452
Views
6
CrossRef citations to date
0
Altmetric
Research Article

The conservation management implications of isolation by distance and high genetic diversity in Great Spotted Kiwi (Apteryx haastii)

ORCID Icon, , & ORCID Icon
Pages 10-22 | Received 10 Aug 2020, Accepted 05 Feb 2021, Published online: 22 Mar 2021

References

  • Allen, J. L., McKenzie, S. K., Sleith, R. S., and Alter, S. E. (2018). First genome-wide analysis of the endangered, endemic lichen Cetradonia linearis reveals isolation by distance and strong population structure. American Journal of Botany 105, 1556–1567. doi:10.1002/ajb2.1150
  • Allendorf, F. W. (1986). Genetic drift and the loss of alleles versus heterozygosity. Zoo Biology 5, 181–190. doi:10.1002/zoo.1430050212
  • Allendorf, F. W., and Ryman, N. (2002). The role of genetics in population viability analysis. In ‘Population Viability Analysis.’ (Eds S. R. Beissinger and D. R. McCullough.) pp. 50–85. (The Chicago University Press: Chicago.)
  • Aoki, S., and Ito, M. 2020. Where should wild species be sampled? New method based on isolation-by-distance objectively gives the answer. Molecular Ecology Resources n/a. doi:10.1111/1755-0998.13179
  • Baillie, S. M., Ritchie, P. A., and Brunton, D. H. (2014). Population genetic connectivity of an endemic New Zealand passerine after large-scale local extirpations: A model of re-colonization potential. Ibis 156, 826–839. doi:10.1111/ibi.12182
  • Baker, A. J., Daugherty, C. H., Colbourne, R., and McLennan, J. L. (1995). Flightless brown kiwis of New Zealand possess extremely subdivided population structure and cryptic species like small mammals. Proceedings of the National Academy of Sciences of the United States of America 92, 8254–8258. doi:10.1073/pnas.92.18.8254
  • Berner, D. (2019). Allele Frequency Difference AFD – An intuitive alternative to fst for quantifying genetic population differentiation. Genes 10, 308. doi:10.3390/genes10040308
  • Berry, O., Tocher, M. D., Gleeson, D. M., and Sarre, S. D. (2005). Effect of vegetation matrix on animal dispersal: Genetic evidence from a study of endangered skinks. Conservation Biology 19, 855–864. Available at http://www.jstor.org/stable/3591075
  • BirdLife International (2016). Apteryx haastii. The IUCN Red List of Threatened Species 2016, e.T22678132A92756666. Accepted 02 July 2020. doi:10.2305/IUCN.UK.2016-3.RLTS.T22678132A92756666.en
  • Boessenkool, S., Taylor, S. S., Tepolt, C. K., Komdeur, J., and Jamieson, I. G. (2007). Large mainland populations of South Island robins retain greater genetic diversity than offshore island refuges. Conservation Genetics 8, 705–714. doi:10.1007/s10592-006-9219-5
  • Charlesworth, B. (1998). Measures of divergence between populations and the effect of forces that reduce variability. Molecular Biology and Evolution 15, 538–543. doi:10.1093/oxfordjournals.molbev.a025953
  • Cook, C. N., and Sgrò, C. M. (2017). Aligning science and policy to achieve evolutionarily enlightened conservation. Conservation Biology 31, 501–512. doi:10.1111/cobi.12863
  • Cornuet, J. M., and Luikart, G. (1996). Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144, 2001–2014. Available at http://www.genetics.org/content/genetics/144/4/2001.full.pdf
  • Department of Conservation. (in prep.). Roroa (Great Spotted Kiwi, Apteryx Haastii) species plan 2019–2029. (Wellington, NZ.)
  • Driscoll, D. A., and Hardy, C. M. (2005). Dispersal and phylogeography of the agamid lizard Amphibolurus nobbi in fragmented and continuous habitat. Molecular Ecology 14, 1613–1629. doi:10.1111/j.1365-294X.2005.02509.x
  • Dussex, N., Wegmann, D., and Robertson, B. C. (2014). Postglacial expansion and not human influence best explains the population structure in the endangered kea (Nestor notabilis). Molecular Ecology 23, 2193–2209. doi:10.1111/mec.12729
  • Falush, D., Stephens, M., and Pritchard, J. K. (2003). Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics 164, 1567–1587. Available at https://www.ncbi.nlm.nih.gov/pubmed/12930761
  • Falush, D., Stephens, M., and Pritchard, J. K. (2007). Inference of population structure using multilocus genotype data: Dominant markers and null alleles. Molecular Ecology Notes 7, 574–578. doi:10.1111/j.1471-8286.2007.01758.x
  • Frankham, R., Ballou, J. D., Ralls, K., Eldridge, M., Dudash, M. R., Fenster, C. B., Lacy, R. C., et al. (2019). ‘A Practical Guide for Genetic Management of Fragmented Animal and Plant Populations.’ (Oxford University press: Oxford, UK.)
  • Germano, J., Barlow, S., Castro, I., Colbourne, R., Cox, M., Gillies, C., Hackwell, K., et al. (2018). Kiwi (Apteryx spp.) recovery plan 2018–2028. Department of Conservation Threatened Species Recovery Plan 64.
  • Goudet, J. (1995). FSTAT (Version 1.2): A computer program to calculate F-statistics. Journal of Heredity 86, 485–486. doi:10.1093/oxfordjournals.jhered.a111627
  • Goudet, J. (2005). HIERFSTAT, a package for R to compute and test hierarchical F-statistics. Molecular Ecology Notes 5, 184–186. doi:10.1111/j.1471-8286.2004.00828.x
  • Grosser, S., Abdelkrim, J., Wing, J., Robertson, B. C., and Gemmell, N. J. (2017). Strong isolation by distance argues for separate population management of endangered blue duck (Hymenolaimus malacorhynchos). Conservation Genetics 18, 327–341. doi:10.1007/s10592-016-0908-4
  • Grueber, C. E., Knafler, G. J., King, T. M., Senior, A. M., Grosser, S., Robertson, B., Weston, K. A., et al. (2015). Toll-like receptor diversity in 10 threatened bird species: Relationship with microsatellite heterozygosity. Conservation Genetics 16, 595–611. doi:10.1007/s10592-014-0685-x
  • Hardy, O. J., and Vekemans, X. (2002). SPAGEDi: A versatile computer program to analyse spatial genetic structure at the individual or population levels. Molecular Ecology Notes 2, 618–620. doi:10.1046/j.1471-8286.2002.00305.x
  • Hedrick, P. W. (1999). Perspective: Highly variable loci and their interpretation in evolution and conservation. Evolution 53, 313–318. doi:10.2307/2640768
  • Herbert, J., and Daugherty, C. H. (2002). Genetic variation, systematics and management of kiwi. In ‘Some Early 1990s Studies in Kiwi (Apteryx Spp.) Genetics and Management. Science & Research Internal Report 191.’ (Ed. F. Overmars.) pp. 11–34. (Department of Conservation: Wellington, New Zealand.)
  • Hoban, S., Bruford, M., D’Urban Jackson, J., Lopes-Fernandes, M., Heuertz, M., Hohenlohe, P. A., Paz-Vinas, I., et al. (2020). Genetic diversity targets and indicators in the CBD post-2020 global biodiversity framework must be improved. Biological Conservation 248, 108654. doi:10.1016/j.biocon.2020.108654
  • Holm, S. (1979). A simple sequentially rejective multiple test procedure. Scandinavian Journal of Statistics 6, 65–70.
  • Innes, J., Eppink, F. V., and Robertson, H. (2015). Saving a national icon: Preliminary estimation of the additional cost of achieving kiwi population stability or 2% growth. Landcare Research contract report LC2136 prepared for Kiwi for kiwis/The Kiwi Trust, Private Bag 68908, Auckland 1145.
  • Jahn, P., Harper, G. A., and Gilchrist, J. (2013). Home range sharing in family units of great spotted kiwi (Apteryx haastii) at Nelson Lakes National Park. Notornis 60, 201–209.
  • Jakobsson, M., Edge, M. D., and Rosenberg, N. A. (2013). The relationship between FST and the frequency of the most frequent allele. Genetics 193, 515 LP–528. doi:10.1534/genetics.112.144758
  • Jamieson, I. G., Wallis, G. P., and Briskie, J. V. (2006). Inbreeding and endangered species management: Is New Zealand out of step with the rest of the world? Conservation Biology 20, 38–47. doi:10.1111/j.1523-1739.2005.00282.x
  • Jost, L. (2008). GST and its relatives do not measure differentiation. Molecular Ecology 17, 4015–4026. doi:10.1111/j.1365-294X.2008.03887.x
  • Keye, C., Roschak, C., and Ross, J. (2011). Summer home range size and population density of great spotted kiwi (Apteryx haastii) in the North Branch of the Hurunui River, New Zealand. Notornis 58, 22–30.
  • Laikre, L. (2010). Genetic diversity is overlooked in international conservation policy implementation. Conservation Genetics 11, 349–354. doi:10.1007/s10592-009-0037-4
  • Laikre, L., Hoban, S., Bruford, M. W., Segelbacher, G., Allendorf, F. W., Gajardo, G., Rodríguez, A. G., et al. (2020). Post-2020 goals overlook genetic diversity Ed J. Sills. Science 367, 1083 LP–1085. doi:10.1126/science.abb2748
  • Lawson, D. J., van Dorp, L., and Falush, D. (2018). A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots. Nature Communications 9, 3258. doi:10.1038/s41467-018-05257-7
  • Lloyd, B. D. (2003). The demographic history of the New Zealand short-tailed bat Mystacina tuberculata inferred from modified control region sequences. Molecular Ecology 12, 1895–1911. doi:10.1046/j.1365-294X.2003.01879.x
  • Luikart, G., and Cornuet, J.-M. (1998). Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data. Conservation Biology 12, 228–237. doi:10.1111/j.1523-1739.1998.96388.x
  • Matisoo-Smith, E., and Daugherty, C. (2012). Africa to Aotearoa: The longest migration. Journal of the Royal Society of New Zealand 42, 87–92. doi:10.1080/03036758.2012.673495
  • McLennan, J., and McCann, T. (2002). Genetic variability, distribution and abundance of great spotted kiwi (Apteryx haastii). In ‘Some Early 1990s Studies in Kiwi (Apteryx Spp.) Genetics and Management. Science & Research Internal Report 191.’ (Ed. F. Overmars.) pp. 35–56. (Department of Conservation: Wellington.)
  • Meirmans, P. G. (2012). The trouble with isolation by distance. Molecular Ecology 21, 2839–2846. doi:10.1111/j.1365-294X.2012.05578.x
  • Mills, L. S., and Allendorf, F. W. (1996). The one-migrant-per-generation rule in conservation and management. Conservation Biology 10, 1509–1518. doi:10.1046/j.1523-1739.1996.10061509.x
  • O’ Donnell, C. F. J., Richter, S., Dool, S., Monks, J. M., and Kerth, G. (2016). Genetic diversity is maintained in the endangered New Zealand long-tailed bat (Chalinolobus tuberculatus) despite a closed social structure and regular population crashes. Conservation Genetics 17, 91–102. doi:10.1007/s10592-015-0763-8
  • Orloci, L. (1978). ‘Multivariate Analysis in Vegetation Research.’ (W Junk Publishers: The Haugue, Netherlands.)
  • Palsbøll, P. J., Bérubé, M., and Allendorf, W. F. (2007). Identification of management units using population genetic data. Trends in Ecology & Evolution 22, 11–16. doi:10.1016/j.tree.2006.09.003
  • Peakall, R., Ruibal, M., and Lindenmayer, D. B. (2003). Spatial autocorrelation analysis offers new insights into gene flow in the Australian bush rate, Rattus fuscipes. Evolution 57, 1182–1195. doi:10.1111/j.0014-3820.2003.tb00327.x
  • Peakall, R., and Smouse, P. E. (2006). GENALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6, 288–295. doi:10.1111/j.1471-8286.2005.01155.x
  • Peakall, R., and Smouse, P. E. (2012). GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research - An update. Bioinformatics 28, 2537–2539. doi:10.1093/bioinformatics/bts460
  • Perez, M. F., Franco, F. F., Bombonato, J. R., Bonatelli, I. A. S., Khan, G., Romeiro-Brito, M., Fegies, A. C., et al. (2018). Assessing population structure in the face of isolation by distance: Are we neglecting the problem? Diversity and Distributions 24, 1883–1889. doi:10.1111/ddi.12816
  • Pierson, J. C., Coates, D. J., Oostermeijer, J. G. B., Beissinger, S. R., Bragg, J. G., Sunnucks, P., Schumaker, N. H., et al. (2016). Genetic factors in threatened species recovery plans on three continents. Frontiers in Ecology and the Environment 14, 433–440. doi:10.1002/fee.1323
  • Piry, S., Luikart, G., and Cornuet, J.-M. (1999). Computer note. BOTTLENECK: A computer program for detecting recent reductions in the effective size using allele frequency data. Journal of Heredity 90, 502–503. doi:10.1093/jhered/90.4.502
  • Pritchard, J. K., Stephens, M., and Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics 155, 945–959. Available at https://www.genetics.org/content/genetics/155/2/945.full.pdf
  • Pritchard, J. K., Wen, X., and Falush, D. (2007). ‘Documentation for Structure Software: Version 2.2.’ pp. 1–36.
  • Prunier, J. G., Kaufmann, B., Fenet, S., Picard, D., Pompanon, F., Joly, P., and Lena, J. P. (2013). Optimizing the trade-off between spatial and genetic sampling efforts in patchy populations: Towards a better assessment of functional connectivity using an individual-based sampling scheme. Molecular Ecology 22, 5516–5530. doi:10.1111/mec.12499
  • Ralls, K., Ballou, J. D., Dudash, M. R., Eldridge, M. D. B., Fenster, C. B., Lacy, R. C., Sunnucks, P., et al. (2018). Call for a paradigm shift in the genetic management of fragmented populations. Conservation Letters 11, e12412. doi:10.1111/conl.12412
  • Ramstad, K. M., Pfunder, M., Robertson, H. A., Colbourne, R. M., Allendorf, F. W., and Daugherty, C. H. (2010). Fourteen microsatellite loci cross-amplify in all five kiwi species (Apteryx spp) and reveal extremely low genetic variation in little spotted kiwi (A. owenii). Conservation Genetics Resources 2, 333–336. doi:10.1007/s12686-010-9233-2
  • Raymond, M., and Rousset, F. (1995). GENEPOP (version-1.2) - Population-genetics software for exact tests and ecumenicism. Journal of Heredity 86, 248–249. doi:10.1093/oxfordjournals.jhered.a111573
  • Robertson, B. C. (2006). The role of genetics in kakapo recovery. Notornis 53, 173–183.
  • Robertson, H., and Colbourne, R. (2003) . ‘Kiwi (Apteryx Spp.) Best Practice Manual.’ (New Zealand Department of Conservation: Wellington, NZ.)
  • Robertson, H. A., Baird, K., Dowding, J. E., Elliott, G. P., Hitchmough, R. A., Miskelly, C. M., McArthur, N., et al. (2017). Conservation status of New Zealand birds, 2016. Department of Conservation New Zealand Threat Classification Series 19. Available at https://www.doc.govt.nz/globalassets/documents/science-and-technical/nztcs19entire.pdf
  • SCBD (2010). Decision adopted by the conference of the parties to the convention on biological diversity at its tenth meeting. X/2. The Strategic Plan for Biodiversity 2011–2020 and the Aichi Biodiversity Targets. Available at https://www.cbd.int/doc/decisions/cop-10/cop-10-dec-02-en.pdf
  • SCBD (2020). ‘Preparation of the post-2020 Global Biodiversity Framework: Recommendation submitted by the Co-Chairs.’ Available at https://www.cbd.int/conferences/post2020/wg2020-02/documents
  • Schregel, J., Remm, J., Eiken, H. G., Swenson, J. E., Saarma, U., and Hagen, S. B. (2018). Multi-level patterns in population genetics: Variogram series detects a hidden isolation-by-distance-dominated structure of Scandinavian brown bears Ursus arctos. Methods in Ecology and Evolution 9, 1324–1334. doi:10.1111/2041-210X.12980
  • Schwartz, M. K., and McKelvey, K. S. (2008). Why sampling scheme matters: The effect of sampling scheme on landscape genetic results. Conservation Genetics 10, 441. doi:10.1007/s10592-008-9622-1
  • Slatkin, M. (1993). Isolation by distance in equilibrium and non-equilibrium populations. Evolution 47, 264–279. doi:10.2307/2410134
  • Smouse, P. E., and Peakall, R. (1999). Spatial autocorrelation analysis of individual multiallele and multilocus genetic structure. Heredity 82, 561–573. doi:10.1038/sj.hdy.6885180
  • Taylor, B. L., and Dizon, A. E. (1999). First policy then science: Why a management unit based solely on genetic criteria cannot work. Molecular Ecology 8, S11–S16. doi:10.1046/j.1365-294X.1999.00797.x
  • Taylor, H. R., Colbourne, R. M., Robertson, H. A., Nelson, N. J., Allendorf, F. W., and Ramstad, K. M. (2017a). Cryptic inbreeding depression in a growing population of a long-lived species. Molecular Ecology 26, 799–813. doi:10.1111/mec.13977
  • Taylor, H. R., Dussex, N., and van Heezik, Y. (2017b). Bridging the conservation genetics gap by identifying barriers to implementation for conservation practitioners. Global Ecology and Conservation 10, 231–242. doi:10.1016/j.gecco.2017.04.001
  • Toy, R., and Toy, S. (2020). Post-translocation dispersal and home range establishment of Roroa (Great Spotted Kiwi, Apteryx Haastii): Need for long-term monitoring and aflexible management strategy’. Notornis 67, 511–525.
  • Wahlund, S. (1928). Zusammensetzung von populationen und korrelationrscheinungen vom standpunkt der vererbungslehre aus betrachtet. Hereditas 11, 65–106. doi:10.1111/j.1601-5223.1928.tb02483.x
  • Weeks, A. R., Thavornkanlapachai, R., Weiser, E. L., and Heinze, D. (2015). Conserving and enhancing genetic diversity in translocation programmes. In ‘Advances in Reintroduction Biology of Australian and New Zealand Fauna.’ (Eds D. P. Armstrong, M. W. Hayward, D. Moro, and P. J. Seddon.) pp. 127–139. (CSIRO Publishing: Collingwood, VIC, Australia.)
  • Weir, B. S., and Cockerham, C. C. (1984). Estimating F-statistics for the analysis of population structure. Evolution 38, 1358–1370. doi:10.2307/2408641
  • Wright, S. (1943). Isolation by distance. Genetics 28, 114 LP–138. Available at http://www.genetics.org/content/28/2/114.abstract
  • Wright, S. (1946). Isolation by distance under diverse systems of mating. Genetics 31, 39–59. Available at https://pubmed.ncbi.nlm.nih.gov/21009706
  • Wright, S. (1978). ‘Evolution and the Genetics of Populations, Volume 4: Variability within and among Natural Populations.’ (University of Chicago Press: Chicago, IL.)

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.