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30/05/2022, 17:00
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Alita Burmeister, Andrew Farr (MPI for Evolutionary Biology), Clara Moreno-Fenoll, Fatima Hussain, Loukas Theodosiou (MPI for Evolutionary Biology), Tanush Jagdish30/05/2022, 19:45
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Ben Kerr (University of Washington)30/05/2022, 20:00
The passage of genes from parents to offspring is a fundamental rule of heredity. However, bacteria violate this rule of strict vertical inheritance by shuttling DNA between cells through horizontal gene transfer (HGT). Common vehicles for HGT are conjugative plasmids, extrachromosomal pieces of DNA encoding the machinery for their own transfer. In addition to standard vertical transmission,...
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Berenike Maier (University of Cologne )31/05/2022, 09:00
In their natural habitats, bacteria live in close contact with other species. Genomic studies reveal plentiful evidence of horizontal gene transfer across different species. However, little is known about its rates and fitness effects. What are limiting factors of cross-species gene transfer? How does gene transfer affect bacterial fitness? While gene transfer can benefit bacteria during...
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Frederic Bertels (MPI for Evolutionary Biology)31/05/2022, 09:45
While independently replicating sequences, such as transposons, are common in bacterial genomes, they usually do not persist for long periods of time. To be maintained in the gene pool bacterial mobile genetic elements require to jump hosts. In contrast, short sequence repeats known as REPINs – whose replication is dependent on a non-jumping RAYT transposase – persist for millions of years in...
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Eitan Yaffe (Stanford University )31/05/2022, 10:45
Microbes living in natural communities develop antimicrobial resistance (AMR) through complex evolutionary trajectories. Fundamental features of this process emerge only in natural settings and therefore remain poorly understood. How are real-world AMR-associated genetic traits distributed between genes, intergenic regulatory regions, and mobile elements? Following an antibiotic exposure, are...
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Sinead Collins (University of Edinburgh)31/05/2022, 11:05
While we often track evolution for single traits in microbes, understanding and projecting their ecological functions often requires considering their integrated multitrait phenotypes. For example, understanding how the responses of phytoplankton to environmental change translate into changes in ocean primary production changes depends not only on the direct responses to selection (e.g....
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Audrey Menegaz Proenca (Freie Universität Berlin )31/05/2022, 14:30
No two cells are identical, even when sharing the same genetic code. This variability among phenotypes can be found in cell populations regardless of the complexity of the organism — from mammalian neural tissues to bacterial colonies. In the latter, genetically and morphologically identical bacteria often exhibit a myriad of growth states, resulting in drastic fitness variability. Most of...
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Joao Ascensao (University of California, Berkeley )31/05/2022, 14:50
The fitness effects of all possible mutations available to an organism largely shapes the dynamics of evolutionary adaptation. Tremendous progress has been made in quantifying the strength and abundance of selected mutations available to single microbial species in simple environments, lacking strong ecological interactions. However, the adaptive potential of strains that are part of...
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31/05/2022, 19:15
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Silvia De Monte (MPI for Evolutionary Biology)01/06/2022, 09:00
Biological functions of many cellular assemblages, ranging from multicellular organisms to microbial communities, rely on diversity among the composing units. Such division of labour is often seen through the lens of game theory, where the accent is posed on the success of different strategies in short-term competition (e.g. one cell type grows faster than another - like in cancer). Such...
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Sonja Lehtinen (ETH Zurich )01/06/2022, 10:00
Bacterial genes can either reside on the chromosome or on plasmids, extrachromosomal genetic structures that can be transferred from cell to cell. The distribution of genes between plasmid and chromosome is not random: certain types of genes are particularly likely to be plasmid-associated. This includes a number of clinically important traits, such as antibiotic resistance and virulence...
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Julien Barrere (Harvard University )01/06/2022, 11:00
The evolution of multicellularity has opened new evolutionary paths to increased diversity and complexity. This transition from single cells to multicellularity involved three processes: cells remained attached to one another and formed groups, cells within these new groups differentiated to perform different tasks, and the emergent groups adapted their life cycles by evolving new reproductive...
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William Ratcliff (Georgia Tech)01/06/2022, 11:20
The origin of multicellularity was one of the most significant innovations in the history of life. Our understanding of the evolutionary processes underlying this transition remains limited, however, mainly because extant multicellular lineages are ancient and most transitional forms have been lost to extinction. We bridge this knowledge gap by evolving novel multicellularity in vivo, using...
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Shaul Pollak (MIT )01/06/2022, 12:05
Bacteria often interact with their environment through extracellular molecules that increase access to limiting resources. These secretions can act as public goods, creating incentives for exploiters to invade and “steal” public goods away from producers. This phenomenon has been studied extensively in vitro, but little is known about the occurrence and impact of public good exploiters in the...
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01/06/2022, 13:30
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01/06/2022, 19:30
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Harmit Malik (Fred Hutchinson Cancer Research Center and HHMI )02/06/2022, 09:00
The evolutionary battle between viruses and the immune system is likened to a high-stakes arms race. The immune system makes antiviral proteins, called restriction factors, which can stop the virus from replicating. In response, viruses evolve to evade the effects of restriction factors. To counter this, restriction factors evolve too, and the cycle continues, in which both sides rapidly...
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Jenna Gallie (MPI for Evolutionary Biology)02/06/2022, 10:00
Large-scale duplications are a highly dynamic class of mutation. They arise and are subsequently lost – often without a trace – at rates far exceeding those typically observed for SNPs. The transient nature of large duplications means that their contribution to evolutionary processes is often overlooked. We are following the dynamics of adaptive, large-scale duplications in evolving...
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Michael Desai (Harvard University )02/06/2022, 11:00
In response to infection or vaccination, our immune system creates antibodies that bind strongly to relevant antigens through an evolutionary process called affinity maturation, which involves rounds of somatic hypermutation and selection. A key aspect of this process is the binding affinity landscape, which describes the mapping between antibody sequence and binding affinity to various...
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Sandeep Venkataram (University of California, San Diego )02/06/2022, 11:45
From phytoplankton producing the planet’s oxygen to wildebeest grazing the Serengeti, each species modifies their ecosystem. These ecological changes can precipitate adaptive evolution, which in turn can lead to further changes in the ecosystem. Previous studies have shown that this coupling between ecological and evolutionary processes is often driven by interactions between species. While...
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Sotaro Takano (National Institute for Materials Science(NIMS, Japan) )02/06/2022, 12:05
Author: Sotaro Takano, Jean C.C. Vila, Alvaro Sanchez, Djordje Bajić
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Microorganisms typically display a wide, and often overlapping, range of metabolic capabilities. In theory, this should favor competitive exclusion, and thus seems at odds with the pervasive coexistence and the diversity observed in natural microbiomes. One form of resource specialization that could partly explain the... -
Dmitri Petrov (Stanford University)02/06/2022, 15:30
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Kara Schmidlin (Arizona State University )02/06/2022, 16:15
There is great deal of interest in exploiting evolutionary tradeoffs to combat drug resistance. Instances of drug resistance have been steadily increasing creating considerable human health and economic impacts. In the United States, the CDC reports that ~35,000 deaths and $55 billion can be attributed to drug resistant infections per year. Collateral sensitivity (CS), where developing...
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02/06/2022, 19:00
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Vivek Mutalik03/06/2022, 09:00
Unbiased and comprehensive genetic screens that are easily scalable to diverse bacterial pathogens would be valuable for obtaining a detailed understanding of antibiotic cross-resistance profiles, phage infection pathways and co-evolutionary landscapes of phage- and antibiotic resistance phenotypes. Recently, we have developed high-throughput barcoded genetic screening technologies that are...
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Louise Flanagan (University of Bath )03/06/2022, 09:45
Gene regulatory networks are essential to organism survival as they allow rapid adaptation through altering gene expression profiles. These regulatory networks can be key sites of evolutionary change and they provide important insights into the adaptability of various organisms to environmental shifts such as climate change. Mutations drive their evolution, but mutation biases can drive...
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Oskar Hallatschek (Berkeley, Uni Leipzig )03/06/2022, 10:45
Tremendous progress has been made in quantifying fitness landscapes and elucidating how the effects of available mutations affect the dynamics of single microbial species in simple environments lacking strong ecological interactions. However, it remains largely unclear how natural selection depends and feeds back onto the spatial and community structure characteristic of most natural...
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Xiaoqian Yu (University of Vienna )03/06/2022, 11:30
Populations are fundamental units of ecology and evolution, and delineating ecologically meaningful populations among microbes is important for identifying how they adapt to and interact with their local environment. Here, we develop a method to assign closely related isolates to populations by inferring their gene flow information through a tri-partitioning of SNPs distributed across the...
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Jennifer Pentz (Umea University )03/06/2022, 11:50
Whether evolution is predictable has become an outstanding question in the field of evolutionary biology and requires knowledge of the complex genotype-fitness map. Experimental evolution studies have begun to shed light on this, but it has not yet been determined if predictions can be extended between different species. Here, we use the Pseudomonas fluorescens SBW25 wrinkly spreader (WS)...
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Arjan de Visser (Wageningen University & Research )03/06/2022, 13:15
Random mutations and demographic events make evolution inherently stochastic, despite the deterministic force of natural selection. In order to better understand the genetic and ecological factors that drive evolutionary predictability, we use the evolution of resistance to beta-lactam antibiotics in Escherichia coli as experimental model. I will present recent work on the joint effect of...
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Meike Wortel (University of Amsterdam )03/06/2022, 14:00
Fitness landscapes map genotypes to fitness, visualizing possible evolutionary paths. These landscapes are studied both at the conceptual level and made explicit by measuring the fitness of nearby genotypes to create empirical fitness landscapes. Since the mapping of the genotype to fitness depends on the environment, several approaches have been taken to include the environment. One of them...
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Rahul Unni (MPI Evolutionary Biology)
The basic evolutionary principle of adaptation by natural selection applies to the natural microbial populations in our microbiomes. Disease-mediated changes in the intestinal environment would impose different selection pressures on the microbiome to what we would expect in healthy individuals, resulting in selection for disease-specific microbial traits. Inflammatory bowel disease (IBD)...
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Angela Phillips (Harvard University )
Several broadly neutralizing antibodies (bnAbs) that confer protection against diverse influenza strains have been identified. Still, our understanding of the evolutionary pathways leading to these rare antibodies, and thus how best to elicit them, remains limited. To address this, we measure equilibrium dissociation constants of combinatorially complete mutational libraries (of up to ~100k...
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Alecia Rokes (University of Pittsburgh )
Antimicrobial resistance (AMR) is a rapidly worsening global health issue, with an increasing number of bacterial infections becoming impossible to treat with most drugs. Of serious concern is Acinetobacter baumannii, a nosocomial and highly multidrug resistant (MDR) pathogen. Although resistance is often attained through common mechanisms, such as increased drug efflux and modifications to...
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Rozenn Pineau (Georgia Institute of Technology )
The evolution of multicellularity created new ecosystems, fundamentally changing Earth’s ecology (Szathmáry & Smith, 1995). While multicellularity has evolved numerous times in diverse lineages (Knoll et al. 2011), no prior work has directly examined the impact of this major evolutionary transition on multicellular diversity. Using long-term experimental evolution, we show that the evolution...
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Davis Weaver (Case Western Reserve University )
Drug resistant pathogens are a wide-spread and deadly phenomenon that infect nearly 3 million individuals in the United States each year. If microbial resistance continues to develop at the current rate, bacterial infections are expected to surpass cancer as the leading cause of death worldwide by 2050. Novel approaches to designing therapy that explicitly take into account the adaptive nature...
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Mahfuza Akter (Clarkson University)
When exposed to antibiotics, a population of bacteria may evolve resistance through the combination of random mutation and natural selection driving fixation of antibiotic resistance mutations. However, in a natural environment, a complex suite of stressors simultaneously drive natural selection and depending on their trade-offs and/ or interactions may impact adaptive evolution. Spatial...
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Michael Barnett (MPI for Evolutionary Biology)
Evolution can be viewed as a game where the object is to keep playing. From this perspective, focus is brought to the properties of lineages that enable their success over long spans of evolutionary time, rather than the phenotypes and performance of individuals in the contemporary environment. One property required for long-term evolutionary success is the ability of a lineage to translate...
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Duncan Greig (UCL)
How can organisms cope with environmental change? Some evolutionary strategies, such as adaptive tracking (adapting directly to a changed environment via mutations) or phenotypic plasticity (sensing and responding to previously-experienced changes via physiology or development) can be readily tested experimentally. But adaptive bet-hedging, the strategy of producing random variation to insure...
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Cara Weisman (Princeton University)
“Lineage-specific” genes appear to have homologs only in a restricted group of related species, strikingly absent from the rest of the tree of life. They are often interpreted as novel genes, receiving much interest related to their apparent potential to underlie evolutionary innovation. An alternative, “null” hypothesis is that these genes are not meaningfully novel: they do have existing...
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Artur Rego-Costa (Harvard University )
The past decades of experimental evolution in controlled laboratory conditions have established that microbial evolutionary dynamics are largely complicated by clonal interference and hitchhiking, making the process of adaptation hard to model and predict. Harnessing evolutionary knowledge for applied purposes is further complicated by how the various relevant microbial populations in health...
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Jona Kayser (Max Planck Zentrum für Physik und Medizin, Erlangen, Germany )
Many cellular populations are tightly packed, including microbial colonies and biofilms, or tissues and tumours in multicellular organisms. However, little is known about how ensuing mechanical cell-cell interactions reshape evolutionary dynamics and critical outcomes, such as drug resistance. Here, I will show how growth-induced collective motion inherently suppresses the differential...
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Lydia Robert (INRAE )
Mutations are the source of genetic variation upon which natural selection acts and therefore the driving force of evolution. In order to understand the generation of diversity among life forms, from the variety of Galapagos finches to the spread of antibiotic resistant bacterial strains, as well as the diversity between cells in an organism, such as in cancer evolution, we need a quantitative...
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Kyle Card (Cleveland Clinic)
The evolution of antibiotic resistance is a serious and growing problem. The ability to predict a pathogen’s capacity to evolve resistance is therefore a critical public-health goal. In previous work, we found that differences between genetic backgrounds can sometimes lead to unpredictable responses in phenotypic resistance and influence its genetic basis by channeling evolution down...
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Rike Stelkens (Stockholm University )
The genomes of hybrids often show substantial deviations from the features of the parent genomes, including genomic instabilities characterized by chromosomal rearrangements, gains, and losses. This plastic genomic architecture generates phenotypic diversity, giving hybrids access to new ecological niches. We asked if there are any generalizable patterns and predictability in the type and...
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Tera Levin (University of Pittsburgh)
Hosts and pathogens frequently engage in physiological and evolutionary 'battles for iron', as each adapts to sequester this essential nutrient. We focus on the battle for iron between the intracellular bacterium Legionella pneumophila and its natural hosts, free-living amoebae. Amoebae restrict Legionella replication by pumping iron out of the Legionella-containing vacuole. In turn, the...
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Daniel Schultz (Dartmouth College Geisel School of Medicine )
Microbes inhabit natural environments that are remarkably dynamic, with sudden environmental shifts that require immediate action by the cell. The genetic control of cellular responses therefore evolve according to the specific demands of their environment, resulting in different strategies such as transcriptional regulation or stochastic switching. However, when microbes are exposed to...
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Danna Gifford (University of Manchester )
Resistance evolution is often described as an instantaneous event--the acquisition of a resistance mutation or a gene via horizontal transfer. However, in antibiotic fitness landscapes, this is often only the initial foothold on an adaptive peak, with many more steps required before reaching a fitness optimum. How important are these initial footholds for determining ultimate evolutionary...
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Julie Chuong (New York University)
Detecting and predicting heritable changes in DNA that lead to adaptation is an essential goal in evolutionary biology. Copy number variants (CNVs) -- gains and losses of genomic sequences -- are a pervasive class of mutation and source of genetic variation that frequently underlie rapid adaptation. Although mechanisms of CNV formation have been identified, the role of local genomic...
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Alfonso Santos-Lopez (Hospital Universitario Ramón y Cajal )
History, chance, and selection are the fundamental factors that drive and constrain evolution. We designed evolution experiments to disentangle and quantify effects of these forces on the evolution of antibiotic resistance. Previously, we showed that selection of the pathogen Acinetobacter baumannii in both structured and unstructured environments containing the antibiotic ciprofloxacin...
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Bram van Dijk (MPI for Evolutionary Biology)
Eukaryotes and prokaryotes have distinct genome architectures, with marked differences in genome size, the ratio coding/non-coding DNA, and the abundance of transposable elements (TEs). As TEs replicate independently of their hosts, the proliferation of TEs is thought to have driven genome expansion in eukaryotes. However, prokaryotes also have TEs in intergenic spaces, so why do prokaryotes...
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Jeff Smith (University of Missouri-St Louis)
Plasmids are mobile genetic elements that horizontally transfer antibiotic resistance and virulence factor genes among bacteria. It's unclear if plasmids persist only through selection for the genes they carry or if they are infectious enough to persist as genomic parasites. Here we show that plasmids' infectious potential is severely underestimated by theoretical models and experimental...
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Subrata Mishra (Affiliation )
Gene duplications have been proven to introduce variation by providing basic genetic material mainly those with adaptive functions. The pervasive choice of evolutionary pathway in the form of duplications in all three domains of life , including mammals, plants, yeast, bacteria, and archaea has been observed by analysis of their respective genomes. The significance of gene duplication can be...
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