Cyprinid phylogeny based on Bayesian and maximum likelihood analyses of partitioned data: Implications for Cyprinidae systematics

Science China Life Sciences

Volumn 55, Issue 9, 2012, Pages 761-773

  Wang, XuZhen ^a   Gan, XiaoNi ^a   Li, JunBing ^a   Mayden, Richard L ^b   He, ShunPing ^a  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b SAINT LOUIS UNIVERSITY   (United States)

Author keywords

Cyprinidae; molecular dating; partitioned analyses; phylogeny

Indexed keywords

ACHEILOGNATHINAE; CYPRINIDAE; CYPRININAE; GOBIONINAE; LEUCISCINAE; PISCES; RASBORINAE;

EID: 84867138194     PISSN: 16747305     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11427-012-4366-z     Document Type: Article

References (61)

1. Nelson J S, ed. Fishes of the World. New York: John Wiley and Sons Inc., 2006.
2. Howes G J. Systematics and biogeography: an overview. In: Winfield I J, Nelson J S, eds. Cyprinid Fishes: Systematics, Biology and Exploitation. London: Chapman and Hall, 1991. 1-33.
3. Hensel K. Review of the classification and of the opinions on the evolution of Cyprinoidei (Eventognathi) with an annotated list of genera and subgenera described since 1921. Annot Zool Bot, 1970, 57: 1-45.
4. Chen Y Y, ed. Fauna Sinica, Osteichthys: Cypriniformes (Part II). Beijing: Science Press, 1998.
5. Gosline W A. Unbranched dorsal-fin rays and subfamily classification in the fish family Cyprinidae. Occas Pap Mus Zool Univ Mich, 1978, 684: 1-21.
6. Chu Y T. Comparative studies on the scales and on the pharyngeals and their teeth in Chinese Cyprinids, with particular reference to taxonomy and evolution. Biol Bull St John's Univ (Shanghai), 1935, 2: 1-225.
7. Wu X, ed. The Cyprinid Fishes of China (in Chinese). Shanghai: Shanghai Science and Technology Press, 1964.
8. Chen X L, Yue P Q, Lin R D. Major groups within the family Cyprinidae and their phylogenetic relationships. Acta Zootaxon Sin, 1984, 9: 424-440.
9. Cavender T M, Coburn M M. Phylogenetic relationships of North American Cyprinidae. In: Mayden R L, ed. Systematics, Historical Ecology and North American Freshwater Fishes. Stanford, California: Stanford University Press, 1992. 293-327.
10. Zardoya R, Doadrio I. Molecular evidence on the evolutionary and biogeographical patterns of European Cyprinids. J Mol Evol, 1999, 49: 227-237.
11. Briolay J, Galtier N, Brito R M, et al. Molecular phylogeny of Cyprinidae inferred from cytochrome b DNA sequences. Mol Phylogenet Evol, 1998, 9: 100-108.
12. Gilles A, Lecointre G, Faure E, et al. Mitochondrial phylogeny of the European Cyprinids: implications for their systematics, reticulate evolution, and colonization time. Mol Phylogenet Evol, 1998, 10: 132-143.
13. Gilles A, Lecointre G, Miquelis A, et al. Partial combination applied to phylogeny of European Cyprinids using the mitochondrial control region. Mol Phylogenet Evol, 2001, 19: 22-33.
14. Zardoya R, Doadrio I. Phylogenetic relationships of Iberian Cyprinids: systematic and biogeographical implications. Proc R Soc B Biol Sci, 1998, 265: 1365-1372.
15. Durand J D, Tsigenopoulos C S, Unlu E, et al. Phylogeny and biogeography of the family Cyprinidae in the Middle East inferred from cytochrome b DNA-evolutionary significance of this region. Mol Phylogenet Evol, 2002, 22: 91-100.
16. Hanfling B, Brandl R. Phylogenetics of European Cyprinids: insights from allozymes. J Fish Biol, 2000, 57: 265-276.
17. Fu C Z, Wu J H, Chen J K, et al. Freshwater fish biodiversity in the Yangtze River Basin of China: patterns, threats and conservation. Biodivers Conserv, 2003, 12: 1649-1685.
18. Cunha C, Mesquita N, Dowling T E, et al. Phylogenetic relationships of Eurasian and American Cyprinids using cytochrome b sequences. J Fish Biol, 2002, 61: 929-944.
19. He S, Liu H, Chen Y, et al. Molecular phylogenetic relationships of Eastern Asian Cyprinidae (Pisces: Cypriniformes) inferred from cytochrome b sequences. Sci China Ser C-Life Sci, 2004, 47: 130-138.
20. Liu H, Chen Y. Phylogeny of the East Asian Cyprinids inferred from sequences of the mitochondrial DNA control region. Can J Zool, 2003, 81: 1938-1946.
21. Ronquist F, Huelsenbeck J P. Mrbayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 2003, 19: 1572-1574.
22. Stamatakis A. Raxml-Vi-Hpc: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 2006, 22: 2688-2690.
23. McGuire J A, Witt C C, Altshuler D L, et al. Phylogenetic systematics and biogeography of hummingbirds: Bayesian and maximum likelihood analyses of partitioned data and selection of an appropriate partitioning strategy. Syst Biol, 2007, 56: 837-856.
24. Fink S V, Fink W L. Interrelationships of the ostariophysan fishes (Teleostei). Zool J Linn Soc, 1981, 72: 297-353.
25. Wang X, Wang J, He S, et al. The complete mitochondrial genome of the Chinese hook snout carp Opsariichthys bidens (Actinopterygii: Cypriniformes) and an alternative pattern of mitogenomic evolution in vertebrate. Gene, 2007, 399: 11-19.
26. Sambrook J, Fritsch E, Maniatis T, ed. Molecular Cloning: A Laboratory Manual. New York: Cold Spring Harbor Laboratory Press, 1989.
27. Xiao W H, Zhang Y P, Liu H Z. Molecular systematics of Xenocyprinae (Teleostei: Cyprinidae): taxonomy, biogeography, and coevolution of a special group restricted in East Asia. Mol Phylogenet Evol, 2001, 18: 163-173.
28. Li J, Wang X, Kong X, et al. Variation patterns of the mitochondrial 16s rRNA gene with secondary structure constraints and their application to phylogeny of Cyprinine fishes (Teleostei: Cypriniformes). Mol Phylogenet Evol, 2008, 47: 472-487.
29. Lovejoy N R, Collette B B. Phylogenetic relationships of new world needlefishes (Teleostei: Belonidae) and the biogeography of transitions between marine and freshwater habitats. Copeia, 2001, 2: 324-338.
30. Thompson J D, Gibson T J, Plewniak F, et al. The Clustal X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res, 1997, 25: 4876-4882.
31. De Rijk P, Wuyts J, van de Peer Y, et al. The European large subunit ribosomal RNA database. Nucleic Acids Res, 2000, 28: 177-178.
32. Gutell R R, Gray M W, Schnare M N. A compilation of large subunit (23s and 23s-like) ribosomal RNA structures. Nucleic Acids Res, 1993, 21: 3055-3074.
33. Gutell R R, Fox G E. A compilation of large subunit RNA sequences presented in a structural format. Nucleic Acids Res, 1988, 16: r175-269.
34. Swofford D L. Paup*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4. 0b10. 2003.
35. Posada D, Crandall K A. Modeltest: testing the model of DNA substitution. Bioinformatics, 1998, 14: 817-818.
36. Posada D, Buckley T R. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst Biol, 2004, 53: 793-808.
37. Lemmon A R, Moriarty E C. The importance of proper model assumption in Bayesian phylogenetics. Syst Biol, 2004, 53: 265-277.
38. Huelsenbeck J, Rannala B. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst Biol, 2004, 53: 904-913.
39. Wilgenbusch J, Warren D, Swofford D. Awty: A System for Graphical Exploration of Mcmc Convergence in Bayesian Phylogenetic Inference. 2004.
40. Kass R E, Raftery A E. Bayes factors. J Am Stat Assoc, 1995, 90: 773-795.
41. Nylander J A A, Ronquist F, Huelsenbeck J P, et al. Bayesian phylogenetic analysis of combined data. Syst Biol, 2004, 53: 47-67.
42. Schwarz G. Estimating the dimension of a model. Ann Stat, 1978, 6: 461-464.
43. Minin V, Abdo Z, Joyce P, et al. Performance-based selection of likelihood models for phylogeny estimation. Syst Biol, 2003, 52: 674-683.
44. Abdo Z, Minin V N, Joyce P, et al. Accounting for uncertainty in the tree topology has little effect on the decision-theoretic approach to model selection in phylogeny estimation. Mol Biol Evol, 2005, 22: 691-703.
45. Sullivan J, Abdo Z, Joyce P, et al. Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation. Mol Biol Evol, 2005, 22: 1386-1392.
46. Raftery A. Hypothesis testing and model selection. In: Gilks W R, Spiegelhalter D J, Richardson S, eds. Markov Chain Monte Carlo in Practice. London: Chapman and Hall, 1996. 163-187.
47. Castoe T A, Sasa M M, Parkinson C L. Modeling nucleotide evolution at the mesoscale: the phylogeny of the neotropical pitvipers of the Porthidium group (Viperidae: Crotalinae). Mol Phylogenet Evol, 2005, 37: 881-898.
48. Castoe T A, Parkinson C L. Bayesian mixed models and the phylogeny of pitvipers (Viperidae: Serpentes). Mol Phylogenet Evol, 2006, 39: 91-110.
49. Brandley M C, Schmitz A, Reeder T W. Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Syst Biol, 2005, 54: 373-390.
50. Shimodaira H. An approximately unbiased test of phylogenetic tree selection. Syst Biol, 2002, 51: 492-508.
51. Sanderson M J. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol Biol Evol, 1997, 14: 1218-1231.
52. Sanderson M J. R8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics, 2003, 19: 301-302.
53. Felsenstein J. Phylip (Phylogeny Inference Package) Version 3. 5 C. 1993.
54. Cavender T M. The fossil record of the Cyprinidae. In: Winfield I J, Nelson J S, eds. Cyprinid Fishes: Systematics, Biology and Exploitation. London: Chapman and Hall, 1991. 34-54.
55. Hierholzer E, Mörs T. Cypriniden-Schlundzähne (Osteichthyes: Teleostei) aus dem Tertiär von Hambach (Niederrheinische Bucht, Nw-Deutschland). Palaeontographica, Abteilung A, 2003, 269: 1-38.
56. Sytchevskaya E. Freshwater Ichthyofauna of the Neogene of Mongolia. Tr Sovm Sovets-Mongol Paleontol Eksped, 1989, 39: 1-144.
57. Schulz-Mirbach T, Reichenbacher B. Reconstruction of oligocene and neogene freshwater fish faunas-an actualistic study on cypriniform otoliths. Acta Palaeontol Pol, 2006, 51: 283-304.
58. Liu H, Su T. Pliocene fishes from the Yushe Basin, Shanxi. Vertebr Palasiat, 1962, 6: 1-25.
59. Tang K L, Agnew M K, Hirt M V, et al. Systematics of the subfamily Danioninae (Teleostei: Cypriniformes: Cyprinidae). Mol Phylogenet Evol, 2010, 57: 189-214.
60. Chen W J, Mayden R L. Molecular systematics of the Cyprinoidea (Teleostei: Cypriniformes), the world's largest clade of freshwater fishes: further evidence from six nuclear genes. Mol Phylogenet Evol, 2009, 52: 544-549.
61. Wang X, Li J, He S. Molecular evidence for the monophyly of East Asian groups of Cyprinidae (Teleostei: Cypriniformes) derived from the nuclear recombination activating gene 2 sequences. Mol Phylogenet Evol, 2007, 42: 157-170.