Observations and perspectives on the diversification of genomes

TL;DR

This paper explores how statistical analysis of genomic data reveals relationships between genetic code evolution and the tree of life, supporting the three-domain model and providing a new phylogenomic approach.

Contribution

It introduces a biodiversity space based on codon distributions, reconstructs the three-domain tree, and proposes a simple phylogenomic method linked to prebiotic evolution.

Findings

Supports the three-domain tree of life over the eocyte tree.

Reconstructs an evolutionary tree of codons consistent with recruitment order.

Proposes a statistical explanation for triplet codon length and genome adaptation.

Abstract

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.