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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

(A) SNP frequencies in mature miRs among populations of C. remanei. Most variants are found in a single population and at low frequency, with noticeable exceptions for instance for SNPs in mir-64a, mir-248, mir-787, block2892, and block3297. Columns represent separate populations and rows represent distinct SNPs. Each circle represents the frequencies of the ancestral or major allele (in purple) and the derived or minor allele (in blue). The different alleles and their position relative to the start of the mature miR are indicated in the right panels. Ancestral alleles identified by comparison with C. latens are marked with a thick line. SNPs located in a same miRNA are joined by a horizontal bar. (B) A 14-bp long deletion present in 22% of the population from Ontario removes the seed motif of the mature miR in miRNA block2890 and also alters the hairpin structure.
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evu239-F3: (A) SNP frequencies in mature miRs among populations of C. remanei. Most variants are found in a single population and at low frequency, with noticeable exceptions for instance for SNPs in mir-64a, mir-248, mir-787, block2892, and block3297. Columns represent separate populations and rows represent distinct SNPs. Each circle represents the frequencies of the ancestral or major allele (in purple) and the derived or minor allele (in blue). The different alleles and their position relative to the start of the mature miR are indicated in the right panels. Ancestral alleles identified by comparison with C. latens are marked with a thick line. SNPs located in a same miRNA are joined by a horizontal bar. (B) A 14-bp long deletion present in 22% of the population from Ontario removes the seed motif of the mature miR in miRNA block2890 and also alters the hairpin structure.

Mentions: We contrasted variation in mature miR sequence among C. remanei populations to explore the possibility that population-specific variants and differences in allele frequencies between populations could reflect local adaptation to different parts of the species range. Most of the SNPs in mature miRs are unique to a single population and occur at low frequency, indicative of ongoing species-wide purifying selection to eliminate new detrimental mutations. Of the 23 SNPs in miR sequence, however, six appeared in two or all three populations of C. remanei (fig. 3A). Moreover, eight miRNAs (block2890, block2892, block2981, block3297, mir-35i, mir-64a, mir-787, and mir-7606) have SNPs with minor allele frequency ≥25% in at least one population. For instance, the major allele in the Ohio population at position 22 in mir-787 is fixed in the population sample from Ontario, whereas the minor allele is fixed in the population sample from Germany (fig. 3A). Thus, despite the potential contribution to heterogeneity in gene regulation among individuals, most observed SNPs in the mature miRNA may have limited long-term impact on the evolution of gene regulation. And yet, our analysis also identifies candidate miRNAs that may be involved in differential gene expression among populations.Fig. 3.—


Microevolution of nematode miRNAs reveals diverse modes of selection.

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

(A) SNP frequencies in mature miRs among populations of C. remanei. Most variants are found in a single population and at low frequency, with noticeable exceptions for instance for SNPs in mir-64a, mir-248, mir-787, block2892, and block3297. Columns represent separate populations and rows represent distinct SNPs. Each circle represents the frequencies of the ancestral or major allele (in purple) and the derived or minor allele (in blue). The different alleles and their position relative to the start of the mature miR are indicated in the right panels. Ancestral alleles identified by comparison with C. latens are marked with a thick line. SNPs located in a same miRNA are joined by a horizontal bar. (B) A 14-bp long deletion present in 22% of the population from Ontario removes the seed motif of the mature miR in miRNA block2890 and also alters the hairpin structure.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evu239-F3: (A) SNP frequencies in mature miRs among populations of C. remanei. Most variants are found in a single population and at low frequency, with noticeable exceptions for instance for SNPs in mir-64a, mir-248, mir-787, block2892, and block3297. Columns represent separate populations and rows represent distinct SNPs. Each circle represents the frequencies of the ancestral or major allele (in purple) and the derived or minor allele (in blue). The different alleles and their position relative to the start of the mature miR are indicated in the right panels. Ancestral alleles identified by comparison with C. latens are marked with a thick line. SNPs located in a same miRNA are joined by a horizontal bar. (B) A 14-bp long deletion present in 22% of the population from Ontario removes the seed motif of the mature miR in miRNA block2890 and also alters the hairpin structure.
Mentions: We contrasted variation in mature miR sequence among C. remanei populations to explore the possibility that population-specific variants and differences in allele frequencies between populations could reflect local adaptation to different parts of the species range. Most of the SNPs in mature miRs are unique to a single population and occur at low frequency, indicative of ongoing species-wide purifying selection to eliminate new detrimental mutations. Of the 23 SNPs in miR sequence, however, six appeared in two or all three populations of C. remanei (fig. 3A). Moreover, eight miRNAs (block2890, block2892, block2981, block3297, mir-35i, mir-64a, mir-787, and mir-7606) have SNPs with minor allele frequency ≥25% in at least one population. For instance, the major allele in the Ohio population at position 22 in mir-787 is fixed in the population sample from Ontario, whereas the minor allele is fixed in the population sample from Germany (fig. 3A). Thus, despite the potential contribution to heterogeneity in gene regulation among individuals, most observed SNPs in the mature miRNA may have limited long-term impact on the evolution of gene regulation. And yet, our analysis also identifies candidate miRNAs that may be involved in differential gene expression among populations.Fig. 3.—

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