UNIVERSITÀ POLITECNICA DELLE MARCHE DIPARTIMENTO SCIENZE DELLA VITA E DELL’AMBIENTE XXIX ciclo Corso di Dottorato in SCIENZE DELLA VITA E DELL’AMBIENTE Curriculum Biologia ed Ecologia Marina GENETIC DIVERSITY AND STOCK STRUCTURE IN TELEOSTS OF INTEREST TO FISHERIES Dottoranda: Tutor: Dr. Tatiana Fioravanti Chiar.mo Prof. Vincenzo Caputo Barucchi A.A. 2013/2016 CONTENTS THESIS OBJECTIVES ........................................................................................................... 1 INTRODUCTION ................................................................................................................... 3 Stock definition and identification ....................................................................................... 4 Genetic markers ................................................................................................................... 6 Genetic variations and stock management ....................................................................... 10 Usefulness of ancient and historical DNA studies ............................................................. 14 Target species of this PhD work ......................................................................................... 18 Aphia minuta .................................................................................................................. 18 Engraulis encrasicolus ................................................................................................... 21 Salmo trutta complex ..................................................................................................... 25 References ......................................................................................................................... 31 CHAPTER I ........................................................................................................................... 49 Evidences for the role of demography, selective pressure and hydrographic boundaries in shaping the genetic structure of the transparent goby, Aphia minuta , Risso 1820. ......... 50 Abstract .......................................................................................................................... 50 Introduction .................................................................................................................... 51 Materials and Methods ................................................................................................... 54 Results ............................................................................................................................ 59 Discussion ...................................................................................................................... 62 Figures and Tables ......................................................................................................... 69 References ...................................................................................................................... 73 CHAPTER II .......................................................................................................................... 84 Biocomplexity in Populations of European Anchovy in the Adriatic Sea ........................... 85 Abstract .......................................................................................................................... 85 Introduction .................................................................................................................... 85 Materials and Methods ................................................................................................... 88 Results ............................................................................................................................ 96 Discussion .................................................................................................................... 101 Figures and Tables ....................................................................................................... 110 References .................................................................................................................... 117 CHAPTER III ...................................................................................................................... 129 Coupling Demographic and Genetic Variability from Archived Collections of European Anchovy ( Engraulis encrasicolus ) ..................................................................................... 130 Abstract ........................................................................................................................ 130 Introduction .................................................................................................................. 130 Materials and Methods ................................................................................................. 133 Results .......................................................................................................................... 141 Discussion .................................................................................................................... 145 Figures and Tables ....................................................................................................... 151 References .................................................................................................................... 157 CHAPTER IV ...................................................................................................................... 167 The Effects of Paleoclimatic Events on Mediterranean Trout: Preliminary Evidences from Ancient DNA ..................................................................................................................... 168 Abstract ........................................................................................................................ 168 Introduction .................................................................................................................. 168 Materials and Methods ................................................................................................. 172 Results .......................................................................................................................... 176 Discussion .................................................................................................................... 178 Figures and Tables ....................................................................................................... 183 References .................................................................................................................... 189 APPENDIX .......................................................................................................................... 197 Supplementary materials CHAPTER I ............................................................................... 198 Supplementary materials CHAPTER II .............................................................................. 201 Supplementary materials CHAPTER III ............................................................................. 231 Supplementary materials CHAPTER IV ............................................................................. 239 LIST OF PAPERS PUBLISHED ........................................................................................ 243 Other papers at which I have collaborated during my PhD: ................................................ 244 THESIS OBJECTIVES The “ Food and Health Organization ” of the United Nations (FAO 2016) has showed that the global amount of fish capture in 2014 was 93 million tonnes, of which 81.5 million tonnes from marine fisheries and 11.9 million tonnes from inland fisheries. FAO (2016) has also reported that 31.4% of fish stocks are exploited at a biological unsustainable level and can be considered overfished. In addition, the collapse of marine species due to high fishing efforts can be also influenced by life history traits and climate variability (Pinsky & Byler 2015). The effects of climate changes severely affect freshwater biodiversity (Sala et al. 2000). In fact freshwater fishes are negatively impacted especially by high temperature, low levels of oxygen dissolved and modification in water flow (Ficke et al. 2007), which will lead to a drastic reduction in freshwater fish species in the next years (Xenopolous et al. 2005). The acquisition of information on the current genetic population structure and on how the genetic diversity has changed across time as results of overexploitation and/or environmental changes can be useful to develop new management and conservation strategies in order to prevent the size reduction of populations, their genetic impoverishment and losses in global biodiversity. This PhD work consist of four parts, the first two provide useful information with regard to the genetic population structure of two pelagic species of interest to fisheries within the Mediterranean area (La Mesa et al. 2005; Morello & Arneri 2009), the Transparent goby ( Aphia minuta ) and the European anchovy ( Engraulis encrasicolus ). The genetic structure of these pelagic species was analysed using microsatellites as molecular markers and some hypotheses were provided to explain 1 which forces, among life history traits, historical events, hydrographic barriers and environmental conditions, shaped it. In addition, for E. encrasicolus a series of demographic fluctuations were observed in Adriatic Sea during the last 40 years, with a demographic