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Conservation Genetics

, Volume 11, Issue 3, pp 1043–1049 | Cite as

Detecting bottlenecks using BOTTLENECK 1.2.02 in wild populations: the importance of the microsatellite structure

  • Romane CristescuEmail author
  • William Bruce Sherwin
  • Kathrine Handasyde
  • Valma Cahill
  • Desmond W. Cooper
Research Article

Abstract

Reduced, or bottlenecked, populations are more prone to adverse events. Thus, the detection of genetic bottleneck signatures in wildlife is an important issue for conservation. BOTTLENECK 1.2.02 is a software commonly used for detecting genetic characteristics of past bottlenecks. Here we test the efficiency with which this software detects bottlenecks in two koala populations of known history. The sign test performed well for both populations, particularly under the infinite alleles model for mutation. This suggests this model could be the more realistic for marsupial microsatellites than other mutation models. Under the allele frequency distribution test, the two populations falsely appeared to be at mutation/drift equilibrium. However, this test could detect the bottleneck when only imperfect repeat microsatellites were included in the analysis. We thus recommend further investigation of imperfect repeat microsatellites, which could be more powerful for bottleneck detection. These results underline the cautious approach researchers and conservationists should take when studying the past of unknown populations.

Keywords

Bottleneck Infinite alleles model Marsupial Perfect and imperfect repeat microsatellites 

Abbreviation

IAM

Infinite alleles model

SMM

Stepwise mutation model

TPM

Two phase model

Notes

Acknowledgments

This worked has been funded by ARC linkage grant (LPO560344). We thank K. Carlyon for providing koala samples, B. L. Carlsson and A. Wilton for technical assistance. We also thank the Rangers from French Island National Park (Parks Victoria) and the members of the Koala Management Program (Department for Environment and Heritage) for their support and assistance in the field. We would also like to thank two anonymous reviewers for their most helpful comments.

References

  1. Amos W, Balmford A (2001) When does conservation genetics matter? Heredity 87:257–265CrossRefPubMedGoogle Scholar
  2. Bijlsma R, Bundgaard J, Boerema AC (2000) Does inbreeding affect the extinction risk of small populations?: predictions from Drosophila. J Evol Biol 13(3):502–514CrossRefGoogle Scholar
  3. Bouzat JL, Cheng HH, Lewin HA et al (1998) Genetic evaluation of a demographic bottleneck in the greater prairie chicken. Conserv Biol 12(4):836–843CrossRefGoogle Scholar
  4. Brook BW, Tonkyn DW, O’Grady JJ et al (2002) Contribution of inbreeding to extinction risk in threatened species. Conserv Ecol 6(1):16. Available from http://www.consecol.org/vol16/iss11/art16 Google Scholar
  5. Chakraborty R, Nei M (1977) Bottleneck effects on average heterozygosity and genetic distance with stepwise mutation model. Evolution Int J org Evolution 31(2):347–356Google Scholar
  6. Cornuet JM, Luikart G (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144(4):2001–2014PubMedGoogle Scholar
  7. Cristescu R, Cahill V, Handasyde K et al (2009) Inbreeding and testicular abnormalities in a bottlenecked population of koalas, Phascolarctos cinereus. Wildl Res 36(4):299–308CrossRefGoogle Scholar
  8. Di Rienzo A, Peterson AC, Garza JC et al (1994) Mutational processes of simple-sequence repeat loci in human populations. Proc Natl Acad Sci U S A 91(8):3166–3170CrossRefPubMedGoogle Scholar
  9. Frankham R (2005) Genetics and extinction. Biol Conserv 126(2):131–140CrossRefGoogle Scholar
  10. Garza JC, Williamson EG (2001) Detection of reduction in population size using data from microsatellite loci. Mol Ecol 10(2):305–318CrossRefPubMedGoogle Scholar
  11. Gibson M, Irvin M (2003) Tree condition assessment of selected sites on French Island. Report to Parks Victoria, Melbourne, Centre for Environmental Management University of Ballarat, p 47Google Scholar
  12. Goldstein DB, Clark AG (1995) Microsatellite variation in North American populations of Drosophila melanogaster. Nucleic Acids Res 23(19):3882–3886CrossRefPubMedGoogle Scholar
  13. He W, Lin L, Shen F et al (2008) Genetic diversities of the giant panda (Ailuropoda melanoleuca) in Wanglang and Baoxing nature reserves. Conserv Genet 9(6):1541–1546CrossRefGoogle Scholar
  14. Hedrick P, Miller P (1992) Conservation genetics: techniques and fundamentals. Ecol Appl 2:30–46CrossRefGoogle Scholar
  15. Hoelzel AR, Halley J, O’Brien SJ et al (1993) Elephant seal genetic variation and the use of simulation models to investigate historical population bottlenecks. J Hered 84(6):443–449PubMedGoogle Scholar
  16. Houlden BA, England P, Sherwin WB (1996a) Paternity exclusion in koalas using hypervariable microsatellites. J Hered 87(2):149–152PubMedGoogle Scholar
  17. Houlden BA, England PR, Taylor AC et al (1996b) Low genetic variability of the koala Phascolarctos cinereus in south-eastern Australia following a severe population bottleneck. Mol Ecol 5(2):269–281PubMedGoogle Scholar
  18. Hull J, Anderson R, Bradbury M et al (2008) Population structure and genetic diversity in Swainson’s Hawks (Buteo swainsoni): implications for conservation. Conserv Genet 9(2):305–316CrossRefGoogle Scholar
  19. Jimenez JA, Hughes KA, Alaks G et al (1994) An experimental study of inbreeding depression in a natural habitat. Science 266(5183):271–273CrossRefPubMedGoogle Scholar
  20. Lande R (1994) Risk of population extinction from fixation of new deleterious mutations. Evolution Int J org Evolution 48:1460–1469Google Scholar
  21. Le Page SL, Livermore RA, Cooper DW et al (2000) Genetic analysis of a documented population bottleneck: introduced Bennett’s wallabies (Macropus rufogriseus rufogriseus) in New Zealand. Mol Ecol 9(6):753–763CrossRefPubMedGoogle Scholar
  22. Luikart G, Cornuet JM (1998) Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data. Conserv Biol 12(1):228–237CrossRefGoogle Scholar
  23. Luikart G, Allendorf FW, Cornuet JM et al (1998) Distortion of allele frequency distributions provides a test for recent population bottlenecks. J Hered 89(3):238–247CrossRefPubMedGoogle Scholar
  24. Lynch M, Conery J, Burger R (1995) Mutation accumulation and the extinction of small populations. Am Nat 146(4):489–518CrossRefGoogle Scholar
  25. Madsen T, Stille B, Shine R (1996) Inbreeding depression in an isolated population of adders Vipera berus. Biol Conserv 75(2):113–118CrossRefGoogle Scholar
  26. Martin RW (1981) Age-specific fertility in three populations of the koala, Phascolarctos cinereus Goldfuss, in Victoria. Wildl Res 8(2):275–283CrossRefGoogle Scholar
  27. Martin R, Handasyde K (1999) The koala: natural history, conservation and management, Australian natural history series. University of New South Wales Press Ltd., Hong KongGoogle Scholar
  28. Maruyama T, Fuerst PA (1985) Population bottlenecks and nonequilibrium models in population genetics, II. Number of alleles in a small population that was formed by a recent bottleneck. Genetics 111(3):675–689PubMedGoogle Scholar
  29. Masters P, Duka T, Berris S et al (2004) Koalas on Kangaroo Island: from introduction to pest status in less than a century. Wildl Res 31(3):267–272CrossRefGoogle Scholar
  30. Mills LS, Smouse PE (1994) Demographic consequences of inbreeding in remnant populations. Am Nat 144(3):412–431CrossRefGoogle Scholar
  31. Nei M (1987) Molecular evolutionary genetics. Colombia University Press, New YorkGoogle Scholar
  32. Nei M, Li WH (1976) The transient distribution of allele frequencies under mutation pressure. Genet Res 28(3):205–214CrossRefPubMedGoogle Scholar
  33. Nei M, Maruyama T, Chakraborty R (1975) The bottleneck effect and genetic variability in populations. Evolution Int J org Evolution 29(1):1–10Google Scholar
  34. Newman D, Pilson D (1997) Increased probability of extinction due to decreased genetic effective population size: experimental populations of Clarkia pulchella. Evolution Int J org Evolution 51(2):354–362Google Scholar
  35. O’Brien SJ, Roelke ME, Marker L et al (1985) Genetic basis for species vulnerability in the cheetah. Science 227(4693):1428–1434CrossRefPubMedGoogle Scholar
  36. O’Brien SJ, Wildt DE, Bush M et al (1987) East African cheetahs: evidence for two population bottlenecks? Proc Natl Acad Sci 84(2):508–511CrossRefPubMedGoogle Scholar
  37. Ovenden JR, White RW (1990) Mitochondrial and allozyme genetics of incipient speciation in a landlocked population of Galaxias truttaceus (Pisces: Galaxiidae). Genetics 124(3):701–716PubMedGoogle Scholar
  38. Packer C, Pusey AE, Rowley H et al (1991) Case study of a population bottleneck: lions of the Ngorongoro crater. Conserv Biol 5(2):219–230CrossRefGoogle Scholar
  39. Piry S, Luikart G, Cornuet JM (1999) BOTTLENECK: A computer program for detecting recent reductions in the effective population size using allele frequency data. J Hered 90(4):502–503CrossRefGoogle Scholar
  40. Schlötterer C (2000) Evolutionary dynamics of microsatellite DNA. Chromosoma 109(6):365–371CrossRefPubMedGoogle Scholar
  41. Schlötterer C, Tautz D (1992) Slippage synthesis of simple sequence DNA. Nucleic Acids Res 20(2):211–215CrossRefPubMedGoogle Scholar
  42. Sherwin WB, Murray ND (1990) Population and conservation genetics of marsupials. Aust J Zool 37(2–4):161–180Google Scholar
  43. Taylor A, Sherwin W, Wayne R (1994) Genetic variation of microsatellite loci in a bottleneck species: the northern hairy nosed wombat Lasiorhinus krefftii. Mol Ecol 3:277–290CrossRefPubMedGoogle Scholar
  44. Thomas A, White JBS (2007) Genetic diversity and population size: island populations of the common shrew, Sorex araneus. Mol Ecol 16(10):2005–2016CrossRefGoogle Scholar
  45. Vazquez JF, Perez T, Albornoz J et al (2000) Estimation of microsatellite mutation rates in Drosophila melanogaster. Genet Res 76(3):323–326CrossRefGoogle Scholar
  46. Vucetich JA, Waite TA (1999) Erosion of heterozygosity in fluctuating populations. Conserv Biol 13(4):860–868CrossRefGoogle Scholar
  47. Weber JL (1990) Informativeness of human (Dc-Da)N.(Dg-Dt)N polymorphisms. Genomics 7(4):524–530CrossRefPubMedGoogle Scholar
  48. Whitehouse AM, Harley EH (2001) Post-bottleneck genetic diversity of elephant populations in South Africa, revealed using microsatellite analysis. Mol Ecol 10(9):2139–2149CrossRefPubMedGoogle Scholar
  49. Wierdl M, Dominska M, Petes TD (1997) Microsatellite instability in yeast: dependence on the length of the microsatellite. Genetics 146(3):769–779PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Romane Cristescu
    • 1
    Email author
  • William Bruce Sherwin
    • 1
  • Kathrine Handasyde
    • 2
  • Valma Cahill
    • 3
  • Desmond W. Cooper
    • 1
  1. 1.Evolution and Ecology Research Centre, School of Biological, Earth and Environmental SciencesUniversity of New South WalesKensingtonAustralia
  2. 2.Department of ZoologyUniversity of MelbourneMelbourneAustralia
  3. 3.Dubbo CollegeDubboAustralia

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