Appendix C. Description of the mammalian phylogeny and the sources used to construct it.
We constructed a phylogeny for the 1197 species in our database (Fig. C1) as follows. The placental ordinal topology followed Murphy et al. (2001); see also Springer et al. (2004). In this scheme the order Insectivora is polyphyletic and reclassified into Afrosoricida (golden moles and tenrecs) and Eulipotyphla (hedgehogs, moles and shrews), and Cetacea is nested within Artiodactyla. For the purposes of ordinal comparisons (e.g., Fig. 3) we considered Cetacea and Artiodactyla separately.
Relationships within the major placental orders represented in our database were resolved using information in the following sources: Afrosoricida and Euliptophyla, (Quérouil et al. 2001, Grenyer and Purvis 2003); Artiodactyla and Cetacea, (Gatesy et al. 1992, Árnason and Gullberg 1994, Sæther and Gordon 1994, Pitra et al. 1997, Hassanin et al. 1998, Messenger and McGuire 1998, Ursing and Arnason 1998, LeDuc et al. 1999, Ursing et al. 2000); Carnivora, (Bininda-Edmonds et al. 1999); Chiroptera, (Jones et al. 2002); Lagomorpha, (Stoner et al. 2003); Perissodactyla, (Norman and Ashley 2000); Primates, (Purvis 1995); Rodentia, (Robinson et al. 1997, Martin et al. 2000, Ebensperger and Cofré 2001, Michaux et al. 2001, Steppan et al. 2004a, Steppan et al. 2004b); Xenarthra, (Delsuc et al. 2002).
The marsupial phylogeny was derived from Kirsch et al. (1997) and Johnson et al. (2002).
Because branch lengths were unavailable for large portions of the phylogeny, we estimated branch lengths by setting the height of each node equal to the number of daughter taxa minus one (Grafen 1989).
![]() |
FIG. C1. The phylogeny used for the 1197 mammal species included in our analysis, showing the major groupings. Branch lengths are proportional to the number of taxa below each node. |
LITERATURE CITED
Árnason, U., and A. Gullberg. 1994. Relationship of baleen whales established by cytochrome b gene sequence comparison. Nature 367:726728.
Bininda-Edmonds, O. R. P., J. L. Gittleman, and A. Purvis. 1999. Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia). Biological Reviews 74:143175.
Delsuc, F., M. Scally, O. Madsen, M. J. Stanhope, W. W. de Jong, F. Catzeflis, M. S. Springer, and J. P. Douzery. 2002. Molecular phylogeny of living Xenarthans and the impact of character and taxon sampling on the placental tree rooting. Molecular Biology and Evolution 19:16561671.
Ebensperger, L. A., and H. Cofré. 2001. On the evolution of group-living in the New World cursorial hystricognath rodents. Behavioral Ecology 12:227236.
Gatesy, J., D. Yelon, R. DeSalle, and E. S. Vrba. 1992. Phylogeny of the Bovidae (Artiodactyla, Mammalia), based on mitochondrial ribosomal DNA sequences. Molecular Biology and Evolution 9:433446.
Grafen, A. 1989. The phylogenetic regression. Philosophical Transactions of the Royal Society London, Series B 326:119157.
Grenyer, R., and A. Purvis. 2003. A composite species-level phylogeny of the 'Insectivora' (Mammalia: order Lipotyphla Haeckel, 1866). Journal of Zoology, London 260:245257.
Hassanin, A., E. Pasquet, and J.-D. Vigne. 1998. Molecular systematics of the subfamily Caprinae (Artiodactyla, Bovidae) as determined from cytochrome b sequences. Journal of Mammalian Evolution 5:217236.
Johnson, C. N., S. Delean, and A. Balmford. 2002. Phylogeny and selectivity of extinction in Australian marsupials. Animal Conservation 5:135142.
Jones, K. E., A. Purvis, A. MacLarnon, O. R. P. Bininda-Edmonds, and N. B. Simmons. 2002. A phylogenetic supertree of the bats (Mammalia: Chiroptera). Biological Reviews 77:223259.
Kirsch, J. A. W., F.-J. Lapointe, and M. S. Springer. 1997. DNA-hybridisation studies of marsupials and their implications for Metatherian classification. Australian Journal of Zoology 45:211280.
LeDuc, R. G., W. F. Perrin, and A. E. Dizon. 1999. Phylogenetic relationships among the Delphinid Cetaceans based on full cytochrome B sequences. Marine Mammal Science 15:619648.
Martin, Y., G. Gerlach, C. Schlötterer, and A. Meyer. 2000. Molecular phylogeny of European Muroid rodents based on complete cytochrome b sequences. Molecular Phylogenetics and Evolution 16:3747.
Messenger, S. L., and J. A. McGuire. 1998. Morphology, molecules, and the phylogenetics of Cetaceans. Systematic Biology 47:90124.
Michaux, J., A. Reyes, and F. Catzeflis. 2001. Evolutionary history of the most speciose mammals: molecular phylogeny of Muroid rodents. Molecular Biology and Evolution 18:20172031.
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. 2001. Resoultion of the early placental mammal radiation using Bayesian phylogenetics. Science 294:23482351.
Norman, J. E., and M. V. Ashley. 2000. Phylogenetics of Perissodactyla and tests of the molecular clock. Journal of Molecular Evolution 50:1121.
Pitra, C., R. Fürbass, and H.-M. Seyfert. 1997. Molecular phylogeny of the tribe Bovini (Mammalia: Artiodactyla): alternative placement of Anoa. Journal of Evolutionary Biology 10:589600.
Purvis, A. 1995. A composite estimate of primate phylogeny. Philosophical Transactions of the Royal Society of London B 348:405421.
Quérouil, S., R. Hutterer, P. Barrière, M. Colyn, J. C. K. Peterhans, and E. Verheyen. 2001. Phylogeny and evolution of African shrews (Mammalia: Soricidae) inferred from 16s rRNA sequences. Molecular Phylogenetics and Evolution 20:185195.
Robinson, M., F. Catzeflis, J. Briolay, and D. Mouchiroud. 1997. Molecular phylogeny of rodents, with special emphasis on Murids: evidence from nuclear gene LCAT. Molecular Phylogenetics and Evolution 8:423434.
Sæther, B.-E., and I. J. Gordon. 1994. The adaptive significance of reproductive strategies in ungulates. Proceedings of the Royal Society of London B 256:263268.
Springer, M. S., M. J. Stanhope, O. Madsen, and W. W. de Jong. 2004. Molecules consolidate the placental mammal tree. Trends in Ecology and Evolution 19:430438.
Steppan, S. J., R. M. Adkins, and J. Anderson. 2004a. Phylogeny and divergence-date estimates of rapid radiations in muroid rodents based on multiple nuclear genes. Systematic Biology 53:533553.
Steppan, S. J., B. L. Storz, and R. S. Hoffmann. 2004b. Nuclear DNA phylogeny of the squirrels (Mammalia: Rodentia) and the evolution of arboreality from c-myc and RAGI. Molecular Phylogenetics and Evolution 30:703719.
Stoner, C. J., O. R. P. Bininda-Edmonds, and T. Caro. 2003. The adaptive significance of coloration in lagomorphs. Biological Journal of the Linnean Society 79:309328.
Ursing, B. M., and U. Arnason. 1998. Analyses of mitochondrial genomes strongly support a hippopotamus-whale clade. Proceedings of the Royal Society of London B 265:22512255.
Ursing, B. M., K. E. Slack, and U. Arnason. 2000. Subordinal artiodactyl relationships in the light of phylogenetic analysis of 12 mitochondrial protein-coding genes. Zoologica Scripta 29:8388.