Divergence across Australia's Carpentarian barrier: Statistical phylogeography of the red-backed fairy wren (Malurus melanocephalus)

Evolution

Volumn 62, Issue 12, 2008, Pages 3117-3134

  Lee, June Y ^a   Edwards, Scott V ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

Anonymous loci; Carpentarian barrier; Historical demography; Malurus melanocephalus; Phylogeography

Indexed keywords

DEMOGRAPHIC HISTORY; DIVERGENCE; GENE FLOW; GENETIC MARKER; MITOCHONDRIAL DNA; PASSERINE; PHYLOGEOGRAPHY; POPULATION STRUCTURE; TAXONOMY;

ANIMAL; ARTICLE; AUSTRALIA; BIOLOGICAL MODEL; CLUSTER ANALYSIS; COMPARATIVE STUDY; DNA SEQUENCE; GENE FLOW; GENETIC MARKER; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM; SONGBIRD;

ANIMALS; AUSTRALIA; BASE SEQUENCE; CLUSTER ANALYSIS; GENE FLOW; GENETIC MARKERS; GENETIC VARIATION; GENETICS, POPULATION; GEOGRAPHY; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PASSERIFORMES; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

AUSTRALASIA; AUSTRALIA;

CARPENTARIA; MALURUS MELANOCEPHALUS; PASSERIFORMES; TROGLODYTINAE;

EID: 57249086459     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2008.00543.x     Document Type: Article

References (99)

1. Arbogast, B. S., and G. J. Kenagy. 2001. Comparative phylogeography as an integrative approach to historical biogeography. J. Biogeogr. 28 : 819 825.
2. Avise, J. C. 1998. The history and purview of phylogeography: a personal reflection. Mol. Ecol. 7 : 371 379.
3. Avise, J. C. 2000. Phylogeography. Harvard Univ. Press, Cambridge, MA.
4. Avise, J. C., and D. Walker. 1998. Pleistocene phylogeographic effects on avian populations and the speciation process. Proc. R. Soc. Lond. B 265 : 457 463.
5. Avise, J. C., J. Arnold, R. M. Ball, E. Bermingham, T. Lamb, J. E. Neigel, C. A. Reeb, and N. C. Saunders. 1987. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annu. Rev. Ecol. Syst. 18 : 489 522.
6. Backström, N., S. Fagerberg, and H. Ellegren. 2008. Genomics of wild bird populations: a gene-based set of references makers spread across the avian genome. Mol. Ecol. 17 : 964 980.
7. Bazin, E., S. Glémin, and N. Galtier. 2006. Population size does not influence mitochondrial genetic diversity in animals. Science 312 : 570 572.
8. Becquet, C., and M. Przeworski. 2007. A new approach to estimate parameters of speciation models with application to apes. Genome Res. 17 : 1505 1519.
9. Bensch, S., D. E. Irwin, J. H. Irwin, L. Kvist, and S. Åkesson. 2006. Conflicting patterns of mitochondrial and nuclear DNA diversity in Phylloscopus warblers. Mol. Ecol. 15 : 161 171.
10. Boles, W. E. 1988. Comments on the subspecies of Australian native and introduced finches. Emu 88 : 20 24.
11. Brito, P. H., and S. V. Edwards. 2008. Multilocus phylogeography and phylogenetics using sequence-based markers. Genetica Online First doi :.
12. Brumfield, R. T., P. Beerli, D. A. Nickerson, and S. V. Edwards. 2003. The utility of single nucleotide polymorphisms in inferences of population history. Trends Ecol. Evol. 18 : 249 256.
13. Cardinal, B. R., and L. Christidis. 2000. Mitochondrial DNA and morphology reveal three geographically distinct lineages of the large bentwing bat (Miniopterus schreibersii) in Australia. Aust. J. Zool. 48 : 1 19.
14. Carstens, B. C., and L. L. Knowles. 2007. Shifting distributions and speciation: species divergence during rapid climate change. Mol. Ecol. 16 : 619 627.
15. Carstens, B. C., J. D. Degenhardt, A. L. Stevenson, and J. Sullivan. 2005. Accounting for coalescent stochasticity in testing phylogeographical hypotheses: modelling Pleistocene population structure in the Idaho giant salamander Dicamptodon aterrimus. Mol. Ecol. 14 : 255 265.
16. Castillo-Davis, C. I., S. L. Mekhedov, D. L. Hartl, E. V. Koonin, and F. A. Kondrashov. 2002. Selection for short introns in highly expressed genes. Nat. Genet. 31 : 415 418.
17. Christidis, L., and R. Schodde. 1997. Relationships within the Australo-Papuan fairy-wrens (Aves: Malurinae): an evaluation of the utility of allozyme data. Aust. J. Zool. 45 : 113 129.
18. Collins, R. A. 1988. Evidence of natural selection to maintain a functional domain outside of the 'core' in a large subclass of group I introns. Nucleic Acids Res. 16 : 2705 2715.
19. Cracraft, J. 1986. Origin of evolution of continental biotas: speciation and historical congruence within the Australian avifauna. Evolution 40 : 977 996.
20. Cracraft, J. 2001. Avian evolution, Gondwana biogeography and the Cretaceous-Tertiary mass extinction event. Proc. R. Soc. Lond. B 268 : 459 469.
21. Di Rienzo, A., P. Donnelly, C. Toomajian, B. Sisk, A. Hill, M. L. Petzl-Erler, G. K. Haines, and D. H. Barch. 1998. Heterogeneity of microsatellite mutations within and between loci, and implications for human demographic histories. Genetics 148 : 1269 1284.
22. Dolman, G., and C. Moritz. 2006. A multilocus perspective on refugial isolation and divergence in rainforest skinks (Carlia). Evolution 60 : 573 582.
23. Driskell, A. C., S. Pruett-Jones, K. A. Tarvin, and S. Hagevik. 2002. Evolutionary relationships among blue- and black-plumaged populations of the white-winged fairy-wren (Malurus leucopterus). Aust. J. Zool. 50 : 581 595.
24. Edwards, S. V. 1993. Long-distance gene flow in a cooperative breeder detected in genealogies of mitochondrial DNA sequences. Proc. R. Soc. Lond. B 252 : 177 85.
25. Edwards, S. V., and P. Beerli. 2000. Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54 : 1839 1854.
26. Edwards, S. V., S. B. Kingan, J. D. Calkins, C. N. Balakrishnan, W. B. Jennings, W. J. Swanson, and M. Sorenson. 2005. Speciation in birds: genes, geography, and sexual selection. Proc. Natl. Acad. Sci. USA 102 : 6550 6557.
27. Ellegren, H. 2007. Molecular evolutionary genomics of birds. Cyto. Genome Res. 117 : 120 130.
28. Excoffier, L., and S. Schneider. 2005. Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol. Bioinform. Online. 1 : 47 50.
29. Ford, J. 1974. Speciation in Australian birds adapted to arid habitats. Emu 74 : 161 168.
30. Ford, J. 1977. Subspeciation in the white-throated warbler of Australia and New Guinea. Emu 78 : 90 92.
31. Ford, J. 1987a. Hybrid zones in Australian birds. Emu 87 : 158 178.
32. Ford, J. 1987b. Minor isolates and minor geographical barriers in avian speciation in continental Australia. Emu 87 : 90 102.
33. Ford, F., and D. Blair. 2005. Neat patterns with a messy history: Savannah refuges in northern Australia. Mammal Study 30 : S45 S50.
34. Hagelberg, E., N. Goldman, P. Lio, S. Whelan, W. Schiefenhövel, J. B. Clegg, and D. K. Bowden. 2000. Evidence for mitochondrial DNA recombination in a human population of island Melanesia. Proc. R. Soc. Lond. B 267 : 1595 1596.
35. Hare, M. P. 2001. Prospects for nuclear phylogeography. TRENDS Ecol. Evol. 16 : 700 706.
36. Hewitt, G. M. 2001. Speciation, hybrid zones and phylogeography - or seeing genes in space and time. Mol. Ecol. 10 : 537 549.
37. Hey, J., and C. A. Machado. 2003. The study of structured populations - new hope for a difficult and divided science. Nat. Rev. 4 : 535 543.
38. Hey, J., and R. Nielsen. 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.
39. Hong, X., D. G. Scofield, and M. Lynch. 2006. Intron size, abundance, and distribution within untranslated regions of genes. Mol. Biol. Evol. 23 : 2392 2404.
40. Hopkins, M. S., A. W. Graham, R. Hewett, J. Ash, and J. Head. 1990. Evidence of late Pleistocene fires and eucalypt forest from a north Queensland humid tropical rainforest site. Aust. J. Ecol. 15 : 345 347.
41. Hudson, R. R. 2000. A new statistic for detecting genetic differentiation. Genetics 155 : 2011 2014.
42. Huelsenbeck, J. P., and F. Ronquist. 2001. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17 : 754 755.
43. Hughes, J. M., A. M. Baker, G. De Zylva, and P. B. Mather. 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. Biol. J. Linn. Soc. 74 : 25 34.
44. Hughes, J. M., C. L. Lange, P. B. Mather, and A. Robinson. 2002. A comparison of fitness components among different plumage morphs of the Australian magpie Gymnorhina tibicen. Emu 102 : 331 338.
45. James, C. H., and C. Moritz. 2000. Intraspecific phylogeography in the sedge frog Litoria fallax (Hylidae) indicates pre-Pleistocene vicariance of an open forest species from eastern Australia. Mol. Ecol. 9 : 349 358.
46. Jennings, W. B., and S. V. Edwards. 2005. Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees. Evolution 59 : 2033 2047.
47. Johnson, K. P. 2004. Deletion bias in avian introns over evolutionary timescales. Mol. Biol. Evol. 21 : 599 602.
48. Johnson, N. K., and C. Cicero. 2004. New mitochondrial DNA data affirm the importance of Pleistocene speciation in North American birds. Evolution 58 : 1122 1130.
49. Joseph, L., and C. Moritz. 1994. Mitochondrial DNA phylogeography of birds in eastern Australian rainforest: first fragment. Aust. J. Zool. 42 : 385 403.
50. Joseph, L., and T. Wilke. 2007. Lack of phylogeographic structure in three widespread Australian birds reinforces emerging challenges in Australian historical biogeography. J. Biogeogr. 34 : 612 624.
51. Karl, S. A., and J. C. Avise. 1993. PCR-based assays of Mendelian polymorphisms from anonymous single-copy nuclear DNA: techniques and applications for population genetics. Mol. Biol. Evol. 10 : 342 361.
52. Karubian, J. 2002. Costs and benefits of variable breeding plumage in the red-backed fairy-wren. Evolution 56 : 1673 1682.
53. Katzman, S., A. D. Kern, G. Bejerano, G. Fewell, L. Fulton, R. K. Wilson, S. R. Salama, and D. Haussler. 2007. Human genome ultraconserved elements are ultraselected. Science 317 : 915.
54. Keast, A. 1961. Bird speciation on the Australian continent. Bull. Mus. Compar. Zool. 123 : 305 495.
55. Kershaw, A. P. 1994. Pleistocene vegetation of the humid tropics of northeastern Queensland, Australia. Palaeogeogr. Palaeoclimatol. Palaeoecol. 109 : 399 412.
56. Klicka, J., and R. M. Zink. 1999. Pleistocene effects on North America songbird evolution. Proc. R. Soc. Lond. B 266 : 695.
57. Knowles, L. L. 2004. The burgeoning field of statistical phylogeography. J. Evol. Biol. 17 : 1 10.
58. Knowles, L. L., and W. P. Maddison. 2002. Statistical phylogeography. Mol. Ecol. 11 : 2623 2635.
59. Kuhner, M. K., J. Yamato, and J. Felsenstein. 2000. Maximum likelihood estimation of recombination rates from population data. Genetics 156 : 1393 1401.
60. Kuo, C., and J. C. Avise. 2005. Phylogeographic breaks in low-dispersal species: the emergence of concordance across gene trees. Genetica 124 : 179 186.
61. Leaché, A. D., S. C. Crews, and M. J. Hickerson. 2007. Two waves of diversification in mammals and reptiles of Baja California revealed by hierarchical Bayesian analysis. Biol. Letts. 3 : 646 650.
62. Lovette, I. J. 2004. Mitochondrial dating and mixed-support for the "2% rule" in birds. Auk 121 : 1 6.
63. MacDonald, J. D. 1969. Variation in the black-faced woodswallow. Emu 69 : 168 171.
64. Maddison, D. R., and W. P. Maddison. 2000. MacClade version 4: analysis of phylogeny and character evolution. Sinauer Associates, Sunderland, MA.
65. McCracken, K. G., and M. Sorenson. 2005. Is homoplasy or lineage sorting the source of incongruent mtDNA and nuclear gene trees in the stiff-tailed ducks (Nomonyx-Oxyura)? Syst. Biol. 54 : 35 55.
66. Nei, M., and W. Li. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 76 : 5269 5273.
67. Nickerson, D. A., V. O. Tobe, and S. L. Taylor. 1997. PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res. 25 : 2745 2751.
68. Nielsen, R. 2000. Estimation of population parameters and recombination rates from single nucleotide polymorphism. Genetics 154 : 931 942.
69. Nielsen, R., and J. Wakeley. 2001. Distinguishing migration from isolation: a Markov Chain Monte Carlo approach. Genetics 158 : 885 896.
70. Nix, H. A., and J. D. Kalma. 1972. Climate as a dominant control in the biogeography of northern Australia and New Guinea. Pp. 61 91 in D. Walker, ed. Bridge and barrier: the natural and cultural history of Torres Strait. Australian National Univ., Canberra.
71. Nylander, J. A. A. 2004. MrModeltest 2.0. Program distributed by the author. Evolutionary Biology Centre, Uppsala Univ.
72. Ollier, C. D. 1982. The great escarpment of eastern Australia: tectonic and geomorphic significance. J. Geol. Soc. Aust. 29 : 13 23.
73. Pakendorf, B., and M. Stoneking. 2005. Mitochondrial DNA and human evolution. Annu. Rev. Genom. Hum. Genet. 6 : 165 183.
74. Plunzhnikov, A., and P. Donnelly. 1996. Optimal sequencing strategies for surveying molecular genetic diversity. Genetics 144 : 1247 1262.
75. Pritchard, J. K., M. Stephens, and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155 : 945 959.
76. Rannala, B., and Z. Yang. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164 : 1645 1656.
77. Rowley, I., and E. Russell. 1997. Fairy-wrens and Grasswrens. Oxford Univ. Press Inc., New York.
78. Rozas, J., and J. C. D. B. Sanchez. 2003. DNAsp, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19 : 2496 2497.
79. Schodde, R. 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.
80. Schodde, R., and I. J. Mason. 1999. The directory of Australian birds. CSIRO Publishing, Canberra.
81. Slatkin, M., and W. P. Maddison. 1989. A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 123 : 603 613.
82. Smart, J. 1977. Late Quaternary sea-level changes, Gulf of Carpentaria, Australia. Geology 5 : 755 759.
83. Sorenson, M., J. C. Ast, D. E. Dimcheff, T. Yuri, and D. P. Mindell. 1999. Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. Mol. Phylogenet. Evol. 12 : 105 114.
84. Sorenson, M., C. N. Balakrishnan, and R. B. Payne. 2004. Clade-limited colonization in brood parasitic finches (Vidua spp.). Syst. Biol. 53 : 140 153.
85. Stephens, M., N. J. Smith, and P. Donnelly. 2001. A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68 : 978 989.
86. Swofford, D. L. 2003. PAUP*. Phylogenetic analysis using parsimony (*and other methods) version 4. Sinauer Associates, Sunderland, MA.
87. Toon, A., J. Hughes, A. Baker, and P. Mather. 2003. Discordance between morphology and genetic structure among three plumage morphs of the Australian magpie. Emu 103 : 337 343.
88. Toon, A., P. B. Mather, A. M. Baker, K. L. Durrant, and J. M. Hughes. 2007. Pleistocene refugia in an arid landscape: analysis of a widely distributed Australian passerine. Mol. Ecol. 16 : 2525 2541.
89. Tsaousis, A. D., D. P. Martin, E. D. Ladoukakis, D. Posada, and E. Zouros. 2005. Widespread recombination in published animal mtDNA sequences. Mol. Biol. Evol. 22 : 925 933.
90. Wakeley, J., R. Nielsen, S. N. Liu-Cordero, and K. Ardlie. 2001. The discovery of single-nucleotide polymorphisms - and inferences about human demographic history. Am. J. Hum. Genet. 69 : 1332 47.
91. Waltari, E., and S. V. Edwards. 2002. Evolutionary dynamics of intron size, genome size, and physiological correlates in Archosaurs. Am. Nat. 160 : 539 552.
92. Webster, M. S., C. W. Varian, and J. Karubian. 2008. Plumage color and reproductive success in the red-backed fairy-wren: why be a dull breeder? Behav. Ecol. 19 : 517 524.
93. Weir, J. T. and D. Schluter. 2008. Calibrating the avian molecular clock. Mol. Ecol. 17 : 2321 2328.
94. Wooller, R. D., D. A. Saunders, J. S. Bradley, and C. P. De Rebeira. 1985. Geographical variation in size of an Australian honeyeater (Aves: Meliphagidae): an example of Bergmann's rule. Biol. J. Linn. Soc. 25 : 355 363.
95. Worthington-Wilmer, J., L. Hall, E. Barratt, and C. Moritz. 1999. Genetic structure and male-mediated gene flow in the ghost bat (Macroderma gigas). Evolution 53 : 1582 1591.
96. Yang, Z. 1997. On the esitmation of ancestral population sizes of modern humans. Genet. Res. 69 : 111 116.
97. Zhao, Z., L. Jin, Y. Fu, M. Ramsay, T. Jenkins, E. Leskinen, P. Pamilo, M. Trexler, L. Patthy, L. B. Jorde, et al. 2000. Worldwide DNA sequence variation in a 10-kilobase noncoding region on human chromosome 22. Proc. Natl. Acad. Sci. USA 97 : 11354 11358.
98. Zink, R. M. 2007. Ecological exchangeability versus neutral molecular markers: the case of the great tit. Anim. Conserv. 10 : 369 373.
99. Zink, R. M., and G. F. Barrowclough. 2008. Mitochondrial DNA under siege in avian phylogeography. Mol. Ecol. 17 : 2107 2121.