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Parasitic Plants Have Increased Rates of Molecular Evolution Across All Three Genomes

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Parasitic Plants Have Increased Rates of Molecular Evolution Across All Three Genomes

Lindell Bromham et al. BMC Evol Biol.

Abstract

Background: Theoretical models and experimental evidence suggest that rates of molecular evolution could be raised in parasitic organisms compared to non-parasitic taxa. Parasitic plants provide an ideal test for these predictions, as there are at least a dozen independent origins of the parasitic lifestyle in angiosperms. Studies of a number of parasitic plant lineages have suggested faster rates of molecular evolution, but the results of some studies have been mixed. Comparative analysis of all parasitic plant lineages, including sequences from all three genomes, is needed to examine the generality of the relationship between rates of molecular evolution and parasitism in plants.

Results: We analysed DNA sequence data from the mitochondrial, nuclear and chloroplast genomes for 12 independent evolutionary origins of parasitism in angiosperms. We demonstrated that parasitic lineages have a faster rate of molecular evolution than their non-parasitic relatives in sequences for all three genomes, for both synonymous and nonsynonymous substitutions.

Conclusions: Our results prove that raised rates of molecular evolution are a general feature of parasitic plants, not confined to a few taxa or specific genes. We discuss possible causes for this relationship, including increased positive selection associated with host-parasite arms races, relaxed selection, reduced population size or repeated bottlenecks, increased mutation rates, and indirect causal links with generation time and body size. We find no evidence that faster rates are due to smaller effective populations sizes or changes in selection pressure. Instead, our results suggest that parasitic plants have a higher mutation rate than their close non-parasitic relatives. This may be due to a direct connection, where some aspect of the parasitic lifestyle drives the evolution of raised mutation rates. Alternatively, this pattern may be driven by an indirect connection between rates and parasitism: for example, parasitic plants tend to be smaller than their non-parasitic relatives, which may result in more cell generations per year, thus a higher rate of mutations arising from DNA copy errors per unit time. Demonstration that adoption of a parasitic lifestyle influences the rate of genomic evolution is relevant to attempts to infer molecular phylogenies of parasitic plants and to estimate their evolutionary divergence times using sequence data.

Figures

Figure 1
Figure 1
Scatter plot of comparisons between phylogenetically independent pairs of parasitic plants and their nonparasitic relatives. Points were calculated as the value of the nonparasitic clade subtracted from the parasitic clade, so that if the parasite has a faster rate then the difference is greater than 0. Each line represents a single substitution class in one of the three plant genomes, and each comparison is represented either by a red dot if the parasitic clade has the greater substitution rate or a blue dot if the nonparasitic clade has the higher substitution rate. The points have been slightly jittered to allow overlapping points to be seen clearly.

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