Morphology and placental mammal phylogeny

Systematic Biology

Volumn 57, Issue 3, 2008, Pages 499-503

  Springer, Mark S ^a   Meredith, Robert W ^a   Eizirik, Eduardo ^b   Teeling, Emma ^c   Murphy, William J ^d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b PONTIFICAL CATHOLIC UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

^c UNIVERSITY COLLEGE DUBLIN   (Ireland)

^d TEXAS A AND M UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EUTHERIA;

EID: 45849100517     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1080/10635150802164504     Document Type: Review

References (45)

1. Amrine-Madsen, H., K.-P. Koepfli, R. K. Wayne, and M. S. Springer. 2003. A new phylogenetic marker, apolipoprotein B, provides compelling evidence for eutherian relationships. Mol. Phylogenet. Evol. 28:225-240.
2. Asher, R. J., J. H. Geisler, and M. R. Sánchez-Villagra. 2008. Morphology, paleontology, and placental mammal phylogeny. Syst. Biol. 57:311-317.
3. Asher, R. J., M. J. Novacek, and J. G. Geisler. 2003. Relationships of endemic African mammals and their fossil relatives based on morphological and molecular evidence. J. Mamm. Evol. 10:131-194.
4. Cannarozzi, G., A. Schneider, and G. Gonnet. 2007. A phylogenomic study of human, dog, and mouse. PLoS Comput. Biol. 3:9-14.
5. D'Erchia, A. M., C. Gissi, G. Pesole, C. Saccone, and U. Arnason. 1996. The guinea-pig is not a rodent. Nature 381:597-600.
6. de Jong, W. W., M. A. M. van Dijk, C. Poux, G. Kappe, T. van Rheede, and O. Madsen. 2003. Indels in protein-coding sequences of Euarchontoglires constrain the rooting of the eutherian tree. Mol. Phylogenet. Evol. 28:328-340.
7. Delsuc, F., M. Scally, O. Madsen, M. J. Stanhope, W. W. de Jong, F. M. Catzeflis, M. S. Springer, and E. J. P. Douzery. 2002. Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting. Mol. Biol. Evol. 19:1656-1671.
8. Fleming, M. A., J. D. Potter, C. J. Ramirez, G. K. Ostrander, and E. A. Ostrander. 2003. Understanding missense mutations in the BRCA1 gene: An evolutionary approach. Proc. Natl. Acad. Sci. USA 100:1151-1156.
9. Gunnel, G. F., and N. B. Simmons. 2005. Fossil evidence and the origin of bats. J. Mamm. Evol. 12:209-246.
10. Hallstrom, B. M., M. Kullberg, M. A. Nilsson, and A. Janke. 2007. Phylogenomic data analyses provide evidence that Xenarthra and Afrotheria are sister groups. Mol. Biol. Evol. 24:2059-2068.
11. Horovitz, I. 2004. Eutherian mammal systematics and the origins of South American ungulates as based on postcranial osteology. Bull. Carneg. Mus. Nat. Hist. 36:63-79.
12. Horovitz, I., and M. R. Sánchez-Villagra. 2003. A morphological analysis of marsupial mammal higher-level phylogenetic relationships. Cladistics 19:181-212.
13. Hudelot, C., V. Gowri-Shankar, H. Jow, M. Rattray, and P. G. Higgs. 2003. RNA-based phylogenetic methods: Application to mammalian mitochondrial RNA sequences. Mol. Phylogenet. Evol. 28:241-252.
14. Huttley, G. A., M. J. Wakefield, and S. Easteal. 2007. Rates of genome evolution and branching order from whole genome analysis. Mol. Biol. Evol. 24:1702-1730.
15. Kitazoe, Y., H. Kishino, T. Okabayashi, T. Watabe, N. Nakajima, Y. Okuhara, and Y. Kurihara. 2005. Multidimensional vector space representation for convergent evolution and molecular phylogeny. Mol. Biol. Evol. 22:704-715.
16. Kjer, K. M., and R. L. Honeycutt. 2007. Site specific rates of mitochondrial genomes and the phylogeny of Eutheria. BMC Evol. Biol. 7:8.
17. Kriegs, J. O., G. Churakov, M. Keifmann, U. Jordan, J. Brosius, and J. Schmitz. 2006. Retroposed elements as archives for the evolutionary history of placental mammals. PLoS Biol. 4:e91.
18. Lunter, G. 2007. Dog as an outgroup to human and mouse. PLoS Comput. Biol. 3:e74.
19. Luo, Z.-X., and J. R. Wible. 2005. A Late Jurassic digging mammal and early mammalian diversification. Science 308:103-107.
20. Luo, Z.-X, Q. Ji, J. R. Wible, and C.-Y. Yuan. 2003. An early Cretaceous tribosphenic mammal and metatherian evolution. Science 203:1934-1940.
21. Madsen, O., M. Scally, C. J. Douady, D. J. Kao, W. DeBry, R. Adkins, H. Amrine, M. J. Stanhope, W. W. de Jong, and M. S. Springer. 2001. Parallel adaptive radiations in two major clades of placental mammals. Nature 409:610-614.
22. Meredith, R. W. 2007. Phylogeny and evolution of diprotodontian marsupials. PhD Dissertation, University of California, Riverside.
23. Murphy, W. J., E. Eizirik, W. E. Johnson, Y. P. Zhang, O. A. Ryder, and S. J. O'Brien. 2001a. Molecular phylogenetics and the origins of placental mammals. Nature 409:614-618.
24. Murphy, W. J., E. Eizirik, S. J. O'Brien, O. Madsen, M. Scally, C. J. Douady, E. Teeling, O. A. Ryder, M. J. Stanhope, W. W. de Jong, and M. S. Springer. 2001b. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294:2348-2351.
25. Murphy, W. J., P. A. Pevzner, and S. J. O'Brien. 2004. Mammalian phylogenomics comes of age. Trends Genet. 20:631-639.
26. Nikolaev, S., J. I. Montoya-Burgos, E. H. Margulies, NISC Comparative Sequencing Program, J. Rougemont, B. Nyffeler, and S. E. Antonarakis. 2007. Early history of mammals is elucidated with the ENCODE multiple species sequencing data. PLoS Genet. 3:e2.
27. Nishihara, H., M. Hasegawa, and N. Okada. 2006. Pegasoferae, an unexpected mammalian clade revealed by tracking acient retroposon insertions. Proc. Natl. Acad. Sci. USA 103:9929-9934.
28. Poux, C., van Rheede, T., O. Madsen, and W. W. de Jong. 2002. Sequence gaps join mice and men: Phylogenetic evidence from deletions in two proteins. Mol. Biol. Evol. 19:2035-2037.
29. Reyes, A., C. Gissi, F. Catzeflis, E. Nevo, G. Pesole, and C. Saccone. 2004. Congruent mammalian trees from mitochondrial and nuclear genes using Bayesian methods. Mol. Biol. Evol. 21:397-403.
30. Roca, A., G. K. Bar-Gal, E. Eizirik, K. M. Helgen, R. Maria, M. S. Springer, S. J. O'Brien, and W. J. Murphy. 2004. Mesozoic origin for West Indian insectivores. Nature 429:649-651.
31. Sánchez-Villagra, M., S. Ladeveze, I. Horovitz, C. Argot, J. J. Hooker, T. E. Macrini, T. Martin, S. Moore-Fay, C. de Muizon, T. Schmelzle, and R. J. Asher. 2007. Exceptionally preserved North American Paleogene metatherians: Adaptations and discovery of a major gap in the opossum fossil record. Biol. Lett. 3:318-322.
32. Scally, M., O. Madsen, C. J. Doouady, W. W. de Jong, M. J. Stanhope, and M. S. Springer. 2001. Molecular evidence for the major clades of placental mammals. J. Mamm. Evol. 8:239-277.
33. Shoshani, J., and M. C. McKenna. 1998. Higher taxonomic relationships among extant mammals based on morphology, with selected comparisons of results from molecular data. Mol. Phylogenet. Evol. 9:572-584.
34. Simmons, N. B., and J. H. Geisler. 1998. Phylogenetic relationships of Icaronycteris, Archaeonycteris, Hassianycteris, and Palaeochiropteryx to extant bat lineages, with comments on the evolution of echolocation and foraging strategies in Microchiroptera. Bull. Am. Mus. Nat. Hist. 235:1-182.
35. Springer, M. S., A. Burk-Herrick, R. Meredith, E. Eizirik, E. Teeling, S. J. O'Brien, and W. J. Murphy. 2007. The adequacy of morphology for reconstructing the early history of placental mammals. Syst. Biol. 56:673-684.
36. Springer, M. S., M. J. Stanhope, O. Madsen, and W. W. de Jong. 2004. Molecules consolidate the placental mammal tree. Trends Ecol. Evol. 19:430-438.
37. Springer, M. S., E. C. Teeling, O. Madsen, M. J. Stanhope, and W. W. de Jong. 2001. Integrated fossil and molecular data reconstruct bat echolocation. Proc. Natl. Acad. Sci. USA 98:6241-6246.
38. Swofford, D. L. 2003. PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4.0b10. Sinauer Associates, Sunderland, Massachusetts.
39. Thomas, J. W., et al. (70 other authors). 2003. Comparative analyses of multi-species sequences from targeted genomic regions. Nature 424:788-793.
40. van Dijk, M. A. M., E. Paradis, F. Catzeflis, and W. W. de Jong. 1999. The virtues of gaps: Xenarthran (edentate) monophyly supported by a unique deletion in αA-crystallin. Syst. Biol. 48:94-106.
41. Waddell, P. J., H. Kishino, and R. Ota. 2001. A phylogenetic foundation for comparative mammalian genomics. Genome Informatics 12:141-154.
42. Waddell, P. J., and S. Shelley. 2003. Evaluating placental interordinal phylogenies with novel sequences including RAG1, γ-fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models. Mol. Phylogenet. Evol. 28:197-224.
43. Waters, P. D., G. Dobigny, P. J. Waddell, and T. J. Robinson. 2007. Evolutionary history of LINE-1 in the major clades of placental mammals. PLoS ONE 2:e158.
44. Wible, J. R., G. W. Rougier, M. J. Novacek, and R. J. Asher. 2007. Cretaceous eutherians and Laurasian origin for placental mammals near the K/T boundary. Nature 447:1003-1006.
45. Wildman, D. E., M. Uddin, J. C. Opazo, G. Liu, V. Lefort, S. Guindon, O. Gascuel, W. I. Grossman, R. Romero, and M. Goodman. 2007. Genomics, biogeography, and the diversification of placental mammals. Proc. Natl. Acad. Sci. USA 104:14395-14400.