Table S1. Species and Tissue Samples Used in This Study, Related to Figure 1 and Experimental Procedures. Provider class. Number of replicates

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1 Tble S1. nd Tissue Smples Used in This Study, Relted to Figure 1 nd Experimentl Procedures common nme scientific nme Age of sexul mturity / lifespn clss Number of replictes Sex Age Age group Tissue preprtion b Humn Hsp Homo spiens 12-1 yers / 80 yers Addenbrookes Hospitl (UK) Hospitl 4 All M unknown dult Mcque Mmul Vervet Csb Mcc multt Chlorocebus ethiops sbeus 4 yers / 20 yers 2- yers / yers Medicl Council (UK) Vervet Colony (US) 4 M, M, M, F unknown, 18,, 11 (yers) dult, juvenile 3 All F 8, 9, 9 (yers) dult Mrmoset Cjc Cllithrix jcchus 1. yers / 12 yers 3 All M unknown dult Mouse Mmus Mus musculus domesticus 6-8 weeks / 1-3 yers Chrles river (UK) 4 All M 10 weeks dult Rt Rnor Rttus norvegicus weeks / 1-3 yers 3 All M 10 weeks dult Guine pig Cpor Cvi porcellus 3- weeks / 4-8 yers 3 All M 10 weeks dult Nked mole rt Hgl Heterocephlus glber 8-12 months / 30 yers UIC (US) 3 All M 1 yer dult Rbbit Ocun Oryctolgus cuniculus -6 months / 8-12 yers 3 All M 7,12,12 (months) juvenile, dults Tree shrew Tbel Tupi belngeri 4- months / 9-12 yers Crdiff University (UK) 3 M, M, F 16, 3, 6 (months) dult, juveniles Cow Btu Bos turus 8-12 months / 1 yers B&K ltd (UK) Commerci l 4 All M 2, 1., 2, 2 (yers) dult S 1

2 common nme scientific nme Age of sexul mturity / lifespn clss Number of replictes Sex Age Age group Tissue preprtion b Dolphin Ddel (short-beked common dolphin nd white-beked dolphin) Sei whle Bbor Sowerby s beked whle Mbid Delphinus delphis Lgenorhynchus lbirostris Blenopter borelis Mesoplodon bidens 12-1 yers / 22 yers uknown / 2 yers 8-10 yers / 0-70 yers 7 yers / unknown UK Cetcen Strndings Investigtion Progrmme, Zoologicl Society of London (UK) Specilised reserch progrmme 1 M unknown dult frozen 1 F unknown dult frozen 1 F unknown juvenile frozen 2 Both F unknown juvenile frozen Pig Sscr Sus scrof 6 months / 10-1 yers 3 All M 2 yers dult Dog Cfm Cnis fmiliris 1 yer / 12-1 yers 3 All M 2., 1, 1 (yers) dult, juveniles Ct Fct Felis ctus -10 months / 1 yers Isoquimen ltd (Spin) 2 Both F 1. yers dult Ferret Mfur Mustel putorius furo 6 months / 8 yers B&K ltd (UK) 3 All M 8, 6, 6 (months) dult, juveniles Opossum Mdom Tsmnin Devil Shr Monodelphis domestic Srcophilus hrrisii 4- months / 4-8 yers 2 yers / -6 yers MRC Ntionl Institute for Medicl (UK) Copenhgen Zoo (Denmrk) 3 All M 6 months juveniles Zoo 2 F, M 8, 7. (yers) dult frozen bbrevitions used in the mnuscript re given in bold b see Extended Experimentl Procedures (Chromtin immunoprecipittion nd high through-put sequencing). S 2

3 Tble S2. Qulity Assessment of Reds Alignments nd Peks Detection, Relted to Figure 1 nd Experimentl Procedures Alignment genome nd version Aligned (%) Control reds b Peks reproducibility (%) c Replicte-specific peks d Uniquely ligned (%) H3K4me3 H3K27c H3K4me3 H3K27c Humn GRCh37.p12/hg ,33 Mcque MMUL1.0/rheMc ,3 10,183 Vervet MMUL1.0/rheMc ,093 9,341 Mrmoset C_jcchus3.2.1/clJc ,49 11,28 Mouse GRCm38.p2/mm ,66 Rt Rnor.0/rn ,2 8,30 Guine pig cvpor ,77 Nked mole rt HetGl1.0/hetGl ,301 Rbbit OryCun2.0/oryCun ,06 14,628 Tree shrew tupbel ,904 6,44 Cow UMD3.1/bosTu ,64 Dolphin turtru ,646 17,022 Sei whle turtru Beked whle turtru ,769 12,377 Pig Sscrof10.2/susScr ,1 9,380 Dog CnFm3.1/cnFm ,608 Ct Felis_ctus_6.2/felCt ,308 8,849 Ferret MusPutFur1.0/musFur ,973 9,420 Opossum mondom ,208 9,717 Tsmnin Devil Devil_7.0/srHr ,23 14, Ensembl genome versions were used, nd the equivlent UCSC genome version is given fter slsh. Both mcque nd vervet ChIP-seq reds were ligned to the Mcc multt mcque genome, nd ll reds from ll cetcen smples were ligned to the Tursiops trunctus dolphin genome. b Averge percentge of reds in the control experiments (totl DNA) tht cn be either ligned or uniquely ligned to the reference genome. c Averge percentge of peks per experiment tht re replicted in t lest one other experiment (see Experimentl Procedures, Short reds lignment nd pek clling). d Averge number of peks specific to n individul, i.e. not replicted in ny other experiment. S 3

4 Tble S3: Assocition Tests between Liver-Specific Genes nd Highly-Conserved or Recently-Evolved Humn Promoters nd Enhncers, Relted to Figures nd 6 Wilcoxon test Men proportion of promoters/enhncers in: Promoters/enhncers ssocited with liver-specific Liver-specific ssocited with promoters/enhncers Genomic elements set Highly-conserved promoters Highly-conserved enhncers Recently-evolved humn promoters Recently-evolved humn enhncers Liverspecific All p-vlue Elements in liversp Totl elements All other elements Totl elements in liversp p-vlue Liversp within All liver-sp All other Genes within ,13 1, , , , , ,363 18, ,084 4, Liver-specific were identified s described in Methods, using publicly vilble expression dt from 16 humn tissues (Petryszk et l., p-vlue 2014). S 4

5 Tble S4. Number of Linege-Specific nd Recently-Evolved Elements Identified in Primtes, Rodents, Ungultes nd Crnivores, Relted to Figure 6 PRIMATES RODENTS UNGULATES CARNIVORES MARSUPIALS PRIMATES RODENTS UNGULATES CARNIVORES MARSUPIALS STRICT ASSESSMENT OF ACTIVITY CONSERVATION (REPRODUCIBLE ORTHOLOGOUS PEAKS) b Promoters c Highlyconservespecifievolveconservespecifievolved Linege- Recently- Enhncers c Highly- Linege- Recently- Humn 11, ,177 10,434 Mcque 10,729 22, Vervet 9,704 16, Mrmoset 10,808 31,649 Mouse 12,443 2,847 18,61 7,930 Rt 13,782 22,471 Guine pig 11,986 2, Nked mole rt 11,300 2, Rbbit 8,790 19,11 1,872 Tree shrew 13,426 19, Cow 12,972 2,108 32,371 13,929 Dolphin 1,019 14,770 Sei whle 17, , Beked whle 11,63 16,432 Pig 10,103 23,822 Dog 10,329 1,793 20,220 9,012 Ct 9, , Ferret 13,140 21,377 Opossum 1,211 23,271 Tsmnin devil 10,496 19,983 LENIENT ASSESSMENT OF ACTIVITY CONSERVATION (ANY SIGNAL AT ANY ORTHOLOGOUS LOCATION) b Promoters c Highlyconservespecifievolved Linege- Recently- Enhncers c Humn 11, ,177 Mcque 10,729 22, Vervet 9,704 16,769 Mrmoset 10,808 31,649 Mouse 12,443 2,602 18,61 Rt 13,782 22,471 Guine pig 11,986 2, Nked mole rt 11,300 2,238 Rbbit 8,790 19,11 2,47 Tree shrew 13,426 19,642 Cow 12,972 1,941 32,371 Dolphin 1,019 14,770 Sei whle 17, ,381 Beked whle 11,63 16,432 Pig 10,103 23,822 Dog 10,329 1,69 20,220 Ct 9, ,238 Ferret 13,140 21,377 Opossum 1,211 23,271 Tsmnin devil 10,496 19, Highlyconserved Linegespecific Recentlyevolved 8,699 6,891 12,111 7, Strict ssessment: n ctive region in species A is defined s conserved in species B if the orthologous locus in species B ws reproducibly ctive in two replictes or more. Lenient ssessment: n ctive region in species A is defined s conserved in species B if ny replicte in species B showed significnt ctivity t the orthologous locus (p < 10 -, no FDR correction). b Reference species in ech linege re indicted in bold. Additionl species in the EPO multiple lignment, used to identify highly-conserved elements, re indicted in blue. c Numbers given re totl promoters or enhncers experimentlly identified from ech species ChIP-seq dt. S

6 Tble S. Assocition Tests between Positively Selected Genes (PSGs) nd Recently-Evolved Enhncers in Nked Mole Rt nd Dolphin, Relted to Figure 7 Wilcoxon test Men proportion of recently-evolved enhncers in: Recently-evolved enhncers ssocited with PSGs PSGs ssocited with recently-evolved enhncers PSG set Recentlyevolved PSGs All p- vlue Rec-ev in Rec-ev enhncers All other enhncers Totl enhncers p- vlue PSGs with rec-ev PSGs All other Genes with rec-ev p- vlue enhncers PSGs in PSGs enhncers enhncers Dolphin_Sun Dolphin Whle_Yim b Dolphin NMR_Kim c Nked mole rt Genes under positive selection in dolphin, s identified in (Sun et l., 2013). b Genes under positive selection in whle (Yim et l., 2014) were used s negtive control. c Positively selected in nked mole rt, originlly identified in (Kim et l., 2011). S 6