To explain differences in gut microbial communities we must determine how processes regulating microbial community assembly (colonization, persistence) differ among hosts and affect microbiota ...composition. We surveyed the gut microbiota of threespine stickleback (Gasterosteus aculeatus) from 10 geographically clustered populations and sequenced environmental samples to track potential colonizing microbes and quantify the effects of host environment and genotype. Gut microbiota composition and diversity varied among populations. These among-population differences were associated with multiple covarying ecological variables: habitat type (lake, stream, estuary), lake geomorphology and food- (but not water-) associated microbiota. Fish genotype also covaried with gut microbiota composition; more genetically divergent populations exhibited more divergent gut microbiota. Our results suggest that population level differences in stickleback gut microbiota may depend more on internal sorting processes (host genotype) than on colonization processes (transient environmental effects).
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, SBMB, SBNM, UL, UM, UPUK
•This paper reviews the similarities across Problem Structuring Methods.•Based on a literature review we build a framework to define these methods.•The framework contains four pillars: ontology, ...epistemology, axiology & methodology.•Each pillar poses questions examining an approach for problem structuring method characteristics.•The framework is evaluated to understand if it can identify these methods.
Problem structuring methods (PSMs) are a class of qualitative operational research (OR) modelling approaches that were first developed approximately 40 years ago. Different definitions of PSMs have been proposed, some focusing on the types of problems that PSMs typically address, others on how they address these problems. Despite this, there is no clear framework for what characteristics need to be present in an approach to warrant it being regarded as a PSM. This presents a challenge to understanding what constitutes a PSM and the acceptance of new PSMs. This exploratory paper develops a framework from a literature review to identify similarities between PSMs. The framework reflects that PSMs hold different philosophical assumptions to traditional OR and, thus, the framework is structured according to the four pillars of ontological, epistemological, axiological and methodological assumptions an approach makes. Across these assumptions, the framework poses 13 questions to determine if an approach could be a PSM. The effectiveness of the framework is understood by applying it to eight OR approaches to see if it successfully identifies PSMs.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Spatial genetic variation is shaped in part by an organism's dispersal ability. We present a deep learning tool, disperseNN2, for estimating the mean per-generation dispersal distance from ...georeferenced polymorphism data. Our neural network performs feature extraction on pairs of genotypes, and uses the geographic information that comes with each sample. These attributes led disperseNN2 to outperform a state-of-the-art deep learning method that does not use explicit spatial information: the mean relative absolute error was reduced by 33% and 48% using sample sizes of 10 and 100 individuals, respectively. disperseNN2 is particularly useful for non-model organisms or systems with sparse genomic resources, as it uses unphased, single nucleotide polymorphisms as its input. The software is open source and available from https://github.com/kr-colab/disperseNN2, with documentation located at https://dispersenn2.readthedocs.io/en/latest/.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Diversity is essential to climate resilience in food and farming. Traditionally, agrobiodiversity has been cultivated and sustained through communities’ relationships with seeds. A fluid process of ...saving, preserving, and exchanging seeds allows for regional adaptation and transformation. This process results in seed diversity at the crop, variety, and genetic level. Over the last century, agrobiodiversity has declined at an alarming rate, and simultaneously there has been an erosion of community seed-keeping practices. A reaction to these interrelated crises has been an increased push to preserve biodiversity through institutional seed preservation efforts (also called ex situ preservation), which focus on genetic preservation of seeds in controlled environments. The seeds are genetic resources that are made available to plant breeders, who solve agronomic problems by creating improved cultivars for farmers. This is very different from community seed-keeping (also called in situ preservation), which values seed-people relationships and fosters natural agrobiodiversity and regional adaptation. Seeds are seen in direct connection to food, and saved for immediate and practical reasons like yield, flavor, and resistance to biotic stressors. In traditional communities, seeds are often perceived as kin, as ancestors or living beings with both histories and futures. For institutional seed preservation, collecting and maintaining seed diversity is an imperative insurance policy against future challenges. Ironically, this model erodes community-based seed-keeping efforts and increases dependence on institutional seed preservation to maintain genetic diversity. In this paper, we explore declining agrobiodiversity and community seed-keeping and share our experiences working with a diverse range of varieties from The Heirloom Collard Project (HCP). We propose that radical seed diversity can jump-start autonomous, community-based seed-keeping efforts, increasing agrobiodiversity and, ultimately, the climate resilience of food systems.
Criminal organizations, like legitimate organizations, adapt to shifts in markets, competition, regulations, and enforcement. Exogenous shocks can be consequential moments of power consolidation, ...resource hoarding, and inequality amplification in legitimate organizations, but especially in criminal organizations. This research examines how the exogenous shock of the U.S. prohibition of the production, transportation, and sale of alcohol in 1920 restructured power and inequality in Chicago organized crime. I analyze a unique relational database on organized crime from the early 1900s via a criminal network that tripled in size and centralized during Prohibition. Before Prohibition, Chicago organized crime was small, decentralized, and somewhat inclusive of women at the margins. However, during Prohibition, the organized crime network grew, consolidated the organizational elites, and left out the most vulnerable participants from the most profitable opportunities. This historical case illuminates how profits and organizational restructuring outside of (or in response to) regulatory environments can displace people at the margins.
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BFBNIB, INZLJ, NMLJ, NUK, OILJ, PNG, SAZU, UKNU, UL, UM, UPUK, ZRSKP
Bureaucratic and patrimonial theories of organized crime tend to miss the history and mobility of crime groups integrating into and organizing with legitimate society. The network property of ...multiplexity—when more than one type of relationship exists between a pair of actors—offers a theoretical and empirical inroad to analyzing overlapping relationships of seemingly disparate social spheres. Using the historical case of organized crime in Chicago and a unique relational database coded from more than 5,000 pages of archival documents, we map the web of multiplex relationships among bootleggers, politicians, union members, businessmen, families, and friends. We analyze the overlap of criminal, personal, and legitimate networks containing 1,030 individuals and 3,726 mutual dyads between them. Multiplexity is rare in these data: only 10 percent of the mutual dyads contain multiplex ties. However, results from bivariate exponential random graph models demonstrate that multiplexity is a relevant structural property binding the three networks together. Even among our sample of criminals, we find dependencies between the criminal and personal networks and the criminal and legitimate networks. Although not pervasive, multiplexity glued these worlds of organized crime together above and beyond the personalities of famous gangsters, ethnic homophily, and other endogenous network processes.
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BFBNIB, INZLJ, NMLJ, NUK, OILJ, PNG, SAZU, UKNU, UL, UM, UPUK, ZRSKP
Previous studies of service reconfiguration in healthcare have explored the influence of power on processes and outcomes. However, in these accounts the moral agency of managers is often ...underemphasised. This paper draws on the theoretical tools provided by the sociology of morality to help deepen understanding of the interaction between power and moral agency in service reconfiguration in healthcare. It presents results from a qualitative study of a pan-organisational service reconfiguration in the NHS in England, involving nineteen in-depth interviews with those leading the change and the analysis of twelve programme documents. We combine concepts of the moral background and epistemic governance to interpret participants' conviction that the service change was 'the right thing to do'. The paper shows how epistemic work carried out by service change regulations shaped the moral background within which participants worked. This, in turn, channelled their moral agency - specifically their commitment to patient care - in a way that also reflected central priorities. The paper adds to sociological understandings of service reconfiguration through considering the interaction of structure, agency and power, while also developing the concept of the moral background to show how power relations can influence moral beliefs.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
• There are two theories about how allocation of metabolic products occurs. The allometric biomass partitioning theory (APT) suggests that all plants follow common allometric scaling rules. The ...optimal partitioning theory (OPT) predicts that plants allocate more biomass to the organ capturing the most limiting resource.
• Whole-plant harvests of mature and juvenile tropical deciduous trees, evergreen trees, and lianas and model simulations were used to address the following knowledge gaps: (1) Do mature lianas comply with the APT scaling laws or do they invest less biomass in stems compared to trees? (2) Do juveniles follow the same allocation patterns as mature individuals? (3) Is either leaf phenology or life form a predictor of rooting depth?
• It was found that: (1) mature lianas followed the same allometric scaling laws as trees; (2) juveniles and mature individuals do not follow the same allocation patterns; and (3) mature lianas had shallowest coarse roots and evergreen trees had the deepest.
• It was demonstrated that: (1) mature lianas invested proportionally similar biomass to stems as trees and not less, as expected; (2) lianas were not deeper-rooted than trees as had been previously proposed; and (3) evergreen trees had the deepest roots, which is necessary to maintain canopy during simulated dry seasons.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NMLJ, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
The architecture of the extracellular matrix (ECM) directs cell behavior by providing spatial and mechanical cues to which cells respond. In addition to soluble chemical factors, physical ...interactions between the cell and ECM regulate primary cell processes, including differentiation, migration, and proliferation. Advances in microtechnology and, more recently, nanotechnology provide a powerful means to study the influence of the ECM on cell behavior. By recapitulating local architectures that cells encounter in vivo, we can elucidate and dissect the fundamental signal transduction pathways that control cell behavior in critical developmental, physiological, and pathological processes.
Regulation of gene expression is a critical link between genotype and phenotype explaining substantial heritable variation within species. However, we are only beginning to understand the ways that ...specific gene regulatory mechanisms contribute to adaptive divergence of populations. In plants, the post-transcriptional regulatory mechanism of alternative splicing (AS) plays an important role in both development and abiotic stress response, making it a compelling potential target of natural selection. AS allows organisms to generate multiple different transcripts/proteins from a single gene and thus may provide a source of evolutionary novelty. Here, we examine whether variation in alternative splicing and gene expression levels might contribute to adaptation and incipient speciation of dune-adapted prairie sunflowers in Great Sand Dunes National Park, Colorado, USA. We conducted a common garden experiment to assess transcriptomic variation among ecotypes and analyzed differential expression, differential splicing, and gene coexpression. We show that individual genes are strongly differentiated for both transcript level and alternative isoform proportions, even when grown in a common environment, and that gene coexpression networks are disrupted between ecotypes. Furthermore, we examined how genome-wide patterns of sequence divergence correspond to divergence in transcript levels and isoform proportions and find evidence for both cis and trans-regulation. Together, our results emphasize that alternative splicing has been an underappreciated mechanism providing source material for natural selection at short evolutionary time scales.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
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