Prediction of reduction in aggressive behaviour of growing pigs using skin lesion traits as selection criteria.

Aggression at regrouping is a common issue in pig farming. Skin lesions are genetically and phenotypically correlated with aggression and have been shown to have a significant heritable component. This study predicts the magnitude of reduction in complex aggressive behavioural traits when using lesion numbers on different body regions at two different time points as selection criteria, to identify the optimum skin lesion trait for selection purposes. In total, 1146 pigs were mixed into new social groups, and skin lesions were counted 24 h (SL24h) and 3 weeks (SL3wk) post-mixing, on the anterior, centre and posterior regions of the body. An animal model was used to estimate genetic parameters for skin lesion traits and 14 aggressive behavioural traits. Estimated breeding values (EBVs) and phenotypic values were scaled and standardised to allow direct comparison across multiple traits. Individuals with SL24h and SL3wk EBVs in the least aggressive 10% of the population were compared with the population mean to predict the expected genetic and phenotypic response in aggressive behaviour to selection. At mixing, selection for low anterior lesions was predicted to affect substantially more behavioural traits of aggressiveness than lesions obtained on other body parts, with EBVs between -0.21 and -1.17 SD below the population mean. Individuals with low central SL24h EBVs also had low EBVs for aggressive traits (-0.33 to -0.55). Individuals with high SL3wk EBVs had low EBVs for aggression at mixing (between -0.24 and -0.53 SD below the population mean), although this was predicted to affect fewer traits than selection against SL24h. These results suggest that selection against anterior SL24h would result in the greatest genetic and phenotypic reduction in aggressive behaviour recorded at mixing. Selection for increased SL3wk was predicted to reduce aggression at mixing; however, current understanding about aggressive behaviour under stable social conditions is insufficient to recommend using this trait for selection purposes.

Genetic associations of short- and long-term aggressiveness identified by skin lesion with growth, feed efficiency, and carcass characteristics in growing pigs.

The objective of this study was to investigate the genetic relationships between skin lesion traits in group housed growing pigs as a measure of short- (in a newly mixed group) and long- (in a socially stable group) term aggression and commonly used commercial performance measures: growth, feed intake, feed efficiency, and carcass traits. Data on 2,413 growing pigs (138 groups) were available. Pigs were mixed into new social groups of 18 animals, and skin lesions were counted 24 h (SL24h) and 5 wk (SL5wk) postmixing. The animal model was used to estimate genetic parameters for skin lesion traits, test daily gain, lifetime daily gain, daily feed intake, feed efficiency (calculated as test daily gain divided by daily feed intake), loin depth, back fat, and HCW. Skin lesions had a heritable component, ranging from 0.08 for anterior SL24h to 0.22 for central SL5wk and would, therefore, be suitable as a method of phenotyping aggression for selection purposes. Significant positive genetic correlations were found between SL24h and SL5wk (0.46 to 0.81). Positive genetic correlations were also found between SL24h (central and posterior body regions) or SL5wk (all body regions) and the production traits lifetime daily gain, test daily gain, and HCW (0.29 to 0.54). Central SL24h, anterior SL5wk, and posterior SL5wk were found to correlate positively with feed efficiency (0.39 to 0.50), suggesting that pigs with more lesions convert feed more efficiently. Where significant, the magnitude of phenotypic correlations was low but positive (0.07 to 0.10). These results suggest that, genetically, animals that receive many lesions show improved performance compared to those with few lesions, except for anterior SL24h, which had previously been shown to be genetically positively correlated with the initiation of nonreciprocal attacks. It may, therefore, be possible, via selection against anterior skin lesions at mixing, to reduce this form of 1-sided aggression without adversely affecting production traits.

Behavioural cues of reproductive status in seahorses Hippocampus abdominalis.

A method is described to assess the reproductive status of male Hippocampus abdominalis on the basis of behavioural traits. The non-invasive nature of this technique minimizes handling stress and reduces sampling requirements for experimental work. It represents a useful tool to assist researchers in sample collection for studies of reproduction and development in viviparous syngnathids, which are emerging as important model species.

Identification of a uniquely southern African clade of coastal pipefishes Syngnathus spp.

The taxonomic status of two southern African coastal pipefish species, Syngnathus temminckii and Syngnathus watermeyeri, was investigated using a combination of morphological and genetic data. Morphological data showed that S. temminckii is distinct from the broadly distributed European pipefish Syngnathus acus, and a molecular phylogeny reconstructed using mitochondrial DNA recovered S. temminckii and S. watermeyeri as sister taxa. The southern African species share an evolutionary origin with north-eastern Atlantic Ocean and Mediterranean Sea species, including S. acus. These data support the existence of a distinct southern African clade of Syngnathus pipefishes that has diverged in situ to form the two species present in the region today.

Thermally assisted quantum annealing of a 16-qubit problem.

Efforts to develop useful quantum computers have been blocked primarily by environmental noise. Quantum annealing is a scheme of quantum computation that is predicted to be more robust against noise, because despite the thermal environment mixing the system's state in the energy basis, the system partially retains coherence in the computational basis, and hence is able to establish well-defined eigenstates. Here we examine the environment's effect on quantum annealing using 16 qubits of a superconducting quantum processor. For a problem instance with an isolated small-gap anticrossing between the lowest two energy levels, we experimentally demonstrate that, even with annealing times eight orders of magnitude longer than the predicted single-qubit decoherence time, the probabilities of performing a successful computation are similar to those expected for a fully coherent system. Moreover, for the problem studied, we show that quantum annealing can take advantage of a thermal environment to achieve a speedup factor of up to 1,000 over a closed system.

Bias, accuracy, and impact of indirect genetic effects in infectious diseases.

Selection for improved host response to infectious disease offers a desirable alternative to chemical treatment but has proven difficult in practice, due to low heritability estimates of disease traits. Disease data from field studies is often binary, indicating whether an individual has become infected or not following exposure to an infectious disease. Numerous studies have shown that from this data one can infer genetic variation in individuals' underlying susceptibility. In a previous study, we showed that with an indirect genetic effect (IGE) model it is possible to capture some genetic variation in infectivity, if present, as well as in susceptibility. Infectivity is the propensity of transmitting infection upon contact with a susceptible individual. It is an important factor determining the severity of an epidemic. However, there are severe shortcomings with the Standard IGE models as they do not accommodate the dynamic nature of disease data. Here we adjust the Standard IGE model to (1) make expression of infectivity dependent on the individuals' disease status (Case Model) and (2) to include timing of infection (Case-ordered Model). The models are evaluated by comparing impact of selection, bias, and accuracy of each model using simulated binary disease data. These were generated for populations with known variation in susceptibility and infectivity thus allowing comparisons between estimated and true breeding values. Overall the Case Model provided better estimates for host genetic susceptibility and infectivity compared to the Standard Model in terms of bias, impact, and accuracy. Furthermore, these estimates were strongly influenced by epidemiological characteristics. However, surprisingly, the Case-Ordered model performed considerably worse than the Standard and the Case Models, pointing toward limitations in incorporating disease dynamics into conventional variance component estimation methodology and software used in animal breeding.

The evolutionary origins of Syngnathidae: pipefishes and seahorses.

Despite their importance as evolutionary and ecological model systems, the phylogenetic relationships among gasterosteiforms remain poorly understood, complicating efforts to understand the evolutionary origins of the exceptional morphological and behavioural diversity of this group. The present review summarizes current knowledge on the origin and evolution of syngnathids, a gasterosteiform family with a highly developed form of male parental care, combining inferences based on morphological and molecular data with paleontological evidence documenting the evolutionary history of the group. Molecular methods have provided new tools for the study of syngnathid relationships and have played an important role in recent conservation efforts. Despite recent insights into syngnathid evolution, however, a survey of the literature reveals a strong taxonomic bias towards studies on the species-rich genera Hippocampus and Syngnathus, with a lack of data for many morphologically unique members of the family. The study of the evolutionary pressures responsible for generating the high diversity of syngnathids would benefit from a wider perspective, providing a comparative framework in which to investigate the evolution of the genetic, morphological and behavioural traits of the group as a whole.

The role of mathematical models of host-pathogen interactions for livestock health and production - a review.

Compared with the application of mathematical models to study human diseases, models that describe animal responses to pathogen challenges are relatively rare. The aim of this review is to explain and show the role of mathematical host-pathogen interaction models in providing underpinning knowledge for improving animal health and sustaining livestock production. Existing host-pathogen interaction models can be assigned to one of three categories: (i) models of the infection and immune system dynamics, (ii) models that describe the impact of pathogen challenge on health, survival and production and (iii) models that consider the co-evolution of host and pathogen. State-of-the-art approaches are presented and discussed for models belonging to the first two categories only, as they concentrate on the host-pathogen dynamics within individuals. Models of the third category fall more into the class of epidemiological models, which deserve a review by themselves. An extensive review of published models reveals a rich spectrum of methodologies and approaches adopted in different modelling studies, and a strong discrepancy between models concerning diseases in animals and models aimed at tackling diseases in humans (most of which belong to the first category), with the latter being generally more sophisticated. The importance of accounting for the impact of infection not only on health but also on production poses a considerable challenge to the study of host-pathogen interactions in livestock. This has led to relatively simplistic representations of host-pathogen interaction in existing models for livestock diseases. Although these have proven appropriate for investigating hypotheses concerning the relationships between health and production traits, they do not provide predictions of an animal's response to pathogen challenge of sufficient accuracy that would be required for the design of appropriate disease control strategies. A synthesis between the modelling methodologies adopted in categories 1 and 2 would therefore be desirable. The progress achieved in mathematical modelling to study immunological processes relevant to human diseases, together with the current advances in the generation and analysis of biological data related to animal diseases, offers a great opportunity to develop a new generation of host-pathogen interaction models that take on a fundamental role in the study and control of disease in livestock.

Meta-analysis of the effect of the halothane gene on 6 variables of pig meat quality and on carcass leanness.

Technological meat quality is a significant economic factor in pork production, and numerous publications have shown that it is strongly influenced both by genetic status and by rearing and slaughter conditions. The quality of meat is often described by meat pH at different times postmortem, as well as by color and drip loss, whereas carcass quality is often characterized by lean percentage. A meta-analysis of findings relating to 3,530 pigs reported in 23 publications was carried out to assess the effects of the halothane gene, sex, breed, and slaughter weight of animals on 7 selected variables: pH at 45 min postmortem, ultimate pH, reflectance (L*-value), redness (a*-value), yellowness (b*-value), drip loss, and lean percentage. Two statistical methods were used in the meta-analysis: the method of effect size and the better known random effects model. The method of effect size was associated with Markov chain Monte Carlo techniques for implementing Bayesian hierarchical models to avoid the problems of limited data and publication bias. The results of our meta-analysis showed that the halothane genotype had a significant effect on all analyzed pork quality variables. Between-study variance was evaluated with the Cochran (1954) Q-test of heterogeneity. Meta-regression was used to explain this variance, with covariates such as breed, sex, slaughter weight, and fasting duration being integrated into different regression models. The halothane gene effect was associated with the breed effect only for the following variables: L*-value, b*-value, and drip loss. Slaughter weight contributed significantly only to the explanation of differences in ultimate pH between homozygous genotypes. In response to inconsistencies reported in the literature regarding the difference between the genotypes NN and Nn, results of the meta-analysis showed that the difference between these 2 genotypes was significant for all the analyzed variables except the a*-value.

Clinical and pathological responses of pigs from two genetically diverse commercial lines to porcine reproductive and respiratory syndrome virus infection.

The response to infection from porcine reproductive and respiratory syndrome virus (PRRSV) for 2 genetically diverse commercial pig lines was investigated. Seventy-two pigs from each line, aged 6 wk, were challenged with PRRSV VR-2385, and 66 litter-mates served as control. The clinical response to infection was monitored throughout the study and pigs were necropsied at 10 or 21 d postinfection. Previous analyses showed significant line differences in susceptibility to PRRSV infection. This study also revealed significant line differences in growth during infection. Line B, characterized by faster growth rate than line A in the absence of infection, suffered more severe clinical disease and greater reduction in BW growth after infection. Correlations between growth and disease-related traits were generally negative, albeit weak. Correlations were also weak among most clinical and pathological traits. Clinical disease traits such as respiratory scores and rectal temperatures were poor indicators of virus levels, pathological damage, or growth during PRRSV infection. Relationships between traits varied over time, indicating that different disease-related mechanisms may operate at different time scales and, therefore, that the time of assessing host responses may influence the conclusions drawn about biological significance. Three possible mechanisms underlying growth under PRRSV infection were proposed based on evidence from this and previous studies. It was concluded that a comprehensive framework describing the interaction between the biological mechanisms and the genetic influence on these would be desirable for achieving progress in the genetic control of this economically important disease.

Sexual size dimorphism predicts the frequency of multiple mating in the sex-role reversed pipefish Syngnathus typhle.

The sex-role reversed pipefish Syngnathus typhle is a member of the Syngnathidae, a family of fishes in which males brood embryos on their body surface. As in most ectotherms, embryonic development is highly temperature dependent in syngnathids and male brooding periods are extended when water temperatures are reduced. The influence of temperature on reproduction is expected to effectively truncate the breeding season and reduce fecundity in cold waters, potentially enhancing the opportunity for both fecundity and sexual selection. We studied spatial variation in the morphology and reproductive biology of S. typhle in five European populations which vary in latitude and water temperature. Microsatellite analyses indicated that the average number of male mates per population ranged between 1.3 and 3.7. The frequency of multiple mating by males was negatively correlated with the degree of sexual size dimorphism in each population, suggesting that disproportionate increases in female fecundity may be able to compensate for increased male brood pouch capacity. Both sexes were larger and males had an increased brood size where water temperatures during the breeding season were lower. Morphological variation among populations may be mediated by differences in fecundity selection associated with different optimal reproductive strategies in cold and warm water environments.

Genetic monogamy despite social promiscuity in the pot-bellied seahorse (Hippocampus abdominalis).

Sexual selection theory predicts a positive correlation between relative parental investment and mate choice. In syngnathid fishes (seahorses and pipefish), males brood offspring in specialized brooding structures. While female-female mating competition has been demonstrated in some pipefishes, all seahorses (genus Hippocampus) studied to date have been found to have conventional sex roles with greater male-male competition for access to mates despite possessing the most complex brood structures in the family. Although multiple mating is common in pipefish, seahorses are again exceptional, exhibiting strict genetic monogamy. Both demographic and behavioural explanations have been offered to explain the lack of multiple mating in seahorse species, but these hypotheses have not yet been explicitly addressed. We investigated mating systems and brood parentage of the pot-bellied seahorse, Hippocampus abdominalis, a temperate-water species that is socially promiscuous with conventional sex roles in laboratory populations. We observed promiscuous courtship behaviour and sex-role reversal in high density, female-biased field populations of H. abdominalis. We hypothesize that sex roles are plastic in H. abdominalis, depending on local population density and sex ratio. Despite promiscuous courtship behaviour, all assayed male seahorses were genetically monogamous in both laboratory and wild populations. Physiological limitations associated with embryo incubation may explain the absence of multiple mating in seahorses and may have played an important role in the development of the unique reproductive behaviour typical in these species.

Using mechanistic animal growth models to estimate genetic parameters of biological traits.

Mechanistic animal growth models can incorporate a description of the genotype as represented by underlying biological traits that aim to specify the animal's genetic potential for performance, independent from the environmental factors captured by the models. It can be argued that these traits may therefore be more closely associated to genetic potential, or components of genetic merit that are more robust across environments, than the environmentally dependent phenotypic traits currently used for genetic evaluation. The prediction of merit for underlying biological traits can be valuable for breeding and development of selection strategies across environments.Model inversion has been identified as a valid method for obtaining estimates of phenotypic and genetic components of the biological traits representing the genotype in the mechanistic model. The present study shows how these estimates were obtained for two existing pig breeds based on genetic and phenotypic components of existing performance trait records. Some of the resulting parameter estimates associated with each breed differ substantially, implying that the genetic differences between the breeds are represented in the underlying biological traits. The estimated heritabilities for the genetic potentials for growth, carcass composition and feed efficiency as represented by biological traits exceed the heritability estimates of related phenotypic traits that are currently used in evaluation processes for both breeds. The estimated heritabilities for maintenance energy requirements are however relatively small, suggesting that traits associated with basic survival processes have low heritability, provided that maintenance processes are appropriately represented by the model.The results of this study suggest that mechanistic animal growth models can be useful to animal breeding through the introduction of new biological traits that are less influenced by environmental factors than phenotypic traits currently used. Potential value comes from the estimation of underlying biological trait components and the explicit description of their expression across a range of environments as predicted by the model equations.

Genetic signature of recent glaciation on populations of a near-shore marine fish species (Syngnathus leptorhynchus).

Continental glaciation has played a major role in shaping the present-day phylogeography of freshwater and terrestrial species in the Northern Hemisphere. Recent work suggests that coastal glaciation during ice ages may have also had a significant impact on marine species. The bay pipefish, Syngnathus leptorhynchus, is a near-shore Pacific coast fish species with an exceptionally wide latitudinal distribution, ranging from Bahia Santa Maria, Baja California to Prince William Sound, Alaska. Survey data indicate that S. leptorhynchus is experiencing a range expansion at the northern limit of its range, consistent with colonization from southern populations. The present study uses six novel microsatellite markers and mitochondrial DNA (mtDNA) sequence data to study the present-day population genetic structure of four coastal populations of S. leptorhynchus. Deficits in mtDNA and nuclear DNA diversity in northern populations from regions glaciated during the last glacial maximum (LGM) [c. 18 000 years before present (bp)] suggest that these populations were effected by glacial events. Direct estimates of population divergence times derived from both isolation and isolation-with-migration models of evolution are also consistent with a postglacial phylogenetic history of populations north of the LGM. Sequence data further indicate that a population at the southern end of the species range has been separated from the three northern populations since long before the last interglacial event (c. 130 000 years bp), suggesting that topographical features along the Pacific coast may maintain population separation in regions unimpacted by coastal glaciation.

Interspecies mating in sympatric species of Syngnathus pipefish.

Hybridization is thought to be an important source of novel genetic variation, and interspecific hybridization may increase the adaptive potential of wild populations. While hybridization has not been previously reported in syngnathid fishes (seahorses and pipefish), the sympatric occurrence of closely related species at high densities increases the probability of interspecies mating in this group. Southern California is home to five species of Syngnathus pipefish, and these species frequently co-occur in near-shore eelgrass beds along the California coast. Recent work has identified exceptionally high levels of genetic diversity in southern populations of Syngnathus leptorhynchus, a widespread species which ranges from Mexico to Alaska. Microsatellite genotyping and mitochondrial sequence data are used here to study the population genetics of S. leptorhynchus and S. auliscus at a site in San Diego Bay where they are found to co-occur at high densities. While no adult hybrids were detected in the study population, analysis of male broods indicates that interspecies mating is occurring between the two species. The lack of premating isolating mechanisms between these two relatives suggests that hybridization may be common in sympatric species of Syngnathus.

The relationship between body dimensions of living pigs and their carcass composition.

The performance of a visual image analysis (VIA) system was tested with regards to its potential to determine in vivo carcass composition and conformation, either alone, or in conjunction with other in vivo measures such as live weight and backfat depth. Pigs of both sexes of a commercial type were reared and slaughtered at weights ranging from 50 to 120 kg. Feeding was ad libitum on diets ranging from 0.14 to 0.19 kgkg(-1) crude protein content to produce animals of a range of body condition. Two analyses were carried out: the first analysis addressed the relationship between dimensionless carcass and VIA indices; the second analysis assessed the relationship between carcass composition and VIA body shape using detrended carcass and VIA data, which were produced by removal of allometric growth trends. A statistically significant relationship (P<0.05) between in vivo VIA body size and shape and carcass muscle dimensions and composition was found for most body regions. Adjusted R(2) statistics ranged between 0.13 and 0.54 for relative fat weights and between 0.14 and 0.51 for relative lean weights. The predictive power of the regression models, indicated by R(2)-like statistics for prediction, was approximately 70% of the adjusted R(2) values. The descriptive and predictive powers of the corresponding models generally strengthened if VIA indices were combined with other in vivo measurements. The relationships between in vivo and carcass measures remained statistically significant (P<0.05) after removal of the growth trends, although adjusted R(2) statistics generally decreased. The predictive power of models corresponding to the detrended measures was, however, weak. The results show in vivo VIA measurements to be useful in the estimation of muscle size, carcass conformation and composition, all of which are of significant importance to the pig production, marketing and processing industries.

Determination of CD59 protein in normal human serum by enzyme immunoassay, using octyl-glucoside detergent to release glycosyl-phosphatidylinositol-CD59 from lipid complex.

In this study we have optimised the enzyme immunoassay (ELISA) to quantify CD59 antigen in human serum or plasma. The glycosyl-phosphatidylinositol (GPI)-linked form of CD59 is known to complex with serum high-density lipoprotein. For ELISA optimisation, therefore, we investigated the effect of detergents, added to the sample diluent, on the determined values of CD59. Values obtained in the presence of octyl-glucoside (OG) for 20 adults aged 18-35 years and 17 children 1-5 years old were, respectively, 33-119 ng/ml (mean +/- S.D.: 66+/-22 ng/ml) and 37-143 ng/ml (76+/-33 ng/ml). These results were higher than those measured without OG and were in contrast with published results showing absence, or eight to nine times lower levels, of the protein in serum. A known range for serum concentrations of CD59 in healthy individuals will establish an important reference point for clinical work and for the investigation of diseases involving the complement membrane attack complex (MAC) and its regulation.

Male pregnancy in seahorses and pipefishes (family Syngnathidae): rapid diversification of paternal brood pouch morphology inferred from a molecular phylogeny.

In contrast to the majority of vertebrate species, primary male parental care is common in fishes and encompasses a remarkable diversity of adaptations. Seahorses and pipefishes (Family Syngnathidae) exhibit some of the most specialized forms of paternal care in animals and so are ideally suited to the study of the evolution of male parental care. During mating, female syngnathids transfer eggs to specialized morphological structures that are located on either the abdomen or tail of the male. The male provides all postfertilization parental care and has morphological and physiological adaptations to osmoregulate, aerate, and even nourish the developing embryos. While all syngnathid species are adapted for paternal care, the brooding structure with which this is accomplished varies between species, from simple ventral gluing areas to much more complex structures such as the completely enclosed pouches of the seahorses. Our combined cytochrome b-, 12S rDNA-, and 16S rDNA-based molecular phylogeny of syngnathid fishes demonstrates that rapid diversification of male brooding structures has been associated with the major evolutionary radiation of the group, suggesting that development and diversification of structures involved in paternal care may have been key evolutionary innovations of the Syngnathidae. Molecular analyses also highlight geographical centers of biodiversity and suggest interoceanic migration of Syngnathus pipefishes from their center of origin in the Pacific.

An aberrant form of CD59 derived from HeLa cells.

We isolated a CD59 cDNA from a HeLa cell library which encoded a mutated form of CD59, having a single base substitution (G to T) that changed Arg55 to Met. Since this mutation occurred in the vicinity of the putative active site of CD59, we expressed the aberrant form of the protein in Chinese hamster ovary cells in order to test for effects upon function. We found that the mutation did not influence complement inhibitory activity of CD59. However, the epitopes recognised by the function-blocking CD59 monoclonal antibodies BRIC229 and YTH 53.1 were significantly affected. The G to T substitution caused loss of an Mnl I restriction site which permitted PCR-RFLP analysis. All of 52 human subjects studied, and our in-house HeLa cells, were homozygous for the normal CD59 sequence, indicating that the altered sequence was not due to normal variation in the general population. Therefore this mutation probably arose spontaneously in the HeLa cell line used to generate the commercially obtained cDNA library.