Microevolution of nematode miRNAs reveals diverse modes of selection.
Bottom Line: We also show that new miRNAs evolve faster than older miRNAs but that selection nevertheless favors their persistence.Moreover, we demonstrate substantial nucleotide divergence of pre-miRNA hairpin alleles between populations and sister species.These findings from the first global survey of miRNA microevolution in Caenorhabditis support the idea that changes in gene expression, mediated through divergence in miRNA regulation, can contribute to phenotypic novelty and adaptation to specific environments in the present day as well as the distant past.
Affiliation: Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada email@example.com.Show MeSH
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Mentions: Given this abundance of allelic variants in miRNA sequences, how does the pattern of nucleotide polymorphism implicate natural selection? SNP density differs drastically across structural regions of the miRNAs, indicating strongest selective constraint for the mature and star miRNA regions and lowest constraint for sites located in loops (fig. 1B). However, purifying selection reduces nucleotide variation across the entire hairpin sequence, leaving a clear signature relative to genomic locations that flank miRNAs (fig. 2A and C). When we quantified nucleotide polymorphism and sequence divergence separately for the mature miR in the hairpin, we observed 18 times less polymorphism than for synonymous sites, used as a proxy for selective neutrality. This pattern is indicative of potent purifying selection on miRNA sequences and extends even to miRNA backbone sequences (the hairpin minus the miR), which contain three times less polymorphism than synonymous sites (fig. 2B and D). The same pattern holds for the populations of C. remanei from Ontario and Germany and for nucleotide divergence in orthologous regions between C. remanei and C. latens (supplementary tables S2–S4, Supplementary Material online).Fig. 2.—
Affiliation: Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada firstname.lastname@example.org.