The Maluridae: Inferring avian biology and evolutionary history from DNA sequences

Emu

Volumn 113, Issue 3, 2013, Pages 195-207

  Joseph, Leo ^a   Edwards, Scott V ^b   McLean, Alison J ^c  

^a CSIRO   (Australia)

^b HARVARD UNIVERSITY   (United States)

^c GRIFFITH UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTATION; BEHAVIORAL ECOLOGY; BIOGEOGRAPHY; DNA; GENE EXPRESSION; PASSERINE; PLUMAGE; TAXONOMY;

EID: 84882410593     PISSN: 01584197     EISSN: None     Source Type: Journal    
DOI: 10.1071/MU12081     Document Type: Review

References (108)

1. Austin, J., Joseph, L., Pedler, L., and Black, A. (2013). Uncovering cryptic evolutionary diversity in extant and extinct populations of the southern Australian arid zone Western and Thick-billed Grasswrens (Paseriformes: Maluridae: Amytornis). Conservation Genetics. [Published online ahead of print 7 June 2013] doi:10.1007/s10592-013-0504-9
2. Avise, J. C., Arnold, J., Ball, R. M., Bermingham, E., Lamb, T., Neigel, J., 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
3. Balakrishnan, C. N., Lee, J. Y., and Edwards, S. V. (2010). Phylogeography and phylogenetics in the nuclear age. In 'In Search of the Causes of Evolution: From Field Observations to Mechanisms'. (Eds P. Grant and R. Grant.) pp. 65-88. (Princeton University Press: Princeton, NJ.)
4. Barker, F. K., Barrowclough, G. F., and Groth, J. G. (2002). A phylogenetic hypothesis for passerine birds: taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data. Proceedings of the Royal Society of London-B. Biological Sciences 269, 295-308. doi:10.1098/rspb.2001.1883
5. Barker, F. K., Cibois, A., Schikler, P., Feinstein, J., and Cracraft, J. (2004). Phylogeny and diversification of the largest avian radiation. Proceedings of the National Academy of Sciences of the United States of America 101, 11 040-11 045. doi:10.1073/pnas.0401892101
6. Black, A. B. (2004). The 'Immarna' grasswrens of R. C. Chandler: locality, habitat, identity and taxonomic implications. South Australian Ornithologist 34, 199-211.
7. Black, A. B. (2011a). Subspecies of the Thick-billed Grasswren Amytornis modestus (Aves-Maluridae). Transactions of the Royal Society of South Australia 135, 26-38.
8. Black, A. B. (2011b). Western Australia, home of the Grass-Wren (Amytornis textilis). Amytornis 3, 1-12.
9. Black, A., Carpenter, G., and Pedler, L. (2009). Distribution and habitats of the Thick-billed Grasswren Amytornis textilis subspecies myall. South Australian Ornithologist 35, 161-177.
10. Black, A. B., Joseph, L., Pedler, L. P., and Carpenter, G. A. (2010). A taxonomic framework for interpreting evolution within the Amytornis textilis-modestus complex of grasswrens. Emu 110, 358-363. doi:10.10 71/MU10045
11. Brito, P., and Edwards, S. V. (2009). Multilocus phylogeography and phylogenetics using sequence-based markers. Genetica 135, 439-455. doi:10.1007/s10709-008-9293-3
12. Byrne, M., Yeates, D., Joseph, L., Kearney, M., Bowler, J., Williams,M. A. J., Cooper, S., Donnellan, S. C., Keogh, J. S., Leys, R., Melville, J., Murphy, D. J., Porch, N., and Wyrwoll, K.-H. (2008). Birth of a biome: insights into the assembly and maintenance of the Australian arid zone biota. Molecular Ecology 17, 4398-4417. doi:10.1111/j.1365-294X.2008.03 899.x
13. Caparroz, R., Miyaki, C., and Baker, A. (2009). Contrasting phylogeographic patterns in mitochondrial DNA and microsatellites: evidence of female philopatry and male-biased gene flow among regional populations of the Blue-and-yellow Macaw (Psittaciformes: Ara ararauna) in Brazil. The Auk 126, 359-370. doi:10.1525/auk.2009.07183
14. Chivas, A. R., Garcia, A., and van der Kaars, S. (2001). Sea-level and environmental changes since the last interglacial in the Gulf of Carpentaria, Australia: an overview. Quaternary International 83-85, 19-46. doi:10.1016/S1040-6182(01)00029-5
15. Christidis, L. (1999). Evolution and biogeography of the Australian grasswrens Amytornis (Aves: Maluridae). Australian Journal of Zoology 47, 113-124. doi:10.1071/ZO98054
16. Christidis, L., and Schodde, R. (1997). Relationships within the Australo-Papuan fairywrens (Aves: Malurinae): an evaluation of the utility of allozyme data. Australian Journal of Zoology 45, 113-129. doi:10.1071/ZO96068
17. Christidis, L., Horton, P., and Norman, J. A. (2008). Subspeciation in the Short-tailed Grasswren (Amytornis merrotsyi, Maluridae). Emu 108, 275-282. doi:10.1071/MU08011
18. Christidis, L., Rheindt, F. E., Boles, W. E., and Norman, J. A. (2010). Plumage patterns are good indicators of taxonomic diversity, but not of phylogenetic affinities, in Australian grasswrens Amytornis (Aves: Maluridae). Molecular Phylogenetics and Evolution 57, 868-877. doi:10.1016/j.ympev.2010.08. 029
19. Cracraft, J. (1991). Patterns of diversification within continental biotas: hierarchical congruence among the areas of endemism of Australian vertebrates. Australian Systematic Botany 4, 211-227. doi:10.1071/SB99 10211
20. Condon, H. T. (1951). Notes on the birds of South Australia: occurrence, distribution and taxonomy. South Australian Ornithologist 20, 26-68
21. Cook, B. D., Adams, M., Mather, P., and Hughes, J. (2012). Statistical phylogeographic tests of competing 'Lake Carpentaria hypotheses' in the mouth-brooding freshwater fish, Glossamia aprion (Apogonidae). Marine and Freshwater Research 63, 450-456. doi:10.1071/MF11222
22. Cracraft, J. (1986). Origin and evolution of continental biotas: speciation and historical congruence within the Australian avifauna. Evolution 40, 977-996. doi:10.2307/2408757
23. Cracraft, J., and Feinstein, J. (2000). What is not a bird of paradise? Molecular and morphological evidence places Macgregoria in the Meliphagidae and the Cnemophilinae near the base of the corvoid tree. Proceedings of the Royal Society of London-B. Biological Sciences 267, 233-241. doi:10.1098/rspb.2000. 0992
24. D'Horta, F. M., Cabanne, G. S., Meyer, D., and Miyaki, C. Y. (2011). The genetic effects of Late Quaternary climatic changes over a tropical latitudinal gradient: diversification of an Atlantic Forest passerine. Molecular Ecology 20, 1923-1935. doi:10.1111/j.1365-294X.2011.05063.x
25. de Bruyn, M., Wilson, J. C., and Mather, P. B. (2004). Reconciling geography and genealogy: phylogeography of giant freshwater prawns from the Lake Carpentaria region. Molecular Ecology 13, 3515-3526. doi:10.1111/j.1365-294X. 2004.02348.x
26. Dolman, G., and Joseph, L. (2012). A species assemblage approach to comparative phylogeography of birds in southern Australia. Ecology and Evolution 2, 354-369. doi:10.1002/ece3.87
27. Dolman, G., and Moritz, C. (2006). A multi-locus perspective on refugial isolation and divergence in rainforest skinks (Carlia). Evolution 60, 573-582.
28. Donnellan, S. C., Armstrong, J., Pickett, M., Milne, T., Baulderstone, J., Hollfelder, T., and Bertozzi, T. (2009). Systematic and conservation implications of mitochondrial DNA diversity in emu-wrens, Stipiturus (Aves: Maluridae). Emu 109, 143-152. doi:10.1071/MU07011
29. Double, M. C., Peakall, R., Beck, N. R., and Cockburn, A. (2005). Dispersal, philopatry, and infidelity: dissecting local genetic structure in Superb Fairy-wrens (Malurus cyaneus). Evolution 59, 625-635.
30. Doucet, S. M., Shawkey, M. D., Rathburn, M. K., Mays, H. L., and Montgomerie, R. (2004). Concordant evolution of plumage colour, feather microstructure and a melanocortin receptor gene between mainland and island populations of a fairy-wren. Proceedings of the Royal Society of London-B. Biological Sciences 271, 1663-1670. doi:10.1098/rspb.2004.2779
31. Driskell, A. C., Pruett-Jones, S., Tarvin, K. A., and Hagevik, S. (2002). Evolutionary relationships among blue-and black-plumaged populations of the White-winged Fairy-wren (Malurus leucopterus). Australian Journal of Zoology 50, 581-595. doi:10.1071/ZO02019
32. Driskell, A. C., Prum, R. O., and Pruett-Jones, S. (2010). The evolution of black plumage from blue in Australian fairy-wrens (Maluridae): genetic and structural evidence. Journal of Avian Biology 41, 505-514. doi:10. 1111/j.1600-048X.2009.04823.x
33. Driskell, A. C., Norman, J. A., Pruett-Jones, S., Mangall, E., Sonsthagen, S., and Christidis, L. (2011). A multigene phylogeny examining evolutionary and ecological relationships in the Australo-Papuan wrens of the subfamily Malurinae (Aves). Molecular Phylogenetics and Evolution 60, 480-485. doi:10.1016/j.ympev.2011.03.030
34. Dudaniec, R., Schlotfeldt, B., Bertozzi, T., Donnellan, S. C., and Kleindorfer, S. (2011). Genetic and morphological divergence in island and mainland birds: informing conservation priorities. Biological Conservation 144, 2902-2912. doi:10.1016/j.biocon.2011.08.007
35. Edwards, S. V. (1993). Long-distance gene flow in a cooperative breeder detected in genealogies of mitochondrial DNA sequences. Proceedings of the Royal Society of London-B. Biological Sciences 252, 177-185. doi:10.1098/rspb.1993. 0063
36. Edwards, S. V. (2009). Is a new and general theory of molecular systematics emerging? Evolution 63, 1-19. doi:10.1111/j.1558-5646. 2008.00549.x
37. Edwards, D. L., Roberts, J. D., and Keogh, J. S. (2007). Impact of Plio-Pleistocene arid cycling on the population history of a southwestern Australian frog. Molecular Ecology 16, 2782-2796. doi:10.1111/j.13 65-294X.2007.03374.x
38. Edwards, S. V., Cameron Devitt, S., and Fujita, M. (2012). Phylogeography. In 'Encyclopedia of Theoretical Ecology'. (Eds A. Hastings and L. Gross.) pp. 557-565. (University of California Press: Berkeley, CA.)
39. Endler, J. A. (1993). The colour of light in forests and its implications. Ecological Monographs 63, 1-27. doi:10.2307/2937121
40. Ericson, P. G. P., Christidis, L., Cooper, A., Irestedt, M.,, Jackson, J., Johansson, U. S., and Norman, J. A. (2002). A Gondwanan origin of passerine birds supported by DNA sequences of the endemic New Zealand wrens. Proceedings of the Royal Society of London-B. Biological Sciences 269, 235-241.
41. Ford, J. (1966). Taxonomy and variation of the chestnut-shouldered wrens of Western Australia. Emu 66, 47-57. doi:10.1071/MU966047
42. Ford, J. (1974). Speciation in Australian birds adapted to arid habitats. Emu 74, 161-168. doi:10.1071/MU974161
43. Ford, J. (1987). Minor isolates and minor geographical barriers in avian speciation in continental Australia. Emu 87, 90-102. doi:10.1071/MU9870090
44. Ford, J., and Johnstone, R. E. (1991). Hybridisation between Malurus lamberti rogersi and Malurus lamberti assimilis in north-western Australia. Emu 91, 251-254. doi:10.1071/MU9910251
45. Gardner, J. L., Trueman, J. W. H., Ebert, D., Joseph, L., and Magrath, R. D. (2010). Phylogeny and evolution of the Meliphagoidea, the largest radiation of Australasian songbirds. Molecular Phylogenetics and Evolution 55, 1087-1102. doi:10.1016/j.ympev.2010.02.005
46. Greenwood, P. J. (1980). Mating systems, philopatry and dispersal in birds and mammals. Animal Behaviour 28, 1140-1162. doi:10.1016/S0003-3472(80) 80103-5
47. Gutiérrez-Pinto, N., Cuervo, A. M., Miranda, J., Perez-Eman, J. L.,Brumfield, R. T., and Cadena, C. D. (2012). Non-monophyly and deep genetic differentiation across low-elevation barriers in a Neotropical montane bird (Basileuterus tristriatus; Aves: Parulidae). Molecular Phylogenetics and Evolution 64, 156-165. doi:10.1016/j.ympev.2012.03.011
48. Harrison, C. J. O. (1972). A re-examination of the chestnut-shouldered wren complex of Australia. Bulletin of the British Museum of Natural History (Zoology) 21, 313-328.
49. Hewitt, G. M. (2004). Genetics consequences of climatic oscillations in the Quaternary. Philosophical Transactions of the Royal Society of London-B. Biological Sciences 359, 183-195. doi:10.1098/rstb.2003.1388
50. Higgins, P. J., Peter, J. M., and Steele, W. K. (2001). Handbook of Australian, New Zealand and Antarctic Birds. Tyrant-flycatchers to Chats, vol. 5. (Oxford University Press: Melbourne.)
51. Hopper, S., and Gioia, P. (2004). The southwest Australian floristic region: evolution and conservation of a global hot spot of biodiversity. Annual Review of Ecology Evolution and Systematics 35, 623-650. doi:10.1146/annurev. ecolsys.35.112202.130201
52. Jennings, W. B., and Edwards, S. V. (2005). Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees. Evolution 59, 2033-2047.
53. Johnson, N. K., and Cicero, C. (2004). New mitochondrial DNA data affirm the importance of Pleistocene speciation in North American birds. Evolution 58, 1122-1130.
54. Joseph, L., and Omland, K. E. (2009). Phylogeography: its development and impact in Australo-Papuan ornithology with special reference to paraphyly in Australian birds. Emu 109, 1-23. doi:10.1071/MU08024
55. Joseph, L., Moritz, C., and Hugall, A. (1995). Molecular support for vicariance as a source of diversity in rainforest. Proceedings of the Royal Society of London. Series B, Biological Sciences 260, 177-182. doi:10. 1098/rspb.1995.0077
56. Kearns, A. M., Joseph, L., Edwards, S. V., and Double,M.C. (2009). Inferring the phylogeography and evolutionary history of the Splendid Fairywren Malurus splendens from mitochondrial DNA and spectrophotometry. Journal of Avian Biology 40, 7-17. doi:10.1111/j.1600-048X.2008. 04383.x
57. Kearns, A., Joseph, L., and Cook, L. (2010). The impact of Pleistocene climatic and landscape changes on Australian birds: a test using the Pied Butcherbird (Cracticus nigrogularis). Emu 110, 285-295. doi:10.1071/MU10020
58. Kearns, A. M., Joseph, L., Omland, K., and Cook, L. (2011). Testing the effect of transient Plio-Pleistocene barriers in monsoonal Australo-Papua: did mangrove habitats maintain genetic connectivity in the Black Butcherbird? Molecular Ecology 20, 5042-5059. doi:10.1111/j.1365-294X.2011.05330.x
59. Keast, J. A. (1958). Speciation in the genus Amytornis Stejneger (Passeres: Muscicapidae, Malurinae) in Australia. Australian Journal of Zoology 6, 33-52. doi:10.1071/ZO9580033
60. Keast, J. A. (1961). Bird speciation on the Australian continent. Bulletin of the Museum of Comparative Zoology, Harvard 123, 303-495
61. Kingma, S. A., Hall, M., Segelbacher, G., and Peters, A. (2009). Radical loss of an extreme extra-pair mating system. BMC Ecology 9, 15. doi:10. 1186/1472-6785-9-15
62. Kleindorfer, S., Evans, C., Mihailova, M., Colombelli-Négrel, D., Hoi, H., Griggio, M., Mahr, K., and Robertson, J. (2013). When subspecies matter: resident Superb Fairy-wrens (Malurus cyaneus) distinguish the sex and subspecies of intruder birds. Emu 113, 259-269. doi:10.1071/MU12066
63. Klicka, J., and Zink, R. M. (1999). Pleistocene phylogeographic effects on avian evolution. Proceedings of the Royal Society of London-B. Biological Sciences 266, 695-700. doi:10.1098/rspb.1999.0691
64. Ladiges, P., Parra-O., C., Gibbs, A., Udovicic, F., Nelson, G., and Bayly, M. (2011). Historical biogeographical patterns in continental Australia: congruence among areas of endemism of two major clades of eucalypts. Cladistics 27, 29-41. doi:10.1111/j.1096-0031.2010.00315.x
65. Ladiges, P., Bayly, M., and Nelson, G. (2012). Searching for ancestral areas and artifactual centers of origin in biogeography: with comment on east-west patterns across southern Australia. Systematic Biology 61, 703-708. doi:10.1093/sysbio/sys005
66. LeCroy, M., and Diamond, J. (1995). Plumage variation in the Broad-billed Fairy-wren. Emu 95, 185-193. doi:10.1071/MU9950185
67. Lee, J. Y., and Edwards, S. V. (2008). Divergence across Australia's Carpentarian Barrier: statistical phylogeography of the Red-backed Fairy wren (Malurus melanocephalus). Evolution 62, 3117-3134. doi:10.1111/j.1558-5646.2008. 00543.x
68. Lee, J. Y., Joseph, L., and Edwards, S. V. (2012). A species tree for the Australo-Papuan fairywrens and allies. Systematic Biology 61, 253-271. doi:10.1093/sysbio/syr101
69. Liu, L. (2008). BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics 24, 2542-2543. doi:10.1093/bioinfor matics/btn484
70. Lovette, I. (2004). Mitochondrial dating and mixed support for the '2% rule' in birds. Auk 121, 1-6.
71. Mack, G. (1934). A revision of the genus Malurus. Memoirs of the National Museum Melbourne 8, 100-125.
72. McLean, A. J., Toon, A., Schmidt, D. J., Joseph, L., and Hughes, J. M. (2012). Speciation in chestnut-shouldered fairy-wrens (Malurus spp.) and rapid phenotypic divergence in Variegated Fairy-wrens (Malurus lamberti): a multilocus approach. Molecular Phylogenetics and Evolution 63, 668-678. doi:10.1016/j.ympev.2012.02.016
73. Miller, M. J., Bermingham, E., Klicka, J., Escalante, P., and Winker, K. (2010). Neotropical birds show a humped distribution of within-population genetic diversity along a latitudinal transect. Ecology Letters 13, 576-586. doi:10.1111/j.1461-0248.2010.01454.x
74. MUndy, N. I. (2005). A window on the genetics of evolution: MC1R and plumage colouration in birds. Proceedings of the Royal Society of London-B. Biological Sciences 272, 1633-1640. doi:10.1098/rspb. 2005.3107
75. MUndy, N. I., Badcock, N. S., Hart, T., Scribner, K., Janssen, K., and Nadeau, N. J. (2004). Conserved genetic basis of a quantitative plumage trait involved in mate choice. Science 303, 1870-1873. doi:10.1126/science. 1093834
76. Myers, N., Mittermeier, R. A., Mittermeier, C. G., da Fonseca, G. A. B., and Kent, J. (2000). Biodiversity hotspots for conservation priorities. Nature 403, 853-858. doi:10.1038/35002501
77. Nicholls, J. A., and Austin, J. J. (2005). Phylogeography of an east Australian wet-forest bird, the Satin Bowerbird (Ptilonorhynchus violaceus), derived from mtDNA, and its relationship to morphology. Molecular Ecology 14, 1485-1496. doi:10.1111/j.1365-294X.2005.02544.x
78. Odeen, A., Pruett-Jones, S., Driskell, A. C., Armenta, J. K., and Hastad, O. (2012). Multiple shifts between violet and ultraviolet vision in a family of passerine birds with associated changes in plumage coloration. Proceedings of the Royal Society of London-B. Biological Sciences 279, 1269-1276. doi:10.1098/rspb.2011.1777
79. Parker, S. A. (1972). Remarks on the distribution and taxonomy of the grasswrens Amytornis textilis, modestus and purnelli. Emu 72, 157-166. doi:10.1071/MU972157
80. Parker, S. A. (1982). Notes on Amytornis striatus merrotsyi Mellor, a subspecies of the Striated Grasswren inhabiting the Flinders Ranges. South Australian Ornithologist 29, 13-16.
81. Parker, S. A., May, I., and Head, W. (1978). Some observations on the Eyrean Grasswren Amytornis goyderi (Gould, 1875). Records of the South Australian Museum 17, 361-371.
82. Pavlova, A., Walker, F. M., van der Ree, R., Cesarini, S., and Taylor, A. C. (2010). Threatened populations of the Australian Squirrel Glider (Petaurus norfolcensis) show evidence of evolutionary distinctiveness on a Late Pleistocene timescale. Conservation Genetics 11, 2393-2407. doi:10.1007/s10592- 010-0125-5
83. Pavlova, A., Amos, J. N., Joseph, L., Loynes, K., Austin, J., Keogh, J. S., Stone, G. N., Nicholls, J. A., and Sunnucks, P. (2013). Perched at the cyto-nuclear crossroads: divergent mitochondrial lineages correlate with environment in the face of ongoing nuclear gene flowin an Australian bird. Evolution. [Published online ahead of print 9 April 2013]. doi:10. 1111/evo.12107
84. Rheindt, F., and Edwards, S. V. (2011). Genetic introgression: an integral but neglected component of speciation in birds. Auk 128, 620-632. doi:10.1525/auk.2011.128.4.620
85. Rollins, L. A., Svedin, N., Pryke, S. R., and Griffith, S. C. (2012). The role of the Ord Arid Intrusion in the historical and contemporary genetic division of Long-tailed Finch subspecies in northern Australia. Ecology and Evolution 2, 1208-1219. doi:10.1002/ece3.259
86. Ronquist, F. (2004). Bayesian inference of character evolution. Trends in Ecology & Evolution 19, 475-481. doi:10.1016/j.tree.2004.07.002
87. Ronquist, F., and Huelsenbeck, J. P. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574. doi:10.1093/bioinformatics/btg180
88. Rowley, I. (2001). [Introduction to] Family Maluridae Australopapuan fairy-wrens, emu-wrens and grasswrens. In 'Handbook of Australian, NewZealand and Antarctic Birds. Tyrant-flycatchers to Chats.Volume 5'. (Eds P. J. Higgins, J. M. Peter and W. K. Steele) pp 257-260. (Oxford University Press, Melbourne).
89. Rowley, I., and Russell, E. (1997). 'Fairy-wrens and Grasswrens Maluridae.' (Oxford University Press: New York.)
90. Rowley, I., and Russell, E. (2007). Family Maluridae (Fairy-wrens). In 'Handbook of the Birds of the World. Vol. 12: Picathartes to Tits and Chickadees'. (Eds J. del Hoyo, A. Elliott and D. A. Christie.) pp. 490-531. (Lynx Edicions: Barcelona.)
91. Schlotfeldt, B. E., and Kleindorfer, S. (2006). Adaptive divergence in the Superb Fairy-wren (Malurus cyaneus): a mainland versus island comparison of morphology and foraging behaviour. Emu 106, 309-319. doi:10.1071/MU06004
92. Schneider, C. J., Cunningham, M., and Moritz, C. (1998). Comparative phylogeography and the history of endemic vertebrates in the Wet Tropics rainforests of Australia. Molecular Ecology 7, 487-498. doi:10. 1046/j.1365-294x.1998.00334.x
93. Schodde, R. (1975). 'Interim List of Australian Birds. Passerines.' (Royal Australasian Ornithologists Union: Melbourne.)
94. Schodde, R. (1982). 'The Fairy-Wrens: A Monograph of the Maluridae.' (Lansdowne Editions: Melbourne.)
95. Schodde, R., and Mason, I. J. (1999). 'The Directory of Australian Birds: Passerines.' (CSIRO Publishing: Melbourne.)
96. Sibley, C. G., and Ahlquist, J. E. (1990). 'Phylogeny and Classification of Birds: A Study in Molecular Evolution.' (Yale University Press: New Haven.)
97. 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
98. Theron, E., Hawkins, K., Bermingham, E., Ricklefs, R. E., and Mundy, N. I. (2001). The molecular basis of an avian plumage polymorphism in the wild: a melanocortin-1-receptor point mutation is perfectly associated with the melanic plumage morph of the Bananaquit, Coereba flaveola. Current Biology 11, 550-557. doi:10.1016/S0960-9822(01)00158-0
99. Toon, A., Mather, P. B., Baker, A. M., Durrant, K. L., and Hughes, J. M. (2007). Pleistocene refugia in an arid landscape: analysis of a widely distributed Australian passerine. Molecular Ecology 16, 2525-2541. doi:10.1111/j.1365-294X.2007.03289.x
100. Toon, A., Hughes, J., and Joseph, L. (2010). Multilocus analysis of honeyeaters (Aves: Meliphagidae) highlights the spatio-temporal heterogeneity in the influence of biogeographic barriers in the Australian monsoonal zone. Molecular Ecology 19, 2980-2994. doi:10.1111/j.13 65-294X.2010.04730.x
101. Toon, A., Austin, J., Dolman, G., Pedler, L., and Joseph, L. (2012). Evolution of arid zone birds in Australia: leapfrog distribution patterns and mesicarid connections in quail-thrush. Molecular Phylogenetics and Evolution 62, 286-295. doi:10.1016/j.ympev.2011.09.026
102. Uy, J. A. C., Moyle, R. G., Filardi, C., and Cheviron, Z. A. (2009). Difference in plumage color used in species recognition between incipient species is linked to a single amino acid substitution in the melanocortin-1 receptor. American Naturalist 174, 244-254. doi:10.1086/600084
103. Weir, J. T., and Price, M. (2011). Andean uplift promotes lowland speciation through vicariance and dispersal in Dendrocincla woodcreepers. Molecular Ecology 20, 4550-4563. doi:10.1111/j.1365-294X.2011. 05294.x
104. Weir, J. T., and Schluter, D. (2007). The latitudinal gradient in recent speciation and extinction rates of birds and mammals. Science 315, 1574-1576. doi:10.1126/science.1135590
105. Yu, Y., Harris, A. J., and He, X.-J. (2010). S-DIVA (Statistical Dispersal-Vicariance Analysis): a tool for inferring biogeographic histories. Molecular Phylogenetics and Evolution 56, 848-850. doi:10.1016/j.ym
106. pev.2010.04.011 Yu, Y., Harris, A. J., and He, X. J. (2011). 'RASP (Reconstruct Ancestral State in Phylogenies) 2.0b.' (Sichuan University: Chengdu, China.) Available at http://mnh.scu.edu.cn/soft/blog/RASP [Verified 18 September 2012].
107. 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.2009.04903.x
108. 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.