Recent work by Magnuson, Solomon and Grossman(1) adds to a growing body of evidence indicating that microorganisms possess sophisticated signaling systems that enable them to sense and respond to environmental challenges. Typically, this response results in morphological, physiological and even genetic differentiation, paralleling that observed among higher organisms. These signaling systems may be interpreted as adaptations that maximize the reproductive potential of a population.

Although it has not been much noticed, reproduction is the central theme of François Jacob’s important history of biology, La logique du vivant (The Logic of Life). In a book ostensibly devoted to heredity, this molecular biologist had reproduction integrate levels of organization from organisms to molecules and play a major role in each historical transition between them, not just in the influential argument for a shift “from generation to reproduction.” Moreover, I claim, La logique was the first general history (...) of (research on) reproduction. Earlier histories had tackled only aspects of generation and reproduction; none historicized the latter. Jacob’s innovation came out of the rising prominence of reproduction in neo-Darwinist studies of populations and in his own field, the cellular genetics of bacteria and their viruses, and engagement with history and philosophy of science. The discovery of bacterial “sex” enabled microbial genetics but, ironically, led Jacob to a sexless concept of reproduction. This approach molded a history that reached across the living world but slighted sex and the complexities of reproduction in multicellular organisms. Readers can learn from its strength and limitations. (shrink)

Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or (...) features of entities) over time inevitably underestimates the extent and nature of microbial diversity. These dynamics are not the outcome of the process of vertical descent alone. Other processes, often involving causal interactions between entities from distinct levels of biological organisation, or operating at different time scales, are responsible not only for the destabilisation of pre-existing entities, but also for the emergence and stabilisation of novel entities in the microbial world. In this article we consider microbial entities as more or less stabilised functional wholes, and sketch a network-based ontology that can represent a diverse set of processes including, for example, as well as phylogenetic relations, interactions that stabilise or destabilise the interacting entities, spatial relations, ecological connections, and genetic exchanges. We use this pluralistic framework for evaluating (i) the existing ontological assumptions in evolution (e.g. whether currently recognized entities are adequate for understanding the causes of change and stabilisation in the microbial world), and (ii) for identifying hidden ontological kinds, essentially invisible from within a more limited perspective. We propose to recognize additional classes of entities that provide new insights into the structure of the microbial world, namely “processually equivalent” entities, “processually versatile” entities, and “stabilized” entities. (shrink)

While unicellular microbes such as phytoplankton (marine algae) have long been considered immortal unless eaten by predators, recent research suggests that under specific conditions entire populations of phytoplankton actively kill themselves; their assumed atemporality is being revised as marine ecologists recognize phytoplankton’s important role in the global carbon cycle. Drawing on empirical research into programmed cell death in marine microbes, this article explores how, in their study of microbial death, scientists change not only our understanding of microbial temporality, (...) but also reconstruct the relationship between life and death, biological individuality and assumptions about a natural teleology associated with bounded biological systems and genetic programmes. Reading this research together with a Derridean deconstruction of the limit between human and other animals with respect to death, this article explores how the deconstruction of individuality from within biology may suggest alternatives to our anthropocentric notion of time and embodiment. (shrink)

The gut microbiota is an important component of the human body and its immune‐modulating and metabolic activities are critical to maintain good health. Gut microbes, however, are sensitive to changes in diet, exposure to antibiotics, or infections, all of which cause transient disruptions in the microbial composition, a phenomenon known as dysbiosis. It is now recognized that microbial dysbiosis is at the root of many gastrointestinal disorders. However, the mechanisms through which bacterial dysbiosis initiates disease are not fully (...) understood. Microbially‐derived metabolites and their role in disease have also attracted significant attention. Identification of cancer‐associated bacteria and understanding the contributions of microbial metabolism in health and disease are exciting but challenging areas that will allow defining microbial biomarkers for predicting gastrointestinal disorders. Understanding the complex interactions between gut microbiota, diet, host immune system and host genetics will be critical to developing more personalized therapies and approaches to treat disease. (shrink)

Plasmids are a major type of mobile genetic elements (MGEs) that mediate horizontal gene transfer. The stable maintenance of plasmids plays a critical role in the functions and survival for microbial populations. However, predicting and controlling plasmid persistence and abundance in complex microbial communities remain challenging. Computationally, this challenge arises from the combinatorial explosion associated with the conventional modeling framework. Recently, a plasmid‐centric framework (PCF) has been developed to overcome this computational bottleneck. This framework enables the derivation of (...) a simple metric, the persistence potential, to predict plasmid persistence and abundance. Here, we discuss how PCF can be extended to account for plasmid interactions. We also discuss how such model‐guided predictions of plasmid fates can benefit from the development of new experimental tools and data‐driven computational methods. (shrink)

I propose a T‐cell receptor (TcR)‐based mechanism by which immunity mediates both “genetic self” and “microbial self” thereby, connecting microbiome disease with autoimmunity. The hypothesis is based on simple principles. First, TcR are selected to avoid strong cross‐reactivity with “self,” resulting in selection for a TcR repertoire mimicking “genetic self.” Second, evolution has selected for a “microbial self” that mimics “genetic self” so as to share tolerance. In consequence, our TcR repertoire also mimics microbiome antigenicity, providing a novel (...) mechanism for modulating tolerance to it. Also, the microbiome mimics the TcR repertoire, acting as a secondary immune system. I call this TcR‐microbiome mimicry “holoimmunity” to denote immune tolerance to the “holobiont self.” Logically, microbiome‐host mimicry means that autoimmunity directed at host antigens will also attack components of the microbiome, and conversely, an immunological attack on the microbiome may cross‐react with host antigens producing “holoautoimmunity.”. (shrink)

Mutations that disrupt biological rhythms have existed in microbial and metazoan eukaryotes for some time. They have recently begun to be studied with increasing intensity, both in terms of phenotypic effects of the relevant genetic variants, and with regard to molecular isolation and analysis of the genes defined by two of the ‘clock mutations’. These genetic loci, called period (per) in Drosophila and frequency (frq) in Neurospora, influence not only the basic characteristics of circadian rhythmicity, but also temperature compensation (...) of such daily cycle durations, ‘re‐setting’ of the rhythms' phases, and (for the per mutants) behavioral oscillations associated with much shorter than circadian periodicities. Molecular cloning of Drosophila's per gene, accompanied crucially by the locus's identification in germ‐line transformants, has led to information on its expression ‐ temporally, spatially, and in regard to heterogeneity of mRNA types. Nucleotide‐sequencing analyses of genomic DNA (and/or cDNA) from normal and mutated per alleles have (1) led to the suggestion that this clock gene encodes a family of proteoglycans (which was further indicated by application of antibody reagents obtained by manipulation of one of the gene's exons); and (2) shown that the three types of per mutations ‐ which shorten or lengthen rhythm periodicities or appear to eliminate them ‐ are associated with interesting amino‐acid substitutions or a stop codon, respectively. Analogous molecular findings are awaited from Neurospora, whose frq gene has very recently been cloned and definitively identified, in part via transformation experiments. (shrink)

In the past few decades, increased awareness of environmental pollution has led to the exploitation of microbial metabolic potential in the construction of several genetically engineered microorganisms (GEMs) for bioremediation purposes. At the same time, environmental concerns and regulatory constraints have limited the in situ application of GEMs, the ultimate objective behind their development. In order to address the anticipated risks due to the uncontrolled survival/dispersal of GEMs or recombinant plasmids into the environment, some attempts have been made to (...) construct systems that would contain the released organisms. This article discusses the designing of safer genetically engineered organisms for environmental release with specific emphasis on the use of bacterial plasmid addiction systems to limit their survival thus minimizing the anticipated risk. We also conceptualize a novel strategy to construct “Suicidal Genetically Engineered Microorganisms (SGEMs)” by exploring/combining the knowledge of different plasmid addiction systems (such as antisense RNA‐regulated plasmid addiction, proteic plasmid addiction etc.) and inducible degradative operons of bacteria. BioEssays 27:563–573, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

The future of art is dirt and decomposing shit. A deconstructed intestinal sea of microorganisms, spread out into the soil they were released back into following the extinction of their complex vessel. The genetic information they exchanged with each other as well as with their container, now existing in a vague memory, perhaps a feeling of sadness and longing, as they digest the once cherished artifacts of their human predecessors.

Non‐genetic forms of antimicrobial (drug) resistance can result from cell‐to‐cell variability that is not encoded in the genetic material. Data from recent studies also suggest that non‐genetic mechanisms can facilitate the development of genetic drug resistance. We speculate on how the interplay between non‐genetic and genetic mechanisms may affect microbial adaptation and evolution during drug treatment. We argue that cellular heterogeneity arising from fluctuations in gene expression, epigenetic modifications, as well as genetic changes contribute to drug resistance at different (...) timescales, and that the interplay between these mechanisms enhance pathogen resistance. Accordingly, developing a better understanding of the role of non‐genetic mechanisms in drug resistance and how they interact with genetic mechanisms will enhance our ability to combat antimicrobial resistance. Also see the video abstract here: https://youtu.be/aefGpdh-bgU. (shrink)

We address the controversy in the literature concerning the definition of holobionts and the apparent constraints on their evolution using concepts from community population genetics. The genetics of holobionts, consisting of a host and diverse microbial symbionts, has been neglected in many discussions of the topic, and, where it has been discussed, a gene-centric, species-centric view, based in genomic conflict, has been predominant. Because coevolution takes place between traits or genes in two or more species and not, strictly speaking, (...) between species, it may affect some traits but not others in either host or symbiont. Moreover, when interacting species pairs are embedded in a larger community, indirect ecological effects can alter the expected pairwise dynamics. Mode of symbiont transmission and the degree of host inbreeding both affect the extent of microbial mixing across host lineages and thereby the degree to which selection on one trait of either partner affects other aspects of a holobiont phenotype. We discuss several potential defining criteria for holobionts using community genetics and population genetics models, suggesting their application and limitations. Using community genetics models, we show how conflict between genomes can be self-limiting, while cooperation and mutualism tend to be self-accelerating. It is likely that this bias in the evolutionary dynamics of interaction between hosts and symbionts is an important feature of holobionts. This bias in the evolutionary dynamic could contribute to explaining the absence of cheaters from natural mutualisms, although cheaters are predicted by gene-centered conflict theory to cause the evolutionary instability of mutualisms. Additionally, it may help explain the more frequent origin of mutualisms from parasitic than from free-living systems, an evolutionary trajectory opposite to that predicted by genome conflict theory. (shrink)

Prompted by recent recognitions of the omnipresence of horizontal gene transfer among microbial species and the associated emphasis on exchange, rather than isolation, as the driving force of evolution, this essay will reflect on hybridization as one of the central concerns of nineteenth-century biology. I will argue that an emphasis on horizontal exchange was already endorsed by ‘biology’ when it came into being around 1800 and was brought to full fruition with the emergence of genetics in 1900. The true (...) revolution in nineteenth-century life sciences, I maintain, consisted in a fundamental shift in ontology, which eroded the boundaries between individual and species, and allowed biologists to move up and down the scale of organic complexity. Life became a property extending both ‘downwards’, to the parts that organisms were composed of, as well as ‘upwards’, to the collective entities constituted by the relations of exchange and interaction that organisms engage in to reproduce. This mode of thinking was crystallized by Gregor Mendel and consolidated in the late nineteenth-century conjunction of biochemistry, microbiology and breeding in agro-industrial settings. This conjunction and its implications are especially exemplified by Wilhelm Johannsen’s and Martinus Beijerinck’s work on pure lines and cultures. An understanding of the subsequent constraints imposed by the evolutionary synthesis of the twentieth century on models of genetic systems may require us to rethink the history of biology and displace Darwin’s theory of natural selection from that history’s centre. (shrink)

Obesity is the focus of multiple lines of inquiry that have -- together and separately -- produced many deep insights into the physiology of weight gain and maintenance. We examine three such streams of research and show how they are oriented to obesity intervention through multilevel integrated approaches. The first research programme is concerned with the genetics and biochemistry of fat production, and it links metabolism, physiology, endocrinology and neurochemistry. The second account of obesity is developmental and draws together epigenetic (...) and environmental explanations that can be embedded in an evolutionary framework. The third line of research focuses on the role of gut microbes in the production of obesity, and how microbial activities interact with host genetics, development and metabolism. These interwoven explanatory strategies are driven by an orientation to intervention, both for experimental and therapeutic outcomes. We connect the integrative and intervention-oriented aspects of obesity research through a discussion of translation, broadening the concept to capture the dynamic, iterative processes of scientific practice and therapy development. This system-oriented analysis of obesity research expands the philosophical scrutiny of contemporary developments in the biosciences and biomedicine, and has the potential to enrich philosophy of science and medicine. (shrink)

The role of fixed charges present at the surface of biological membranes is usually described by the Gouy-Chapman-Grahame theory of the electric double-layer where the Grahame equation is applied independently on each side of the membrane and where the capacitive charges are disregarded. In this article, we generalize the Gouy-Chapman-Grahame theory by taking into account both intrinsic charges and capacitive charges, in the density value of the membrane surface charges. In the first part, we show that capacitive charges couple electrostatic (...) potentials present on both sides of the membrane. The intensity of this coupling depends both on the value of the membrane specific capacitance and the transmembrane electric potential difference. In the second part, we suggest some physiological implications of membrane electric double-layers. (shrink)

The Epic of Evolution is a course taught at Northern Arizona University. It engages the task of formulating a new epic myth that is based on the physical, natural, social, and cultural sciences. It aims to serve the need of providing meaning for human living in the vast and complex universe that the sciences now depict for us. It is an interdisciplinary effort in an academic setting that is often divided by specializations; it focuses on values in a climate of (...) relativism; and it concentrates on an enterprise for which there are few textbooks at hand. The course is presented in three segments: the cosmos before humans appeared, the human phenomenon, and scenarios for the future of evolution. (shrink)

Building on the emerging literature on the ethics of social enterprises (SEs), this paper advances the underexplored role of frontline workers (FLWs) as embedded agents at the interface between communities and SEs. Specifically, we uncover the subjectivity of FLWs as they navigate moral ambiguities while performing their professional roles, dealing with rules and regulations within the organizational hierarchy and living as members of local communities. Based on an inductive case study of a microfinance organization in Cameroon, we find that FLWs (...) engage in three rationalization strategies: cautious disengaging, safeguarding self-interest, and justifying relevance. Our findings offer a better understanding of the ethics of SEs by unpacking the subjectivity of FLWs. We highlight a bottom-up account of caring SEs, identify a boundary condition to subjectivity, and present a nuanced view of FLWs in embedded organizations. We also discuss the practical implications for SEs to improve their compassion and cater for the mental wellbeing of FLWs. (shrink)

By exploring whether nanotechnologies have the potential to generate green innovations, we consider the paradox between the negative and positive side-effects that could come with the development of nanotechnologies. Starting from the conceptual framework of green product innovation, the potential green innovation activity of more than 14,000 firms of the nanotech sector is investigated. Using a query-search method, their patenting activity is explored. Results first show that there is an increasing trend toward the creation of fundamental green knowledge by firms (...) involved in nanotechnologies; second, they demonstrate that energy efficiency is the main driver of green knowledge creation in the sector and third they reveal the main characteristics of nanotech firms creating green knowledge. Beyond their contribution to the debate between positive and negative outcomes of nanotechnology developments, these results also enrich the conceptual framework of green product innovation—a key route to achieving sustainability at the same time as growth. (shrink)

The rapidly changing field of genetics affects society through advances in health-care and through implications of genetic research. This study addresses the impacts of new genetic discoveries and technologies on different segments of today's society. The book begins with a chapter on genetic complexity, and subsequent chapters discuss moral and ethical questions arising from today's genetics from the perspectives of health care professionals, the media, the general public, special interest groups and commercial interests.

The 1940s and 1950s were marked by intense debates over the origin of drug resistance in microbes. Bacteriologists had traditionally invoked the notions of ‘training’ and ‘adaptation’ to account for the ability of microbes to acquire new traits. As the field of bacterial genetics emerged, however, its participants rejected ‘Lamarckian’ views of microbial heredity, and offered statistical evidence that drug resistance resulted from the selection of random resistant mutants. Antibiotic resistance became a key issue among those disputing physiological vs. (...) genetic explanations of variation in bacteria. Postwar developments connected with the Lysenko affair gave this debate a new political valence.Proponents of the neo-Darwinian synthesis weighed in with support for the genetic theory. However, certain features of drug resistance seemed inexplicable by mutation and selection, particularly the phenomenon of ‘multiple resistance’—the emergence of resistance in a single strain against several unrelated antibiotics. In the late 1950s, Tsutomu Watanabe and his collaborators solved this puzzle by determining that resistance could be conferred by cytoplasmic resistance factors rather than chromosomal mutation. These R factors could carry resistance to many antibiotics and seemed able to promote their own dissemination in bacterial populations. In the end, the vindication of the genetic view of drug resistance was accompanied by a recasting of the ‘gene’ to include extrachromosomal hereditary units carried on viruses and plasmids. (shrink)

Society has historically not taken a benign view of genetic disease. The laws permitting sterilization of the mentally re tarded~ and those proscribing consanguineous marriages are but two examples. Indeed as far back as the 5th-10th centuries, B.C.E., consanguineous unions were outlawed (Leviticus XVIII, 6). Case law has traditionally tended toward the conservative. It is reactive rather than directive, exerting its influence only after an individual or group has sustained injury and brought suit. In contrast, state legislatures have not been (...) inhibited in enacting statutes. Many of their products can be characterized as hasty, unnecessary, ill-conceived, and based on the heart rather than the head. Moreover the lack of expert consultation sought has also been remarkable. One state legislature, for example, has advocated immunization for sickle cell anemia! Many others have enacted laws for the screening of inborn errors of metabolism, e.g., phenylketon uria, but have poorly defined the lines of responsibility to secure compliance. A spate of specific disease-related bills has emerged in the u.S. Congress, each seeking recognition and appropriations. Sickle cell anemia, hemophilia, Cooley's anemia and Tay-Sachs disease have been among the front-runners for support. Finally, in 1975, Congress has begun to examine an omnibus bill concerning all forms of genetic disease. The bill, termed the National Genetic Diseases Act is, however, still far from being enacted. (shrink)

Progressive supranuclear palsy is a movement disorder with prominent tau neuropathology. Brain diseases with abnormal tau deposits are called tauopathies, the most common of which is Alzheimer's disease. Environmental causes of tauopathies include repetitive head trauma associated with some sports. To identify common genetic variation contributing to risk for tauopathies, we carried out a genome-wide association study of 1,114 individuals with PSP and 3,247 controls followed by a second stage in which we genotyped 1,051 cases and 3,560 controls for the (...) stage 1 SNPs that yielded P ≤ 10-3. We found significant previously unidentified signals associated with PSP risk at STX6, EIF2AK3 and MOBP. We confirmed two independent variants in MAPT affecting risk for PSP, one of which influences MAPT brain expression. The genes implicated encode proteins for vesicle-membrane fusion at the Golgi-endosomal interface, for the endoplasmic reticulum unfolded protein response and for a myelin structural component. © 2011 Nature America, Inc. All rights reserved. (shrink)

BackgroundClinical ethical practice (CEP) is required for healthcare workers (HCWs) to improve health-care delivery. However, there are gaps between accepted ethical standards and CEP in Ethiopia. There have been limited studies conducted on CEP in the country. Therefore, this study aimed to determine the magnitude and associated factors of CEP among healthcare workers in healthcare facilities in Ethiopia.MethodFrom February to April 2021, a mixed-method study was conducted in 24 health facilities, combining quantitative and qualitative methods. Quantitative (survey questionnaire) and qualitative (...) (semi-structured interviews) data were collected. For quantitative and qualitative data analysis, Stata version 14 and Atlas.ti version 7 were utilized. Multiple logistic regression and thematic analysis for quantative and qualitative respectively used.ResultsFrom a total of 432 study participants, 407 HCWs were involved in the quantitative analysis, 36 participants were involved in five focus group discussions (FGDs), and eleven key informant interviews (KIIs) were involved in the qualitative analysis. The score of good CEP was 32.68%. Similarly, the scores of good knowledge and attitude were 33.50% and 25.31%, respectively. In the multiple logistic regression models, satisfaction with the current profession, availability of functional CECs, compassionate leaders, previously thought clinical ethics in pre-service education and good attitude were significant factors associated with CEP. Among these significant factors, knowledge, compassionate leaders, poor infrastructure, a conducive environment and positive attitudes were also determinants of CEP according to qualitative findings.ConclusionsThe CEP in health care services in Ethiopia is low. Satisfaction with the current profession, functional CECs, positive attitude, compassionate leaders and previously thought clinical ethics were significant factors associated with CEP. The Ministry of Health (MoH) should integrate interventions by considering CECs, compassionate leadership, and positive attitudes and enhance the knowledge of health professionals. Additionally, digitalization, intersectoral collaboration and institutionalization are important for promoting CEP. (shrink)

Abstractabstract:Long before COVID-19 made social distancing familiar, people with cystic fibrosis (CF) already practiced such behaviors. CF is held up as a classic example of genetic disease, yet people with CF are also susceptible to bacteria from the environment and from other CF patients. Starting in the 1980s, a bacterial epidemic in the CF population highlighted clashing priorities of connection, physical safety, and environmental protection. Policymakers ultimately called for the physical separation of people with CF from one another via recommendations (...) that reconfigured the CF community. Simultaneously, medical researchers recognized that one highly transmissible CF pathogen called cepacia was being developed for environmental applications and got the EPA to limit cepacia's environmental deployment. Environmental regulations speak to the challenge of useful microbes that harm a minority, but CF cross-infection also involves legal implications for microbial and genetic discrimination, social consequences for CF communities, and ethical questions about balancing autonomy, harms, and benefits. As scientists increasingly study connections between host genetics, microbial genetics, and infectious risks, CF is a vital referent. (shrink)

Microscopy has revealed tremendous diversity of bacterial and eukaryotic forms. Recent molecular analyses show discordance in estimates of biodiversity between morphological and molecular analyses. Moreover, phylogenetic analyses of the diversity of microbial forms reveal evidence of convergence at scales as deep as interdomain: morphologies shared between bacteria and eukaryotes. Here, we highlight examples of such discordance, focusing on exemplary lineages such as testate amoebae, ciliates, and cyanobacteria. These have long histories of morphological study, enabling deeper analyses on both the (...) molecular and morphological sides. We discuss examples in two main categories: (i) morphologically identical (or highly similar) individuals that are genetically distinct and (ii) morphologically distinct individuals that are genetically the same. We argue that hypotheses about discordance can be tested using the concept of neutral morphologies, or more broadly neutral phenotypes, as a null hypothesis. -/- . (shrink)

Enzyme directed genetic mechanisms causing random DNA sequence alterations are ubiquitous in both eukaryotes and prokaryotes. A number of molecular geneticist have invoked adaptation through natural selection to account for this fact, however, alternative explanations have also flourished. The population geneticist G.C. Williams has dismissed the possibility of selection for mutator activity on a priori grounds. In this paper, I attempt a refutation of Williams' argument. In addition, I discuss some conceptual problems related to recent claims made by microbiologists on (...) the adaptiveness of molecular variety generators in the evolution of prokaryotes. A distinction is proposed between selection for mutations caused by a mutator activity and selection for the mutator activity proper. The latter requires a concept of fitness different from the one commonly used in microbiology. (shrink)

Microbial genome sequencing has entered a new phase, where DNA sequence information is gathered from entire microbial communities (metagenomics or environmental genomics) rather than from individual microorganisms. By providing access to the genetic material of vast numbers of organisms, most of which are organisms that have never been isolated or cultivated, a new level of insight is being gained into the diversity and extent of the microbial processes that are presently occuring in environmental communities. By extending metagenomic‐based (...) approaches to the study of very complex and methodologically recalcitrant soil environments, a recent study has found that ammonia‐oxidizing archaea are more abundant in many soils than bacteria.1 These findings not only highlight the undoubtedly critical yet unknown roles that archaea play in global nutrient cycles but illustrate the importance of genomic studies for informing us about the functional capacity of life on Earth. BioEssays 29: 11–14, 2007. © 2006 Wiley Periodicals, Inc. (shrink)

Metaseiulus occidentalis is a representative of an important family of mites (Arthropoda: Chelicerata: Acari: Phytoseiidae) that are effective predators of pest mites in agricultural crops around the world. Like many arthropods, this mite contains multiple genomes, including the genomes of several microbial symbionts as well as its own mitochondrial and nuclear genomes. The mitochondrial genome is “mitey” large at 25 kb, due to duplication and triplication of genes. By contrast, the nuclear genome is “mitey” small at 88 Mb. This (...) mite has a parahaploid genetic system, tolerates inbreeding, and has a haploid chromosome number of 3. This predator was genetically improved for use in agriculture by developing strains that lacked the ability to overwinter in diapause or were resistant to multiple pesticides, and can be genetically modified using recombinant DNA methods. Sequencing the nuclear genome would provide useful insights that could enhance genetic improvement programs that would result in improved pest management, could provide genes needed to resolve the evolutionary relationships of this family, and could serve as a model for understanding the evolution and genetics of chelicerate arthropod predators. (shrink)

Frequent lateral genetic transfer undermines the existence of a unique “tree of life” that relates all organisms. Vertical inheritance is nonetheless of vital interest in the study of microbial evolution, and knowing the “tree of cells” can yield insights into ecological continuity, the rates of change of different cellular characters, and the evolutionary plasticity of genomes. Notwithstanding within-species recombination, the relationships most frequently recovered from genomic data at shallow to moderate taxonomic depths are likely to reflect cellular inheritance. At (...) the same time, it is clear that several types of ‘average signals’ from whole genomes can be highly misleading, and the existence of a central tendency must not be taken as prima facie evidence of vertical descent. Phylogenetic networks offer an attractive solution, since they can be formulated in ways that mitigate the misleading aspects of hybrid evolutionary signals in genomes. But the connections in a network typically show genetic relatedness without distinguishing between vertical and lateral inheritance of genetic material. The solution may lie in a compromise between strict tree-thinking and network paradigms: build a phylogenetic network, but identify the set of connections in the network that are potentially due to vertical descent. Even if a single tree cannot be unambiguously identified, choosing a subnetwork of putative vertical connections can still lead to drastic reductions in the set of candidate vertical hypotheses. (shrink)

This paper investigates the complexity hypothesis in microbial evolutionary genetics from a philosophical vantage. This hypothesis, in its current version, states that genes with high connectivity are likely to be resistant to being horizontally transferred. We defend four claims. There is an important distinction between two different ways in which a gene family can persist: vertically and horizontally. There is a trade-off between these two modes of persistence, such that a gene better at achieving one will be worse at (...) achieving the other. At least some genes are likely to experience selection favoring increased transferability. One consequence of this can be encapsulated as the “simplicity hypothesis”: horizontally persisting genes will experience selection favoring reduced connectivity. In order to make sense of the simplicity hypothesis, we need to consider evolutionary populations that transcend species boundaries. Vertical and horizontal persistence are therefore not two competing ways of succeeding at the same game, but involve playing two different games altogether. The complexity hypothesis can be understood in terms of two related notions: entrenchment and Cuvierian functionalism. This framing reveals previously unrecognized and philosophically interesting connections between reasoning about deep conservation and horizontal transfer. (shrink)

There is an urgent need for novel protection strategies to sustainably secure crop production under changing climates. Studying microbial effectors, defined as microbe‐derived proteins that alter signalling inside plant cells, has advanced our understanding of plant immunity and microbial plant colonisation strategies. Our understanding of effectors in the establishment and beneficial outcome of plant symbioses is less well known. Combining functional and comparative interaction assays uncovered specific symbiont effector targets in highly interconnected plant signalling networks and revealed the (...) potential of effectors in beneficially modulating plant traits. The diverse functionality of symbiont effectors differs from the paradigmatic immuno‐suppressive function of pathogen effectors. These effectors provide solutions for improving crop resilience against climate stress by their evolution‐driven specification in host protein targeting and modulation. Symbiont effectors represent stringent tools not only to identify genetic targets for crop breeding, but to serve as applicable agents in crop management strategies under changing environments. (shrink)