Microsatellite analysis reveals substantial levels of genetic variation but low levels of genetic divergence among isolated populations of Kaka (Nestor meridionalis)

James P. Sainsbury; Terry C. Greene; Ron J. Moorhouse; Charles H. Daugherty; Geoffrey K. Chambers

doi:10.1071/MU06009

RESEARCH ARTICLE

Microsatellite analysis reveals substantial levels of genetic variation but low levels of genetic divergence among isolated populations of Kaka (Nestor meridionalis)

James P. Sainsbury ^A ^E , Terry C. Greene ^B , Ron J. Moorhouse ^C , Charles H. Daugherty ^D and Geoffrey K. Chambers ^D

+ Author Affiliations

- Author Affiliations

^A Institute of Zoology, Zoological Society of London, Regent’s Park, London NW1 4RY, United Kingdom.

^B Science and Research Unit, Department of Conservation, PO Box 13049, Christchurch, New Zealand.

^C Department of Conservation, Private Bag 5, Nelson, New Zealand.

^D Institute for Molecular Systematics, School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand.

^E Corresponding author. Email: james.sainsbury@gmail.com

Emu 106(4) 329-338 https://doi.org/10.1071/MU06009
Submitted: 16 February 2006 Accepted: 13 September 2006 Published: 16 November 2006

Abstract

The Kaka (Nestor meridionalis) is a threatened, endemic forest parrot of New Zealand with a fragmented distribution. We present data from eight microsatellite DNA loci for 126 Kaka from nine locations along the length of New Zealand. The observed patterns of variation reveal little population structure in Kaka, despite substantial levels of genetic variation. Our estimate of R_ST over all populations is low (0.04) and a hierarchical analysis of molecular variance (AMOVA) shows that most allelic variation (93.7%) is within populations rather than divided among them. Further, most inter-population genetic differentiation is attributed to the divergence of the possibly bottlenecked Kapiti Island population from all other populations surveyed. This overall homogeneity probably reflects historic population structure and is being maintained by the ongoing dispersal of individuals between populations. Conservation management of Kaka should reflect this New Zealand-wide gene flow, although special consideration may be given to Kapiti Island.

Acknowledgments

This work was supported by the Institute for Molecular Systematics, the School of Biological Sciences, and the Faculty of Science at Victoria University of Wellington. James Sainsbury was supported by a Victoria University Postgraduate scholarship. The authors thank the New Zealand Department of Conservation, Sue Keall, Julliette Huggins, Les Moran, Ralph Powlesland and Peter Dilks for providing samples. Special thanks go to Elizabeth MacAvoy for valuable technical advice and Mathew (ChiHang) Chan and Brenda Greene and two anonymous referees for reviewing the manuscript.

References

Ardern, S. L. , and Lambert, D. M. (1997). Is the black robin in genetic peril? Molecular Ecology 6, 21–28.
| Crossref | GoogleScholarGoogle Scholar | Boag P. T., and van Noordwijk A. J. (1987). Quantitative genetics. In ‘Avian Genetics: A Population and Ecological Approach’. (Eds F. Cooke and P. A. Buckley.) pp. 45–78. (Academic Press: London.)

Briskie, J. V. , and Mackintosh, M. (2004). Hatching failure increases with severity of population bottlenecks in birds. Proceedings of the National Academy of Sciences, USA 101, 558–561.
| Crossref | GoogleScholarGoogle Scholar | Brzustowski J. (2002). Doh assignment test calculator. Available at http://www2.biology.ualberta.ca/jbrzusto/Doh.php [Verified/Accessed 9 October 2006]

Bull P. C., Gaze P. D., and Robertson C. J. R. (1985). ‘The Atlas of Bird Distribution in New Zealand.’ (Ornithological Society of New Zealand: Wellington.)

Buller W. L. (1865). ‘Essay on the Ornithology of New Zealand.’ (Fergusson and Mitchell: Dunedin.)

Buller W. L. (1873). ‘A History of the Birds of New Zealand.’ (John van Woorst: London.)

Buller W. L. (1888). ‘A History of New Zealand Birds.’ (W. L. Buller: London.)

Buller W. L. (1905). ‘Supplement to the Birds of New Zealand.’ (W. L. Buller: London.)

Chan, C.-H. , Ballantyne, K. N. , Lambert, D. M. , and Chambers, G. K. ()2005.). Characterization of variable microsatellite loci in Forbes’ Parakeet (Cyanoramphus forbesi) and their use in other parrots. Conservation Genetics 6, 651–654.
| Crossref | GoogleScholarGoogle Scholar | Heather B. D., and Robertson H. A. (2000). ‘The Field Guide to the Birds of New Zealand.’ (Viking: Auckland.)

Hedrick, P. W. , Parker, K. M. , and Lee, R. N. (2001). Using microsatellite and MHC variation to identify species, ESUs, and MUs in the endangered Sonoran topminnow. Molecular Ecology 10, 1399–1412.
| Crossref | GoogleScholarGoogle Scholar | PubMed | Higgins P. J. (Ed.) (1999). ‘Handbook of Australian, New Zealand and Antarctic Birds. Vol. 4: Parrots to Dollarbird.’ (Oxford University Press: Melbourne.)

Huggins J. (2001). Genetic variation and conservation of Kaka (Nestor meridionalis). M.Sc. Thesis, Victoria University of Wellington, Wellington, NZ.

Johnson, N. K. (1982). Retain subspecies – at least for the time being. Auk 99, 605–606.
McKensie D. W. (Ed.) (1987). ‘New Zealand Atlas.’ (Department of Survey and Land Information and Heinemann Publishers: Auckland.)

Monroe, B. L., Jr (1982). A modern concept of subspecies. Auk 99, 608–609.
Moorhouse R. J. (1996). Productivity, sexual dimorphism and diet of North Island Kaka (Nestor meridionalis septentrionalis) on Kapiti Island. Ph.D. Thesis, Victoria University of Wellington, Wellington, NZ.

Moorhouse R. J. (2000). Kaka in the South Island. Conservation Science Newsletter 39, NZ Department of Conservation, Wellington.

Moorhouse, R. J. , and Greene, T. C. (1995). Identification of fledgling and juvenile Kaka (Nestor meridionalis). Notornis 42, 187–196.
Peakell R., and Smouse P. E. (2001). ‘GenAlEx v5.04: Genetic Analysis in Excel. Subpopulation Genetics Software for Teaching and Research.’ (Australian National University: Canberra.) Available at http://www.anu.edu.au/BoZo/GenAlEx/ [Accessed/Verified 9 October 2006]

Phillips, A. R. (1982). Subspecies and species: fundamentals, needs, and obstacles. Auk 99, 612–615.
Sambrook J., Fritsch E. F., and Maniatis T. (1989). ‘Molecular Cloning: A Laboratory Manual.’ (Cold Spring Harbor Laboratory Press: New York.)

Schiegg, K. , Pasinelli, G. , Walters, J. R. , and Daniels, S. J. (2002). Inbreeding and experience affect response to climate change by endangered woodpeckers. Proceedings of the Royal Society of London. Series B. Biological Sciences 269, 1153–1159.
| Crossref | GoogleScholarGoogle Scholar | Schneider S., Roessli D., and Excoffier L. (2000). ‘Arlequin: A Software for Population Genetics Data Analysis.’ (Genetics and Biometry Laboratory, Department of Anthropology, University of Geneva.) (http://lgb.unige.ch/arlequin/software/2.000/doc/faq/faqlist.htm#How%20do%20I%20cite%20Arlequin)

Slatkin, M. (1993). Isolation by distance in equilibrium and non-equilibrium populations. Evolution 47, 264–279.
| Crossref | GoogleScholarGoogle Scholar |

Slatkin, M. (1995). A measure of population subdivision based on microsatellite allele frequencies. Genetics 139, 457–462.
| PubMed |

Storer, R. W. (1982). Subspecies and the study of geographic variation. Auk 99, 599–601.

Valsecchi, E. , Palsboll, P. , Hale, P. , Glockner-Ferrari, D. , Ferrari, M. , Clapham, P. , Larsen, F. , Mattila, D. , Sears, R. , Sigurjonsson, J. , Brown, M. , Corkeron, P. , and Amos, B. (1997). Microsatellite genetic distances between oceanic populations of the humpback whale (Megaptera novaeangliae). Molecular Biology and Evolution 14, 355–362.
| PubMed |

Walker, C. W. , Vila, C. , Landa, A. , Linden, M. , and Ellegren, H. (2001). Genetic variation and population structure in Scandinavian wolverine (Gulo gulo) populations. Molecular Ecology 10, 53–63.
| Crossref | GoogleScholarGoogle Scholar | PubMed |

Weir, B. S. , and Cockerham, C. C. (1984). Estimating F-statistics for the analysis of population structure. Evolution 38, 1358–1370.
| Crossref | GoogleScholarGoogle Scholar |

Wilson, P. R. , Karl, B. J. , Toft, R. J. , Beggs, J. R. , and Taylor, R. H. (1998). The role of introduced predators and competitors in the decline of Kaka (Nestor meridionalis) populations in New Zealand. Biological Conservation 83, 175–185.
| Crossref | GoogleScholarGoogle Scholar |

Zusi, R. L. (1982). Infraspecific geographic variation and the subspecies concept. Auk 99, 606–608.

**Appendix 1. Allelic frequencies for each locus and population**
Private alleles (only present in one population) are shown in bold, alleles missing in only one population are shown in italics

Microsatellite analysis reveals substantial levels of genetic variation but low levels of genetic divergence among isolated populations of Kaka (Nestor meridionalis)

Abstract

Acknowledgments

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