Evolutionary Dynamics of Viruses or Microbes, but Not Both

Quantitative Viral Ecology ◽

10.23943/princeton/9780691161549.003.0004 ◽

2016 ◽

Author(s):

Joshua S. Weitz

Keyword(s):

Life History ◽

Evolutionary Dynamics ◽

Selective Pressure ◽

Host Interactions ◽

Intermediate Phenotypes ◽

Strong Selective Pressure ◽

Evolution Of Resistance ◽

Resistance To Infection ◽

Host Evolution ◽

Different Levels

This chapter discusses the evolutionary dynamics of viruses. Preexisting variation in host phenotypes include variants with different levels of susceptibility to viruses, including complete resistance. Formative studies of the basis of the mutation rate relied upon virus–host interactions and the possibility of the evolution of resistance to infection. Viruses represent a strong selective pressure and can induce evolution among hosts. Host evolution, as induced by viruses, includes novel forms of ecological dynamics, including cryptic dynamics. Infection of hosts represents a strong selective pressure for viruses. Viruses that differ in their life history traits vary in their fitness and can invade and replace existing viral strains. The latent period represents a model trait for the further study of the evolution of intermediate phenotypes. Evolution among other traits is also possible, including who infects whom.

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Evolutionary dynamics of bipartite begomoviruses revealed by complete genome analysis

10.1101/2020.06.25.171728 ◽

2020 ◽

Author(s):

César A.D. Xavier ◽

Márcio T. Godinho ◽

Talita B. Mar ◽

Camila G. Ferro ◽

Osvaldo F.L. Sande ◽

...

Keyword(s):

New World ◽

Evolutionary Dynamics ◽

Bipartite Begomoviruses ◽

Evolutionary Analysis ◽

Host Interactions ◽

Coding Regions ◽

Evolutionary Studies ◽

Genetic Clusters ◽

Complete Genome Analysis ◽

Different Levels

ABSTRACTSeveral key evolutionary events marked the evolution of geminiviruses, culminating with the emergence of bipartite genomes represented by viruses classified in the genus Begomovirus. This genus represents the most abundant group of multipartite viruses, contributing significantly to the observed abundance of multipartite species in the virosphere. Although aspects related to virus-host interactions and evolutionary dynamics have been extensively studied, the bipartite nature of these viruses has been little explored in evolutionary studies. We performed a parallel evolutionary analysis of the DNA-A and DNA-B components of New World begomoviruses. A total of 239 full-length DNA-B sequences obtained in this study, combined with 292 DNA-A and 76 DNA-B sequences retrieved from GenBank, were analyzed. The results indicate that the DNA-A and DNA-B respond differentially to evolutionary processes, with the DNA-B being more permissive to variation and more prone to recombination than the DNA-A. Although a clear geographic segregation was observed for both components, differences in the genetic structure between DNA-A and DNA-B were also observed, with cognate components belonging to distinct genetic clusters. DNA-B coding regions evolve under the same selection pressures than DNA-A coding regions. Together, our results indicate an interplay between reassortment and recombination acting at different levels across distinct subpopulations and components.

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Life history, climate and biogeography interactively affect worldwide genetic diversity of plant and animal populations

Nature Communications ◽

10.1038/s41467-021-20958-2 ◽

2021 ◽

Vol 12 (1) ◽

Cited By ~ 1

Author(s):

H. De Kort ◽

J. G. Prunier ◽

S. Ducatez ◽

O. Honnay ◽

M. Baguette ◽

...

Keyword(s):

Genetic Diversity ◽

Life History ◽

Evolutionary Dynamics ◽

Environmental Changes ◽

Peripheral Populations ◽

Plant Dispersal ◽

Weak Support ◽

Animal Populations ◽

Plant Groups ◽

Conservation Genetic

AbstractUnderstanding how biological and environmental factors interactively shape the global distribution of plant and animal genetic diversity is fundamental to biodiversity conservation. Genetic diversity measured in local populations (GDP) is correspondingly assumed representative for population fitness and eco-evolutionary dynamics. For 8356 populations across the globe, we report that plants systematically display much lower GDP than animals, and that life history traits shape GDP patterns both directly (animal longevity and size), and indirectly by mediating core-periphery patterns (animal fecundity and plant dispersal). Particularly in some plant groups, peripheral populations can sustain similar GDP as core populations, emphasizing their potential conservation value. We further find surprisingly weak support for general latitudinal GDP trends. Finally, contemporary rather than past climate contributes to the spatial distribution of GDP, suggesting that contemporary environmental changes affect global patterns of GDP. Our findings generate new perspectives for the conservation of genetic resources at worldwide and taxonomic-wide scales.

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Reverse transcriptase sequences from mulberry LTR retrotransposons: characterization analysis

Open Life Sciences ◽

10.1515/biol-2017-0031 ◽

2017 ◽

Vol 12 (1) ◽

pp. 266-276

Author(s):

Bi Ma ◽

Lulu Kuang ◽

Youchao Xin ◽

Fei Hou ◽

Ningjia He

Keyword(s):

Reverse Transcriptase ◽

Evolutionary Dynamics ◽

Selective Pressure ◽

Sequence Divergence ◽

Degenerate Primers ◽

Random Mutation ◽

Functional Studies ◽

Study Support ◽

Element Transfer

AbstractCopia and Gypsy play important roles in structural, functional and evolutionary dynamics of plant genomes. In this study, a total of 106 and 101, Copia and Gypsy reverse transcriptase (rt) were amplified respectively in the Morus notabilis genome using degenerate primers. All sequences exhibited high levels of heterogeneity, were rich in AT and possessed higher sequence divergence of Copia rt in comparison to Gypsy rt. Two reasons are likely to account for this phenomenon: a) these elements often experience deletions or fragmentation by illegitimate or unequal homologous recombination in the transposition process; b) strong purifying selective pressure drives the evolution of these elements through “selective silencing” with random mutation and eventual deletion from the host genome. Interestingly, mulberry rt clustered with other rt from distantly related taxa according to the phylogenetic analysis. This phenomenon did not result from horizontal transposable element transfer. Results obtained from fluorescence in situ hybridization revealed that most of the hybridization signals were preferentially concentrated in pericentromeric and distal regions of chromosomes, and these elements may play important roles in the regions in which they are found. Results of this study support the continued pursuit of further functional studies of Copia and Gypsy in the mulberry genome.

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Loci, genes, and gene networks associated with life history variation in a model ecological organism,Daphnia pulex(complex)

10.1101/436733 ◽

2018 ◽

Author(s):

Jacob W. Malcom ◽

Thomas E. Juenger ◽

Mathew A. Leibold

Keyword(s):

Gene Expression ◽

Genetic Variation ◽

Life History ◽

Molecular Basis ◽

Life History Traits ◽

Evolutionary Dynamics ◽

Daphnia Pulex ◽

Life History Trait ◽

Life History Variation ◽

Trait Variation

ABSTRACTBackgroundIdentifying the molecular basis of heritable variation provides insight into the underlying mechanisms generating phenotypic variation and the evolutionary history of organismal traits. Life history trait variation is of central importance to ecological and evolutionary dynamics, and contemporary genomic tools permit studies of the basis of this variation in non-genetic model organisms. We used high density genotyping, RNA-Seq gene expression assays, and detailed phenotyping of fourteen ecologically important life history traits in a wild-caught panel of 32Daphnia pulexclones to explore the molecular basis of trait variation in a model ecological species.ResultsWe found extensive phenotypic and a range of heritable genetic variation (~0 < H2< 0.44) in the panel, and accordingly identify 75-261 genes—organized in 3-6 coexpression modules—associated with genetic variation in each trait. The trait-related coexpression modules possess well-supported promoter motifs, and in conjunction with marker variation at trans- loci, suggest a relatively small number of important expression regulators. We further identify a candidate genetic network with SNPs in eight known transcriptional regulators, and dozens of differentially expressed genes, associated with life history variation. The gene-trait associations include numerous un-annotated genes, but also support several a priori hypotheses, including an ecdysone-induced protein and several Gene Ontology pathways.ConclusionThe genetic and gene expression architecture ofDaphnialife history traits is complex, and our results provide numerous candidate loci, genes, and coexpression modules to be tested as the molecular mechanisms that underlieDaphniaeco-evolutionary dynamics.

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Genomic evidence of adaptive evolution in the reptilian SOCS gene family

PeerJ ◽

10.7717/peerj.11677 ◽

2021 ◽

Vol 9 ◽

pp. e11677

Author(s):

Tian Xia ◽

Lei Zhang ◽

Guolei Sun ◽

Xiufeng Yang ◽

Honghai Zhang

Keyword(s):

Negative Selection ◽

Molecular Mechanisms ◽

Evolutionary Dynamics ◽

Theoretical Foundation ◽

Selective Pressure ◽

Rapid Evolution ◽

Cytokine Signaling ◽

Signal Pathways ◽

Branch Model ◽

Comprehensive Study

The suppressor of the cytokine signaling (SOCS) family of proteins play an essential role in inhibiting cytokine receptor signaling by regulating immune signal pathways. Although SOCS gene functions have been examined extensively, no comprehensive study has been performed on this gene family’s molecular evolution in reptiles. In this study, we identified eight canonical SOCS genes using recently-published reptilian genomes. We used phylogenetic analysis to determine that the SOCS genes had highly conserved evolutionary dynamics that we classified into two types. We identified positive SOCS4 selection signals in whole reptile lineages and SOCS2 selection signals in the crocodilian lineage. Selective pressure analyses using the branch model and Z-test revealed that these genes were under different negative selection pressures compared to reptile lineages. We also concluded that the nature of selection pressure varies across different reptile lineages on SOCS3, and the crocodilian lineage has experienced rapid evolution. Our results may provide a theoretical foundation for further analyses of reptilian SOCS genes’ functional and molecular mechanisms, as well as their roles in reptile growth and development.

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Evolutionary dynamics of ‘the’ bdelloid and monogonont rotifer life-history patterns

Developments in Hydrobiology - Rotifera X ◽

10.1007/1-4020-4408-9_5 ◽

2006 ◽

pp. 55-70

Author(s):

Charles E. King ◽

Claudia Ricci ◽

Justin Schonfeld ◽

Manuel Serra

Keyword(s):

Life History ◽

Evolutionary Dynamics ◽

Monogonont Rotifer ◽

Life History Patterns

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Daphnia as a Model for Eco-evolutionary Dynamics

10.1093/oso/9780190620271.003.0016 ◽

2018 ◽

pp. 403-424

Author(s):

Matthew R. Walsh ◽

Michelle Packer ◽

Shannon Beston ◽

Collin Funkhouser ◽

Michael Gillis ◽

...

Keyword(s):

Life History ◽

Evolutionary Dynamics ◽

Model Organism ◽

Life History Evolution ◽

Ecological Processes ◽

Evolutionary Forces ◽

Evolutionary Changes ◽

History Evolution ◽

Ecological Importance ◽

The Many

Much research has shown that variation in ecological processes can drive rapid evolutionary changes over periods of years to decades. Such contemporary adaptation sets the stage for evolution to have reciprocal impacts on the properties of populations, communities, and ecosystems, with ongoing interactions between ecological and evolutionary forces. The importance and generality of these eco-evolutionary dynamics are largely unknown. In this chapter, we promote the use of water fleas (Daphnia sp.) as a model organism in the exploration of eco-evolutionary interactions in nature. The many characteristics of Daphnia that make them suitable for laboratory study in conjunction with their well-known ecological importance in lakes, position Daphnia to contribute new and important insights into eco-evolutionary dynamics. We first review the influence of key environmental stressors in Daphnia evolution. We then highlight recent work documenting the pathway from life history evolution to ecology using Daphnia as a model. This review demonstrates that much is known about the influence of ecology on Daphnia life history evolution, while research exploring the genomic basis of adaptation as well as the influence of Daphnia life history traits on ecological processes is beginning to accumulate.

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Unhatched eggs represent the invisible fraction in two wild bird populations

Biology Letters ◽

10.1098/rsbl.2019.0763 ◽

2020 ◽

Vol 16 (1) ◽

pp. 20190763 ◽

Cited By ~ 4

Author(s):

Nicola Hemmings ◽

Simon Evans

Keyword(s):

Life History ◽

Wild Bird ◽

Evolutionary Dynamics ◽

Population Studies ◽

Bird Species ◽

Fertilization Failure ◽

Bird Populations ◽

Life History Data ◽

Evolutionary Inference ◽

The Invisible

Prenatal mortality is typically overlooked in population studies, which biases evolutionary inference by confounding selection and inheritance. Birds represent an opportunity to include this ‘invisible fraction’ if each egg contains a zygote, but whether hatching failure is caused by fertilization failure versus prenatal mortality is largely unknown. We quantified fertilization failure rates in two bird species that are popular systems for studying evolutionary dynamics and found that overwhelming majorities (99.9%) of laid eggs were fertilized. These systems thus present opportunities to eliminate the invisible fraction from life-history data.

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