Comparison of the phylogenetic performance of neodermatan mitochondrial protein-coding genes

Zoologica Scripta

Volumn 35, Issue 6, 2006, Pages 655-665

  Hardman, Michael ^a   Hardman, Lotta M ^a  

^a FINNISH FOREST RESEARCH INSTITUTE   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 33750304110     PISSN: 03003256     EISSN: 14636409     Source Type: Journal    
DOI: 10.1111/j.1463-6409.2006.00248.x     Document Type: Article

References (48)

1. Avise, J. C. (2000). Phylogeography: the history and formation of species. Harvard University Press.
2. Bowles, J. D. & McManus, D. P. (1994). Genetic characterization of the Asian Taenia, a newly described taeniid cestode of humans. American Journal of Tropical Medicine and Hygiene, 50, 33-44.
3. Bowles, J., Blair, D. & McManus, D. P. (1995). A molecular phylogeny of the genus Echinococcus. Parasitology, 110, 317-328.
4. Cao, Y., Adachi, J. & Hasegawa, M. (1994a). Eutherian phylogeny as inferred from mitochondrial DNA sequence data. Japanese Journal of Genetics, 69, 455-472.
5. Cao, Y., Adachi, J., Janke, A., Pääbo, S. & Hasegawa, M. (1994b). Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: instability of a tree based on a single gene. Journal of Molecular Evolution, 39, 519-527.
6. Cummings, M. P., Otto, S. & Wakeley, J. (1995). Sampling properties of DNA sequence data in phylogenetic analysis. Molecular Biology and Evolution 12, 814-822.
7. Cummings, M. P., Otto, S. & Wakeley, J. (1999). Genes and other samples of DNA sequence data for phylogenetic inference. Biological Bulletin, 196, 345-350.
8. Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783-791.
9. Foster, P. G. (2003). P4 - a python package for phylogenetics. Distributed by the author.
10. Foster, P. G. (2004). Modeling compositional heterogeneity. Systematic Biology, 53, 485-495.
11. Foster, P. G. & Hickley, D. A. (1999). Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. Journal of Molecular Evolution, 48, 284-290.
12. Haukisalmi, V., Wickström, L. M., Henttonen, H., Hantula, J. & Gubányi, A. (2004). Molecular and morphological evidence for multiple species within Paranoplocephala omphalodes (Cestoda, Anoplocephalidae) in Microtus voles (Arvicolinae). Zoologica Scripta, 33, 277-290.
13. Hebert, P. D. N., Cywinska, A., Ball, S. L. & deWaard, J. R. (2003a). Biological identifications through DNA barcodes. Proceedings of the Royal Society of London, Series B, 270, 313-321.
14. Hebert, P. D. N., Ratnasingham, S. & deWaard, J. R. (2003b). Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London, Series B ( Supplement), 270, S96-S99.
15. Huelsenbeck, J. P. (1995). The performance of phylogenetic methods in simulation. Systematic Biology, 44, 17-48.
16. Huelsenbeck, J. P. & Crandall, K. A. (1997). Phylogeny estimation and hypothesis testing using maximum likelihood. Annual Review of Ecology and Systematics, 28, 437-466.
17. Jeon, H. K., Lee, K. H., Kim, K. H., Hwang, U. W. & Eom, K. S. (2005). Complete sequence and structure of the mitochondrial genome of the human tapeworm, Taenia asiatica (Platyhelminthes; Cestoda). Parasitology, 130, 717-726.
18. Kedra, H. A., Swiderski, Z., Tkach, V. V., Dubinski, P., Pawlowski, Z., Stefaniak, J. & Pawlowski, J. (1999). Genetic analysis of Echinococcus granulosus from humans and pigs in Poland, Slovakia and Ukraine. A multicenter study. Acta Parasitologica, 44, 248-254.
19. Kishino, H. & Hasegawa, M. (1989). Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in the Hominoidea. Journal of Molecular Evolution, 29, 170-179.
20. Kokaze, A., Miyadera, H., Kita, K., Machinami, R., Noya, O., Alarcón de Noya, B., Okamoto, M., Horii, T. & Kojima, S. (1997). Phylogenetic identification of Sparganum proliferum as a pseudophyllidean cestode. Parasitology International, 46, 271-279.
21. Le, T. H., Blair, D., Agatsuma, T., Humair, P. F. et al. (10 co-authors) (2000). Phylogenies inferred from mitochondrial gene orders - a cautionary tale from the parasitic flatworms. Molecular Biology and Evolution, 17, 1123-1125.
22. Le, T. H., Blair, D. & McManus, D. P. (2001). Complete DNA sequence and gene organization of the mitochondrial genome of the liverfluke, Fasciola hepatica L. (Platyhelminthes, Trematoda). Parasitology, 123, 609-621.
23. Le, T. H. & McManus, D. P. (2002a). Mitochondrial genomes of parasitic flatworms. Trends in Parasitology, 18, 206-213.
24. Le, T. H., Pearson, M. S., Blair, D., Dai, N., Zhang, L. H. & McManus, D. P. (2002b). Complete mitochondrial genomes confirm the distinctiveness of the horse-dog and sheep-dog strains of Echinococcus granulosus. Parasitology, 124, 97-112.
25. Le, T. H., McManus, D. P. & Blair, D. (2004). Codon usage and bias in mitochondrial genomes of parasitic platyhelminthes. The Korean Journal of Parasitology, 42, 159-167.
26. Macnish, M. G., Morgan-Ryan, U. M., Monis, P. T., Behnke, J. M. & Thompson, R. C. A. (2002). A molecular phylogeny of nuclear and mitochondrial sequences in Hymenolepis nana (Cestoda) supports the existence of a cryptic species. Parasitology, 125, 567-575.
27. Maddison, D. R. & Maddison, W. P. (2000). MacClade 4: Analysis of Phylogeny and Character Evolution. Sunderland, MA: Sinauer Associates.
28. Mariaux, J. & Olson, P. D. (2001). Cestode systematics in the molecular era. In: T. Littlewood & R. Bray (Eds) Interrelationships of the Platyhelminthes. The Systematics Association Special Volume Series 60 (pp. 127-134). London: Taylor & Francis.
29. McManus, D. P., Le, T. H. & Blair, D. (2004). Genomics of parasitic flatworms. International Journal of Parasitology, 34, 153-158.
30. Miya, M. & Nishida, M. (2000). Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterion. Molecular Phylogenetics and Evolution, 17, 437-455.
31. Miyadera, H., Kokaze, A., Kuramochi, T., Kita, K. et al. (8 co-authors) (1995). Phylogenetic relationships within Taenia taeniaeformis variants and other taeniid cestodes inferred from the nucleotide sequence of the cytochrome c oxidase subunit I gene. Parasitological Research, 81, 451-458.
32. Miyadera, H., Kokaze, A., Kuramochi, T., Kita, K., Machinami, R., Noya, O., Alarcon de Noya, B., Okamoto, M. & Kojima, S. (2001). Phylogenetic identification of Sparganum proliferum as a pseudophyllidean cestode by the sequence analyses on mitochondrial COI and nuclear sdhB gene. Parasitology International, 50, 93-104.
33. Morgan, J. A. T. & Blair, D. (1998). Relative merits of nuclear ribosomal internal transcribed spacers and mitochondrial CO1 and ND1 genes for distinguishing among Echinostoma species (Trematoda). Parasitology, 116, 289-297.
34. Nakao, M., Sako, Y. & Ito, A. (2003). The mitochondrial genome of the tapeworm Taenia solium: a finding of the abbreviated stop codon U. Journal of Parasitology, 89, 633-645.
35. von Nickisch-Rosenegk, M., Brown, W. M. & Boore, J. L. (2001). Complete sequence of the mitochondrial genome of the tapeworm Hymenolepis diminuta: gene arrangements indicate that Platyhelminthes are Eutrochozoans. Molecular Biology and Evolution, 18, 721-730.
36. Okamoto, M., Ito, A., Kurosawa, T., Oku, Y., Kamiya, M. & Agatsuma, T. (1995). Intraspecific variation of isoenzymes in Taenia taeniaeformis. International Journal for Parasitology, 25, 221-228.
37. Okamoto, M., Agatsuma, T., Kurosawa, T. & Ito, A. (1997). Phylogenetic relationships of three hymenolepidid species inferred from nuclear ribosomal and mitochondrial DNA sequences. Parasitology, 115, 661-666.
38. Otto, S. P., Cummings, M. P. & Wakeley, J. (1996). Inferring phylogenies from DNA sequence data: the effects of sampling. In: P. H. Harvey, A. J. Leigh Brown, J. Maynard Smith & S. Nee (Eds) New Uses for New Phylogenies (pp. 103-115). Oxford: Oxford University Press.
39. Posada, D. & Crandall, K. A. (1998). Modeltest: testing the model of DNA substitution. Bioinformatics, 14, 817-818.
40. Russo, C. A. M., Takezaki, N. & Nei, M. (1996). Efficiencies of different genes and tree-building methods in recovering a known vertebrate phylogeny. Molecular Biology and Evolution, 13, 525-536.
41. Shimodaira, H. & Hasegawa, M. (1999). Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution, 16, 1114-1116.
42. Slowinski, J. B. (2001). Molecular polytomies. Molecular Phylogenetics and Evolution, 19, 114-120.
43. Swofford, D. L. (2001). PAUP* Phylogenetic Analysis Using Parsimony (*and Other Methods). Sunderland, MA: Sinauer Associates Inc.
44. Telford, M. J., Herniou, E. A., Russell, R. B. & Littlewood, D. T. J. (2000). Changes in mitochondrial genetic codes as phylogenetic characters: two examples from the flatworms. Proceedings of the National Academy of Sciences of the USA, 97, 11359-11364.
45. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. (1997). The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 24, 4876-4882.
46. Vilas, R., Criscione, C. D. & Blouin, M. S. (in press). A comparison between mitochondrial DNA and the ribosomal internal transcribed regions in prospecting for cryptic species of platyhelminth parasites. Parasitology (in press).
47. Wickström, L. M., Haukisalmi, V., Varis, S., Hantula, J. & Henttonen, H. (2005). Molecular phylogeny and systematics of anoplocephaline cestodes in rodents and lagomorphs. Systematic Parasitology, 62, 83-99.
48. Zardoya, R. & Meyer, A. (1996). Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates. Molecular Biology and Evolution, 13, 933-942.