Despite numerous mass extinctions in the Phanerozoic eon, the overall trend in biodiversity evolution was not blocked and the life has never been wiped out. Almost all possible catastrophic events (large igneous province, asteroid impact, climate cha
nge, regression and transgression, anoxia, acidification, sudden release of methane clathrate, multi-cause etc.) have been proposed to explain the mass extinctions. However, we should, above all, clarify at what timescale and at what possible levels should we explain the mass extinction? Even though the mass extinctions occurred at short-timescale and at the species level, we reveal that their cause should be explained in a broader context at tectonic timescale and at both the molecular level and the species level. The main result in this paper is that the Phanerozoic biodiversity evolution has been explained by reconstructing the Sepkoski curve based on climatic, eustatic and genomic data. Consequently, we point out that the P-Tr extinction was caused by the tectonically originated climate instability. We also clarify that the overall trend of biodiversification originated from the underlying genome size evolution, and that the fluctuation of biodiversity originated from the interactions among the earths spheres. The evolution at molecular level had played a significant role for the survival of life from environmental disasters.
The classification of life should be based upon the fundamental mechanism in the evolution of life. We found that the global relationships among species should be circular phylogeny, which is quite different from the common sense based upon phylogene
tic trees. The genealogical circles can be observed clearly according to the analysis of protein length distributions of contemporary species. Thus, we suggest that domains can be defined by distinguished phylogenetic circles, which are global and stable characteristics of living systems. The mechanism in genome size evolution has been clarified; hence main component questions on C-value enigma can be explained. According to the correlations and quasi-periodicity of protein length distributions, we can also classify life into three domains.
There is an intrinsic relationship between the molecular evolution in primordial period and the properties of genomes and proteomes of contemporary species. The genomic data may help us understand the driving force of evolution of life at molecular l
evel. In absence of evidence, numerous problems in molecular evolution had to fall into a twilight zone of speculation and controversy in the past. Here we show that delicate structures of variations of genomic base compositions and amino acid frequencies resulted from the genetic code evolution. And the driving force of evolution of life also originated in the genetic code evolution. The theoretical results on the variations of amino acid frequencies and genomic base compositions agree with the experimental observations very well, not only in the variation trends but also in some fine structures. Inversely, the genomic data of contemporary species can help reconstruct the genetic code chronology and amino acid chronology in primordial period. Our results may shed light on the intrinsic mechanism of molecular evolution and the genetic code evolution.
Much evolutionary information is stored in the fluctuations of protein length distributions. The genome size and non-coding DNA content can be calculated based only on the protein length distributions. So there is intrinsic relationship between the c
oding DNA size and non-coding DNA size. According to the correlations and quasi-periodicity of protein length distributions, we can classify life into three domains. Strong evidences are found to support the order in the structures of protein length distributions.
We show that the holographic principle in quantum gravity imposes a strong constraint on life. The degrees of freedom of an organism can be estimated according to the theory of Boolean networks, which is constrained by the entropy bound. Hence we can
explain the languages in protein sequences or in DNA sequences. The overall evolution of biological complexity can be illustrated. And some general properties of protein length distributions can be explained by a linguistic mechanism.
The Cambrian explosion is a grand challenge to science today and involves multidisciplinary study. This event is generally believed as a result of genetic innovations, environmental factors and ecological interactions, even though there are many conf
licts on nature and timing of metazoan origins. The crux of the matter is that an entire roadmap of the evolution is missing to discern the biological complexity transition and to evaluate the critical role of the Cambrian explosion in the overall evolutionary context. Here we calculate the time of the Cambrian explosion by an innovative and accurate C-value clock; our result (560 million years ago) quite fits the fossil records. We clarify that the intrinsic reason of genome evolution determined the Cambrian explosion. A general formula for evaluating genome size of different species has been found, by which major questions of the C-value enigma can be solved and the genome size evolution can be illustrated. The Cambrian explosion is essentially a major transition of biological complexity, which corresponds to a turning point in genome size evolution. The observed maximum prokaryotic complexity is just a relic of the Cambrian explosion and it is supervised by the maximum information storage capability in the observed universe. Our results open a new prospect of studying metazoan origins and molecular evolution.
The holographic bound in physics constrains the complexity of life. The finite storage capability of information in the observable universe requires the protein linguistics in the evolution of life. We find that the evolution of genetic code determin
es the variance of amino acid frequencies and genomic GC content among species. The elegant linguistic mechanism is confirmed by the experimental observations based on all known entire proteomes.
