Prediction of accuracy of estimated Mendelian sampling terms

This study describes a general framework for predicting the accuracy of Mendelian sampling terms when truncation selection is applied on best linear unbiased prediction (BLUP) estimated breeding values. A selection index approach is followed. The pseudo‐BLUP index is extended to include terms related to the Mendelian sampling term. Predicted accuracies are compared with those obtained through stochastic computer simulation. Good predictions for the accuracy of the Mendelian sampling term were obtained both at selection time and at convergence of long‐term contributions of selected candidates for a range of heritabilities and population structures. The prediction approach developed provides a key tool for obtaining predictions of genetic response from quadratic optimization that maximizes the rate of genetic progress while restricting the rate of inbreeding.     

Validation of the otolith increment deposition ratio using alizarin marks in juveniles of the sparid fishes, Diplodus vulgaris and D. puntazzo

Deposition rate of otolith increments was validated by two immersions in alizarin complexone 10 days apart in juvenile Diplodus vulgaris and D. puntazzo. Alizarin complexone produced a well-defined scarlet band on the otoliths of all individuals. One increment:one day ratio was found for both species.     

Conservation value of dispersed tree cover threatened by pasture management

Trees dispersed in pastures are a prominent feature of many Central American landscapes, particularly in cattle producing regions where farmers retain trees to serve as shade, fodder, timber and firewood. The presence of dispersed trees in pastures is often considered as important for the conservation of biodiversity by providing habitat and enhancing landscape connectivity. However, despite their critical productive and environmental roles, little is known about tree distribution within pastures or how farmers’ management decisions influence the trees themselves and their impact on farm productivity and biodiversity conservation. Here, we present a synthesis of (a) the abundance, composition, and size of dispersed trees in four important cattle producing regions of Costa Rica (Caňas and Río Frío) and Nicaragua (Rivas and Matiguás), based on inventory of 18,669 trees on 1492 ha of pasture, (b) the local knowledge, management and use of trees by cattle farmers, and (c) opportunities for ensuring sustainable management of dispersed trees in pasture-dominated landscapes. Dispersed trees were common in all four landscapes, with mean frequency ranging from 8.0 trees ha⁻¹ in Caňas to 33.4 trees ha⁻¹ in Matiguás. A total of 255 tree species were found in pastures across the four landscapes. The total number of tree species per landscape varied from 72 in Rivas to 101 in Caňas and Rio Frio, with mean species richness per farm ranging from 22.9 in Rio Frio to 45.9 in Matiguás. In all four landscapes, a handful of tree species dominated the pastures, with the ten most abundant species in each landscape accounting for >70% of all trees recorded. Most of these common tree species provide fruits or foliage eaten by cattle, or are important timber or firewood species, and are deliberately retained by farmers for these uses. In all four landscapes, farmers had a detailed knowledge of tree attributes affecting pasture and animal productivity, and influenced tree cover through pasture management activities and occasional tree cutting. Current farm management practices are gradually decreasing the diversity of trees in pastures, and in some cases also tree density, reducing their contribution to farm productivity and biodiversity conservation. To reverse this trend, incentives are required to encourage cattle farmers to retain and enhance tree cover in pastures, through the adoption of pasture management practices that favor the regeneration and persistence of a diverse range of tree species.     

A persistent oxygen anomaly reveals the fate of spilled methane in the deep Gulf of Mexico

Methane was the most abundant hydrocarbon released during the 2010 Deepwater Horizon oil spill in the Gulf of Mexico. Beyond relevancy to this anthropogenic event, this methane release simulates a rapid and relatively short-term natural release from hydrates into deep water. Based on methane and oxygen distributions measured at 207 stations throughout the affected region, we find that within ~120 days from the onset of release ~3.0 × 10(10) to 3.9 × 10(10) moles of oxygen were respired, primarily by methanotrophs, and left behind a residual microbial community containing methanotrophic bacteria. We suggest that a vigorous deepwater bacterial bloom respired nearly all the released methane within this time, and that by analogy, large-scale releases of methane from hydrate in the deep ocean are likely to be met by a similarly rapid methanotrophic response.     

Comparative time-course mineral content study between healthy and diseased picea trees from polluted areas

In connection with our previous biochemical comparative study on healthy and diseased Picea trees from polluted areas we have now measured the nutrient contents in the same needle samples. 540 small samples were processed in a very short time (25 min for each sample) using microwave digestion in HNO₃. Al, Ba, Ca, Cu, Fe, K, Mg, Mn, Sr, and Zn were then simultaneously determined by ICP-AES analysis. This rapid and simple micromethod is briefly described and results of the comparison between healthy and diseased Picea trees are presented and discussed in the light of our previous results, particularly that of putrescine and polyamines which have been reported to accumulate in response to cell mineral deficiencies.     

Association of the prion protein gene with individual tissue weights in Scottish Blackface sheep

This study investigated associations of prion protein (PrP) genotype with body composition and weight traits of Scottish Blackface ewes. Body composition was predicted using computer tomography (CT) scans to estimate muscle, carcass fat, internal fat, and bone weights. The traits were measured at 4 key seasonal production points (pre-mating, pregnancy, midlactation, and weaning) over 4 production cycles (2 to 5 yr old). There were 2,413 records for each of the CT traits measured on 335 ewes, and 26,649 records for each of the body condition score and BW traits for 2,356 ewes. From 1999 to 2004, animals were genotyped to determine polymorphisms at codons 136, 154, and 171, which are associated with scrapie susceptibility. Four alleles were found in the population (ARR, AHQ, ARQ, and VRQ). The data were analyzed using a linear mixed random regression model assuming that the direct additive genetic effect was a 2nd order Legendre polynomial function of time. The PrP genotype was included in the model as a fixed effect along with other fixed factors with significant effects (P < 0.05). Five separate analyses were carried out for each trait, depending on the method of classifying the PrP genotype. In the first analysis, animals were categorized according to the genotype. Only the 5 most common genotypes (ARR/ARR, ARR/AHQ, ARR/ARQ, AHQ/ARQ, and ARQ/ARQ) were included. In the last 4 analyses, animals were categorized according to the number of each PrP allele carried. For CT traits and body condition score, results showed that the PrP genotype has no association with the overall mean of the traits (averaged over age). For BW, ewes without the ARQ allele were at least 0.5 kg heavier than ARQ homozygous and heterozygous ewes. On the other hand, there was a significant interaction between PrP genotype and age of the ewe (i.e., the effect of PrP genotype was not the same at different ages for 5 out of the 6 traits studied). In general, ARQ carrying ewes mobilized more fat reserves at times of nutrient deficiency, such as during lactation, and gained it back more quickly by the mating season (when nutrients became abundant) than non-ARQ carriers. Therefore, selecting against this allele would have consequences on BW and seasonal mobilization of body reserves. The number of VRQ alleles (the most scrapie susceptible allele) carried was not significantly associated with any of the traits.     

Evaluation of Agave lechuguilla by‐product crude extract as a feed additive for juvenile shrimp Litopenaeus vannamei

Agave lechuguilla is a succulent plant species, mainly distributed in the northeast of Mexico and south of the United States of America. The main use for this plant is the fibre´s extraction (known as Tampico fibres), resulting in 15% of fibres and 85% of a by‐product waste named guishe. The lechuguilla collectors, normally incinerate the guishe, thus causing environmental contamination. Interestingly, recent studies showed that guishe contains molecules with nutritional properties, such as saponins, flavonoids and sugars. Therefore, in this work, we evaluated the effect of the crude extract of guishe as a feed additive in whiteleg shrimp diets. According to that, MS‐HPLC analysis of the extract showed the presence of saponins such as diosgenin, smilagenin, hecogenin, manogenin, tigogenin hexose, yucagenin, chlorogenin, diosgenin diglucoside and the flavonol, quercetin. After chemical analysis, the crude extract was included into an experimental diet in four levels; 0% (L0%), 0.1% (L0.1%), 0.3% (L0.3%) and 0.6% (L0.6%). Dietary incorporation of the extract was evaluated by zootechnical performance, haemolymph biochemistry, histomorphology and digestive enzyme activity of shrimps. After 5‐week feeding, the L0.3% diet showed significantly higher growth and better feed utilization among treatments. A significant increase in tubule epithelium height and tubule coverage area from hepatopancreas in shrimp under L0.3% diet compared with the control diet suggest an improvement of the health and nutritional status of the shrimp. Inclusion of L0.3% and L0.6% of the crude extract resulted in a reduction in amylase activity, without effect in glucose levels in the haemolymph. Thus, we suggest that lechuguilla guishe crude extract contains nutritional molecules that may be used as a feed additive to promote shrimp productivity.     

Turnover of Village Chickens Undermines Vaccine Coverage to Control HPAI H5N1

Highly pathogenic avian influenza (HPAI) subtype H5N1 remains an enzootic disease of village chickens in Indonesia, posing ongoing risk at the animal–human interface. Previous modelling showed that the fast natural turnover of chicken populations might undermine herd immunity after vaccination, although actual details of how this effect applies to Indonesia's village chicken population have not been determined. We explored the turnover effect in Indonesia's scavenging and mixed populations of village chickens using an extended Leslie matrix model parameterized with data collected from village chicken flocks in Java region, Indonesia. Population dynamics were simulated for 208 weeks; the turnover effect was simulated for 16 weeks after vaccination in two ‘best case’ scenarios, where the whole population (scenario 1), or birds aged over 14 days (scenario 2), were vaccinated. We found that the scavenging and mixed populations have different productive traits. When steady‐state dynamics are reached, both populations are dominated by females (54.5%), and ‘growers’ and ‘chicks’ represent the most abundant age stages with 39% and 38% in the scavenging, and 60% and 25% in the mixed population, respectively. Simulations showed that the population turnover might reduce the herd immunity below the critical threshold that prevents the re‐emergence of HPAI H5N1 4–8 weeks (scavenging) and 6–9 weeks (mixed population) after vaccination in scenario 1, and 2–6 weeks (scavenging) and 4–7 weeks (mixed population) after vaccination in scenario 2. In conclusion, we found that Indonesia's village chicken population does not have a unique underlying population dynamic and therefore, different turnover effects on herd immunity may be expected after vaccination; nonetheless, our simulations carried out in best case scenarios highlight the limitations of current vaccine technologies to control HPAI H5N1. This suggests that the improvements and complementary strategies are necessary and must be explored.