scholarly journals Competition and coevolution drive the evolution and the diversification of CRISPR immunity

2021 ◽  
Author(s):  
Martin Guillemet ◽  
Helene Chabas ◽  
Antoine Nicot ◽  
Francois Gatchitch ◽  
Enrique Ortega-Abboud ◽  
...  
Keyword(s):  
Host Resistance ◽  
Host Adaptation ◽  
Transient Dynamics ◽  
Resistance Mutations ◽  
Host Diversity ◽  
Selective Pressures ◽  
Negative Frequency Dependent Selection ◽  
Host Evolution ◽  
Phage Population ◽  
Over Time

The diversity of resistance fuels host adaptation to infectious diseases and challenges the ability of pathogens to exploit host populations. Yet, how this host diversity evolves over time remains unclear because it depends on the interplay between intraspecific competition and coevolution with pathogens. Here we study the effect of a coevolving phage population on the diversification of bacterial CRISPR immunity across space and time. We demonstrate that the negative-frequency-dependent selection generated by coevolution is a powerful force that maintains host resistance diversity and selects for new resistance mutations in the host. We also find that host evolution is driven by asymmetries in competitive abilities among different host genotypes. Even if the fittest host genotypes are targeted preferentially by the evolving phages they often escape extinctions through the acquisition of new CRISPR immunity. Together, these fluctuating selective pressures maintain diversity, but not by preserving the pre-existing host composition. Instead, we repeatedly observe the introduction of new resistance genotypes stemming from the fittest hosts in each population. These results highlight the importance of competition on the transient dynamics of host-pathogen coevolution.

scholarly journals Floral Scent and Pollinators of Cypripedium calceolus L. at Different Latitudes

Diversity ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 5
Author(s):  
Herbert Braunschmid ◽  
Robin Guilhot ◽  
Stefan Dötterl
Keyword(s):  
Floral Scent ◽  
Latitudinal Gradients ◽  
Isolated Populations ◽  
Floral Scents ◽  
Selective Pressures ◽  
Octyl Acetate ◽  
Important Trait ◽  
Cypripedium Calceolus ◽  
Negative Frequency Dependent Selection ◽  
Plant Pollinator

Floral scent is an important trait in plant–pollinator interactions. It not only varies among plant species but also among populations within species. Such variability might be caused by various non–selective factors, or, as has been shown in some instances, might be the result of divergent selective pressures exerted by variable pollinator climates. Cypripedium calceolus is a Eurasian deceptive orchid pollinated mainly by bees, which spans wide altitudinal and latitudinal gradients in mainly quite isolated populations. In the present study, we investigated whether pollinators and floral scents vary among different latitudes. Floral scents of three C. calceolus populations in the Southern Alps were collected by dynamic headspace and analyzed by gas chromatography coupled to mass spectrometry (GC/MS). These data were completed by previously published scent data of the Northern Alps and Scandinavia. The scent characteristics were compared with information on pollinators recorded for present study or available in the literature. More than 80 scent compounds were overall recorded from plants of the three regions, mainly aliphatics, terpenoids, and aromatics. Seven compounds were found in all samples, and most samples were dominated by linalool and octyl acetate. Although scents differed among regions and populations, the main compounds were similar among regions. Andrena and Lasioglossum species were the main pollinators in all three regions, with Andrena being relatively more abundant than Lasioglossum in Scandinavia. We discuss natural selection mediated by pollinators and negative frequency–dependent selection as possible reasons for the identified variation of floral scent within and among populations and regions.

scholarly journals Longitudinal and multi-tissue molecular diagnostics track somatic BRCA2 reversion mutations that correct the open reading frame of germline alteration upon clinical relapse

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Shelly Sorrells ◽  
Kelly E. McKinnon ◽  
Ashleigh McBratney ◽  
Christopher Sumey
Keyword(s):  
Disease Progression ◽  
Parp Inhibitor ◽  
Acquired Resistance ◽  
Open Reading Frame ◽  
Genomic Testing ◽  
Clinical Relapse ◽  
Resistance Mutations ◽  
Reading Frame ◽  
Germline Alteration ◽  
Over Time

AbstractBRCA-mutant cancers often develop therapeutic resistance through several mechanisms. Here, we report a case of pathogenic germline BRCA2-driven breast cancer monitored for disease progression and acquired resistance using longitudinal multi-tissue genomic testing. Briefly, genomic testing was performed throughout the course of disease on tumor tissue from multiple sites, circulating tumor DNA from blood plasma, and matched normal tissue. Genomic analyses identified actionable variants for targeted therapies, as well as emerging resistance mutations over time. Two unique BRCA2 somatic alterations (p.N255fs and p.D252fs) were identified upon resistance to PARP inhibitor and platinum treatment, respectively. Both alterations restored the open reading frame of the original germline alteration, likely accounting for acquired resistance. This case exemplifies the evolution of multiple subclonal BRCA reversion alterations over time and demonstrates the value of longitudinal multi-tissue genomic testing for monitoring disease progression, predicting measures of response, and evaluating treatment outcomes in oncology patients.

scholarly journals The study of host–microbiome (co)evolution across levels of selection

2020 ◽  
Vol 375 (1808) ◽  
pp. 20190604 ◽  
Author(s):  
Britt Koskella ◽  
Joy Bergelson
Keyword(s):  
Paradigm Shift ◽  
Dynamic Nature ◽  
Theme Issue ◽  
Critical Question ◽  
Microbiome Composition ◽  
Single Host ◽  
Host Evolution ◽  
Existing Data ◽  
Over Time

Microorganismal diversity can be explained in large part by selection imposed from both the abiotic and biotic environments, including—in the case of host-associated microbiomes—interactions with eukaryotes. As such, the diversity of host-associated microbiomes can be usefully studied across a variety of scales: within a single host over time, among host genotypes within a population, between populations and among host species. A plethora of recent studies across these scales and across diverse systems are: (i) exemplifying the importance of the host genetics in shaping microbiome composition; (ii) uncovering the role of the microbiome in shaping key host phenotypes; and (iii) highlighting the dynamic nature of the microbiome. They have also raised a critical question: do these complex associations fit within our existing understanding of evolution and coevolution, or do these often intimate and seemingly cross-generational interactions follow novel evolutionary rules from those previously identified? Herein, we describe the known importance of (co)evolution in host–microbiome systems, placing the existing data within extant frameworks that have been developed over decades of study, and ask whether there are unique properties of host–microbiome systems that require a paradigm shift. By examining when and how selection can act on the host and its microbiome as a unit (termed, the holobiont), we find that the existing conceptual framework, which focuses on individuals, as well as interactions among individuals and groups, is generally well suited for understanding (co)evolutionary change in these intimate assemblages. This article is part of the theme issue ‘The role of the microbiome in host evolution’.

scholarly journals Genotypic Profile of the Outer Membrane Proteins BabA and BabB in Clinical Isolates of Helicobacter pylori

2006 ◽  
Vol 74 (7) ◽  
pp. 4375-4378 ◽  
Author(s):  
Jeffrey C. Colbeck ◽  
Lori M. Hansen ◽  
Julie M. Fong ◽  
Jay V. Solnick
Keyword(s):  
Helicobacter Pylori ◽  
Outer Membrane Proteins ◽  
Genotypic Diversity ◽  
Blood Group Antigen ◽  
Antigen Binding ◽  
Abo Blood Group ◽  
Selective Pressures ◽  
Different Strains ◽  
Genotypic Profile ◽  
Over Time

ABSTRACT Helicobacter pylori BabA is the ABO blood group antigen binding adhesin, which has a closely related paralogue (BabB) whose function is unknown. PCR and DNA sequence analysis showed extensive genotypic diversity in babA and babB across different strains, as well as within a strain colonizing an individual patient. We hypothesize that diverse profiles of babA and babB reflect selective pressures for adhesion, which may differ across different hosts and within an individual over time.

scholarly journals Viruses rule over adaptation in conserved human proteins

2019 ◽  
Author(s):  
David Castellano ◽  
Lawrence H. Uricchio ◽  
Kasper Munch ◽  
David Enard
Keyword(s):  
Adaptive Evolution ◽  
Significant Role ◽  
Host Adaptation ◽  
Arms Race ◽  
Interacting Proteins ◽  
Cellular Functions ◽  
Host Proteins ◽  
Selective Pressures ◽  
Human Proteins ◽  
Antiviral Proteins

AbstractAdaptive evolution often involves fast-evolving proteins, and the fastest-evolving proteins in primates include antiviral proteins engaged in an arms race with viruses 1-3. Even though fast-evolving antiviral proteins are the most studied cases of primate host adaptation against viruses, viruses predominantly interact with host proteins that are broadly conserved between distant species in order to complete their replication cycle 4. Broadly conserved proteins are generally viewed as playing a negligible role in adaptive evolution. Here, we used a dataset of ~4,500 human proteins known to physically interact with viruses (VIPs for Virus-Interacting Proteins), to test the involvement of broadly conserved proteins in adaptive evolution against viruses. We found that VIPs conserved between animals and fungi have experienced not only high rates of adaption, but also strong adaptive events. Broadly conserved proteins that do not interact with viruses experienced very little adaptation. As a result, the arms race with viruses explains more than 75% of adaptation in the most phylogenetically conserved subset of the human proteome. Our results imply that broadly conserved proteins have played a significant role in adaptation, and that viruses were likely one of very few selective pressures that were able to force the conserved, central pillars of host cellular functions to adapt during evolution.

Within-Host Viral Diversity: A Window into Viral Evolution

2020 ◽  
Vol 7 (1) ◽  
pp. 63-81 ◽  
Author(s):  
Adam S. Lauring
Keyword(s):  
Large Scale ◽  
Evolutionary Dynamics ◽  
Viral Evolution ◽  
Experimental Studies ◽  
Disease Spread ◽  
Viral Diversity ◽  
Host Diversity ◽  
Models Of Disease ◽  
Host Evolution ◽  
Viral Sequencing

The evolutionary dynamics of a virus can differ within hosts and across populations. Studies of within-host evolution provide an important link between experimental studies of virus evolution and large-scale phylodynamic analyses. They can determine the extent to which global processes are recapitulated on local scales and how accurately experimental infections model natural ones. They may also inform epidemiologic models of disease spread and reveal how host-level dynamics contribute to a virus's evolution at a larger scale. Over the last decade, advances in viral sequencing have enabled detailed studies of viral genetic diversity within hosts. I review how within-host diversity is sampled, measured, and expressed, and how comparative studies of viral diversity can be leveraged to elucidate a virus's evolutionary dynamics. These concepts are illustrated with detailed reviews of recent research on the within-host evolution of influenza virus, dengue virus, and cytomegalovirus.

scholarly journals ­­­grapevine (Vitis Spp.) Rootstock Stilbenoid Associations With Host Resistance to and Induction by Root Knot Nematodes, Meloidogyne Incognita

2020 ◽  
Author(s):  
Christopher Wallis
Keyword(s):  
Meloidogyne Incognita ◽  
Host Resistance ◽  
Nematode Resistance ◽  
Cabernet Sauvignon ◽  
Healthy Controls ◽  
Mechanisms Of Resistance ◽  
Breeding Programs ◽  
Root Knot Nematodes ◽  
Vitis Spp ◽  
Over Time

Abstract Objective:The root knot nematodes (RKN)Meloidogyne incognita can severely reduce grapevine yields over time. Grapevine rootstocks have been developed from wild Vitis species that provide resistance to nematode infections. However, the potential biochemical or mechanical mechanisms of resistance have not been thoroughly explored. Therefore, this study measured levels of stilbenoids in roots of non-infected and RKN-infected grapevines with Cabernet Sauvignon scion grafted to susceptible (O39-16) or resistant (Freedom) rootstocks. This was part of a larger effort to assess phenolic compound levels within grapevine rootstocks to determine roles of stilbenoidcompounds in improving nematode resistance and overall plant health.Results: None of the assessed compounds were consistently greater in RKN infected plants versus healthy controls. Stilbenoids putatively identified as pallidol, ɑ-viniferin, miyabenol C, and hopeaphenol were overall much greater in Freedom than O39-16 rootstocks. By contrast, the stilbenoids ampelopsin A, ω-viniferin, and vitisin B were greater in O39-16 than Freedom. O39-16 and Freedom had similar levels of other stilbenoids especially monomers and dimers. Potentially the greater levels of specific stilbenoids present in Freedom than O39-16 provided RKN resistance. If validated, breeding programs could utilize the increased presence of these compounds as a marker for increased resistance to nematodes.

scholarly journals Clonal interference can cause wavelet-like oscillations of multilocus linkage disequilibrium

2018 ◽  
Vol 15 (140) ◽  
pp. 20170921 ◽  
Author(s):  
Victor Garcia ◽  
Emily C. Glassberg ◽  
Arbel Harpak ◽  
Marcus W. Feldman
Keyword(s):  
Human Immunodeficiency Virus ◽  
Linkage Disequilibrium ◽  
Evolutionary Dynamics ◽  
Host Adaptation ◽  
Clonal Interference ◽  
Beneficial Mutations ◽  
Fitness Effects ◽  
Infection Models ◽  
Immunodeficiency Virus ◽  
Over Time

Within-host adaptation of pathogens such as human immunodeficiency virus (HIV) often occurs at more than two loci. Multiple beneficial mutations may arise simultaneously on different genetic backgrounds and interfere, affecting each other's fixation trajectories. Here, we explore how these evolutionary dynamics are mirrored in multilocus linkage disequilibrium (MLD), a measure of multi-way associations between alleles. In the parameter regime corresponding to HIV, we show that deterministic early infection models induce MLD to oscillate over time in a wavelet-like fashion. We find that the frequency of these oscillations is proportional to the rate of adaptation. This signature is robust to drift, but can be eroded by high variation in fitness effects of beneficial mutations. Our findings suggest that MLD oscillations could be used as a signature of interference among multiple equally advantageous mutations and may aid the interpretation of MLD in data.

scholarly journals Proviral sequencing suggests the majority of the HIV reservoir is expressed over time but significant decay is obscured by clonal expansion

2018 ◽  
Author(s):  
Marilia Rita Pinzone ◽  
D. Jake VanBelzen ◽  
Sam Weissman ◽  
Maria Paola Bertuccio ◽  
LaMont Cannon ◽  
...  
Keyword(s):  
Protein Expression ◽  
Clonal Expansion ◽  
Rapid Decline ◽  
Plasma Viremia ◽  
Significant Extent ◽  
Splice Donor ◽  
Time Points ◽  
Selective Pressures ◽  
Over Time ◽  
Viral Outgrowth Assay

AbstractAfter initiating antiretroviral therapy (ART), a rapid decline in plasma viremia is followed by reservoir stabilization. Viral outgrowth assay suggests the reservoir continues to decline slowly, but variation over time and among individuals complicates our understanding of selective pressures during ART. We used full-length sequencing to study more than 800 HIV proviruses of two subjects on ART at four time points over nine years to investigate the selection pressures influencing the dynamics of the reservoir. We found that intact as well as defective proviruses capable of significant protein expression decrease over time. Moreover, proviruses lacking genetic elements to promote viral protein expression, yet containing strong splice donor sequences increase relative to other defectives over time, especially among clones. Our work suggests that HIV expression occurs to a significant extent during ART and results in HIV clearance, but this is obscured by clones generated by donor splice site-enhanced clonal expansion.

scholarly journals Finite-sites multiple mutations interference gives rise to wavelet-like oscillations of multilocus linkage disequilibrium

2016 ◽  
Author(s):  
Victor Garcia ◽  
Emily C. Glassberg ◽  
Arbel Harpak ◽  
Marcus W. Feldman
Keyword(s):  
Human Immunodeficiency Virus ◽  
Linkage Disequilibrium ◽  
Adaptive Dynamics ◽  
Host Adaptation ◽  
Early Infection ◽  
Beneficial Mutations ◽  
Fitness Effects ◽  
Infection Models ◽  
Immunodeficiency Virus ◽  
Over Time

Within-host adaptation of pathogens such as human immunodeficiency virus (HIV) often occurs at more than two loci. Multiple beneficial mutations may arise simultaneously on different genetic backgrounds and interfere, affecting each other's fixation trajectories. Here, we explore how these adaptive dynamics are mirrored in multilocus linkage disequilibrium (MLD), a measure of multi-way associations between alleles. In the parameter regime corresponding to HIV, we show that deterministic early infection models induce MLD to oscillate over time in a wavelet-like fashion. We find that the frequency of these oscillations is proportional to the rate of adaptation. This signature is robust to drift, but can be eroded by high variation in fitness effects of beneficial mutations. Our findings suggest that MLD oscillations could be used as a signature of interference among multiple equally advantageous mutations and may aid the interpretation of MLD in data.

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