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Study population
Demographic and behavioural information was collected on African wild dogs in KZN from January 2001 through August 2008. This population began successfully breeding and expanding in 2001 after the release of artificially-assembled packs into a single protected area. By August 2008, further reintroductions, natural dispersals and pack formations boosted the population to 88 dogs in eight different groups living in three protected areas (Spiering et al. 2009). During the study period, the population included 257 individuals that comprised 10 packs and 36 total pack years, with successful breeding occurring in 32 of these years. Data on pack composition (number of dogs, sex, age classes and litter size at first emergence from the den), location and reproductive status (i.e., breeding, non-breeding, pregnant, lactating) were collected once monthly minimally and as often as 10 times per month for more accessible packs. Packs and dispersing groups were located by radio-telemetry, observations made from a vehicle or on foot and individual wild dogs identified by unique coat patterns and photographic records.
Determining dominance
The alpha male and female in a given pack were recognized on the basis of: 1) reciprocal male and female scent-marking behaviour (Frame et al. 1979); 2) obvious co-incidental male and female movement; and 3) mutual offensive and defensive maneuvers in agonistic encounters with other adult pack members (Girman et al. 1997). The dominance hierarchy also was inferred from gestures of subordination, including laying the ears flat against the head and/or rotating the head away from a higher ranking individual (van Lawick 1970) as well as passive submission that included a subordinate rolling onto its back in the presence of a more dominant dog (Schenkel 1967). In this study, we considered three ways for an individual to gain the dominant position within a pack. First, a wild dog could become dominant by default as the only adult of their sex in the pack. Alternatively, there could be inter-animal competition without physical aggression with a same-sex adult at the initial pack-bonding phase or when the hierarchy was disrupted due to death of the alpha individual. Lastly, the current dominant could be overthrown by a competitor through fighting. As dominant females never disperse (Creel et al. 2004), we assumed that any such individuals missing from a pack had died. Subordinate siblings of the alpha pair were considered ‘potential breeders’, whereas subordinate offspring of the dominant pair were not because alpha individuals apparently share breeding with siblings, but rarely with offspring (Girman et al. 1997; McNutt & Silk 2008; Spiering et al., unpublished observations).
Genetic sampling and genotyping
Biomaterials for molecular genetic evaluations were collected from January 2003 through January 2008. Wild dog tissue and blood samples were obtained opportunistically during immobilization operations for translocation and collaring and when a wild dog carcass was located (Spiering et al. 2009). Non-invasive collection of faeces allowed securing representative samples from a significant-sized population (n = 113 wild dog individuals and 10 packs). Faecal samples were collected fresh from known individuals within 5 to 30 min of deposition and then kept in a cool bag for up to 4 hr before storing in labelled, plastic freezer bags at -20oC until genetic analysis.
Sample collection and detailed DNA extraction protocols are described in Spiering et al. (2009). In brief, DNA was extracted from scat using a QIAamp DNA Stool Mini Kit and from tissue and blood using a QIAamp Tissue and Blood Kit (QIAGEN). Genetic analyses were completed using 19 microsatellites selected from the 2006 International Society for Animal Genetics domestic dog (Canis familiaris) panel that were consistent with other wild dog genetic studies in southern Africa (Moueix 2006). All individuals were genotyped at 17 dinucleotide microsatellite loci (AHT130, AHT137, AHTh171, AHTh260, AHTk211, AHTk253, CXX279, FH2848, INRA21, INU030, INU055, LEI004, REN54P11, REN105L03, REN162C04, REN169D01, REN247M23) and two tetranucleotide loci (FH2054 and FH2328). These loci are commonly used for determining parentage in domestic dogs and, therefore, were selected because they are widely distributed throughout the genome and highly polymorphic. The polymerase chain reaction (PCR) protocols are discussed in Spiering et al. (2009). A combination of the multiple tubes approach (Taberlet et al. 1996) and the maximum likelihood method (Miller et al. 2002) were used to overcome the potential for faecal DNA genotyping errors (Spiering et al. 2009). To detect and eliminate sampling error, we compared matched tissue or blood with faeces, analyzed duplicate samples for individuals and used a significant number of microsatellite markers to verify unique individuals in the dataset (Waits et al. 2001).
CHAPTER 1: GENERAL INTRODUCTION
1.1 Genetics of Small Populations
1.2 Influence of Behaviour on Genetics and Demographics
1.3 Objectives and Scope of the Study
1.4 Natural History of African Wild Dogs
1.5 Study Area and Population
1.6 References
CHAPTER 2: SAMPLING ERROR IN NON-INVASIVE GENETIC ANALYSES OF AN ENDANGERED SOCIAL CARNIVORE
2.1 Abstract
2.2 Introduction
2.3 Methods
2.4 Results
2.5 Discussion
2.6 References
CHAPTER 3: INBREEDING, HETEROZYGOSITY AND FITNESS IN A REINTRODUCED POPULATION OF ENDANGERED AFRICAN WILD DOGS
3.1 Abstract
3.2 Introduction
3.3 Methods
3.4 Results
3.4.1 Relationship between inbreeding coefficient and heterozygosity
3.4.2 Influence of molecular metrics and f on fitness
3.5 Discussion
3.6 References
CHAPTER 4: REPRODUCTIVE SHARING AND PROXIMATE FACTORS MEDIATING COOPERATIVE BREEDING IN THE AFRICAN WILD DOG
4.1 Abstract
4.2 Introduction
4.3 Methods and Materials
4.4 Results
4.5 Discussion
4.6 References
CHAPTER 5: INBREEDING AVOIDANCE INFLUENCES THE VIABILITY OF REINTRODUCED POPULATIONS OF ENDANGERED AFRICAN WILD DOGS
5.1 Abstract
5.2 Introduction
5.3 Methods
5.4 Results
5.5 Discussion
5.6 References
CHAPTER 6: INTEGRATING GENETICS AND DEMOGRAPHICS INTO POPULATION MODELS TO REINTRODUCE VIABLE POPULATIONS OF ENDANGERED AFRICAN WILD DOGS
6.1 Abstract
6.2 Introduction
6.3 Methods
6.4 Results
6.5 Discussion
6.6 References
CHAPTER 7: GENERAL DISCUSSION
7.1 Summary
7.2 Conclusions and Recommendations
7.3 References
APPENDICES
Appendix A: Model inputs for population viability analyses in VORTEX
Appendix B: Studbook file used as initial population in VORTEX
