Emerging Frontiers in the Study of Molecular Evolution

Liberles, David A.; Chang, Belinda S. W.; Geiler-Samerotte, Kerry; Goldman, Aaron D.; Hey, Jody; Kaçar, Betül; Meyer, Michelle M.; Murphy, William J.; Posada, David; Storfer, Andrew

doi:10.1007/s00239-020-09932-6

Cited by 8 publications

(7 citation statements)

References 242 publications

(244 reference statements)

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“…Making further progress in our understanding of the TOL and resolving the phylogenetic placement of taxa near key evolutionary branching points requires advances within a wide range of research topics, which we summarize below ( Liberles et al 2020 , fig. 4 ).…”

Section: How To Make Further Progressmentioning

confidence: 99%

Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere

Spang

Mahendrarajah

Offre

et al. 2022

Genome Biology and Evolution

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The tree of life (TOL) is a powerful framework to depict the evolutionary history of cellular organisms through time, from our microbial origins to the diversification of multicellular eukaryotes that shape the visible biosphere today. During the past decades, our perception of the TOL has fundamentally changed in part due to profound methodological advances which allowed a more objective approach to studying organismal and viral diversity and led to the discovery of major new branches in the TOL as well as viral lineages. Phylogenetic and comparative genomics analyses of this data have, among others, revolutionized our understanding of the deep roots and diversity of microbial life, the origin of the eukaryotic cell, eukaryotic diversity as well as the origin and diversification of viruses. In this review, we provide an overview of some of the recent discoveries on the evolutionary history of cellular organisms and their viruses and discuss a variety of complementary techniques that we consider crucial for making further progress in our understanding of the TOL and its interconnection with the virosphere.

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Section: How To Make Further Progressmentioning

confidence: 99%

Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere

Spang

Mahendrarajah

Offre

et al. 2022

Genome Biology and Evolution

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“…In finding bouts of positive selection, ancestral sequence reconstruction generated experimentally testable hypotheses for studying molecular evolutionary history with potential protein functional change. While other recent reviews have examined this direction more systematically (Gumulya and Gillam 2017 ; Liberles et al 2020 ), an overview of key developments from a historical perspective is presented. The first experimental study using ASR involved the replacement of three amino acid positions in a modern lysozyme protein with inferred ancestral residues at these positions (Malcolm et al 1990 ), and proceeded to dissect possible intermediate pathways for how these amino acid positions evolved under selective constraints during an episode of functional divergence.…”

Section: Early Experimental Applications Of Computational Ancestral Smentioning

confidence: 99%

Ancestral Sequence Reconstruction: From Chemical Paleogenetics to Maximum Likelihood Algorithms and Beyond

2021

Self Cite

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As both a computational and an experimental endeavor, ancestral sequence reconstruction remains a timely and important technique. Modern approaches to conduct ancestral sequence reconstruction for proteins are built upon a conceptual framework from journal founder Emile Zuckerkandl. On top of this, work on maximum likelihood phylogenetics published in Journal of Molecular Evolution in 1996 was one of the first approaches for generating maximum likelihood ancestral sequences of proteins. From its computational history, future model development needs as well as potential applications in areas as diverse as computational systems biology, molecular community ecology, infectious disease therapeutics and other biomedical applications, and biotechnology are discussed. From its past in this journal, there is a bright future for ancestral sequence reconstruction in the field of evolutionary biology.

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“…Identifying the factors that drive molecular change in the genomes of organisms is one of the most central goals of evolutionary biology (1,2). Past research suggests that biotic interactions are fundamental for determining the evolution of organisms in nature (3,4).…”

Section: Main Textmentioning

confidence: 99%

Synergistic coevolution accelerates genome evolution

Preussger

Herbig

Kost

2021

Preprint

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Ecological interactions are key drivers of evolutionary change. Although it is welldocumented that antagonistic coevolution can accelerate molecular evolution, the evolutionary consequences of synergistic coevolution remain poorly understood. Here we show experimentally that also synergistic coevolution can speed up the rate of molecular evolution. Pairs of auxotrophic genotypes of the bacterium Escherichia coli, whose growth depended on a reciprocal exchange of amino acids, were experimentally coevolved, and compared to two control groups of independently growing cells. Coevolution drove the rapid emergence of a strong metabolic cooperation that correlated with a significantly increased number of mutations in coevolved auxotrophs as compared to monoculture controls. These results demonstrate that synergistic coevolution can cause rapid evolution that in the long run may drive diversification of mutualistically interacting species.

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Emerging Frontiers in the Study of Molecular Evolution

Cited by 8 publications

References 242 publications

Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere

Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere

Ancestral Sequence Reconstruction: From Chemical Paleogenetics to Maximum Likelihood Algorithms and Beyond

Synergistic coevolution accelerates genome evolution

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