Positive selection effects on the biochemical properties of fish pyroglutamylated RFamide peptide receptor (QRFPR)

References

• Amores A, Catchen J, Ferrara A, Fontenot Q, Postlethwait JH. 2011. Genome evolution and meiotic maps by massively parallel DNA sequencing: Spotted gar, an outgroup for the teleost genome duplication. Genetics 188:799–808.
   PubMed Web of Science ®Google Scholar
• Atchley WR, Zhao J, Fernandes AD, Drüke T. 2005. Solving the protein sequence metric problem. Proceedings of the National Academy of Science USA 102:6395–6400. doi:10.1073/pnas.0408677102.
   PubMed Web of Science ®Google Scholar
• Bakiu R. 2014. Calreticulin molecular evolution: A strong purifying and episodic diversifying selection result. Biologia 69:270–280. doi:10.2478/s11756-013-0327-7.
   Web of Science ®Google Scholar
• Balaji S, Aruna S, Srinivasan N. 2003. Tolerance to the substitution of buried apolar residues by charged residues in the homologous protein structures. Proteins 53:783–791. doi:10.1002/prot.v53:4.
   PubMed Web of Science ®Google Scholar
• Bamshad M, Wooding SP. 2003. Signatures of natural selection in the human genome. Nature Reviews Genetics 4:99–111. doi:10.1038/nrg999.
   PubMed Web of Science ®Google Scholar
• Braasch I, Guiguen Y, Loker R, Letawa JH, Ferrara A, Bobe J, Postlethwait JH. 2014. Connectivity of vertebrate genomes: Paired-related homeobox (Prrx) genes in spotted gar, basal teleosts, and tetrapods. Comparative Biochemistry and Physiology C 163:24–36.
   Web of Science ®Google Scholar
• Chartrel N, Alonzeau J, Alexandre D, Jeandel L, Alvear-Perez R, Leprince J, Boutin J, Vaudry H, Anouar Y, Llorens-Cortes C. 2011. The RFamide neuropeptide 26RFa and its role in the control of neuroendocrine functions. Frontiers in Neuroendocrinology 32:387–397. doi:10.1016/j.yfrne.2011.04.001.
   PubMed Web of Science ®Google Scholar
• Conant GC, Wagner GP, Stadler PF. 2007. Modeling amino acid substitution patterns in orthologous and paralogous genes. Molecular Phylogenetics and Evolution 42:298–307. doi:10.1016/j.ympev.2006.07.006.
   PubMed Web of Science ®Google Scholar
• Darriba D, Taboada GL, Doallo R, Posada D. 2011. ProtTest 3: Fast selection of best-fit models of protein evolution. Bioinformatics 27:1164–1165. doi:10.1093/bioinformatics/btr088.
   PubMed Web of Science ®Google Scholar
• Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: More models, new heuristics and parallel computing. Nature Methods 9:772.
   PubMed Web of Science ®Google Scholar
• Dunn KA, Jiang W, Field C, Bielawski JP. 2013. Improving evolutionary models for mitochondrial protein data with site-class specific amino acid exchangeability matrices. PLoS One 8:1e55816. doi:10.1371/journal.pone.0055816.
   Web of Science ®Google Scholar
• Fukusumi S, Yoshida H, Fujii R, Murayama M, Komatsu H, Habata Y, Shintani Y, Hinuma S, Fujino M. 2003. A new peptidic ligand and its receptor regulating adrenal function in rats. Journal of Biological Chemistry 278:46387–46395. doi:10.1074/jbc.M305270200.
   PubMed Web of Science ®Google Scholar
• Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Systematic Biology 59:307–321. doi:10.1093/sysbio/syq010.
   PubMed Web of Science ®Google Scholar
• Huelsenbeck JP, Larget B, Swofford D. 2000. A compound Poisson process for relaxing the molecular clock. Genetics 154:1879–1892.
   PubMed Web of Science ®Google Scholar
• Jiang Y, Luo L, Gustafson EL, Yadav D, Laverty M, Murgolo N, Vassileva G, Zeng M, Laz TM, Behan J, Qiu P, Wang L, Wang S, Bayne M, Greene J, Monsma F, Zhang FL. 2003. Identification and characterization of a novel RF-amide peptide ligand for orphan G-protein-coupled receptor SP9155. Journal of Biological Chemistry 278:27652–27657. doi:10.1074/jbc.M302945200.
   PubMed Web of Science ®Google Scholar
• Kosakovsky Pond SL, Frost SDV. 2005. Not so different after all: A comparison of methods for detecting amino acid sites under selection. Molecular Biology and Evolution 22:1208–1222. doi:10.1093/molbev/msi105.
   PubMed Web of Science ®Google Scholar
• Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SDW. 2006. Automated phylogenetic detection of recombination using a genetic algorithm. Molecular Biology and Evolution 23:1891–1901. doi:10.1080/10635150290102456.
   PubMed Web of Science ®Google Scholar
• Larhammar D, Xu B, Bergqvist CA. 2014. Unexpected multiplicity of QRFP receptors in early vertebrate evolution. Frontiers in Neuroscience 8:337. doi:10.3389/fnins.2014.00337. Oct 24; eCollection.
   PubMed Web of Science ®Google Scholar
• Lepage T, Bryant D, Philippe H, Lartillot N. 2007. A general comparison of relaxed molecular clock models. Molecular Biology and Evolution 24:2669–2680. doi:10.1093/molbev/msm193.
   PubMed Web of Science ®Google Scholar
• Leprince J, Neveu C, Lefranc B, Guilhaudis L, Milazzo-Segalas I, Do Rego JC, Tena-Sempere M, Tsutsui K, Vaudry H. 2013. 26RFa. In: Kastin AJ, editor. Handbook of biologically active peptides. 2nd ed. Amsterdam, The Netherlands: Elsevier. pp. 917–923.
   Google Scholar
• Messier W, Stewart CB. 1997. Episodic adaptive evolution of primate lysozymes. Nature 385:151–154. doi:10.1038/385151a0.
   PubMed Web of Science ®Google Scholar
• Murrell B, Wertheim JO, Moola S, Weighill T, Scheffler K. 2012. Detecting individual sites subject to episodic diversifying selection. PLoS Genetics 8:e1002764. doi:10.1371/journal.pgen.1002764.
   PubMed Web of Science ®Google Scholar
• Near TJ, Eytan RI, Dornburg A, Kuhn KL, Moore JA, Davis MP, Wainwright PC, Friedman M, Smith WL. 2012. Resolution of ray-finned fish phylogeny and timing of diversification. Proceedings of the National Academy of Science US 109:13698–13703. doi:10.1073/pnas.1206625109.
   PubMed Web of Science ®Google Scholar
• Notredame C, Higgins DG, Heringa J. 2000. T-Coffee: A novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology 302:205–217. doi:10.1006/jmbi.2000.4042.
   PubMed Web of Science ®Google Scholar
• Pond SL, Frost SD, Muse SV. 2005. HyPhy: Hypothesis testing using phylogenies. Bioinformatics 21:676–679. doi:10.1093/bioinformatics/bti079.
   PubMed Web of Science ®Google Scholar
• Price DA, Greenberg MJ. 1977. Structure of a molluscan cardioexcitatory neuropeptide. Science 197:670–671. doi:10.1126/science.877582.
   PubMed Web of Science ®Google Scholar
• Pyron RA. 2010. A likelihood method for assessing molecular divergence time estimates and the placement of fossil calibrations. Systematic Biology 59:185–194. doi:10.1093/sysbio/syp090.
   PubMed Web of Science ®Google Scholar
• Raffa RB. 1988. The action of FMRFamide (Phe-Met-Arg-Phe-NH2) and related peptides on mammals. Peptides 9:915–922. doi:10.1016/0196-9781(88)90141-6.
   PubMed Web of Science ®Google Scholar
• Ramanjaneya M, Karteris E, Chen J, Rucinski M, Ziolkowska A, Ahmed N, Kagerer S, Jöhren O, Lehnert H, Malendowicz LK. 2013. QRFP induces aldosterone production via PKC and T-type calcium channel-mediated pathways in human adrenocortical cells: Evidence for a novel role of GPR103. American Journal of Physiology-Endocrinology and Metabolism 305:E1049–E1058. doi:10.1152/ajpendo.00191.2013.
   PubMed Web of Science ®Google Scholar
• Rastogi RK, D’Aniello B, Pinelli C, Fiorentino M, Di Fiore MM, Di Meglio M, Iela L. 2001. FMRFamide in the amphibian brain: A comprehensive survey. Microscopy Research and Technique 54:158–172. doi:10.1002/jemt.1130.
   PubMed Web of Science ®Google Scholar
• Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, L L, Suchard MA, Huelsenbeck JP. 2012. MrBayes 3.2: Efficient bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61:539–542. doi:10.1093/sysbio/sys029.
   PubMed Web of Science ®Google Scholar
• Shan Y, Gras R. 2011. 43 genes support the lungfish-coelacanth grouping related to the closest living relative of tetrapods with the Bayesian method under the coalescence model. BMC Research Notes 4:49.
   PubMedGoogle Scholar
• Tamura K, Stecher G, Peterson D, Filipski A, Kumar S, Tamura K, Stecher G, Peterson D, Filipski A. 2013. MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution 30:2725–2729. doi:10.1093/molbev/mst197.
   PubMed Web of Science ®Google Scholar
• Thorne JL, Kishino H. 2002. Divergence time and evolutionary rate estimation with multilocus data. Systematic Biology 51:689–702. doi:10.1080/10635150290102456.
   PubMed Web of Science ®Google Scholar
• Tourasse NJ, Li WH. 2000. Selective constraints, amino acid composition, and the rate of protein evolution. Molecular Biology and Evolution 17:656–664.
   PubMed Web of Science ®Google Scholar
• Tsutsui K, Ukena K. 2006. Hypothalamic LPXRF-amide peptides in vertebrates: Identification, localization and hypophysiotropic activity. Peptides 27:1121–1129.
   PubMed Web of Science ®Google Scholar
• Ukena K, Osugi T, Leprince J, Vaudry H, Tsutsui K. 2014. Molecular evolution of GPCRs: 26Rfa/GPR103. Journal of Molecular Endocrinology 52:T119–131. doi:10.1530/JME-13-0207.
   PubMed Web of Science ®Google Scholar
• Ukena K, Tsutsui K. 2005. A new member of the hypothalamic RF-amide peptide family, LPXRF-amide peptides: Structure, localization, and function. Mass Spectrometry Reviews 24:469–486.
   PubMed Web of Science ®Google Scholar
• Walker RJ, Papaioannou S, Holden-Dye L. 2009. A review of FMRFamide- and RFamide-like peptides in metazoa. Invertebrate Neuroscience 9:111–153. doi:10.1007/s10158-010-0097-7.
   PubMed Web of Science ®Google Scholar
• Xie W, Lewis PO, Fan Y, Kuo L, Chen MH. 2011. Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Systematic Biology 60:150–160. doi:10.1093/sysbio/syq085.
   PubMed Web of Science ®Google Scholar