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Population Genetic Analysis and Characterization of Nuclear Gene Regions and Mitogenomes in Four European "Donax"Speci

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Population Genetic Analysis and Characterization of Nuclear Gene Regions and Mitogenomes in Four European Population genetic analysis and characterization of nuclear gene regions and mitogenomes in four European Donax species Doctoral Thesis 2018 Jenyfer Fernández Pérez Population genetic analysis and characterization of nuclear gene regions and mitogenomes in four European Donax species Jenyfer Fernández Pérez Doctoral Thesis 2018 Directora/Tutora: Josefina Méndez Felpeto Programa Oficial de Doctorado en Biología Celular y Molecular This is a work distributed under the terms of the Creative Commons Attibution- NonCommercial-NoDerivates 4.0 International (CC BY-NC-ND 4.0) License. To see a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/4.0/ You are free to: Share – copy and redistribute the material in any medium or format. The licensor cannot revoke these freedoms as long as you follow the license terms. Under the following terms: Attribution – You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggest the licensor endorses you or your use. NonCommercial – You may not use the material for commercial purposes. NonDerivatives – If you remix, transform, or build upon the material, you may not distribute the modified material. No additional restrictions – You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. Population genetic analysis and characterization of nuclear gene regions and mitogenomes in four European Donax species DEPARTAMENTO DE BIOLOGÍA Memoria que para optar al Título de Doctora con Mención Internacional presenta Jenyfer Fernández Pérez 2018 Directora: Dra. Josefina Méndez Felpeto Financiación de la investigación La realización de esta tesis ha sido posible gracias a la financiación obtenida a través del proyecto “Contribución genética para la recuperación de los bancos naturales de coquina (Donax spp.) en Galicia”, dirigido por la Dra. Josefina Méndez Felpeto y concedido por el Ministerio de Economía, Industria y Competitividad del Gobierno de España (AGL2016-75288-R). La autora de este trabajo ha disfrutado de un contrato temporal con cargo a dicho proyecto (marzo 2017 – julio 2018). Estancias Parte del trabajo ha sido realizado en: – Interdisciplinary Centre of Marine and Environmental Research (CIIMAR) (Universidade do Porto, Portugal) durante una estancia de tres meses en el año 2016, dentro del programa de “Axudas para estadías predoutorais INDITEX-UDC 2016”, y bajo la supervisión de la Dra. Elsa Froufe. – Departamento de Genética de la Universidad de Granada durante una breve estancia en el año 2016, bajo la supervisión del Dr. Juan Pedro Martínez Camacho. Publicaciones Por el momento, parte de este trabajo ha sido publicado en forma de cuatro artículos científicos y dos capítulos de libro: – Fernández-Pérez, J., Nantón, A., Méndez, J., 2018. An alternative method for rapid and specific authentication of four European Donax species, including D. trunculus, a commercially- important bivalve. Eur Food Res. Technol. DOI: 10.1007/s00217-018-3093-5 – Fernández-Pérez, J., Nantón, A., Arias-Pérez, A., Freire, R., Martínez-Patiño, D., Méndez, J., 2018. Mitochondrial DNA analyses of Donax trunculus (Mollusca: Bivalvia) population structure in the Iberian Peninsula, a bivalve with high commercial importance. Aquatic Conserv.: Mar. Freshw. Ecosyst. DOI: 10.1002/aqc.2929 – Fernández-Pérez, J., Nantón, A., Ruiz-Ruano, F.J., Camacho, J.P.M., Méndez, J., 2017. First complete female mitochondrial genome in four bivalve species genus Donax and their relationships within the Veneroida order. PLoS ONE. 19(9),e0184464. – Fernández-Pérez, J., Froufe, E., Nantón, A., Gaspar, M.B., Méndez, J., 2017. Genetic diversity and population genetic analysis of Donax vittatus (Mollusca: Bivalvia) and phylogeny of the genus with mitochondrial and nuclear markers. Estuar. Coast. Shelf Sci. 197,126- 135. – Fernández-Pérez, J., Nantón, A., Rodríguez, L., Febrero, F., Nóvoa, S., Ojea, J., Martínez- Patiño, D., Méndez, J., 2016. Evaluación genética de la coquina Donax trunculus en tres localidades gallegas mediante el marcador mitocondrial 16S. En: Foro Rec. Mar. Ac. Rías Gal. Rey-Méndez, M., Fernández Casal, J., Lodeiros, C., Guerra, A. (eds) 18,233-241. ISBN: 978- 84-608-7689-2. – Nantón, A., Fernández-Pérez, J., Arias-Pérez, A., Freire, R., Méndez, J., 2015. Estudio de la diversidad genética y estructura poblacional de la coquina Donax trunculus de la Península Ibérica mediante marcadores de ADN mitocondrial. En: Foro Rec. Mar. Ac. Rías Gal. Rey- Méndez, M., Fernández Casal, J., Lodeiros, C., Guerra, A. (eds) 17,163-172. ISBN: 978-84- 606-7810-6. A mis padres y a mi hermano A Adrián Agradecimientos En primer lugar, me gustaría mostrar mi agradecimiento más sincero a la Dra. Josefina Méndez Felpeto, por darme la gran oportunidad de formar parte de su equipo y haberme permitido realizar este trabajo. Gracias también por permitirme trabajar en un marco de confianza y libertad fundamentales para la realización de este trabajo y para mi formación profesional, por inculcarme siempre un espíritu ganador, por su tiempo y por compartir conmigo su conocimiento y experiencia. A la Dra. Elsa Froufe por acogerme durante mi estancia en el Interdisciplinary Centre of Marine and Environmental Research (CIIMAR) de la Universidade do Porto (Portugal). Gran parte de este trabajo se debe a ella. Gracias también a todos mis compañeros por el cariño y el buen trato recibido, en especial a André, Cláudia, David y Vanessa. De todos vosotros no sólo he ganado conocimiento, sino valores y vivencias que siempre me acompañarán y me harán recordaros con gran cariño. Al Dr. Juan Pedro Martínez Camacho por abrirme las puertas de su laboratorio, así como por su disposición y amabilidad en todo momento. Gracias también a Paquillo por ser mi consejero y maestro del apasionante mundo de la NGS y, sobre todo, por su disposición y paciencia desde el primer momento. Vuestra colaboración ha sido esencial para el desarrollo de parte de esta Tesis. También quiero agradecer a todos los participantes de los muestreos, tanto de la Xunta de Galicia como del Instituto Português do Mar e da Atmosfera de Portugal, que hicieron posible la obtención de una parte importante de los ejemplares empleados en este trabajo. La mitad de esta tesis no hubiera sido posible sin la colaboración de Miguel Gaspar, Susana y Tea, gracias por el valiosísimo material. Una especial mención a Alberto y Ruth, por su colaboración en parte de este trabajo y por estar siempre dispuestos a ayudarme. Gracias a todos mis compañeros de Genética, tanto a los que se mudaron al CICA, como a los que continúan. En especial quisiera agradecer a Ana, por ser mi madrina de poyata y la guía de mis primeros pasos en el laboratorio, por enseñarme todo sobre la coquina, por su amistad y por su infinita paciencia y perseverancia. A Anita, por su apoyo y por sus valiosas sugerencias. A Luisa, por su ayuda desinteresada, por todas las correcciones de esta tesis, por sus acertados consejos, su constante ánimo y, sobre todo, por contagiarnos a todos con su buen humor. A Rosa, por su inestimable ayuda. A Vero, por preguntarme siempre por cómo me va y por los ánimos brindados en esta última etapa. A Zeltia, por su ánimo y simpatía. Muchas gracias por los buenos momentos compartidos, especialmente por vuestra motivación, apoyo y ayuda prestada en esta etapa final. Resulta fácil sacar un proyecto adelante cuando tu entorno se compone de personas como vosotras. Gracias también a Noe, a la que no sólo se debe el diseño de la portada de este trabajo, si no también muchos buenos momentos vividos en A Coruña. A mis amigos y familia por interesarse siempre por mi trabajo y por su constante ánimo. A Adrián por recordarme que las metas están para ser alcanzadas, por mantenerme con ánimos, por estar siempre pendiente de mí y por hacer que esta etapa fuese más fácil a su lado. Gracias a mi hermano por su apoyo incondicional durante el transcurso de todos estos años y por estar siempre ahí cuando necesitaba un consejo o unas palabras de ánimo. Él es la persona que me hace mirar hacia adelante sin miedo a nada. Finalmente, quisiera agradecer de una manera muy especial a mis padres, a quienes les debo todo. Ellos han sido los promotores de mis sueños y los que han permitido que se hagan realidad. A ellos les dedico esta tesis en reconocimiento a todos los esfuerzos y sacrificios que han hecho por mí. Gracias por todo lo que me habéis enseñado a lo largo de la vida. Quisiera también dejar escrita la dedicatoria de este trabajo a tres personas muy especiales que quise y quiero con toda mi alma, y que me mostraron en su propio ejemplo lo que significa ser una gran persona, Abuelita, Josefa y Miguel. Muchas gracias. Table of contents Table of Contents Table of Contents ….………………………………...……………………………………… 1 Abbreviations and symbols ………………………………………………………………… 5 List of tables and figures …………………………………………………………………… 13 Short abstracts ……………………………………………………………………………… 23 Abstract …………………………………………………………………………………. 25 Resumen ………………………………………………………………………………… 25 Resumo …………………………………………………………………………………. 26 Extended abstract (Spanish) ………………………………………………………………. 27 Introduction ………………………………………………………………………………… 41 Biology of the genus Donax …………………………………………………………….. 43 Importance of Donax species ……………………………………………………………. 45 Genetic studies in European Donax clams ………………………………………………. 48 Genetics aspects of the conservation and management of fishery resources ………...…..
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