Data from: The phylogenetic utility and functional constraint of microRNA flanking sequences

MicroRNAs (miRNAs) have recently risen to prominence as novel factors
responsible for post-transcriptional regulation of gene expression. miRNA
genes have been posited as highly conserved in the clades in which they
exist. Consequently, miRNAs have been used as rare genome change
characters to estimate phylogeny by tracking their gain and loss. However,
their short length (21–23 bp) has limited their perceived utility in
sequenced-based phylogenetic inference. Here, using reference taxa with
established phylogenetic relationships, we demonstrate that miRNA
sequences are of high utility in quantitative, rather than in qualitative,
phylogenetic analysis. The clear orthology among miRNA genes from
different species makes it straightforward to identify and align these
sequences from even fragmentary datasets. We also identify significant
sequence conservation in the regions directly flanking miRNA genes, and
show that this too is of utility in phylogenetic analysis, as well as
highlighting conserved regions that will be of interest to other fields.
Employing miRNA sequences from 12 sequenced drosophilid genomes, together
with a Tribolium castaneum outgroup, we demonstrate that this approach is
robust using Bayesian and maximum-likelihood methods. The utility of these
characters is further demonstrated in the rhabditid nematodes and
primates. As next-generation sequencing makes it more cost-effective to
sequence genomes and small RNA libraries, this methodology provides an
alternative data source for phylogenetic analysis. The approach allows
rapid resolution of relationships between both closely related and rapidly
evolving species, and provides an additional tool for investigation of
relationships within the tree of life.