Additional file 9 - Alignment and parameters used to infer phylogeny from Figure 5. #NEXUS begin mrbayes; set autoclose=yes nowarn=yes; BEGIN DATA; dimensions ntax=11 nchar=930; format missing=? interleave datatype=PROTEIN gap= -; matrix DEREC_2z3cvj MINGLSVGGGQQVAQVTP----TGAAIKLHFAYN-NSNN----NSSSNKN DYAKU_crjp9x MINGLSVGGGQQVAQVTP----TGAAIKLHFAYN-NSNNSSSNNSSSNNN DMELA_crjnm1 MINGLSVGGGQQVAQVTP----TGAAIKLHFAYNNNSNNS---SSSNISN DPSEU_9p8n96 MINGLSVGGGQQQAAANTKAKSSGAAITLHFTYNNNNNNSNSNNISSRSN DVIRI_cnpf85 MINSFSVAGAGAGAAATA-------AITLHFNYNNNSSSS---NNNNNNN AAEGY_vq89q9 MANSVSS---HFGDRIIN-----------MLGSPDQQQSTSDSGVNGNNN CQUIN_8czhs6 MNSTCNQSDQHNSDVKGN-----------SAGSPNQQ-----SGMNGNNN Anste_SoxY MLQNSAFGTPMLDGKPVLP----------EIYSHHQTLDK--LDIVAEPQ Anste_SoxA MLQNSAYGTPLLDGKPVLP----------EINSHHQTVDK--LDTVAEPQ AGAMB_zkh7tk MIQNSAYGNPMLDGASAFP----------DIYIQHQSADK--PDGPP-PS AGAP003896-PA MIQNSAYGNPMLDGASAFP----------DIYIQHQSADK--PDGPP-PS DEREC_2z3cvj --NYNNLK-----TAEPKMSNNK--HYAGRALKIVEKIPGASGVIAATNA DYAKU_crjp9x I-NYSGLK-----TAEPKMSNNK--NYTARALKIVEKIPRASGVIAATSV DMELA_crjnm1 S-NYSGLK-----TSETKMRNNK--NYTGRALKIVEKIPGASGVIATTSG DPSEU_9p8n96 NKNYNNQNHISGHKMDHQMNNNQKESLSTKVLKIIESIRGGGGEAAEAAT DVIRI_cnpf85 N-NSSGIKIVPAASNEHKSQSLIN-NAAPATTKAETNTTTTPKIFQITST AAEGY_vq89q9 LKSFVNNN-----------------IATSDNSNYNVNSHQTKNAASYCLT CQUIN_8czhs6 VKSYVNNN-----------------TATV-NHNYSVNSQQTKNAASYGFT Anste_SoxY QLTIYNNN-----------------NADIAYRNSSSILAPPRYAVERSTP Anste_SoxA QLTICNNN-----------------NANIANRNSTSIVAPPRYAVETPAP AGAMB_zkh7tk NNNIANYT-----------------NRNSGYPYQTCVAPAPARPLVARES AGAP003896-PA NNNIANYT-----------------NRNSGYPYQTCVASAPASLVVARES DEREC_2z3cvj NQGAGSLVGFSPATASYVSGLSRDFLISRELSQRSGDFLT-AAAKMVSQM DYAKU_crjp9x NQGAGSLVGFSPATASYVSGLSRDFLISRELSQRSGDFLT-AAAKMVSQM DMELA_crjnm1 NQGARSLEGYSPAAASYVSGLSRDFLISRELSQRSGEFLT-AAAKMVSQM DPSEU_9p8n96 GKTA-TIAG-TPKAVEDATGGS----VGGGVA--SLNLLP-MPIRRTSLL DVIRI_cnpf85 EVEAKHFLMTFPQQQQQQQQQQQ---QPKQKAGASLKWMPPGKVNTSAST AAEGY_vq89q9 LQNSISLYNFYAKNDKR------------------------DATKEESTS CQUIN_8czhs6 LQKSITMFNLYAKKDKR------------------------DATKEFVVP Anste_SoxY TVEHDVWYG---RLLDHT-----------------------NYTRHTPEP Anste_SoxA TVERDGWYG---RLLDHT-----------------------NYTRHTPEP AGAMB_zkh7tk CVRAEIVKDTQDLAVEFR-----------------------QLSHNVPIK AGAP003896-PA CVRAEIVKDTQDLAVEFR-----------------------QLSHNVPIK DEREC_2z3cvj GAGELRWMPMPRT-KDKPSN---AEAKTL--EREAHGSPENAAKSALADP DYAKU_crjp9x GASELRWLPMPRT-KDKPSNAEEAETKTLVRERDEHGSPGKAAKSALADP DMELA_crjnm1 GASELRWLPISRT-KDKPSSAGEAEAKTLVREGESQGSPGKVAKSALGDP DPSEU_9p8n96 HQAISSTSAITKE-KERPQQ-KTAKPPALALPLLSL-TPQKQQPEPHQGH DVIRI_cnpf85 KEPQLRQVSIQSSSNNKQQQQQQQLQLATTTTGLAKSAFIEAWTMPQQQQ AAEGY_vq89q9 SSTITGNMVDQKDTVDGSQQ------------------KSTIISTTLSTN CQUIN_8czhs6 KDISLNPMTTNKD--QG-----------------------------WSVS Anste_SoxY AAHDVQP-----------------------------------------LK Anste_SoxA AAHDVQP-----------------------------------------LK AGAMB_zkh7tk TEHCIANN----------------------------------------VG AGAP003896-PA TEHCIANN----------------------------------------VG DEREC_2z3cvj QPQRTEDQENAFRRIEDVHNYAKLQD--------------------CSSD DYAKU_crjp9x QPQRTEDQENAFRRIEDVHNYAKLQD--------------------CSSD DMELA_crjnm1 QPQRTEDQENAFRRIEDVHNYAKLQD--------------------CSSD DPSEU_9p8n96 QPQRTEDQEHAFRLVEDVHNYAKLQD--------------------YSED DVIRI_cnpf85 QQQRTEDQENAFRQIEDVHNYAKLQHHHQQQQQQQQQQQQHQHQHSSSSE AAEGY_vq89q9 VHSNMNDLQNQH------HNYSKSYD--------------------SQPD CQUIN_8czhs6 GNS-SNDLQNQH------HNYSKSCH--------------------SNED Anste_SoxY TENNTSQRNDE-----ITPNAADGEE------------------------ Anste_SoxA TEDNTSQRNDE-----ITPNAADGEE------------------------ AGAMB_zkh7tk QGMATNETGGEL---GITTARPKASD------------------------ AGAP003896-PA QDMATNETGGEL---GITTARPKASE------------------------ DEREC_2z3cvj TDDED--DEEEDLDEEEEDDEEEEEA--EIQVQLPVQQEVTRIRREAAEE DYAKU_crjp9x TEDED--DEEEDLDEEEDD---EEEA--DIQVQLPVQQEVTRIRREAAEE DMELA_crjnm1 TDDED--DEEEDLDEEEDD---EEEA--EIQVQLPVQQEVTRIRREAAEE DPSEU_9p8n96 -DGEDLLDDDEDNDDDDDD---EEEQ--QMTVPMRVQ-EVTRIQLEDTEE DVIRI_cnpf85 LGEEDEEDDDDDDDEEDEDDDEEEERGREPTKKTHLNVPINTNNDDDSEE AAEGY_vq89q9 -----------------------------------LKLDTSCDDPIDSDD CQUIN_8czhs6 -----------------------------------VKSEIA-NDPSNDED Anste_SoxY --------------------------------------VLIGTCQQ---- Anste_SoxA --------------------------------------LLIGTCQQ---- AGAMB_zkh7tk --------------------------------------QMLQTVDQKPYE AGAP003896-PA --------------------------------------QMLQTVDQKPYE DEREC_2z3cvj HVDVDVVTVPQPEQ--------------DQDSHQVEPRQLQQ-DQAADTT DYAKU_crjp9x HVDVDVVTVPQQEQ--------------DQESHQVEPQQHQQ-DQATDTT DMELA_crjnm1 HVDVDVVTVPQQEQ--------------DQYSHQVEPRQLQQ-DETADNT DPSEU_9p8n96 HVDV--VTVPQQEL--------------VQQKLQLEPTAVGSPNNETGDR DVIRI_cnpf85 HVEVDVVTVTPTATTVATAAAAAAAAAATAPQLQLQQEQLMS-KVDQEHM AAEGY_vq89q9 HATTDSMNDYVSPA--------------KQSSSSDHIARSQQ---NATPT CQUIN_8czhs6 HFPED--TDSAVAC--------------ENESLAAKPDDFPP---ALSTA Anste_SoxY ----HMVPHAQTP-----------------AEEATQPQDNIA---AAVAC Anste_SoxA ----HMVPHAQTP-----------------AEEVTQPQDNIA---AAVAC AGAMB_zkh7tk AFTHQSITYVQTPA---------------AAGEEREPEDEQD---VGVKA AGAP003896-PA AFTHQSITYVQTPA---------------AAGEEREPEDEQD---VGAKA DEREC_2z3cvj RPEH--HARRPMNAFLIFCKRHRGIVKERYKTLENRAITKILGDWWAALD DYAKU_crjp9x RPEH--HARRPMNAFLIFCKRHRGIVKERYRTLENRAITKILGDWWAALD DMELA_crjnm1 RPEH--HARRPMNAFLIFCKRHRGIVKERYKTLENRAITKILGDWWAALD DPSEU_9p8n96 RPEH--HARRPMNAFLIFCKRHRAIVKERYKSLENRAITKILGDWWAALD DVIRI_cnpf85 RPEH--HARRPMNAFLIFCKRHRAIVKERYKSLENRAITKILGDWWAALD AAEGY_vq89q9 TPDH--HARRPMNAFLIFCKRHRTIVRDRHPNLENRSITKILGDWWANLD CQUIN_8czhs6 TPDH--HARRPMNAFLIFCKRHRTIVRDRHPNLENRSITKILGDWWANLD Anste_SoxY RPKKKAGQRRPMNAFILFCKRHRSVLKEHYPE-ENRETTKKLGKWWKNAT Anste_SoxA SPKKKAGQRRPMNAFLLFCKRHRSVLKEHYPE-ENRAITKKLGKWWKNAT AGAMB_zkh7tk SPKK--EQRRPMNAFLIFCKRHRTMLKNRFPE-ENRAISIKLGKWWRMLT AGAP003896-PA SPKK--EQRRPMNAFLIFCKRHRTMLKNRFPE-ENRAISIKLGKWWRMLT DEREC_2z3cvj EQEKHCFTDLAQQNKDAFFNANPNFKWYKLPAPPLRTL-------ATRPS DYAKU_crjp9x EQEKHCFTDLAQQNKDAFFNANPNFKWYKLPAPPLRTL-------ATRPS DMELA_crjnm1 EQEKHCFTDLAQQNKDAFFNANPNFKWYKLPAPPLRTL-------ATRPS DPSEU_9p8n96 EQEKHCFTDLAQQNKDAFFNANPNFKWYKLPAPPLRTL-------ATRPG DVIRI_cnpf85 EQEKQCFTDLAQQNKDAFFNANPNFKWYKLPAPPLRTL-------ATRPS AAEGY_vq89q9 KDQKASYTNLAKQYKDAFFTAHPDFKWYKLPAPPLRPQ--GIRPVKTEPS CQUIN_8czhs6 KEQKSNYTNLAKQYKDAFFTAHPDFKWYKLPAPPLRPPSFGARIVQPEPT Anste_SoxY AKQKKPYQLLAEKNKTKFLDVNPSFRWCKSSTMASCDK-------NVDDE Anste_SoxA AEQKKPYQLLAEKNKTKFLDVNPGFRWCKSSTMASCDK-------NVDGE AGAMB_zkh7tk TEQKKPFQLLSKEYKNKYLSLNPNFRWCKQPMVPATPS-------TPSPL AGAP003896-PA TEQKKPFQLLSKEYKNKYLSLNPNFRWCKQPMVPATPS-------TPSPL DEREC_2z3cvj ---------------NAAAALL--IPNEDQPQQQVPTSLQMQWAERGEMP DYAKU_crjp9x ---------------NAAAGLL--IPSEEQPQQHVPASLQMQWAERGEMP DMELA_crjnm1 ---------------NASAGLL--IPSEDQPQQQVPTSLQVQWAERGEMP DPSEU_9p8n96 ---------------NAATPAIGGHLTDENPQ-NTQQQVQLQW-ERNELH DVIRI_cnpf85 ---------------NASTGQI----NEEPLQPHAPQQ-HLQWAPNDVAH AAEGY_vq89q9 GLGSEYEYGYGISYETVETKDEEQFDT-DQRTNITT--SEFITGDNELTY CQUIN_8czhs6 ---SSNMVENGLLYELDEPKTVELQDSGDKVTHHACNLEQLINPDSELQ- Anste_SoxY --------------PVLSKVKT---EPMETEPEATLSPDLLEAAQALLSL Anste_SoxA --------------PVLSEGKT---EPMETEPEATISPAHLEAAQALVSL AGAMB_zkh7tk --------------VALAPNPTNGLSLAAVRPEPSFVQDNRESLEAAESL AGAP003896-PA --------------VALAPNATNGLSLAAVRPEPSFVQDNRESLEAAESL DEREC_2z3cvj RA----------MLRPNYFKLADETQMGELSSLLQV-------------- DYAKU_crjp9x RA----------MLRPNYFKLADETQMGELSSLLQV-------------- DMELA_crjnm1 RA----------MLRPNYFKLADETQMGELSSLLQV-------------- DPSEU_9p8n96 AAPMTASLSAAKLLRGNFFKLADETQMGELSALLQA-------------- DVIRI_cnpf85 ------------MLRSNYFKFADETQMGELSALLSANAG----------- AAEGY_vq89q9 GELPTESSPKKKNLEMSVFKLADEAQMGGLNSLMMDAYEGKINQNDSS-S CQUIN_8czhs6 -AMPVA---KKKEPQMGVFKLADEAQMGGLNSLMIDSYEMKANQNFSSGV Anste_SoxY RGSVED------RRPLTTFKLADDSDMESLNKLCVETR------------ Anste_SoxA RGSVED------RRPLTTFKLADDSDMGSLNKLCVETR------------ AGAMB_zkh7tk VQLAQG------KPLLSVFRLADESNMGSLNALCVGP------------- AGAP003896-PA VQLAQG------KPLLSVFRLADESNMGSLNALCVGP------------- DEREC_2z3cvj ----QVQEKDFALQQVLSETSQFLSAHMPGGNSDGNG-------NKRSL- DYAKU_crjp9x ----QVQEKDFALQQVLSETSQFLSTHMPGGNTNGNG-------NKRSL- DMELA_crjnm1 ----QVQEKDFALQQVLSETSQFLSAHMPAGNTNGNG-------NKRSL- DPSEU_9p8n96 ----QVQEKACELQQVLSETSQFLSTHMPGG-------------TKRPIS DVIRI_cnpf85 ----SVPDKDYALQQVLSETTQFLSTHMPSNNNNNNNNNNNCNNNKRLL- AAEGY_vq89q9 PGYCEAKQESTMLDPSSPEPRMTMEPCINMKNHFYSKRPND--VNRELSA CQUIN_8czhs6 LNQSKSDTQNSLFETLSPESKQLTEPCLNMKNHFYSKRPND--TSREMSA Anste_SoxY ----QCGDRADAGQP-WKP-------------------------RYNRVS Anste_SoxA ----QCGDRADAGQP-WKP-------------------------RYNRVA AGAMB_zkh7tk ----NVGSKA---------------------------------------- AGAP003896-PA ----NVGSRADNKEPTWKPPKATQ--------------------TVDREL DEREC_2z3cvj QDSNSSNSSEEEAAS-GSSPNKKVKSSRSCKGKIYQELVNSGQLAAIAKK DYAKU_crjp9x QDSNSSNSSEEEAAS-GSSPNKKAKSSRSCKGKIYQELVNSGQLAAIAKK DMELA_crjnm1 QDNNSSNSSEEEAAS-GSSPNKKVKSSRSCKGKIYQELVNSGQLAAIAKK DPSEU_9p8n96 QDSNSSNSSEEDVGGLGSSPCKKAKSSRSCKGKIYQELVNSGQLAAVPKK DVIRI_cnpf85 -DSGS-NSSEEEERG---TPSKKLKTARSCKGKIYQELINSGQLAAIVKK AAEGY_vq89q9 YDSKRFKRAFDSMHYEYYDEDYTRKTARACKGKRYKEFMTHTRLSSASKK CQUIN_8czhs6 YDSKRFKRAFDSMHYEYYDDDFTKKTSRACKGKRYQEFMTLTKLSSTSKK Anste_SoxY ESDQCSTGVDNVPDQVNDGTESTTRAARSCKAKRYYDFMSHMYPSVQAKR Anste_SoxA ESDQCSTGVGNVPDQVNDGTESTTRAARSCKAKWYYDFMSHMYPSMQTKR AGAMB_zkh7tk --------G----------------------------------------- AGAP003896-PA PAPTPSISGNAVAEPIAAEGRSSPRATRSCKGKKYQELMSRMYPNAHAPQ DEREC_2z3cvj S------------KARSPPAGGMGGNFVDIP---LDAG-PNTPPVSPP-E DYAKU_crjp9x S------------KARSPPAGGMGGNFMDIP---LDAG-PNTPPVSPP-E DMELA_crjnm1 S------------KARLPPAGNMGGNFVDIP---LDAG-PNTPPVSPP-E DPSEU_9p8n96 S------------KSRLNSGGQGAGFFGDAA---VDVASPHSQAVRQQMD DVIRI_cnpf85 S------------KCRLNSGGSNN-----------DAN-SNTPPISPT-N AAEGY_vq89q9 TSKSATVVRAEQPQAAVE--SGPAPIVTEYA---IDDPAPKTNGTLDQNY CQUIN_8czhs6 TSKSATIVK-EEPQASVSGFTG-APEGTMCV---KDVTSLDVS-TNREDL Anste_SoxY A--------------TSSKKTQKAHNDR-------------TSRNRESNT Anste_SoxA A--------------TSSKKTQKAHNDR-------------TSRDRESNT AGAMB_zkh7tk -------------------------------------------------- AGAP003896-PA T--------------KRSPGARMQKDNQKFPKPAT------VAAGGDDQT DEREC_2z3cvj RQGTSPDSMQKHMRSVSESSSSG--FFDLEEKIKELPALSLDAYLQRKRS DYAKU_crjp9x RQGNSPDSMQKNMRSVSESSSSG--FFDLEEKIKELPALSLDAYLQRKRS DMELA_crjnm1 RQGSSPDSMQKHIRSVSESSSSG--FFDLEEKIKELPALSLDAYLQRKRS DPSEU_9p8n96 SLEVATSTSCKHPRSVSESSSSGGGGFDLEEKIKELTALSLDAYLQRKRS DVIRI_cnpf85 NVVASVGQLLPEPETTAVRVAAN--EFDLEEKIRELPALSLDAYLQRKRS AAEGY_vq89q9 SGCIAYEETNIVGKNDPKHFDAS--DFDLDKKINELPCLNLDEYLTKKKD CQUIN_8czhs6 TLDMK-KPMNFAIKSEVKLFDAS--DFDLDTKINELPCLNLDDYLAKKKD Anste_SoxY GCLVEPTDVEALNK----NLERE-----LDKELMNIPALSIDLFRAIQNN Anste_SoxA GCLVEPTDVEALIG----NLDRE-----LDKELMSIPALSIDLFRAIQNN AGAMB_zkh7tk -------------------------------------------------- AGAP003896-PA GFLYSNTAMPELDPLAIDALMME-----LDSKISDLPAMNVGDFCILLNS DEREC_2z3cvj TKKKKKFSGTKKQRNSNSTSGASAASNATAVDATAKGAVPATNEHLVRIK DYAKU_crjp9x TKKKKKFSGTKKQRNSNSTSGTSAASSAAAVDATAKGAVPAANEHLVRIK DMELA_crjnm1 TKKKKKFSGTKKQRNSNSTSGASATSNVAAADAAAKGAVPLSSEQHVRIK DPSEU_9p8n96 TKKKKKFTAGKKQRNSNSTSAGGAACGGGPATGAAGAGKAAANE-LVRKE DVIRI_cnpf85 TKKKKKFSSSKKQRNPNCNTNSTPAATVANVS-TATAAT----------- AAEGY_vq89q9 TKKKKKIKGKFKSTIKPHITVVEQME------------------------ CQUIN_8czhs6 TKKKKKIKGNGKTYIS---------------------------------- Anste_SoxY EQNTTEPCHLASGSKATTKIFMRPSSPEA--------------------- Anste_SoxA EKRRKK-CQ-KSGSKASLKICNLPSPPVAAIC------------------ AGAMB_zkh7tk ------SYT----------------------------------------- AGAP003896-PA EKKRKKSFTKLPKQKLFLNREEQPSTAAS--------------------- DEREC_2z3cvj QQQQQLQAVGSQRRKARKESITRRDVSAIEQEVASILPLTINGSYYFNQS DYAKU_crjp9x QQQQ-LQAVGSQRRKARKESITRRDVSAIEQEVASILPLTINGSYYFNQS DMELA_crjnm1 QQQ--LQAVGSQRRKARKESITRRDVSAIEQEVASILPLTINGSYYFNQS DPSEU_9p8n96 AQRQ-AAVVGSQKRKARKESITRRDVSAIEQEVASILPLTINGCYYFDQT DVIRI_cnpf85 -----VAAVGSQKRKARKESITRRDVSAIEQEVASILPLTINGCYYFNET AAEGY_vq89q9 ------KIVGSRKRKARKESITRRDVSLSDSNLVPEADALFA-------- CQUIN_8czhs6 -------------------------------------------------- Anste_SoxY -------------TTDYTRSTPENRISVVPSTVQPVPPPATNPVGCRKRK Anste_SoxA ---------TTINTNDNTMSTPENRISVVPSTVQPVPPPSTKPVGCRKRK AGAMB_zkh7tk -------------------------------------------------- AGAP003896-PA ------------VTASGVVLQSCNSINGVAPPIATITQPATNGV----DD DEREC_2z3cvj GTP----KAVN----------ASVTSSS-ASPPLSSNSS-SSSSSLSSQA DYAKU_crjp9x GTP----KAVN----------TSVTSSS-NSPPLSSNSS-SSSS-LSSQT DMELA_crjnm1 GAP----KAVN----------APVTSSS-ASPPLSSNSS-SSSSSLSSQA DPSEU_9p8n96 ASPDVEAKAANNSSLTLSTTSTSLSSSSSASPPLSSASSSSSSSSSSSQA DVIRI_cnpf85 RAA---AAAAT-------VAATTATATVAASPPLSSSSS--STLSVYEPA AAEGY_vq89q9 -------------------------------------------------- CQUIN_8czhs6 -------------------------------------------------- Anste_SoxY QPRE---------------------------------------------- Anste_SoxA PPRE---------------------------------------------- AGAMB_zkh7tk -------------------------------------------------- AGAP003896-PA SPLA---------------------------------------------- DEREC_2z3cvj AFDVTSSTSDLLILAEVAANRTELTKSN-- DYAKU_crjp9x AFDVTSSTSDLLILAEVAANRTELTKSN-- DMELA_crjnm1 AFDVTSSTSDLLILAEVAANRTELTKSN-- DPSEU_9p8n96 AFDVTS-TSDLLILAEVAANRTELTKSN-- DVIRI_cnpf85 GYDVTT-TSDLLILAEVAANRTELTKSN-- AAEGY_vq89q9 ----------LATLAEVAANENHIGEKTI- CQUIN_8czhs6 -------------------HE--------- Anste_SoxY -----------------KIIRYVLPRTDQR Anste_SoxA -----------------SITRYVLPTTDQR AGAMB_zkh7tk ------------------------------ AGAP003896-PA -----------------TYYQHKL------ ; prset aamodelpr=mixed; mcmc ngen=100000 file=fasta.out; sump burnin=250; sumt burnin=250; end;