Evolutionary dynamics of origin and loss in the deep history of phospholipase D toxin genes

A successful Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variant, B.1.1.7, has recently been reported in the UK, causing global alarm. Most likely, the new variant emerged in a persistently infected patient, justifying a special focus on these cases. Our aim in this study was to explore certain clinical profiles involving severe immunosuppression that may help explain the prolonged persistence of viable viruses. We present three severely immunosuppressed cases (A, B, and C) with a history of lymphoma and prolonged SARS-CoV-2 shedding (2, 4, and 6 months), two of whom finally died. Whole-genome sequencing of 9 and 10 specimens from Cases A and B revealed extensive within-patient acquisition of diversity, 12 and 28 new single nucleotide polymorphisms, respectively, which suggests ongoing SARS-CoV-2 replication. This diversity was not observed for Case C after analysing 5 sequential nasopharyngeal specimens and one plasma specimen, and was only observed in one bronchoaspirate specimen, although viral viability was still considered based on constant low Ct values throughout the disease and recovery of the virus in cell cultures. The acquired viral diversity in Cases A and B followed different dynamics. For Case A, new single nucleotide polymorphisms were quickly fixed (13–15 days) after emerging as minority variants, while for Case B, higher diversity was observed at a slower emergence: fixation pace (1–2 months). Slower SARS-CoV-2 evolutionary pace was observed for Case A following the administration of hyperimmune plasma. This work adds knowledge on SARS-CoV-2 prolonged shedding in severely immunocompromised patients and demonstrates viral viability, noteworthy acquired intra-patient diversity, and different SARS-CoV-2 evolutionary dynamics in persistent cases.

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Stochastic fluctuations drive non-genetic evolution of proliferation in clonal cancer cell populations

10.1101/2021.06.08.447479 ◽

2021 ◽

Author(s):

Carmen Ortega-Sabater ◽

Gabriel Fernandez-Calvo ◽

Víctor M Pérez-García

Keyword(s):

Evolutionary Dynamics ◽

Growth Dynamics ◽

Driver Mutations ◽

Organizational Changes ◽

Tumour Heterogeneity ◽

Stochastic Fluctuations ◽

Oncological Patients ◽

Single Genotype ◽

History Of ◽

Broad Variety

Evolutionary dynamics allows to understand many changes happening in a broad variety of biological systems, ranging from individuals to complete ecosystems. It is also behind a number of remarkable organizational changes that happen during the natural history of cancers. These reflect tumour heterogeneity, which is present at all cellular levels, including the genome, proteome and phenome, shaping its development and interrelation with its environment. An intriguing observation in different cohorts of oncological patients is that tumours exhibit an increased proliferation as the disease progresses, while the timescales involved are apparently too short for the fixation of sufficient driver mutations to promote an explosive growth. In this paper we discuss how phenotypic plasticity, emerging from a single genotype, may play a key role and provide a ground for a continuous acceleration of the proliferation rate of clonal populations with time. Here we address this question by means of stochastic and deterministic mathematical models that capture proliferation trait heterogeneity in clonal populations and elucidate the contribution of phenotypic transitions on tumour growth dynamics.

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Alien Species vs. Native Species: From Community Ecology to Eco-Evolutionary Dynamics

10.20944/preprints201904.0189.v1 ◽

2019 ◽

Author(s):

Andersonn Silveira Prestes

Keyword(s):

Alien Species ◽

Exotic Species ◽

Native Species ◽

Evolutionary Dynamics ◽

Evolutionary Processes ◽

Native Communities ◽

Individualized Approach ◽

History Of ◽

Relationship Of ◽

The Relationship

The establishment and spread of exotic species is a contemporary major concern. Alien species may become invasive in their new habitat, leading to both/either environmental and/or economic impacts. I briefly reviewed the literature in the last decade about the relationship of exotic species and native communities. I identified that professionals usually approach the subject in two main points of view: (1) researchers tend to point out the impacts of alien species on entire communities, evaluating if the relationship is positive, negative or neutral; (2) they focus on the eco-evolutionary processes involved in the introductions, the dynamics of invasion, and individual study cases. When evaluating the response of introductions to entire communities, evidence seems to be ambiguous and may support positive, negative or neutral relationship, especially depending on the scale approached. The unique eco-evolutionary pathways of each introduction may be a great shortcoming in the searching for generalities. On the other hand, advances have been made in understanding the dynamics of invasion on different lineages through a more selective/individualized approach. I suggest that the dynamics of invasion might be studied through a perspective in which different eco-evolutionary processes, levels of organization (from gene to entire communities), the history of the organism(s) and time are taken into account. Individual cases might be compared in attempt to understand how the relationship exotic and native works and in the search for generalities.

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Comparative Analysis of Chlamydia psittaci Genomes Reveals the Recent Emergence of a Pathogenic Lineage with a Broad Host Range

mBio ◽

10.1128/mbio.00604-12 ◽

2013 ◽

Vol 4 (2) ◽

Cited By ~ 49

Author(s):

Timothy D. Read ◽

Sandeep J. Joseph ◽

Xavier Didelot ◽

Brooke Liang ◽

Lisa Patel ◽

...

Keyword(s):

Chlamydia Trachomatis ◽

New World ◽

Evolutionary Dynamics ◽

Chlamydia Psittaci ◽

South American ◽

Content Type ◽

Sexually Transmitted ◽

Genome Wide ◽

Life Threatening ◽

History Of

ABSTRACT Chlamydia psittaci is an obligate intracellular bacterium. Interest in Chlamydia stems from its high degree of virulence as an intestinal and pulmonary pathogen across a broad range of animals, including humans. C. psittaci human pulmonary infections, referred to as psittacosis, can be life-threatening, which is why the organism was developed as a bioweapon in the 20th century and is listed as a CDC biothreat agent. One remarkable recent result from comparative genomics is the finding of frequent homologous recombination across the genome of the sexually transmitted and trachoma pathogen Chlamydia trachomatis. We sought to determine if similar evolutionary dynamics occurred in C. psittaci. We analyzed 20 C. psittaci genomes from diverse strains representing the nine known serotypes of the organism as well as infections in a range of birds and mammals, including humans. Genome annotation revealed a core genome in all strains of 911 genes. Our analyses showed that C. psittaci has a history of frequently switching hosts and undergoing recombination more often than C. trachomatis. Evolutionary history reconstructions showed genome-wide homologous recombination and evidence of whole-plasmid exchange. Tracking the origins of recombinant segments revealed that some strains have imported DNA from as-yet-unsampled or -unsequenced C. psittaci lineages or other Chlamydiaceae species. Three ancestral populations of C. psittaci were predicted, explaining the current population structure. Molecular clock analysis found that certain strains are part of a clonal epidemic expansion likely introduced into North America by South American bird traders, suggesting that psittacosis is a recently emerged disease originating in New World parrots. IMPORTANCE Chlamydia psittaci is classified as a CDC biothreat agent based on its association with life-threatening lung disease, termed psittacosis, in humans. Because of the recent remarkable findings of frequent recombination across the genome of the human sexually transmitted and ocular trachoma pathogen Chlamydia trachomatis, we sought to determine if similar evolutionary dynamics occur in C. psittaci. Twenty C. psittaci genomes were analyzed from diverse strains that may play a pathogenic role in human disease. Evolution of the strains revealed genome-wide recombination occurring at a higher rate than for C. trachomatis. Certain strains were discovered to be part of a recent epidemic clonal expansion originating in South America. These strains may have been introduced into the United States from South American bird traders, suggesting that psittacosis is a recently emerged disease originating in New World parrots. Our analyses indicate that C. psittaci strains have a history of frequently switching hosts and undergoing recombination.

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Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli

10.1101/017020 ◽

2015 ◽

Cited By ~ 1

Author(s):

Rohan Maddamsetti ◽

Richard E. Lenski ◽

Jeffrey E. Barrick

Keyword(s):

Escherichia Coli ◽

Frequency Dependence ◽

Evolutionary Dynamics ◽

Selective Sweeps ◽

Clonal Interference ◽

Beneficial Mutations ◽

Frequency Dependent ◽

Evolution Experiment ◽

History Of

Twelve replicate populations of Escherichia coli have been evolving in the laboratory for more than 25 years and 60,000 generations. We analyzed bacteria from whole-population samples frozen every 500 generations through 20,000 generations for one well-studied population, called Ara???1. By tracking 42 known mutations in these samples, we reconstructed the history of this population???s genotypic evolution over this period. The evolutionary dynamics of Ara???1 show strong evidence of selective sweeps as well as clonal interference between competing lineages bearing different beneficial mutations. In some cases, sets of several mutations approached fixation simultaneously, often conveying no information about their order of origination; we present several possible explanations for the existence of these mutational cohorts. Against a backdrop of rapid selective sweeps both earlier and later, we found that two clades coexisted for over 6000 generations before one drove the other extinct. In that time, at least nine mutations arose in the clade that prevailed. We found evidence that the clades evolved a frequency-dependent interaction, which prevented the competitive exclusion of either clade, but which eventually collapsed as beneficial mutations accumulated in the clade that prevailed. Clonal interference and frequency dependence can occur even in the simplest microbial populations. Furthermore, frequency dependence may generate dynamics that extend the period of coexistence that would otherwise be sustained by clonal interference alone.

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“Carrefour Louisiane”

Journal of Language Contact ◽

10.1163/19552629-00701006 ◽

2014 ◽

Vol 7 (1) ◽

pp. 124-153 ◽

Cited By ~ 2

Author(s):

Ingrid Neumann-Holzschuh

Keyword(s):

Language Contact ◽

Language Change ◽

Evolutionary Dynamics ◽

Point Of View ◽

New Variety ◽

Dialect Contact ◽

Cajun French ◽

Louisiana French ◽

History Of ◽

Linguistic Behavior

The history of Louisiana French (LF) is closely related to Louisiana’s particular societal and linguistic ecosystem, characterized by a mixed society where new forms of societal organization emerged and were reflected in new forms of linguistic patterns and linguistic behavior. From the beginning, language contact has been of crucial importance for the emergence, evolution and gradual decline of Louisiana French (“Cajun French”). In colonial times, contact between related French lects resulted in the formation of a new variety of regional French in North America with its own features and its own evolutionary dynamics. The continuing contact with English, however, which takes place in an entirely different ecological frame, results in the ongoing attrition of the minority language. The first part of the article deals with early stages of dialect contact in Louisiana; it will be shown that from a diachronic point of view Louisiana French has to be seen as a product of language mixing and dialect leveling. In the second part two specific aspects of current English-French language contact will be discussed. Both aspects serve to illustrate particularities of the linguistic situation in Louisiana now and then as well as the importance of certain universal mechanisms of contact-induced language change.

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Polymorphisms and evolutionary history of retrotransposon insertions in rice promoters

Genome ◽

10.1139/g11-030 ◽

2011 ◽

Vol 54 (8) ◽

pp. 629-638 ◽

Cited By ~ 7

Author(s):

Z. Xu ◽

S. Rafi ◽

W. Ramakrishna

Keyword(s):

Oryza Sativa ◽

Wild Rice ◽

Evolutionary Dynamics ◽

Genomic Sequence ◽

Promoter Regions ◽

Higher Plant ◽

Wild Rice Species ◽

History Of ◽

Aa Genome ◽

Rice Genotypes

Retrotransposons are ubiquitous in higher plant genomes. The presence or absence of retrotransposons in whole genome and high throughput genomic sequence (HTGS) from cultivated and wild rice was investigated to understand the organization and evolution of retrotransposon insertions in promoter regions. Approximately half of the Oryza sativa subsp. japonica ‘Nipponbare’ promoters with retrotransposons conserved in Oryza sativa subsp. indica ‘93-11’ and four wild rice species showed higher sequence conservation in retrotransposon than nonretrotransposon regions. We further investigated, in detail, the evolutionary dynamics of five retrotransposons in the promoter regions of 95 rice genotypes. Our data suggest that four of five insertions (Rp2–Rp5) occurred in the ancestor of AA genome, while the other insertion (Rp1) predates the ancestral divergence of Oryza officinalis (CC genome). Four retrotransposons (Rp2–Rp5) were present in 52% (Rp2), 29% (Rp3), 53% (Rp4), and 43% (Rp5) of the rice genotypes with AA genome type, and the fifth retrotransposon (Rp1) was present in 95% of the rice genotypes with AA, BBCC, or CC genome types. Furthermore, most of these retrotransposons were found to evolve slower than flanking promoter regions, suggesting a role in promoter function for regulating downstream genes.

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Polygenic variation in sexual investment across an ephemerality gradient in Daphnia pulex

10.1101/2021.06.23.449662 ◽

2021 ◽

Author(s):

Karen B Barnard-Kubow ◽

Dörthe Becker ◽

Connor S Murray ◽

Robert Porter ◽

Grace Gutierrez ◽

...

Keyword(s):

Reproductive Strategy ◽

Evolutionary Dynamics ◽

Daphnia Pulex ◽

Clonal Diversity ◽

Basic Question ◽

Male Production ◽

Dynamic Nature ◽

Quantitative Genetic ◽

History Of ◽

Polygenic Variation

Species across the tree of life can switch between asexual and sexual reproduction. In facultatively sexual species, the ability to switch between reproductive modes is often environmentally dependent and subject to local adaptation. However, the ecological and evolutionary factors that influence the maintenance and turnover of polymorphism associated with facultative sex remain unclear. To address this basic question, we studied the ecological and evolutionary dynamics of polymorphism in reproductive strategy in a metapopulation of the model facultative sexual, Daphnia pulex, located in the southern United Kingdom. We found that patterns of clonal diversity, but not genetic diversity varied with ephemerality. Reconstruction of a multi-year pedigree demonstrated the co-existence of clones that were found to differ in their investment into male production. Mapping of quantitative variation in male production using lab-generated and field-collected individuals identified multiple putative QTL underlying this trait, and we identified a plausible candidate gene. The evolutionary history of these QTL suggests that they are relatively young, and male limitation in this system is a rapidly evolving trait. Our work highlights the dynamic nature of the genetic structure and composition of facultative sex across space and time and suggests that quantitative genetic variation in reproductive strategy can undergo rapid evolutionary turnover.

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A multidisciplinary approach to improve and share the understanding of landslide hazard in mountain environments: the PIURO 1618 disaster

10.5194/egusphere-egu21-14567 ◽

2021 ◽

Author(s):

Enrico Pigazzi ◽

Tiziana Apuani ◽

Riccardo Bersezio ◽

Corrado Camera ◽

Alessandro Comunian ◽

...

Keyword(s):

Multidisciplinary Approach ◽

Evolutionary Dynamics ◽

Risk Mitigation ◽

Numerical Models ◽

Cultural Development ◽

Risk And Resilience ◽

Mountain Environments ◽

Huge Impact ◽

History Of ◽

Geomorphological Evolution

<p>Large landslides have affected the geomorphological evolution of most Alpine territories. Some catastrophic events also had a huge impact on the economic and cultural development of human societies. In the Bregaglia Valley and in nearby territories, evidences of settlements date back to the Roman age. In these areas, human activities always coexisted with the natural evolution of the valley, which has been characterized by recurrent natural events such as floods and landslides. Among these, the 1618 Piuro landslide was the one with the strongest impact, remaining impressed on the collective imagination and artistic representations. It erased an entire village and its 1000-2000 inhabitants few km East of Chiavenna, and it is still remembered as one of the worst tragedies in the history of the region. Understanding the evolutionary dynamics of such a geomorphologically active landscape, taking notes from the ancient or recent past, plays a central role in risk assessment and mitigation. In Piuro, such dynamics were investigated through a multidisciplinary approach, starting from the historical and archaeological analyses of the event and involving: (i) the geological/geomorphological characterization of the Last Glacial Maximum, to present palimpsest landscape of the valley through the realization of thematic maps, (ii) the stratigraphic interpretation of new boreholes crossing the landslide deposits and the deeper intra-mountain sedimentary valley fill, (iii) the realization of topographic, petrographic, geophysical (HVSR and MASW) and geo-mechanical surveys. In addition, the implementation of numerical models is on the way, to check different hypotheses on the predisposing factors, triggers, timing and evolution of the 1618 Piuro landslide. To increase the awareness of natural hazards in mountain settings and to promote a risk and resilience culture, all these acquired knowledge will be disseminated and shared with citizen, authorities and scientists in the frame of the Interreg project A.M.AL.PI.18. The fulfilment of a transboundary (Italian-Swiss) geo-cultural path will link other sites of historical and geological relevance through the territories of Bregaglia, Valchiavenna, Moesa and Ticino. Showing and telling the history of catastrophic landslides and their impacts on the involved communities, it will contribute to enhance the perception of beauty and the awareness of geo-hazard. The dissemination of knowledge and awareness is one main goal towards risk mitigation.</p><p>The present work was co-funded through the EU, Regional Development European Fund, by Italian State, Helvetic Confederation and Cantons under the Interreg V-A IT-CH 2014-2020 Cooperation Program - A.M.AL.PI.2018 &#8220;Alpi in Movimento, Movimento nelle Alpi. Piuro 1618-2018", ID 594274 &#8211; Axis 2 &#8220;Cultural and natural enhancement&#8221;.</p>

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Chloroplast phylogenomics and the dynamic evolution of Santalum (Santalaceae)

10.21203/rs.3.rs-154608/v1 ◽

2021 ◽

Author(s):

Xiaojin Liu ◽

Daping Xu ◽

Zhou Hong ◽

Ningnan Zhang ◽

Zhiyi Cui

Keyword(s):

Chloroplast Genome ◽

Evolutionary Dynamics ◽

Divergence Time ◽

Major Type ◽

Time Analysis ◽

Chloroplast Genomes ◽

Extant Species ◽

History Of ◽

Insight Into ◽

Simple Sequence

Abstract Background Santalum (Santalaceae, sandalwood) is a hemiparasitic genus including approximately 15 extant species. It is known for its aromatic heartwood oil, which is used in incense and perfume. Demand for sandalwood-based products has led to drastic over-harvesting, and wild Santalum populations are now threatened. Knowledge of the phylogenetic relationships and genetic diversity will be critical for the conservation and proper management of this genus. Here, we sequenced the chloroplast genome of 11 Santalum species. The data were then used to investigate the chloroplast genome evolutionary dynamics and relationships and divergence time within Santalum and related species. Results The Santalum chloroplast genome contains the typical quadripartite structures, ranging from 143,291 to 144,263 bp. The chloroplast genome contains 124 genes. The whole set of ndh genes and the infA gene were found to lose their function. Between 17 and 31 SSRs were found in the Santalum chloroplast genome, and mononucleotide simple sequence repeats (SSRs) were the major type. The P-distance among the Santalum species was 0.0003 to 0.00828. Three mutation hotspot regions, 14 small inversions, and 460 indels events were discovered in the Santalum chloroplast genome. Our phylogenomic assessment provides improved resolution compared to past analyses. Our divergence time analysis shows that the crown age of Santalum was 8.46 Mya, the first divergence occurred around 6.97 Mya, and diversification was complete within approximately 1 Mya. Conclusions By sequencing the 12 chloroplast genomes of Santalum, we gain insight into the evolution of its chloroplast genomes. The chloroplast genome sequences had sufficient polymorphic information to elucidate the evolutionary history of Santalum.

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