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Tion and Characterization of Novel Serine Proteases in the Bark Beetle Tomicus Yunnanensis

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Tion and Characterization of Novel Serine Proteases in the Bark Beetle Tomicus Yunnanensis D. Fco J. Sánchez García T E S I S D UNIVERSIDAD DE MURCIA O C FACULTAD DE BIOLOGÍA T O R A L Phylogeography, genomics and biosemiotics of bark beetles (Coleoptera: Scolytinae) Filogeografía, genómica y biosemiótica de escarabajos de corteza (Coleoptera: Scolytinae) 2015 D. Francisco Javier Sánchez García 2015 D. Fco J. Sánchez García T E S I S D UNIVERSIDAD DE MURCIA O C FACULTAD DE BIOLOGÍA T O R A L Phylogeography, genomics and biosemiotics of bark beetles (Coleoptera: Scolytinae) Filogeografía, genómica y biosemiótica de escarabajos de corteza (Coleoptera: Scolytinae) 2015 D. Francisco Javier Sánchez García 2015 Supervised by: José Galián Albaladejo Diego Gallego Cambronero Vilmar Machado 1 Table of contents 1 RESUMEN GENERAL.............................................................................................................1 1.1 INTRODUCIÓN............................................................................................................................................2 1.2 OBJECTIVOS..............................................................................................................................................4 1.3 METODOLOGÍA..........................................................................................................................................5 1.4 RESULTADOS.............................................................................................................................................6 2 INTRODUCTION....................................................................................................................10 2.1 TAXONOMY OF THE GENUS TOMICUS............................................................................................................11 2.1.1 Tomicus destruens....................................................................................................................13 2.1.2 Tomicus yunnanensis................................................................................................................14 2.2 SERINE PROTEASES...................................................................................................................................15 2.3 NON-CODING RNA TYPES AND FUNCTIONS...................................................................................................16 2.4 MICRORNAS.........................................................................................................................................17 2.5 NICHE THEORY AND MODELLING..................................................................................................................18 2.5.1 The importance of niche in the delimitation of intraspecific and interspecific entities............19 2.6 BIOSEMIOTICS.........................................................................................................................................19 2.7 REFERENCES...........................................................................................................................................21 3 PLANNING, OBJECTIVES AND HYPOTHESES.............................................................31 3.1 CHAPTER 1. DISTRIBUTION OF TOMICUS DESTRUENS (COLEOPTERA: SCOLYTINAE) MITOCHONDRIAL LINEAGES: PHYLOGEOGRAPHIC INSIGHTS AND NICHE MODELLING......................................................................................33 3.2 CHAPTER 2. IN SILICO PREDICTION AND CHARACTERIZATION OF MICRORNAS FROM THE BARK BEETLE TOMICUS YUNNANENSIS AND VALIDATION IN T. DESTRUENS (COLEOPTERA, SCOLYTINAE)..................................................33 3.3 CHAPTER 3. TRANSCRIPTOME ANALYSIS AND IN SILICO IDENTIFICATION AND CHARACTERIZATION OF SERINE PROTEASES IN THE BARK BEETLE TOMICUS YUNNANENSIS...................................................................................................34 3.4 CHAPTER 4. APPLYING ECO-FIELD AND THE GENERAL THEORY OF RESOURCES TO BARK BEETLES: BEYOND THE NICHE CONSTRUCTION THEORY..........................................................................................................................35 4 PLANTEAMIENTO HIPÓTESIS Y OBJETIVOS..............................................................37 4.1 CAPÍTULO 1. DISTRIBUCIÓN DE LINAJES MITOCONDRIALES DE TOMICUS DESTRUENS (COLEOPTERA: SCOLYTINAE): ENFOQUE FILOGEOGRÁFICO Y MODELADO DE NICHO........................................................................................39 4.2 CAPÍTULO 2. PREDICCIÓN IN SILICO Y CARACTERIZACIÓN DE MICRORNAS DEL ESCARABAJO DE CORTEZA TOMICUS YUNNANENSIS Y VALIDACIÓN EN T. DESTRUENS (COLEOPTERA, SCOLYTINAE).....................................................39 4.3 CAPÍTULO 3. ANÁLISIS IN SILICO DEL TRANSCRIPTOMA Y IDENTIFICACIÓN Y CARACTERIZACIÓN DE PROTEASAS DE SERINA EN EL ESCARABAJO DE LA CORTEZA TOMICUS YUNNANENSIS............................................................................40 4.4 CHAPTER 4. APPLYING ECO-FIELD AND THE GENERAL THEORY OF RESOURCES TO BARK BEETLES: BEYOND THE NICHE CONSTRUCTION THEORY..........................................................................................................................41 5 RESÚMENES...........................................................................................................................44 5.1 CAPÍTULO 1. DISTRIBUCIÓN DE LINAJES MITOCONDRIALES DE TOMICUS DESTRUENS (COLEOPTERA: SCOLYTINAE): ENFOQUE FILOGEOGRÁFICO Y MODELADO DE NICHO........................................................................................45 5.2 CAPÍTULO 2. PREDICCIÓN IN SILICO Y CARACTERIZACIÓN DE MICRORNAS DEL ESCARABAJO DE CORTEZA TOMICUS YUNNANENSIS Y VALIDACIÓN EN T. DESTRUENS (COLEOPTERA, SCOLYTINAE)......................................................47 5.3 CAPÍTULO 3. ANÁLISIS IN SILICO DEL TRANSCRIPTOMA Y IDENTIFICACIÓN Y CARACTERIZACIÓN DE PROTEASAS DE SERINA EN EL ESCARABAJO DE CORTEZA TOMICUS YUNNANENSIS..................................................................................49 5.4 CAPÍTULO 4. APLICANDO EL ECO-FIELD Y LA TEORÍA GENERAL DE RECURSOS A LOS ESCARABAJOS DE CORTEZA: MÁS ALLÁ DE LA TEORÍA DE LA CONSTRUCCIÓN DE NICHO...................................................................................51 6 CHAPTER 1..............................................................................................................................53 6.1 ABSTRACT..............................................................................................................................................55 6.2 INTRODUCTION........................................................................................................................................56 6.3 METHODS...............................................................................................................................................58 6.4 RESULTS.................................................................................................................................................63 6.5 DISCUSSION............................................................................................................................................72 7 CHAPTER 2..............................................................................................................................97 7.1 ABSTRACT..............................................................................................................................................99 7.2 INTRODUCTION........................................................................................................................................99 7.3 MATERIALS AND METHODS......................................................................................................................101 7.4 RESULTS...............................................................................................................................................105 7.5 DISCUSSION..........................................................................................................................................110 8 CHAPTER 3...........................................................................................................................121 8.1 ABSTRACT............................................................................................................................................124 8.2 INTRODUCTION......................................................................................................................................124 8.3 MATERIALS AND METHODS.......................................................................................................................126 8.4 RESULTS AND DISCUSSION.......................................................................................................................128 8.5 FINAL REMARKS.....................................................................................................................................137 9 CHAPTER 4............................................................................................................................145 9.1 ABSTRACT............................................................................................................................................147 9.2 INTRODUCTION......................................................................................................................................147 9.3 ECO-FIELD OF HOST SEARCH AND MATING IN BARK BEETLES. TRIADICS OF EAVESDROPPING EACH OTHER.................151 9.4 SEMIOTIC NICHE AND THE ROLE OF ECO-FIELD..............................................................................................156
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