Inferring population connectivity across the range of the purple-crowned fairy-wren (Malurus coronatus) from mitochondrial DNA and morphology: Implications for conservation management

Australian Journal of Zoology

Volumn 60, Issue 3, 2012, Pages 199-209

  Skroblin, Anja ^a,b   Lanfear, Robert ^a,c   Cockburn, Andrew ^a   Legge, Sarah ^b,d  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

^b AUSTRALIAN WILDLIFE CONSERVANCY   (Australia)

^c NATIONAL EVOLUTIONARY SYNTHESIS CENTER   (United States)

^d CHARLES DARWIN UNIVERSITY   (Australia)

Author keywords

conservation biology; northern Australia; phylogeography; wildlife management

Indexed keywords

CONSERVATION GENETICS; ENDEMIC SPECIES; GENE FLOW; HABITAT FRAGMENTATION; MITOCHONDRIAL DNA; MORPHOLOGY; NATURE CONSERVATION; PASSERINE; PHYLOGENETICS; PHYLOGEOGRAPHY; RANGE EXPANSION; SUBSPECIES;

AUSTRALIA;

MALURUS CORONATUS; TROGLODYTINAE;

EID: 84869065687     PISSN: 0004959X     EISSN: None     Source Type: Journal    
DOI: 10.1071/ZO12093     Document Type: Article

References (67)

1. Avise, J.C., Arnold, J., Ball, R.M., Bermingham, E., Lamb, T., Neigel, J.E., Reeb, C.A., and Saunders, N.C. (1987). Intraspecific phylogeography: The mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics 18, 489-522.
2. Barrett, G., Silcocks, A., Barry, S., Cunningham, R., and Poulter, R. (2003).'The New Atlas of Australian Birds. (Royal Australasian Ornithologists Union: Melbourne.)
3. Berger, J. (1990). Persistence of different-sized populations: An empirical assessment of rapid extinctions in bighorn sheep. Conservation Biology 4, 91-98. doi:10.1111/j.1523-1739.1990.tb00271.x
4. Bowman, D.M. J.S., Brown, G.K., Braby, M.F., Brown, J.R., Cook, L.G., Crisp, M.D., Ford, F., Haberle, S., Hughes, J., Isagi, Y., Joseph, L., McBride, J., Nelson, G., and Ladiges, P.Y. (2010). Biogeography of the Australian monsoon tropics. Journal of Biogeography 37, 201-216.doi:10.1111/j.1365-2699.2009. 02210.x
5. Brooker, M., and Brooker, L. (2001). Breeding biology, reproductive success and survival of blue-breasted fairy-wrens in fragmented habitat in the Western Australian wheatbelt. Wildlife Research 28, 205-214.doi:10.1071/WR00012
6. Clement, M., Posada, D., and Crandall, K.A. (2000). TCS: A computer program to estimate gene genealogies. Molecular Ecology 9, 1657-1659.doi:10. 1046/j.1365-294x.2000.01020.x
7. Cox, J., and Engstrom, R.T. (2001). Influence of the spatial pattern of conserved lands on the persistence of a large population of red-cockaded woodpeckers. Biological Conservation 100, 137-150. doi:10.1016/ S0006-3207(00)00214-7 Crandall, K.A., Bininda-Emonds, O.R. P., Mace, G.M., and Wayne, R.K. (2000). Considering evolutionary processes in conservation biology. Trends in Ecology & Evolution 15, 290-295. doi:10.1016/S0169-5347(00)01876-0
8. DEWHA (2009). Malurus coronatus coronatus. In 'Species Profile and Threats Database. (Department of the Environment, Water, Heritage and the Arts: Canberra.)
9. Diniz-Filho, J.A. F., de Campos Telles, M.P., Bonatto, S.L., Eizirik, E., de Freitas, T.R. O., de Marco, P., Santos, F.R., Sole-Cava, A., and Soares, T.N. (2008). Mapping the evolutionary twilight zone: molecular markers, populations and geography. Journal of Biogeography 35, 753-763.doi:10.1111/j. 1365-2699.2008.01912.x
10. Drummond, A., Ashton, B., Buxton, S., Cheung, M., Cooper, A., Heled, J., Kearse, M., Moir, R., Stones-Havas, S., Sturrock, S., Thierer, T., and Wilson, A. (2010). Geneious v5.1. Available from http://www.geneious. com Eldridge, M.D. B., Potter, S., and Cooper, S.J. B. (2012). Biogeographic barriers in north-western Australia: An overview and standardisation of nomenclature. Australian Journal of Zoology 59, 270-272. doi:10.1071/ ZO12012 Excoffier, L., Smouse, P.E., and Quattro, J.M. (1992). Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics 131, 479-491.
11. Fahrig, L., and Merriam, G. (1985). Habitat patch connectivity and population survival. Ecology 66, 1762-1768. doi:10.2307/2937372
12. Fahrig, L., and Merriam, G. (1994). Conservation of fragmented populations. Conservation Biology 8, 50-59. doi:10.1046/j.1523-1739.1994. 08010050.x
13. Fedy, B.C., Martin, K., Ritland, C., and Young, J. (2008). Genetic and ecological data provide incongruent interpretations of population structure and dispersal in naturally subdivided populations of white-tailed ptarmigan (Lagopus leucura). Molecular Ecology 17, 1905-1917.doi:10.1111/j.1365-294X.2008.03720.x
14. Ford, J. (1978). Geographical isolation and morphological and habitat differentiation between birds of the Kimberley and the Northern Territory. Emu 78, 25-35. doi:10.1071/MU9780025
15. Fujita, M.K., McGuire, J.A., Donnellan, S.C., and Moritz, C. (2010). Diversification and persistence at the aridYmonsoonal interface: Australiawide biogeography of the Bynoe's gecko (Heteronotia binoei; Gekkonidae). Evolution 64, 2293-2314.
16. Garnett, S.T., Szabo, J.K., and Dutson, G. (2011). 'The Action Plan for Australian Birds 2010. (CSIRO Publishing: Melbourne.) Hackett, S.J. (1996). Molecular phylogenetics and biogeography of tanagers in the Genus Ramphocelus (Aves). Molecular Phylogenetics and Evolution 5, 368-382. doi:10.1006/mpev.1996. 0032
17. Halliburton, R. (2004). 'Introduction to Population Genetics. (Pearson Education: Upper Saddle River, NJ.) Higgins, P.J., Peter, J.M., and Steele, W.K. E. (2001). 'Handbook of Australian, New Zealand and Antarctic Birds. Volume 5: Tyrantflycatchers to Chats. (Oxford University Press: Melbourne.)
18. Holsinger, K.E. (2000). Demography and extinction in small populations. In 'Genetics, Demography and Viability of Fragmented Populations. (Eds A.G. Young and G.M. Clarke.) pp. 55-74. (Cambridge University Press: Cambridge.)
19. Howeth, J.G., McGaugh, S.E., and Hendrickson, D.A. (2008). Contrasting demographic and genetic estimates of dispersal in the endangered Coahuilan box turtle: A contemporary approach to conservation. Molecular Ecology 17, 4209-4221. [In English] doi:10.1111/j.1365-294X.2008.03904.x
20. Huelsenbeck, J.P., and Ronquist, F. (2001).MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17, 754-755. doi:10.1093/bioinformatics/17.8.754
21. Joseph, L., and Wilke, T. (2006). Molecular resolution of population history, systematics and historical biogeography of the Australian ringneck parrots Barnardius: Are we there yet? Emu 106, 49-62.doi:10.1071/MU05035
22. Kearns, A.M., Joseph, L., Edwards, S.V., and Double,M.C. (2009). Inferring the phylogeography and evolutionary history of the splendid fairy-wren Malurus splendens from mitochondrial DNA and spectrophotometry. Journal of Avian Biology 40, 7-17. doi:10.1111/j.1600-048X.2008.
23. .x Lanfear, R., Calcott, B., Ho, S.Y. W., and Guindon, S. (2012). Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution 29, 1695-1701. doi:10.1093/molbev/mss020
24. Librado, P., and Rozas, J. (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451-1452.doi:10.1093/ bioinformatics/btp187
25. McDonald-Madden, E.V. E., Baxter, P.W. J., and Possingham, H.P. (2008). Subpopulation triage: how to allocate conservation effort among populations. Conservation Biology 22, 656-665. doi:10.1111/j.1523-1739.2008.00918.x
26. Meiri, S., and Dayan, T. (2003). On the validity of Bergmann's rule. Journal of Biogeography 30, 331-351. doi:10.1046/j.1365-2699.2003.00837.x
27. Melville, J., Ritchie, E.G., Chapple, S.N. J., Glor, R.E., and Schulte, J.A. II (2011). Evolutionary origins and diversification of dragon lizards in Australia's tropical savannas. Molecular Phylogenetics and Evolution 58, 257-270. doi:10.1016/j.ympev.2010.11.025
28. 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
29. Montgomery, M.E., Ballou, J.D., Nurthen, R.K., England, P.R., Briscoe, D.A., and Frankham, R. (1997). Minimizing kinship in captive breeding programs. Zoo Biology 16, 377-389. doi:10.1002/(SICI)1098-2361(1997)16:5<377::AID- ZOO1>3.0.CO;2-7
30. Moritz, C. (1994). Defining 'Evolutionarily Significant Units' for conservation. Trends in Ecology & Evolution 9, 373-375. doi:10.1016/0169- 5347(94)90057-4
31. Moritz, C. (1999). Conservation units and translocations: strategies for conserving evolutionary processes. Hereditas 130, 217-228.doi:10.1111/j.1601- 5223.1999.00217.x
32. Moritz, C. (2002). Strategies to protect biological diversity and the evolutionary processes that sustain it. Systematic Biology 51, 238-254.doi:10.1080/10635150252899752
33. Moritz, C., Dowling, T.E., and Brown, W.M. (1987). Evolution of animal mitochondrial DNA: Relevance for population biology and systematics. Annual Review of Ecology and Systematics 18, 269-292. doi:10.1146/annurev.es.18.110187. 001413
34. National Land and Resources Audit (2002). Australian catchment, river and estuary assessment 2002. Natural Heritage Trust, Canberra.
35. Paetkau, D. (1999). Using genetics to identify intraspecific conservation units: A critique of current methods. Conservation Biology 13, 1507-1509.doi:10.1046/j.1523-1739.1999.98507.x
36. Palsboll, P.J., Berube, M., and Allendorf, F.W. (2007). Identification of management units using population genetic data. Trends in Ecology &Evolution 22, 11-16. doi:10.1016/j.tree.2006.09.003
37. Peakall, R., and Smouse, P.E. (2006).GENALEX6: 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
38. Phillimore, A.B., and Owens, I.P. F. (2006). Are subspecies useful in evolutionary and conservation biology? Proceedings of the Royal Society of London. Series B, Biological Sciences 273, 1049-1053. doi:10.1098/rspb.2005.3425
39. Pimm, S.L., Jones, H.L., and Diamond, J. (1988). On the risk of extinction. American Naturalist 132, 757-785. doi:10.1086/284889
40. Potter, S., Eldridge, M.D.B., Taggart, D.A., and Cooper, S.J.B. (2012). Multiple biogeographical barriers identified across the monsoon tropics of northern Australia: phylogeographic analysis of the brachyotis group of rock-wallabies. Molecular Ecology 21, 2254-2269.
41. Prugh, L.R., Hodges, K.E., Sinclair, A.R. E., and Brashares, J.S. (2008). Effect of habitat area and isolation on fragmented animal populations. Proceedings of the National Academy of Sciences of the United States of America 105, 20770-20775. doi:10.1073/pnas.0806080105
42. Rambaut, A., andDrummond, A.J. (2007). Tracer v1.4. Available from http://beast.bio.ed.ac.uk/Tracer Ray, C. (2001). Maintaining genetic diversity despite local extinctions: Effects of population scale. Biological Conservation 100, 3-14. doi:10.1016/S0006-3207(00)00202-0
43. Remsen, J.V. (2005). Pattern, process, and rigor meet classification. The Auk 122, 403-413. doi:10.1642/0004-8038(2005)122[0403:PPARMC]2.0.CO;2
44. Rising, J.D., Jackson, D.A., and Fokidis, H.B. (2009). Geographic variation in plumage pattern and colouration of savannah sparrows. The Wilson Journal of Ornithology 121, 253-264. doi:10.1676/08-077.1
45. Ronquist, F., van der Mark, P., and Huelsenbeck, J.P. (2009). Bayesian phylogenetic analysis using MrBayes. In 'The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing. (Eds P.Lemey, M.Salemi and A.Vandanne.) pp. 210-266. (Cambridge University Press: Cambridge.)
46. Rowley, I. (1993). The purple-crowned fairy-wren Malurus coronatus. I.History, distribution and present status. Emu 93, 220-234. doi:10.1071/MU9930220
47. Rowley, I., and Russell, E. (1993). The purple-crowned fairy-wren Malurus coronatus II Breeding biology, social organisation, demography and management. Emu 93, 235-250. doi:10.1071/MU9930235
48. Rubinoff, D., and Holland, B.S. (2005). Between two extremes: mitochondrialDNAis neither the panacea nor the nemesis of phylogenetic and taxonomic inference. Systematic Biology 54, 952-961. doi:10.1080/ 10635150500234674
49. Schodde, R. (1982). 'The Fairy-Wrens: A Monograph of the Maluridae. (Lansdowne Editions: Melbourne.)
50. Segelbacher, G., Cushman, S., Epperson, B., Fortin, M.-J., Francois, O., Hardy, O., Holderegger, R., Taberlet, P., Waits, L., and Manel, S. (2010). Applications of landscape genetics in conservation biology: concepts and challenges. Conservation Genetics 11, 375-385. doi:10.1007/s10592- 009-0044-5
51. Selkoe, K.A., and Toonen, R.J. (2006). Microsatellites for ecologists: A practical guide to using and evaluating microsatellite markers. Ecology Letters 9, 615-629. doi:10.1111/j.1461-0248.2006.00889.x
52. Skroblin, A., and Legge, S. (2010). The distribution and status of the western subspecies of the purple-crowned fairy-wren (Malurus coronatus coronatus). Emu 110, 339-347. doi:10.1071/MU10029
53. Skroblin, A., and Legge, S. (2011). The influence of fine-scale habitat requirements and riparian degradation on the distribution of the purplecrowned fairy-wren (Malurus coronatus coronatus) in northern Australia. Austral Ecology Online early.
54. Smith, L.A., and Johnstone, R.E. (1977). Status of the purple-crowned wren (Malurus coronatus) and buff-sided robin (Poecilodryas superciliosa) in Western Australia. Western Australian Naturalist 13, 185-188.
55. Sorenson, M.D., and Quinn, T.W. (1998). Numts: A challenge for avian systematics and population biology. The Auk 115, 214-221. doi:10.2307/4089130
56. Sorenson, M.D., Ast, J.C., Dimcheff, D.E., Yuri, T., and Mindell, D.P. (1999). Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. Molecular Phylogenetics and Evolution 12, 105-114. doi:10.1006/mpev.1998.0602
57. Spielman, D., Brook, B.W., and Frankham, R. (2004). Most species are not driven to extinction before genetic factors impact them. Proceedings of the National Academy of Sciences of the United States of America 101, 15261-15264. doi:10.1073/pnas.0403809101
58. Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688-2690. doi:10.1093/bioinformatics/btl446
59. Thrall, P.H., Burdon, J.J., and Murray, B.R. (2000). The metapopulaton paradigm: A fragmented view of conservation biology. In 'Genetics, Demography and Viabiltiy of Fragmented Populations. (Eds A.G. Young and G.M. Clarke.) pp. 75-95. (Cambridge University Press: Cambridge.)
60. Unmack, P.J. (2001). Biogeography of Australian freshwater fishes. Journal of Biogeography 28, 1053-1089. doi:10.1046/j.1365-2699. 2001.00615.x
61. van Doorn, A. (2007). Ecology and conservation of the purple-crowned fairywren (Malurus coronatus coronatus) in the Northern Territory, Australia. Ph.D. Thesis, University of Florida, Gainsville.
62. Zhang, D., and Hewitt, G.M. (1996). Nuclear integrations: challenges for mitochondrial DNA markers. Trends in Ecology & Evolution 11, 247-251. doi:10.1016/0169-5347(96)10031-8
63. Zink, R.M. (2004). The role of subspecies in obscuring avian biological diversity and misleading conservation policy. Proceedings. Biological Sciences 271, 561-564. doi:10.1098/rspb.2003.2617
64. Zink, R.M. (2005). Natural selection on mitochondrial DNA in Parus and its relevance for phylogeographic studies. Proceedings. Biological Sciences 272, 71-78. doi:10.1098/rspb.2004.2908
65. Zink, R.M. (2010). Drawbacks with the use of microsatellites in phylogeography: The song sparrow Melospiza melodia as a case study. Journal of Avian Biology 41, 1-7. doi:10.1111/j.1600-048X.2009.
66. Zink, R.M., and Barrowclough, G.F. (2008). Mitochondrial DNA under siege in avian phylogeography. Molecular Ecology 17, 2107-2121.doi:10.1111/j.1365- 294X.2008.03737.x
67. Zink, R.M., Drovetski, S.V., and Rohwer, S. (2006). Selective neutrality of mitochondrial ND2 sequences, phylogeography and species limits in Sitta europaea. Molecular Phylogenetics and Evolution 40, 679-686.doi:10.1016/j.ympev. 2005.11.002