Additional file 2.

Phylogenies for each vertebrate clade. Supplemental figures S1 through S39. Phylogenies for each sampled vertebrate clade based on a partitioned Bayesian analysis of combined data (first tree), mitochondrial DNA (second tree), and nuclear DNA (third tree). An asterisk next to a node indicates strong support, (Pp) ≥ 0.95. Small white circles on a node indicate (Pp) < 0.95 and these values are listed. Integers next to each node in the combined tree correspond to clade numbers used in analyses. The outgroup taxa are excluded for all groups to facilitate presentation of branch lengths, and the root is indicated with an open circle. Figures S1, S2, S3: balistid fish; Figures S4, S5, S6: scarine fish; Figures S7, S8, S9: hemiphractid frogs; Figures S10, S11, S12: hylid frogs; Figures S13, S14, S15: phrynosomatid lizards; Figures S16, S17, S18: alcid birds; Figures S19, S20, S21: caprimulgid birds; Figures S22, S23, S24: cotingid birds; Figures S25, S26, S27: dicaeid birds; Figures S28, S29, S30: emydid turtles; Figures S31, S32, S33: cervid mammals; Figures S34, S35, S36: murid rodents (Philippines); Figures S37, S38, S39: murid rodents (Sahul = Australia-New Guinea). PDF file.

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Fisher-Reid and Wiens BMC Evolutionary Biology 2011 11:300   doi:10.1186/1471-2148-11-300