Mitochondrial genealogy of Western Australian barramundi: Applications of inbreeding coefficients and coalescent analysis for separating temporal population processes

Journal of Fish Biology

Volumn 54, Issue 6, 1999, Pages 1197-1209

  Doupe R G ^a   Horwitz, P ^a   Lymbery, A J ^b  

^a EDITH COWAN UNIVERSITY   (Australia)

^b DEPARTMENT OF AGRICULTURE AND FOOD WESTERN AUSTRALIA   (Australia)

Author keywords

Barramundi phylogenies; Coalescent theory; F statistics; Gene flow; mtDNA

Indexed keywords

GENE FLOW; PHYLOGENETICS; POPULATION GENETICS; TEMPORAL DISTRIBUTION;

AUSTRALIA;

LATES CALCARIFER;

EID: 0032983912     PISSN: 00221112     EISSN: None     Source Type: Journal    
DOI: 10.1006/jfbi.1999.0952     Document Type: Article

References (46)

1. Aplin K. P., Baverstock P. R., Donnellan S. C. Albumin immunological evidence for the time and mode of origin of the New Guinean terrestrial mammal fauna. Science in New Guinea. 19:1993;131-145.
2. Avise J. C. Molecular population structure and the biogeographic history of a regional fauna: a case history with lessons for conservation biology. Oikos. 63:1992;62-76.
3. Avise J. C. Molecular Markers, Natural History and Evolution. 1994;Chapman & Hall, New York.
4. Barton N. H., Wilson I. Genealogies and geography. Philosophical Transactions of the Royal Society of London. 349:1995;49-59.
5. Berggren W. A., Burckle L. H., Cita M. B., Cooke M. B. S., Funnell B. M., Gartner S., Hays J. D., Kennett J. P., Opdyke N. D., Pastouret L., Shackleton N. J., Takayanagi Y. Towards a Quaternary time scale. Quaternary Research. 13:1980;277-302.
6. Bernatchez L., Guyomard R., Bonhomme F. DNA sequence variation of the mitochondrial control region among geographically and morphologically remote European brown trout Salmo trutta populations. Molecular Ecology. 1:1992;161-173.
7. Billington N., Hebert P. D. N. Mitochondrial DNA diversity in fishes and its implications for introductions. Billington N., Hebert P. D. N. The Ecological and Genetic Implications of Fish Introduction (FIN). Canadian Journal of Fisheries and Aquatic Sciences. 48:1991;80-94.
8. Birky C. W. III, Maruyama T., Fuerst P. An approach to population and evolutionary genetic theory for genes in mitochondria and chloroplasts, and some results. Genetics. 103:1983;513-527.
9. Chappell J. A revised sea-level record for the last 300,000 years from Papua New Guinea. Search. 14:1983;99-101.
10. Chenoweth S. F., Hughes J. M. Genetic population structure of the catadromous Perciform: Macquaria novemaculeata (Percichthyidae). Heredity. 80:1997;187-197.
11. Chenoweth S. F., Hughes J. M., Keenan C. P., Lavery S. Concordance between dispersal and mitochondrial gene flow: isolation by distance in a tropical teleost, Lates calcarifer. Heredity. 80:1998;187-197.
12. Chenoweth S. F., Hughes J. M., Keenan C. P., Lavery S. When oceans meet: a teleost shows secondary intergradation at an Indian-Pacific interface. Proceedings of the Royal Society of London B. 265:1998;415-420.
13. Edwards S. V. Mitochondrial gene genealogy and gene flow among island and mainland populations of a sedentary songbird, the Grey-Crowned Babbler (Pomatostomus temporalis). Evolution. 47:1993;1118-1137.
14. Excoffier L., Smouse P. E., Quattro J. M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics. 131:1992;479-491.
15. Fajen A., Breden F. Mitochondrial DNA sequence variation among natural populations of the Trinidad guppy, Poecilia reticulata. Evolution. 46:1992;1457-1465.
16. Felsenstein J. How can we infer geography and history from gene frequencies? Journal of Theoretical Biology. 96:1982;9-20.
17. Felsenstein J. PHYLIP (Phylogeny Inference Package), version 3.5c. 1993;Department of Genetics, University of Washington, Seattle.
18. Hallerman E. M., Beckmann J. S. DNA-level Polymorphism as a tool in fisheries science. Canadian Journal of Fisheries and Aquatic Sciences. 45:1988;1075-1087.
19. Hillis D. M., Bull J. J. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology. 42:1993;182-192.
20. Hudson R. R. Gene genealogies and the coalescent process. Futuyama D., Antonovics J. Oxford Surveys in Evolutionary Biology. 1990;1-44 Oxford University Press, Oxford.
21. Hudson R. R., Slatkin M., Maddison W. P. Examination of levels of gene flow from DNA sequence data. Genetics. 132:1992;583-589.
22. Keenan C. P. Recent evolution of population structure in Australian barramundi, Lates calcarifer (Bloch): an example of isolation by distance in one dimension. Australian Journal of Marine and Freshwater Research. 45:1994;1123-1148.
23. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution. 16:1980;111-120.
24. Kocher T. D., Thomas W. K., Meyer A., Edwards S. V., Pääbo S., Villablanca F. X., Wilson A. C. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proceedings of the National Academy of Sciences USA. 86:1989;6196-6200.
25. Lynch M., Crease T. J. The analysis of population survey data on DNA sequence variation. Molecular Biology and Evolution. 7:1990;377-394.
26. Maddison W. P., Maddison D. R. MacClade: Analysis of Phylogeny and Character Evolution. 1992;Sinauer Associates, Sunderland.
27. Meyer A. DNA technology and phylogeny of fish. Beaumont A. R. Genetics and Evolution of Aquatic Organisms. 1994;219-249 Chapman & Hall, London.
28. Meyer A., Kocher T. D., Basasibwaki P. Monophyletic origin of Lake Victoria cichlid fish suggested by mitochondrial DNA sequences. Nature. 347:1990;550-553.
29. Milligan B. G., Leebens-Mack J., Strand A. E. Conservation genetics: beyond the maintenance of marker diversity. Molecular Ecology. 3:1994;423-435.
30. Moritz C., Dowling T. E., Brown W. M. Evolution of animal mitochondrial DNA: relevance for population biology and systematics. Annual Review of Ecology and Systematics. 18:1987;269-292.
31. Nei M. Evolutonary Molecular Genetics. 1987;University of Columbia Press, New York.
32. Nielsen E. E., Hansen M. M., Loeschcke V. Genetic structure of European populations of Salmo salar L. (Atlantic salmon) inferred from mitochondrial DNA. Heredity. 77:1996;351-358.
33. Ovenden J. R. Mitochondrial DNA and marine stock assessment: a review. Australian Journal of Marine and Freshwater Research. 41:1990;835-853.
34. Reynolds J., Weir B. S., Cockerham C. C. Estimation of the coancestry coefficient: basis for a short term genetic distance. Genetics. 105:1983;767-779.
35. Rozas J., Rozas R. DnaSP version 2.0: a novel software package for extensive molecular population genetics analysis. Computer Applications in Bioscience. 13:1997;307-311.
36. Sambrook J., Fritsch E. F., Maniatis T. Molecular Cloning: A Laboratory Manual. 1989;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
37. Shackleton N. J. Oxygen isotopes, ice volume and sea level. Quaternary Science Reviews. 6:1987;783-790.
38. Shaklee J. B., Salini J. Genetic variation and population subdivision in Australian barramundi, Lates calcarifer (Bloch). Australian Journal of Marine and Freshwater Research. 36:1985;203-218.
39. Shaklee J. B., Salini J., Garrett R. N. Electrophoretic characterization of multiple genetic stocks of barramundi (Lates calcarifer) in Queensland, Australia. Transactions of the American Fisheries Society. 122:1993;685-701.
40. Slatkin M., Maddison W. P. A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics. 123:1989;603-613.
41. Swofford D. L. Phylogenetic Analysis Using Parsimony. Version 3.1. 1993;Laboratory of Molecular Systematics, Smithsonian Institute, Washington.
42. Tajima F. Evolutionary relationships of DNA sequences in finite populations. Genetics. 105:1983;437-460.
43. Torgersen T., Hutchinson M. F., Searle D. E., Nix H. A. General bathymetry of the Gulf of Carpentaria and the Quaternary physiography of Lake Carpentaria. Palaeogeography, Palaeoclimatology, Palaeoecology. 41:1983;207-225.
44. Torgersen T., Jones M. R., Stephens A. W., Searle D. E., Ullman W. J. Late Quaternary hydrological changes in the Gulf of Carpentaria. Nature (London). 313:1985;785-787.
45. Wright S. Evolution in Mendelian populations. Genetics. 16:1931;97-159.
46. Wright S. The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution. 19:1965;395-420.