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Mertensiella luschani Xenopus laevis Agkistrodon piscivorus Ovophis okinavensis Pantherophis guttatus Dinodon semicarinatus Boa constrictor Python regius Xenopeltis unicolor Cylindrophis ruffus Acrochordus granulatus Leptotyphlops dulcis Typhlops reticulatus Rhineura floridana Geocalamus acutus Amphisbaena schmidti Diplometopon zarudnyi Bipes tridactylus Bipes canaliculatus Bipes biporus > 1.0 0.8 - 1.0 0.0 - 0.8 0.1 sub./site Iguana iguana Sceloporus occidentalis Anolis carolinensis Abronia graminea Ophisaurus attnuatus Varanus komodoensis Varanus salvator Shinisaurus crocodilurus Cordylus warreni Eumeces egregius Sphenodon punctatus Caiman crocodilus Alligator sinensis Alligator mississippiensis Gavialis gangeticus Crocodylus moreletii Tinamus major Dromaius novaehollandiae Apteryx haastii Struthio camelus Rhea americana Smithornis sharpei Corvus frugilegus Vidua chalybeata Buteo buteo Ciconia ciconia Ciconia boyciana Falco peregrinus Gallus gallus Dogania subplana Chrysemys picta Chelonia mydas Pelomedusa subrufa Bos taurus Hylobates lar Gorilla gorilla Homo sapiens Pan paniscus Pongo pygmaeus Papio hamadryas Macaca sylvanus Cebus albifrons Lemur catta Nycticebus coucang Tarsius bancanus Figure S7. Results of traditional dN/dS estimates for the COI gene using the alternative (mitochondrial gene-based) topology from Fig. S1, with branches colored based on dN/dS ratios. Branch lengths are based on all mitochondrial protein-coding genes, optimized on this topology in PAUP* under a GTRI model. Estimates of dN/dS are from codon model-based analyses conducted HyPhy (See Supplementary Methods).