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UIF USFF QBSBNFUFST BOE MJLFMJIPPE WBMVF BSF TBWFE UP UIF QPTUFSJPS TBNQMF 'JHVSF  TIPXT B UZQJDBM SFDPSE PG MJLFMJIPPE PS FMFWBUJPO GPS IJMM DMJNCJOH PWFS UIF TFBSDI *G BMM HPFT XFMM BॏFS BO JOJUJBM QFSJPE PG XJME PTDJMMBUJPO UIF TFBSDI SFBDIFT B SFBTPOBCMZ MFWFM NBYJNVN TUBUF य़F JOJUJBM QFSJPE ۘ UIF ۠CVSOJOۡ ۘ JT EJTDBSEFE BOE UIF SFNBJOEFS PG UIF TBNQMF SFQSFTFOUT NPSFPSMFTT FRVBMMZ IJHIMZ MJLFMZ TFUT PG QBSBNFUFST TUSJDUMZ TQFBLJOH UIFZ BSF TBNQMFE JO QSPQPSUJPO UP UIFJS MJLFMJIPPE  *O QIZMPHFOFUJD JOGFSFODF UIFTF QBSBNFUFST UZQJDBMMZ JODMVEF USFF UPQPMPHZ CSBODI MFOHUIT BOE USBOTJUJPO QSPCBCJMJUJFT  &WPMVUJPOBSZ NPEFMT *O 4FDUJPO  JU XBT NFOUJPOFE UIBU POF PG UIF HSFBU UIFPSFUJDBM XFBLOFTTFT PG HMP॒PDISPOPMPHZ XBT UIBU JU BTTVNFE B DPOTUBOU SBUF PG DIBOHF 3BUF PG DIBOHF JT JODMVEFE JO MJLFMJIPPE BOBMZTFT BT UIF DMPDL NPEFM " TUSJDU DMPDL DPSSFTQPOET UP UIF DPOTUBOU SBUF PG DIBOHF BTTVNQUJPO BOE JO CJPMPHZ BT JO MJOHVJTUJDT JU IBT CFFO TIPXO FNQJSJDBMMZ UP CF JOBQQSPQSJBUF JO NBOZ DBTFT 'FMTFOTUFJO  ۗ  4FWFSBM PUIFS NPSF SFBMJTUJD DMPDL NPEFMT IBWF CFFO EFWJTFE 4P DBMMFE SFMBYFE DMPDL NFUIPET SFMBY UIF TUSJDU DMPDL BTTVNQUJPO CZ BMMPXJOH SBUFT UP WBSZ BDSPTT UIF USFF DIPTFO GSPN B QSPCBCJMJUZ EJTUSJCVUJPO XIPTF NFBO JT EFUFSNJOFE CZ UIF SBUF PG UIF QBSFOU CSBODI %SVNNPOE FU BM   य़JT SFMBYFE DMPDL QBSBNFUFS JT JODPSQPSBUFE BT QBSU 

−950 −1050 −1100

Model B: Post−burnin harmonic mean = −1025

−1200

−1150

Log Likelihood

−1000

Model A: Post−burnin harmonic mean = −1001

0

200

400

600

800

1000

1200

Iteration (x 10000)

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USFBUT SBUF WBSJBUJPO BT B TFSJFT PG JOEFQFOEFOU MPDBM DMPDLT FBDI FYUFOEJOH PWFS B TVCSFHJPO PG UIF DPNQMFUF USFF य़F OVNCFS PG EJTUJODU MPDBM DMPDLT SFRVJSFE UP BDDPVOU GPS UIF PCTFSWFE EBUB JT B QBSBNFUFS FTUJNBUFE CZ UIJT NPEFM XIJDI NBLFT UIJT UFDI OJRVF BQQMJDBCMF UP RVFTUJPOT PG DMBEFTQFDJ੗D SBUF WBSJBUJPO " OPUF TIPVME BMTP CF NBEF IFSF PG OP DMPDL NPEFMT *O DBTFT XIFSF JU JT VODMFBS XIJDI DMPDL NPEFM JT BQQSPQSJBUF GPS B EBUB TFU JU NJHIU CF UFNQUJOH UP VTF B NPEFM XIJDI FOGPSDFT OP DMPDL BU BMM #VU UIJT XPVME CF B NJTUBLF B OP DMPDLT NPEFM FYQMJDJUMZ TUBUFT UIBU UIFSF JT OP MJNJU PO UIF FWPMVUJPOBSZ WBSJBUJPO CFUXFFO CSBODIFT ۘ BO BTTVNQUJPO XIJDI JT FWFO MFTT MJLFMZ UP CF B HPPE ੗U UP UIF SFBM FWPMVUJPO QSPDFTTFT UIBO BOZ PG UIF PUIFS DMPDL NPEFMT BWBJMBCMF 1ZCVT   "MPOH XJUI UIF DMPDL NPEFM XIJDI TQFDJ੗FT IPX SBUFT DIBOHF HMPCBMMZ BDSPTT CSBODIFT B TVCTUJUVUJPO NPEFM NVTU BMTP CF TQFDJ੗FE JOEJDBUJOH IPX SBUFT EJ੖FS GSPN DIBSBDUFS UP DIBSBDUFS FH GSPN DPHOBUF TFU UP DPHOBUF TFU  .PEFM DPNQMFYJUZ JT EF੗OFE CZ UIF OVNCFS PG QBSBN FUFST UIF NPEFM IBT BOE JO HFOFSBM B HPPE NPEFM TIPVME IBWF BT GFX QBSBNFUFST BT QPTTJCMF 4FDUJPO   य़F CBTJD TVCTUJUVUJPO NPEFMT GPS CJOBSZ EBUB BSF UIF TJNQMF POFSBUF PS UXPSBUF NPEFMT 'JHVSF B  *O B POFSBUF NPEFM B TJOHMF QBSBNFUFS R FYQSFTTFT UIF QSPCBCJMJUZ UIBU B DIBSBDUFS TUBUF  XJMM UVSO JOUP  PS WJDF WFSTB *O B UXPSBUF NPEFM UIF QSPCBCJMJUZ UIBU  XJMM UVSO JOUP  R JT FTUJNBUFE TFQBSBUFMZ GSPN UIF QSPCBCJMJUZ UIBU  XJMM UVSO JOUP  R  य़JT JT 

(ii)

b

Rooted trees (i)

(i)

a

0

1

(ii)

0 1

c

(iii) 1 0

1 0

(iii)

Unrooted tree

a

b

c

b

a

c

c

a

b

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(a) Binary simple (no rate variation) q One rate (reversible) model

(b) Gamma (among site rate variation) q01 q10 Two rates

(c) Covarion (site-specific rate variation)

(d) Stochastic Dollo (cognate-birth, word-death)

'JHVSF  4VCTUJUVUJPO NPEFMT (BJOT BOE MPTTFT PG SF੘FYFT PG DPHOBUF TFUT BSF NPEFMMFE BT B

PDDVSJOH BU B TJOHMF SBUF PS BU B EJTUJODU SBUF GPS HBJOT BOE B GPS MPTTFT C EJ੖FSFOU SBUFT GPS EJ੖FSFOU DPHOBUF TFUT D EJ੖FSFOU SBUFT GPS EJ੖FSFOU CSBODIFT BOE E B SBUF PG JOOPWBUJPO BOE B SBUF PG MPTT  *OUFSQSFUJOH UIF SFTVMUT 

.PEFM ࠩPJDF

य़F MJLFMJIPPE TDPSF PG BO BOBMZTJT JT UIF QSPCBCJMJUZ GPS UIF PCTFSWFE EBUB UP FWPMWF HJWFO B QBSUJDVMBS NPEFM &WFO BTTVNJOH UIBU GPS FBDI NPEFM UIF PQUJNBM QBSBNFUFS WBMVFT IBWF CFFO JOGFSSFE TPNF NPEFMT TUJMM ੗U CF॒FS UIBO PUIFST य़F EJ੖FSFODF JO BDDFQUBCJMJUZ PG UXP NPEFMT DBO CF FYQSFTTFE CZ UIF #BZFT 'BDUPS XIJDI JT DBMDVMBUFE BT UIF SBUJP PG - )‫ ܒ‬UIF MJLFMJIPPE PG IZQPUIFTJT POF BMTP FYQSFTTFE BT ۠1S %])‫ ۡ ܒ‬UIF QSPCBCJMJUZ PG UIF EBUB % VOEFS )‫ ܒ‬UP UIF MJLFMJIPPE PG - )‫ ܓ‬PS ۠1S %])‫ ۡ ܓ‬BT GPMMPXT #'‫ ܓܒ‬

- )‫ ܒ‬ - )‫ ܓ‬

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5SFF TBNQMF

य़F SFTVMUT PG B #BZFTJBO QIZMPHFOFUJD JOGFSFODF BOBMZTJT BSF B TBNQMF PG USFFT BT XFMM BT MPHT PG PUIFS NPEFM QBSBNFUFST PG JOUFSFTU BTTPDJBUFE XJUI FBDI PG UIFTF USFFT

TBNQMFE JO QSPQPS 

#'‫ܓܒ‬  UP   UP   UP  

MPH#'‫ܓܒ‬  UP   UP   UP  

&WJEFODF GPS )‫ ܒ‬PWFS )‫ܓ‬ /FHMJHJCMF 1PTJUJWF 4USPOH 7FSZ TUSPOH

5BCMF  (VJEFMJOFT GPS UIF JOUFSQSFUBUJPO PG #BZFT 'BDUPST BOE -PH #BZFT 'BDUPST BॏFS ,BTT BOE 3BॏFSZ  

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