Supplemental Table S2



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Supplemental Table S2








H1/H2/H3




Warren et al. 2008

3 / 0

Theria monophyly / paraphyly

Kriegs et al. 2006

4 / 0

Placentalia monophyly / paraphyly

this study

5 / 9 / 8

Exafroplacentalia/Epitheria/Atlantogenata

Kriegs et al. 2006

0 / 2 / 0

Exafroplacentalia/Epitheria/Atlantogenata

Murphy et al. 2007

0 / 0 / 2

Exafroplacentalia/Epitheria/Atlantogenata

Krull et al. 2007

5 / 0

Xenarthra monophyly / paraphyly

Nishihara et al. 2005

Nishihara et al. 2006



7 / 0

Afrotheria monophyly / paraphyly

Kriegs et al. 2006

Nishihara et al. 2006



21 / 0

Boreotheria monophyly / paraphyly

Kriegs et al. 2006

Nishihara et al. 2006



13 / 0

Laurasiatheria monopyhly / paraphyly

Kriegs et al. 2006

Nishihara et al. 2006



16 / 0

Supraprimates monophyly / paraphyly

(Euarchontoglires)



Nishihara et al. 2006

4 / 1

Pegasoferae monophyly / paraphyly

Kriegs et al. 2007

5 / 0

Euarchonta monophyly / paraphyly

Nishihara et al. 2006

Kriegs et al. 2007



11 / 0

Glires monophyly / paraphyly

Martignetti and Brosius 1993

Farwick et al. 2006



2 / 0

Rodentia monophyly / paraphyly

Schmitz et al. 2002

4 / 0

Primate monophyly / paraphyly

Other supportive/conflicting patterns of diagnostic retroposon insertions in higher level-mammalian clades. Alternative hypotheses (H1-3). Gray backgrounds denote conflicting splits.


Literature

Farwick, A., Jordan, U., Fuellen, G., Huchon, D., Catzeflis, F., Brosius, J., and Schmitz, J. 2006. Automated scanning for phylogenetically informative transposed elements in rodents. Syst. Biol. 55: 936-948.

Kriegs, J.O., Churakov, G., Jurka, J., Brosius, J., and Schmitz, J. 2007. Evolutionary history of 7SL RNA-derived SINEs in Supraprimates. Trends Genet. 23: 158-161.

Kriegs, J.O., Churakov, G., Kiefmann, M., Jordan, U., Brosius, J., and Schmitz, J. 2006. Retroposed elements as archives for the evolutionary history of placental mammals. PLoS Biol. 4: e91.

Martignetti, J.A. and Brosius, J. 1993. BC200 RNA: a neural RNA polymerase III product encoded by a monomeric Alu element. Proc. Natl. Acad. Sci. 90: 11563-11567.

Moeller-Krull, M., Delsuc, F., Churakov, G., Marker, C., Superina, M., Brosius, J., Douzery, E.J., and Schmitz, J. 2007. Retroposed elements and their flanking regions resolve the evolutionary history of xenarthran mammals (armadillos, anteaters, and sloths). Mol. Biol. Evol. 24: 2573-2582.

Murphy, W.J., Pringle, T.H., Crider, T.A., Springer, M.S., and Miller, W. 2007. Using genomic data to unravel the root of the placental mammal phylogeny. Genome Res. 17: 413-421.

Nishihara, H., Hasegawa, M., and Okada, N. 2006. Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions. Proc. Natl. Acad. Sci. 103: 9929-9934.



Schmitz, J. and Zischler, H. 2003. A novel family of tRNA-derived SINEs in the colugo and two new retrotransposable markers separating dermopterans from primates. Mol. Phylogenet. Evol. 28: 341-349.

Warren, W.C. Hillier, L.W. Marshall Graves, J.A. Birney, E. Ponting, C.P. Gruetzner, F. Belov, K. Miller, W. Clarke, L. Chinwalla, A.T. et al. 2008. Genome analysis of the platypus reveals unique signatures of evolution. Nature 453: 175-183.

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