Development of a Genomic Prediction Pipeline for Maintaining Comparable Sample Sizes in Training and Testing Sets across Prediction Schemes Accounting for the Genotype-by-Environment Interaction

The global growing population is experiencing challenges to satisfy the food chain supply in a world that faces rapid changes in environmental conditions complicating the development of stable cultivars. Emergent methodologies aided by molecular marker information such as marker assisted selection (MAS) and genomic selection (GS) have been widely adopted to assist the development of improved genotypes. In general, the implementation of GS is not straightforward, and it usually requires cross-validation studies to find the optimum set of factors (training set sizes, number of markers, quality controls, etc.) to use in real breeding applications. In most cases, these different scenarios (combination of several factors) vary just in the levels of a single factor keeping fixed the other levels of the other factors allowing the use of previously developed routines (code reuse). In this study we present a set of structured modules than are easily to assemble for constructing complex genomic prediction pipelines from scratch. Also, we proposed a novel method for selecting training-testing sets of similar sample sizes across different cross-validation schemes (CV2, predicting tested genotypes in observed environments; CV1, predicting untested genotypes in observed environments; CV0, predicting tested genotypes in novel environments; and CV00, predicting untested genotypes in novel environments). To show how our implementation works, we considered two real data sets. These correspond to selected samples of the USDA soybean collection (D1: 324 genotypes observed in 6 environments scored for 9 traits) and of the Soybean Nested Association Mapping (SoyNAM) experiment (D2: 324 genotypes observed in 6 environments scored for 6 traits). In addition, three prediction models which consider the effect of environments and lines (M1: E + L), environments, lines and main effect of markers (M2: E + L + G), and also the inclusion of the interaction between makers and environments (M3: E + L + G + G×E) were considered. The results confirm that under CV2 and CV1 schemes, moderate improvements in predictive ability can be obtained with the inclusion of the interaction component, while for CV0 mixed results were observed, and for CV00 no improvements were shown. However, for this last scenario the inclusion of weather and soil data potentially could enhance the results of the interaction model.

Parasites differentially impact crayfish personality in different contexts

The expression of an individual animal’s behaviour can be placed along many different personality spectra. Parasite load can alter animal behaviour and, thus, fitness. The personality traits of rusty crayfish, Faxonius rusticus, were analysed in three different behavioural contexts: foraging, exploration, and threatened. Each crayfish was tested in each context 3 times, giving a total of 9 assays per crayfish. After assays were completed, crayfish were dissected, and the hepatopancreas of each crayfish was photo analysed to determine the parasite load of the trematode, Microphallus spp. A composite personality score for each assay and parasite load was loaded into a PCA. The PCA model showed that as parasite load increased, crayfish became bolder in threatening contexts and less exploratory in novel environments, whether or not a food stimulus was present. Thus, parasite load alters the placement of crayfish on different personality spectra, but this change is context specific.

Idiographic personality coherence: A quasi experimental longitudinal ESM study

Personality is a study of persons. However, persons exist within contexts, and personality coherence emerges from persons in contexts. But persons and environments bidirectionally influence each other, with persons selecting into and modifying their contexts, which also have lasting influences on personality. Thus, environmental change should produce changes in personality. Alternatively, environmental changes may produce few changes. This paradoxical viewpoint is based on the idea that novel environments have no predefined appropriate way to behave, which allows preexisting personality systems to stay coherent. We test these two perspectives by examining longitudinal consistency idiographic personality coherence using a quasi-experimental design (N = 50; total assessments = 5093). Personality coherence was assessed up to one year before the COVID-19 pandemic and again during lockdown. We also test antecedents and consequences of consistency, examining both what prospectively predicts consistency and what consistency prospectively predicts. Overall, consistency was modest but there were strong individual differences, indicating some people were quite consistent despite environmental upheaval. Moreover, there were relatively few antecedents and consequences of consistency, with the exception of some goals and domains of satisfaction predicting consistency, leaving open the question of why changes in coherence occur.

The Role of Culture in Evolutionary Theories of Human Cooperation

Evolutionarily-minded scholars working on the most puzzling aspects of human cooperation-one-shot, anonymous interactions among non-kin where reputational information is not available-can be roughly divided into two camps. In the first, researchers argue for the existence of evolved capacities for genuinely altruistic human cooperation, and in their models emphasize the role of intergroup competition and selection, as well as group norms and markers of membership that reduce intragroup variability. Researchers in the second camp explain cooperation in terms of individual-level decision-making facilitated by evolved cognitive mechanisms associated with well-established self- and kin-maximization models, as well as by ‘misfires’ that may result from these mechanisms interacting with novel environments. This essay argues that the manner in which culture provides information that de-anonymizes intragroup strangers suggests that neither evolved capacities for genuine altruism nor widespread misfires are necessary to account for anonymous, one-shot cooperation.

Idiographic Personality Coherence: A Quasi Experimental Longitudinal ESM Study

Personality is a study of persons. However, persons exist within contexts, and personality coherence emerges from persons in contexts. But persons and environments bidirectionally influence each other, with persons selecting into and modifying their contexts, which also have lasting influences on personality. Thus, environmental change should produce changes in personality. Alternatively, environmental changes may produce few changes. This paradoxical viewpoint is based on the idea that novel environments have no predefined appropriate way to behave, which allows preexisting personality systems to stay coherent (Caspi & Moffitt, 1993). We test these two perspectives by examining longitudinal consistency idiographic personality coherence using a quasi-experimental design (N = 50; total assessments = 5,093). Personality coherence was assessed up to one year before the COVID-19 pandemic and again during lockdown. We also test antecedents and consequences of consistency, examining both what prospectively predicts consistency as well as what consistency prospectively predicts. Overall, consistency was modest but there were strong individual differences, indicating some people were quite consistent despite environmental upheaval. Moreover, there were relatively few antecedents and consequences of consistency, with the exception of some goals and domains of satisfaction predicting consistency, leaving open the question of why changes in coherence occurs.

Genetic variation in Luman/CREB3 and association with stress and meat quality traits in Yorkshire pigs

LUMAN/CREB3 is a stress regulatory gene that affects activity of the hypothalamic-pituitary-adrenal axis in mice and presents a promising avenue for exploring variable stress-responsiveness in pigs. Pigs with similar characteristics to LUMAN-deficient mice, including greater resilience to stress and receptivity to human handling, would be valuable in the pork industry from animal welfare and production efficiency perspectives. We previously identified eight genetic variations and five haplotypes throughout the LUMAN locus in Yorkshire pigs. In this study we analysed associations between LUMAN variations with behavioural stress response during three tests (open field test, novel object test, and human approach test), physiological stress-responsiveness (cortisol), and carcass/meat quality measurements from purebred Yorkshire pigs. Haplotypes A1 and A2 were associated with decreased activity levels in novel environments and greater plasma cortisol concentrations at slaughter. Haplotype A1 was associated with lower carcass scratch scores and meat with lower cooking losses and greater tenderness. Haplotypes B1 and B2 were associated with the opposite traits including increased activity levels in novel environments and characteristics for lower meat quality including greater cooking losses, lower marbling, and paler coloured meat. We conclude that DNA variations in the LUMAN locus could potentially be used as genetic markers for stress resistance and meat quality in pig breeding.