Emu Emu Society
Journal of BirdLife Australia
ROWLEY REVIEW

ROWLEY REVIEW. Phylogeography: its development and impact in Australo-Papuan ornithology with special reference to paraphyly in Australian birds

Leo Joseph A C and Kevin E. Omland B
+ Author Affiliations
- Author Affiliations

A Australian National Wildlife Collection, CSIRO Sustainable Ecosystems, GPO Box 284, Canberra, ACT 2601, Australia.

B Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.

C Corresponding author. Email: leo.joseph@csiro.au

Emu 109(1) 1-23 https://doi.org/10.1071/MU08024
Submitted: 12 May 2008  Accepted: 18 September 2008   Published: 20 January 2009

Abstract

With examples from Australo-Papuan ornithology, we examine the technical and theoretical roots of molecular phylogeography and review its development. We describe the progression from ad hoc interpretation of gene trees in single species phylogeographic studies through to comparative phylogeography and currently advocated model-testing approaches. Mitochondrial DNA (mtDNA) sequences have provided most advances to date, although we demonstrate and advocate the future use of multilocus datasets analysed with coalescent methods. We examine interrelationships among speciation research, historical biogeography, phylogeography and landscape genetics. Mitochondrial paraphyly, in which individuals of one species or population have mtDNA that is more closely related to that of another than to their own, emerges in 44% of Australian studies to date as a common, important result in Australian avian phylogeography. Accordingly, we explore at length its most common causes and its impact on case studies in Australo-Papuan avian phylogeography. The impact of so much paraphyly on avian phylogeography and taxonomy is a major theme of the review. We suggest a full research agenda for avian phylogeography in the Australo-Papuan region that spans diverse topics: the need for more studies of pelagic birds, spatio-temporal links between New Guinea and Australia, island populations, testing of long-established biogeographical hypotheses, and integration of molecular and non-molecular datasets into integrated evolutionary understanding of species and populations. Studying the full continuum of divergences from landscape genetics, to phylogeography, to recently diverged species with evidence of paraphyly, to highly divergent species with many fixed differences will lead to a more complete understanding of the processes and patterns of avian evolution.


Acknowledgements

We especially thank Scott Edwards for his detailed comments on two drafts. We also thank Gaynor Dolman, Michael Double, and anonymous reviewers for critically commenting on a draft, and David Winkler for discussion. We thank our colleagues and collaborators for their help in many projects,especially J. Peters and T. Wilke. Kevin E. Omland (KEO) is funded by an US National Science Foundation, Systematics Program CAREER Grant (DEB – 0347083). KEO’s contribution was made while on sabbatical leave at the Australian National University, Canberra, supported by a Visiting Fellowship from the School of Botany and Zoology (BoZo). KEO thanks William Foley, Andrew Cockburn, Mike Crisp, and other members of the Crisp Laboratory and BoZo for interesting discussions. Responsibility for views expressed, of course, lies with L. Joseph and K. E. Omland.


References

Abbott, I. (1974). The avifauna of Kangaroo Island and causes of its impoverishment. Emu 74, 124–134.


Abbott, C. L. , and Double, M. C. (2003a). Genetic structure, conservation genetics and evidence of speciation by range expansion in shy and white-capped albatrosses. Molecular Ecology 12, 2953–2962.
CrossRef | PubMed |

Abbott, C. L. , and Double, M. C. (2003b). Phylogeography of shy and white-capped albatrosses inferred from mitochondrial DNA sequences: implications for population history and taxonomy. Molecular Ecology 12, 2747–2758.
CrossRef | CAS | PubMed |

Akey, J. M. , Eberle, M. A. , Rieder, M. J. , Carlson, C. S. , Shriver, M. D. , Nickerson, D. A. , and Kruglyak, L. (2004). Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biology 2(10), e286.
CrossRef | PubMed |

Allen, E. S. , and Omland, K. E. (2003). Novel intron phylogeny supports plumage convergence in orioles (Icterus). Auk 120, 961–970.
CrossRef |

Austin, J. , White, R. , and Ovenden, J. (1994). Population genetic structure of a philopatric, colonially nesting seabird, the Short-tailed Shearwater (Puffinus tenuirostris). Auk 111, 70–79.


Avise J. C. (2000). ‘Phylogeography, The History and Formation of Species.’ (Harvard University Press: Cambridge, MA.)

Avise, J. C. , and Aquadro, C. F. (1982). A comparative summary of genetic distances in vertebrates. Evolutionary Biology 15, 151–185.


Avise, J. C. , and Walker, D. (1998). Pleistocene phylogeographic effects on avian populations and the speciation process. Proceedings of the Royal Society of London. Series B: Biological Sciences 265, 457–463.
CrossRef | CAS |

Avise, J. C. , Patton, J. C. , and Aquadro, C. F. (1980a). Evolutionary genetics of birds. Comparative molecular evolution in New World warblers and rodents. Journal of Heredity 71, 303–310.
CAS |

Avise, J. C. , Patton, J. C. , and Aquadro, C. F. (1980b). Evolutionary genetics of birds. II. Conservative protein evolution in North American sparrows and relatives. Systematic Zoology 29, 323–334.
CrossRef |

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.


Avise, J. C. , Ankey, C. D. , and Nelson, W. S. (1990). Mitochondrial gene trees and the evolutionary relationship of mallard and black ducks. Evolution 44, 1109–1119.
CrossRef |

Axelsson, A. , Hultin-Rosenberg, L. , Brandström, M. , Zwahlén, M. , Clayton, D. , and Ellegren, H. (2008). Natural selection in avian protein-coding genes expressed in brain. Molecular Ecology 17, 3008–3017.
CrossRef | CAS | PubMed |

Backström, N. , Fagerberg, S. , and Ellegren, H. (2008). Genomics of natural bird populations: a gene-based set of reference markers evenly spread across the avian genome. Molecular Ecology 17, 964–980.
CrossRef | PubMed |

Baker, A. M. , Mather, P. B. , and Hughes, J. M. (2000). Population genetic structure of Australian magpies: evidence for regional differences in juvenile dispersal behaviour. Heredity 85, 167–176.
CrossRef | CAS | PubMed |

Baker, M. C. , Maker, M. S. , and Tilghman, L. (2006). Differing effects of isolation on evolution of bird songs: examples from an island–mainland comparison of three species. Biological Journal of the Linnaean Society 89, 331–342.
CrossRef |

Ballard, J. , and Rand, D. M. (2005). The population biology of mitochondrial DNA and its phylogenetic implications. Annual Review of Ecology, Evolution, and Systematics 36, 621–642.
CrossRef |

Ballard, J. , and Whitlock, M. (2004). The incomplete natural history of mitochondria. Molecular Ecology 13, 729–744.
CrossRef | PubMed |

Beheregaray, L. B. (2008). Twenty years of phylogeography: the state of the field and the challenges for the Southern Hemisphere. Molecular Ecology 17, 3754–3774.
PubMed |

Bermingham, E. , and Moritz, C. (1998). Comparative phylogeography: concepts and applications. Molecular Ecology 7, 367–369.
CrossRef |

Birky, C. W. , Fuerst, P. , and Maruyama, T. (1989). Organelle gene diversity under migration, mutation, and drift: equilibrium expectations, approach to equilibrium, effects of heteroplasmic cells, and comparison to nuclear genes. Genetics 121, 613–627.
PubMed |

Boulet, M. , and Gibbs, H. L. (2006). Lineage origin and expansion of a Neotropical migrant songbird after recent glaciation events. Molecular Ecology 15, 2505–2525.
CrossRef | CAS | PubMed |

Brito, P. (2007). Contrasting patterns of mitochondrial and microsatellite genetic structure among Western European populations of tawny owls (Strix aluco). Molecular Ecology 16, 3423–3437.
CrossRef | CAS | PubMed |

Brito, P. , and Edwards, S. V. (2008). Multilocus phylogeography and phylogenetics using sequence-based markers. Genetica ,in press
CrossRef |

Brumfield, R. , Jernigan, J. W. , McDonald, D. B. , and Braun, M. J. (2001). Evolutionary implications of divergent clines in an avian (Manacus : Aves) hybrid zone. Evolution 55, 2070–2087.
CAS | PubMed |

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.
CrossRef | CAS | PubMed |

Castelloe, J. , and Templeton, A. R. (1994). Root probabilities for intraspecific gene trees under neutral coalescent theory. Molecular Phylogenetics and Evolution 3, 102–113.
CrossRef | CAS | PubMed |

Chen, C. , Durand, E. , Forbes, F. , and François, O. (2007). Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison study. Molecular Ecology Notes 7, 747–756.
CrossRef |

Cheviron, Z. , Whitehead, A. , and Brumfield, R. (2008). Transcriptomic variation and plasticity in Rufous-collared Sparrows (Zonotrichia capensis) along an altitudinal gradient. Molecular Ecology 17, 4556–4569.
CrossRef | CAS | PubMed |

Christidis L. , and Boles W. E. (2008). ‘Systematics and Taxonomy of Australian Birds.’ (CSIRO Publishing: Melbourne.)

Christidis, L. , Horton, P. , and Norman, J. (2008). Subspeciation in the Short-tailed Grasswren (Amytornis merrotsyi, Maluridae). Emu 108, 275–282.
CrossRef |

Clegg, S. M. , Degnan, S. M. , Kikkawa, J. , Moritz, C. , Estoup, A. , and Owens, I. P. F. (2002). Genetic consequences of sequential founder events by an island-colonizing bird. Proceedings of the National Academy of Sciences, USA 99, 8127–8132.
CrossRef | CAS |

Congdon, B. C. , Piatt, J. F. , Martin, K. , and Friesen, V. L. (2000). Mechanisms of population differentiation in marbled murrelets: historical versus contemporary processes. Evolution 54, 974–986.
CAS | PubMed |

Cook, L. , and Crisp, M. (2005). Directional asymmetry of long-distance dispersal and colonization could mislead reconstructions of biogeography. Journal of Biogeography 32, 741–754.
CrossRef |

Crandall, K. , Bininda-Emonds, O. , Mace, G. , and Wayne, R. (2000). Considering evolutionary processes in conservation biology. Trends in Ecology & Evolution 15, 290–295.
CrossRef |

de Queiroz K. (1998). The general lineage concept of species, species criteria, and the process of speciation: a conceptual unification and terminological recommendations. In ‘Endless Forms: Species and Speciation’. (Eds D. J. Howard and S. H. Berlocher.) pp. 57–75. (Oxford University Press: New York.)

de Queiroz, K. (2007). Species concepts and species delimitation. Systematic Biology 56, 879–886.
CrossRef | PubMed |

Degnan, S. M. (1993a). The perils of single gene trees – mitochondrial versus single-copy nuclear DNA variation in white-eyes (Aves : Zosteropidae). Molecular Ecology 2, 219–225.
CrossRef |

Degnan, S. M. (1993b). Genetic variability and population differentiation inferred from DNA-fingerprinting in silvereyes (Aves : Zosteropidae). Evolution 47, 1105–1117.
CrossRef |

Degnan, S. M. , and Moritz, C. (1992). Phylogeography of mitochondrial DNA in two species of white-eyes in Australia. Auk 109, 800–811.


Diniz-Filho, J. , Telles, M. , Bonatto, S. , Eizirik, E. , de Freitas, T. , de Marco, P. , Santos, F. , Sole-Cava, A. , and Soares, T. (2008). Mapping the evolutionary twilight zone: molecular markers, populations and geography. Journal of Biogeography 35, 753–763.
CrossRef |

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. Series B: Biological Sciences 271, 1663–1670.
CrossRef | CAS |

Driskell, A. , and Christidis, L. (2004). Phylogeny and evolution of the Australo-Papuan honeyeaters (Passeriformes, Meliphagidae). Molecular Phylogenetics and Evolution 31, 943–960.
CrossRef | CAS | PubMed |

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.
CrossRef |

Dumbacher, J. , and Fleischer, R. (2001). Phylogenetic evidence for colour pattern convergence in toxic pitohuis: mullerian mimicry in birds? Proceedings of the Royal Society of London. Series B: Biological Sciences 268, 1971–1976.
CrossRef | CAS |

Edwards, S. V. (1993a). Long-distance gene flow in a cooperative breeder detected in genealogies of mitochondrial DNA sequences. Proceedings of the Royal Society of London. Series B: Biological Sciences 252, 177–185.
CrossRef | CAS |

Edwards, S. V. (1993b). Island and mainland populations of a sedentary songbird, the grey-crowned babbler (Pomatostomus temporalis). Evolution 47, 1118–1137.
CrossRef | CAS |

Edwards, S. V. (2008a). Book Review: Speciation in Birds by Trevor Price. Emu 108, 97–99.
CrossRef |

Edwards, S. V. (2008b). Bird speciation: selection and the origin of species. Evolution 62, 991–995.
CrossRef |

Edwards, S. V. , and Beerli, P. (2000). Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54, 1839–1854.
CAS | PubMed |

Edwards, S. V. , and Wilson, A. (1990). Phylogenetically informative length polymorphism and sequence variability in mitochondrial DNA of Australian songbirds (Pomatostomus). Genetics 126, 695–711.
CAS | PubMed |

Edwards, S. , Kingan, S. , Calkins, J. , Balakrishnan, C. , Jennings, W. , Swanson, W. , and Sorenson, M. (2005). Speciation in birds: genes, geography, and sexual selection. Proceedings of the National Academy of Sciences, USA 102, 6550–6557.
CrossRef | CAS |

Ellegren, H. (2008). Sequencing goes 454 and takes large-scale genomics into the wild. Molecular Ecology 17, 1629–1631.
CrossRef | CAS | PubMed |

Excoffier, L. , and Heckel, G. (2006). Computer programs for population genetics data analysis: a survival guide. Nature Genetics Reviews 7, 745–758.
CrossRef | CAS |

Fleischer, R. , McIntosh, C. E. , and Tarr, C. L. (1998). Evolution on a volcanic conveyor belt: using phylogeographic reconstructions and K–Ar-based ages of the Hawaiian Islands to estimate molecular evolutionary rates. Molecular Ecology 7, 533–545.
CrossRef | CAS | PubMed |

Ford, H. A. (1981). A comment on the relationships between miners Manorina spp. in South Australia. Emu 81, 247–250.


Ford, J. (1974a). Speciation in Australian birds adapted to arid habitats. Emu 74, 161–168.


Ford, J. (1974b). Concepts of subspecies and hybrid zones, and their application in Australian ornithology. Emu 74, 113–123.


Ford, J. R. (1987). Hybrid zones in Australian birds. Emu 87, 158–178.


Funk, D. J. , and Omland, K. (2003). Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology, Evolution, and Systematics 34, 397–423.
CrossRef |

Garnett, S. , and Christidis, L. (2007). Implications of changing species definitions for conservation purposes. Bird Conservation International 17, 187–195.
CrossRef |

Garrick, R. C. , Dyer, R. J. , Beheregaray, L. B. , and Sunnucks, P. (2008a). Babies and bathwater: a comment on the premature obituary for nested clade phylogeographical analysis. Molecular Ecology 17, 1401–1403.
CrossRef | CAS | PubMed |

Garrick, R. C. , Rowell, D. , Simmons, C. , Hillis, D. , and Sunnucks, P. (2008b). Fine-scale phylogeographic congruence despite demographic incongruence in two low-mobility saproxylic springtails. Evolution 62, 1103–1118.
CrossRef | PubMed |

Gay, L. , Neubauer, G. , Zagalska-Neubauer, M. , Debain, C. , Pons, J.-M. , David, P. , and Crochet, P.-A. (2007). Molecular and morphological patterns of introgression between two large white-headed gull species in a zone of recent secondary contact. Molecular Ecology 16, 3215–3227.
CrossRef | CAS | PubMed |

Grant, P. R. , and Grant, B. R. (1992). Hybridization of bird species. Science 256, 193–197.
CrossRef | PubMed |

Hebert, P. D. , Stoeckle, M. Y. , Zemlak, T. S. , and Francis, C. M. (2004). Identification of birds through DNA barcodes. PLoS Biology 2(10), e312.
CrossRef | PubMed |

Helbig, A. , Knox, A. G. , Parkin, D. T. , Sangster, G. , and Collinson, M. (2002). Guidelines for assigning species rank. Ibis 144, 518–525.
CrossRef |

Hey, J. (2005). On the number of New World founders: a population genetic portrait of the peopling of the Americas. PLoS Biology 3(6), e193.
CrossRef | PubMed |

Hey, J. , and Nielsen, R. (2004). Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167, 747–760.
CrossRef | CAS | PubMed |

Hillis D. M. , Moritz C. , and Mable B. K. (1996). ‘Molecular Systematics.’ 2nd edn. (Sinauer: Sunderland, MA.)

Ho, S. Y. W. (2007). Calibrating molecular estimates of substitution rates and divergence times in birds. Journal of Avian Biology 38, 409–414.


Hudson, M. E. (2008). Sequencing breakthroughs for genomic ecology and evolutionary biology. Molecular Ecology Resources 8, 3–17.
CrossRef | CAS |

Hudson, R. R. , and Turelli, M. (2003). Stochasticity overrules the ‘three-times rule’: genetic drift, genetic draft, and coalescence times for nuclear loci versus mitochondrial DNA. Evolution 57, 182–190.
PubMed |

Hugall, A. , Moritz, C. , Moussalli, A. , and Stanisic, J. (2002). Reconciling paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail Gnarosophia bellendenkerensis (Brazier, 1875). Proceedings of the National Academy of Sciences, USA 99, 6112–6117.
CrossRef | CAS |

Hughes, J. M. , Baker, A. M. , De Zylva, G. , and Mather, P. B. (2001). A phylogeographic analysis of southern and eastern populations of the Australian magpie: evidence for selection in maintenance of the distribution of two plumage morphs. Biological Journal of the Linnaean Society 74, 25–34.
CrossRef |

International Chicken Genome Sequencing Consortium (2004). Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695–716.
CrossRef | PubMed |

Jennings, W. B. , and Edwards, S. V. (2005). Speciational history of Australian grass finches (Poephila) inferred from 30 gene trees. Evolution 59, 2033–2047.
CAS | PubMed |

Johnson, J. , Watson, R. T. , and Mindell, D. (2005). Prioritizing species conservation: does the Cape Verde kite exist? Proceedings of the Royal Society of London. Series B: Biological Sciences 272, 1365–1371.
CrossRef |

Johnson, K. P. , and Sorenson, M. D. (1999). Phylogeny and biogeography of dabbling ducks (genus : Anas): a comparison of molecular and morphological evidence. Auk 116, 792–805.


Jonsson, K. , Bowie, R. , Moyle, R. , Christidis, L. , Filardi, C. , Norman, J. , and Fjeldsa, J. (2008). Molecular phylogenetics and diversification within one of the most geographically variable bird species complexes Pachycephala pectoralis/melanura. Journal of Avian Biology 39, 473–478.
CrossRef |

Joseph, L. (2002). Geographical variation, taxonomy and distribution of some Amazonian Pyrrhura parakeets. Ornitologia Neotropical 13, 337–363.


Joseph L. (2008a). The changing faces of systematics and biogeography in Australian ornithology in the latter half of the twentieth century: a young turk’s view. In ‘Contributions to the History of Australasian Ornithology’. Memoirs of the Nuttall Ornithological Club 14. (Eds W. E. Davis Jr, H. F. Recher, W. E. Boles and J. A. Jackson.) pp 253–303. (Nuttall Ornithological Club: Cambridge, MA.)

Joseph, L. (2008b). Book Review: Systematics and Taxonomy of Australian Birds by Les Christidis and Walter E. Boles. Emu 108, 365–368.
CrossRef |

Joseph, L. , and Hope, R. (1984). Aspects of genetic relationships and variation in parrots of the Crimson Rosella Platycercus elegans complex (Aves : Psittacidae). Transactions of the Royal Society of South Australia 108, 77–84.


Joseph, L. , and Moritz, C. (1993a). Phylogeny and historical aspects of the ecology of eastern Australian scrubwrens Sericornis spp. – evidence from mitochondrial DNA. Molecular Ecology 2, 161–170.
CrossRef | CAS | PubMed |

Joseph, L. , and Moritz, C. (1993b). Hybridization between the White-browed and Atherton Scrubwrens: detection with mitochondrial DNA. Emu 93, 93–99.


Joseph, L. , and Moritz, C. (1994). Mitochondrial-DNA phylogeography of birds in eastern Australian rain-forests – first fragments. Australian Journal of Zoology 42, 385–403.
CrossRef | CAS |

Joseph, L. , and Wilke, T. (2004). When DNA throws a spanner in the taxonomic works: testing for monophyly in the Dusky-capped Flycatcher Myiarchus tuberculifer and its South American subspecies M. t. atriceps Cabanis, 1883. Emu 104, 197–204.
CrossRef |

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.
CrossRef | CAS |

Joseph, L. , and Wilke, T. (2007). Lack of phylogeographic structure in three widespread Australian birds reinforces emerging challenges in Australian historical biogeography. Journal of Biogeography 34, 612–624.
CrossRef |

Joseph, L. , Moritz, C. , and Hugall, A. (1993). A mitochondrial DNA perspective on the historical biogeography of middle eastern Queensland rainforest birds. Memoirs of the Queensland Museum 34, 201–214.


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.
CrossRef | CAS |

Joseph, L. , Slikas, B. , Alpers, D. , and Schodde, R. (2001). Molecular systematics and phylogeography of New Guinean logrunners (Orthonychidae). Emu 101, 273–280.
CrossRef |

Joseph, L. , Wilke, T. , and Alpers, D. (2002). Reconciling genetic expectations from host specificity with historical population dynamics in an avian brood parasite, Horsfield’s Bronze-Cuckoo Chalcites basalis of Australia. Molecular Ecology 11, 829–837.
CrossRef | CAS | PubMed |

Joseph, L. , Wilke, T. , and Alpers, D. (2003). Independent evolution of migration on the South American landscape in a long-distance temperate–tropical bird, Swainson’s Flycatcher (Myiarchus swainsoni). Journal of Biogeography 30, 925–937.
CrossRef |

Joseph, L. , Wilke, T. , ten Have, J. , and Chesser, R. T. (2006). Implications of mitochondrial DNA polyphyly in two ecologically undifferentiated but morphologically distinct migratory birds, the Masked and White-browed Woodswallows Artamus spp. of inland Australia. Journal of Avian Biology 37, 625–636.
CrossRef |

Joseph, L. , Dolman, G. , Donnellan, S. , Saint, K. , Berg, M. , and Bennett, A. (2008). Where and when does a ring start and end? Testing the ring species hypothesis in a species complex of Australian parrots. Proceedings of the Royal Society of London. Series B: Biological Sciences 275, 2431–2440.
CrossRef |

Joseph, L. , Adcock, G. , Linde, C. , Omland, K. , Heinsohn, R. , Chesser, R. T. , and Roshier, D. (in press). A tangled tale of two teal: population history of the Grey and Chestnut Teal of Australia. Journal of Avian Biology ,


Kearns, A. M. , Joseph, L. , Edwards, S. V. , and Double, M. C. (2008). Inferring the phylogeography and evolutionary history of the Splendid Fairy-wren (Malurus splendens) from mitochondrial DNA and spectrophotometry. Journal of Avian Biology ,in press
CrossRef |

Keast, J. A. (1961). Bird speciation on the Australian continent. Bulletin of the Museum of Comparative Zoology, Harvard 123, 303–495.


Kerr, K. C. R. , Stoeckle, M. Y. , Dove, C. J. , Weigt, L. A. , Francis, C. M. , and Hebert, P. D. N. (2007). Comprehensive DNA barcode coverage of North American birds. Molecular Ecology Notes 7, 535–543.
CrossRef | CAS | PubMed |

Kimura, M. , and Ohta, T. (1969). The average number of generations until fixation of a mutant gene in a finite population. Genetics 61, 763–771.
PubMed |

Kingman, J. F. C. (2000). Origins of the coalescent: 1974–1982. Genetics 156, 1461–1463.
CAS | PubMed |

Kleindorfer, S. , Lambert, S. , and Paton, D. (2006). Ticks (Ixodes sp.) and blood parasites (Haemoproteus spp.) in New Holland Honeyeaters (Phylidonyris novaehollandiae): evidence for site specificity and fitness costs. Emu 106, 113–118.
CrossRef |

Knowles, L. L. (2004). The burgeoning field of statistical phylogeography. Journal of Evolutionary Biology 17, 1–10.
CrossRef | CAS | PubMed |

Knowles, L. L. (2008). Why does a method that fails continue to be used? Evolution 62, 2713–2717.
CrossRef | PubMed |

Knowles, L. L. , and Carstens, B. C. (2007). Estimating a geographically explicit model of population divergence. Evolution 61, 477–493.
CrossRef | PubMed |

Knowles, L. L. , and Maddison, W. P. (2002). Statistical phylogeography. Molecular Ecology 11, 2623–2635.
CrossRef | PubMed |

Knowles, L. L. , Carstens, B. C. , and Keat, M. L. (2007). Coupling genetic and ecological-niche models to examine how past population distributions contribute to divergence. Current Biology 17, 940–946.
CrossRef | CAS | PubMed |

Kozak, K. , Graham, C. , and Wiens, J. (2008). Integrating GIS-based environmental data into evolutionary biology. Trends in Ecology & Evolution 23, 141–148.


Kuo, C.-H. , and Avise, J. C. (2005). Phylogeographic breaks in low-dispersal species: the emergence of concordance across gene trees. Genetica 124, 179–186.
CrossRef | PubMed |

Ladoukakis, E. D. , and Eyre-Walker, A. (2004). Evolutionary genetics: direct evidence of recombination in human mitochondrial DNA. Heredity 93, 321–321.
CrossRef | CAS | PubMed |

Latch, E. K. , Dharmarajan, G. , Glaubitz, J. C. , and Rhodes, O. E. (2006). Relative performance of Bayesian clustering software for inferring population substructure and individual assignment at low levels of population differentiation. Conservation Genetics 7, 295–302.
CrossRef |

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.
CrossRef | PubMed |

Liu, L. , Pearl, D. K. , Brumfield, R. T. , and Edwards, S. V. (2008). Estimating species trees using multiple-allele DNA sequence data. Evolution 62, 2080–2091.
CrossRef | PubMed |

Lovette, I. (2004). Mitochondrial dating and mixed support for the ‘2% rule’ in birds. Auk 121, 1–6.
CrossRef |

Macdonald, J. D. (1969). Notes on the taxonomy of Neositta. Emu 69, 169–174.


Maddison, W. P. (1997). Gene trees in species trees. Systematic Biology 46, 523–536.
CrossRef |

Maddison, W. P. , and Knowles, L. L. (2006). Inferring phylogeny despite incomplete lineage sorting. Systematic Biology 55, 21–30.
CrossRef | PubMed |

Manel, S. , Schwartz, M. K. , Luikart, G. , and Taberlet, P. (2003). Landscape genetics: combining landscape ecology and population genetics. Trends in Ecology & Evolution 18, 189–197.
CrossRef |

McGuigan, K. , McDonald, K. , Parris, K. , and Moritz, C. (1998). Mitochondrial DNA diversity and historical biogeography of a wet forest-restricted frog (Litoria pearsoniana) from mid-east Australia. Molecular Ecology 7, 175–186.
CrossRef | CAS | PubMed |

Miura, G. L. , and Edwards, S. V. (2001). Cryptic differentiation and geographic variation in genetic diversity of Hall’s Babbler Pomatostomus halli. Journal of Avian Biology 32, 102–110.
CrossRef |

Moore, W. S. (1995). Inferring phylogenies from mtDNA variation – mitochondrial-gene trees versus nuclear-gene trees. Evolution 49, 718–726.
CrossRef |

Moritz, C. (1994). Applications of mitochondrial DNA analysis in conservation: a critical review. Molecular Ecology 3, 401–412.
CrossRef | CAS |

Moritz, C. , and Cicero, C. (2004). DNA barcoding: promise and pitfalls. PLoS Biology 2(10), e354.
CrossRef | PubMed |

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.
CrossRef |

Murphy, S. A. , Double, M. C. , and Legge, S. M. (2007). The phylogeography of palm cockatoos, Probosciger aterrimus, in the dynamic Australo-Papuan region. Journal of Biogeography 34, 1534–1545.
CrossRef |

Neigel J. E. , and Avise J. C. (1986). Phylogenetic relationships of mitochondrial DNA under various demographic models of speciation. In ‘Evolutionary Processes and Theory’. (Eds E. Nevo and S. Karlin.) pp. 515–534. (Academic Press: New York.)

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.
CrossRef | CAS | PubMed |

Nicholls, J. A. , Austin, J. , Moritz, C. , and Goldizen, A. (2006). Genetic population structure and call variation in a passerine bird, the satin bowerbird, Ptilonorhynchus violaceus. Evolution 60, 1279–1290.
CAS | PubMed |

Norman, J. A. , Christidis, L. , Joseph, L. , Slikas, B. , and Alpers, D. (2002). Unravelling a biogeographical knot: origin of the ‘leapfrog’ distribution pattern of Australo-Papuan sooty owls (Strigiformes) and logrunners (Passeriformes). Proceedings of the Royal Society of London. Series B: Biological Sciences 269, 2127–2133.
CrossRef | CAS |

Norman, J. , Rheindt, F. , Rowe, D. , and Christidis, L. (2007). Speciation dynamics in the Australo-Papuan Meliphaga honeyeaters. Molecular Phylogenetics and Evolution 42, 80–91.
CrossRef | CAS | PubMed |

Omland, K. E. (1997). Examining two standard assumptions of ancestral reconstructions: repeated loss of dichromatism in dabbling ducks (Anatini). Evolution 51, 1636–1646.
CrossRef |

Omland, K. E. , Tarr, C. L. , Boarman, W. I. , Marzluff, J. M. , and Fleischer, R. C. (2000). Cryptic genetic variation and paraphyly in ravens. Proceedings of the Royal Society of London. Series B: Biological Sciences 267, 2475–2482.
CrossRef | CAS |

Omland, K. E. , Baker, J. M. , and Peters, J. L. (2006). Genetic signatures of intermediate divergence: population history of Old and New World Holarctic ravens (Corvus corax). Molecular Ecology 15, 795–808.
CrossRef | PubMed |

Ovenden, J. , Mackinlay, A. , and Crozier, R. (1987). Systematics and mitochondrial genome evolution of Australian rosellas (Aves : Platycercidae). Molecular Biology and Evolution 4, 526–543.
CAS |

Page R. , and Holmes E. C. (1998). ‘Molecular Evolution: A Phylogenetic Approach.’ (Blackwell Science: Oxford, UK.)

Palumbi, S. R. , and Cipriano, F. (1998). Species identification using genetic tools: the value of nuclear and mitochondrial gene sequences in whale conservation. Journal of Heredity 89, 459–464.
CrossRef | CAS | PubMed |

Palumbi, S. R. , Cipriano, F. , and Hare, M. P. (2001). Predicting nuclear gene coalescence from mitochondrial data: the three-times rule. Evolution 55, 859–868.
CrossRef | CAS | PubMed |

Parsons, T. J. , Olson, S. L. , and Braun, M. J. (1993). Unidirectional spread of secondary sexual plumage traits across an avian hybrid zone. Science 260, 1643–1646.
CrossRef | PubMed |

Pavlova, A. , Rohwer, S. , Drovetski, S. , and Zink, R. M. (2006). Different post-Pleistocene histories of Eurasian parids. Journal of Heredity 97, 389–402.
CrossRef | CAS | PubMed |

Peck, D. , and Congdon, B. (2004). Reconciling historical processes and population structure in the sooty tern Sterna fuscata. Journal of Avian Biology 35, 327–335.
CrossRef |

Penhallurick, J. , and Wink, M. (2004). Analysis of the taxonomy and nomenclature of the Procellariiformes based on complete nucleotide sequences of the mitochondrial cytochrome b gene. Emu 104, 125–147.
CrossRef | CAS |

Peters, J. L. , Zhuravlev, Y. , Fefelov, I. , Logie, A. , and Omland, K. E. (2007). Nuclear loci and coalescent methods support ancient hybridization as cause of mitochondrial paraphyly between Gadwall and Falcated duck (Anas spp.). Evolution 61, 1992–2006.
CrossRef | CAS | PubMed |

Peters, J. L. , Zhuravlev, Y. , Fefelov, I. , Humphries, E. M. , and Omland, K. E. (2008). Multilocus phylogeography of a Holarctic duck: colonization of North America from Eurasia by gadwall (Anas strepera). Evolution 62, 1469–1483.
CrossRef | CAS | PubMed |

Peterson, A. T. (2006). Application of molecular clocks in ornithology revisited. Journal of Avian Biology 37, 541–544.
CrossRef |

Peterson, A. T. , and Nyári, A. S. (2007). Ecological niche conservatism and Pleistocene refugia in the thrush-like mourner, Schiffornis sp., in the Neotropics. Evolution 62, 173–183.
PubMed |

Petit, R. J. (2008a). The coup de grâce for nested clade phylogeographic analysis? Molecular Ecology 17, 516–518.
CrossRef | PubMed |

Petit, R. J. (2008b). On the falsifiability of the nested clade phylogeographic analysis method. Molecular Ecology 17, 1404.
CrossRef |

Phillimore, A. , and Owens, I. (2006). Are subspecies useful in evolutionary and conservation biology? Proceedings of the Royal Society of London. Series B: Biological Sciences 273, 1049–1053.
CrossRef |

Price T. (2008). ‘Speciation in Birds.’ (Roberts and Company: Greenwood Village, CO.)

Rand, D. M. (2001). The units of selection on mitochondrial DNA. Annual Review of Ecology and Systematics 32, 415–448.
CrossRef |

Remsen, J. (2005). Pattern, process, and rigor meet classification. Auk 122, 403–413.
CrossRef |

Rheindt, F. , and Austin, J. (2005). Major analytical and conceptual shortcomings in a recent taxonomic revision of the Procellariiformes – a reply to Penhallurick and Wink (2004). Emu 105, 181–186.
CrossRef |

Rhymer, J. M. , Williams, M. J. , and Kingsford, R. T. (2004). Implications of phylogeography and population genetics for subspecies taxonomy of Grey (Pacific Black) Duck Anas superciliosa and its conservation in New Zealand. Pacific Conservation Biology 10, 57–66.


Ribas, C. , Joseph, L. , and Miyaki, C. (2006). Molecular systematics and patterns of diversification in Pyrrhura (Psittacidae) with special reference to the picta-leucotis complex. Auk 123, 660–680.
CrossRef |

Rosenberg, N. (2007). Statistical tests for taxonomic distinctiveness from observations of monophyly. Evolution 61, 317–323.
CrossRef | PubMed |

Roy M. S. , da Silva J. M. C. , Arctander P. , Garcia-Moreno J. , and Fjeldså J. (1997). The speciation of South American and African birds in montane regions. In ‘Avian Molecular Evolution and Systematics’. (Ed. D. P. Mindell.) pp. 325–344. (Academic Press: San Diego, CA.)

Ruegg, K. , Hijmans, R. J. , and Moritz, C. (2006). Climate change and the origin of migratory pathways in the Swainson’s Thrush, Catharus ustulatus. Journal of Biogeography 33, 1172–1182.
CrossRef |

Schlotfeldt, B. , 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, 309–320.
CrossRef |

Schodde R. (1982). Origin, adaptation and evolution of birds in arid Australia. In ‘Evolution of the Flora and Fauna of Arid Australia’. (Eds W. R. Barker and P. J. M. Greenslade.) pp. 191–224. (Peacock Publications: Adelaide.)

Schodde R. (2006). Australia’s bird fauna today – origins and development. In ‘Evolution and Biogeography of Australasian Vertebrates’. (Eds J. R. Merrick, M. Archer, G. Hickey and M. Lee.) pp. 413–458. (AusciPub: Sydney.)

Schodde R. , and Mason I. (1999). ‘Directory of Australian Birds. Vol. 2. Passerines.’ (CSIRO Publishing: Melbourne.)

Sharman, G. B. , Close, R. L. , and Maynes, G. M. (1989). Chromosome evolution, phylogeny and speciation of rock wallabies (Petrogale : Macropodidae). Australian Journal of Zoology 37, 351–363.
CrossRef |

Sites, J. W. , and Marshall, J. C. (2004). Operational criteria for delimiting species. Annual Review of Ecology Evolution and Systematics 35, 199–227.
CrossRef |

Sorenson, M. D. , and Quinn, T. W. (1998). Numts: a challenge for avian systematics and population biology. Auk 115, 214–221.


Stapley, J. , Birkhead, T. , Burke, T. , and Slate, J. (2008). Linkage map of the zebra finch Taeniopygia guttata provides new insights into avian genome evolution. Genetics 179, 651–667.
CrossRef | CAS | PubMed |

Swenson, N. G. (2008). The past and future influence of geographic information systems on hybrid zone, phylogeographic and speciation research. Journal of Evolutionary Biology 21, 421–434.
CrossRef | CAS | PubMed |

Tavares, E. S. , and Baker, A. J. (2008). Single mitochondrial gene barcodes reliably identify sister-species in diverse clades of birds. BMC Evolutionary Biology 8, 81.
CrossRef | PubMed |

Templeton, A. R. (2004). Statistical phylogeography: methods of evaluating and minimizing inference errors. Molecular Ecology 13, 789–809.
CrossRef | PubMed |

Templeton, A. R. (2008). Nested clade analysis: an extensively validated method for strong phylogeographic inference. Molecular Ecology 17, 1877–1880.
CrossRef | PubMed |

Templeton, A. R. , Routman, E. , and Phillips, C. A. (1995). Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum. Genetics 140, 767–782.
CAS | PubMed |

Toon, A. , Hughes, J. , Baker, A. , and Mather, P. (2003). Discordance between morphology and genetic structure among three plumage forms of the Australian magpie. Emu 103, 337–343.
CrossRef |

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.
CrossRef | CAS | PubMed |

Tsaousis, A. D. , Martin, D. P. , Ladoukakis, E. D. , Posada, D. , and Zouros, E. (2005). Widespread recombination in published animal mtDNA sequences. Molecular Biology and Evolution 22, 925–933.
CrossRef | CAS | PubMed |

Watson, D. (2005). Diagnosable versus distinct: evaluating species limits in birds. Bioscience 55, 60–68.
CrossRef |

Weir, J. T. , and Schluter, D. (2008). Calibrating the avian molecular clock. Molecular Ecology 17, 2321–2328.
CrossRef | CAS | PubMed |

Wiens, J. A. , and Servedio, M. R. (2000). Species delimitation in systematics: inferring diagnostic differences between species. Proceedings of the Royal Society of London. Series B: Biological Sciences 267, 631–636.
CrossRef | CAS |

Wilkins, J. F. (2004). A separation-of-timescales approach to the coalescent in a continuous population. Genetics 168, 2227–2244.
CrossRef | PubMed |

Wilson, E. O. , and Brown, W. L. (1953). The subspecies concept and its taxonomic application. Systematic Zoology 2, 97–111.
CrossRef |

Wooller, R. D. , Saunders, D. A. , Bradley, J. S. , and de Rebeira, C. P. (1985). Geographical variation in size of an Australian honeyeater (Aves : Meliphagidae): an example of Bergmann’s rule. Biological Journal of the Linnaean Society 25, 355–363.
CrossRef |

Yang, S.-J. , Lei, F.-M. , Qu, Y.-H. , and Yin, Z.-H. (2005). Intraspecific phylogeography of the White-rumped Snowfinch (Onychostruthus taczanowskii) endemic to the Tibetan Plateau based on mtDNA sequences. Journal of Zoology 268, 187–192.
CrossRef |

Zink R. M. (1997). Phylogeographic studies of North American birds. In ‘Avian Molecular Evolution and Systematics’. (Ed. D. P. Mindell.) pp. 301–324. (Academic Press: San Diego, CA.)

Zink, R. M. (2004). The role of subspecies in obscuring avian biological diversity and misleading conservation policy. Proceedings of the Royal Society of London. Series B: Biological Sciences 271, 561–564.
CrossRef |

Zink, R. M. , and Barrowclough, G. (2008). Mitochondrial DNA under siege in avian phylogeography. Molecular Ecology 17, 2107–2121.
CrossRef | CAS | PubMed |

Zink, R. M. , and McKay, B. (2008). Book Review: Speciation in Birds by Trevor Price. Auk 125, 504–505.
CrossRef |


Full Text PDF (635 KB) Export Citation

View Altmetrics