The ecology and evolution of pangenomes

Since the first genome-scale comparisons, it has been evident that the genomes of many species are unbound by strict vertical descent: Large differences in gene content can occur among genomes belonging to the same prokaryotic species, with only a fraction of genes being universal to all genomes. These insights gave rise to the pangenome concept. The pangenome is defined as the set of all the genes present in a given species and can be subdivided into the accessory genome, present in only some of the genomes, and the core genome, present in all the genomes. Pangenomes arise due to gene gain by genomes from other species through horizontal gene transfer and differential gene loss among genomes, and have been described in both prokaryotes and eukaryotes. Our current view of pangenome variation is phenomenological and incomplete. In this review, we outline the mechanistic, ecological and evolutionary drivers of and barriers to horizontal gene transfer that are likely to structure pangenomes. We highlight the key role of conflict between the host chromosome(s) and the mobile genetic elements that mediate gene exchange. We identify shortcomings in our current models of pangenome evolution and suggest directions for future research to allow a more complete understanding of how and why pangenomes evolve

Co-evolution, opportunity seeking and institutional change: Entrepreneurship and the Indian telecommunications industry 1923-2009

"This is an Author's Original Manuscript of an article submitted for consideration in Business History [copyright Taylor & Francis]; Business History is available online at http://www.tandfonline.com/." 10.1080/00076791.2012.687538In this paper, we demonstrate the importance for entrepreneurship of historical contexts and processes, and the co-evolution of institutions, practices, discourses and cultural norms. Drawing on discourse and institutional theories, we develop a model of the entrepreneurial field, and apply this in analysing the rise to global prominence of the Indian telecommunications industry. We draw on entrepreneurial life histories to show how various discourses and discursive processes ultimately worked to generate change and the creation of new business opportunities. We propose that entrepreneurship involves more than individual acts of business creation, but also implies collective endeavours to shape the future direction of the entrepreneurial field

Mutation update for the SATB2 gene

SATB2-associated syndrome (SAS) is an autosomal dominant neurodevelopmental disorder caused by alterations in the SATB2 gene. Here we present a review of published pathogenic variants in the SATB2 gene to date and report 38 novel alterations found in 57 additional previously unreported individuals. Overall, we present a compilation of 120 unique variants identified in 155 unrelated families ranging from single nucleotide coding variants to genomic rearrangements distributed throughout the entire coding region of SATB2. Single nucleotide variants predicted to result in the occurrence of a premature stop codon were the most commonly seen (51/120=42.5%) followed by missense variants (31/120=25.8%). We review the rather limited functional characterization of pathogenic variants and discuss current understanding of the consequences of the different molecular alterations. We present an expansive phenotypic review along with novel genotype-phenotype correlations. Lastly, we discuss current knowledge on animal models and present future prospects. This review should help provide better guidance for the care of individuals diagnosed with SAS

Temporal, spatial, and structural patterns of adult trembling aspen and white spruce mortality in Quebec's boreal forest

Temporal, spatial, and structural patterns of adult trembling aspen (Populus tremuloides Michx.) and white spruce (Picea glauca (Moench) Voss) mortality were studied in intact 150-year-old stands in the southwestern boreal forest of Quebec. For both species, mortality decreases (number of dead trees/total number of trees) with distance from the lake edge until 100-150 m, from which point it slightly increases. Strong peaks in mortality were found for 40- to 60-year-old aspen mainly between 1974 and 1992. Such mortality in relatively young aspen is likely related to competition for light from the dominant canopy trees. Also, the recruitment of this young aspen cohort is presumably the result of a stand breakup that occurred when the initial aspen-dominated stand was between 90 and 110 years old. For spruce, strong peaks in mortality were found in 110- to 150-year-old trees and they occurred mainly after 1980. No clear explanation could be found for these peaks, but we suggest that they may be related to senescence or weakening of the trees following the last spruce budworm outbreak. Suppressed and codominant aspen had a much higher mortality ratio than spruce in the same height class, while more surprisingly, no difference in mortality rate was found between dominant trees of the two species. Most spruce trees were found as standing dead, which leads us to reject the hypothesis that windthrow is an important cause of mortality for spruce in our forests

Microclimate variability and long-term persistence of fragmented woodland

Favourable microclimates are predicted to buffer fragmented populations against the effects of environmental change, but ecological timeseries are often too short to establish the extent to which such microsites facilitate population persistence through multiple climate shifts. We investigate the effects of microclimatic heterogeneity on woodland resilience through millennial climate and disturbance shifts near northwest European woodland range limits. We use palaeoecological data from northern Scotland to study the effects of fragmentation on community composition and diversity in a potentially favourable microclimate, and compare palynological timeseries of tree abundance from five sites to assess the effects of favourable (low-lying sheltered) versus more marginal (higher altitude) settings on population persistence and stability. The sheltered site shows persistence of tree cover through Holocene climatic and anthropogenic shifts, including climatically-driven regional woodland contraction around 4400calBP (calendar years before present), when surviving woods became compositionally differentiated into upland pine and low-lying deciduous communities. A favourable microclimate can thus buffer woodlands against environmental shifts and increase continuity of canopy cover, but it does not generate stable communities. Compositional reorganisation is an essential stress response mechanism and should be accommodated by conservation managers. The replacement of deciduous taxa byPinus sylvestrisafter 1060calBP represents the decoupling of pine distribution from climate drivers by management intervention. As a result, current microrefugial woodland composition reflects late Holocene human intervention. Alternative models of community composition and behaviour from palaeoecology provide a stronger foundation for managing microsite communities than relict woods in contrasting environmental settings

The parent?infant dyad and the construction of the subjective self

Developmental psychology and psychopathology has in the past been more concerned with the quality of self-representation than with the development of the subjective agency which underpins our experience of feeling, thought and action, a key function of mentalisation. This review begins by contrasting a Cartesian view of pre-wired introspective subjectivity with a constructionist model based on the assumption of an innate contingency detector which orients the infant towards aspects of the social world that react congruently and in a specifically cued informative manner that expresses and facilitates the assimilation of cultural knowledge. Research on the neural mechanisms associated with mentalisation and social influences on its development are reviewed. It is suggested that the infant focuses on the attachment figure as a source of reliable information about the world. The construction of the sense of a subjective self is then an aspect of acquiring knowledge about the world through the caregiver's pedagogical communicative displays which in this context focuses on the child's thoughts and feelings. We argue that a number of possible mechanisms, including complementary activation of attachment and mentalisation, the disruptive effect of maltreatment on parent-child communication, the biobehavioural overlap of cues for learning and cues for attachment, may have a role in ensuring that the quality of relationship with the caregiver influences the development of the child's experience of thoughts and feelings

Global maps of soil temperature.

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km <sup>2</sup> resolution for 0-5 and 5-15 cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km <sup>2</sup> pixels (summarized from 8519 unique temperature sensors) across all the world's major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (-0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications