UNIVERSITA' DEGLI STUDI DI PADOVA ___________________________________________________________________ SCUOLA DI DOTTORATO DI RICERCA IN SCIENZE DELLE PRODUZIONI VEGETALI INDIRIZZO PROTEZIONE DELLE COLTURE - CICLO XXII Dipartimento Di Agronomia Ambientale e Produzioni Vegetali Genetics and genomics of pine processionary moths and their parasitoids Direttore della Scuola : Ch.mo Prof. Andrea Battisti Supervisore : Ch.mo Prof. Andrea Battisti Dottorando : Mauro Simonato DATA CONSEGNA TESI 01 febbraio 2010 Declaration I hereby declare that this submission is my own work and that, to the best of my knowledge and belief, it contains no material previously published or written by another person nor material which to a substantial extent has been accepted for the award of any other degree or diploma of the university or other institute of higher learning, except where due acknowledgment has been made in the text. February 1st, 2010 Mauro Simonato A copy of the thesis will be available at http://paduaresearch.cab.unipd.it/ Dichiarazione Con la presente affermo che questa tesi è frutto del mio lavoro e che, per quanto io ne sia a conoscenza, non contiene materiale precedentemente pubblicato o scritto da un'altra persona né materiale che è stato utilizzato per l’ottenimento di qualunque altro titolo o diploma dell'università o altro istituto di apprendimento, a eccezione del caso in cui ciò venga riconosciuto nel testo. 1 febbraio 2010 Mauro Simonato Una copia della tesi sarà disponibile presso http://paduaresearch.cab.unipd.it/ Table of contents Table of contents................................................................................................................ 5 Riassunto ........................................................................................................................... 9 Summary.......................................................................................................................... 11 Chapter 1 - Introduction .................................................................................................... 13 Objective and contents of the thesis .............................................................................. 21 References ....................................................................................................................... 22 Chapter 2 - Phylogeography of the pine processionary moth Thaumetopoea wilkinsoni in the Near East Introduction..................................................................................................................... 31 Materials and methods..................................................................................................... 32 Sampling and DNA protocols ....................................................................................... 32 Data analysis................................................................................................................. 33 Results ............................................................................................................................. 34 Mitochondrial DNA phylogeography............................................................................ 34 Comparison between mitochondrial and nuclear markers.............................................. 35 Discussion........................................................................................................................ 37 Mitochondrial phylogeographic patterns and female colonization routes....................... 37 Unexpected patterns of nuclear diversity, and sex-biased gene flow.............................. 38 References ....................................................................................................................... 39 Chapter 3 - Quaternary history and contemporary patterns in a currently expanding species Background ..................................................................................................................... 46 Results ............................................................................................................................. 48 Phylogenetic inference and node datation...................................................................... 48 Haplotype distribution and haplotype network .............................................................. 51 Discussion........................................................................................................................ 52 5 Overall phylogenetic patterns around the Mediterranean Basin......................................52 Phylogeographical patterns and within-clade structures.................................................53 Evolution of insular populations....................................................................................54 Contemporary patterns in a historical context................................................................54 Conclusion .......................................................................................................................55 Methods............................................................................................................................55 Moth sampling ..............................................................................................................55 DNA protocols..............................................................................................................55 Data analyses ................................................................................................................56 References........................................................................................................................57 Additional material...........................................................................................................59 The role of topography in structuring the demographic history of the pine processionary moth, Thaumetopoea pityocampa (Lepidoptera: Notodontidae)..................................66 Abstract.........................................................................................................................66 Chapter 4 - The complete mitochondrial genome of the bag-shelter moth Ochrogaster lunifer (Lepidoptera, Notodontidae) Background......................................................................................................................72 Results and discussion .....................................................................................................72 Genome organization, structure and composition ..........................................................72 Protein-coding genes.....................................................................................................74 Transfer and ribosomal RNA genes...............................................................................79 Non coding regions .......................................................................................................81 Conclusion .......................................................................................................................81 Methods............................................................................................................................83 Sample origin and DNA extraction................................................................................83 PCR amplification and sequencing of Ochrogaster lunifer mtDNA...............................83 Sequence assembly and annotation................................................................................83 Genomic analysis ..........................................................................................................83 Abbreviations................................................................................................................83 6 References ....................................................................................................................... 84 Chapter 5 - Testing host plant associated differentiation on two parthenogenetic parasitoid species feeding on the same insect host in a forest system Introduction..................................................................................................................... 89 Materials and methods..................................................................................................... 91 Sample collection ......................................................................................................... 91 DNA extraction and fingerprint analysis ....................................................................... 91 Assays for intracellular symbionts ................................................................................ 92 Data analysis................................................................................................................. 93 Results ............................................................................................................................. 94 Assays for intracellular symbionts ................................................................................ 94 Genetic data analysis .................................................................................................... 95 Discussion........................................................................................................................ 96 Tables and figures.......................................................................................................... 100 References ....................................................................................................................