No genome is an island: toward a 21st century agenda for evolution

Shapiro, James A.

doi:10.1111/nyas.14044

Cited by 27 publications

(22 citation statements)

References 205 publications

(423 reference statements)

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“…In this manner and through a number of highly integrated linkages, phenotypic adaptations are the result of complex cell-centered processes that alter the content and expression of the genome [ 62 ]. Consequently, Shapiro indicates that it is reasonable to doubt that such disparate mechanisms can function, each in their own manner, and still yield productive evolutionary outcomes [ 165 ].…”

Section: Discussionmentioning

confidence: 99%

Non-Random Genome Editing and Natural Cellular Engineering in Cognition-Based Evolution

Miller

Enguita

Leitão

2021

Cells

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Neo-Darwinism presumes that biological variation is a product of random genetic replication errors and natural selection. Cognition-Based Evolution (CBE) asserts a comprehensive alternative approach to phenotypic variation and the generation of biological novelty. In CBE, evolutionary variation is the product of natural cellular engineering that permits purposive genetic adjustments as cellular problem-solving. CBE upholds that the cornerstone of biology is the intelligent measuring cell. Since all biological information that is available to cells is ambiguous, multicellularity arises from the cellular requirement to maximize the validity of available environmental information. This is best accomplished through collective measurement purposed towards maintaining and optimizing individual cellular states of homeorhesis as dynamic flux that sustains cellular equipoise. The collective action of the multicellular measurement and assessment of information and its collaborative communication is natural cellular engineering. Its yield is linked cellular ecologies and mutualized niche constructions that comprise biofilms and holobionts. In this context, biological variation is the product of collective differential assessment of ambiguous environmental cues by networking intelligent cells. Such concerted action is enabled by non-random natural genomic editing in response to epigenetic impacts and environmental stresses. Random genetic activity can be either constrained or deployed as a ‘harnessing of stochasticity’. Therefore, genes are cellular tools. Selection filters cellular solutions to environmental stresses to assure continuous cellular-organismal-environmental complementarity. Since all multicellular eukaryotes are holobionts as vast assemblages of participants of each of the three cellular domains (Prokaryota, Archaea, Eukaryota) and the virome, multicellular variation is necessarily a product of co-engineering among them.

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Section: Discussionmentioning

confidence: 99%

Non-Random Genome Editing and Natural Cellular Engineering in Cognition-Based Evolution

Miller

Enguita

Leitão

2021

Cells

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“…Because of the universal occurrence of the PC in the oceans, it may serve as a basis for monitoring the health of the oceans and climate change. Ecological transitions and changes in the oceans trigger natural genetic engineering and genome changes on a massive scale [25,143]. The PC has evolved in multiple ecologic niches in the global ocean and participates in relevant biogeochemical cycles, such as the recently postulated parasitic arsenic cycle between Eurycolium and Pelagibacter ubique [144,145].…”

Section: Discussionmentioning

confidence: 99%

“…The PC is cited as an example of the evolution of dependencies of free-living organisms through adaptive gene losses, better known as the Black Queen hypothesis [31,32], summarized by Shapiro (2019) [25] as "no genome is an island", to stress continuous biosphere communications during evolution.…”

Section: Introductionmentioning

confidence: 99%

Unlocking the genomic taxonomy of theProchlorococcuscollective

Tschoeke

Vidal

Campeão

et al. 2020

Preprint

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1Prochlorococcus is the most abundant photosynthetic prokaryote on our planet. The extensive ecological literature on the Prochlorococcus collective (PC) is based on the assumption that it comprises one single genus comprising the species Prochlorococcus marinus, containing itself a collective of ecotypes. Ecologists adopt the distributed genome hypothesis of an open pan-genome to explain the observed genomic diversity and evolution patterns of the ecotypes within PC. Novel genomic data for the PC prompted us to revisit this group, applying the current methods used in genomic taxonomy. As a result, we were able to distinguish the five genera: Prochlorococcus, Eurycolium, Prolificoccus, Thaumococcus and Riococcus. The novel genera have distinct genomic and ecological attributes.

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“…Reticulate evolution studies track how over the course of ontogeny, non-or distinctly related entities interact in such a way that it impacts phylogeny. Reticulate interactions can occur through symbiosis [3,4], symbiogenesis [5][6][7][8][9][10], lateral gene transfer [11,12], infective heredity [13] mediated by mobile genetic elements [14,15] and overall organismal mobility, and hybridization [16,17].…”

Section: Reticulate Evolutionmentioning

confidence: 99%

Testing the “(Neo-)Darwinian” Principles against Reticulate Evolution: How Variation, Adaptation, Heredity and Fitness, Constraints and Affordances, Speciation, and Extinction Surpass Organisms and Species

Gontier

2020

Information

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Variation, adaptation, heredity and fitness, constraints and affordances, speciation, and extinction form the building blocks of the (Neo-)Darwinian research program, and several of these have been called “Darwinian principles.” Here, we suggest that caution should be taken in calling these principles Darwinian because of the important role played by reticulate evolutionary mechanisms and processes in also bringing about these phenomena. Reticulate mechanisms and processes include symbiosis, symbiogenesis, lateral gene transfer, infective heredity mediated by genetic and organismal mobility, and hybridization. Because the “Darwinian principles” are brought about by both vertical and reticulate evolutionary mechanisms and processes, they should be understood as foundational for a more pluralistic theory of evolution, one that surpasses the classic scope of the Modern and the Neo-Darwinian Synthesis. Reticulate evolution moreover demonstrates that what conventional (Neo-)Darwinian theories treat as intra-species features of evolution frequently involve reticulate interactions between organisms from very different taxonomic categories. Variation, adaptation, heredity and fitness, constraints and affordances, speciation, and extinction therefore cannot be understood as “traits” or “properties” of genes, organisms, species, or ecosystems because the phenomena are irreducible to specific units and levels of an evolutionary hierarchy. Instead, these general principles of evolution need to be understood as common goods that come about through interactions between different units and levels of evolutionary hierarchies, and they are exherent rather than inherent properties of individuals.

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No genome is an island: toward a 21st century agenda for evolution

Cited by 27 publications

References 205 publications

Non-Random Genome Editing and Natural Cellular Engineering in Cognition-Based Evolution

Non-Random Genome Editing and Natural Cellular Engineering in Cognition-Based Evolution

Unlocking the genomic taxonomy of theProchlorococcuscollective

Testing the “(Neo-)Darwinian” Principles against Reticulate Evolution: How Variation, Adaptation, Heredity and Fitness, Constraints and Affordances, Speciation, and Extinction Surpass Organisms and Species

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