Brown WM, Prager EM, Wang A, Wilson AC: Mitochondrial DNA sequences of primates: tempo and mode of evolution. J Mol Evol. 1982, 18: 225-239. 10.1007/BF01734101.
Article
CAS
PubMed
Google Scholar
Moore WS: Inferring phylogenies from mtDNA variation: Mitochondrial-gene trees versus nuclear-gene trees. Evolution. 1995, 49: 718-726. 10.2307/2410325.
Article
Google Scholar
Cummings MP, Otto SP, Wakeley J: Sampling properties of DNA sequence data in phylogenetic analysis. Mol Biol Evol. 1995, 12: 814-822.
CAS
PubMed
Google Scholar
Saitou N, Nei M: The number of nucleotides required to determine the branching order of three species with special reference to the human-chimpanzee-gorilla divergence. J Mol Evol. 1986, 24: 189-204. 10.1007/BF02099966.
Article
CAS
PubMed
Google Scholar
Ruvolo M, Disotell TR, Allard MW, Brown WM, Honeycutt RL: Resolution of the African homonid trichotomy by use of a mitochondrial gene sequence. Proc Natl Acad Sci USA. 1991, 88: 1570-1574. 10.1073/pnas.88.4.1570.
Article
CAS
PubMed
PubMed Central
Google Scholar
DeFilippis VR, Moore WS: Resolution of phylogenetic relationships among recently evolved species as a function of amount of DNA sequence: An empirical study based on woodpeckers (Aves: Picidae). Mol Phyl Evol. 2000, 16: 143-160. 10.1006/mpev.2000.0780.
Article
CAS
Google Scholar
Rokas A, Carroll SB: More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol Biol Evol. 2005, 22: 1337-1344. 10.1093/molbev/msi121.
Article
CAS
PubMed
Google Scholar
Rohland N, Malaspinas AS, Pollack JL, Slatkin M, Matheus P, Hofreiter M: Proboscidean mitogenomics: Chronology and mode of elephant evolution using mastodon as outgroup. PLoS Biol. 2007, 5: e207-10.1371/journal.pbio.0050207.
Article
PubMed
PubMed Central
Google Scholar
Maddison W: Reconstructing character evolution on polytomous cladograms. Cladistics. 1989, 5: 365-377. 10.1111/j.1096-0031.1989.tb00569.x.
Article
Google Scholar
Willerslev E, Gilbert MTP, Binladen J, et al: Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution. BMC Evol Biol. 2009, 9: 95-10.1186/1471-2148-9-95.
Article
PubMed
PubMed Central
Google Scholar
Hudson RR: Gene genealogies and the coalescent process. Oxford Surv Evol Biol. 1990, 7: 1-44.
Google Scholar
Hoelzer GA, Melnick DJ: Patterns of speciation and limits to phylogenetic resolution. Trends Ecol Evol. 1994, 9: 104-107. 10.1016/0169-5347(94)90207-0.
Article
CAS
PubMed
Google Scholar
Jackman TR, Larson A, de Queiroz K, Losos JB: Phylogenetic relationships and tempo of early diversification in Anolis lizards. Syst Biol. 1999, 48: 254-285. 10.1080/106351599260283.
Article
Google Scholar
Walsh HE, Kidd MG, Moum T, Friesen VL: Polytomies and the power of phylogenetic inference. Evolution. 1999, 53: 932-937. 10.2307/2640732.
Article
Google Scholar
Bolnick DI: Multi-species outcomes in a common model of sympatric speciation. J Theor Biol. 2006, 241: 734-744.
Article
PubMed
Google Scholar
Meyer M, Stenzel U, Hofreiter M: Parallel tagged sequencing on the 454 platform. Nature Protocols. 2008, 3: 267-278. 10.1038/nprot.2007.520.
Article
CAS
PubMed
Google Scholar
Morin PA, Archer FI, Foote AD, et al: Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species. Genome Res. 2010, 20: 908-916. 10.1101/gr.102954.109.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shen YY, Liang L, Sun YB, Yue BS, Yang XJ, Murphy RW, Zhang YP: A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the Phasianidae. BMC Evol Biol. 2010, 10: 132-10.1186/1471-2148-10-132.
Article
PubMed
PubMed Central
Google Scholar
Shimodaira H, Hasegawa M: Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol. 1999, 16: 1114-1116.
Article
CAS
Google Scholar
Slowinski JB: Molecular polytomies. Mol Phyl Evol. 2001, 19: 114-120. 10.1006/mpev.2000.0897.
Article
CAS
Google Scholar
LeDuc RG, Perrin WF, Dizon AE: Phylogenetic relationships among the Delphinid cetaceans based on full cytochrome b sequences. Mar Mamm Sci. 1999, 15: 619-648. 10.1111/j.1748-7692.1999.tb00833.x.
Article
Google Scholar
May-Collado L, Agnarsson I: Cytochrome b and Bayesian inference of whale phylogeny. Mol Phyl Evol. 2006, 38: 344-354. 10.1016/j.ympev.2005.09.019.
Article
CAS
Google Scholar
Nishida S, Goto M, Pastene LA, Kanda N, Koike H: Phylogenetic relationships among cetaceans revealed by Y-chromosome sequences. Zool Sci. 2007, 24: 723-732. 10.2108/zsj.24.723.
Article
PubMed
Google Scholar
Caballero S, Jackson J, Mignucci-Giannoni AA, Barrios-Garrido H, Beltrán-Pedreros S, Montiel-Villalobos MG, Robertson KM, Baker CS: Molecular systematics of South American dolphins Sotalia: sister taxa determination and phylogenetic relationships, with insights into a multilocus phylogeny of the Delphinidae. Mol Phyl Evol. 2008, 46: 252-268. 10.1016/j.ympev.2007.10.015.
Article
CAS
Google Scholar
Kingston SE, Adams LD, Rosel PE: Testing mitochondrial sequences and anonymous nuclear markers for phylogeny reconstruction in a rapidly radiating group: molecular systematics of the Delphinidae (Cetacea: Odontoceti: Delphinidae). BMC Evol Biol. 2009, 9: 245-10.1186/1471-2148-9-245.
Article
PubMed
PubMed Central
Google Scholar
McGowen MR, Spaulding M, Gatesy J: Divergence date estimation and a comprehensive molecular tree of extant cetaceans. Mol Phyl Evol. 2009, 53: 891-906. 10.1016/j.ympev.2009.08.018.
Article
CAS
Google Scholar
Steeman ME, Hebsgaard MB, Fordyce RE, et al: Radiation of extant cetaceans driven by restructuring of the oceans. Syst Biol. 2009, 58: 573-585. 10.1093/sysbio/syp060.
Article
PubMed
PubMed Central
Google Scholar
Xiong YE, Brandley MC, Xu S, Zhou K, Yang G: Seven new dolphin mitochondrial genomes and a time-calibrated phylogeny of whales. BMC Evol Biol. 2009, 9: 20-10.1186/1471-2148-9-20.
Article
PubMed
PubMed Central
Google Scholar
Perrin WF: Dolphins, porpoises, and whales. An action plan for the conservation of biological diversity: 1988-1992, IUCN, Gland, Switzerland. 1989
Google Scholar
Lartillot N, Philippe H: Computing Bayes factor using thermodynamic integration. Syst Biol. 2005, 55: 195-207. 10.1080/10635150500433722.
Article
Google Scholar
Xie W, Lewis PO, Fan Y, Kuo L, Chen M-H: Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Syst Biol. 2011.
Google Scholar
Haq BH, Hardenbol J, Vail PR: Chronology of fluctuating sea levels since the Triassic. Science. 1987, 235: 1156-1162. 10.1126/science.235.4793.1156.
Article
CAS
PubMed
Google Scholar
Beasley I, Robertson KM, Arnold P: Description of a new dolphin, the Australian snubfin dolphin Orcaella heinsohni sp. N. (Cetacea, Delphinidae). Mar Mam Sci. 2005, 21: 365-400. 10.1111/j.1748-7692.2005.tb01239.x.
Article
Google Scholar
Dwyer GS, Cronin TM, Baker PA, Raymo ME, Buzas JS, Corrège T: North Atlantic deepwater temperature change during late Pliocene and late Quaternary climactic cycles. Science. 1995, 270: 1347-1351. 10.1126/science.270.5240.1347.
Article
CAS
Google Scholar
Ravelo AC, Andreasen DH, Lyle M, Olivarez-Lyle A, Wara MW: Regional climate shifts caused by gradual global cooling in the Pliocene epoch. Nature. 2004, 429: 263-267. 10.1038/nature02567.
Article
CAS
PubMed
Google Scholar
Wara MW, Ravelo A-C, Delaney ML: Permanent El Niño-like conditions during the Pliocene warm period. Science. 2005, 309: 758-761. 10.1126/science.1112596.
Article
CAS
PubMed
Google Scholar
Lawrence KT, Liu Z, Herbert TD: Evolution of the Eastern Tropical Pacific through Pio-Pleistocene glaciation. Science. 2006, 312: 79-83. 10.1126/science.1120395.
Article
CAS
PubMed
Google Scholar
Weisrock DW, Shaffer HB, Storz BL, Storz SR, Voss AR: Multiple nuclear gene sequences identify species boundaries in the rapidly radiating clade of Mexican ambystomatid salamanders. Mol Ecol. 2006, 15: 2489-2503. 10.1111/j.1365-294X.2006.02961.x.
Article
CAS
PubMed
Google Scholar
Springer MS, DeBry RW, Douady C, Amrine HM, Madsen O, de Jong WW, Stanhope MJ: Mitochondrial Versus Nuclear Gene Sequences in Deep-Level Mammalian Phylogeny Reconstruction. Mol Biol Evol. 2001, 18 (2): 132-143.
Article
CAS
PubMed
Google Scholar
McCracken KG, Sorenson MD: Is homoplasy or lineage sorting the source of incongruent mtDNA and nuclear gene trees in the stiff-tailed ducks (Nomonyx-Oxyura). Syst Biol. 2005, 54: 35-55. 10.1080/10635150590910249.
Article
PubMed
Google Scholar
Milinkovitch , LeDuc , Tiedemann , Dizon : Applications of Molecular Data in Cetacean Taxonomy and Population Genetics with Special Emphasis on Defining Species Boundaries. 'Marine Mammals: Biology and Conservation'. Edited by: Evans PGH, J A. 2002, Kluwer Academic Press, 325-359.
Chapter
Google Scholar
Oremus M, Gales R, Dalebout ML, Funahashi N, Endo T, Kage T, Steel D, Baker SC: Worldwide mitochondrial DNA diversity and phylogeography of pilot whales (Globicephala spp). Biol J Linn Soc. 2009, 98: 729-744. 10.1111/j.1095-8312.2009.01325.x.
Article
Google Scholar
Pollock DD, Zwickl DJ, McGuire JA, Hillis DM: Increased taxon sampling is advantageous for phylogenetic inference. Syst Biol. 2002, 51 (4): 664-671. 10.1080/10635150290102357.
Article
PubMed
PubMed Central
Google Scholar
Zwickl DJ, Hillis DM: Increased taxon sampling greatly reduces phylogenetic error. Syst Biol. 2002, 51 (4): 588-598. 10.1080/10635150290102339.
Article
PubMed
Google Scholar
Harlin-Cognato AD, Honeycutt RL: Multi-locus phylogeny of dolphins in the subfamily Lissodelphininae: character synergy improves phylogenetic resolution. BMC Evol Biol. 2006, 6: 87-10.1186/1471-2148-6-87.
Article
PubMed
PubMed Central
Google Scholar
Palsbøll PJ, Larsen F, Hansen ES: Sampling of skin biopsies from free-ranging large cetaceans in West Greenland: development of new biopsy tips and bolt designs. Rep Int Whaling Commn. 1991, 71-79. Special 13
Amos W, Hoelzel AR: Long-term preservation of whale skin for DNA analysis. Rep Int Whaling Commn. 1991, 99-103. Special 13
Arnason U, Gullberg A, Janke A: Mitogenomic analyses provide new insights into cetacean origin and evolution. Gene. 2004, 333: 27-34. 10.1016/j.gene.2004.02.010.
Article
CAS
PubMed
Google Scholar
Yan J, Zhou K, Yang G: Molecular phylogenetics of river dolphin's and the baiji mitochondrial genome. Mol Phyl Evol. 2005, 37: 743-750. 10.1016/j.ympev.2005.06.009.
Article
CAS
Google Scholar
Keane TM, Creevey CJ, Pentony MM, Naughton TJ, McInerney JO: Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol. 2006, 6: 29-10.1186/1471-2148-6-29.
Article
PubMed
PubMed Central
Google Scholar
Luo A, Qiao H, Zhang Y, Shi W, Ho SYW, Xu W, Zhang A, Zhu C: Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets. BMC Evol Biol. 2010, 10: 242-10.1186/1471-2148-10-242.
Article
PubMed
PubMed Central
Google Scholar
Yang Z: Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol Biol Evol. 1993, 10: 1396-1401.
CAS
PubMed
Google Scholar
Drummond AJ, Rambaut A: BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 2007, 7: 214-10.1186/1471-2148-7-214.
Article
PubMed
PubMed Central
Google Scholar
Drummond AJ, Ho SYW, Phillips MJ, Rambaut A: Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006, 4: e88-10.1371/journal.pbio.0040088.
Article
PubMed
PubMed Central
Google Scholar
Aguirre-Fernandez G, Barnes LG, Aranda-Manteca FJ, Fernandez-Rivera JR: Protoglobicephala mexicana, a new genus and species of Pliocene fossil dolphin (Cetacea; Odontoceti; Delphinidae) from the gulf of California, Mexico. Boletin de la Sociodad Geologica Mexicana. 2009, 61 (2): 245-265.
Google Scholar
Ho SYW, Lanfear R: Characterising rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks. Mitochondrial DNA. 2010, 21 (3-4): 138-146. 10.3109/19401736.2010.494727.
Article
CAS
PubMed
Google Scholar
Rambaut A, Drummond A: Tracer, version 1.4. 2007, [http://tree.bio.ed.ac.uk/software/tracer]
Google Scholar
Suchard MA, Weiss RE, Sinsheimer JS: Bayesian selection of continuous-time Markov chain evolutionary models. Mol Biol Evol. 2001, 18 (6): 1001-1013.
Article
CAS
PubMed
Google Scholar
Huelsenbeck JP, Ronquist F: MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics Applications Note. 2001, 17 (8): 754-755.
Article
CAS
Google Scholar
Guindon S, Gascuel O: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003, 52 (5): 696-704. 10.1080/10635150390235520.
Article
PubMed
Google Scholar
Posada D, Crandall KA: Modeltest: testing the model of DNA substitution. Bioinformatics. 1998, 14 (9): 817-818. 10.1093/bioinformatics/14.9.817.
Article
CAS
PubMed
Google Scholar
Shimodaira H, Hasegawa M: CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics. 2001, 17 (12): 1246-1247. 10.1093/bioinformatics/17.12.1246.
Article
CAS
PubMed
Google Scholar
Huson DH, Richter DC, Rausch C, Dezulian T, Franz M, Rupp R: Dendroscope: An interactive viewer for large phyogenetic trees. BMC Bioinformatics. 2007, 8: 460-10.1186/1471-2105-8-460.
Article
PubMed
PubMed Central
Google Scholar