Figure S2. - PLOS

ML phylogeny using autosome data partition ABE 1 Alouatta belzebul ACA 3 Alouatta caraya ASA 1 Alouatta sara APL 1 Alouatta palliata ABZ 1 Ateles belzebuth AGO 2 Ateles geoffroyi AFC 7 Ateles fusciceps AHY 1 Ateles hybridus ACM 1 Ateles chamek APC 1 Ateles paniscus BAR 1 Brachyteles arachnoides BHY 1 Brachyteles hypoxanthus LAC 2 Lagothrix cana LLG 1 Lagothrix lagotricha ALM 1 Aotus lemurinus griseimembra ATR 1 Aotus trivirgatus ANA 1 Aotus nancymaae AZA 1 Aotus azarae AZB 1 Aotus azarae boliviensis AZI 1 Aotus azarae infulatus CAI 1 Callithrix aurita CGE 4 Callithrix geoffroyi CJA 1 Callithrix jacchus CPE 10 Callithrix penicillata CKU 1 Callithrix kuhlii CAR 1 Mico argentata MHU 1 Mico humeralifer CPY 5 Cebuella pygmaea CGO 1 Callimico goeldii LCH 1 Leontopithecus chrysomelas LRO 244 Leontopithecus rosalia SBI 1 Saguinus bicolor SSI 1 Saguinus martinsi SMD 1 Saguinus midas SGE 3 Saguinus geoffroyi SOE 3 Saguinus oedipus SIM 2 Saguinus imperator SLA 1 Saguinus labiatus SMY 3 Saguinus mystax SFU 6 Saguinus fuscicollis CAP 13 Cebus apella CRO 1 Cebus robustus CXA 1 Cebus xanthosternos CCP 3 Cebus capucinus CEA 1 Cebus albifrons COV 1 Cebus olivaceus SAU 1 Saimiri ustus SOO 1 Saimiri oerstedii oerstedii SSC 7 Saimiri sciureus SBO 3 Saimiri boliviensis boliviensis CAM 1 Cacajao melanocephalus CCL 1 Cacajao calvus CIS 1 Chiropotes israelita CSA 2 Chiropotes satanas chiropotes PIR 1 Pithecia irrorata PPT 1 Pithecia pithecia CBS 1 Callicebus brunneus CMH 1 Callicebus moloch CCU 2 Callicebus cupreus CCG 1 Callicebus caligatus CDO 1 Callicebus donacophilus CCO 1 Callicebus coimbrai CLP 1 Callicebus personatus CNI 1 Callicebus nigrifrons ANI 1 Allenopithecus nigroviridis CAE 4 Chlorocebus cynosuros CAE 8 Chlorocebus aethiops CSB 1 Chlorocebus sabaeus CIH 1 Cercopithecus lhoesti EPA 9 Erythrocebus patas CAB 1 Cercopithecus albogularis kolbi CMT 1 Cercopithecus mitis CAS 1 Cercopithecus ascanius schmidti CCE 1 Cercopithecus cephus CPP 1 Cercopithecus petaurista petaurista CDA 3 Cercopithecus diana CNE 1 Cercopithecus neglectus CWW 1 Cercopithecus wolfi wolfi CMO 2 Cercopithecus mona CHH 1 Cercopithecus hamlyni hamlyni MOG 1 Miopithecus ogouensis CAC 1 Cercocebus agilis CCY 1 Cercocebus chrysogaster CTR 1 Cercocebus torquatus MLE 2 Mandrillus leucophaeus MSP 12 Mandrillus sphinx LAA 1 Lophocebus albigena LAT 2 Lophocebus aterrimus PAN 10 Papio anubis PHM 1 Papio hamadryas PPP 2 Papio papio TGE 2 Theropithecus gelada MAC 1 Macaca arctoides MTH 3 Macaca thibetana MCY 3 Macaca cyclopis MFS 2 Macaca fuscata MMA 14 Macaca mulatta MFA 18 Macaca fascicularis MCA 1 Macaca maura MTO 6 Macaca tonkeana MNG 3 Macaca nigra Moc 1 Macaca orchreata MNE 5 Macaca nemestrina MSI 7 Macaca silenus MSE 1 Macaca siberu MSY 3 Macaca sylvanus CAN 1 Colobus angolensis palliatus CGU 7 Colobus guereza CPO 2 Colobus polykomos PBD 1 Piliocolobus badius NLA 2 Nasalis larvatus PCN 2 Pygathrix cinerea PNE 2 Pygathrix nemaeus PNI 1 Pygathrix nigripes RBR 1 Rhinopithecus brelichi SEE 1 Semnopithecus entellus entellus SEF 2 Semnopithecus entellus SHE 1 Semnopithecus hector TVV 2 Trachypithecus vetulus monticola TAU 1 Trachypithecus auratus TOB 4 Trachypithecus obscurus TPH 1 Trachypithecus phayrei TDE 1 Trachypithecus delacouri TFR 1 Trachypithecus francoisi THA 1 Trachypithecus hatinhensis PCM 1 Presbytis comata PME 2 Presbytis melalophos GGO 9 Gorilla gorilla HSA 34 Homo sapiens PPN 8 Pan paniscus PTR 104 Pan troglodytes verus PTR 60 Pan troglodytes troglodytes PPY 155 Pongo abelii PPY 157 Pongo pygmaeus HAG 6 Hylobates agilis HMU 6 Hylobates muelleri HLA 1 Hylobates lar SSY 2 Symphalangus syndactylus HCO 3 Nomascus leucogenys NSI 1 Nomascus siki NCN 2 Nomascus concolor NGA 2 Nomascus gabriellae TBA 1 Tarsius bancanus TSY 1 Tarsius syrichta

ALN 1 Avahi laniger PDI 2 Propithecus diadema PED 1 Propithecus edwardsi PTA 1 Propithecus tattersalli PVC 2 Propithecus verreauxi coquereli PVE 1 Propithecus verreauxi EFL 4 Eulemur fulvus ERF 1 Eulemur rufus EFL 15 Eulemur collaris EFL 7 Eulemur albifrons EFL 16 Eulemur sanfordi EMO 1 Eulemur mongoz EMC 1 Eulemur macaco EMC 5 Eulemur macaco flavifrons ECR 2 Eulemur coronatus ERB 4 Eulemur rubriventer HGR 1 Hapalemur griseus HOC 1 Hapalemur occidentalis LCT 10 Lemur catta VVA 2 Varecia variegata variegata VVA 7 Varecia variegata rubra CMD 1 Cheirogaleus medius CMI 3 Microcebus murinus subspecies1 MMR 2 Microcebus murinus subspecies2 MCE 1 Mirza zaza LAN 1 Lepilemur ankaranensis LSP 1 Lepilemur septentrionalis LDO 1 Lepilemur dorsalis LER 1 Lepilemur ruficaudatus LJA 1 Lepilemur jamesi DMD 5 Daubentonia madagascariensis CVA 5 Galeopterus variegatus CVO 1 Cynocephalus volans TGL 4 Tupaia glis TMI 1 Tupaia minor 0.005 substitutions/site

ACL 1 Arctocebus calabarensis PEP 2 Perodicticus potto LTA 2 Loris tardigradus NBE 1 Nycticebus bengalensis NCO 2 Nycticebus coucang NPY 1 Nycticebus pygmaeus GGR 2 Otolemur garnettii OCR 1 Otolemur crassicaudatus GMO 4 Galago moholi GSE 1 Galago senegalensis GTH 1 Galago thomasi

rabbit rabbit