Nucleotide substitution type dependence of generation time effect of molecular evolution

Accelerated evolutionary rates in tropical and oceanic parmelioid lichens (Ascomycota)

Background

The rate of nucleotide substitutions is not constant across the Tree of Life, and departures from a molecular clock have been commonly reported. Within parmelioid lichens, the largest group of macrolichens, large discrepancies in branch lengths between clades were found in previous studies. Using an extended taxon sampling, we test for presence of significant rate discrepancies within and between these clades and test our a priori hypothesis that such rate discrepancies may be explained by shifts in moisture regime or other environmental conditions.

Results

In this paper, the first statistical evidence for accelerated evolutionary rate in lichenized ascomycetes is presented. Our results give clear evidence for a faster rate of evolution in two Hypotrachyna clades that includes species occurring in tropical and oceanic habitats in comparison with clades consisting of species occurring in semi-arid and temperate habitats. Further we explore potential links between evolutionary rates and shifts in habitat by comparing alternative Ornstein-Uhlenbeck models.

Conclusion

Although there was only weak support for a shift at the base of a second tropical clade, where the observed nucleotide substitution rate is high, overall support for a shift in environmental conditions at cladogenesis is very strong. This suggests that speciation in some lichen clades has proceeded by dispersal into a novel environment, followed by radiation within that environment. We found moderate support for a shift in moisture regime at the base of one tropical clade and a clade occurring in semi-arid regions and a shift in minimum temperature at the base of a boreal-temperate clade.

Accelerated molecular evolution in halophilic crustaceans

In contrast to the stable ionic composition of the oceans, inland waters show striking diversity, possessing salt concentrations varying from I mM to 5 M. Although species diversity is highest in fresh water, some lineages have colonized hypersaline environments where they encounter elevated levels of both ultraviolet (UV) radiation and osmotic stress. This study compares rates of evolution in halophilic and freshwater taxa for two groups of microcrustaceans, anostracans and daphniids, from Australia and North America. The results establish that halophilic species show consistent rate acceleration, involving elevated levels of both insertion/deletion events and of nucleotide substitutions. The elevated pace of molecular evolution does not appear to be linked to selection or to other agents that are known to influence the supply rate of mutations, such as UV exposure, generation length, or shifts in metabolic rate. However, variance in ionic strength, which is known to have potent effects on DNA-protein interactions as well as on the structural properties of DNA and proteins, might account for the lowered fidelity of DNA replication in life from hypersaline settings. Regardless of its cause, the consistent rate acceleration in halophiles suggests that past efforts to employ sequence divergences to date events, such as the age of asexual lineages in Artemia, have resulted in serious overestimates. More generally, the results indicate that coordinated shifts in rates of molecular evolution may occur in lineages exposed to extreme environmental conditions.

A synthetic theory of molecular evolution

According to the neo-Darwinian view of evolution evolution rate nu depends solely on the environment variation rate gamma, whereas in the non-Darwinian view evolution rate is determined mainly by the mutation rate mu. We have studied two kinds of population genetics models which exhibit both types of evolution in different parametric regions: one is a dynamical model representing infinite population, and the other is a Markov process model representing a nearly monomorphic finite population. In the infinite population model, after proving general time-derivative and mu-derivative formulas for the population average of quantitative traits, we show that if the mutation rate is adaptively determined, mu must be larger than nu in the stationary state. Loads of evolution are obtained in both regions. A high evolution rate such as nu = 1 per genome per generation is consistent with Haldane's value of tolerable load if and only if the functional constraint is not large and selection is weak, independent of whether the evolution is neo-Darwinian or non-Darwinian. As the selection intensity increases, nu is shown to change discontinuously from nearly mu to gamma at the transition point. In the finite population model, the transition of v is not discontinuous, but is very steep. On the other hand, no steep change of polymorphism takes place at the transition point. The steepness of the transition in our model suggests that real molecular evolution can be divided into either neo-Darwinian or non-Darwinian,and that the intermediate type of evolution is rather rare.

Sex biases in the mutation rate

Men have more germ-line cell divisions than women. Does this lead to a higher mutation rate in males? Most estimates of the proportion of mutations originating in men come either from direct observation of disease-inducing mutations or from analysis of the relative rate of evolution of sex-linked and autosomal genes in primates. The latter mode of analysis has also been applied to other mammals, birds and files. For unknown reasons, this method produces contradictory results. A majority of estimates using the best direct methods in humans indicate a male bias for point mutations, but the variance in estimates is high. It is unclear how the evolutionary and direct data correspond and a consensus as to the extent of any male bias is not presently possible. While the number of germ-line cell divisions might contribute to differences, this by no means accounts for all of the data.