The Genetic and Phenotypic consequences of translocations of deer (Genus Cervus) in Scotland Graeme Mackie Swanson Thesis submitted for the degree of Doctor of Philosophy University of Edinburgh 1999 ii 1! I hereby declare that this thesis was composed by myself and that the work described within was carried out by me, unless otherwise acknowledged. Graeme Mackie Swanson 26th April 2000 To Lisbeth and Rory "The Japanese are a most satisfactory little deer.." Viscount Powerscourt (1884) CONTENTS . 1 ABSTRACT .4 iNTRODUCTION .......................................................................................................................... 6 1 .1 G1L INTRODUCTION .............................................................................................................. 6 1.1.1 Conservation genetics..........................................................................................................7 1 .2 Ti-IEGENTJsCERVUS ...................................................................................................................... 9 1.2.1 Phenotype............................................................................................................................ 9 1.2.2 Genotype........................................................................................................................... 10 1.2.3 Phylogeny.......................................................................................................................... 15 1.2.4 Taxonomy .......................................................................................................................... 15 1.3 TRANSLOCATIONS ....................................................................................................................... 15 1.3.1 Red deer and wapiti........................................................................................................... 15 1.3.2 Sika................................................................................................................................... 18 1.4 HYBRIDISATION WITHN THE CERVINAE ...................................................................................... 18 1.4.1 Background....................................................................................................................... 18 1.4.2 Scottish studies.................................................................................................................. 24 1.4.3 Consequences of hybridisation........................................................................................... 27 1.5 OBJECTIVESOFSTIJDY ................................................................................................................ 28 1 .6 SPECIFIC AIMS ............................................................................................................................ 30 2 MATERIALS AND METHODS FOR GENETIC STUDY........................................................31 2.1 SAMPLING REGIME 31 2.1.1 Overview.......................................................................................................................... 31 2.1.2 Intensive Argyll study....................................................................................................... 31 2.1.3 Extensive Scotland wide survey......................................................................................... 36 2.2 MOLECULAR MARKERS ............................................................................................................. 39 2.2.1 Diagnostic Markers.......................................................................................................... 39 2.2.2 Number of markers........................................................................................................... 40 2.2.3 Nuclear Markers............................................................................................................... 40 2.2.4 Mitochondrial Markers..................................................................................................... 42 2.3 LABORATORY TECHNIQUES ....................................................................................................... 43 2.3.1 Overview .......................................................................................................................... 43 2.3.2 Sample Collection and Storage......................................................................................... 43 2.3.3 Extraction......................................................................................................................... 44 2.3.4 Microsatellite Markers...................................................................................................... 44 2.3.5 D-Loop Mitochondrial Marker......................................................................................... 45 3 GENETIC DATA SET ................................................................................................................. 46 3 .1 INTRODUCTION ........................................................................................................................... 46 3.2 OVERVIEW.................................................................................................................................. 46 3.3 SUMMARY STATISTICS................................................................................................................ 47 3.3.1 Allele Frequencies.............................................................................................................47 BM6438 .........................................................................................................................................49 BOVIRBP ...................................................................................................................................... 50 FCBJ93 ......................................................................................................................................... 51 MMOJ2 .......................................................................................................................................... 52 R1v1188........................................................................................................................................... 53 INRAO5 . ......................................................................................................................................... 55 RM095 ...........................................................................................................................................57 Table 3.1 Argyll mitochondrial DNA haplotypes listed by population and phenotype....................58 3.3.2 Heterozygosity...................................................................................................................58 3.3.3 Inbreeding Coefficient (F,)................................................................................................60 3.4 CoNcLusions ............................................................................................................................63 HYBRIDISATION ....................................................................................................................... 64 4 .1 INTRODUCTION ........................................................................................................................... 64 4.2 ANALYSIS METHODS .................................................................................................................. 64 4.2.1 IdentifIcation of hybrids..................................................................................................... 64 4.2.2 Calculation of hybrid indices............................................................................................. 67 4.3 RESULTS ..................................................................................................................................... 67 4.3.1 Extensive Scotland wide survey.......................................................................................... 67 4.3.2 Intensive Argyll Study........................................................................................................ 73 4.4 DiscussioN ................................................................................................................................ 73 4.5 SUMMARY .................................................................................................................................. 76 GENETIC VARIATION WITHIN RED & SIKA...................................................................... 78 5 .1 BACKGROUND ............................................................................................................................ 78 5.2 GENETIC VARIATION ................................................................................................................... 79 5.2.1 Introduction....................................................................................................................... 79 5.2.2 Methods............................................................................................................................. 80 5.2.3 Results............................................................................................................................... 82 5 .3 DISCuSSION ................................................................................................................................ 85 5.3.1 Differences between sika deer populations........................................................................