Combining genetic data to identify relatedness among founders in a genetically depauperate parrot, the Kakapo (Strigops habroptilus)

Conservation Genetics

Volumn 15, Issue 5, 2014, Pages 1013-1020

  Bergner, Laura M ^a   Jamieson, Ian G ^a   Robertson, Bruce C ^a  

^a UNIVERSITY OF OTAGO   (New Zealand)

Author keywords

Inbreeding; Microsatellites; mtDNA control region; Pedigree; Relatedness; Sibship inference

Indexed keywords

ENDEMIC SPECIES; EXTINCTION; GENETIC VARIATION; HATCHING; INBREEDING DEPRESSION; PASSERINE; POPULATION BOTTLENECK; RELATEDNESS;

NEW ZEALAND; SOUTH ISLAND; SOUTHLAND; STEWART ISLAND;

PSITTACIDAE; STRIGOPS HABROPTILUS;

EID: 84907083349     PISSN: 15660621     EISSN: 15729737     Source Type: Journal    
DOI: 10.1007/s10592-014-0595-y     Document Type: Article

References (51)

1. Ballard JWO, Whitlock MC (2004) The incomplete natural history of mitochondria. Mol Ecol 13:729–744
2. Ballou JD, Lacy RC (1995) Identifying genetically important individuals for management of genetic variation in pedigreed populations. In: Ballou JD, Gilpin M, Foose TJ (eds) Population management for survival and recovery. Columbia University Press, New York, pp 76–111
3. Blouin MS (2003) DNA-based methods for pedigree reconstruction and kinship analysis in natural populations. Trends Ecol Evol 18:503–511
4. 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
5. Eason DK, Elliott GP, Merton DV, Jansen PW, Harper GA, Moorhouse RJ (2006) Breeding biology of kakapo (Strigops habroptilus) on offshore island sanctuaries, 1990–2002. Notornis 53:27–36
6. Elliott GP, Merton DV, Jansen PW (2001) Intensive management of a critically endangered species: the kakapo. Biol Conserv 99:121–133
7. Ewing SR, Nager RG, Nicoll MAC, Aumjaud A, Jones CG, Keller LF (2008) Inbreeding and loss of genetic variation in a reintroduced population of Mauritius kestrel. Conserv Biol 22:395–404
8. Frankham R, Ballou JD, Briscoe DA (2010) Introduction to conservation genetics, 2nd edn. Cambridge University Press, Cambridge
9. Gautschi B, Jacob G, Negro JJ, Godoy JA, Mullar JP, Schmid B (2003) Analysis of relatedness and determination of the source of founders in the captive bearded vulture, Gypaetus barbatus, population. Conserv Genet 4:479–490
10. Goncalves da Silva A, Lalonde DR, Quse V, Shoemaker A, Russello MA (2010) Genetic approaches refine ex situ Lowland Tapir (Tapirus terrestris) conservation. J Hered 101:581–590
11. Grueber CE, Jamieson IG (2008) Quantifying and managing the loss of genetic variation in a free-ranging population of takahe through the use of pedigrees. Conserv Genet 9:645–651
12. Guerier AS, Bishop JM, Crawford SJ, Schmidt-Küntzel A, Stratford KJ (2012) Parentage analysis in a managed free ranging population of southern white rhinoceros: genetic diversity, pedigrees and management. Conserv Genet 13:811–822
13. Henkel JR, Jones KL, Hereford SG, Savoie ML, Leibo SP, Howard JJ (2012) Integrating microsatellite and pedigree analyses to facilitate the captive management of the endangered Mississippi sandhill crane (Grus canadensis pulla). Zoo Biol 31:322–335
14. Herbinger CM, O’Reilly PT, Verspoor E (2006) Unravelling first-generation pedigrees in wild endangered salmon populations using molecular genetic markers. Mol Ecol 15:2261–2275
15. IUCN 2011. IUCN red list of threatened species. Version 2011.2. www.iucnredlist.org. Downloaded on 20 February 2012
16. 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
17. Jamieson IG (2010) Founder effects, inbreeding, and loss of genetic diversity in four avian reintroduction programs. Conserv Biol 25:115–123
18. Jones OR, Wang J (2010) COLONY: a program for parentage and sibship inference from multilocus genotype data. Mol Ecol Resour 10:551–555
19. Jones KL, Glenn TC, Lacy RC, Pierce JR, Unruh N, Mirande CM, Chavez-Ramirez F (2002) Refining the whooping crane studbook by incorporating microsatellite DNA and leg-banding analyses. Conserv Biol 16:789–799
20. Karaket T, Poompuang S (2012) CERVUS vs. COLONY for successful parentage and sibship determinations in freshwater prawn Macrobrachium rosenbergii de Man. Aquaculture 324–325:307–311
21. Kvist L, Martens J, Nazarenko AA, Orell M (2003) Paternal leakage of mitochondrial DNA in the great tit (Parus major). Mol Biol Evol 20:243–247
22. Lacy RC (1989) Analysis of founder representation in pedigrees: founder equivalents and founder genome equivalents. Zoo Biol 8:111–123
23. Lloyd B, Powlesland R (1994) The decline of Kakapo and attempts at conservation by translocation. Biol Conserv 69:75–85
24. Lynch M, Ritland K (1999) Estimation of pairwise relatedness with molecular markers. Genetics 152:1753–1766
25. Miller HC, Lambert DM, Millar CD, Robertson BC, Minot EO (2003) Minisatellite DNA profiling detects lineages and parentage in the endangered kakapo. Conserv Genet 4:265–274
26. Neill E (2008) Kakapo recovery plan, 2006–2016. Department of Conservation New Zealand, Wellington
27. Pemberton JM (2008) Wild pedigrees: the way forward. Proc R Soc B 275:613–621
28. Powlesland RG, Roberts A, Lloyd BD, Merton DV (1995) Number, fate, and distribution of kakapo (Strigops habroptilus) found on Stewart Island, New Zealand, 1979–92. N Z J Zool 22:239–248
29. Powlesland RG, Merton DV, Cockrem JF (2006) A parrot apart: the natural history of the kakapo (Strigops habroptilus), and the context of its conservation management. Notornis 53:3–26
30. Queller DC, Goodnight KF (1989) Estimating relatedness using genetic markers. Evolution 43:258–275
31. R Development Core Team (2012) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org/. Accessed 25 June 2012
32. Ralls K, Ballou JD (2004) Genetic status and management of California condors. Condor 106:215–228
33. Read KD, Lemay MA, Acheson S, Boulding EG (2012) Using molecular pedigree reconstruction to evaluate the long-term survival of outplanted hatchery-reared larval and juvenile northern abalone (Haliotis kamtschatkana). Conserv Genet 13:801–810
34. Riehl C (2012) Mating system and reproductive skew in a communally breeding cuckoo: hard-working males do not sire more young. Anim Behav 84:707–714
35. Robertson BC (2006) The role of genetics in kakapo recovery. Notornis 53:173–183
36. Robertson BC, Minot EO, Lambert DM (2000) Microsatellite primers for the kakapo (Strigops habroptilus) and their utility in other parrots. Conserv Genet 1:93–95
37. Robertson BC, Frauenfelder N, Eason DK, Elliot G, Moorhouse R (2009) Thirty polymorphic microsatellite loci from the critically endangered kakapo (Strigops habroptilus). Mol Ecol Resour 9:664–666
38. Robertson BC, Blanco JM, Adams SL, Eason DK, Vercoe DA, Moorhouse RJ (2011) Artificial insemination allows genetic management of the kakapo Strigops habroptilus. Conference abstract, presented at the 25th International Congress for Conservation Biology, Auckland, NZ. 5–9 December 2011
39. Rudnick JA, Lacy RC (2008) The impact of assumptions about founder relationships on the effectiveness of captive breeding strategies. Conserv Genet 9:1439–1450
40. Russello MA, Amato G (2004) Ex situ population management in the absence of pedigree information. Mol Ecol 13:2829–2840
41. Swinnerton KJ, Groombridge JJ, Jones CG, Burn RW, Mungroo Y (2004) Inbreeding depression and founder diversity among captive and free-living populations of the endangered pink pigeon Columba mayeri. Anim Conserv 7:353–364
42. Tzika AC, Remy C, Gibson R, Milinkovitch MC (2008) Molecular genetic analysis of a captive-breeding program: the vulnerable endemic Jamaican yellow boa. Conserv Genet 10:69–77
43. van de Casteele T, Galbusera P, Matthysen E (2001) A comparison of microsatellite-based pairwise relatedness estimators. Mol Ecol 10:1539–1549
44. Walling CA, Pemberton JM, Hadfield JD, Kruuk LEB (2010) Comparing parentage inference software: reanalysis of a red deer pedigree. Mol Ecol 19:1914–1928
45. Walsh PS, Metzger DA, Higuchi R (1991) Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 10:506–513
46. Wang J (2007) Triadic IBD coefficients and applications to estimating pairwise relatedness. Genet Res 89:135–153
47. Wang J (2011) COANCESTRY: a program for simulating, estimating and analysing relatedness and inbreeding coefficients. Mol Ecol Resour 11:141–145
48. Wang J, Santure AW (2009) Parentage and sibship inference from multilocus genotype data under polygamy. Genetics 181:1579–1594
49. Weir BS, Anderson AD, Hepler AB (2006) Genetic relatedness analysis: modern data and new challenges. Nat Rev Genet 7:771–780
50. White K (2012) The role of inbreeding in the reproductive fitness of kakapo (Strigops habroptilus). Masters Thesis, University of Otago
51. Willis K (2001) Unpedigreed populations and worst-case scenarios. Zoo Biol 20:305–314