Discontinuous DNA variation in the evolution of plant species

Quantum Patterns of Genome Size Variation in Angiosperms

Aims:

The discontinuous pattern of genome size variation in angiosperms is an unsolved problem related to genome evolution. In this study, we introduced a genome evolution operator and solved the related eigenvalue equation to deduce the discontinuous pattern.

Background:

Genome is a well-defined system for studying the evolution of species. One of the basic problems is the genome size evolution. The DNA amounts for angiosperm species are highly variable, differing over 1000-fold. One big surprise is the discovery of the discontinuous distribution of nuclear DNA amounts in many angiosperm genera.

Objective:

The discontinuous distribution of nuclear DNA amounts has certain regularity, much like a group of quantum states in atomic physics. The quantum pattern has not been explained by all the evolutionary theories so far and we shall interpret it through the quantum simulation of genome evolution.

Methods:

We introduced a genome evolution operator H to deduce the distribution of DNA amount. The nuclear DNA amount in angiosperms is studied from the eigenvalue equation of the genome evolution operator H. The operator H is introduced by physical simulation and it is defined as a function of the genome size N and the derivative with respect to the size.

Results:

The discontinuity of DNA size distribution and its synergetic occurrence in related angiosperms species are successfully deduced from the solution of the equation. The results agree well with the existing experimental data of Aloe, Clarkia, Nicotiana, Lathyrus, Allium and other genera.

Conclusion:

The success of our approach may infer the existence of a set of genomic evolutionary equations satisfying classical-quantum duality. The classical phase of evolution means it obeys the classical deterministic law, while the quantum phase means it obeys the quantum stochastic law. The discontinuity of DNA size distribution provides novel evidences on the quantum evolution of angiosperms. It has been realized that the discontinuous pattern is due to the existence of some unknown evolutionary constraints. However, our study indicates that these constraints on the angiosperm genome essentially originate from quantum.

A continuous morphological approach to study the evolution of pollen in a phylogenetic context: An example with the order Myrtales

The study of pollen morphology has historically allowed evolutionary biologists to assess phylogenetic relationships among Angiosperms, as well as to better understand the fossil record. During this process, pollen has mainly been studied by discretizing some of its main characteristics such as size, shape, and exine ornamentation. One large plant clade in which pollen has been used this way for phylogenetic inference and character mapping is the order Myrtales, composed by the small families Alzateaceae, Crypteroniaceae, and Penaeaceae (collectively the "CAP clade"), as well as the large families Combretaceae, Lythraceae, Melastomataceae, Myrtaceae, Onagraceae and Vochysiaceae. In this study, we present a novel way to study pollen evolution by using quantitative size and shape variables. We use morphometric and morphospace methods to evaluate pollen change in the order Myrtales using a time-calibrated, supermatrix phylogeny. We then test for conservatism, divergence, and morphological convergence of pollen and for correlation between the latitudinal gradient and pollen size and shape. To obtain an estimate of shape, Myrtales pollen images were extracted from the literature, and their outlines analyzed using elliptic Fourier methods. Shape and size variables were then analyzed in a phylogenetic framework under an Ornstein-Uhlenbeck process to test for shifts in size and shape during the evolutionary history of Myrtales. Few shifts in Myrtales pollen morphology were found which indicates morphological conservatism. Heterocolpate, small pollen is ancestral with largest pollen in Onagraceae. Convergent shifts in shape but not size occurred in Myrtaceae and Onagraceae and are correlated to shifts in latitude and biogeography. A quantitative approach was applied for the first time to examine pollen evolution across a large time scale. Using phylogenetic based morphometrics and an OU process, hypotheses of pollen size and shape were tested across Myrtales. Convergent pollen shifts and position in the latitudinal gradient support the selective role of harmomegathy, the mechanism by which pollen grains accommodate their volume in response to water loss.

The problem of the eukaryotic genome size

The current state of knowledge concerning the unsolved problem of the huge interspecific eukaryotic genome size variations not correlating with the species phenotypic complexity (C-value enigma also known as C-value paradox) is reviewed. Characteristic features of eukaryotic genome structure and molecular mechanisms that are the basis of genome size changes are examined in connection with the C-value enigma. It is emphasized that endogenous mutagens, including reactive oxygen species, create a constant nuclear environment where any genome evolves. An original quantitative model and general conception are proposed to explain the C-value enigma. In accordance with the theory, the noncoding sequences of the eukaryotic genome provide genes with global and differential protection against chemical mutagens and (in addition to the anti-mutagenesis and DNA repair systems) form a new, third system that protects eukaryotic genetic information. The joint action of these systems controls the spontaneous mutation rate in coding sequences of the eukaryotic genome. It is hypothesized that the genome size is inversely proportional to functional efficiency of the anti-mutagenesis and/or DNA repair systems in a particular biological species. In this connection, a model of eukaryotic genome evolution is proposed.