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: We discovered a total of 381 SNPs and 32 indels located within 129 miRNA gene hairpins in an Ohio population of C. remanei (fig. 1A and supplementary table S1, Supplementary Material online). This gene collection comprises a large majority of the miRNAs in the genome: 83% of miRNAs identified in de Wit et al. (2009) and 69% of miRBase release 20 miRNAs (Kozomara and Griffiths-Jones 2011) that include a recent update of Caenorhabditis miRNAs (Shi et al. 2013). Nearly one-third (29%) of miRNA hairpins had no polymorphisms at all, although polymorphic miRNAs contained up to 20 variable sites. Subsequent analysis of C. remanei strains from Germany and Ontario revealed respectively 153 and 151 SNPs and 11 and 10 indels in a subset of 38 miRNA genes that we had found to have allelic variation within Ohio (supplementary table S1, Supplementary Material online). And, for the 79 miRNAs that we sequenced in the closely related species C. latens, we identified 302 nt substitutions and 37 indel differences between the 2 species. This wealth and density of mutations in miRNA genes within a single species and between sister species thus provide a powerful substrate to test the processes driving their microevolutionary dynamics.Fig. 1.—
Affiliation: Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada firstname.lastname@example.org.