110′2?43 ￥6?úd Mark A. Hershkovitz and Detlef D.Leipe National Center for Biotechnology Information National Library of Medicine National Institutes of Health Bethesda,Maryland V 2?43 ￥6?:-è0J,XEˉêG2?è2?43 ￥6?úd?U|?ê5ùA?E-oEˉêG2??E?E?2?43 ￥6?úd|??9,XEˉêG2??8*üúq ò><?Eˉê??9￡E?èE-tEˉê?￡E?Z à ?B2?,XEˉêG2?èùàZú$Eˉê? ? ′???(=/?Eˉê1 ?ú$Eˉê `(=/?Eˉê,X4D ü? ′ ”clade”E-tA??1YE à/*,X à?B2?? üà7[,X?úè12?43 ￥6?:Yê>/?F+?ú2O: (cladistics)? ü)?·2?43 ￥6?:-è0Jè-è0J,XG?&??4￡á a*ó(=,X6?:(MUê5ùJa(M?è5à*ó(=?ú$?Jc?? 1u0′,X,?,X?￡E??t?6?,X2?43 ￥6?úd?"?èE-t,??E?by,óèá ?6? r)?,X (Hills et al.,1993)?<Q' ?à?4￡A?AuZ?G￡,X*üb2?43 ￥6?,X1k"??E?/? `Au1k /?cèE-o?"?,X ?M4? `r*ü?E?qC*bDB,X4§X `??è ′!8GbE-o?"?,Xì &? `5&?,X%?&?]A??Zú2O: `2?43 ￥6?:óT,X&áK?AòNl? Avise, 1994:Saitou, 1996; Li, 1997; Swofford et al., 1996a?? Hillis1?? 1993?ò4￡UJ1T ) ?4?E?2?43 ￥ 6?:? !¨CKA??JW:/￥5à??è*üAu1k,X?"?Eˉ> 2?43 ￥6?úd\??kJíA?,X4§pè5àè?Jí ,X EL=′"á ?FS!,X×JW:/￥?8F??YrP` ?.è5à2?43 ￥6?údát ?6??1Y rP` ?.è7??3?o?3rP`ê5ù+?!|rP`? 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Thorne and Kishino, 1992?? ′!8è B!¨í4§p?0?Eˉê? aè?NO 5×<% oê,X ?6??è3AèèVp BJW,X!¨í4§pk?tJá?ìê,XEˉê?è E-t ?ìê,XEˉê?áè6?ó$μC?-è0J,XL??U? !¨í ?DA? ü!¨í??)??oc?  3èJKSz ? ?,XèV)?)úE-o  3 indel(??,X!&?? G??UèE- a?bEˉê? _,XY?U2??!¨Vèùà 8?GLE@6Nt6Eó)[?è5àè,ìG,X ?D ü!D?a!¨í|D,XEˉê?hA1±??7è?!¨í ?DhA1Lc-Eˉê,Xú ?|? ?ê ? Thompson et al., 1994?è ?YE- !6?±A?.? ?JíG!,X′)[6?ó$μC?c?C_?,XL??U× !¨í ?DhA1LcêA×H? Thompson et al., 1994, Hughey et al., 1996?è1L!6é9E? ?,XE￥c?5àD7è!¨íc?,XμCG￡áC?è ?1E?E?L!"E￥c?,X!¨íúG?9L!6 E-/???? CULSTAL/?cPNRZE-?/???? ?D|? ?ê?è5à SAM/?cé9Zc?G?? y*ü ?4§Xê5ùP?4{4§XEˉ> !¨í  B`4{ê5ùY4{c?4§XEˉ> !¨íè!¨CK,èyy*ü?4{c?Eˉ> !¨í,X ?μz?UQè ′ ü à$d?A?è?à?,èAxá4§X,X±\?P?b1T )(MU? 8?GLè!ü ?GL?,X à$d ±\?è5àèè0?C?bá4§X,X!¨í/?cE? ?1e2??o(M!^,XG6(!&?èE-o!&? Eˉê,Xs6?  3?rLTè ?b2?43 ￥6?,X4§X?G?!¨íJ"uYúK?Nl1Têè3Aèèc ?!¨í?NOá￠4§XEˉêè5à4§XEˉêí à2?43 ￥6?±??7è?Y?tv2??,X1/?c ?V ò 9.2?è*ü9í 2a' DNAEˉ> 4§X!¨í,X? Gutell et al., 1994?èE-t/?c?U5× 3,ìG a·,X ?è,ìG??NOE?E?2?43 ￥6??,X?t(à0?,X>9S?0U ?|Dk ? cf. Harvey and Pagel, 1991?? D:ìê Yo!¨í/?c?!¨Vè MACAW, SAM? B?t43Au? _Eˉ> ìêèE-o43Au à2?43 ￥6? ? _,XG2?Já#ù.??? B?t2?43 ￥6?? _"uYr"?!¨EW?G?!¨í?"?,Xìw,X? 4§?íb2?43 ￥6?údè?Q,X!¨í/?c? 6? NI-?è 4/32110′2?43 ￥6?úd 2005 1 18file://E:\wcb\*ó(=μC:?A￥??110′2?43 ￥6?úd .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om íb?t4-n,X2?43 ￥6?K?NlèVpNXá-1F'J,X2?43 ￥6?G2?è\L?-1F'?E?*ü,X !¨í?"?? cf. Morrison and Ellis, 1997???89Aèè?àJáC2?,èy^Au1k!¨í 4§p¤x4-??/?cè ′??/?cá6? ￥)?!¨í,XJíA?×?JFwoù ? ü!¨í/?cù ?!¨Vè CLUSTAL and TREE in ProPack?,X??/?cè(M??U"??E-?&?? Feng and Doolittle, 1996?è ′ üE-o/?cù,X??/?cètáù??à?NOE?E?ú$4§X &#0;s6? `.? ? a·E?/?0??onèJè4§ ü oê?o(à0?,X2?43 ￥6?A?BèíHt!¨ íEˉ> 5×3? ￠!¨í¤ a2?43 ￥6?DBL? ü¤o!¨íè!¨íKSz ? ?,XèE-êè2?43 ￥6?DBL? à!¨íá?`<  ü× GS ü ?oKSzá ?,X!¨íèDBL?3 ?6? à!¨í4§pá?7è ?t\1T ),X_$èYêí? à ?L??U?)ú1?t `1`t?-?$!&?èáL??U<F?,X!¨í4§pèE-tA±Nl?à ü aM6 A|A? a·? _,XêíE??#] ?? Vp!¨í?)? ? ?KSzè?àE? ? 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Eú×E-t? _1YM-?,X?Büè ′ üY,X.? ?Ne)["uYNX-1,X ?ê? ü2?43 ￥ 6?,X(M!^ Z ?èá àc?,X.? ?Ne)[á à><aè!Eˉ ` ? ?Eó)[rLT ?6??á à×5à ?43,X a·G?ê5ùEó)[?L á6?ù?E-tM2M-?)?W×8V,X4§úA|A??t ?bM2 M-? a·? _? “log&#0;det”?,X???"?èE-t?"?ú?¤o?t ?oEY?,XAu1k? "?? E? è(MU0ú(??,XG??L F??ê?ê? E?E???3Eˉ> E?è'' 3 ?1￠Eó)[-?L >!*ók?!¨VèVpn?tE@ê,XJ?tè ￥*ó,XNe)[!￡tNt6,X?áèFwB!8  ?1.Bn?tG??L è!¨Vè A&#0;G,XE@6·?è5à A&#0;T,XNt6·?? ò 9.4???8V4z?"???ní?|4?2?èê5ùAèá àc?1Y,ì à.? ?,X·?Lê?E- 8V4z?"?,X?t5&? &#0;&#0;Ao???[? üLc a,X??!9PxèE-+n?^Nt6,XD NI-?è 6/32110′2?43 ￥6?úd 2005 1 18file://E:\wcb\*ó(=μC:?A￥??110′2?43 ￥6?úd .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om L!7??"è5ào"^Fwo?U??E@6,Xc?L? ü?CK? ?)?/?êKè ?Eú,X 8?GL a·? _F? ?1*ü ò 9.5/,X?L +è ?J?tEó)[ `JWEó)[,X??× ü??4? üè?? ?1E? ?YAt ?DèJ!￡?tEó)[ ?DF? (à0?,X? Swofford et al., 1996a× Li, 1997??VpG>5,X.? ?Ne)[á,ì1èíL??UNqê ,X ?D×VpG>5,X.? ?Ne)[á,ì1è HnE-oNe)[,ì1èFw2?43 ￥6?Eˉê?,X? 4?4§pú??Jí? 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PAUP,X￡E??(MUí DNAc?,X a·? _Eˉ> ??8×,X?tEWQ,X1*+9èWS*ü' ?"? àêA?At ?Eú,X a·Eó)[? gammaú×,X . 6(? ?D `á ?,X!&?,X!¨_? ò 9.7??E-o ?D ?1E?E?,ì1,Xê5ù?n,X.? ?Ne)[Eˉ> ?E? è?)?t ü)ú,X2?43 ￥6?Eˉê? ?!¨Vè\?? ?1k?t,ìF?E2y,XEˉê??F?E?*übE-t/?cè ′\aèí ? D,X ü\?/?zT ?(MU0ú??,XE ?è5àáEˉê?,X§%4§X? Swofford et al., 1996b??E-t/?cíb 50tc?5à??èJá?5?C t?,XêKè?Vpc?EW?è ê5ùêKèEW2?è ?1íA?P`,XEˉê?Eˉ> 2?1Tè ü±+-<F?,X2?43 ￥6?8× è `4§X,X àêè ￡?ú2OD,??E?E?E-o1k,X a· ?Dè?à ?1E?E?!¨EW+EW? ?D `EW? ?Dú?A? k,X' úè?n?t1Tê,X? _ ú ü)ú?!¨VèAt a·2O? ú ?1￡?? t??Yêíè . ?D `á ?!&?,X!¨_ ?1,ìfó6è1?àhA1!¨EW!￡?t )(àS*üê k,X' ú `?t àêS*üêk,X' ú?"??è ` MP1 ? MEá àè*üá à,X ?D k MLú ?1,èy!¨EW? Swofford et al., 1996b?? íb4ê-?<?,QBü,X DNAc?è B ,Xú!;/?zèYêí\a èY*ü,X ?ê ?TF? 1?! `1`!,X4ê-?!&?è5à üHtDBL?è1Y!&?E? 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Swofford et al., 1996a?èFwC±/????"?ú?G?X,ór,X Eˉê??' 5àè'c?0U ?E?OE `êèú!;/?z?E?TL$??íú!;c?,XJ? ü¤t(Mn!&? ￥*ó0U ? aè a4á,X0U ?á1u ￥*ó ü ??5c?èF?á?aE??è?,X? ??rLTè a4á,X ??\ ?6??Sk!?t!&?6á?,ì1,X(??è￠5à#;]!?t0U ?è ′!8è4±??D ?bC±/?,X???"?F??J\íE- á ???,Xó6Eˉ> ?!7? ürL ?0èS*ü,XEó)[?L F??\Y n? ü??3,X,ì1,X.? ?íèrLT, ü?n !¨_,X!&?èE-o!&?4￡ ?Z? ?0U ?è5àèèLc-Htc???/?z,XrtèE-o!&?,X !¨_3 ürt?Yo/?c?7??Lc? ??Au1k?á!7.B,XC±/?Eˉ> è!¨?Aèè MEGA/?c ? Kumar et al., 1994? ?J\í?-?$ `!ü ?GLDB?Au1k?JíA?,XC±/?×L8M2c?,XH' ??/?z\?èE-t/?crBüTú?±A?4-?JíA?,X4§p? ?G?c???S*ü??' ?"?,X a·Eó)[Au1kk?? *ü,XC±/???/?cS*ü,X? _ L$bêKè ?Eú? _è ?ù ?\YL$,X′t a·? _× PAUP 4.0 ?T?#A?êKè ?Eú? _,XY ?êèùà*ü??' ?"?￠DBA?k,XrL? _è1 ?J\íM2M-?DB,X log&#0;detC±/????"?k,X? _? a??' ?"?,ì!¨èC±/????"?,XAu1kz\?è ?1S*üc?Eˉê,X,ì à? _è E-Wà??U,Xì&??E-t?"?,X5&?#;Z,ór,X(MU0úDB?? *ü,XC±/???? "?átG!í4?1k?"?? UPGMAè unweighted pair group method with arithmetic mean??,ìF?E2y?"?? NJè neighbor joining? `íC±/?Eˉê?,XLtEˉ> ìê,X? "?èùà??Eˉê?"?? 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FM??"?A?"?E?E?^Y ?6???3,XC±/?,ìíbEˉê?Y ?6? ,XC?XKSz,X#?,XG?U?êèúEˉê???3,X ?G?C±/?,X üE?zU?ê ? Felsenstein, 1997??Y?o ?G￡è üa íJíA?Eˉ> t,X?)úTát? ?í ?ê,X JM2`<(à0?,Xè ′Y,XEˉê?YF?,X?q, ü,XJíA?F?7??>Au1kZ? ? ? Rzhetsky and Nei, 1992?? ??Eˉê?"?? ME,Minimum Evolution? ??Eˉê?"?S*ü à FM,ì à,X??Au1k?C?XKSzè' a BC?XKSzìê??-á,XEˉê ?×3AèèW?U"ú??3,XC±/?,ìíb ?bEˉê?,XC±/?,X#?,XG???ê ? Rzhetsky and Nei, 1992; Swofford et al., 1996a; Felsenstein, 1997?? à FM?"?á àè ME?"?JáS*üY ?6?,X ?G?c?C±/? `Y ?6?,X,ìG,XEˉê?C?XKSzè5à  Bê8V&?,XC±/? ?nEˉê?YF?8V&?,X!5Bè' a BE-o??3&?Kè,X??Au1kA? ?èíYF?,X?qKSzEˉ> ìê?bE-t?"??/?W#\L8Z FMAu1k,XqC*?? 0J03 ??t ?bC±/?,X??/?c?Q,X ME ` FM"?Q,X/?c/?cèWà ü?3-è0J ak,X?4?′",ì à? Huelsenbeck, 1995?? ME üAu1k/?c,Xh*üC^9C^S"ˉZèùà METREE? Rzhetsky and Nei, 1994? ` PAUPF? üS*ü ME?íb<?,QBüDBè PHYLIP,X FM/?c¤oZ??,XêKè ?Eú a·? _è "uYí!&?YF?,X a·Eó)[??Eˉ> ?!7? MEGA? Kumar et al., 1994? ` METREEECê ùùà?tJ\í<?,QBü,X gamma?!7è ?Y à?t s?? “p&#0;C±/??,Xú!;? _ ?"uYC±/??!7ê5ù#Q?!7?4§ üê!Eˉ> ?!7èE-/??"? ?Y'ú!;\?ê! ü)ú ? Rzhetsky and Nei, 1994?? MEGA3Au1k à,X `?,X!&?,Xú/?C±/?è ?Y'"u Y a·ê5ù.? ?Ne)[#Q,Xêíè1 ?"uYí!&?YF?,XEó)[??Eˉ> ?!7,XêíèE-t? "?! ü)ú? ′!8èíb4±??DDBL?5à??èí 8?GLDBh*ü?tèt)ú?,X? _ ?6?? !¨ MEGA?"??UQ? ?3-è0J??èíb?t?8× è,XEˉê?6(?0NKèè UPGMA,X ??0?\?? Huelsenbeck, 1995???àJáC2?S*üE-/??"?è5à1 üE-G??¤ ?E-t?"?è ′ ü)? ü,X? ((=T4￡ ??)? UPGMA,Xh*üèE-?&? ?1+'!,X?((=?)?,X UPGMA“ ? ′Eˉê? ” A?a? Huelsenbeck, 1995?? \' è NJ??,X/?cèJè{*ó,XEˉê? à MEEˉê?,ì!¨è<Qá6?Aè? è3?4￡ M2 ,ìE￥Z? Rzhetsky and Nei, 1992; Li, 1997??è NJ ?{*ó?tEˉê?? BD B4§XèY?G￡á à,XEˉê? ?6? ` NJEˉê?? Qè*?7?!¨ NJEˉê?Qk?? Swofford et al.1996a???à,X?t? MAH? ` D.Hillis?t?E?A???4￡ ?7?(à0? kZ?o?<Q ' \??DBL?èíbE-oDBL?è NJ4-?,XEˉê?\232?×S*ü PAUP?"?,X?y E￥? closest?EYNM aèEˉ> E?!9tèkZ?tEWQ,XC±/?Eˉê?? Swoffordè 1997?? (MU0ú???"? NI-?è 10/32110′2?43 ￥6?úd 2005 1 18file://E:\wcb\*ó(=μC:?A￥??110′2?43 ￥6?úd .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om L8Z üY,Xúd!9PxF??*ü(MU0úDB1êè ?b(MU0ú,X???"?!?′E à?? E-Sk?à6?óA??t!¨í!￡?t.? ?!&?íJWY,X.? ?!&?,XqC*??? *ü ,X ?b(MU0ú,X???"???8V4z?"? `??' ?"?? ??8V4z?"?? MPè Maximum Parsimony? ??8V4z?"??/?ìê??èE-t??FI~9 5?? sí? Occam’s razor??í DB?Q,X?·G?3?1T ),Xè5à?1T ),XL??U,X(M?n3??? ürLh*üè MPEˉ ê??-á,X &#0;3 ?ê??,XEˉê?è BnèE-tEˉê?,XG> ?ê??èê5ùAè  à6??"? MPY?o ?G￡a(MU0ú(?? ?,X ?> ? ?á,ì0ú? Swofford et al., 1996a?? Z6?óù? a·#Qè MP?NOt×!¨VèNt6,X ?6,ìíbE@6???T[?>t?Eˉ > t,X?1T ),X?"??0??tt!9Px?L è üE-t?L G?èG?*üEó)[,X?DèE- tEó)[+TM6￡E?,X ML?"?A?k,X?!9Px?L t ?6??U? ￡6 MP,XAu1kEóz? Vp!¨íYF?,X!&?.Br, üE-Eó)[??èFw MP?"??;> k\áQ? 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PDF XCHANGE ww w.d ocu track.c om ',XD,??UqC*bú2O5x,XDG￡?ìê???!¨VAèè MP?U!¨ ML?k??? ?DA?n?!¨ VAèèát,X MP?U!¨t,X?k?×NX5BZ?G￡ ?D,X ML?U!¨NX5B?G￡ ?Dê5ùí ?DEˉ > à!9ìê?U?k???Au1k.@ê1 ?Au1kECê?íECê,XqC*?EW?פo1k"? ?U!¨JW1k"??פoECêA??4?/?פoECêL$ Y,G?,XEˉê?,XDG￡ `/?2O??e 2?/?cE?? ?DB4§X,XE ??VpDB?·dk\232?èFwú?kEW?,XE￥"ì ê,XEˉê?èE-oEˉê??NOG??A?1.BnJ?ìê,XEˉê?? ?qx61k"?á??H+??!9Px?0?,XEˉê?? Swofford et al., 1996a??E-t1k"? ,X8× è\Sè? ?1{*óY ?6?,X )?Eˉê??0K1k"??è3 ?1 ?A? ??U,X? ? Y?/?e2??"?±A? ?1R?ìê,XEˉê??0K"? `?q &#0;C?C?"?? BB?? Swofford et al., 1996a??íb?t\?,XDBL?èE-?/??"?F?\ár*ü?íú2O5xDG￡,XL$  ?U a?bDB4§X `Au1kEózèíbCYE? 20tú2O5x,XDBL?è BB?"?\??kh *ü?0K"??U Bìê??èí!￡?t ?6?,XEˉê?Eˉ> A?? BB?"?¤o?tFEe?"?è 1.BnFwoEˉê?kA?,Xè5à o?oEˉê? ?11T ) #;],X? ′!8 BB?"?E? ?U!¨0K"??k?? 4±??Dúd?"?F?S*ü  ￥?,Xe2?? Swofford et al., 1996a??  ￥?)?e2?? ,ìE￥,X ?ìê,XEˉê??￡?oS?è' a￠kìê?·?ENJ??á à,X1k"? *üá à/?z,X2?.B?e2?E-ooS `ENJ??Oi3?6,X/?c? 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F?ù ?YE-tEYNM? ú ?D,X7?éD?"? ú ?D,X7?éD?"? àáú ?D,X7?éD?"?á àè!5ùS*üZ?3,X?' ,ór,Xá ?è5àá<.,Xá ?? üEˉ> 2?43 ￥6?,Xc?údèa s?DBL???,ì à,Xá D BL?E?E??t(M!^,Xc?Eˉê? _k,XèDBL?E?ùà BE-t? _k,X?GEˉê? §%4§X? Huelsenbeck et al., 1996a?è' a ?1S*üóHCw,X?"?í!￡?tDBL?Eˉ > úd?írP`Eˉê?,X?q ú?,X?n?"? à′ ?D,X7?éD?"??',ì à? 0?/?E?"uY>JW?"??AìVEˉê?/,Xú2O5x,X?)ú4?,X )tB2?? ? Huelsenbeck et al., 1996a, 1996b??P`E?,X#A?nèú ?D,X7?éD?"?E?á6?1k ′ ?D,X7?éD?"?ê,X?/?EY?? ü!￡?tá ?,Xúdè,ór,XEˉê?? n6?ó{*ó?3DB,XEˉê??,Xú ?6??!¨!￡?tá ?,X?Q,XEˉê?,XúF??U? ?ê5ù???ú?? òí/Z #?,X?t,ór,X!7??ú×??)ó?,X ?EY,XEˉê ?§%,Xú??,XG??U? ?1+E-t!7?? ò9?n?ú ?D,X7?éD?"? ?1 à?)? ??"? # àS*ü?,?!èE-t?"?,XL$ ′2? üb/?c*ó??3DB,X ?> ??Y?t/? cè6?ó ü1?????3c?DB?? _ùà?t a·2O _?E@ê `Nt6?è.? ?Ne)[á ,ì1èíbYF?!&?,XEó)[??A?nê5ù"uYA?n gamma?!7?E-t/?c ?1 ü05ù,X Web0- &?TRèE-t0-&?+ Berkeley4èx? ???0′? aL,X InternetC$d?><?? 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MOLPHY,X*üEèùà NEXUS, MEGA ` PHYLIP[ê?Kè,XDB[ê,X?E@6èE?ùà￠ EMBLê5ù GeneBank,X 8?GLc?[ê ¤ a4ê-?  3?J,X ML/?c à PHYLIP,X ML/?c\,ìè!5ù,X!ü ?GL a·? _,X 8× è\Sè5àèY\?EYNM6?óEˉ> ?Eó,X  ￥?,Xe2?èJùà?tEYNM6?óS*ü 7?éDúd?3AèèEˉ> ?t$?,X7?éDúdè5ênE-tEˉê?,X=-F? ú!7.B,X?1e2?èQ,X MLEˉê??Eg?4§pùà?qKSzA?1 ???#??údú/? ,X?-?$!5B ?6?,X? MOPHYS*ü PAUP¤o,X 8?GL a·? _,X?t$L?è1uWA?S *ü5ù7?> ?n ?DD?)? üS*ü,X MOLPHY5??t7?éDEYNMè3á6?ù?!&?YF?,XEó )[???? PAML PAML? Yang et al., 1996??tEECêù???0′4§,X?><?è6?óEˉ> ML? _,X? 0? `Eˉê?,X?0?è6?óEˉ> BayesianEˉê?,X?0?è6?óEˉ> ?3rP`è6?óEˉ> ?b ' ?"?,XEˉê?,Xúdè6?óEˉ> Eˉê?A?1 ?DB `Eˉê?,X43Au?E-tECêù?4￡ ü Macintosh 68K ` PowerPCAu1kT4êA￥E?E?èE?Y?tM24êA￥,X Unix(? GNU gccê5ù Sun ANSI C??íb?-?$DB `!ü ?GLDBèE-t/?c¤oZ?Ao4?,X `?&I#,X ?D?n ` A???íb 8?GLDB? BASEML ` BASEMLG?è a·? _,X8× è à PAUP,X? S"ˉè ?6? ùàZYk5×<%,X? _? 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NI-?è 22/32110′2?43 ￥6?úd 2005 1 18file://E:\wcb\*ó(=μC:?A￥??110′2?43 ￥6?úd .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om àá6? ? ′YE-Yt?"?{*óZ,ì à,XEˉê?èAx?4￡E?Z,ìíb,ór2? 43 ￥6?,X?tEWQ,XA??áL,Xè+á à?"?k,X4§p,X?7è?Já6??' ? G-4§p43Au:+,X?ê5ù·><E-,ór,X2?43 ￥*ó ??è ′E??7è?,X ′2??? 3. EY?ê è,Xú2O5x àY ü,Xú2O5x,XEY?íbúd,XE ?,ì',X??J'ê è,Xú 2O5x à?tê5ù′tY ü,Xú2O5x1Y?t,ì à,Xá à? ,X2??!¨?Aèè4??#Q ê5ù?4?Ne)[?êèK?Nl?áê? Leipe et al., 1993?? ′!8 ü)ú,X."?*ü81 Ftê è,Xú2O5xAu1k!￡?túdè?1Y üú2O5x,X§%4§X,X?7è?? 4. ?U#ùGf ?A?/?c ?14-?á à,X1(?Eˉê??è?? ′c??)? üEg9[ê ,XNNcá à? PHYLIP, PAUP1 ?JW2?43 ￥6?ECê¤oZ?t#?EEYNMè ?1Y'; á à,X?#?E,X?Eg9NNcG??E¤1k?Vpá1u? s ′è?NO ü? ?E¤> Au1kEˉ ê?è?+eYK?Nl,X,Xc?hA15B üEg9[ê,X4§è1L!"Eˉê?G??f×?"? ? ?tEW?,X??§%4§X?E-t§%4§X9$db??,XYK?Nl,Xc??,XBóM6E ?,X ?6??? 110′#] ?,X ′(M5%C$d? 2?43 ￥6?:,XC$d? PHYLOGENETIC RESOURCES?? üt2?:oú?,X ?*ó(=: .(=OZY?t ′(M5%0-&?è4?4?kM2 QVp4íE-tNZ 3óHCwè?Q6?ó^E-t  ±, ü ;￡ G??E-t0-&?eL?,X2?43 ￥6?:,X/?cJá B5JW0-&?Fw ?èW,XNIM6G?ù ?ZA??a2?43 ￥6?:YG,XJòyèJùà?( (=??4???K?4?? #???A?E?-11 ??G￡,Xú$*ó(=: `ú2O*ó(=:DBg? http://www.ucmp.berkeley.edu/subway/phylogen.html 2?43 ￥6?:,X/?c? PHYLOGENY PROGRAMS?? E?E?E-t5%0-##??)?Y,X2?43 ￥6?:,XECêtM2 Q,XEY?? üE-t0-&?Y?4z?,Rt 2?43 ￥6?:,X/?c1T ),X￡E?èY';/?c?"??KS/??"?è' ?"?è8V4z?"?1? `E¤> ,XAu1kG ?? Unix,Mac,Pc1?4?4?CK9? oêèWE?¤oZE-oECê,X?EQ5% ê5ù ? ECê,X?(5% ? http://evolution.genetics.washington.edu/phylip/software.html 2?43 ￥6?:Au1kúd/?c? PHYLOGENETIC ANALYSIS COMPUTER PROGRAMS?? E-tGb*ó Q?,X5%NI?W¤o,X2?43 ￥6?:/?c"uYT?t5%0-Fw?è/?c,X AèaètAoèJèL8Z+?/?c1êèWE?¤oZc?4êEe < `Ja?oú$*ó(=:,XEC ê1K? http://phylogeny.arizona.edu/tree/programs/programs.html 8V4z1k"?údECê? PARSIMONY ANALYSIS SOFTWARE?? E-t0-&?+ IWHS? Iternational Willi Hennig Society?4èx,Xè?K?-è0J8V4z1k"?èJ NI-?è 23/32110′2?43 ￥6?úd 2005 1 18file://E:\wcb\*ó(=μC:?A￥??110′2?43 ￥6?úd .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om A??/?c à PAUPê5ù Hennig86f,ìE ?? http://www.vims.edu/~mes/hennig/software.html *ó(=,?)ú$Eˉê? BIOCATALOG MOLECULAR EVOLUTION?? ?#*ó(=μC:-è0J¤oZ?G￡2?43 ￥6?:ECê,XJòy?E-t0-&?¤o,X STATALIGN/?c "(à?′`,XèJa0-&?F?"uY? http://www.ebi.ac.uk:/biocat/phylogeny.html NI? ROD PAGE’S HOME PAGE?? E-tNI¤oZ?G￡,X2?43 ￥6?:,XúdECêèE-o/?c ?b8ípê5ù??0k?02?43 ,Xèùà?M6¤,X TreeView/?c? http://taxonomy.zoology.gla.ac.uk/rod/rod.html A? ac?? READSEQ?? E-G?Y?t[ê?E@ê/?cè ?1^?/??,Xc?[êE@ê? o?/??,Xc?[ê? E-t0-&?,XNIM6TY?t?B?ü2lC? copy—and—paste?0k · `?t??9° )è*ü ?1 EY? 14/? *ü,Xc?[ê?,X?/?0Eg??? http://dot.imgen.bcm.tmc.edu:933/seq util/Optiions/readseq.html c?Eg9Eg?? SEQIO?? E-t0-&?Y?tECêùèJùàZ READSEQ/?c,X ?;> (èE?YJWA??,XGbDBg e2?,XECê `ú$*ó(=:?à ?6??*ü,XAu1k1K?E-tECêù ?!¨ READSEQ/?cák ?è?NO?EQ a]>?!6?S*ü?Vp ??Eˉ> 1T ) c?[ê?E@êè READSEQ?U?k ?? http://wwwcsif.cs.ucdavis.edu/~knight/seqio.html PHYLIP? E-?túd2?43 ￥6?,X!C ECêèYGECê,X1T-á?4? ?1 ü4?Kù??èECê ``H `L??U?EQ? http://evolution.genetics.washington.edu/phylip.html +?/?c? TREEVIEW?? E-t0-&?,X+?ECê ?b8íp `??0k?02?43,XèWA? a??,X NEXUS ` PHYLIP?,X2? 43 ￥6??[ê?E-tECêA?*ü G??n? `JW?o1T ),X8V&?è2?43 ￥6?? ?1' Dê5ù±, ü?t[ê? ü8íp PICTè ü??0k?02?43 ò[ê?è1?1 a ?)ú?E-t/?cíb?((=,X2?43 ￥6??,X￡4?\Y}? NI-?è 24/32110′2?43 ￥6?úd 2005 1 18file://E:\wcb\*ó(=μC:?A￥??110′2?43 ￥6?úd .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om http://taxonomy.zoology.gla.ac.uk/rod/treeview.html üRDP?TEˉ> 2?43 ￥6?n!? SUGGESTING A PHYLOGENETIC PLACEMENT ON THE RDP TREE?? E-NMáuA?*ü 7?> Eg9?!??,X RNAc?è^E-!?c?*ü?Eó DNAml+?/?cn!?Y ,X RDP? Ribosomal Database Project??T?E-NMáu?k???èW ?1 üá?úJs ,XêKèG?E¨ 2?t?4zù ? 20t(=/?,X2?43 ￥6??èWE?á6?Eˉ> Oi,Xúd? http://rdp.life.uiuc.edu/RDP/commands/sgtree.html 7èA?? M2 óA? Dave Swofford¤oZ PAUP 4.0,X#A?(1 ? à Dave Swofford ` Jack Sullivan Eˉ> ,X úY,?,XA|A?? M.A.H0 ??*ó(=1/?μC?,X? á .? a ?aE-NM10,X? óA? NIH ` ???:?? ò/? ò 9.1? EYn,Xá(=?,ó9? ` s*ó*ó(=,X 5.8s rDNAc?,X CLUSTALéD??ú2O `,ìh4ym+!?· ><,Xc? üJW ?Y￡E?? Hershkovitz and Lewis, 1996??Ojy*ü CLUSTAL,X(Mn,X ? üE-G?S*ü,XT?Ax?0N!5.úEˉ> ?G?!¨íè' a B ?G?!¨íkc???Kè,X ,ì?èkE-tE￥,ìE2,X?C±/??Eˉê??Au1k,ì?êqB,X ?G?!¨í,ì à.? ? ,X!¨_èá*ü5×<%0N!,X!5B?E-tEˉê?? ?1,?0?t?4?4§pè3 ?10?t? G?!¨í,XNX?!9Px?á1ua èE-tEˉê?F??>,| PHILIP?,XEˉê?[ê?íb ?G?!¨í/?c5à??èE-tEˉê?,X§%4§Xú?nc?Eg9,XNNc??êM6,XL? ü?!¨ í?è5à?qKSzú?nc?,XG??E-tEˉê???? Hershkovitz and Lewis, 1996?Y ′tú4?è à?-1A?Bá6?  ü?!¨VèJ\ ê? `4v;?,X??× y2Oá(= `8¨;§,X )? ??èE-oá!7.B ′2?F?úA?D?G?!¨í?E-tEˉê?+ PAUP,X8íp(,X+?/?c 0 `' Dè a4￡E?Z8íp,X ò6/?ct15à?,X? PAUP,XEˉê?Kù?? ` 0,X ?? #A? V?????;> ?t PAUP[êèJú2O á/? àEˉê? á/?,ì à×???*ü GETTREES Q? é9Eˉê?[êè?nEYNM1±+-Eˉê?[ê,X?qKSz×???*ü PRINT TREES Q?+ ?Eˉê?èa ??nEg9,X?qKSz,X*üEè×???*ü ?,X' DEˉê?9° )? Print Trees?,XNX??EYNM? Preview option?úEˉê?,| PICT[ê?"??èíb PAUP+?1 K,XS*üè;> ,XDB[ê?c? `!¨í?,XY?JáG??Uè ?L??Uú2O á,ì à ?1? üDB[ê ?6??YNqê,Xú2Oè ??U*ü DELETE TAXA Q?úJ?+9 G ?? ò 9.2? 4§X RNAc?!¨í,X2?43 ￥6?A?B??$??n,X?tc?,X!¨íèE-t!¨í B`4{4§ X,ì à,X.? ?í?k,XèKèY?!? ?KS?+=+6?A??,X)?6? loop?  3??%?? n,X`4{4§XG!íG2?,XAèa??&è D?? A&#0;Tc? ` G&#0;Cc? ?oEY?,X2?43 ￥6? G2???&?,X!¨í à2?43 ￥*ó,ì?7èèa′Gè ′ A&#0;T ` G&#0;C,X a· ? ￥*ó NI-?è 25/32110′2?43 ￥6?úd 2005 1 18file://E:\wcb\*ó(=μC:?A￥??110′2?43 ￥6?úd .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! 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PDF XCHANGE ww w.d ocu track.c om LcEˉê?,X?)?tF??U?k??y?9?Eˉ> 1` ?rP`èú￠ 18SDBL??L8 >$á(=,XDB?ú2O5x ?1 B á+ê5ù4ê ?>ê?L8è5à>$á(=DQDB[ê ,X! 10tú2O5x? üE-/????èJ43Au?U!¨1Y 500t(MU0ú ` 10tú2O5x,X2?43,X+  ? 0.16; p=0.5??k??!7D?è/? 18Sc?"uY2?43 ￥6?μ ?9?·?E-o ,XG 2??*üE-o 18SDB1 ? 10t>$á(=k,X MPú 312úèE-tú ?!¨?Q,XLcEˉê ?ú/á?Q?&?? ò 9.10 *üPHYLIP/?cEˉ> 7?éDúd,X10#/?? SEQBOOTy ??t PHYLIP?,X[ê0Eg9D Bè' aY';*ü ?n,XD,??!¨V 1000 ??úJtá?Eg?[ê,X4§p ?1*ü9Au1k 1000tC±/?-?L ?Vp DNADBè*ü DNADIST×Vp<?,QBüDBèS*ü PROTDIST? ü E-t!9Pxè,ó:,XDB? 8?GLè!ü ?GL?>#;è+?tc?Kè,Xú!;DG￡ a·?' aè NEIGHBOR/?cú?E-o? 1000t?-?L ,X!￡?tF??0??tEˉê??' aè CONSENSE /?cú 1000tEˉê?EW?tèJè ü?qT?"?7?éDD?, übEg?[ê,X CONSENSEEˉê?,X§%4§X ?1*ü?)[4êEeECê'?è5àEˉê?[ê ?1?( ￥> 0 Eˉ?!9?)ú? Treetool ` TREEVIEWA?*ü íEˉê?Eˉ> ?0 `?)ú?G??.Bn? èG?? f×?qèú2?43? òE@ê?￡ òBè11?èJè ?1ú[ê,| *ü,X ò6? ?￡ PICT??<Q' E-o/?cá ü PHYLIPECêù?*ü<.4???"??èaàF?!C ?k ,X???0′4§,X?><?? ò/E?/Z?o ü7?éDúdE?/?Eˉ> DB?)úê*ü,X á à,X[ê?? ?1?L$ è!￡t[êF?t ?ZA??Y?èE-ot ?,XY? ü?b ? ? `iF?? ?5×[) Adachi J.and Hasegama,M.(1996).MOLPHY Version2.3.Programs for Molecular phylogenetics based on maximum likelihood(Tokyo:Institute of Statustical Mathematics). Avise J.C.(1994).Molecular Markers,Natural and Evolution(New York: Chapman & Hall). Baldauf,S.L,Palmer,J.D.,and Doolittle,W.F.(1996).The root of the universal tree and the and the orugin Efron,B.(1979).Bootsrapping methods:Another look at the jackknife.Ann.Stat.7,1 26. Dayhoff,M.O.,Schwarez,R.M.,and Orcutt,B.C.(1978).A model of evolutionary change in proteins.In Atlas of protein sequence and structure M.O.Dayhoff,ed. (washington,DC.,National Biomedical Research Foundation),pp 345 362. Faith,D.P.,and Trueman,J.W.H.(1996).When the topology depnsent permutation test (T PTP)ing the null hypothesis of nonmonophyly,(b)rejecting the null hypothesis of "no structure,"(c)Felsenstein,J.(1985).Confidence intervals on phylogeies:An approach using the bootstrap.Evolution39,783 791. Felsenstein,J.(1997).An alternative lesst approsch to inferring phylogenies from pairwise distances.Syst.Biol.46,101 111. 228 PHYLOGENETIC ANALYSIS NI-?è 28/32110′2?43 ￥6?úd 2005 1 18file://E:\wcb\*ó(=μC:?A￥??110′2?43 ￥6?úd .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Felsenstein,J.,and kishino,H.(1993)Is there something wrong with the bootstrap on phylogenies. A reply to Hillis and Bull.Systematic biology42,193 200. Feng,D.F.,and Doolittle,R.F.(1996).progressive alignment of amino acid sequences and con struction of phylogenetic trees from them.Methods Enzymoi.266,368 382. Gstesy,J.,Desalle,R.,and wheeler,w.(1993).Alignment ambiguous nucleotide sites and the Gutell,R.R.,Lsrsen,N.,and woese,C.R.(1994).Lessons from an evolving rRNA:16S and 23S rRNA structures from a comparative perpective.Microbiol.Rev 58,10 26. Harver,P.H.,and pagel,M.D.(1991).The comparative Method in Evolutionary Biology (Oxfrord:Oxford University press). Hein,J.(1990).Unified approach to alignment and phylogenies.Methods Enzymol.183,626 645. Hein,J.(1994).TreeAlin.Methods MOL.Bion 25,349 364. Helbig,A.J.,and seibold,I.(1996).Deep level diagnostic value of the rDNA ITS region.Hershkovitz,M.A.,and Bull,J.J.(1996).Are storks and new world vultures paraphyletic?Mol.phyloenet.Evol 13,1276 1295. Hershkovitz,M.A.,and Lewis,L.A.(1996).Deep level diagnostic as a method for assessing confidence in phylogenenbeck,J.P.(1992) Hillis,D.M.,Allsrd,M.W.,and miyamoto,M.M.(1993).Analysis of DNA sequence sara:phylo Hillis,D.M.,Huelsenbeck,J.P.,and cunningham,C.W.(1994)Application and accuracy of molecular phylogenies.methods Enzymol.224,456 487. Hillos,D,M.,Huelsenbeck,J,P(1995).perfromance of phlogenetoc methods in simulation.syst Biol,44,17 48. Huelsenbeck,J.P.,Hillis,D,M.,and Grate,L.(1996b)SAM:sequence slinment and modelling software:University of california Baskin center for compuer Engineering and modelling software University of California,Baskin Center for Computer Enguneering and Information Sciences . http:\\www.cse.ucsc.edu\research\compbio\sam doc.html) Kishino,H.,and Hasegawa,M,(1989).Evaluation of the maximum lielihood estimate of the evolutionary tree topologies.Comput.Appl.Biosci.10,189 191. 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Biol. 44, 384 399 T? NI ?? NI E¨ 2,? ) E¨ 29 X NI-?è 32/32110′2?43 ￥6?úd 2005 1 18file://E:\wcb\*ó(=μC:?A￥??110′2?43 ￥6?úd .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om