Section 11 Genetics Management of Captive Populations

1. Section 11 Genetics Management of Captive Populations Traditionally, the objective of captive breeding programs was simply preservation of species and increase of numbers. Now, managers of zoos, botanic gardens, and wildlife parks almost universally accept the necessity to retain species as dynamic evolutionary entities and to maintain genetic health both for long-term viability and hopefully for subsequent release to natural habitats.

2. Captive breeding programs can assist conservation efforts • by: • establishing populations in secure ex-situ locations • educating and engaging the public on conservation issues • providing a focus for fund-raising efforts for conservation • providing individuals for research on the basic biology of the species, knowledge can then be applied to conservation of the species in the wild • providing individuals for reintroduction programs

3. Extent of Captive Breeding and Propagation Activity Approximately 1,150 zoos and aquaria worldwide currently house about 1,232,000 individual animals, including 584,000 individual fish, 202,000 mammals, 351,000 birds, 74,000 reptiles, and 21,000 amphibians. About 5 -- 10% of the available space in zoos are used for endangered species. With the changes in priority, there could be breeding space for about 800 endangered species in zoos and wildlife parks.

4. In contrast, an estimated 2,000 -- 3,000 species ofterrestrial vertebrates alone will require captive breeding within the forseeable future. Unfortunately, zoos can only maintain a certain number of individuals and these small, breeding groups can rapidly become inbred and potentially non-viable. By the early 1980s, zoo managers recognized that their contribution to conservation could best be made through regional and international cooperative breeding programs and through collaborations with in-situ conservation programs.

5. In North America, Species Survival Plans (SSP), coordinated by the American Zoo and Aquarium Association, were first developed in 1981. SSPs involve the coordinated management of all captive individuals held by cooperating institutions, and are now in place for many endangered species. Regional and international studbooks are used to make recommendations on which animals should be bred, with whom, how often, and where.

6. Individual institutions permit their animals to be managed under one genetic and demographic objective, determined by the coordinator, and animals are frequently moved among participating institutions for breeding to optimize genetic management. Similar programs have been developed in Australia, Europe, Japan, New Zealand, South Africa, and Central America. Information on pedigrees, individual histories, breeding experiences, and health records are collected at each zoo and maintained by the International Species Information System (ISIS) in Minnesota.

7. Zoos also contribute to both ex-situ and in-situ • conservation through involvement with the Conservation • Breeding Specialist Group (CBSG) of the Species • Survival Commission of the IUCN. • Their programs include: • Conservation Assessment and Management Plans (CAMPs) • that provide initial assessments of the global status • and initial research and management • recommendations.

8. Population and habitat viability assessments that provide • detailed quantitative assessment, evaluation of • management options, and recommendations for • conservation action. • Zoo conservation planning. • Providing expertise relating to captive breeding. • Coordinating meetings and workshops on topics required • to advance conservation.

9. Stages in Captive Breeding and Reintroduction • Captive breeding and reintroduction may be viewed as a • process involving the following six stages: • Decline of wild populations and its genetic consequences • Founding a captive population • Growing the captive population to a secure size • Managing the captive population over generations • Selecting individuals for reintroduction • Managing the reintroduced population (probably • fragmented) in the wild.

10. Genetic issues important in the first stage are the rate of decline of the wild population, the size to which it declines, and the resulting loss of genetic diversity and inbreeding it has suffered prior to captive breeding. Captive populations must be managed through 3 phases, foundation, growth, and maintenance. Management during each of these phases focuses on different priorities. During foundation, population size is usually small, and knowledge of the husbandry of the species lacking.

11. During this phase, management focuses on basic research to develop husbandry techniques and efforts to ensure reproduction of founders. During the growth phase, the focus is on rapid reproduction and expansion of the population to multiple facilities. During the maintenance phase, the population is managed at zero population growth, at a size determined by the genetic goals of the program. Typically, individuals are not removed from the captive population (e.g. for reintroduction) until the population size approaches this target size.

12. Founding Captive Populations Potential founders may come from different sources or be of unknown origin. It is therefore essential to resolve any taxonomic uncertainties, or the need for separate management units prior to foundation. This avoids outbreeding depression or a population of undesirable hybrids.

13. It was not until late in the program that it was discovered that several of the founders of the Asiatic lion captive breeding program were identified as actually African lions, resulting in termination of the program, but only after substantial resources had been expended in its development and support. The founding process sets the genetic characteristics for, and ultimately affects the conservation value of, the captive breeding program.

14. If the population is to encompass the genetic diversity in the wild and minimize subsequent inbreeding, then a fully representative sample of founders is required. Some selection is however inevitable during the foundation as typically only a moderate proportion of wild-caught individuals successfully breed in captivity. For example, of the 242 wild-caught golden lion tamarins in the captive breeding program, only 48 individuals contributed to the current gene pool with 2/3 of the gene pool prior to management being derived from just one prolific male.

15. The need to acquire a solid genetic base, the effects of selection in reducing the number of contributing founders, and economics all argue for establishing populations with large numbers of founders. Unfortunately, most captive breeding populations have become established using an inadequate number of founders. Some captive populations were only founded when the endangered species was at a “last gasp”, when few founders were available.

16. Founders for most other captive breeding programs were the few animals (or ancestors of animals) that were already in captivity at the time the program was initiated. Genetic Consequence of Small Founder Numbers Population bottlenecks at foundation lead to loss of genetic diversity, resulting in inbreeding, and reduced fitness. To avoid bottlenecks, it is recommended that a minimum of 20 -- 30 genetically effective founders by used.

17. As discussed earlier, the relationship between number of founders and the proportion of heterozygosity that they capture is given by: H = [1 - (1/2Ne)] Thus, even 10 contributing founders capture 98% of the heterozygosity in an outbreeding species while 30 founders captures over 98% of the heterozygosity.

18. The number of founders required to capture allelic diversity depends more on the number and frequency of alleles, but typically requires more individuals than needed to capture heterozygosity, with more founders needed if rare alleles are present. For a locus with two alleles, the probability that a random sample of n founders contains at least one copy of each allele P(A1, A2) is given by: P(A1, A2) = 1 - (1 - p)2n - (1 - q)2n Where p is the frequency of A1 and q is freq. of A2.

19. At least 30 founders are need to meet the recommendation of 95% certainty of capture of allele with frequency of 0.05. For the rarer allele, at a frequency of 1%, even 50 founders only have about a 60% chance of capturing the allele. Rare alleles are unlikely to be sampled unless founder numbers are very high.

20. Growth of Captive Populations The second phase of captive breeding programs is to multiply the population size as rapidly as possible up to the desired size set by the genetic and demographic objectives of the program. Genetic management is de-emphasized during this phase as it may conflict with the goal of rapid population growth.

21. Offspring must be produced from all adults, not just the genetically most valuable. Some animals display strong mating preferences and may refuse to mate in genetically ideal crosses. If a genetically undesirable pairing is broken up in a monogamous species, new pairings may not mate for several years, slowing population growth. Genetic management during this phase is usually limited to avoiding pairings between close relativesl.

22. How is Target Population Size Set? The current goal of most captive breeding programs for endangered species is to retain 90% of the genetic diversity for 100 years. For a population with a stable size, the effective populations size required to meet this goal is inversely proportional to the generation length as: Ne = 475/L, where L is the generation length in years.

23. The founding phase has a significant impact on the required Ne, and it is likely to be greater than the value predicted. The required number of individuals depends critically on the founder effects, Ne/N ratio, generation length, and on how quickly the population increases after the bottleneck. The Ne/N ratio depends on variance in family size, sex- ratio, mating system, and fluctuations in N.

24. Genetic Management of Captive Populations Genetic Deterioration in Captivity -- As the population approaches its target size, the focus increasingly shifts to more intense genetic management. The objective becomes maintaining demographic stability and counteracting deleterious genetic changes including: inbreeding depression, loss of genetic variation, accumulation of new deleterious mutations, genetic adaptations to captivity that are deleterious in the wild, outbreeding depression.

25. Inbreeding depression, loss of genetic diversity and genetic adaptation to captivity are expected in all closed captive populations. The accumulation of new deleterious mutations is only a long-term concern and is of unknown importance. The most immediate threat during foundation is inbreeding depression.

26. The effects of inbreeding depression, loss of genetic diversity, and mutational accumulations are all more severe in smaller than larger populations. Conversely, genetic adaptation to captivity is more extensive in larger than smaller populations. While this is beneficial in captivity, its deleterious effects are only felt when the population is returned to the wild. All deleterious changes in captivity are likely to be more deleterious when populations are reintroduced into harsher wild environmental conditions.

27. Loss of Genetic Diversity -- Captive populations of threatened species lose genetic diversity at foundation, and because of small subsequent population size. We can recast an earlier equation to illustrate both the effect of Ne/N and the effect of founder, versus subsequent population numbers, as follows: Ht/HO = [1 - (1/2Nfo)]{1 - 1/[2N(Ne/N)]}t - 1 Where, Nfo = number of effective founders.

28. Ht/HO = [1 - (1/2Nfo)]{1 - 1/[2N(Ne/N)]}t - 1 Reflects the effect of subsequent pop. reductions Reflects the Founder Effect From this equation, genetic variation in captive breeding programs can be retained by:

29. Maximizing the initial genetic variation by using adequate numbers of founders. Minimizing the number of generations by breeding from older individuals, or using cryoprservation Maximizing population size Maximizing Ne/N

30. Current Genetic Management of Captive Populations -- The current target of genetic management is a loss of genetic diversity, and a concomitant increase in inbreeding coefficient, no more than 10% over 100 years. Unfortunately, due to small founder numbers and/or limitations in space, such goals are unattainable in many populations, and the genetic objective is often relaxed. Targets may be lowered to 80% for 100 years, or 90% for 50 years.

31. Maximizing Ne/N As captive breeding resources are clearly limited, and the number of species requiring captive breeding to save them from extinction is increasing, it is important to maximize Ne for each species using the minimum number of individuals. The following procedures can be used to maximize Ne/N

32. Equalizing family size so that Ne approximates 2N -- this recommendation can double the effective captive breeding resource and it is being applied in practice. Equalizing the sex-ratio of breeders -- i.e. avoiding harems if possible. This is difficult to achieve in mammals as most are polygamous and many breed best with harem structures. Many mammals are maintained in harems to avoid injury or death from male-male aggression, and this is sometimes practiced for species that do not naturally have harems.

33. Equalizing population sizes across generations -- Following the foundation and growth phases, captive populations are typically maintained at relatively stable sizes. Maximizing generation length -- The may be done by (a) allowing parents to reproduce from sexual maturity, with successively euthanasia of offspring as new siblings are produced (not ethically acceptable to many), (b) retaining all offspring, but only using later-born siblings to be parents of subsequent generations (wasteful in terms of resources), (c) delaying reproduction until they are older; this risks death, or sterility before breeding,

34. (d) breeding parents when young, and then avoiding reproduction (often with contraceptives) until older, and breeding them again, or (e) cryopreservation of embryos, or gametes; often the technology to do this is not available for the species. The procedures, while theoretically sound, are not widely practiced, although there is some use of (d).

35. Minimizing Kinship The individuals used to found captive populations typically make very unequal contributions to subsequent generations. A range of procedures including Maximum avoidance of inbreeding Genome Uniqueness Founder Importance Minimizing kinship But what is the optimum way to manage pedigreed captive populations of threatened species?

36. Ballou and Lacy (1995) compared the above four procedures using both theoretical predictions and computer simulations and found that minimizing kinship was best for retaining genetic variation. In brief, minimizing kinship involves choosing individuals with the lowest relationship in the population as parents of subsequent generations. This reduces inequalities of founder contributions.

37. The kinship (or coancestry) of two individuals is directly related to inbreeding, and, in fact, is the inbreeding coefficient of their offspring (if they had them). The mean kinship is: N mki = kij/N j=1 Where kij is kinship between i and j, and N is the number of individuals in the population.

38. The rationale behind the use of mean kinship in genetic management is illuminated by noting the relationship of average mean kinship to genetic diversity (Ht/Ho): 1 - mk = Ht/Ho where mk is the average mean kinship in the population. Consequently, if kinship is minimized, heterozygosity is maximized.

39. Individuals with low mean kinships have fewer relatives in the population of individuals with high mean kinship and therefore, carry fewer common alleles and thus are the most valuable individuals. Under a mean kinship breeding program, individuals with lower mean kinship are given breeding priority.

40. A B C D E The kinship of Robert to the other named individuals is zero. Kinship of Louise and Rita is most easily obtained by computing the inbreeding coefficient of hypothetical offspring X from a mating between them using the pedigree method. G I J F H Thelma Louise Rita Robert

41. A B C D E G I J F H Thelma Louise Rita Robert Paths n FA Contribution to FX LFAHR 5 0 (1/2)5 LGAHR 5 0 (1/2)5 LFBHR 5 0 (1/2)5 LGBHR 5 0 (1/2)5 FX = 4/32 = 1/8

42. Thus, KL-Ri = KRi-L = FX = 1/8 The kinship of Rita with herself is the probability that 2 random gametes from her contain alleles that are identical by descent. As Rita is NOT inbred, she does not herself contain alleles that are identical by descent. If she is labeled with a genotype of A5A6, then Rita’s kinship with herself is:

43. kRi-Ri = P[both A5] + P[both A6] = 1/4 + 1/4 = 1/2 This is the same value as the F for the progeny of selfing. Robert is inbred, so his kinship with himself is increased, as follows: kRo-Ro =1/2(1+FRo) and since Robert results from a full-sib mating, his inbreeding coefficient FRo = 1/4, and kRo-Ro =1/2[1+1/4] = 5/8

44. Kinship and mean kinship for the named individuals in the pedigree. Thelma Louise Rita Robert Mean k Thelma 5/8 9/32 1/8 0 0.258 Louise 9/32 5/8 1/8 0 0.258 Rita 1/8 1/8 1/2 0 0.187 Robert 0 0 0 5/8 0.156 Rationale behind use of mean kinship in genetic management is due to: 1 - mean k = Ht/HO. Thus, if kinship is minimized, heterozygosity is maximized.

45. Individuals with low mean k are most valuable. They have fewer relatives in the population than individuals with higher mean k and therefore carry fewer common alleles. Under a mean kinship breeding program, individuals with lower mean k are given breeding priority. Managing by mean k would then increase the contribution of genes from Robert and decrease those of Thelma and Louise.

46. When applying minimizing kinship to threatened populations, the mean k for each individual is calculated from pedigrees. Parents to be used for breeding are chosen as those with the lowest mean k. Two additional considerations are required to determine specific matings:

47. Mates are chosen such that matings between individuals with quite different mean kinships are avoided as they limit management options in the future. For example, if a valuable individual is mated to one of low value, increasing the contribution of the under- represented individual also increases the contribution of its over represented matel. Matings of close relatives is avoided to minimize inbreeding.

48. Limitations of Management by Minimizing Kinship: Does not directly address the probable changes in reproductive fitness. Does not necessarily minimize inbreeding, but it is very close to minimization of inbreeding strategy. Equalization of family sizes minimizes genetic adaptations to captivity for a given sized population however, maximization of Ne is a single, large population promotes genetic adaptation to captivity.

49. Reproductive Technology & Genome Resource Banks Reproductive technologies, developed for use in domestic animals, promise to have significant input to conservation of threatened species. Artificial Insemination (AI) -- AI with frozen semen can be used in transportation of genetic material, rather than animals, with great reductions in cost. AI can also be used to equalize sex-ratios of breeders by inseminating females with semen from males other than local dominant, or sole, male.

50. Based on available data, AI is only being used routinely in the management of the black-footed ferret, cheetah, giant panda, and whooping crane and its use is just beginning in elephants. Cryopreservation -- Cryopreservation of gametes, embryos, seeds, or tissues has many potential benefits for conservation, as it literally deep-freezes tissues, and the genes they contain, away from the deleterious environmental and genetic influences.