Usingmolecular methods to improve the genetic management of captive breeding programs for threatened species

Molecular Approaches in Natural Resource Conservation and Management

Volumn , Issue , 2010, Pages 267-295

  Ivy, Jamie A ^a   Lacy, Robert C ^b  

^a Department of Collections San Diego Zoo ^*  (United States)

^b BROOKFIELD ZOO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84857532622     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1017/CBO9780511777592.012     Document Type: Chapter

References (82)

1. Allendorf FW (1993) Delay of adaptation to captive breeding by equalizing family size. Conservation Biology, 7, 416-419.
2. Arnold SJ (1995) Monitoring quantitative genetic variation and evolution in captive populations. In: Population Management for Survival and Recovery: Analytical Methods and Strategies in Small Population Conservation (eds. Ballou JD, Gilpin M, Foose TJ), pp. 293-317. Columbia University Press, New York.
3. Baillie JEM, Hilton-Taylor C, Stuart SN, editors (2004) IUCN Red List of Threatened Species. A Global Species Assessment. IUCN, Gland, Switzerland, and Cambridge, UK.
4. Ballou JD, Foose TJ (1996) Demographic and genetic management of captive populations. In: Wild Mammals in Captivity (eds. Kleiman DG, Lumpkin S, AllenM, HarrisH, Thompson K), pp. 263-283. University of Chicago Press, Chicago.
5. Ballou JD, Lacy RC (1995) Identifying genetically important individuals for management of genetic diversity in pedigreed populations. In: Population Management for Survival and Recovery: Analytical Methods and Strategies in Small Population Conservation (eds. Ballou JD, Gilpin M, Foose TJ), pp. 76-111. Columbia University Press, New York.
6. Ballou JD, Mickelberg J (2009) International Population Management Plan for Ex-situ Golden Lion Tamarins. National Zoological Park, Washington, DC.
7. Benirschke K (1984) The frozen zoo concept. Zoo Biology, 3, 325-328.
8. Bink MCAM, Anderson AD, van de Weg WE, Thompson EA (2008) Comparison of markerbased pairwise relatedness estimators on a pedigreed plant population. Theoretical and Applied Genetics, 117, 843-855.
9. Blouin MS, Parsons M, Lacille V, Lotz S (1996) Use of microsatellite loci to classify individuals by relatedness. Molecular Ecology, 5, 393-401.
10. Bryant EH, Reed DH (1999) Fitness decline under relaxed selection in captive populations. Conservation Biology, 13, 665-669.
11. Butchart SHM, Stattersfield AJ, Baillie J et al. (2005) Using Red List Indices to measure progress towards the 2010 target and beyond. Philosophical Transactions of the Royal Society of London-Series B: Biological Sciences, 360, 255-268.
12. Cosson L, Grassman LL Jr, Zubaid A et al. (2007) Genetic diversity of captive binturongs (Arctictis binturong, Viverridae, Carnivora): implications for conservation. Journal of Zoology, 271, 386-395.
13. Csillery K, Johnson T, Beraldi D et al. (2006) Performance of marker-based relatedness estimators in natural populations of outbred vertebrates. Genetics, 173, 2091-2101.
14. DeWoody JA (2005) Molecular approaches to the study of parentage, relatedness, and fitness: practical applications for wild animals. Journal of Wildlife Management, 69, 1400- 1418.
15. Earnhardt JM, Thompson SD, Marhevsky E (2001) Interactions of target population size, population parameters, and program management of viability of captive populations. Zoo Biology, 20, 169-183.
16. Ely JJ, Dye B, Frels WI et al. (2005) Subspecies composition and founder contribution of the captive U.S. chimpanzee (Pan troglodytes) population. American Journal of Primatology, 67, 223-241.
17. Falconer DS, Mackay TFC (1996) Introduction to Quantitative Genetics, 4th edn. Pearson/ Prentice, Harlow, UK.
18. Fernandez J, Toro MA (1999) The use of mathematical programming to control inbreeding in selection schemes. Journal of Animal Breeding and Genetics, 116, 447-466.
19. Field D, Chemnick L, Robbins M, Garner K, Ryder OA (1998) Paternity determination in captive lowland gorillas and orangutans and wild mountain gorillas by microsatellite analysis. Primates, 39, 199-209.
20. Foose TJ, Lande R, Flesness NR, Rabb G, Read B (1986) Propagation plans. Zoo Biology, 5, 139-146.
21. Frankham R, Hemmer H, Ryder OA et al. (1986) Selection in captive environments. Zoo Biology, 5, 127-138.
22. Frankham R, Loebel DA (1992) Modeling problems in conservation genetics using captive Drosophila populations: rapid genetic adaptation to captivity. Zoo Biology, 11, 333- 342.
23. Frankham R, Manning H, Margan SH, Briscoe DA (2000) Does equalisation of family sizes reduce genetic adaptation to captivity? Animal Conservation, 3, 357-363.
24. Frentiu FD, Clegg SM, Chittock J et al. (2008) Pedigree-free animal models: the relatedness matrix reloaded. Proceedings of the Royal Society of London-Series B: Biological Sciences, 275, 639-648.
25. Gascon C, Collins JP, Moore RD et al. (2007) Amphibian Conservation Action Plan. IUCN/SSC Amphibian Specialist Group. Gland, Switzerland.
26. Gautschi B, Jacob G, Negro JJ et al. (2003) Analysis of relatedness and determination of the source of founders in the captive bearded vulture, Gypaetus barbatus, population. Conservation Genetics, 4, 479-490.
27. Glaubitz JC, Rhodes EO Jr, DeWoody JA (2003) Prospects for inferring pairwise relationships with single nucleotide polymorphisms. Molecular Ecology, 12, 1039-1047.
28. Haig SM, Ballou JD, Casna NJ (1994) Identification of kin structure among Guam rail founders: a comparison of pedigrees and DNA profiles. Molecular Ecology, 3, 109- 119.
29. Haldane JBS (1924) A mathematical theory of natural and artificial selection. Part I. Transactions of the Cambridge Philosophical Society, 23, 10-41.
30. HedrickPW (2001) Conservation genetics: where are we now?Trends in Ecology and Evolution, 16, 629-636.
31. Hedrick PW (2002) The importance of the major histocompatibility complex in declining populations. In: Reproduction and Integrated Conservation Science (eds. Wildt DE, Holt B). Cambridge University Press, Cambridge.
32. Hedrick PW, Miller PS, Geffen E, Wayne R (1997) Genetic evaluation of the three captive Mexican wolf lineages. Zoo Biology, 16, 47-69.
33. Hu J, Pan H, Wan Q, Fang S (2007) Nuclear DNA microsatellite analysis of genetic diversity in captive populations of Chinese water deer. Small Ruminant Research, 67, 252-256.
34. Hughes AL (1991) MHC polymorphism and the design of captive breeding programs. Conservation Biology, 5, 249-251.
35. International Union for Conservation of Nature (IUCN) (2008) Available at http://www. iucnredlist.org.
36. Ivy JA, Miller A, Lacy RC, DeWoody JA (2009) Methods and prospects for using molecular data in captive breeding programs: an empirical example using parma wallabies (Macropus parma). Journal of Heredity, 100, 441-454.
37. Iyengar A, Gilbert T, Woodfine T et al. (2007) Remnants of ancient genetic diversity preserved within captive groups of scimitar-horned oryx (Oryx dammah). Molecular Ecology, 16, 2436-2449.
38. Jones AG, Ardren WR (2003) Methods of parentage analysis in natural populations. Molecular Ecology, 12, 2511-2523.
39. Jones KL, Glenn TC, Lacy RC et al. (2002) Refining the whooping crane studbook by incorporating microsatellite DNA and leg banding analyses. Conservation Biology, 16, 789-799.
40. Kimura M, Crow JF (1963) On the maximum avoidance of inbreeding. Genetical Research, 4, 399-415.
41. King JL (1965) The effect of litter culling - or family planning - on the rate of natural selection. Genetics, 51, 425-429.
42. Kruuk LEB, Hill WG (2008) Introduction. Evolutionary dynamics of wild populations: the use of long-term pedigree data. Proceedings of the Royal Society of London-Series B: Biological Sciences, 275, 593-596.
43. Lacy RC (1994) Managing genetic diversity in captive populations of animals. In: Restoration of Endangered Species (eds. BowlesML, Whelan CJ), pp. 63-89. Cambridge University Press, Cambridge.
44. Lacy RC (1995) Clarification of genetic terms and their use in the management of captive populations. Zoo Biology, 14, 565-577.
45. Lacy RC (2000) Should we select genetic alleles in our conservation breeding programs? Zoo Biology, 19, 279-282.
46. Lacy RC, Ballou JD (1998) Effectiveness of selection in reducing the genetic load in populations of Peromyscus polionotus during generations of inbreeding. Evolution, 52, 900- 909.
47. Lande R (1995) Breeding plans for small populations based on the dynamics of quantitative genetic variance. In: Population Management for Survival and Recovery: Analytical Methods and Strategies in Small Population Conservation (eds. Ballou JD, Gilpin M, Foose TJ), pp. 318-340. Columbia University Press, New York.
48. Lynch M, Ritland K (1999) Estimation of pairwise relatedness with molecular markers. Genetics, 152, 1753-1766.
49. Lynch M, Walsh B (1998) Genetic analysis of quantitative traits. Sinauer, Sunderland, MA.
50. Milligan BG (2003) Maximum-likelihood estimation of relatedness. Genetics, 163, 1153- 1167.
51. NeiM (1973) Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences USA, 70, 3321-3323.
52. Norton JE, Ashley MV (2004) Genetic variability and population differentiation in captive Baird's tapirs (Tapirus bairdii). Zoo Biology, 23, 521-531.
53. Pelletier F, Réale D, Watters J, Boakes EH, Garant D (2009) Value of captive populations for quantitative genetics research. Trends in Ecology and Evolution, 24, 263-270.
54. Petric A, Long S (2008) Population Analysis and Breeding Plan: Okapi (Okapia johnstoni) Species Survival Plan. Association of Zoos and Aquariums, Silver Spring, MD.
55. Petrie M, Moller AP (1991) Laying eggs in others' nests: intraspecific brood parasitism in birds. Trends in Ecology and Evolution, 6, 315-320.
56. Piper WH, Rabenold PP (1992) Use of fragment-sharing estimates from DNA fingerprinting to determine relatedness in a tropical wren. Molecular Ecology, 1, 69-78.
57. Princée FPG (1995) Overcoming the constraints of social structure and incomplete pedigree data through low-intensity genetic management. In: Population Management for Survival and Recovery: Analytical Methods and Strategies in Small Population Conservation (eds. Ballou JD, Gilpin M, Foose TJ), pp. 124-154. Columbia University Press, New York.
58. Queller DC, Goodnight KF (1989) Estimating relatedness using genetic markers. Evolution, 43, 258-275.
59. Ramirez O, Altet L, Ensenat C et al. (2006) Genetic assessment of the Iberian wolf Canis lupus signatus captive breeding program. Conservation Genetics, 7, 861-878.
60. Reddy A, Prakash V, Shivaji S (2007) A rapid, non-invasive, PCR-based method for identification of sex of the endangered Old World vultures (white-backed and long-billed vultures) - implications for captive breeding programmes. Current Science, 92, 659- 662.
61. Ritland K (1996) Estimators for pairwise relatedness and individual inbreeding coefficients. Genetical Research, 67, 175-185.
62. Roff DA (1997) Evolutionary Quantitative Genetics. Chapman & Hall, New York.
63. Rudnick JA, Lacy RC (2008) The impact of assumptions about founder relationships on the effectiveness of captive breeding strategies. Conservation Genetics, 9, 1439-1450.
64. Ruokonen M, Andersson A, Tegelstrom H (2007) Using historical captive stocks in conservation: the case of the lesser white-fronted goose. Conservation Genetics, 8, 197- 207.
65. Russello MA, Hyseni C, Gibbs JP et al. (2007) Lineage identification of Galapagos tortoises in captivity worldwide. Animal Conservation, 10, 304-311.
66. Schad K, editor (2008) Amphibian Population Management Guidelines. Amphibian Ark Amphibian Population Management Workshop; December 10-11, 2007; San Diego, CA. Amphibian Ark, available at www.amphibianark.org.
67. Selvin S (1980) Probability of nonpaternity determined by multiple allele codominant systems. American Journal of Human Genetics, 32, 276-278.
68. Sonesson AK, Meuwissen THE (2001) Minimization of rate of inbreeding for small populations with overlapping generations. Genetical Research, 77, 285-292.
69. Soule M, Gilpin M, Conway W, Foose T (1986) The millennium ark: how long a voyage, how many staterooms, how many passengers? Zoo Biology, 5, 101-113.
70. Spinks PQ, Shaffer HB (2007) Conservation phylogenetics of the Asian box turtles (Geoemydidae, Cuora): mitochondrial introgression, numts, and inferences from multiple nuclear loci. Conservation Genetics, 8, 641-657.
71. Thompson EA (1995) Genetic importance and genomic descent. In: Population Management for Survival and Recovery: Analytical Methods and Strategies in Small Population Conservation (eds. Ballou JD, Gilpin M, Foose TJ), pp. 76-111. Columbia University Press, New York.
72. Tzika AC, Remy C, Gibson R, Milinkovitch MC (2009) Molecular genetic analysis of a captive-breeding program: the vulnerable endemic Jamaican yellow boa. Conservation Genetics, 10, 69-77.
73. Van de Casteele T, Galbusera P, Matthysen E (2001) A comparison of microsatellite-based pairwise relatedness estimators. Molecular Ecology, 10, 1539-1549.
74. Vrijenhoek RC, Leberg PL (1991) Let's not throw out the baby with the bathwater: a comment on management for MHC diversity in captive populations. Conservation Biology, 5, 252-254.
75. Wang J (2003) Maximum likelihood estimation of admixture proportions from genetic data. Genetics, 164, 747-765.
76. Wang, J (2004) Monitoring and managing genetic variation in group breeding populations without individual pedigrees. Conservation Genetics, 5, 813-825.
77. Wang JL (2002) An estimator for pairwise relatedness using molecular markers. Genetics, 160, 1203-1215.
78. Willis K (1993) Use of animals with unknown ancestries in scientifically managed breeding programs. Zoo Biology, 12, 161-172.
79. Willis K (2001) Unpedigreed populations and worst-case scenarios. Zoo Biology, 20, 305- 314.
80. Yom-Tov Y (1980) Intraspecific nest parasitism in birds. Biological Reviews of the Cambridge Philosophical Society, 55, 93-108.
81. Zhang YP, Ryder OA, Zhao QG et al. (2005) Non-invasive giant panda paternity exclusion. Zoo Biology, 13, 569-573.
82. Zink AG (2000) The evolution of intraspecific brood parasitism in birds and insects. American Naturalist, 155, 395-405.