7 Glyceraldehyde 3-Phosphate GAPDH % SYM+G+e NM_ BC JU JU JU %% 45 /

Transcription

1 tropicalis, X. laevis, H. curtipes, P. carvalhoi, and R. dorsalis (ST accession, XL accession, H accession, P accession, and R accession respectively), and number of reads per partition for H. curtipes, P. carvalhoi, and R. dorsalis (H, P, and R respectively). Sequences with portions that have less than 200 base pairs of continuous sequence are not archived by GenBank and the accession number is therefore indicated with "XXX"; these sequences are available in the files in the Dryad database with three "N"s reflecting gaps. ATP Synthase, H+ Transporting, ATP5F HKY+I+d NM_ NM_ JU JU JU06253 %& ' ( Mitochondrial FO Complex, Subunit B 2 Desmin, Gene DES GTR+G+d NM_ NM_ ))) ))) ))) *+ %, *& 3 Scaffold Attachment Factor A SAF-A GTR+I+d BC BC ))) ))) ))) ** ( ' 4 Ribosomal Protein L4 RPL GTR+G+d BC NM_ JU06263 JU0626 JU06262 *-( -+ *, 5 Elongation Factor- Delta EEFD HKY+I+d NM_ BC JU06266 JU JU * 6 Fragile X Mental Retardation, FXR 7 ** GTR+G+d XM_ BC3884. ))) ))) ))) & ( Autosomal Homolog 7 Glyceraldehyde 3-Phosphate GAPDH % SYM+G+e NM_ BC JU06260 JU JU %% 45 / Dehydrogenase 8 Hematopoietic Prostaglandin D HPGDS &+ GTR+G+d NM_ NM_ JU JU JU (' 68 + Synthase 9 Heat Shock 70kDa Protein 9 HSPA %, GTR+I+d NM_ NM_ JU JU JU *- 3 ' 0 Poly(A) Binding Protein, PABPC / GTR+G+d NM_ NM_ JU JU06264 JU *& +( & Cytoplasmic Ferritin Light Chain FERRITIN * K80+I+e NM_ NM_ JU JU JU ** * ' 2 Proteasome (Prosome, PSMD HKY+G+d CR BC ))) ))) ))). 5 / Macropain) 26S Subunit, Non- ATPase, 3 Ribosomal Protein L5 RPL %, K80+I+e NM_ NM_ JU JU JU ** Ribosomal Protein S3 RPS %( SYM+G+e NM_ BC JU JU JU06262 %& 2 / 5 Uncoupling Protein 2 UCP GTR+G+d NM_ NM_ JU JU JU **& / * (Mitochondrial, Proton Carrier) 6 Adiponectin Receptor 2 ADIPOR HKY+I+d XM_ NM_ ))) ))) ))) & * % 7 Eukaryotic Translation EEFG (+ GTR+I+d NM_ NM_ JU JU JU /- /( ( Elongation Factor Gamma 8 Heterogeneous Nuclear HNRPDL 05 6 *% HKY+I+d NM_ NM_ ))) ))) ))) + ' * Ribonucleoprotein D-like 9 Heat Shock 70kDa Protein 5a N/A *. SYM+G+e XM_ NM_ ))) ))) ))) +/ %% & 20 Heat Shock 70kDa Protein -like HSPAL & GTR+G+d XM_ NM_ JU JU JU '( *% *% 2 Ribosomal Protein S6 RPS GTR+G+d NM_ NM_ JU JU JU & -% - 22 ATP Synthase, H+ Transporting, ATP5C %+ GTR+G+d NM_ NM_ JU JU JU (- %% % Mitochondrial F Complex, Gamma Polypeptide 23 Acyl-CoA Dehydrogenase, C-4 ACADM %. GTR+I+d XM_ NM_ JU06254 JU JU *. % to C-2 Straight Chain 24 Prolyl 4-Hydroxylase, Beta P4HB 35 3 ' GTR+G+d BC6026. NM_ ))) ))) ))) (/ ( ** Polypeptide 25 Phosphatidylethanolamine PEBP 05 7 *, K80+I+e NM_ NM_ ))) ))) ))). %, - Binding Protein 26 Peptidylprolyl Isomerase B PPIB 05 2 ' K80+I+e NM_ NM_ ))) ))) ))) (+ ( ( (Cyclophilin B) 27 Staphylococcal Nuclease and SND *+ GTR+G+d NM_ NM_ JU JU JU */ - - Tudor Domain Containing 28 Small Nuclear Ribonucleoprotein SNRPD *( K80+I+e NM_ NM_ ))) ))) ))) * - * D3 Polypeptide 8kDa 29 Keratin 9 KRT %, HKY+I+d NM_ NM_ ))) ))) ))) && *+ *

2 30 ATP Synthase, H+ Transporting, ATP5O K80+G+e NM_ BC JU JU JU %& '( ' Mitochondrial F Complex, O Subunit 3 Basic Transcription Factor 3 BTF HKY+I+d NM_ NM_ ))) ))) ))) %( '* ' 32 Tubulin, Alpha 3C TUBA3C SYM+I+e BC NM_ JU JU JU %+,, 33 Pinin, Desmoaome Associate protein PNN HKY+G+d NM_ NM_ JU JU JU '- ' ( 34 DEAD (Asp-Glu-Ala-Asp) Box DDX HKY+G+d NM_ NM_ JU06257 JU06255 JU06256 *, '& ( Polypeptide 2 35 Ribosomal Protein S27a RSPS27A K80+G+e NM_ NM_ ))) ))) ))) '+ %% % 36 LUC7-like LUC7L 23 2 K80+I+e NM_ NM_ ))) ))) ))), ' % 37 Glutaminyl-tRNA Synthetase QARS K80+G+e XR_ NM_ ))) ))) ))) '* ' ( 38 Amyloid Beta (A4) Precursor-like APLP SYM+G+e XM_ AJ ))) ))) ))) '*, ' Protein 2 39 DEAD (Asp-Glu-Ala-Asp) Box DDX3X GTR+G+d NM_ NM_ ))) ))) ))) + ' '- Polypeptide 3, X-linked 40 Glycoprotein, Synaptic 2 GPSN GTR+I+d NM_ NM_ ))) ))) ))) ' %. 4 NDP Dipeptidase 2 CNDP SYM+G+e NM_ NM_ ))) ))) ))). ( ' (Metallopeptidase M20 Family) 42 Ribosomal Protein L8 RPL K80+G+e NM_ X JU06257 JU JU (. (, + 43 Nonmuscle Myosin II Heavy Chain A MYH SYM+I+e XM_ BC ))) ))) ))) '/ '', 44 Stress-Induced-Phosphoprotein STIP GTR+G+d NM_ NM_ ))) ))) ))) %/ + ( 45 Nucleosome Assembly Protein -Like NAPL GTR+G+d NM_ NM_ JU JU JU06250 ** */ +, Transcript Variant 2 46 Non-Metastatic Cells 2, Protein NME2 4 0 SYM+G+e NM_ BC ))) ))) ))) %+ (, * (NM23B) Expressed In (NME2) 47 RNA Binding Motif Protein 39 RBM GTR+G+d NM_ NM_ ))) ))) ))) ' ' ( 48 Ribosomal Protein L3 RPL GTR+I+d NM_ NM_ JU JU JU &* *+ * 49 Ribosomal Protein S20 RPS SYM+I+e NM_ BC JU JU JU *- *& % 50 Tyrosine 3- YWHAB K80+G+e NM_0006. NM_ ))) ))) ))) ' %. % Monooxygenase/Tryptophan 5- Monooxygenase Activation Protein, Beta Polypeptide 5 Chromosome 4 Open Reading C4ORF 53 3 GTR+G+d XM_ NM_ ))) ))) ))) (. % Frame Ribosomal Protein S7 RPS GTR+I+d NM_ NM_ JU JU JU062588,. */ % 53 Heat Shock Protein 90kDa Beta HSP90B GTR+G+d BC2250. NM_ ))) ))) ))) '*/ /( ( (Grp94), Member 54 Ribosomal Protein SA RPSA SYM+I+e NM_ NM_ JU JU JU (/ ++ ( 55 Tubulin, Beta 3 TUBB K80+G+e NM_ BC JU JU JU % ( / 56 Ribosomal Protein S5 RPS K80+I+e BC6332. NM_ ))) ))) ))) +%,& + 57 Ribosomal Protein L27 RPL K80+I+e NM_ NM_ ))) ))) ))) (- (* ' 58 Ribosomal Protein L27a RPL27A GTR+G+d NM_ NM_ JU JU JU %/ %, % 59 40S Ribosomal Small Subunit Protein S0 RPS SYM+G+e NM_ BC ))) ))) ))) (- '+ ' 2

3 60 NSA2 Ribosome Biogenesis NSA HKY+G+d NM_ NM_ %%% %%% %%% &' &( ) Homolog 6 Cytochrome C Oxidase Subunit COX5A GTR+I+d NM_ NM_ %%% %%% %%% ' )* & Va 62 Ribosomal Protein L26 RPL GTR+G+d NM_ BC JU06254 JU06252 JU ,,' + 63 Eukaryotic Translation Initiation EIF3E HKY+G+d BC BC JU JU JU )-. + Factor 3, Subunit E 64 Ribosomal Protein L7 RPL GTR+G+d NM_ NM_ JU JU06255 JU (.,' + 65 Pancreatic Progenitor Cell PPDPF K80+I+e NM_ NM_ %%% %%% %%% ) ( & Differentiation and Proliferation Factor Homolog 66 Aminoacyl trna Synthetase AIMP SYM+I+e NM_ NM_ %%% %%% %%% ) - ) Complex-Interacting Multifunctional Protein 67 Ribosomal Protein, Large, P0 RPLP SYM+G+e NM_ NM_ JU JU JU (* (*. 68 Eukaryotic Translation EEFA SYM+G+e BC BC3044. JU JU JU /& )*' &+ Elongation Factor Alpha 69 Transketolase TKT K80+G+e NM_ NM_ JU JU JU ' ++, 70 H3 Histone, Family 3A H3F3A SYM+I+e NM_ NM_ %%% %%% %%%. + & 7 Tripartite Motif-Containing 7 TRIM K80+I+e XM_ NM_ %%% %%% %%% ) ) & 72 Methionine Aminopeptidase 2 METAP GTR+G+d XM_ NM_ %%% %%% %%% ). ), 73 Ribosomal Protein S4, X-Linked RPS4X SYM+I+e NM_ NM_ JU JU JU &-,/. 74 Chaperonin Containing TCP, CCT GTR+G+d NM_ NM_ JU JU JU )) ) ) Subunit 5 75 Alcohol Dehydrogenase B ADHB GTR+G+d NM_ BC %%% %%% %%% - &/ ) (Class I), Beta Polypeptide 76 Ribosomal Protein S3A RPS3A GTR+G+d NM_ NM_ JU JU JU062528,/ &). 77 Actin, Alpha 2, Smooth Muscle, ACTA SYM+G+e NM_ NM_ %%% %%% %%% ) ) &, Aorta 78 Actin, Gamma ACTG GTR+I+d NM_ NM_ JU06263 JU JU )* &, 79 Glutamyl-Prolyl-tRNA EPRS GTR+G+d XM_ NM_ %%% %%% %%% )& )& ( Synthetase 80 ATP Synthase, H+ Transporting, ATP5B GTR+I+d NM_ NM_ JU JU JU062636,, &. ) Mitochondrial F Complex, Beta Polypeptide 8 ATP Synthase, H+ Transporting, ATP5G SYM+I+e BC NM_ JU JU JU062558,&,&, Mitochondrial Fo Complex, Subunit C3 (Subunit 9) 82 Ribosomal Protein S25 RPS GTR+G+d NM_ NM_ %%% %%% %%% (, +* ) 83 Solute Carrier family 25 SLC25A HKY+G+d NM_ NM_ JU JU06258 JU ,,* ' (Mitochondrial Carrier; Phosphate Carrier), Member 3 84 Ribosomal Protein L37a RPL37A K80+I+e NM_ NM_ %%% %%% %%% &/ &* ) 85 Heat Shock 70kDa Protein HSPA K80+G+e XM_ NM_ JU JU JU ) / )' 86 GTP Binding Protein 4 GTPBP GTR+I+d XM_ NM_ *.&..( 0*.&..& 0*.&.., ),,' )* 87 DEAD (Asp-Glu-Ala-Asp) Box DDX GTR+G+d XM_ BC %%% %%% %%% )) )& & Polypeptide 46, Transcript Variant 2 88 Radixin RDX 20 HKY+G+d XM_ BC %%% %%% %%% ) ) & 3

4 GHIIJ2528:9KL;M96J2;'F;N48:78H2AF 89 Alcohol Dehydrogenase 5 (Class ADH GTR+I+d NM_0005 AY JU06269 JU06267 JU06268 %& % % III), Chi Polypeptide Tubulin, Beta 2B TUBB2B SYM+I+e NM_ NM_ JU06266 JU06264 JU06265 ' ' ( 9 Epiplakin EPPK K80+G+e BC BC ))) ))) ))) * + % 92 Moesin MSN K80+I+e XM_ NM_ ))) ))) ))) ', & % 93 Arginyl-tRNA Synthetase RARS K80+G+e NM_ BC ))) ))) ))) '- ' ' 94 Tubulin, Alpha 4b TUBA4B GTR+G+d BC705. NM_ ))) ))) ))) & *. 95 Nuclear Receptor Coactivator 2 NCOA HKY+G+d NM_0042 NM_ ))) ))) ))) * * % 96 Transaldolase TALDO HKY+G+d NM_ NM_ JU JU06252 JU ', & ' 97 Coiled-Coil Domain Containing CCDC09B K80+I+e NM_ NM_ ))) ))) ))) ' ' ' 09B Enhancer of Polycomb Homolog EPC HKY+I+d NM_ NM_ ))) ))) ))) ' & % Ribosomal Protein L23 RPL HKY+I+d NM_0002 NM_ JU JU JU06256 '+ %/ ' 00 Heat Shock Protein 90kDa Alpha HSP90AA SYM+G+e NM_ NM_ JU JU JU '-, /% '- (Cytosolic), Class A Member, Gene Glucose-6-Phosphate Isomerase GPL SYM+I+e NM_0000 NM_ ))) ))) ))) %+ ' ' 02 RAB0, Member RAS Oncogene RAB HKY+G+d NM_00267 NM_ ))) ))) ))) ' ' ' Family Ribosomal Protein L3 RPL GTR+G+d NM_00266 NM_ JU06260 JU JU /* %/ ( 04 Eukaryotic Translation Initiation EIF3M GTR+G+d NM_ NM_ ))) ))) ))) '. /. Factor 3, Subunit M Ribosomal Protein L0a RPL0A HKY+G+d NM_00265 NM_ JU JU06258 JU06259 &, /-, 06 Seryl-tRNA Synthetase SARS K80+G+e BC NM_ ))) ))) ))) '* ' ' 07 Vesicle-Associated Membrane N/A GTR+G+d NM_ NM_ % %++/ 0-+%+++ &/ %, ' Protein-Associated Protein B/C $ :748;<3:7=9:78>;?282@; ';98A;% <B,.&*-/C; DE/*/(/+ <B,.&*-*C; JU DE/*/(-'F' C;DE/*/(// 09 Solute Carrier Family 8 (Sodium/Calcium Exchanger), Member 3 0 Chemokine (C-X-C Motif) Receptor 4 RAG,RAG GTR+I+d XP_ , XP_ SLC8A GTR+G+d XM_ NM_ , NM_ NM_ EF EF0735. AY CXCR GTR+G+d NM_ NM_ AY AY AY Histone H3.2-Like H2A GTR+G+d XM_ BC0843. JU JU DQ Sodium/Calcium Exchanger NCX GTR+I+d AY X AY AY5237. AY Gene, Exon 2 3 Rhodopsin RHO HKY+G+d NM_ NM_ DQ DQ DQ Mitochondrial DNA 2S,6S GTR+G+d AY AY AY58623 AY5862 AY

5 Supplemental Figure : Posterior densities of mutation rates from *BEAST analysis 3 with the HKY codon model. An arrowhead indicates the posterior density for the loop region of the mitochondrial DNA rdna Posterior density Mutation rate (substitutions per site per billion years) 5

6 Supplemental Figure 2: Posterior densities of relative mutation rate from *BEAST analysis 3 with the HKY codon model for (A) the first codon position, (B) the second codon position, and (C) the third codon position of the 3 autosomal partitions. 30 A Posterior density 80 0 B 0 0 C Relative mutation rate 6

7 Correction terms for *BEAST analyses *BEAST Analysis correction term The analysis has five taxa with an outgroup, or four taxa monophyly, and the calibration is on the parent of Pipa. There are 6 3 ranked trees: 9 of those have 3 internal nodes above the calibrated parent, 6 have 2 above and below, and the remaining 3 have 2 below and one (the root) above. As described in Appendix 3 of Heled and Drummond (20), the total density for a above ) and b below is: λh e λ(a+)h e λh b f a,b (h) =λe (a +)! b! So the total correction is: f(h) = 5! 8 (9f 3,0(h)+6f 2, (h)+3f,2 (h)) = 5λe 3λh e 2λh 4e λh +6 6 *BEAST Analysis 2 correction term The correction term for this analysis is given by equation in Heled and Drummond (20) *BEAST Analysis 3 correction term The total per case is: e λh e 0 λh a e λh 0 b f a,b (h 0,h )=λe 2λh 0 λe λh dand total the correction total correction is is: (a )! f(h 0,h )= 5! 8 (9f 3,0(h 0,h )+6f 2, (h 0,h )+3f,2 (h 0,h )) =0e λ(h +2h 0 ) e λh 0 +2e λh 3e λh 0 b! 7