Testing the effect of transient Plio-Pleistocene barriers in monsoonal Australo-Papua: Did mangrove habitats maintain genetic connectivity in the Black Butcherbird?

Molecular Ecology

Volumn 20, Issue 23, 2011, Pages 5042-5059

  Kearns, Anna M ^a   Joseph, Leo ^b   Omland, Kevin E ^c   Cook, Lyn G ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b CSIRO   (Australia)

^c UNIVERSITY OF MARYLAND BALTIMORE COUNTY   (United States)

Author keywords

Australian Monsoon Tropics; Carpentarian Barrier; Cordillera range; incomplete lineage sorting; last glacial maximum; Torres Strait

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; AUSTRALIA; BAYES THEOREM; BIOLOGICAL MODEL; DNA SEQUENCE; ECOSYSTEM; FEMALE; GENE FLOW; GENETICS; HAPLOTYPE; HISTOLOGY; MALE; PAPUA NEW GUINEA; PHYLOGENY; PHYLOGEOGRAPHY; POPULATION GENETICS; REPRODUCTIVE ISOLATION; SONGBIRD; STATISTICAL MODEL;

ANIMALS; AUSTRALIA; BAYES THEOREM; DNA, MITOCHONDRIAL; ECOSYSTEM; FEMALE; GENE FLOW; GENETICS, POPULATION; HAPLOTYPES; LIKELIHOOD FUNCTIONS; MALE; MODELS, GENETIC; NEW GUINEA; PASSERIFORMES; PHYLOGENY; PHYLOGEOGRAPHY; REPRODUCTIVE ISOLATION; SEQUENCE ANALYSIS, DNA;

CARPENTARIA; CRACTICUS QUOYI;

EID: 81855207249     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2011.05330.x     Document Type: Article

References (88)

1. Amadon D, (1951) Taxonomic notes on the Australian butcher-birds (family Cracticidae). American Museum Novitates, 1504, 1-33.
2. Avise JC, (2000) Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge.
3. Black AB, (1986) The taxonomic affinity of the New Guinean Magpie Gymnorhina tibicen papuana. Emu, 86, 65-70.
4. Bowler JM, Hope GS, Jennings JN, Singh G, Walker D, (1976) Late quaternary climates of Australia and New Guinea. Quaternary Research, 6, 359-394.
5. Chappell J, Omura A, Esat T, et al. (1996) Reconciliation of late quaternary sea levels derived from coral terraces at Huon Peninsula with deep sea oxygen isotope records. Earth and Planetary Science Letters, 141, 227-236.
6. Chivas AR, Garcia A, Van Kaars Der S, et al. (2001) Sea-level and environmental changes since the last interglacial in the Gulf of Carpentaria, Australia: an overview. Quaternary International, 83, 19-46.
7. Clement M, Posada D, Crandall KA, (2000) TCS: a computer program to estimate gene genealogies. Molecular Ecology, 9, 1657-1659.
8. Deiner K, Lemmon AR, Mack AL, Fleischer RC, Dumbacher JP, (2011) A passerine bird's evolution corroborates the geologic history of the island of New Guinea. PLoS ONE, 6, e19479, doi:.
9. Dolman G, Moritz C, (2006) A multilocus perspective on refugial isolation and divergence in rainforest skinks (Carlia). Evolution, 60, 573-582.
10. Drovetski SV, Zink RM, Rohwer S, et al. (2004) Complex biogeographic history of a Holarctic passerine. Proceedings of the Royal Society of London Series B-Biological Sciences, 271, 545-551.
11. Drummond AJ, Rambaut A, (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
12. Dumbacher JP, Fleischer RC, (2001) Phylogenetic evidence for colour pattern convergence in toxic pitohuis: Müllerian mimicry in birds? Proceedings of the Royal Society of London Series B-Biological Sciences, 268, 1971-1976.
13. Edwards SV, (1993) 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.
14. Ellegren H, (2007) Molecular evolutionary genomics of birds. Cytogenetic and Genome Research, 117, 120-130.
15. Flannery T, (1990) The Mammals of New Guinea. Robert Brown and Associates, Carina, Queensland, Australia.
16. Ford J, (1982) Origin, evolution and speciation of birds specialized to mangroves in Australia. Emu, 82, 12-23.
17. Ford J, (1983) Taxonomic notes on some mangrove-inhabiting birds in Australasia. Records of the Western Australian Museum, 10, 381-415.
18. Ford J, (1987) Hybrid zones in Australian birds. Emu, 87, 158-178.
19. Guindon S, Gascuel O, (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52, 696-704.
20. Hackett SJ, (1996) Molecular phylogenetics and biogeography of tanagers in the genus Ramphocelus (Aves). Molecular Phylogenetics and Evolution, 5, 368-382.
21. Heine C, Muller DR, Steinberger B, DiCaprio L, (2010) Integrating deep Earth dynamics in paleogeographic reconstructions of Australia. Tectonophysics, 483, 135-150.
22. Heinsohn T, Hope G, (2006) The Torresian connections: zoogeography of New Guinea. In: Evolution and Biogeography of Australian Vertebrates (eds, Merrick JR, Archer M, Hickey GM, Lee MSY,), pp. 71-93. Australian Scientific Publishing, Oatlands, New South Wales.
23. Hope G, Kershaw AP, Kaars SVD, et al. (2004) History of vegetation and habitat change in the Austral-Asian region. Quaternary International, 118-119, 103-126.
24. Huelsenbeck JP, Ronquist F, (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17, 754-755.
25. Jennings WB, Edwards SV, (2005) Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees. Evolution, 59, 2033-2047.
26. Joseph L, Omland KE, (2009) Phylogeography: its development and impact in Australo-Papuan ornithology with special reference to paraphyly in Australian birds. Emu, 109, 1-23.
27. Joseph L, Moritz C, 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.
28. Joseph L, Slikas B, Alpers D, Schodde R, (2001) Molecular systematics and phylogeography of New Guinean logrunners (Orthonychidae). Emu, 101, 273-280.
29. Joseph L, Zeriga T, Adcock GJ, Langmore NE, (2011) Phylogeography and taxonomy of the Little Bronze-Cuckoo (Chalcites minutillus) in Australia. Emu, 111, 113-119.
30. Kearns AM, Joseph L, Cook LG, (2010) The impact of Pleistocene changes of climate and landscape on Australian birds: a test using the Pied Butcherbird (Cracticus nigrogularis). Emu, 110, 285-295.
31. Keast A, (1961) Bird speciation on the Australian continent. Bulletin of the Museum of Comparative Zoology, 123, 307-495.
32. Kirchman JJ, Shannon JH, Goodman SM, Bates JM, (2001) Phylogeny and systematics of ground rollers (Brachypteraciidae) of Madagascar. The Auk, 118, 849-863.
33. Krajewski C, Moyer GR, Sipiorski JT, Fain MG, Westerman M, (2004) Molecular systematics of the enigmatic 'phascolosoricine' marsupials of New Guinea. Australian Journal of Zoology, 52, 389-415.
34. Lambeck K, Chappell J, (2001) Sea level change through the last glacial cycle. Science, 292, 679-686.
35. Langford R, Wilford G, Truswell EM, Isern AR, (1995) Paleogeographic Atlas of Australia, Volume 10-Cainozoic. Australian Geological Survey Organization, Canberra.
36. Lee JY, Edwards SV, (2008) Divergence across Australia's Carpentarian barrier: statistical phylogeography of the red-backed fairy wren (Malurus melanocephalus). Evolution, 62, 3117-3134.
37. Macdonald JD, (1969) Notes on the taxonomy of Neositta (Results of the Harold Hall Australian Expedition, No. 18). Emu, 69, 169-174.
38. Macqueen P, Seddon JM, Austin JJ, Hamilton S, Goldizen AW, (2010) Phylogenetics of the pademelons (Macropodidae: Thylogale) and historical biogeography of the Australo-Papuan region. Molecular Phylogenetics and Evolution, 57, 1134-1148.
39. Macqueen P, Goldizen AW, Austin JJ, Sedoon JM, (2011) Phylogeography of the pademelons (Marsupialia: Macropodidae: Thylogale) in New Guinea reflects both geological and climatic events during the Plio-Pleistocene. Journal of Biogeography, 38, 1732-1747.
40. Martin HA, (2006) Cenozoic climatic change and the development of the arid vegetation in Australia. Journal of Arid Environments, 66, 533-563.
41. Mathews GM, (1927) Systema Avium Australasianarum: A Systematic List of the Birds of the Australasian Region. British Ornithologists Union, London.
42. Mees GF, (1964) Notes on two small collections of birds from New Guinea. Zoologische Verhandelingen, 66, 1-37.
43. Murphy SA, Double MC, Legge SM, (2007) The phylogeography of palm cockatoos, Probosciger aterrimus, in the dynamic Australo-Papuan region. Journal of Biogeography, 34, 1534-1545.
44. Naish T, Powell R, Levy R, et al. (2009) Obliquity-paced Pliocene West Antarctic ice sheet oscillations. Nature, 458, 322-328.
45. Neigel JE, Avise JC, (1986) Phylogenetic relationships of mitochondrial DNA under various demographic models of speciation. In: Evolutionary Processes and Theory (ed., Karlin S, Nevo,), pp. 515-534. Academic Press, New York.
46. Nicholls JA, Austin JJ, (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.
47. Nicholls JA, Double MC, Rowell DM, Magrath RD, (2000) The evolution of cooperative and pair breeding in thornbills Acanthiza (Pardalotidae). Journal of Avian Biology, 31, 165-176.
48. Nix HA, Kalma JD, (1972) Climate as a dominant control in the biogeography of Northern Australia and New Guinea. In: Bridge and Barrier: The Natural and Cultural History of Torres Strait (ed., Walker D,), pp. 61-92. The Australian National University, Canberra.
49. Norman JA, Christidis L, Joseph L, Slikas B, 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.
50. Norman JA, Rheindt FE, Rowe DL, Christidis L, (2007) Speciation dynamics in the Australo-Papuan Meliphaga honeyeaters. Molecular Phylogenetics and Evolution, 42, 80-91.
51. Omland KE, Baker JM, Peters JL, (2006) Genetic signatures of intermediate divergence: population history of Old and New World Holarctic ravens (Corvus corax). Molecular Ecology, 15, 795-808.
52. Peakall R, Smouse PE, (2001) GenAlEx V5: Genetic Analysis in Excel. Population Genetic Software for Teaching and Research. Australian National University, Canberra.
53. Peters JL, Omland KE, Johnson KP, (2007) Population structure and mitochondrial polyphyly in North American gadwalls (Anas strepera). The Auk, 124, 444-462.
54. Pigram CJ, Davies HL, (1987) Terranes and the accretion history of the New Guinea Orogen. BMR Journal of Australian Geology and Geophysics, 10, 193-211.
55. Posada D, (2008) jModelTest: phylogenetic model averaging. Molecular Biology and Evolution, 25, 1253-1256.
56. R Core Development Team (2009) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
57. Rambaut A, Drummond AJ, (2007) Tracer v1.4. Available from (last accessed 20, October 2011).
58. Rawlings LH, Donnellan SC, (2003) Phylogeographic analysis of the green python, Morelia viridis, reveals cryptic diversity. Molecular Phylogenetics and Evolution, 27, 36-44.
59. Rheindt FE, Christidis L, Cabanne GS, Miyaki C, Norman JA, (2009) The timing of neotropical speciation dynamics: a reconstruction of Myiopagis flycatcher diversification using phylogenetic and paleogeographic data. Molecular Phylogenetics and Evolution, 53, 961-971.
60. Rowe C, (2007a) A palynological investigation of Holocene vegetation change in Torres Strait, seasonal tropics of northern Australia. Palaeogeography, Palaeoclimatology, Palaeoecology, 251, 83-103.
61. Rowe C, (2007b) Vegetation change following mid-Holocene marine transgression of the Torres Strait shelf: a record from the island of Mua, northern Australia. Holocene, 17, 927-937.
62. Rozas J, Sánchez-Delbarrio JC, Messeguer X, Rozas R, (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19, 2496-2497.
63. Russell E, Rowley I, (2009) Family Cracticidae (Butcherbirds). In: Handbook of the Birds of the World, Volume 14: Bush-Shrikes to Old World Sparrows (eds, Del Hoyo J, Elliott A, Christie D,), pp. 308-342. Lynx Edicions, Barcelona.
64. Sandiford M, (2007) The tilting continent: a new constraint on the dynamic topographic field from Australia. Earth and Planetary Science Letters, 261, 152-163.
65. Schneider CJ, Cunningham M, Moritz C, (1998) Comparative phylogeography and the history of endemic vertebrates in the wet tropics rainforests of Australia. Molecular Ecology, 7, 487-498.
66. Schodde R, (1982) Origin, adaptation and evolution of birds in arid Australia. In: Evolution of the Flora and Fauna of Arid Australia (eds, Barker WR, Greenslade PJM,), pp. 191-224. Peacock Publications, Adelaide.
67. Schodde R, (2006) Australia's bird fauna today-origins and development. In: Evolution and Biogeography of Australasian Vertebrates (eds, Merrick JR, Archer M, Hickey GM, Lee MSY,), pp. 413-458. AusciPub, Sydney.
68. Schodde R, Calaby JH, (1972) The biogeography of the Australo-Papuan bird and mammal faunas in relation to Torres Strait. In: Bridge and Barrier: The Natural and Cultural History of Torres Strait (ed., Walker D,), pp. 257-300. Australian National University, Canberra.
69. Schodde R, Mason IJ, (1999) The Directory of Australian Birds: Passerines. CSIRO Publishing, Melbourne.
70. Shearman P, Bryan J, (2011) A bioregional analysis of the distribution of rainforest cover, deforestation and degradation in Papua New Guinea. Austral Ecology, 36, 9-24.
71. Stamatakis A, (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22, 2688-2690.
72. Stephens M, Donnelly P, (2003) A comparison of bayesian methods for haplotype reconstruction from population genotype data. The American Journal of Human Genetics, 73, 1162-1169.
73. Storr GM, (1973) List of Queensland Birds. Special Publications of the Western Australian Museum.
74. Swofford DL, (2003) PAUP*. Phylogenetic Analysis Using Parsimony (and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
75. Toon A, Hughes JM, Joseph L, (2010) Multilocus analysis of honeyeaters (Aves: Meliphagidae) highlights spatio-temporal heterogeneity in the influence of biogeographic barriers in the Australian monsoonal zone. Molecular Ecology, 19, 2980-2994.
76. Torgersen T, Luly J, De Deckker P, et al. (1988) Late quaternary environments of the Carpentaria Basin, Australia. Palaeogeography, Palaeoclimatology, Palaeoecology, 67, 245-261.
77. Van Der Kaars WA, (1991) Palynology of eastern Indonesian marine piston-cores: a late quaternary vegetational and climatic record for Australasia. Palaeogeography, Palaeoclimatology, Palaeoecology, 85, 239-252.
78. Veevers JJ, (ed.) (2000) Billion-Year Earth History of Australia and Neighbours in Gondwanaland. GEMOC Press, Sydney.
79. Voris HK, (2000) Maps of Pleistocene sea levels in Southeast Asia: shorelines, river systems and time durations. Journal of Biogeography, 27, 1153-1167.
80. Weir JT, Schluter D, (2008) Calibrating the avian molecular clock. Molecular Ecology, 17, 2321-2328.
81. Westerman M, Springer MS, Krajewski C, (2001) Molecular relationships of the New Guinean bandicoot genera Microperoryctes and Echymipera (Marsupialia: Peramelina). Journal of Mammalian Evolution, 8, 93-105.
82. Williams DJ, O'shea M, Daguerre RL, et al. (2008) Origin of the eastern brownsnake, Pseudonaja textilis (Duméril, Bibron and Duméril) (Serpentes: Elapidae: Hydrophiinae) in New Guinea: evidence of multiple dispersals from Australia, and comments on the status of Pseudonaja textilis pughi Hoser 2003. Zootaxa, 1703, 47-61.
83. Williams M, Cook E, Van Kaars Der S, Barrows T, Shulmeister J, Kershaw P, (2009) Glacial and deglacial climatic patterns in Australia and surrounding regions from 35 000 to 10 000 years ago reconstructed from terrestrial and near-shore proxy data. Quaternary Science Reviews, 28, 2398-2419.
84. Woodroffe CD, Grindrod J, (1991) Mangrove biogeography: the role of quaternary environmental and sea-level change. Journal of Biogeography, 18, 479-492.
85. Woodroffe CD, Thom BG, Chappell J, (1985) Development of widespread mangrove swamps in mid-Holocene times in northern Australia. Nature, 317, 711-713.
86. Wüster W, Dumbrell AJ, Hay C, Pook CE, Williams DJ, Fry BG, (2005) Snakes across the Strait: trans-Torresian phylogeographic relationships in three genera of Australasian snakes (Serpentes: Elapidae: Acanthophis, Oxyuranus, and Pseudechis). Molecular Phylogenetics and Evolution, 34, 1-14.
87. Yokoyama Y, Purcell A, Lambeck K, Johnston P, (2001) Shore-line reconstruction around Australia during the last glacial maximum and late glacial stage. Quaternary International, 83-85, 9-18.
88. Zwiers PB, Borgia G, Fleischer RC, (2008) Plumage based classification of the bowerbird genus Sericulus evaluated using a multi-gene, multi-genome analysis. Molecular Phylogenetics and Evolution, 46, 923-931.