Evolutionary Constraints to Viroid Evolution.docVIP

Viruses 2009, 1, 241-254; doi:10.3390/v1020241 OPEN ACCESS viruses ISSN 1999-4915 /journal/viruses Review Evolutionary Constraints to Viroid Evolution Santiago F. Elena 1,2,*, Gustavo Gómez 1 and José-Antonio Daròs 1 1 Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Campus UPV CPI access G, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain; E-Mails: ggomez@ibmcp.upv.es (G.G.); jadaros@ibmcp.upv.es (J.-A.D.) 2 The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA * Author to whom correspondence should be addressed; E-mail: sfelena@ibmcp.upv.es; Tel.: +34 963 877 895; Fax: +34 963 877 859. Received: 10 July 2009; in revised form: 27 August 2009 / Accepted: 27 August 2009 / Published: 2 September 2009 Abstract: We suggest that viroids are trapped into adaptive peaks as the result of adaptive constraints. The first one is imposed by the necessity to fold into packed structures to escape from RNA silencing. This creates antagonistic epistases, which make future adaptive trajectories contingent upon the first mutation and slow down the rate of adaptation. This second constraint can only be surpassed by increasing genetic redundancy or by recombination. Eigen’s paradox imposes a limit to the increase in genome complexity in the absence of mechanisms reducing mutation rate. Therefore, recombination appears as the only possible route to evolutionary innovation in viroids. Keywords: epistasis; evolutionary constraints; genome complexity; mutation rate; RNA folding; viroid evolution 1. Introduction Whether evolution is erratic due to historical contingencies or it is directed along similar paths by adaptive constraints is unclear. This is a very much discussed topic among evolutionary biologists that, of course, has relevance also for our understanding of viroid evolution and diversification into the two families including several genera that have been so far reco