The phylogeography of dusky dolphins (Lagenorhynchus obscurus): A critical examination of network methods and rooting procedures

Molecular Ecology

Volumn 12, Issue 7, 2003, Pages 1781-1792

  Cassens, I ^a   Van Waerebeek, K ^b   Best, P B ^c   Crespo, E A ^d   Reyes, J ^e   Milinkovitch, Michel C ^a,f  

^a FREE UNIVERSITY OF BRUSSELS   (Belgium)

^b Peruvian Ctr for Cetacean Research   (Peru)

^c UNIVERSITY OF PRETORIA   (South Africa)

^d CENTRO NACIONAL PATAGÓNICO   (Argentina)

^e Areas Costeras y Recursos Marinos ^*  (Peru)

^f UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

Author keywords

Cetacea; Conservation genetics; mtDNA; Network methods; Phylogeography; Rooting techniques

Indexed keywords

ANIMALS; BASE SEQUENCE; CONSERVATION OF NATURAL RESOURCES; CYTOCHROMES B; DOLPHINS; EVOLUTION, MOLECULAR; GENETICS, POPULATION; GEOGRAPHY; MOLECULAR SEQUENCE DATA; OCEANS AND SEAS; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

CETACEA; CORYPHAENIDAE; LAGENORHYNCHUS; LAGENORHYNCHUS OBLIQUIDENS; LAGENORHYNCHUS OBSCURUS; MAMMALIA; VERTEBRATA;

EID: 0038645591     PISSN: 09621083     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-294X.2003.01876.x     Document Type: Article

References (53)

1. Avise JC (1994) Molecular Markers, Natural History, and Evolution. Chapman & Hall, New York.
2. Avise JC (2000) Phylogeography: the History and Formation of Species. Harvard University Press, Cambridge, MA.
3. Bandelt HJ, Dress AWM (1992) A canonical decomposition theory for metrics on a finite set. Advances in Mathematics, 92, 47-105.
4. Bandelt HJ, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16, 37-48.
5. Berta A, Sumich JL (1999) Marine Mammals Evolutionary Biology. Academic Press, San Diego, CA.
6. Bouzat JL, Lewin HA, Paige KN (1998) The ghost of genetic diversity past: historical DNA analysis of the greater prairie chicken. American Naturalist, 152, 1-6.
7. Cassens I, Vicario S, Waddell VG et al. (2000) Independent adaptation to riverine habitats allowed survival of ancient cetacean lineages. Proceedings of the National Academy of Science USA, 97, 11343-11347.
8. Castelloe J, Templeton AR (1994) Root probabilities for intraspecific gene trees under neutral coalescent theory. Molecular Phylogenetics and Evolution, 3, 102-113.
9. Clement M, Posada D, Crandall KA (2000) TCS: a computer program to estimate gene genealogies. Molecular Ecology, 9, 1657-1659.
10. Crandall KA (1996) Multiple interspecies transmissions of human and simian T-cell leukemia/lymphoma virus type I sequences. Molecular Biology and Evolution, 13, 115-131.
11. Crandall KA, Templeton AR (1996) Applications of intraspecific phylogenetics. In: New Uses for New Phylogenies (eds Harvey PH, Leigh Brown AJ, Maynard Smith J, Nee S), pp. 81-99. Oxford University Press, New York.
12. Crespo EA, Corcuera JF, Lopez Cazorla A (1994) Interactions between marine mammals and fisheries in some coastal fishing areas of Argentina. Report of the International Whaling Commission (Special Issue), 15, 269-281.
13. Crespo EA, Pedraza SN, Coscarella M et al. (1997a) Distribution and school size of dusky dolphins, Lagenorhynchus obscurus (Gray, 1828), in the southwestern South Atlantic Ocean. Report of the International Whaling Commission (Special Issue), 47, 693-697.
14. Crespo EA, Pedraza SN, Dans SL et al. (1997b) Direct and indirect effects of the highseas fisheries on the marine mammal populations in the northern and central Patagonian coast. Journal of Northwest Atlantic Fishery Science, 22, 189-207.
15. Dans SL, Crespo EA, Garcia NA et al. (1997) Incidental mortality of Patagonian dusky dolphins in mid-water trawling: retrospective effects from the early 1980s. Report of the International Whaling Commission (Special Issue), 47, 699-703.
16. Donnelly P, Tavaré S (1986) The ages of alleles and a coalescent. Advances in Applied Probability, 18, 1-19.
17. Excoffier L, Smouse PE (1994) Using allele frequencies and geographic subdivision to reconstruct gene trees within a species: molecular variance parsimony. Genetics, 136, 343-359.
18. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131, 479-491.
19. Good JM, Sullivan J (2001) Phylogeography of the red-tailed chipmunk (Tamias ruficaudus), a northern Rocky Mountain endemic. Molecular Ecology, 10, 2683-2695.
20. Grant WS, Bowen BW (1998) Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. Journal of Heredity, 89, 415-426.
21. Hillis DM, Moritz C, Mable BK (1996) Molecular Systematics. Sinauer Associates, Inc, Sunderland, MA.
22. Hochberg Y (1974) Some generalizations of the T-method in simultaneous inference. Journal of Multivariance Analysis, 4, 224-234.
23. Hurwood DA, Hughes JM (2001) Nested clade analysis of the freshwater shrimp, Caridina zebra (Decapoda: Atyidae), from north-eastern Australia. Molecular Ecology, 10, 113-125.
24. Huson DH (1998) SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics, 14, 68-73.
25. LeDuc RG, Perrin WF, Dizon AE (1999) Phylogenetic relationships among the delphinid cetaceans based on full cytochrome b sequences. Marine Mammal Science, 15, 619-648.
26. Mardulyn P (2001) Phylogeography of the Vosges mountains populations of Gonioctena pallida (Coleoptera: Chrysomelidae): a nested clade analysis of mitochondrial DNA haplotypes. Molecular Ecology, 10, 1751-1763.
27. Mllinkovitch MC, LeDuc RG, Adachi J et al. (1996) Effects of character weighting and species sampling on phylogeny reconstruction: a case study based on DNA sequence data in cetaceans. Genetics, 144, 1817-1833.
28. Milinkovitch MC, LeDuc RG, Tiedemann R, Dizon AE (2002) Applications of molecular data in cetacean taxonomy and population genetics with special emphasis on defining species boundaries. In: Marine Mammals: Biology and Conservation (eds Evans PGH, Raga JA), pp. 325-359. Kluwer Academic/Plenum Publishers, New York.
29. Nei M (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
30. O'Corry-Crowe GM, Suydam RS, Rosenberg A, Frost KJ, Dizon AE (1997) Phylogeography, population structure and dispersal patterns of the beluga whale Delphinapterus leucas in the Western Nearctic revealed by mitochondrial DNA. Molecular Ecology, 6, 955-970.
31. Pichler FB, Robineau D, Goodall RNP et al. (2001) Origin and radiation of Southern Hemisphere coastal dolphins (genus Cephalorhynchus). Molecular Ecology, 10, 2215-2223.
32. Posada D, Crandall KA (2001) Intraspecific gene genealogies: trees grafting into networks. Trends in Ecology and Evolution, 16, 37-45.
33. Prim RC (1957) Shortest connection networks and some generalizations. Bell Systems Technical Journal, 36, 1389-1401.
34. Rice DW (1998) Marine Mammals of the World Systematics and Distribution. Allen Press, Inc., Lawrence, KS.
35. Rohlf FJ (1973) Algorithm 76. Hierarchical clustering using the minimum spanning tree. Computer Journal, 16, 93-95.
36. Rosel PE, Tiedemann R, Walton MJ (1999) Genetic evidence for restricted trans-Atlantic movements of the harbour porpoise, Phocoena phocoena. Marine Biology, 133, 583-591.
37. Schneider S, Roessli D, Excoffier L (2000) ARLEQUIN, version 2.000: a Software for Population Genetics Data Analysis Genetics and Biometry Laboratory. University of Geneva, Geneva, Switzerland.
38. Swofford DL (2000) PAUP*, Phylogenetic Analysis Using Parsimony (*and Other Methods). Sinauer Associates, Sunderland, MA.
39. Templeton AR (1992) Human origins and analysis of mitochondrial DNA sequences. Science, 255, 737.
40. Templeton AR (1993) The 'Eve' hypotheses: a genetic critique and reanalyis. American Anthropologist, 95, 51-72.
41. Templeton AR, Crandall KA, Sing CF (1992) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics, 132, 619-633.
42. Van Waerebeek K (1992) Records of dusky dolphins Lagenorhynchus obscurus (Gray, 1828) in the eastern South Pacific. Beaufortia, 43, 45-61.
43. Van Waerebeek K (1993a) External features of the dusky dolphin Lagenorhynchus obscurus (Gray, 1828) from Peruvian waters. Estudios Oceanologicos, 12, 37-53.
44. Van Waerebeek K (1993b) Geographic variation and sexual dimorphism in the skull of the dusky dolphin, Lagenorhynchus obscurus (Gray, 1828). Fishery Bulletin, 91, 754-774.
45. Van Waerebeek K (1994) A note on the status of the dusky dolphin (Lagenorhynchus obscurus) off Peru. Report of the International Whaling Commission (Special Issue), 15, 525-527.
46. Van Waerebeek K, Read AJ (1994) Reproduction of dusky dolphins, Lagenorhynchus obscurus, from coastal Peru. Journal of Mammalogy, 75, 1054-1062.
47. Van Waerebeek K, Reyes JC (1990) Catch of small cetaceans at Pucusana port, central Peru, during 1987. Biological Conservation, 51, 15-22.
48. Van Waerebeek K, Reyes JC (1994a) Interactions between small cetaceans and Peruvian fisheries in 1988-89 and analysis of trends. Report of the International Whaling Commission (Special Issue), 15, 495-502.
49. Van Waerebeek K, Reyes JC (1994b) Post-ban small cetacean takes off Peru: a review. Report of the International Whaling Commission (Special Issue), 15, 503-520.
50. Van Waerebeek K, Reyes JC, Alfaro J (1993) Helminth parasites and phoronts of dusky dolphins Lagenorhynchus obscurus (Gray, 1828) from Peru. Aquatic Mammals, 19, 159-169.
51. Van Waerebeek K, Van Bree PJH, Best PB (1995) On the identity of Prodelphinus petersii Luetken, 1889 and records of dusky dolphin Lagenorhynchus obscurus (Gray, 1828) from the southern Indian and Atlantic Oceans. South African Journal of Marine Science, 16, 25-35.
52. Van Waerebeek K, Van Bressem M-F, Felix F et al. (1997) Mortality of dolphins and porpoises in coastal fisheries off Peru and southern Ecuador in 1994. Biological Conservation, 81, 43-49.
53. Wheeler WC (1990) Nucleic acid sequence phylogeny and random outgroups. Cladistics, 6, 363-367.