Using phylogenetic analyses and reference datasets to validate the species identities of cetacean sequences in GenBank

Molecular Phylogenetics and Evolution

Volumn 40, Issue 3, 2006, Pages 866-871

  Ross, Howard A ^a   Murugan, Sumathi ^a  

^a UNIVERSITY OF AUCKLAND   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME B; MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; CETACEA; CLASSIFICATION; COMPARATIVE STUDY; GENETICS; NUCLEIC ACID DATABASE; NUCLEOTIDE SEQUENCE; PHYLOGENY; REGULATOR GENE; VALIDATION STUDY;

ANIMALS; BASE SEQUENCE; CETACEA; CYTOCHROMES B; DATABASES, NUCLEIC ACID; DNA, MITOCHONDRIAL; LOCUS CONTROL REGION; PHYLOGENY;

CETACEA;

EID: 33746746994     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2006.04.007     Document Type: Article

References (30)

1. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search. Nucleic Acids Res. 25 (1997) 3389-3402
2. Baker C.S., Cipriano F., and Palumbi S.R. Molecular genetic identification of whale and dolphin products from commercial markets in Korea and Japan. Mol. Ecol. 5 (1996) 671-685
3. Baker A.J., Daugherty C.H., Colbourne R., and McLennan J.L. Flightless brown kiwis of New Zealand possess extremely subdivided population structure and cryptic species like small mammals. Proc. Natl. Acad. Sci. USA 92 (1995) 8254-8258
4. Baker C.S., and Lento G.M. Forensic genetic identification of marine mammals. In: Perrin W.F., Würsig B., and Thewissen J.G.M. (Eds). Encyclopedia of marine mammals (2002), Academic Press, San Diego 450-453
5. Baker C.S., Lento G.M., Cipriano F., and Palumbi S.R. Predicted decline of protected whales based on molecular genetic monitoring of Japanese and Korean markets. Proc. R. Soc. Lond. B 267 (2000) 1191-1199
6. Baker C.S., and Palumbi S.R. Which whales are hunted? A molecular genetic approach to monitoring whaling. Science 265 (1994) 1538-1539
7. Baker, C.S., Ross, H.A., Lavery, S., Rodrigo, A.G., Dalebout, M.L., 2004. Progress on an applied molecular taxonomy of cetacean species. In: Reeves, R.R., Perrin, W.F., Taylor, B.L., Baker, C.S., Mesnick, S.L. (Eds.), Report of the Workshop on Shortcomings of Cetacean Taxonomy in relation to needs of Conservation and Management. NOAA-TM-NMFS-SWFSC-363. National Oceanic and Atmospheric Administration, La Jolla, CA, pp. 85-91.
8. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Rapp B.A., and Wheeler D.L. GenBank. Nucleic Acids Res. 30 (2002) 17-20
9. Bollongino R., Burger J., and Hummel S. DNA typing from elephant tusks and rhinoceros horn-Strategies and applications in wildlife conservation and animal forensics. Forensic Sci. Int. 136 Suppl. 1 (2003) 374-375
10. Branicki W., Kupiec T., and Pawlowski R. Validation of cytochrome b sequence analysis as a method of species identification. J. Forensic Sci. 48 (2003) 1-5
11. Cipriano, F., 2004. Cetacean sequence data: What is and isn't in GENBANK. In: Reeves, R.R., Perrin, W.F., Taylor, B.L., Baker, C.S., Mesnick, S.L. (Eds.), Report of the Workshop on Shortcomings of Cetacean Taxonomy in Relation to Needs of Conservation and Management. NOAA-TM-NMFS-SWFSC-363. National Oceanic and Atmospheric Administration, La Jolla, CA, pp. 82-84.
12. Dalebout M.L., Baker C.S., Mead J.G., Cockcroft V.G., and Yamada T.K. A comprehensive and validated molecular taxonomy of beaked whales, family Ziphiidae. J. Hered. 95 (2004) 459-473
13. Dalebout M.L., Mead J.G., Baker C.S., Baker A.N., and Van Helden A.L. A new species of beaked whale Mesoplodon perrini sp. n. (Cetacea: Ziphiidae) discovered through phylogenetic analyses of mitochondrial DNA sequences. Mar. Mammal Sci. 18 (2002) 577-608
14. DeSalle R., and Birstein V.J. PRC identification of black caviar. Nature 381 (1996) 197-198
15. Dizon, A., Baker, C.S., Cipriano, F., Lento, G.M., Palsbøll, P., Reeves, R., 2000. Molecular genetic identification of whales, dolphins and porpoises. In: Proceedings of a Workshop on the Forensic use of Molecular Techniques to Identify Wildlife Products in the Market Place. NOAA Technical Memorandum NMFS NOAA-TM-NMFS-SWFSC-286, La Jolla, California.
16. Forster P. To err is human. Ann. Hum. Genet. 67 (2003) 2-4
17. Funk D.J., and Omland K.E. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu. Rev. Ecol. Syst. 34 (2003) 397-423
18. Hare M.P., Cipriano F., and Palumbi S.R. Genetic evidence on the demography of speciation in allopatric dolphin species. Evolution 56 (2002) 804-816
19. Hebert P.D.N., Cywinska A., Ball S.L., and deWaard J.R. Biological identifications through DNA barcodes. Proc. R. Soc. Lond. B 270 (2003) 313-321
20. Hebert P.D.N., Stroeckle M.Y., Zemlak T.S., and Francis C.M. Identification of birds through DNA barcodes. PLoS Biol. 2 (2004) e312
21. Jarman S.N., Gales N.J., Tierney M., Gill P.C., and Elliott N.G. A DNA-based method for identification of krill species and its application to analysing the diet of marine vertebrate predators. Mol. Ecol. 11 (2002) 2679-2690
22. Lambert D.M., Baker A.J., Huynen L., Haddrath O., Hebert P.D.N., and Millar C.D. Is a large-scale DNA-based inventory of ancient life possible?. J. Hered. 96 (2005) 1-6
23. Matisoo-Smith E., Roberts R.M., Irwin G.J., Allen J.S., Penny D., and Lambert D.M. Patterns of prehistoric human mobility in Polynesia indicated by mtDNA from the Pacific rat. Proc. Natl. Acad. Sci. USA 95 (1998) 15145-15150
24. Reeves, R.R., Perrin, W.F., Taylor, B.L., Baker, C.S., Mesnick, S.L., 2004. Report of the Workshop on Shortcomings of Cetacean Taxonomy in Relation to Needs of Conservation and Management. NOAA Technical Memorandum NOAA-NMFS-SWFSC-363, National Oceanic and Atmospheric Administration, La Jolla, CA.
25. Roca A.L., Georgiadis N., Pecon-Slattery J., and O'Brien S.J. Genetic evidence for two species of elephant in Africa. Science 293 (2001) 1473-1475
26. Rosenbaum H.C., Brownell Jr. R.L., Brown M.W., Schaeff C.V.P., White B.N., Makik S., Pastene L.A., Patenaude N.J., Baker C.S., Goto M., Best P.B., Clapham P.J., Hamilton P., Moore M., Payne R., Rowntree V., Tynan C.T., Bannister J.L., and DeSalle R. World-wide genetic differentiation of Eubalaena: questioning the number of right whale species. Mol. Ecol. 9 (2000) 1793-1802
27. Ross H.A., Lento G.M., Dalebout M.L., Goode M., Ewing G., McLaren P., Rodrigo A.G., Lavery S., and Baker C.S. DNA Surveillance: web-based molecular identification of whales, dolphins, and porpoises. J. Hered. 94 (2003) 111-114
28. Savolainen P., Zhang Y.-p., Luo J., Lundeberg J., and Leitner T. Genetic evidence for an East Asian origin of domestic dogs. Science 298 (2002) 1610-1613
29. Wada S., Oishi M., and Yamada T.K. A newly discovered species of living baleen whale. Nature 426 (2003) 278-281
30. Wu H., Wan Q.-H., Fang S.-G., and Zhang S.-Y. Application of mitochondrial DNA sequence analysis in the forensic identification of Chinese sika deer subspecies. Forensic Sci. Int. 148 (2005) 101-105