Funded by the CSIRO Office of the Chief Executive for GD's OCE Postdoctoral Fellowship and lab costs.
A species assemblage approach to comparative phylogeography of birds in southern Australia
Version of Record online: 6 JAN 2012
© 2011 The Authors. MicrobiologyOpen published by Blackwell Publishing Ltd.
This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
Ecology and Evolution
Volume 2, Issue 2, pages 354–369, February 2012
How to Cite
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
- Issue online: 20 FEB 2012
- Version of Record online: 6 JAN 2012
- Received: 04 October 2011; Revised: 01 November 2011; Accepted: 06 November 2011
- 2002. Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Ann. Rev. Ecol. Evol. Syst. 33:707–740. , , , , and .
- 1998. Pleistocene phylogeographic effects on avian populations and the speciation process. Proc. Roy. Soc. Lond. Ser. B Biol. Sci. 265:457–463. , and .
- 2000. Phylogeography: the history and formation of species. Harvard Univ. Press, Cambridge , MA .
- 2004. The incomplete natural history of mitochondria. Mol. Ecol. 13:729–744. , and .
- 2010. Two pulses of diversification across the Isthmus of Tehuantepec in a montane Mexican bird fauna. Proc. Roy. Soc. B Biol. Sci. 277:2675–2681. , and .
- 2010. Approximate Bayesian computation in evolution and ecology. Pp. 379–406 in : Annual review of ecology, evolution, and systematics, Vol 41. Annual Reviews, Palo Alto .
- 2011. Decline of a biome: evolution, contraction, fragmentation, extinction and invasion of the Australian mesic zone biota. J. Biogeogr. 38:1636–1656. , , , , , , , , , and et al.
- 2008. Birth of a biome: insights into the assembly and maintenance of the Australian arid zone biota. Mol. Ecol. 17:4398–4417. , , , , , , , , , and et al.
- 2008. Evidence for multiple refugia at different time scales during Pleistocene climatic oscillations in southern Australia inferred from phylogeography. Quat. Sci. Rev. 27:2576–2585.
- 1993. The effect of deleterious mutations on neutral molecular variation. Genetics 134:1289–1303. , , and .
- 2008. Systematics and taxonomy of Australian birds. CSIRO Publishing, Melbourne . , and .
- 2007. A congruent molecular signature of vicariance across multiple plant lineages. Mol. Phylogenet. Evol. 43:1106–1117. , and .
- 2006. A multi-locus perspective on refugial isolation and divergence in rainforest skinks (Carlia). Evolution 60:573–582. , and .
- 2009. Systematic and conservation implications of mitochondrial DNA diversity in emu-wrens, Stipiturus (Aves: Maluridae). Emu 109:143–152. , , , et al.
- 2000. Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54:1839–1854. , and .
- 1974. Speciation in Australian birds adapted to arid habitats. Emu 74:161–168.
- 2005. Global cooling initiated stony deserts in central Australia 2–4 Ma, dated by cosmogenic Ne-21–Be-10. Geology 33:993–996. , , , et al.
- 2008. Fine-scale phylogeographic congruence despite demographic incongruence in two low-mobility saprolyxic springtails. Evolution 62:1103–1118. , , , , and .
- 2000. Genetic drift in an infinite population: The pseudohitchhiking model. Genetics 155:909–919.
- 2010. East–west genetic differentiation in Musk Ducks (Biziura lobata) of Australia suggests late Pleistocene divergence at the Nullarbor Plain. Conserv. Genet. 1–16. , , , et al.
- 1987. Chronology of fluctuating sea levels since the Triassic. Science 235:1156–1166. , , and .
- 2001. Prospects for nuclear gene phylogeography. Trends Ecol. Evol. 16:700–706.
- 1996. Some genetic consequences of ice ages, and their role in divergence and speciation. Biol. J. Linn. Soc. 58:247–276.
- 2004. Genetic consequences of climatic oscillations in the Quaternary. Phil. Trans Roy. Soc. Lond. B 359:183–195.
- 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. , and .
- 2007. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc. Natl. Acad. Sci. USA. 104:2785–2790. , and .
- 2006. Test for simultaneous divergence using approximate Bayesian computation. Evolution 60:2435–2453. , , and .
- 2007. msBayes: Pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation. BMC Bioinformatics 8:268. , , and .
- 2002. Handbook of Australian, New Zealand and Antarctic birds. Oxford Univ. Press, Melbourne . , and .
- 2001. Handbook of Australian, New Zealand and Antarctic birds Oxford Univ. Press, Melbourne . , , and .
- 1999. Handbook of Australian, New Zealand and Antarctic birds Oxford Univ. Press, Melbourne .
- 2007. Calibrating molecular estimates of substitution rates and divergence times in birds. J. Avian Biol. 38:409–414.
- 2007. Responses of Quaternary rainforest vertebrates to climate change in Australia. Earth and Planetary Science Letters 264:317–331. , , , and .
- 2003. Stochasticity overrules the “three-times rule”: genetic drift, genetic draft, and coalescence times for nuclear loci versus mitochondrial DNA. Evolution 57:182–190. , and .
- 2002. Reconciling paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail Gnarosophia bellendenkerensis (Brazier 1875). Proc. Natl. Acad. Sci. USA. 99:6112–6117. , , , and .
- 2010. Colonization and/or mitochondrial selective sweeps across the North Atlantic intertidal assemblage revealed by multi-taxa approximate Bayesian computation. Mol. Ecol. 19:4505–4519. , , , and .
- 1961. The Theory of Probability. Oxford University Press, Oxford .
- 2005. Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees. Evolution 59:2033–2047. , and .
- 2009. Phylogeography: its development and impact in Australo-Papuan ornithology with special reference to paraphyly in Australian birds. Emu 109:1–23. , and .
- 2006. Molecular resolution of population history, systematics and historical biogeography of the Australian ringneck parrots Barnardius: are we there yet? Emu 106:49–62. , and .
- 2007. Lack of phylogeographic structure in three widespread Australian birds reinforces emerging challenges in Australian historical biogeography. J. Biogeogr. 34:612–624. , and .
- 1995. Molecular support for vicariance as a source of diversity in rain-forest. Proc. Roy. Soc. Lond. Ser. B Biol. Sci. 260:177–182. , , and .
- 2009. Inferring the phylogeography and evolutionary history of the splendid fairy-wren Malurus splendens from mitochondrial DNA and spectrophotometry. J. Avian Biol. 40:7–17. , , , and .
- 1961. Bird speciation on the Australian continent. Bulletin of the museum of comparative zoology 123:303–495.
- 1994. The Neogene: a time of transition. Pp. 299–327 in R. S. Hill , ed. History of the Australian vegetation: Cretaceous to recent. Cambridge Univ. Press, Cambridge . , , and .
- 2005. Phylogeographic breaks in low-dispersal species: the emergence of concordance across gene trees. Genetica 124:179–186. , and .
- 2007. Two waves of diversification in mammals and reptiles of Baja California revealed by hierarchical Bayesian analysis. Biol. Lett. 3:646–650. , , and .
- 2008. Divergence across Australia's Carpentarian Barrier: statistical phylogeography of the red-backed fairy-wren(Malurus melanocephalus). Evolution 62:3117–3134. , and .
- 2004. The eustatic and tectonic origin of Neogene unconformities from the Great Australian Bight. Mar. Geol. 203:57–81. , , , and .
- 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452. , and .
- 1994. Early Tertiary vegetation: evidence from spores and pollen. Pp. 189–261 in : R. S. Hill , ed. History of the Australian vegetation: Cretaceous to recent. Cambridge Univ. Press, Cambridge . , , , and .
- 2006. Cenozoic climatic change and the development of the arid vegetation in Australia. J. Arid Environ. 66:533–563.
- 1974. The hitch-hiking effect of a favourable gene. Genet. Res. 23:23–35. , and .
- 1991. Adaptive protein evolution at the Adh locus in Drosophila . Nature 351:652–654. , and .
- 1987. A biological survey of the Nullarbor region, South and Western Australia in 1984 . South Australian Department of Environment and Planning, Adelaide . , and .
- 2010. Plio-Pleistocene climate change and the onset of aridity in southeastern Australia. Global and Planetary Change 71:55–72. , and .
- 1988. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 16:1215–1215. , , and .
- 2001. Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 158:885–896. , and .
- 2009. Comparative phylogeography among hydrothermal vent species along the East Pacific Rise reveals vicariant processes and population expansion in the South. Mol. Ecol. 18:3903–3917. , , , et al.
- 2007. An arid-adapted middle Pleistocene vertebrate fauna from south-central Australia. Nature 445:422–425. , , , et al.
- 2008. Phylogeographic insights into cryptic glacial refugia. Trends Ecol. Evol. 23:564–571. , and .
- 2001. Comparative phylogeography of two open forest frogs from eastern Australia. Biol. J. Linn. Soc. 74:157–170. , and .
- 1999. The directory of Australian birds. A taxonomic and zoogeographic atlas of the biodiversity of birds in Australia and its territories. Passerines. CSIRO Publishing, Melbourne . , and .
- 1982. Origin, adaptation and evolution of birds in arid Australia. Pp.191–224 in : W. R. Barker and P. J. M. Greenslade , eds. Evolution of the flora and fauna of arid Australia. Peacock Publications, Adelaide .
- 1995. Karst and mound spring deposits. Pp. 257–261 in : J. F. Drexel and W. V. Preiss , eds. The Geology of South Australia. Department of Mines and Energy, Adelaide . , and .
- 2001. Comparative phylogeography of three rainforest-restricted lizards from mid-east Queensland. Aust. J. Zool. 49:119–127. , , , and .
- 2010. Multilocus analysis of honeyeaters (Aves: Meliphagidae) highlights spatio-temporal heterogeneity in the influence of biogeographic barriers in the Australian monsoonal zone. Mol. Ecol. 19:2980–2994. , , and .
- 2007. Pleistocene refugia in an arid landscape: analysis of a widely distributed Australian passerine. Mol. Ecol. 16:2525–2541. , , , , and .
- 2008. Genetic patterns of differentiation among five landbird species from the Queen Charlotte Islands, British Columbia. The Auk 125:461–472. , and .
- 2006. Karst evolution of the Nullarbor Plain, Australia. Pp. 65–78 in : R. S. Harmon and C. Wicks , eds. Perspectives on karst geomorphology, hydrology, and geochemistry—a tribute volume to Derek C. Ford and William B. White. Geological Society of America, Washington, DC . , and .
- 2008. Calibrating the avian molecular clock. Mol. Ecol. 17:2321–2328. , and .
- 2009. Glacial and deglacial climatic patterns in Australia and surrounding regions from 35,000 to 10,000 years ago reconstructed from terrestrial and nearshore proxy data. Quat. Sci. Rev. 28:2398–2419. , , et al.
- 2005. Natural selection on mitochondrial DNA in Parus and its relevance for phylogeographic studies. Proc. Roy. Soc. B Biol. Sci. 272:71–78.