Conservation Genetics

, Volume 11, Issue 4, pp 1363–1374 | Cite as

Species limits and population differentiation in New Zealand snipes (Scolopacidae: Coenocorypha)

  • Allan J. BakerEmail author
  • Colin M. Miskelly
  • Oliver Haddrath
Research Article


At least four species of New Zealand snipes (Coenocorypha) became extinct following the introduction of predatory mammals, and another two species suffered massive range reductions. To investigate species limits and population differentiation in six of the seven remaining offshore populations, we assayed variation in nine microsatellite loci and 1,980 base pairs of four mitochondrial DNA (mtDNA) genes. Genetic diversity in all populations except the largest one on Adams Island in the Auckland Islands was very low in both genomes. Alleles were fixed at many microsatellite loci and for single mtDNA haplotypes, particularly in the populations in the Chathams, Snares, Antipodes and Campbell Islands. Strong population structure has developed, and Chathams and Snares Islands populations are effectively genetically isolated from one another and from the more southern island populations. Based on reciprocal monophyly of lineages and their morphological distinctiveness we recommend that three phylogenetic species should be recognized, C. pusilla in the Chatham Islands, C. huegeli in the Snares Islands and C. aucklandica in the southern islands. The populations of C. aucklandica in the Auckland Islands, Antipodes Island and Campbell Island may warrant recognition as subspecies, and all should be managed as separate conservation units.


New Zealand snipes Genetic structure Random drift Human-induced population reductions Species limits 



We thank BDG Synthesis, the Natural Sciences and Engineering Research Council of Canada (grant A 200 to AJB), and the New Zealand Department of Conservation (DOC) for financial support for fieldwork and labwork. Snipe blood and feather samples were collected with the assistance of Dave Barker, Karen Barlow, Jeremy Carroll, Graeme Elliott, James Fraser, Sheryl Hamilton, Christine Reed, Kath Walker, Murray Willans, and Al Wiltshire. Access to nature reserves and collection of samples was authorised by the DOC Southland and Wellington Conservancies. Figure 1 was prepared by Chris Edkins, DOC.


  1. Aikman H, Miskelly C (2004) Birds of the Chatham Islands. Department of Conservation, WellingtonGoogle Scholar
  2. Bandelt H-J, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48PubMedGoogle Scholar
  3. Barker D, Carroll J, Edmonds H, Fraser J, Miskelly CM (2005) Discovery of a previously unknown Coenocorypha snipe in the Campbell Island group, New Zealand subantarctic. Notornis 52:143–149Google Scholar
  4. Beerli P (2004) Migrate: documentation and program, part of LAMARC version 2.0. Revised December 23, 2004. Distributed over the internet,
  5. Beerli P, Felsenstein J (1999) Maximum likelihood estimation of migration rates and population numbers of two populations using a coalescent approach. Genetics 152:763–773PubMedGoogle Scholar
  6. Beerli P, Felsenstein J (2001) Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc Nat Acad Sci USA 98:4563–4568CrossRefPubMedGoogle Scholar
  7. Bell LC (1955) Notes on the birds of the Chatham Islands. Notornis 6:65–68Google Scholar
  8. Bell BD (1974) Mangere Island. Wildlife—a review, vol 5. New Zealand Wildlife Service, Department of Internal Affairs, Wellington, pp 31–34Google Scholar
  9. Dallas JF (1992) Estimation of microsatellite mutation rates in recombinant inbred strains of mouse. Mamm Genome 3:452–456CrossRefPubMedGoogle Scholar
  10. Dawson EW (1955) The birds of the Chatham Islands 1954 Expedition. Notornis 6:78–82Google Scholar
  11. Dean AD, Greenwald JE (1995) Use of filtered pipet tips to elute DNA from agarose gels. Biotechniques 18:980PubMedGoogle Scholar
  12. Dib C, Faure S, Fizames C et al (1996) A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature 380:152–154CrossRefPubMedGoogle Scholar
  13. England PR, Graham HR, Osler GHR, Woodworth LM, Montgomery ME, David A, Briscoe DA, Frankham R (2003) Effects of intense versus diffuse population bottlenecks on microsatellite genetic diversity and evolutionary potential. Conserv Genet 4:595–604CrossRefGoogle Scholar
  14. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure: extensions to linked loci and correlated allele frequencies. Genetics 164:1567–1587PubMedGoogle Scholar
  15. Fleming CA (1982) George Edward Lodge, the unpublished New Zealand bird paintings. Nova Pacifica, WellingtonGoogle Scholar
  16. Fu Y-X (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915–925PubMedGoogle Scholar
  17. Fu Y-X, Li W-H (1993) Statistical tests of neutrality of mutations. Genetics 133:693–709PubMedGoogle Scholar
  18. Glaubitz JC (2004) CONVERT: a user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Mol Ecol Notes 4:309–310CrossRefGoogle Scholar
  19. Hagelberg EH (1994) Mitochondrial DNA from ancient bones. In: Herrman B, Hummel S (eds) Ancient DNA. Springer, New York, pp 195–205Google Scholar
  20. Hamilton MB, Pincus EL, Di Fiore A, Fleischer RC (1999) Universal linker and ligation procedures for construction of genomic DNA libraries enriched for microsatellites. Biotechniques 27:501–507Google Scholar
  21. Higgins PJ, Davies SJJF (1996) Handbook of Australian, New Zealand and Antarctic birds vol 3 Snipe to pigeons. Oxford University Press, MelbourneGoogle Scholar
  22. Holdaway RN, Worthy TH, Tennyson AJD (2001) A working list of breeding bird species of the New Zealand region at first human contact. New Zealand J Zool 28:119–187CrossRefGoogle Scholar
  23. Jamieson IG, Wallis GP, Briskie JV (2006) Inbreeding and endangered species management: is New Zealand out of step with the rest of the world? Conserv Biol 20:38–47CrossRefPubMedGoogle Scholar
  24. Lacy RC (1997) Importance of genetic variation in the viability of mammalian populations. J Mammal 78:320–335CrossRefGoogle Scholar
  25. Millener PR (1999) The history of the Chatham Islands’ bird fauna of the last 7000 years, a chronicle of change and extinction. In: Proceedings of the 4th international meeting of the society of avian paleontology and evolution (Washington DC, June 1996) Smithsonian contributions to paleobiology, vol 89, pp 85–109Google Scholar
  26. Miskelly CM (1987) The identity of the hakawai. Notornis 34:95–116Google Scholar
  27. Miskelly CM (1988) The Little Barrier Island snipe. Notornis 35:273–281Google Scholar
  28. Miskelly CM (1990) Breeding systems of New Zealand snipe Coenocorypha aucklandica and Chatham Island snipe C. pusilla; are they food limited? Ibis 132:366–379CrossRefGoogle Scholar
  29. Miskelly CM (2000) Historical records of snipe from Campbell Island, New Zealand. Notornis 47:131–140Google Scholar
  30. Miskelly CM, Fraser JR (2006a) Campbell Island snipe (Coenocorypha undescribed sp) recolonise subantarctic Campbell Island following rat eradication. Notornis 53:353–359Google Scholar
  31. Miskelly C, Fraser J (2006b) Campbell Island snipe survey, January 2006. Department of Conservation, WellingtonGoogle Scholar
  32. Miskelly CM, Sagar PM, Tennyson AJD, Scofield RP (2001) Birds of the Snares Islands, New Zealand. Notornis 48:1–40Google Scholar
  33. Miskelly CM, Walker KJ, Elliott GP (2006) Breeding ecology of three subantarctic snipes (genus Coenocorypha). Notornis 53:361–374Google Scholar
  34. Miskelly CM, Dowding JE, Elliott GP, Powlesland RG, Robertson HA, Sagar PM, Scofield RP, Taylor GA (2008) Conservation status of New Zealand birds, 2008. Notornis 55:117–135Google Scholar
  35. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New YorkGoogle Scholar
  36. Nielsen R, Wakeley J (2001) Distinguishing migration from isolation: a Markov Chain Monte Carlo approach. Genetics 158:885–896PubMedGoogle Scholar
  37. Nilsson RJ, Kennedy ES, West JA (1994) The birdlife of South East Island (Rangatira), Chatham Islands, New Zealand. Notornis 41(supplement):109–125Google Scholar
  38. Pereira SL, Baker AJ (2006) A mitogenomics timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock. Mol Bio Evol 23:1731–1740CrossRefGoogle Scholar
  39. Posada D, Crandall KA (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14:817–818CrossRefPubMedGoogle Scholar
  40. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedGoogle Scholar
  41. Ramakrishnan U, Hadly EA, Mountain JL (2005) Detecting past population bottlenecks using temporal genetic data. Mol Ecol 14:2915–2922CrossRefPubMedGoogle Scholar
  42. Raymond M, Rousset F (1995) GENEPOP: population genetics software for exact tests and ecumenicism. J Heredity 86:248–249Google Scholar
  43. Reed DH, Briscoe DA, Frankham R (2002) Inbreeding and extinction: the effect of environmental stress and lineage. Conserv Genet 3:301–307CrossRefGoogle Scholar
  44. Roberts A, Miskelly C (2003) Recovery plan for the snipe species of New Zealand and the Chatham Islands (Coenocorypha spp) tutukiwi, 2003–2015. Department of Conservation, WellingtonGoogle Scholar
  45. Rozas J, Sanchez-DelBarrio JC, Messequer X, Rozas R (2003) DNAsp, DNA polymorphism analysis by the coalescent and other methods. Bioinformatics 19:2496–2497CrossRefPubMedGoogle Scholar
  46. Saccheri IJ, Wilson IJ, Nichols RA, Bruford MW, Brakefield PM (1999) Inbreeding of bottlenecked butterfly populations: estimation using the likelihood of changes in marker allele frequencies. Genetics 151:1053–1063PubMedGoogle Scholar
  47. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning. Cold Spring Harbor Laboratory, Cold Spring HarborGoogle Scholar
  48. Schneider S, Roessli D, Excoffier L (2000) Arlequin ver 2000: a software for population genetics data analysis. Genetics and Biometry Laboratory, University of Geneva, SwitzerlandGoogle Scholar
  49. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18:233–234CrossRefPubMedGoogle Scholar
  50. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595PubMedGoogle Scholar
  51. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–526PubMedGoogle Scholar
  52. Tennyson AJD, Millener PR (1994) Bird extinctions and fossil bones from Mangere Island, Chatham Islands. Notornis 41(supplement):165–178Google Scholar
  53. Turbott EG (1990) Checklist of the birds of New Zealand and the Ross Dependency, Antarctica. Random Century and Ornithological Society of New Zealand, AucklandGoogle Scholar
  54. Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) Micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538CrossRefGoogle Scholar
  55. Whitlock MC (2000) Fixation of new alleles and the extinction of small populations: drift load, beneficial alleles, and sexual selection. Evolution Int J org Evolution 54:1855–1861Google Scholar
  56. Woodworth LM, Montgomery ME, Briscoe DA, Frankham R (2002) Rapid genetic deterioration in captive populations: causes and conservation implications. Conserv Genet 3:277–288CrossRefGoogle Scholar
  57. Worthy TH (2003) A new extinct species of snipe Coenocorypha from Vitilevu, Fiji. Bulletin of the British Ornithologists’ Club 123:90–103Google Scholar
  58. Worthy TH, Holdaway RN (2002) The lost world of the moa, prehistoric life of New Zealand. Canterbury University Press, ChristchurchGoogle Scholar
  59. Worthy TH, Miskelly CM, Ching BA (2002) Taxonomy of North and South Island snipes (Aves: Scolopacidae: Coenocorypha) with analysis of a remarkable collection of snipe bones from Greymouth, New Zealand. New Zealand J Zool 29:231–244CrossRefGoogle Scholar
  60. Yeh FC, Boyle TJB (1997) Population genetic analysis of co-dominant and dominant markers and quantitative traits. Belg J Bot 129:157Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Allan J. Baker
    • 1
    • 2
    Email author
  • Colin M. Miskelly
    • 3
  • Oliver Haddrath
    • 1
  1. 1.Department of Natural HistoryRoyal Ontario MuseumTorontoCanada
  2. 2.Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoCanada
  3. 3.Department of ConservationWellingtonNew Zealand

Personalised recommendations