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Ecological Determinants of Potyvirus Emergence in Wild Ecosystems

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Ecological Determinants of Potyvirus Emergence in Wild Ecosystems DEPARTAMENTO DE BIOTECNOLOGÍA-BIOLOGÍA VEGETAL ESCUELA TÉCNICA SUPERIOR DE INGENIERÍA AGRONÓMICA, ALIMENTARIA Y DE BIOSISTEMAS UNIVERSIDAD POLITÉCNICA DE MADRID ECOLOGICAL DETERMINANTS OF POTYVIRUS EMERGENCE IN WILD ECOSYSTEMS DOCTORAL THESIS CRISTINA RODRÍGUEZ NEVADO Master's Degree in Genetics and Cell Biology 2018 DEPARTAMENTO DE BIOTECNOLOGÍA-BIOLOGÍA VEGETAL ESCUELA TÉCNICA SUPERIOR DE INGENIERÍA AGRONÓMICA, ALIMENTARIA Y DE BIOSISTEMAS UNIVERSIDAD POLITÉCNICA DE MADRID ECOLOGICAL DETERMINANTS OF POTYVIRUS EMERGENCE IN WILD ECOSYSTEMS DOCTORAL THESIS CRISTINA RODRÍGUEZ NEVADO Master's Degree in Genetics and Cell Biology Supervisor: JESÚS ISRAEL PAGÁN MUÑOZ Universidad Politécnica de Madrid PhD Madrid, 2018 UNIVERESIDAD POLITÉCNICA DE MADRID Tribunal nombrado por el Magfco. y Excmo. Sr. Rector de la Universidad Politécnica de Madrid, el día de de 2018 Presidente: D/Dª Secretario: D/Dª Vocal: D/Dª Vocal: D/Dª Vocal: D/Dª Suplente: D/Dª Suplente: D/Dª Realizado el acto de defensa y lectura de Tesis el día de de 2018 En el Centro de Biotecnología y Genómica de Plantas, UPM-INIA. EL PRESIDENTE LOS VOCALES EL SECRETARIO AGRADECIMIENTOS Esta tesis ha sido realizada en el grupo Determinantes de Transmisión y Especiación de los Virus de Plantas dirigido por el Dr. Jesús Israel Pagán Muñoz perteneciente al Centro de Biotecnología y Genómica de Plantas UPM- INIA, (CBGP-UPM-INIA). Me gustaría expresar mi agradecimiento a las siguientes personas por su contribución en la elaboración del presente trabajo: Dr. Jesús Israel Pagán Muñoz por la dirección de este trabajo, por la búsqueda de las localizaciones en los ecosistemas estudiados y por su ayuda en los muestreos de campo. Además, quiero destacar su importante labor en mi formación científica y su valiosa dedicación a la planificación y supervisión de esta tesis. Dr. Fernando García-Arenal Rodríguez, por ampliar mi formación en virología y por haber facilitado los medios necesarios para la elaboración de este trabajo dentro de su grupo Interacción Planta-Virus y Co-evolución. Dra. Rosario G. Gavilán García (Universidad Complutense de Madrid, UCM) por la identificación de las plantas muestreadas en los ecosistemas de este estudio y por sus recomendaciones para realizar la caracterización ecológica de los mismos. Dr. Edward Holmes (The University of Sydney, Australia) por sus enseñanzas sobre los métodos filodinámicos y filogenéticos empleados en este trabajo, así como por concederme la oportunidad y los medios necesarios para desarrollar parte del mismo durante mi estancia en la Universidad de Sídney. Dras. Beatriz García Jiménez (Centro Nacional de Biotecnología, CNB) por su colaboración en el desarrollo de los análisis de Aprendizaje Automático y por sus explicaciones sobre la elaboración de los mismos y Nuria Montes Casado (Instituto de Investigación Sanitaria Hospital Universitario de La Princesa, Madrid) por su ayuda y colaboración en el desarrollo de los análisis de estadística multivariante. A Viji Vijayan por su asistencia en la purificación del virus MeRV, y a Marina García de Lomana, Alberto Cobos y Maria Luisa López Herranz por su excelente ayuda técnica sin la cual este trabajo no habría sido posible. Por último, quiero reconocer a la UPM por el apoyo económico recibido gracias a las “Ayudas para estancias breves en España y en el extranjero para los beneficiarios de los programas predoctorales oficiales de formación de investigadores”, según la Resolución del 26 de mayo de 2015 (Convocatoria 2015). Este trabajo ha sido financiado por una beca Marie Curie de Integración Profesional (“Marie Curie Career Integration Grant”, PCIG11-GA-2012-322100) (Años 2013-2016). Quisiera agradecer a Israel Pagán la oportunidad de formar parte de su grupo. Gracias por su inestimable ayuda, paciencia y la confianza depositada en mí para la realización de este trabajo. Gracias también por su valiosa orientación científica y personal durante estos años. Quiero agradecer también su ayuda y apoyo a todas las personas que forman o formaron parte del laboratorio. En especial a Nuria Montes y Livia Donaire por su acogida y atención desde que llegué, siempre dispuestas a ayudarme y transmitirme sus conocimientos. Os he echado de menos. A mi compañera en el grupo, Viji Vijayan por todo lo que hemos compartido juntas durante esta experiencia. A Miguel Ángel Mora y Antolín López por sus ocurrencias, que nos hacen pasar ratos tan divertidos. También quiero agradecer a las Dras. Aurora Fraile, Soledad Sacristán y María Ángeles Ayllón por sus útiles consejos y contribuciones en las dudas científicas durante este trabajo. Quisiera dar las gracias también a Marisa López por su siempre eficiente ayuda técnica en los últimos meses. A todos, mi más sincero agradecimiento. Gracias a todos los estudiantes que me han ayudado en los muestreos de campo y en el laboratorio por su dedicación, entusiasmo y simpatía, en especial a Alberto y Marina, por los buenos ratos en el campo y las interesantes conversaciones entre extracto y extracto que me animaban el día. También quisiera agradecer su ayuda a todos los compañeros de las antípodas. Todos ellos hicieron que, a pesar de la gran distancia, me sintiera como en casa y que mi estancia fuera una experiencia magnífica. Gracias a mis amigos por su comprensión y buenos consejos. En especial, gracias a David, por todo su apoyo y ánimos en los momentos de incertidumbre. Gracias por las sonrisas, la energía positiva y la fuerza que me contagias cada día. Y, sobre todo, gracias a mi familia. A mi abuela, que me pudo acompañar hasta el principio de esta etapa, por su infinito cariño, y a mis padres, por su afecto y la ayuda que siempre he recibido de ellos antes y después de volar del nido. Por vuestro apoyo incondicional, muchísimas gracias. INDEX INDEX ........................................................................................................................... I RESUMEN .................................................................................................................... V ABSTRACT ................................................................................................................. XI 1. INTRODUCTION .................................................................................................... 15 1.1. Importance of plant viruses ........................................................................... 17 1.2. Ecological factors driving emergence of plant viruses ............................... 19 1.2.1. Biotic factors ............................................................................................... 20 1.2.1.1. Species biodiversity ............................................................................... 20 1.2.1.2. Community composition ......................................................................... 22 1.2.1.3. Host density and biomass ...................................................................... 23 1.2.1.4. Pathogen host range .............................................................................. 24 1.2.2. Abiotic factors ................................................................................................ 26 1.2.2.1. Effect of abiotic factors on host physiology .............................................. 26 1.2.2.2. Effect of abiotic factors on the vector population ...................................... 27 1.3. Genetic diversity of plant virus populations ................................................ 28 1.3.1. Generation of genetic diversity in plant virus populations ............................ 28 1.3.1.1. Mutation ................................................................................................. 29 1.3.1.2. Recombination ....................................................................................... 30 1.3.1.3. Processes that Shape the Genetic Diversity of Plant Virus Populations . 30 1.3.2. Ecological factors affecting virus population genetic diversity ..................... 32 1.3.3. Virus emergence and speciation ................................................................. 33 1.4. Wild ecosystems in the Iberian Peninsula .................................................... 34 1.4.1. Riparian forest ............................................................................................ 37 1.4.2. Evergreen oak forest .................................................................................. 39 1.5. The genus Potyvirus ...................................................................................... 41 1.5.1 Molecular biology ......................................................................................... 41 1.5.2. Ecology, epidemiology and disease control ................................................ 44 1.5.3. Genetic diversity and evolution ................................................................... 47 2. OBJECTIVES ......................................................................................................... 49 3. MATERIALS AND METHODS................................................................................ 53 3.1. Plant sampling and data collection in wild ecosystems .............................. 55 3.1.1. Description of sampling locations ................................................................ 55 3.1.2. Plant sampling design ................................................................................. 56 I 3.1.3. Monitoring and estimation of ecological factors ........................................... 57 3.1.4. Analysis of the sampling effort ...................................................................
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