Experimental evolution is not just for model organisms

Burnetti, Anthony; Ratcliff, William C.

doi:10.1371/journal.pbio.3001587

Cited by 3 publications

(1 citation statement)

References 12 publications

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“…The Richard Lenski’s long-term evolution experiment (LTEE) with a laboratory population of Escherichia coli sampled through 60,000 generations shows the relationships between rates of genomic evolution and organismal adaptation (Barrick et al , 2009; Good et al , 2017). Experimental evolution of a major evolutionary innovation (the origin of multicellularity) has been also carried out on both experimentally tractable model organisms (Ratcliff et al , 2012), as well as in a unicellular relative of animals (Burnetti and Ratcliff, 2022). In the same way, computer simulations of digital organisms revealed important aspects of evolutionary dynamics (Adami, Ofria and Collier, 2000).…”

Section: Introductionmentioning

confidence: 99%

Adaptive trends of sequence compositional complexity over pandemic time in the SARS-CoV-2 coronavirus

Oliver

Bernaola‐Galván

Perfectti

et al. 2021

Preprint

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In the brief time since the outbreak of the COVID-19 pandemic, and despite its proofreading mechanism, the SARS-CoV-2 coronavirus has accumulated a significant amount of genetic variability through recombination and mutation events. To test evolutionary trends that could inform us on the adaptive process of the virus to its human host, we summarize all this variability in the Sequence Compositional Complexity (SCC), a measure of genome heterogeneity that captures the mutational and recombinational changes accumulated by a nucleotide sequence along time. Despite the brief time elapsed, we detected many differences in the number and length of compositional domains, as well as in their nucleotide frequencies, in more than 12,000 high-quality coronavirus genomes from across the globe. These differences in SCC are phylogenetically structured, as revealed by significant phylogenetic signal. Phylogenetic ridge regression shows that SCC followed a generalized decreasing trend along the ongoing process of pathogen evolution. In contrast, SCC evolutionary rate increased with time, showing that it accelerates toward the present. In addition, a low rate set of genomes was detected in all the genome groups, suggesting the existence of a stepwise distribution of rates, a strong indication of selection in favor of different dominant strains. Coronavirus variants reveal an exacerbation of this trend: non-significant SCC regression, low phylogenetic signal and, concomitantly, a threefold increase in the evolutionary rate. Altogether, these results show an accelerated decline of genome heterogeneity along with the SARS-CoV-2 pandemic expansion, a process that might be related to viral adaptation to the human host, perhaps paralleling the transformation of the current pandemic to epidemic.

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Section: Introductionmentioning

confidence: 99%

Adaptive trends of sequence compositional complexity over pandemic time in the SARS-CoV-2 coronavirus

Oliver

Bernaola‐Galván

Perfectti

et al. 2021

Preprint

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Revisiting the Design of the Long-Term Evolution Experiment with Escherichia coli

Lenski

2023

J Mol Evol

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Cephalopod-omics: Emerging Fields and Technologies in Cephalopod Biology

Baden

Briseno

Coffing

et al. 2023

Integrative and Comparative Biology

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Few animal groups can claim the level of wonder that cephalopods instill in the minds of researchers and the general public. Much of cephalopod biology, however, remains unexplored: the largest invertebrate brain, difficult husbandry conditions, complex (meta-)genomes, among many other things, have hindered progress in addressing key questions. However, recent technological advancements in sequencing, imaging, and genetic manipulation have opened new avenues for exploring the biology of these extraordinary animals. The cephalopod molecular biology community is thus experiencing a large influx of researchers, emerging from different fields, accelerating the pace of research in this clade. In the first post-pandemic event at the Cephalopod International Advisory Council (CIAC) conference in April 2022, over 40 participants from all over the world met and discussed key challenges and perspectives for current cephalopod molecular biology and evolution. Our particular focus was on the fields of comparative and regulatory genomics, gene manipulation, single cell transcriptomics, metagenomics and microbial interactions. This article is a result of this joint effort, summarizing the latest insights from these emerging fields, their bottlenecks and potential solutions. The article highlights the interdisciplinary nature of the cephalopod -omics community and provides an emphasis on continuous consolidation of efforts and collaboration in this rapidly evolving field.

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Experimental evolution is not just for model organisms

Cited by 3 publications

References 12 publications

Adaptive trends of sequence compositional complexity over pandemic time in the SARS-CoV-2 coronavirus

Adaptive trends of sequence compositional complexity over pandemic time in the SARS-CoV-2 coronavirus

Revisiting the Design of the Long-Term Evolution Experiment with Escherichia coli

Cephalopod-omics: Emerging Fields and Technologies in Cephalopod Biology

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