An R Framework for the Partitioning of Linkage Disequilibrium between and Within Populations

Patterns of linkage disequilibrium (LD) across the genome result from a myriad of contributing factors including selection and genetic drift. Natural selection can increase LD near individually selected loci, or it can influence LD between epistatically selected groups of loci. Statistics have previously been derived which compare levels of linkage disequilibrium in subpopulations relative to the total population. These statistics may be leveraged to identify loci that may be under selection or epistatic selection. This is a powerful approach, but to date no framework exists to support its use on a genome-wide scale. We present ohtadstats, an R package designed to facilitate the implementation of Ohta’s D statistics in a variety of use cases. Statistics calculated by this package can be used to determine whether a locus is under selection or not, and can provide insight into the nature of the selection that is taking place (hard sweep or epistatic selection). This package is available on the Comprehensive R Archive Network (CRAN).   Funding statement: This research was supported by funding from the USDA Agricultural Research Service. PFP is funded by the University of Missouri Life Sciences Fellowship and a training grant from the National Institute of Health (T32GM008396)

Biological and psychological markers of stress in humans: Focus on the Trier Social Stress Test

Validated biological and psychological markers of acute stress in humans are an important tool in translational research. The Trier Social Stress Test (TSST), involving public interview and mental arithmetic performance, is among the most popular methods of inducing acute stress in experimental settings, and reliably increases hypothalamic-pituitary-adrenal axis activation. However, although much research has focused on HPA axis activity, the TSST also affects the sympathetic-adrenal-medullary system, the immune system, cardiovascular outputs, gastric function and cognition. We critically assess the utility of different biological and psychological markers, with guidance for future research, and discuss factors which can moderate TSST effects. We outline the effects of the TSST in stress-related disorders, and if these responses can be abrogated by pharmacological and psychological treatments. Modified TSST protocols are discussed, and the TSST is compared to alternative methods of inducing acute stress. Our analysis suggests that multiple readouts are necessary to derive maximum information; this strategy will enhance our understanding of the psychobiology of stress and provide the means to assess novel therapeutic agents

Ecological Drivers of and Responses by Arctic Benthic Communities, with an Emphasis on Kongsfjorden, Svalbard

Knowledge on the causes and consequences that structure benthic communities is essential to understand and conserve Arctic ecosystems. This review aims to summarize the current knowledge on the effects of abiotic and biotic factors on species interactions and community traits, i.e. diversity, structure, and functioning of Arctic coastal hard- and soft-bottom habitats, with emphasis on Kongsfjorden (Svalbard). Current evidence indicates that descriptive and mensurative studies on the distribution of species prevail and few studies allow inferences on the underlying processes generating observed patterns. Furthermore, Arctic hard- and soft-bottom communities show some fundamental differences in their ecology. The recovery in hard-bottom communities from disturbance, for instance, takes exceptionally long (i.e. > decadal) due to slow growth and/or sporadic recruitment, while it is considerably shorter in soft-bottom communities. Also, Arctic hard-bottom communities display strong competitive hierarchies that appear negligible in communities populating sedimentary shores. This review concludes with a suggestion to shift the focus in Arctic benthos research from pattern to processes and the identification of major research gaps. These include (i) the apparent demarcation of studies being devoted to either rocky or to sedimentary shores, which hamper studies on habitat connectivity, (ii) the lack of studies addressing the effects of pathogens and diseases on community ecology, and (iii) the incomplete assessment of potentially significant drivers of community ecology, such as trophic interactions, recruitment success, and competition