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COMPLEX SYSTEMS 2022年第3期31卷 287-309页

作者： Langdon, William B. UCL Dept Comp Sci Gower St London WC1E 6BT England

Large arithmetic expressions are dissipative: they lose information and are robust to perturbations. Lack of conservation gives resilience to fluctuations. The limited precision of floating point and the mixture of linear and nonlinear operations make such functions anti-fragile and give a largely stable locally flat plateau a rich fitness landscape. This slows long-term evolution of complex programs, suggesting a need for depthaware crossover and mutation operators in tree-based genetic programming. It also suggests that deeply nested computer program source code is error tolerant because disruptions tend to fail to propagate, and therefore the optimal placement of test oracles is as close to software defects as practical.

关键词： information loss irreversible computing entropy evolvability arithmetic software mutational robustness optimal test oracle placement evolution of complexity data dependent computational irreducibility effective computational equivalence experimental mathematics algorithmic information dynamics

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Mammals with Small Populations Do Not Exhibit Larger Genomes

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MOLECULAR BIOLOGY AND evolution 2021年第9期38卷 3737-3741页

作者： Roddy, Adam B. Alvarez-Ponce, David Roy, Scott W. Florida Int Univ Dept Biol Sci Inst Environm Miami FL 33199 USA Univ Nevada Dept Biol Reno NV 89557 USA San Francisco State Univ Dept Biol San Francisco CA 94132 USA

Genome size in cellular organisms varies by six orders of magnitude, yet the cause of this large variation remains unexplained. The influential Drift-Barrier Hypothesis proposes that large genomes tend to evolve in small populations due to inefficient selection. However, to our knowledge no explicit tests of the Drift-Barrier Hypothesis have been reported. We performed the first explicit test, by comparing estimated census population size and genome size in mammals while incorporating potential covariates and the effect of shared evolutionary history. We found a lack of correlation between census population size and genome size among 199 species of mammals. These results suggest that population size is not the predominant factor influencing genome size and that the Drift-Barrier Hypothesis should be considered provisional.

关键词： evolution of complexity C-value paradox population genomics drift barrier hypothesis genome complexity

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Higher level constructive neutral evolution

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BIOLOGY & PHILOSOPHY 2022年第4期37卷 23-23页

作者： Brunet, T. D. P. Univ Exeter Dept Sociol Philosophy & Anthropol Amory BldgRennes Dr Exeter EX4 4RJ Devon England

Constructive Neutral evolution (CNE) theory provides selectively neutral explanations of the origin and maintenance of biological complexity. This essay provides an analysis of CNE as an explanatory strategy defined by a tripartite set of conditions, and shows how this applies to cases of the evolution of complexity at higher-levels of the biological hierarchy. CNE was initially deployed to help explain a variety of complex molecular structures and processes, including spliceosomal splicing, trypansomal pan-editing, scrambled genes in ciliates, duplicate gene retention and fungal ATP synthetase structure. CNE has also been generalized to apply to phenomena at the cellular level, including protein-protein interaction network modularity, obligate microbial symbioses, eukaryogenesis and microbial unculturability. This essay further extends CNE to cases of complexity at levels of organization higher than the molecular and cellular. These are (1) multicellular phenotypic complexity, (2) multicellular ecological complexity and, (3) some cases of cultural complexity.

关键词： Constructive neutral evolution Neutral evolution evolution of complexity Obligate symbiosis Cultural complexity

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Transposable Elements in the evolution of Gene Regulatory Networks

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RUSSIAN JOURNAL OF GENETICS 2019年第1期55卷 24-34页

作者： Pirogov, S. A. Maksimenko, O. G. Georgiev, P. G. Russian Acad Sci Inst Gene Biol Moscow 119334 Russia

Over the past decade, there has been an active study of the interactions between the population of transposable elements (TEs) and the rest of the genome. Many regulatory sequences of TEs have been used for different genes regulation and genome organization. These regulatory sequences can be transcription factor binding sites, enhancers, and insulators. TEs may contain promoters that can be domesticated during substitution of original gene promoters or during de novo formation of long noncoding RNAs. In addition, there are many examples of domestication of TE-encoded proteins, for example, transposases, proteases, and Gag proteins. This review highlights the role of TEs in the evolution of gene regulatory networks and the principles determining it.

关键词： transposable elements regulation of gene expression genome evolution evolution of complexity exaptation

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Physical foundations of biological complexity

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2018年第37期115卷 E8678-E8687页

作者： Wolf, Yuri I. Katsnelson, Mikhail I. Koonin, Eugene V. Natl Lib Med Natl Ctr Biotechnol Informat Bethesda MD 20894 USA Radboud Univ Nijmegen Inst Mol & Mat NL-6525 AJ Nijmegen Netherlands

Biological systems reach hierarchical complexity that has no counterpart outside the realm of biology. Undoubtedly, biological entities obey the fundamental physical laws. Can today's physics provide an explanatory framework for understanding the evolution of biological complexity? We argue that the physical foundation for understanding the origin and evolution of complexity can be gleaned at the interface between the theory of frustrated states resulting in pattern formation in glass-like media and the theory of self organized criticality (SOC). On the one hand, SOC has been shown to emerge in spin-glass systems of high dimensionality. On the other hand, SOC is often viewed as the most appropriate physical description of evolutionary transitions in biology. We unify these two faces of SOC by showing that emergence of complex features in biological evolution typically, if not always, is triggered by frustration that is caused by competing interactions at different organizational levels. Such competing interactions lead to SOC, which represents the optimal conditions for the emergence of complexity. Competing interactions and frustrated states permeate biology at all organizational levels and are tightly linked to the ubiquitous competition for limiting resources. This perspective extends from the comparatively simple phenomena occurring in glasses to large-scale events of biological evolution, such as major evolutionary transitions. Frustration caused by competing interactions in multidimensional systems could be the general driving force behind the emergence of complexity, within and beyond the domain of biology.

关键词： evolution of complexity competing interactions frustrated states spin glasses self-organized criticality

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The generality of Constructive Neutral evolution

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BIOLOGY & PHILOSOPHY 2018年第1-2期33卷 2-2页

作者： Brunet, T. D. P. Doolittle, W. Ford Univ Cambridge Dept Hist & Philosophy Sci Free Sch Lane Cambridge CB2 3RH England Dalhousie Univ Dept Biochem & Mol Biol POB 15000 Halifax NS B3H 4R2 Canada

Constructive Neutral evolution (CNE) is an evolutionary mechanism that can explain much molecular inter-dependence and organismal complexity without assuming positive selection favoring such dependency or complexity, either directly or as a byproduct of adaptation. It differs from but complements other nonselective explanations for complexity, such as genetic drift and the Zero Force evolutionary Law, by being ratchet-like in character. With CNE, purifying selection maintains dependencies or complexities that were neutrally evolved. Preliminary treatments use it to explain specific genetic and molecular structures or processes, such as retained gene duplications, the spliceosome, and RNA editing. Here we aim to expand the scope of such explanation beyond the molecular level, integrating CNE with Multi-Level Selection theory, and arguing that several popular higherlevel selection scenarios are in fact instances of CNE. Suitably contextualized, CNE occurs at any level in the biological hierarchy at which natural selection as normally construed occurs. As examples, we focus on modularity in protein-protein interaction networks or "interactomes," the origin of eukaryotic cells and the evolution of co-dependence in microbial communities-a variant of the "Black Queen Hypothesis" which we call the "Gray Queen Hypothesis".

关键词： Constructive Neutral evolution evolution of complexity Black Queen Hypothesis Eukaryogenesis Protein-protein interaction networks Interactome

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Domestication of self-splicing introns during eukaryogenesis: the rise of the complex spliceosomal machinery

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BIOLOGY DIRECT 2017年第1期12卷 30-30页

作者： Vosseberg, Julian Snel, Berend Univ Utrecht Dept Biol Theoret Biol & Bioinformat Padualaan 8 NL-3584 CH Utrecht Netherlands

The spliceosome is a eukaryote-specific complex that is essential for the removal of introns from pre-mRNA. It consists of five small nuclear RNAs (snRNAs) and over a hundred proteins, making it one of the most complex molecular machineries. Most of this complexity has emerged during eukaryogenesis, a period that is characterised by a drastic increase in cellular and genomic complexity. Although not fully resolved, recent findings have started to shed some light on how and why the spliceosome originated. In this paper we review how the spliceosome has evolved and discuss its origin and subsequent evolution in light of different general hypotheses on the evolution of complexity. Comparative analyses have established that the catalytic core of this ribonucleoprotein (RNP) complex, as well as the spliceosomal introns, evolved from self-splicing group II introns. Most snRNAs evolved from intron fragments and the essential Prp8 protein originated from the protein that is encoded by group II introns. Proteins that functioned in other RNA processes were added to this core and extensive duplications of these proteins substantially increased the complexity of the spliceosome prior to the eukaryotic diversification. The splicing machinery became even more complex in animals and plants, yet was simplified in eukaryotes with streamlined genomes. Apparently, the spliceosome did not evolve its complexity gradually, but in rapid bursts, followed by stagnation or even simplification. We argue that although both adaptive and neutral evolution have been involved in the evolution of the spliceosome, especially the latter was responsible for the emergence of an enormously complex eukaryotic splicing machinery from simple self-splicing sequences.

关键词： Spliceosome Splicing Introns evolution of complexity Eukaryogenesis

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Non-functional genes repaired at the RNA level

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COMPTES RENDUS BIOLOGIES 2016年第7-8期339卷 289-295页

作者： Burger, Gertraud Univ Montreal Dept Biochem Robert Cedergren Ctr Bioinformat & Genom Montreal PQ Canada

Genomes and genes continuously evolve. Gene sequences undergo substitutions, deletions or nucleotide insertions;mobile genetic elements invade genomes and interleave in genes;chromosomes break, even within genes, and pieces reseal in reshuffled order. To maintain functional gene products and assure an organism's survival, two principal strategies are used - either repair of the gene itself or of its product. I will introduce common types of gene aberrations and how gene function is restored secondarily, and then focus on systematically fragmented genes found in a poorly studied protist group, the diplonemids. Expression of their broken genes involves restitching of pieces at the RNA-level, and substantial RNA editing, to compensate for point mutations. I will conclude with thoughts on how such a grotesquely unorthodox system may have evolved, and why this group of organisms persists and thrives since tens of millions of years. (C) 2016 Academie des sciences. Published by Elsevier Masson SAS. All rights reserved.

关键词： Gene fragmentation Trans-splicing Insertion and substitution RNA editing evolution of complexity Protists Diplonemids

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Root of Dictyostelia based on 213 universal proteins

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MOLECULAR PHYLOGENETICS AND evolution 2015年 92卷 53-62页

作者： Sheikh, Sanea Gloeckner, Gernot Kuwayama, Hidekazu Schaap, Pauline Urushihara, Hideko Baldauf, Sandra L. Uppsala Univ Uppsala Sweden Freie Univ Berlin Germany Univ Tsukuba Tsukuba Ibaraki 305 Japan Univ Dundee Dundee DD1 4HN Scotland

Dictyostelia are common soil microbes that can aggregate when starved to form multicellular fruiting bodies, a characteristic that has also led to their long history of study and widespread use as model systems. Ribosomal RNA phylogeny of Dictyostelia identified four major divisions (Groups 1-4), none of which correspond to traditional genera. Group 1 was also tentatively identified as sister lineage to the other three Groups, although not consistently or with strong support. We tested the dictyostelid root using universal protein-coding genes identified by exhaustive comparison of six completely sequenced dictyostelid genomes, which include representatives of all four major molecular Groups. A set of 213 genes are low-copy number in all genomes, present in at least one amoebozoan outgroup taxon (Acanthamoeba castellanii or Physarum polycephalum), and phylogenetically congruent Phylogenetic analysis of a concatenation of the deduced protein sequences produces a single topology dividing Dictyostelia into two major divisions: Groups 1 + 2 and Groups 3 + 4. All clades in the tree are fully supported by maximum likelihood and Bayesian inference, and all alternative roots are unambiguously rejected by the approximately unbiased (AU) test. The 1 + 2, 3 + 4 root is also fully supported even after deleting clusters with strong individual support for this root, or concatenating all clusters with low support for alternative roots. The 213 putatively ancestral amoebozoan proteins encode a wide variety of functions including 21 KOG categories out of a total of 25. These comprehensive analyses and consistent results indicate that it is time for full taxonomic revision of Dictyostelia, which will also enable more effective exploitation of its unique potential as an evolutionary model system. (C) 2015 Elsevier Inc. All rights reserved.

关键词： Aggregative multi-cellularity Universal genes Multigene phylogeny evolution of complexity

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Stochastic evolution of staying together

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JOURNAL OF THEORETICAL BIOLOGY 2014年 360卷 129-136页

作者： Ghang, Whan Nowak, Martin A. Harvard Univ Program Evolutionary Dynam Cambridge MA 02138 USA Harvard Univ Dept Math Cambridge MA 02138 USA Harvard Univ Dept Organism & Evolutionary Biol Cambridge MA 02138 USA

Staying together means that replicating units do not separate after reproduction, but remain attached to each other or in close proximity. Staying together is a driving force for evolution of complexity, including the evolution of multi-cellularity and eusociality. We analyze the fixation probability of a mutant that has the ability to stay together. We assume that the size of the complex affects the reproductive rate of its units and the probability of staying together. We examine the combined effect of natural selection and random drift on the emergence of staying together in a finite sized population. The number of states in the underlying stochastic process is an exponential function of population size. We develop a framework for any intensity of selection and give closed form solutions for special cases. We derive general results for the limit of weak selection. (C) 2014 Elsevier Ltd. All rights reserved.

关键词： evolution of complexity Multi-cellularity Fixation probability Finite population

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