Institute of Biodiversity, Animal Health & Comparative Medicine

1. Institute of Biodiversity, Animal Health & Comparative Medicine Pictus, Pedigrees and MHC: an integrated approach for genetic management of captive African wild dogs Clare Marsden, Hanny Verberkmoes, Rob Thomas and Barbara Mable

2. African Wild Dogs • Lycaon pictus: one of most endangered canids • Threatened by: habitat loss, persecution, disease • Last 100 years: 98% reduction in population size; 95% reduction in range • Status: <5,000 individuals found in small, fragmented populations • Captive population in Zoos: 632 (312 in Europe) not genetically managed PhD Project: Clare Marsden Comparing variation at adaptive and neutral genes: Have past bottlenecks reduced genetic diversity in the wild? How much diversity is maintained in zoos and can management be improved? Can genetic markers be used to trace extinction/recolonisation events?

3. African Wild Dogs • Lycaon pictus: one of most endangered canids • Threatened by: habitat loss, persecution, disease • Last 100 years: 98% reduction in population size; 95% reduction in range • Status: <5,000 individuals found in small, fragmented populations • Captive population in Zoos: 632 (312 in Europe) not genetically managed PhD Project: Clare Marsden Comparing variation at adaptive and neutral genes: Have past bottlenecks reduced genetic diversity in the wild? How much diversity is maintained in zoos and can management be improved? Can genetic markers be used to trace extinction/recolonisation events?

5. How did this project come about? • Brainstorming Session: • Sarah Cleaveland (wildlife veterinarian) • Dan Haydon (theoretical ecologist/epidemiologist) • Rob Thomas (Conservation and Research Manager, Royal Zoological Society of Scotland-Edinburgh Zoo) • me (Evolutionary Geneticist) • Lorna Kennedy (canid immune gene expert) • Why study genetics of wild and captive populations? • Severe bottlenecks could have meant reduction in genetic diversity in wild but hadn’t been studied • Unknown genetic variation in captive populations • Viral diseases problematic in wild populations but genetics unknown • Social structure means that low success rate of sharing of animals across zoos but unknown whether due to relatedness of individuals

6. How did this project come about? • Brainstorming Session: • Sarah Cleaveland (wildlife veterinarian) • Dan Haydon (theoretical ecologist/epidemiologist) • Rob Thomas (Conservation and Research Manager, Royal Zoological Society of Scotland-Edinburgh Zoo) • me (Evolutionary Geneticist) • Lorna Kennedy (canid immune gene expert) • Innovation • Most studies only consider variation at DNA markers that have no effect on fitness (“neutral” markers) • We also used immune genes (Major Histocompatibility Complex, MHC) as proxy for adaptive variation • Immune genes have been implicated in mate choice • Immune genes might indicate whether wild of captive populations at risk of disease due to low variation

7. Why did it work? Outstanding student!! Collaborative support from Studbook keeper Collaborations with field researchers

8. African wild dog EEP EEP (European Endangered Species Programme): ~ 270 African wild dogs ~ 44 zoos holding groups of wild dogs ~ 10-12 successful breeding groups (max capacity) Research aims: • Determine the ancestry and level of genetic diversity conserved in the EEP • Assess how management could improve the genetic status of the population • inbreeding; risk of disease; breeding success

9. Initial Challenges • No records on breeding success tied to samples • No samples kept from diseased animals • No pedigree • Lack of sample sharing between zoos • Incomplete records of original source of animals

10. Initial Challenges • No records on breeding success tied to samples • Couldn’t assess breeding success in relation to immune gene variation • No samples kept from diseased animals • Couldn’t assess risk of disease in relation to immune gene variation

11. Initial Challenges • No pedigree • Clare and Hanny worked together to produce pedigree based on studbook records • Lack of sample sharing between zoos • Clare and Hanny worked together to establish system for collecting and sharing samples • Incomplete records of original source of animals • Genetics combined with pedigree to solve • Clare and Hanny implemented management plan across zoos based on genetic variation

12. Geneticquestions • What is the genetic status of the EEP? • Pedigree based on existing records • Where did the EEP founders come from? • Genetic analysis of neutral markers compared to wild populations • How much genetic diversity is found in the EEP? • Genetic analysis of neutral markers and immune genes compared to wild populations • What impact will recent South African imports have on the EEP? • Genetic analysis of source of new imports

13. What is the genetic status of the EEP? Pedigree analyses KEY Male Family 1 Family 2 Father Mother Father Mother Female Generation 1 Inbred Generation 2 Daughter Daughter Daughter Son Son Son Daughter Daughter Son Son

14. EEP African wild dog pedigree

15. EEP African wild dog pedigree Very few descendents Many descendents ONLY 18/80 wild founders have left descendents. Unequal founder contributions

16. EEP African wild dog pedigree Bred with 3 males 20 offspring 1 offspring 4 litters from 1 pair 80% of EEP wild dogs never breed Reproductive skew

17. What is the genetic status of the EEP? A large amount of genetic variation has been lost: • Only 18/80 WILD founders have left descendents • 80% of EEP wild dogs die before breeding. Over- and under-representation of founder lineages Wild dog social structure increases genetic risks: • Reproductive skew (Alpha pair monopolise breeding) • Large litters

18. Where do the founders of the EEP originate from in the wild? Stud book Namibia, South Africa, Unknown Mitochondrial DNA • Maternally inherited gene • “Neutral” genetic marker • Can be used to trace back to dead founders

19. Sampling from zoos #5572 ♀ Date______ Sampling coordinated through stud book keeper Clare Marsden Glasgow University Zoo sampling kits • Pre-labelled sampling tubes • Sampling and sedation instructions • UK import licence • Pre-labelled envelopes

20. Sampling from zoos #5572 ♀ Date______ 75% response rate Sampling coordinated through stud book keeper Clare Marsden Glasgow University Zoo sampling kits • Pre-labelled sampling tubes • Sampling and sedation instructions • UK import licence • Pre-labelled envelopes

21. Where do the founders of the EEP originate from in the wild? Expect Stud book Namibia, South Africa, Unknown • Results • Founders have a diverse origin • Wider than S. Africa & Namibia • 3) EU zoos have a more diverse origin than S. African zoos • 4) Risk that some imports from wild populations EU zoos S. African zoos Namibia South Africa

22. Genetics: Assessed level of variation at a set of immunity genes involved with disease resistance Major Histocompatibility Complex (MHC) Variation at these genes is important because it determines the range of diseases you can fight How much genetic diversity is found in the EEP?

23. How much genetic diversity is found in the EEP? Genetics: Assessed level of variation at a set of immunity genes (Major Histocompatability Complex) Southern African wild: 14 genetic variants (alleles) EU zoos: 11/14 variants + 1 variant not found in the wild Genetics: Assessed level of variation at a set of immunity genes (Major Histocompatibility Complex)

24. How much genetic diversity is found in the EEP? Genetics: Assessed level of variation at a set of immunity genes (Major Histocompatability Complex) Southern African wild: 14 genetic variants (alleles) EU zoos: 11/14 variants + 1 variant not found in the wild Genetics: Assessed level of variation at a set of immunity genes (Major Histocompatability Complex) The EU zoos contain a lot of the diversity found in the wild

25. How much genetic diversity is found in the EEP?

26. How much genetic diversity is found in the EEP? High diversity but concentration of alleles in some parts of pedigree suggests inbreeding and unequal reproduction

27. How much genetic diversity is found in the EEP?

28. How much genetic diversity is found in the EEP? Bias in MHC alleles in some families could suggest selection (diseases?) but sample sizes small and no disease records

29. What impact will recent South African imports have on the EEP? EU zoos have imported ~ 20 African wild dogs from South African captive facilities in the last 10 years • Positive impact: • New genetic variation • 3/11 variants introduced by South African animals • Reduce inbreeding • Cautions: • Unknown parentage/ancestry • inbreeding? • outbreeding depression? • Genetics suggest some sampled from wild • impacts on wild populations • encourages poaching?

30. Genetic questions • What is the genetic status of the EEP? • Loss of variation in the past. Current over and under-representation of some lineages 2) Where did the EEP founders come from? • A range of countries in Southern Africa, not just Namibia & S. Africa. EEP is more diverse than S. African zoos 3) How much genetic diversity is found in the EEP? • A large proportion of the diversity found in wild populations in Southern Africa but could be managed better • What impact will recent South African imports have on the EEP? • Introduce new genetic variation but risks might outweigh benefits

31. Management implications? SMALL CHANGES => BIG IMPACT • Try to limit reproduction to 2-3 litters/pair and 2-3 siblings per family • Form breeding groups with animals from different lineages; bias under-represented lineages • Integrate S. African imports into the EEP

32. Lessons Learned • Value of coordinating samples, stud book records, behavioural data and health records • Benefits of collaborative approach and networking • Value of genetics for “forensics” of imports • Genetics demonstrated more variation than expected based on studbook records • 5 years on, management plan resulted in births with more genetic variation in the EEP • Interest in genetic management from other zoo networks (USA, Australia) Remaining Challenges • Continuity and implementation • Sample and data storage • Biology of species/quality of zoo facilities

33. Aalborg zoo Amneville zoo Artis zoo Attica zoo Basel zoo Belfast zoo Boras zoo Colchester zoo Dortmund zoo Dublin zoo Duisburg zoo Dvurkralv zoo Ebeltoft zoo Edinburgh zoo Eskilstun zoo Friguia zoo Hilvarenbeek zoo Howletts wild park Kerkrade zoo Kolmarden zoo La Palmyr zoo Le Pal zoo Lisieux zoo London zoo Lympne wild park Munich zoo Peaugres zoo Pont-Scorff zoo Ramat-Gan zoo Roma zoo Rostock zoo West Midlands Acknowledgments PhD supervisors Contributing zoos • Barbara Mable • Dan Haydon • Lorna Kennedy Chief collaborators • Hanny Verberkmoes • Rosie Woodroffe • Greg Rasmussen • Sarah Cleaveland • Rob Thomas PhD funding • Natural Environment Research Council • Royal Zoological Society of Scotland