to cyanobacteria among plastids contain 'eukaryotic carboxysomes': bicarbonate enrichment within cyanelles should be considerably higher than in chloroplasts with their pyrenoid-based CCM. Thus, the stress-bearing function of the peptidoglycan layer, the other unique heritage, would be indispensable. An isolation method for cyanelle 'carboxysomes' was developed and the protein components other than Rubisco analyzed by MS. Rubisco activase was identified and corroborated by western blotting. The well-established cyanelle in vitro import system allows to use them as 'honorary cyanobacteria': assembly processes of supramolecular structures as phycobilisomes and carboxysomes thus can be studied after import of nucleus-encoded precursor proteins and subsequent fractionation. Even minor components can easily be tracked and a surprisingly dynamic view is obtained. Labeled pre-activase was imported into isolated cyanelles and 30% of the mature protein was found to be incorporated into the carboxysome fraction. A final decision between carboxysome or pyrenoid must await the identification of cyanelle carbonic anhydrase and, especially, the demonstration of shell proteins.     

A core of rhizosphere bacterial taxa associates with two of the world’s most isolated plant congeners

Plant and Soil - The hydrolysis of organic P in soils is a relevant aspect contributing to the supply P to plants, which is affected by adsorbent capacity and biological properties of soils. This...     

Unravelling genetics at the top: mountain islands or isolated belts?

Background and Aims

In mountain plant populations, local adaptation has been described as one of the main responses to climate warming, allowing plants to persist under stressful conditions. This is especially the case for marginal populations at their lowest elevation, as they are highly vulnerable. Adequate levels of genetic diversity are required for selection to take place, while high levels of altitudinal gene flow are seen as a major limiting factor potentially precluding local adaptation processes. Thus, a compromise between genetic diversity and gene flow seems necessary to guarantee persistence under oncoming conditions. It is therefore critical to determine if gene flow occurs preferentially between mountains at similar altitudinal belts, promoting local adaptation at the lowest populations, or conversely along altitude within each mountain.

Methods

Microsatellite markers were used to unravel genetic diversity and population structure, inbreeding and gene flow of populations at two nearby altitudinal gradients of Silene ciliata, a Mediterranean high-mountain cushion plant.

Key Results

Genetic diversity and inbreeding coefficients were similar in all populations. Substantial gene flow was found both along altitudinal gradients and horizontally within each elevation belt, although greater values were obtained along altitudinal gradients. Gene flow may be responsible for the homogeneous levels of genetic diversity found among populations. Bayesian cluster analyses also suggested that shifts along altitudinal gradients are the most plausible scenario.

Conclusions

Past population shifts associated with glaciations and interglacial periods in temperate mountains may partially explain current distributions of genetic diversity and population structure. In spite of the predominance of gene flow along the altitudinal gradients, local genetic differentiation of one of the lower populations together with the detection of one outlier locus might support the existence of different selection forces at low altitudes.     

Keep in touch: Does spatial overlap correlate with contact rate frequency?

Quantifying animal contact rate is crucial both in fundamental and applied studies to understand the evolution of sociality and predict the spread of infectious diseases. Researchers typically use home-range overlap among individuals as a proxy of contact rate, assuming a positive correlation. However, very few studies have assessed how the correlation between home-range overlap and contact rate may vary with ecological context. We used proximity loggers to quantify intraspecific contact rate among raccoons (Procyon lotor) and explored the correlation between contact rate and home-range overlap in different seasons. We monitored 15 female raccoons that formed 121 dyads during summer 2010 and winter 2011. We compared contact rate with the 5 most common overlap indices: home-range overlap proportion, home-range overlap probability, utilization distribution overlap index (UDOI), volume of intersection index, and Bhattacharyya's affinity index. Our results generally supported the contention of a positive and significant correlation between home-range overlap and intraspecific contact rate in raccoons. The strength of the relationship differed among seasons and indices, being weaker during winter than summer for home-range overlap proportion and home-range overlap probability. When contact rates were high, their frequency had stronger correlations with the UDOI and volume of intersection index indices than with the other indices. Our results suggest that the UDOI performs better than other indices, as we obtained a good contact rate–home-range overlap correlation with this index with animals both aggregated and randomly distributed in space. © 2012 The Wildlife Society.     

Inflammatory bowel disease: maladaptation of the vigilant genotype in a hyper-clean world?

Children born of Asian Indian parents who are raised in environmentally hygienic Western societies appear to be highly prone to two diseases, ulcerative colitis and Crohn's disease, collectively known as inflammatory bowel disease or IBD. These ethnically Indian children are similar to an inbred mouse strain, NOD/Lt. Mice of this strain remain diabetes-free when raised in standard mouse colonies, but develop an autoimmune diabetes at high rates when kept in pathogen-free environments. I propose that certain human habitats have, over eons, selected for "vigilant genotypes," wherein combinations of alleles at critical loci result in aggressive immune responses to pathogens. This genetic configuration is adaptive in the selective environment but maladaptive in more hygienic environments, resulting in dysregulated immune effectors. One manifestation of such dysregulation is organ-specific autoimmunity, such as IBD.     

Are human beings part of the rest of nature?

Unified explanations seek to situate the traits of human beings in a causal framework that also explains the trait values found in nonhuman species. Disunified explanations claim that the traits of human beings are due to causal processes not at work in the rest of nature. This paper outlines a methodology for testing hypotheses of these two types. Implications are drawn concerning evolutionary psychology, adaptationism, and anti-adaptationism. This revised version was published online in July 2006 with corrections to the Cover Date.     

Limited benefits of non-crop vegetation on spiders in Australian vineyards: regional or crop differences?

In crops, invertebrate natural enemies such as spiders have been documented as responding to non-crop vegetation at the local and landscape scales, particularly in northern Europe. Much of this information is based on data from arable or annual crops and it is possible that spider numbers in more persistent perennial systems including vineyards may be less dependent on non-crop vegetation. To test the relationship between spider abundance and non-crop vegetation within the context of Australian vineyards, we sampled spiders in 54 vineyards with adjacent non-crop vegetation, from three different regions. Landscape composition in the area surrounding each of the 54 sites was characterized at 11 spatial scales from 95?m to 3?km radius and spiders were sampled monthly using canopy sticky traps and ground pitfall traps. There were only weak relationships between pasture or woody vegetation and the abundance of spiders in vineyards at all spatial scales. At the local scale, abundance of most spider families tended to be greater in vineyards with adjacent pasture. At the landscape scale there were inconsistent patterns. We discuss possible reasons for these apparent contrasting patterns between perennial and annual crops and European compared to Australian agroecosystems.