Extending pedigree analysis for uncertain parentage and diverse breeding systems

Journal of Heredity

Volumn 103, Issue 2, 2012, Pages 197-205

  Lacy, Robert C ^a  

^a BROOKFIELD ZOO   (United States)

Author keywords

conservation genetics; inbreeding coefficient; kinship; population management; software

Indexed keywords

ARTICLE; BREEDING; CLONING; DIPLOIDY; HEREDITY; HOMOZYGOSITY; PARENTHOOD; PEDIGREE ANALYSIS; PRIORITY JOURNAL; PROGENY;

ALGORITHMS; BREEDING; CONSERVATION OF NATURAL RESOURCES; GENETIC VARIATION; GENETICS, POPULATION; MODELS, GENETIC; PEDIGREE; SOFTWARE;

EID: 84857604027     PISSN: 00221503     EISSN: 14657333     Source Type: Journal    
DOI: 10.1093/jhered/esr135     Document Type: Article

References (37)

1. Ballou JD, Lacy RC. 1995. Identifying genetically important individuals for management of genetic diversity in pedigreed populations. In: Ballou JD, Gilpin M, Foose TJ, editors. Population management for survival & recovery. Analytical methods and strategies in small population conservation. New York: Columbia University Press. p. 76-111.
2. Ballou JD, Lacy RC, Pollak JP. 2011. PMx: software for demographic and genetic analysis and management of pedigreed populations. Version 1.0. Brookfield (IL): Chicago Zoological Society.
3. Ballou JD, Lees C, Faust LJ, Long S, Lynch C, Bingaman Lackey L, Foose TJ. 2010. Demographic and genetic management of captive populations. In: Kleiman DG, Thompson KV, Baer CK, editors. Wild mammals in captivity: principles and techniques for zoo management. 2nd ed. Chicago (IL): University of Chicago Press. p. 219-252.
4. Booth W, Johnson DH, Moore S, Schal C, Vargo EL. 2011. Evidence for viable, non-clonal but fatherless Boa constrictors. Biol Lett. 7:253-256.
5. Burlingham-Johnson A, Clarke D, Pearce-Kelly P. 1994. CERCI: a computer system for the demographic and genetic analysis of captive invertebrates, fish and other populations of colony animals. Int Zoo Yearb. 33:278-283.
6. Caballero A, Toro M.A. 2000. Interrelations between effective population size and other pedigree tools for the management of conserved populations. Genet Res. 75:331-343. (Pubitemid 30398388)
7. Dubach J, Sajewicz A, Pawley R. 1997. Parthenogenesis in the Arafuran file snake (Acrochordus arafurae). Herpetol Nat Hist. 5:11-18.
8. Falconer DS, Mackay TFC. 1996. Introduction to quantitative genetics. 4th ed. Harlow (UK): Longman.
9. Fernández J, Toro MA, Caballero A. 2001. Practical implementations of optimal management strategies in conservation programmes: a mate selection method. Anim Biodivers Conserv. 24:17-24. (Pubitemid 34812897)
10. Fernández J, Toro MA, Caballero A. 2003. Fixed contributions designs versus minimization of global coancestry to control inbreeding in small populations. Genetics. 165:885-894. (Pubitemid 37337650)
11. Fernández J, Toro MA, Caballero A. 2004. Managing individuals' contributions to maximize the allele diversity maintained in small, conserved populations. Conserv Biol. 18:1-10.
12. Fernández J, Villanueva B, Pong-Wong R, Toro M.A. 2005. Efficiency of the use of pedigree and molecular marker information in conservation programs. Genetics. 170:1313-1321. (Pubitemid 41105484)
13. Flesness NR. 1977. Gene pool conservation and computer analysis. Int Zoo Yearb. 17:77-81.
14. Foose TJ, Ballou JD. 1988. Population management: theory and practice. Int Zoo Yearb. 27:26-41.
15. ISIS. 2011. SPARKS (Single Population Analysis and Records Keeping System). Version 1.6. Eagan (MN): International Species Information System.
16. Ivy JA, Lacy RC. 2010. Using molecular methods to improve the genetic management of captive breeding programs for threatened species. In: DeWoody JA, Bickham JW, Michler CH, Nicols KM, Rhodes OE, Woeste KE, editors. Molecular approaches in natural resource conservation and management. Cambridge (UK): Cambridge University Press. p. 267-295.
17. Ivy JA, Lacy RC. 2012. A comparison of strategies for selecting breeding pairs to preserve maximal genetic diversity in breeding programs. J Hered.
18. 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). J Hered. 100:441-454.
19. Lacy RC. 1989. Analysis of founder representation in pedigrees: founder equivalents and founder genome equivalents. Zoo Biol. 8:111-124.
20. Lacy RC. 1994. Managing genetic diversity in captive populations of animals. In: Bowles ML, Whelan CJ, editors. Restoration and recovery of endangered plants and animals. Cambridge (UK): Cambridge University Press. p. 63-89.
21. Lacy RC. 1995. Clarification of genetic terms and their use in the management of captive populations. Zoo Biol. 14:565-577.
22. Lacy RC. 2009. Stopping evolution: genetic management of captive populations. In: Amato G, DeSalle R, Ryder OA, Rosenbaum, HC, editors. Conservation genetics in the age of genomics. New York: Columbia University Press. p. 58-81.
23. Lacy RC, Ballou JD, Pollak JP. 2011. PMx: software package for demographic and genetic analysis and management of pedigreed populations. Methods Ecol Evol. Advance Access published September 5, 2011, doi:10.1111/j.2041-210X.2011.00148.x
24. Lacy RC, Ballou JD, Princée F, Starfield A, Thompson E. 1995. Pedigree analysis. In: Ballou JD, Gilpin M, Foose TJ, editors. Population management for survival & recovery. Analytical methods and strategies in small population conservation. New York: Columbia University Press. p. 57-75.
25. Leus K, Traylor-Holzer K, Lacy RC. 2011. Genetic and demographic population management in zoos and aquariums: recent developments, future challenges and opportunities for scientific research. Int Zoo Yearb. 45:213-225.
26. MacCluer JW, VandeBerg JL, Read B, Ryder OA. 1986. Pedigree analysis by computer simulation. Zoo Biol. 5:147-160.
27. Maynard Smith J. 1978. The evolution of sex. Cambridge (UK): Cambridge University Press.
28. Nei M. 1973. Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA. 70:3321-3323.
29. Oliehoek P. 2009. Genetic conservation of endangered animal populations [PhD thesis]. [Wageningen (Netherlands)]: Wageningen University.
30. Pearce-Kelly P, Morgan R, Honan P, Barrett P, Perrotti L, Magdich M, Daniel BA, Sullivan E, Veltman K, Clarke D, et al. 2007. The conservation value of insect breeding programmes: rationale, evaluation tools and example programme case studies. In: Stewart AJA, New TR, Lewis OT, editors. Insect conservation biology. Oxfordshire (UK): CABI. p. 57-73.
31. Penning M, McGregor Reid G, Koldewey H, Dick G, Andrews B, Arai K, Garratt P, Gendron S, Lange J, Tanner K, et al., editors. 2009. Turning the tide: a global aquarium strategy for conservation and sustainability. Bern (Switzerland): World Association of Zoos and Aquariums.
32. Rudnick JA, Lacy RC. 2008. The impact of assumptions about founder relationships on the effectiveness of captive breeding strategies. Conserv Genet. 9:1439-1450.
33. Stöck M, Ustinova J, Betto-Colliard C, Schartl M, Moritz C, Perrin N. 2011. Simultaneous Mendelian and clonal genome transmission in a sexually reproducing, all-triploid vertebrate. Proc R Soc B Biol Sci. doi: 10.1098/rspb.2011.1738
34. Wang J. 2004. Monitoring and managing genetic variation in group breeding populations without individual pedigrees. Conserv Genet. 5:813-825. (Pubitemid 41201443)
35. Watts PC, Buley KR, Sanderson S, Boardman W, Ciofi C, Gibson R. 2006. Parthenogenesis in Komodo dragons. Nature. 444:1021-1022. (Pubitemid 46018511)
36. Willis K. 1993. Use of animals with unknown ancestries in scientifically managed breeding programs. Zoo Biol. 12:161-172.
37. Willis K. 2001. Unpedigreed populations and worst-case scenarios. Zoo Biol. 20:305-314.