POPULATION GENETICS (E LEWALLEN AND C BONIN, SECTION EDITORS) MicroRNA Applications in Marine Biology Carolina A. Bonin 1 & Andre J. van Wijnen 2 & Eric A. Lewallen 3 # Springer Nature Switzerland AG 2019 Abstract Purpose of Review MicroRNAs (miRNAs) are single-stranded, short (~ 22 nt) non-coding RNAs that control gene expression in most metazoan taxa. These vital post-transcriptional regulators are emerging as a novel class of relatively well-conserved biomarkers useful to molecular ecologists working on non-model marine organisms. The purpose of this review is to provide researchers with a brief background on miRNAs and to explore recent applications in marine biology. Recent Findings MiRNA datasets have been broadly employed in studies concerning commercially important species (oysters and crustaceans), phylogenetics (particularly deep evolutionary splits), and environmental stressor responses (temperature and salinity). Most progress has been made in the characterization of cnidarian miRNAs and bivalve and crustacean immune-related miRNAs. The use of miRNAs in phylogenetics is still under debate due to the secondary loss of miRNAs in some lineages, but they have been successfully applied in the resolution of deep evolutionary splits. Finally, miRNAs have been investigated in abiotic stress responses, but data interpretation is limited by the high number of species-specific miRNAs detected in these studies. Improvements in miRNA database curation and functional annotation should provide more confidence in their use. Summary Due to their evolutionary conservation, resilience to degradation, and amenable bioinformatics workflows, miRNAs are a powerful molecular tool in marine genomics. MiRNA investigations regarding environmental stress response will be particularly useful due to their potential to reveal physiological alterations and disease. Thus, they may be ultimately utilized as bio-indicators of environmental health. Keywords Marine invertebrates . Epigenetics . Ecological genomics . Phylogenomics . Epigenomics Introduction In the late 1990s, miRNAs were initially serendipitously dis- covered in studies on Caenorhabditis elegans genes lin-4 and let-7, which are involved in the timing of cellular events dur- ing development. These studies revealed that these genes did not produce typical mRNAs, but rather short non-coding RNAs [1, 2]. Both genes had complementary antisense base- paring within 3′ UTRs of mRNA targets. This finding generated the hypothesis that small non-coding RNA frag- ments were involved in repressing mRNA translation and therefore, the regulation of gene expression. Since their discovery, nearly three decades ago, it has be- come apparent that miRNAs are found in both the animal and plant kingdoms. They may have originated during a very an- cient evolutionary time (“RNA world”) when archaic primi- tive cells evolved using RNAs as the major biochemical and genetic molecules for sustaining biological replication of early life forms [3, 4]. Since the discovery of miRNAs, more than 2500 miRNAs have been identified in humans and > 250 oth- er species have annotated miRNAs [5]. Along with the expan- sion in miRNA identification, miRNAs’ pervasive role in reg- ulating gene expression has been confirmed: > 60% of human protein-coding genes are under selective pressure to maintain pairing to miRNAs [6]. Furthermore, it is apparent that the disruption or alteration of miRNA-mediated gene regulation is coupled with the pathology of well-characterized diseases [7]. Indeed, loss of function studies in mice attempting to disrupt specific miRNAs have yielded a plethora of physio- logic effects such as deafness, epilepsy, retinal degeneration, This article is part of the Topical Collection on Population Genetics * Carolina A. Bonin CAROLINA.LEWALLEN@HAMPTONU.EDU 1 Department of Marine and Environmental Sciences, Hampton University, Hampton, VA, USA 2 Department of Biochemistry & Molecular Biology and Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA 3 Department of Biological Sciences, Hampton University, Hampton, VA, USA Current Molecular Biology Reports https://doi.org/10.1007/s40610-019-00124-w