Constructive Neutral Evolution 20 Years Later

Muñoz-Gómez, Sergio A.; Bilolikar, Gaurav; Wideman, Jeremy G.; Geiler-Samerotte, Kerry

doi:10.1007/s00239-021-09996-y

Cited by 56 publications

(47 citation statements)

References 77 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Previous research suggests how many proteins, i.e., enzymes, begin as generalists with many interacting partners, and later evolve more specialized interactions 52 , 59 , whereas ribosomal proteins may have evolved toward multiple functions while primarily acting as stabilizers of rRNA 60 . Indeed, our results seem to corroborate the “constructive neutral evolution” 61 , in that new nodes added to the network may not initially affect the resilience but over time contribute to the network’s complexity. Under this interpretation, novel proteins may be initially conserved in the network, simply by being tolerated and adding to the network resilience, as suggested in research on de novo genes 62 .…”

Section: Discussionsupporting

confidence: 76%

A computational exploration of resilience and evolvability of protein–protein interaction networks

et al. 2021

View full text Add to dashboard Cite

Protein–protein interaction (PPI) networks represent complex intra-cellular protein interactions, and the presence or absence of such interactions can lead to biological changes in an organism. Recent network-based approaches have shown that a phenotype’s PPI network’s resilience to environmental perturbations is related to its placement in the tree of life; though we still do not know how or why certain intra-cellular factors can bring about this resilience. Here, we explore the influence of gene expression and network properties on PPI networks’ resilience. We use publicly available data of PPIs for E. coli, S. cerevisiae, and H. sapiens, where we compute changes in network resilience as new nodes (proteins) are added to the networks under three node addition mechanisms—random, degree-based, and gene-expression-based attachments. By calculating the resilience of the resulting networks, we estimate the effectiveness of these node addition mechanisms. We demonstrate that adding nodes with gene-expression-based preferential attachment (as opposed to random or degree-based) preserves and can increase the original resilience of PPI network in all three species, regardless of gene expression distribution or network structure. These findings introduce a general notion of prospective resilience, which highlights the key role of network structures in understanding the evolvability of phenotypic traits.

show abstract

Section: Discussionsupporting

confidence: 76%

A computational exploration of resilience and evolvability of protein–protein interaction networks

et al. 2021

View full text Add to dashboard Cite

show abstract

“…The framework here is consistent with adaptive rationales, but does not exclude models such as CNE (Stoltzfus 1999;Muñoz-Gómez et al 2021). CNE describes a multi-step process in which neutral, non-adaptive change opens capacities for complementation and co-dependency.…”

Section: Constructive Neutral Evolution (Cne)mentioning

confidence: 99%

Adaptation and Exaptation: From Small Molecules to Feathers

et al. 2022

View full text Add to dashboard Cite

Evolution works by adaptation and exaptation. At an organismal level, exaptation and adaptation are seen in the formation of organelles and the advent of multicellularity. At the sub-organismal level, molecular systems such as proteins and RNAs readily undergo adaptation and exaptation. Here we suggest that the concepts of adaptation and exaptation are universal, synergistic, and recursive and apply to small molecules such as metabolites, cofactors, and the building blocks of extant polymers. For example, adenosine has been extensively adapted and exapted throughout biological evolution. Chemical variants of adenosine that are products of adaptation include 2′ deoxyadenosine in DNA and a wide array of modified forms in mRNAs, tRNAs, rRNAs, and viral RNAs. Adenosine and its variants have been extensively exapted for various functions, including informational polymers (RNA, DNA), energy storage (ATP), metabolism (e.g., coenzyme A), and signaling (cyclic AMP). According to Gould, Vrba, and Darwin, exaptation imposes a general constraint on interpretation of history and origins; because of exaptation, extant function should not be used to explain evolutionary history. While this notion is accepted in evolutionary biology, it can also guide the study of the chemical origins of life. We propose that (i) evolutionary theory is broadly applicable from the dawn of life to the present time from molecules to organisms, (ii) exaptation and adaptation were important and simultaneous processes, and (iii) robust origin of life models can be constructed without conflating extant utility with historical basis of origins.

show abstract

“…However, because Darwin had no mechanism for the origin of variation, stating that only positive selection is genuinely “Darwinian” is, in our opinion, inadequate. Perhaps a stronger argument in support of WEM is that modern evolutionary theory has no problem in recognizing that other evolutionary processes can lead to evolutionary adaptive novelties ( Koonin 2011 ; Brosius 2019 ; Muñoz-Gómez et al 2021 ).…”

Section: Beyond Se and The Multiple Origins Of Functional Elementsmentioning

confidence: 99%

What We Talk About When We Talk About “Junk DNA”

Fagundes

Bisso‐Machado

Figueiredo

et al. 2022

Genome Biology and Evolution

View full text Add to dashboard Cite

“Junk DNA” is a popular yet controversial concept that states that organisms carry in their genomes DNA that has no positive impact on their fitness. Nonetheless, biochemical functions have been identified for an increasing fraction of DNA elements traditionally seen as “Junk DNA”. These findings have been interpreted as fundamentally undermining the “Junk DNA” concept. Here, we reinforce previous arguments that this interpretation relies on an inadequate concept of biological function that does not consider the selected effect of a given genomic structure, which is central to the “Junk DNA” concept. Next, we suggest that another (though ignored) confounding factor is that the discussion about biological functions includes two different dimensions: a horizontal, ecological dimension that reflects how a given genomic element affects fitness in a specific time, and a vertical, temporal dimension that reflects how a given genomic element persisted along time. We suggest that “Junk DNA” should be used exclusively relative to the horizontal dimension, while for the vertical dimension, we propose a new term, “Spam DNA”, that reflects the fact that a given genomic element may persist in the genome even if not selected for on their origin. Importantly, these concepts are complementary. An element can be both “Spam DNA” and “Junk DNA”, and “Spam DNA” can also be recruited to perform evolved biological functions, as illustrated in processes of exaptation or constructive neutral evolution.

show abstract

Constructive Neutral Evolution 20 Years Later

Cited by 56 publications

References 77 publications

A computational exploration of resilience and evolvability of protein–protein interaction networks

A computational exploration of resilience and evolvability of protein–protein interaction networks

Adaptation and Exaptation: From Small Molecules to Feathers

What We Talk About When We Talk About “Junk DNA”

Contact Info

Product

Resources

About