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Register a new userObservations and perspectives on the prebiotic sequence evolution
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Dirson Jian Li
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The post-genomic era has brought opportunities to bridge traditionally separate fields of early history of life and brought new insight into origin and evolution of biodiversity. According to distributions of codons in genome sequences, I found a relationship between the genetic code and the tree of life. This remote and profound relationship involves the origin and evolution of the genetic code and the diversification and expansion of genomes. Here, a prebiotic picture of the triplex nucleic acid evolution is proposed to explain the origin of the genetic code, where the transition from disorder to order in the origin of life might be due to the increasing stabilities of triplex base pairs. The codon degeneracy can be obtained in detail based on the coevolution of the genetic code with amino acids, or equivalently, the coevolution of tRNAs with aaRSs. This theory is based on experimental data such as the stability of triplex base pairs and the statistical features of genomic codon distributions. Several experimentally testable proposals have been developed. This study should be regarded as an exploratory attempt to reveal the early evolution of life based on sequence information in a statistical manner.
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Rich information on the prebiotic evolution is still stored in contemporary genomic data. The statistical mechanism at the sequence level may play a significant role in the prebiotic evolution. Based on statistical analysis of genome sequences, it has been observed that there is a close relationship between the evolution of the genetic code and the organisation of genomes. A biodiversity space for species is constructed based on comparing the distributions of codons in genomes for different species according to recruitment order of codons in the prebiotic evolution, by which a closely relationship between the evolution of the genetic code and the tree of life has been confirmed. On one hand, the three domain tree of life can be reconstructed according to the distance matrix of species in this biodiversity space, which supports the three-domain tree rather than the eocyte tree. On the other hand, an evolutionary tree of codons can be obtained by comparing the distributions of the 64 codons in genomes, which agrees with the recruitment order of codons on the roadmap. This is a simple phylogenomic method to study the origins of metazoan, the evolution of primates, etc. This study should be regarded as an exploratory attempt to explain the diversification of the three domains of life by statistical mechanism in prebiotic sequence evolution. It is indicated that the number of bases in the triplet codons might be explained statistically by the number of strands in the triplex DNAs. The adaptation of life to the changing environment might be due to assembly of redundant genomes at the sequence level.
Many models for the origin of life have focused on understanding how evolution can drive the refinement of a preexisting enzyme, such as the evolution of efficient replicase activity. Here we present a model for what was, arguably, an even earlier stage of chemical evolution, when polymer sequence diversity was generated and sustained before, and during, the onset of functional selection. The model includes regular environmental cycles (e.g. hydration-dehydration cycles) that drive polymers between times of replication and functional activity, which coincide with times of different monomer and polymer diffusivity. Kinetic Monte Carlo simulations demonstrate that this proposed prebiotic scenario provides a robust mechanism for the exploration of sequence space. Introduction of a polymer sequence with monomer synthetase activity illustrates that functional sequences can become established in a preexisting pool of otherwise non-functional sequences. Functional selection does not dominate system dynamics and sequence diversity remains high, permitting the emergence and spread of more than one functional sequence. It is also observed that polymers spontaneously form clusters in simulations where polymers diffuse more slowly than monomers, a feature that is reminiscent of a previous proposal that the earliest stages of life could have been defined by the collective evolution of a system-wide cooperation of polymer aggregates. Overall, the results presented demonstrate the merits of considering plausible prebiotic polymer chemistries and environments that would have allowed for the rapid turnover of monomer resources and for regularly varying monomer/polymer diffusivities.
The coexistence between different types of templates has been the choice solution to the information crisis of prebiotic evolution, triggered by the finding that a single RNA-like template cannot carry enough information to code for any useful replicase. In principle, confining $d$ distinct templates of length $L$ in a package or protocell, whose survival depends on the coexistence of the templates it holds in, could resolve this crisis provided that $d$ is made sufficiently large. Here we review the prototypical package model of Niesert et al. 1981 which guarantees the greatest possible region of viability of the protocell population, and show that this model, and hence the entire package approach, does not resolve the information crisis. This is so because to secure survival the total information content of the protocell, $Ld$, must tend to a constant value that depends only on the spontaneous error rate per nucleotide of the template replication mechanism. As a result, an increase of $d$ must be followed by a decrease of $L$ to ensure the protocell viability, so that the net information gain is null.
Based on statistical analysis of the complete genome sequences, a remote relationship has been observed between the evolution of the genetic code and the three domain tree of life. The existence of such a remote relationship need to be explained. The unity of the living system throughout the history of life relies on the common features of life: the homochirality, the genetic code and the universal genome format. The universal genome format has been observed in the genomic codon distributions as a common feature of life at the sequence level. A main aim of this article is to reconstruct and to explain the Phanerozoic biodiversity curve. It has been observed that the exponential growth rate of the Phanerozoic biodiversity curve is about equal to the exponential growth rate of genome size evolution. Hence it is strongly indicated that the expansion of genomes causes the exponential trend of the Phanerozoic biodiversity curve, where the conservative property during the evolution of life is guaranteed by the universal genome format at the sequence level. In addition, a consensus curve based on the climatic and eustatic data is obtained to explain the fluctuations of the Phanerozoic biodiversity curve. Thus, the reconstructed biodiversity curve based on genomic, climatic and eustatic data agrees with Sepkoskis curve based on fossil data. The five mass extinctions can be discerned in this reconstructed biodiversity curve, which indicates a tectonic cause of the mass extinctions. And the declining origination rate and extinction rate throughout the Phanerozoic eon might be due to the growth trend in genome size evolution.
A model of genome evolution is proposed. Based on three assumptions the evolutionary theory of a genome is formulated. The general law on the direction of genome evolution is given. Both the deterministic classical equation and the stochastic quantum equation are proposed. It is proved that the classical equation can be put in a form of the least action principle and the latter can be used for obtaining the quantum generalization of the evolutionary law. The wave equation and uncertainty relation for the quantum evolution are deduced logically. It is shown that the classical trajectory is a limiting case of the general quantum evolution depicted in the coarse-grained time. The observed smooth/sudden evolution is interpreted by the alternating occurrence of the classical and quantum phases. The speciation event is explained by the quantum transition in quantum phase. Fundamental constants of time dimension, the quantization constant and the evolutionary inertia, are introduced for characterizing the genome evolution. The size of minimum genome is deduced from the quantum uncertainty lower bound. The present work shows the quantum law may be more general than thought, since it plays key roles not only in atomic physics, but also in genome evolution.
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