Cytogenetic and molecular characterization of lacertid lizard species from the Iberian Peninsula Verónica Rojo Oróns Doctoral Thesis 2015 Supervisors: Dr Horacio Naveira Fachal, Dr Andrés Martínez Lage Department of Cell and Molecular Biology D. HORACIO NAVEIRA FACHAL, DOCTOR EN BIOLOGÍA Y CATEDRÁTICO DE UNIVERSIDAD DEL ÁREA DE GENÉTICA DEL DEPARTAMENTO DE BIOLOGÍA CELULAR Y MOLECULAR DE LA UNIVERSIDADE DA CORUÑA, Y D. ANDRÉS MARTÍNEZ LAGE, DOCTOR EN BIOLOGÍA Y PROFESOR TITULAR DE UNIVERSIDAD EN EL ÁREA DE GENÉTICA DEL DEPARTAMENTO DE BIOLOGÍA CELULAR Y MOLECULAR DE LA UNIVERSIDADE DA CORUÑA, INFORMAN QUE el trabajo titulado "Cytogenetic and molecular characterization of lacertid lizard species from the Iberian Peninsula", presentado por Dña. VERÓNICA ROJO ORÓNS para optar al título de Doctora en Biología con Mención Internacional por la Universidade da Coruña, ha sido realizado bajo nuestra dirección. Considerándolo finalizado, autorizamos su presentación y defensa. A CORUÑA, A 22 DE SEPTIEMBRE DE 2015 Fdo. Dr. Horacio Naveira Fachal Fdo. Dr. Andrés Martínez Lage Fdo. Verónica Rojo Oróns To my dear Rodri To my granny Acknowledgements Firstly, I would like to thank my supervisors, Horacio Naveira and Andrés Martínez, for trusting me and for the opportunity to work on such an interesting project. Thank you for your patient, guidance, and for sharing your knowledge and experience with me! Many thanks to Ana González and Pedro Galán for their significant contributions to this research. Ana, thanks for your friendship and all your support in scientific and non-scientific questions. Pedro, thank you for collecting all the specimens for this thesis, and for your invaluable wealth of knowledge about lacertids. I am very grateful to all the people who generously hosted me during my fruitful internships abroad: Ettore Olmo, Vincenzo Caputo Barucchi, Massimo Giovannotti, Paola Nisi Cerioni, Andrea Splendiani and Paolo Ruggeri, at the Universitá Politecnica delle Marche (Ancona); Malcolm Ferguson-Smith, Jorge Pereira, Fumio Kasai and Willem Rens, at the University of Cambridge. These research internships have been an exciting learning experience, and essential for the completion of this thesis. My special thanks to Massimo, for his infinite patient to show me the tips and tricks of cell cultures and FISH. Thank you for your support and valuable advice over all these years. Thanks also to Adriana Canapa and Marco Barucca for their warm welcome, and to Çinel, Bruna, Sara and Sabrina, for our good moments in Ancona. Back to Coruña, thanks to my colleagues at the Evolutionary Biology Group and, especially, to my wonderful lab partners (past, present, and newcomers): Álex, David, Joaquín, Rosa, my Panoquita, Elba, Neus, Nuria, Luis, Iván, Inés, Eva...I’ve been really lucky to work with you! Thank you very much for the many good times we enjoyed (and I’m sure we will still enjoy) in and outside the lab. Many thanks to Rosa García Díaz and her magic hands, for their brilliant technical skills, and to Nani, Raquel, and Miriam, from the University Research Support Services, for their willing assistance on DNA sequencing. I would also like to thank the great AllGenetics team and, especially, Joaquín, Álex and Antón, for giving me the opportunity to work and learn from them. To my friends (you know who you are), for being always there and for helping me forget about everything when I needed it. And, of course, for your interest in this lizards’ "thing"! I am forever grateful to my amazing family. To Rosa, Pedro, and Lucas, for their energizing support throughout this odyssey, and for bringing back happiness into our lives. To Rubén; thank you for your incredible patient and understanding, and for always making me end the day with a smile. To Cris, for sharing with me a bit of her talent and making this beautiful cover design. And, especially, to my parents, for their unconditional love, encouragement and support. This thesis, and everything I achieved, is thanks to you. Finally, I wish to thank the thesis committee and the external reviewers who read and commented the draft of this thesis report. I was supported by a FPU (Formación de Profesorado Universitario) grant, from the Spanish Ministry of Education, Culture and Sport, and by a Research Internship Grant, from the Universidade da Coruña. Contents Abbreviations v Short abstracts ix Extended abstract (in Spanish) xiii Introduction 1 1. Reptilian karyotype evolution 3 1.1 Chromosome numbers and karyotypic structure 3 1.2 Conservation of chromosomal synteny 5 2. The evolution of sex-determining mechanisms in reptiles 7 2.1 The evolution of sex chromosomes 8 2.1.1 Long-term preservation of homomorphic sex chromosomes 10 2.2 Sex chromosomes in reptiles 11 2.3 Multiple origins of reptilian sex chromosomes 16 2.4 Turnover of sex chromosomes vs. the evolutionary trap hypothesis 17 3. Satellite DNA: features and evolution 20 4. The study species 22 4.1 The family Lacertidae 22 4.2 The genus Iberolacerta 23 5. References 27 Aims and objectives 45 Chapter I: Karyological characterization of the endemic Iberian rock lizard, Iberolacerta monticola (Squamata, Lacertidae): insights into sex chromosome 49 evolution Chapter II: Comparative chromosome painting in lacertid lizards: 81 highly conserved karyotypes but independent origins of sex chromosomes? Chapter III: Evolutionary dynamics of two satellite DNA families in Rock lizards of the genus Iberolacerta (Squamata, Lacertidae): different histories but 127 common traits Conclusions 173 Annexes 177 Annex I: Karyological characterization of the endemic Iberian rock lizard, 179 Iberolacerta monticola (Squamata, Lacertidae): insights into sex chromosome evolution. Cytogenetic and Genome Research 2014; 142: 28–39 Annex II: Isolation and characterization of two satellite DNAs in some 193 Iberian rock lizards (Squamata, Lacertidae). Journal of Experimental Zoology Part B Molecular and Developmental Evolution 2014; 322B: 13–26. Annex III: Evolutionary dynamics of two satellite DNA families in Rock 209 lizards of the genus Iberolacerta (Squamata, Lacertidae): different histories but common traits. Chromosome Research (in press) Abbreviations 2n Diploid chromosome number 4xT 4x SSC, 0.05% Tween-20 μL Microlitre μm Micromolar ºC Degree Celsius Nucleotide diversity ACSL1 Acyl-CoA synthetase long-chain family member 1 ADAM12 ADAM Metallopeptidase Domain 12 Ag-staining Silver-staining ATP2A2 ATPase, Ca++ transporting, cardiac muscle, slow twitch 2 ATP5A1 ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle BLAST Basic Local Alignment Search Tool C19orf47 Chromosome 19 open reading frame 47 CCD Charge coupled device CDH8 Cadherin 8, type 2 CGH Comparative genomic hybridization CMA3 Chromomycin A3 COL5A1 Collagen, type V, alpha 1 Cy3 Cyanine 3 DAPI 4′,6-Diamidino-2-phenylindole DDBJ DNA DataBank of Japan DMRT1 Doublesex and mab-3 related transcription factor 1 DNA Deoxyribonucleic acid DNase Deoxyribonuclease dNTP Deoxynucleotide triphosphate v DOP-PCR Degenerate oligonucleotide primer–polymerase chain reaction dUTP 2'-Deoxyuridine 5'-triphosphate EEF2 Eukaryotic elongation factor 2 EMBL European Molecular Biology Laboratory ESD Environmental sex determination FBXW11 F-Box And WD Repeat Domain Containing 11 FCA Factorial correspondence analysis FISH Fluorescence in situ hybridization FITC Fluorescein Iso-Thyocianate g Relative centrifugal force (RCF) GMPPA GDP-mannose pyrophosphorylase A GSD Genotypic sex determination h Hour HEPES 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid iCGH Interspecies comparative genomic hybridization IgG Immunoglobulin G IPO5 Importin 5 ITS Interstitial telomeric site IUPAC International Union of Pure and Applied Chemistry KCl Potassium chloride LLitre MMolar mg Milligram MgCl2 Magnesium Chloride min Minute mL Millilitre mM Millimolar vi mmol Millimol mya Million years ago MYST2 MYST histone acetyltransferase 2 myr Million years NaCl Sodium Chloride ng Nanogram NCBI National Center for Biotechnology Information NOR Nucleolar organizing region OAF Out at first homolog OCA2 Oculocutaneous Albinism II OSGIN1 Oxidative stress induced growth inhibitor 1 PCR Polymerase chain reaction PIK3CD Phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta RAD-seq Restriction size-associated DNA sequencing RNase Ribonuclease RNF19B Ring finger protein 19B rRNA Ribosomal ribonucleic acid s Second satDNA Satellite DNA SBNO1 Strawberry notch homolog 1 (Drosophila) SH3PXD2A SH3 And PX Domains 2A SKIL SKI-Like Proto-Oncogene SNP Single nucleotide polymorphism SOX5 (Sex determining region Y)-box 5 SS18 Synovial sarcoma translocation, chromosome 18 SSC Saline sodium citrate TKT Transketolase vii TOP2A Topoisomerase (DNA) II alpha TRIM37 Tripartite motif containing 37 Tris Tris(hydroxymethyl)aminomethane TRITC Tetramethylrhodamine TSD Temperature-dependent sex determination UV Ultraviolet WAC WW domain containing adaptor with coiled-coil WDR43 WD Repeat Domain 43 WT1 Wilms Tumor 1 ZNF326 Zinc Finger Protein 326 viii SHORT ABSTRACTS Abstract Reptiles, with their great diversity of sex-determining systems, have long been regarded as a model group for studying the evolution of sex determination and sex chromosomes. They also hold a key phylogenetic position to elucidate the organization and evolution of amniote genomes. This PhD thesis aims to contribute to this understanding by investigating sex chromosomes and karyotype evolution in lacertid lizards, with a focus on rock lizard species (genus Iberolacerta)