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      The Role of microRNAs in the Repeated Parallel Diversification of Lineages of Midas Cichlid Fish from Nicaragua

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          Abstract

          Cichlid fishes are an ideal model system for studying biological diversification because they provide textbook examples of rapid speciation. To date, there has been little focus on the role of gene regulation during cichlid speciation. However, in recent years, gene regulation has been recognized as a powerful force linking diversification in gene function to speciation. Here, we investigated the potential role of miRNA regulation in the diversification of six cichlid species of the Midas cichlid lineage ( Amphilophus spp.) inhabiting the Nicaraguan crater lakes. Using several genomic resources, we inferred 236 Midas miRNA genes that were used to predict the miRNA target sites on 8,232 Midas 3′-UTRs. Using population genomic calculations of SNP diversity, we found the miRNA genes to be more conserved than protein coding genes. In contrast to what has been observed in other cichlid fish, but similar to what has been typically found in other groups, we observed genomic signatures of purifying selection on the miRNA targets by comparing these sites with the less conserved nontarget portion of the 3′-UTRs. However, in one species pair that has putatively speciated sympatrically in crater Lake Apoyo, we recovered a different pattern of relaxed purifying selection and high genetic divergence at miRNA targets. Our results suggest that sequence evolution at miRNA binding sites could be a critical genomic mechanism contributing to the rapid phenotypic evolution of Midas cichlids.

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          A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data.

          Heng Li (2011)
          Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate genotypes may not be easily obtained (e.g. multi-sample low-coverage sequencing or somatic mutation discovery). These applications press for the development of new methods for analyzing sequence data with uncertainty. We present a statistical framework for calling SNPs, discovering somatic mutations, inferring population genetical parameters and performing association tests directly based on sequencing data without explicit genotyping or linkage-based imputation. On real data, we demonstrate that our method achieves comparable accuracy to alternative methods for estimating site allele count, for inferring allele frequency spectrum and for association mapping. We also highlight the necessity of using symmetric datasets for finding somatic mutations and confirm that for discovering rare events, mismapping is frequently the leading source of errors. http://samtools.sourceforge.net. hengli@broadinstitute.org.
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            MicroRNA profiling: approaches and considerations.

            MicroRNAs (miRNAs) are small RNAs that post-transcriptionally regulate the expression of thousands of genes in a broad range of organisms in both normal physiological contexts and in disease contexts. miRNA expression profiling is gaining popularity because miRNAs, as key regulators in gene expression networks, can influence many biological processes and also show promise as biomarkers for disease. Technological advances have spawned a multitude of platforms for miRNA profiling, and an understanding of the strengths and pitfalls of different approaches can aid in their effective use. Here, we review the major considerations for carrying out and interpreting results of miRNA-profiling studies.
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              MicroRNA Targets in Drosophila

              Additional data files Additional data file 1, 2, 3 and 4. Supplementary Material Additional data file 1 Additional data file 1 Click here for additional data file Additional data file 2 Additional data file 2 Click here for additional data file Additional data file 3 Additional data file 3 Click here for additional data file Additional data file 4 Additional data file 4 Click here for additional data file
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                Author and article information

                Journal
                Genome Biol Evol
                Genome Biol Evol
                gbe
                gbe
                Genome Biology and Evolution
                Oxford University Press
                1759-6653
                May 2016
                29 April 2016
                29 April 2016
                : 8
                : 5
                : 1543-1555
                Affiliations
                1Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
                2School of Earth Environmental & Biological Sciences, Queensland University of Technology, Brisbane, QLD, Australia
                Author notes

                Associate editor: Jay Storz

                *Corresponding author: E-mail: axel.meyer@ 123456uni-konstanz.de .
                Article
                evw097
                10.1093/gbe/evw097
                4898811
                27189980
                49b81522-d336-43c3-865d-4c30fb398763
                © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

                History
                : 24 April 2016
                Page count
                Pages: 13
                Categories
                Research Article

                Genetics
                mirna,gene regulation,neotropical cichlids,adaptation,sympatric speciation,purifying selection

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