Application of SNPs for population genetics of nonmodel organisms:new opportunities and challenges

Recent improvements in the speed, cost and accuracy of next generation sequencing are revolutionizing the discovery of single nucleotide polymorphisms (SNPs). SNPs are increasingly being used as an addition to the molecular ecology toolkit in nonmodel organisms, but their efficient use remains challenging. Here, we discuss common issues when employing SNP markers, including the high numbers of markers typically employed, the effects of ascertainment bias and the inclusion of nonneutral loci in a marker panel. We provide a critique of considerations specifically associated with the application and population genetic analysis of SNPs in nonmodel taxa, focusing specifically on some of the most commonly applied methods.

Board invited review:The importance of the gestation period for welfare of calves: Maternal stressors and difficult births

The prenatal period is of critical importance in defining how individuals respond to their environment throughout life. Stress experienced by pregnant females has been shown to have detrimental effects on offspring biology in humans and a variety of other species. It also is becoming increasingly apparent that prenatal events can have important consequences for the behavior, health, and productivity of offspring in farmed species. Pregnant cattle may experience many potentially important stressors, for instance, relating to their social environment, housing system and physical environment, interactions with humans and husbandry procedures, and their state of health. We examined the available literature to provide a review of the implications of prenatal stress for offspring welfare in cattle. The long-term effects of dystocia on cattle offspring also are reviewed. To ensure a transparent and repeatable selection process, a systematic review approach was adopted. The research literature clearly demonstrates that prenatal stress and difficult births in beef and dairy cattle both have implications for offspring welfare and performance. Common husbandry practices, such as transport, were shown to influence offspring biology and the importance of environmental variables, including thermal stress and drought, also were highlighted. Maternal disease during pregnancy was shown to negatively impact offspring welfare. Moreover, dystocia-affected calves suffer increased mortality and morbidity, decreased transfer of passive immunity, and important physiological and behavioral changes. This review also identified considerable gaps in our knowledge and understanding of the effects of prenatal stress in cattle. © 2012 American Society of Animal Science. All rights reserved.

Temperament test for re-homed dogs validated through direct behavioral observation in shelter and home environment

This study was the first attempt to carry out a validation of a temperament test (TT) for shelter dogs that addressed the topics of inter- and intra-raters agreements, test-retest reliability, and validity. The TT consisted of 22 subtests. Each dog was approached and handled by an unfamiliar person and made to interact with a same- and an opposite-gender conspecific. Dogs were tested twice in the shelter and once in their new homes 4 months after adoption to evaluate consistency in behavioral assessment. Playfulness, trainability, problem solving abilities, food possessiveness, and reactivity to sudden stimuli were also evaluated. Testers scored dogs' responses in terms of confidence, fearfulness, and aggressiveness. Results highlighted strengths and limits of this TT that was devised to help shelter staff in matching dogs' personality and owners' expectations. Methodological constraints when working with sheltered dogs are unavoidable; however, the test proved to be overall feasible, reliable, and valid although further studies are needed to address the critical issues that emerged. © 2011 Elsevier Inc.

Validity of model devices used to assess canine temperament in behavioral tests

Temperament tests are widely accepted as instruments for profiling behavioral variability in dogs, and they are applied in numerous areas of investigation (e.g. suitability for adoption or for breeding). During testing, to elicit a dog's reaction toward novel stimuli and predict its behavior in everyday life, model devices such as a child-like doll, or a fake dog, are often employed. However, the reliability of these devices to accurately stimulate dogs' reactions to children or dogs, is unknown and perhaps overestimated. This may be a particular concern in the case of aggressive behavior toward humans, a significant public health issue. The aim of this study was to: (1) evaluate the correlation between dogs' reactions to these devices, and owners' reports of their dog's aggression history (using the C-BARQ ??); (2) compare reactions toward the devices of dogs with and without histories of aggression. Subjects were selected among those visiting for behavioral consultation at the Veterinary Hospital of the University of Pennsylvania, and previously categorized as aggressive toward unfamiliar children, conspecifics, or as non-aggressive dogs (control). The test consisted of different components: an unfamiliar female tester approaching the dog; the presentation of a child-like doll, an ambiguous object, and a fake plastic dog. All tests were videotaped and durations of behaviors were later analyzed on the basis of a specified ethogram. Dogs' reactions were compared to C-BARQ scores, and interesting correlations emerged for 'dog-directed aggression/fear' (R = 0.48, P = 0.004), and 'stranger-directed aggression' (R = 0.58, P <0.001) factors. Dogs differed in their reactions toward the devices: the child-like doll and the fake dog elicited more social behaviors than the ambiguous object used as a control stimulus. Issues concerning the reliability of these tools to assess canine temperament are discussed. ?? 2012 Elsevier B.V. All rights reserved.