DOES BEHAVIOURAL PLASTICITY CONTRIBUTE TO The European rabbit, Oryctolagus cuniculus, ... territorial intrusion approach to observing wild rabbit behaviour in arid and semi-arid environments

DOES BEHAVIOURAL PLASTICITY CONTRIBUTE TO DIFFERENCES IN POPULATION GENETIC

STRUCTURE IN WILD RABBIT POPULATIONS IN ARID AND SEMI-ARID AUSTRALIA?

Mr Geoffrey Anthony de Zylva – B. App. Sc., Hons. School of Natural Resource Sciences Queensland University of Technology

Submitted for the degree of Doctor of Philosophy (Science), in 2007.

Keywords

Oryctolagus cuniculus

European Rabbit

Australia

DNA

mtDNA

microsatellite

behaviour

flexible behaviour

genetic variability

metapopulations

genetic bottleneck

Abstract

The European rabbit, Oryctolagus cuniculus, was introduced to Australia in 1859

and quickly became a significant vertebrate pest species in the country across a wide

distribution. In arid and semi-arid environments, rabbit populations exist as

metapopulations – undergoing frequent extinction recolonisation cycles. Previous

studies identified population genetic structuring at the regional level between arid

and semi-arid environments, and habitat heterogeneity was suggested as a possible

causal factor. For the most part, rabbit behaviour has been overlooked as a factor

that could contribute to explaining population genetic structure in arid and semi-arid

environments.

This study utilised a combination of genetic sampling techniques and a simulated

territorial intrusion approach to observing wild rabbit behaviour in arid and semi-

arid environments. The genetic component of the study compared population

samples from each region using four polymorphic microsatellite loci. The

behavioural component examined variation in the level of territoriality exhibited by

three study populations in the arid region towards rabbits of known versus unknown

origins (resident vs transgressor (simulating dispersal)).

A difference was observed in population genetic structure determined from nuclear

markers between arid and semi-arid regions, which supports findings of previous

research using mitochondrial DNA data in the same area. Additionally, differences

in aggressive response to known vs unknown rabbits were identified in parts of the

arid region, which together with the effects of habitat heterogeneity and connectivity

may explain the observed differences in population genetic structure.

Knowledge of behavioural plasticity and its effect on relative dispersal success and

population genetic structure may contribute to improved management and control of

feral rabbit populations at the regional level within Australia; and may assist with

conservation efforts in the species’ natural range in Europe.

Table of Contents CH1 - INTRODUCTION .......................................................................................................................... 1

DISPERSAL, HABITAT VARIABILITY, AND GENE FLOW ............................................................ 1 MODELLING GENE FLOW ......................................................................................................... 3 METAPOPULATIONS.................................................................................................................. 5 BEHAVIOURAL DIVERSITY AND GENETIC DETERMINATION..................................................... 10 GROUP LIVING, COOPERATION, AND SOCIALITY ..................................................................... 10 RESOURCE DEFENCE ............................................................................................................... 13 BEHAVIOURAL FLEXIBILITY..................................................................................................... 15 THE EUROPEAN RABBIT ........................................................................................................... 16

CH2 – EXPERIMENTAL DESIGN AND METHODOLOGY ......................................................................... 24 DESCRIPTION OF STUDY SITES ................................................................................................. 25 POPULATION SAMPLING ........................................................................................................... 27 GENETIC METHODS ................................................................................................................. 28 BEHAVIOURAL METHODS ........................................................................................................ 29

CH3 – GENETIC ANALYSIS .................................................................................................................. 32 MATERIALS AND METHODS ..................................................................................................... 33 DNA EXTRACTION................................................................................................................... 34 POLYMERASE CHAIN REACTION (PCR).................................................................................... 35 RESULTS................................................................................................................................... 41 DISCUSSION.............................................................................................................................. 50

CH4 – RABBIT BEHAVIOUR.................................................................................................................. 57 MATERIALS AND METHODS ..................................................................................................... 57 ANALYSIS METHODS – HABITAT CONDITIONS ......................................................................... 60 ANALYSIS METHODS – BEHAVIOUR ........................................................................................ 61 RESULTS................................................................................................................................... 64 DISCUSSION………………………………………………………………………………… 103

CH5 - GENERAL DISCUSSION.............................................................................................................111 POPULATION GENETICS..........................................................................................................111 BEHAVIOURAL ECOLOGY .......................................................................................................114 PEST MANAGEMENT ISSUES ...................................................................................................119 FUTURE DIRECTIONS OF RESEARCH AND CONCLUSION..........................................................123

APPENDIX 1 – LIST OF ALL RABBIT BEHAVIOURS ...............................................................................125 BIBLIOGRAPHY ..................................................................................................................................127

List of Tables and Figures FIGURE 1.1 - TYPES OF METAPOPULATION ............................................................................................ 6 FIGURE 2.1 – AREAS OF STUDY ............................................................................................................ 27 TABLE 3.1 – MICROSATELLITE PRIMERS ............................................................................................... 35 TABLE 3.2 – PCR AND ELECTROPHORESIS CONDITIONS (TA = ANNEALING TEMPERATURE)................... 38 TABLE 3.3 – POPULATION SAMPLE SIZES AT EACH LOCUS ..................................................................... 39 TABLE 3.4 – NUMBER OF ALLELES PER LOCUS PER POPULATION ........................................................... 41 TABLE 3.5 – MEAN ALLELIC STATISTICS ACROSS ALL LOCI FOR EACH POPULATION.............................. 42 TABLE 3.6 – SIGNIFICANT GENIC DIFFERENTIATION FOR POPULATION PAIRS ACROSS ALL LOCI ............ 43 TABLE 3.7 – MATRIX OF SIGNIFICANT GENIC DIFFERENTIATION BETWEEN POPULATION PAIRS ............. 44 TABLE 3.8 – PAIRWISE POPULATION FST VALUES.................................................................................. 45 TABLE 3.9 – SIGNIFICANCE OF PAIRWISE POPULATION FST VALUES...................................................... 45 FIGURE 3.1 – SORTED MEAN FIS............................................................................................................ 46 TABLE 3.10 – AMOVA SUMMARY TABLE ............................................................................................ 47 FIGURE 3.2 – AMOVA SUMMARY PIE CHART...................................................................................... 47 FIGURE 3.3 – RANDOMISATION OF PHIPT ............................................................................................. 48 FIGURE 3.4 - UPGMA TREE FOR NEI SIMILARITY MATRIX .................................................................... 49 TABLE 3.11 – SPECIES WITH REDUCED GENETIC DIVERSITY .................................................................. 51 TABLE 4.1 – SITE LOCATIONS................................................................................................................ 58 FIGURE 4.1 – VISION FIELD OF VIDEO CAMERA ..................................................................................... 60 TABLE 4.2 – BEHAVIOUR OBSERVED ON VIDEO..................................................................................... 62 TABLE 4.3 - WARREN COUNT DATA .............................................