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Microevolution of nematode miRNAs reveals diverse modes of selection.

Jovelin R, Cutter AD - Genome Biol Evol (2014)

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada richard.jovelin@utoronto.ca.

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Related in: MedlinePlus

miRNA loci experience strong purifying selection to maintain regulatory interactions and to preserve the integrity of the hairpin structure. Average nucleotide differences within population (A) and between species (B), calculated using a sliding window, are lower in the region corresponding to the miRNA hairpin, represented by a black box. Black lines indicate mean nucleotide diversity and divergence and the blue areas indicate the 95% confidence interval. Nucleotide differences in the mature miR and in the backbone (hairpin − miR) are lower than nucleotide differences at synonymous sites of protein-coding genes (C, D). Similarly, both paired and unpaired sites of the miRNA hairpin show signatures of purifying selection when compared with synonymous changes (C, D). Median polymorphism and divergence are shown by a horizontal line. The box represents the IQR between the first and third quartile. The whiskers extend to the furthest data point within 1.5 times the IQR from the box. Means with different letters are significantly different with Wilcoxon two-sample tests. IQR, interquartile range.
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evu239-F2: miRNA loci experience strong purifying selection to maintain regulatory interactions and to preserve the integrity of the hairpin structure. Average nucleotide differences within population (A) and between species (B), calculated using a sliding window, are lower in the region corresponding to the miRNA hairpin, represented by a black box. Black lines indicate mean nucleotide diversity and divergence and the blue areas indicate the 95% confidence interval. Nucleotide differences in the mature miR and in the backbone (hairpin − miR) are lower than nucleotide differences at synonymous sites of protein-coding genes (C, D). Similarly, both paired and unpaired sites of the miRNA hairpin show signatures of purifying selection when compared with synonymous changes (C, D). Median polymorphism and divergence are shown by a horizontal line. The box represents the IQR between the first and third quartile. The whiskers extend to the furthest data point within 1.5 times the IQR from the box. Means with different letters are significantly different with Wilcoxon two-sample tests. IQR, interquartile range.

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.—


Microevolution of nematode miRNAs reveals diverse modes of selection.

Jovelin R, Cutter AD - Genome Biol Evol (2014)

miRNA loci experience strong purifying selection to maintain regulatory interactions and to preserve the integrity of the hairpin structure. Average nucleotide differences within population (A) and between species (B), calculated using a sliding window, are lower in the region corresponding to the miRNA hairpin, represented by a black box. Black lines indicate mean nucleotide diversity and divergence and the blue areas indicate the 95% confidence interval. Nucleotide differences in the mature miR and in the backbone (hairpin − miR) are lower than nucleotide differences at synonymous sites of protein-coding genes (C, D). Similarly, both paired and unpaired sites of the miRNA hairpin show signatures of purifying selection when compared with synonymous changes (C, D). Median polymorphism and divergence are shown by a horizontal line. The box represents the IQR between the first and third quartile. The whiskers extend to the furthest data point within 1.5 times the IQR from the box. Means with different letters are significantly different with Wilcoxon two-sample tests. IQR, interquartile range.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4255771&req=5

evu239-F2: miRNA loci experience strong purifying selection to maintain regulatory interactions and to preserve the integrity of the hairpin structure. Average nucleotide differences within population (A) and between species (B), calculated using a sliding window, are lower in the region corresponding to the miRNA hairpin, represented by a black box. Black lines indicate mean nucleotide diversity and divergence and the blue areas indicate the 95% confidence interval. Nucleotide differences in the mature miR and in the backbone (hairpin − miR) are lower than nucleotide differences at synonymous sites of protein-coding genes (C, D). Similarly, both paired and unpaired sites of the miRNA hairpin show signatures of purifying selection when compared with synonymous changes (C, D). Median polymorphism and divergence are shown by a horizontal line. The box represents the IQR between the first and third quartile. The whiskers extend to the furthest data point within 1.5 times the IQR from the box. Means with different letters are significantly different with Wilcoxon two-sample tests. IQR, interquartile range.
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.—

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada richard.jovelin@utoronto.ca.

Show MeSH
Related in: MedlinePlus