Journal
GENOME BIOLOGY AND EVOLUTION
Volume 10, Issue 6, Pages 1457-1470Publisher
OXFORD UNIV PRESS
DOI: 10.1093/gbe/evy096
Keywords
microRNAs; annotation; evolution; birth; death; phylogeny
Categories
Funding
- Irish Research Council for Science Engineering and Technology
- Engineering and Physical Sciences Research Council
- Australian Research Council [DE140101879]
- SE Norway Health Authority [2014041]
- National Aeronautics and Space Agency-Ames grant
- Wolfson Merit Award, Biological Sciences Research Council [BB/N000919/1]
- Natural Environment Research Council [NE/P013678/1, NE/N002067/1]
- Australian Research Council [DE140101879] Funding Source: Australian Research Council
- NERC [NE/P013678/1, NE/N002067/1] Funding Source: UKRI
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microRNAs are conserved noncoding regulatory factors implicated in diverse physiological and developmental processes in multi-cellular organisms, as causal macroevolutionary agents and for phylogeny inference. However, the conservation and phylogenetic utility of microRNAs has been questioned on evidence of pervasive loss. Here, we show that apparent widespread losses are, largely, an artefact of poorly sampled and annotated microRNAomes. Using a curated data set of animal microRNAomes, we reject the view that miRNA families are never lost, but they are rarely lost (92% are never lost). A small number of families account for a majority of losses (1.7% of families account for >45% losses), and losses are associated with lineages exhibiting phenotypic simplification. Phylogenetic analyses based on the presence/absence of microRNA families among animal lineages, and based on microRNA sequences among Osteichthyes, demonstrate the power of these small data sets in phylogenetic inference. Perceptions of widespread evolutionary loss of microRNA families are due to the uncritical use of public archives corrupted by spurious microRNA annotations, and failure to discriminate false absences that occur because of incomplete microRNAome annotation.
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