A Method for Determining the Position ancl Sizc of

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A Method for Determining the Position ancl Sizc of Optimal Sequcncc Regions for Phylogenetic Analysis N,I..J.

IVl¿¡rtinrl Ir. Gonz:ílcz-Ctudclas,2 Ii. Sollrilro,s

.1.

I)opazoa

rl'ccnolouí¡ p:trr Di:rgnírstico c Invcstigacitin (Tl)l) S.A., c/Contlcs tlc Torrcunitz 5,2ltO2ll Mtulritl, Spain Dc¡mllrtructtt tlc Gcni'tic:r, Univcrsitut tlc V:rtünciu, C/l)r. Molirrcr 50,46 I(X), llurjirssol, Vlk:nci:r, S¡tlirr

2

rCcntnr tlc lnvcstignciírn cn S:rnitl¡tl Aninurl. INIA,2lll30, Vultlcolnlrs, Matlritl, Splrin

{ Ccntro Nlciourl tlc Biotc'crrología-CSIC. Univcrsitlutl Autórrolna, 2S049 Crrntohl¡rnco, Murlritl, S¡lrin llcccivcrl: 4 Nove.n¡trcr 1994 / Acccptc.tl:

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M:rrch

199.5

Abslr:rct. Thc uvuilallility ol' ljrst urrtl ¡rccur'¡tlc scwith thc usc ol'PCIl. has lecl to a ¡llolil'cration ol'stuclies of'variability lrt Lhc rlolccrrlar Icvcl in populations. Ncvcrtlrclcss, it is of'lcrr irnprrctical to crxuutinc lortt gcnornic strctchcs ancl a large rrurnbcr ol' indivicluals at the sanre tirre. In order to optirnize this kirrd of study, wc suggcst a hcuristic proccclurc filr rletcction ol' thc shortcst lcgion whlt.l (which nrrcly catt bc observcd in rcal clata) this cltllllo[ be cotrsiclcred strictly truc lbr short seqttcnccs, rnainly bec¿tttsc thc cl'lbct of"'noisy," unilrlbrnrativo strctches is not ncgligiblc. 'l-lrcrcf «lrc, tlrc ¡losition ol' Llrc l'r'lrgrncttt artalyzctl sccnls to be a ttrost inrpr'css, Ncw York JLrkcs'l'l'1, Canttrr Cll ( l9(r9) Evolution ol'protcin ttlolccttlcs' ln: Munro l-lN (ctl) Mlt¡ll¡nltlinlt ¡rrotcirt ttrctabolisln' Aclrtlcnlic Ptcss' Ncw l-loctz.cl

York, ¡r 2l

Jurk¡r J, Milosuvllcvic A (1991) Itr:constrrlction itntl lrnirlysis ol'hutll¡ttr Atu gcncs. J Mol Dvol 32: 105-l2l Knowlos NJ, Mart¡trrrrttl O, Sunttlcl Al{ (l98tl) Antigcrric ¡ttrtl nrolcc-

trl¡trcltitr¡tclcriz¡t(itltrtrl.isollrlr:stll.rocotlttrttt[¡t.c:tksol.ltxrt.ltnd.

llt,.th

tliscirsc

vir,s

ir¡ llro Fctlo.ul

llcp.trlic ol'Gortttlttry, ttgy'trrf ol'

lltc Scssitl¡l ot.thc li.csclrch Grtlu¡: ol.tho Stlrnding.|.cclrt¡ical Ctrllr. rnilrcc ol'llrc IJuroPcun c()nrrDission lirr thc corrtrtrl ol' Fotf-lrntlrttoulh Discltsc, I\'lrguc, Cz,cchoslovakilt, F'A'O" llornc, ¡r 149 Kurllur S. 'l'u¡ut¡r¡l K. Nci M (1994) MIICA: ¡.lrtllcstllilr cvoltttionitry gcnctics arurlysis sol'twltlc lirr nricrocotnptltcrs' Collll)ut Appl Bio-

sci l0:ltl9-l9l l-inz U, Dctling U, lltrbsanrcrl-Waigttxtnn H (1990) Syslcnllltic studics on pilt.ilntclcrs inl'lucncing lhc pcrlirrrnarrcc 1¡l' ¡l¡¡r ¡rolytDcrasc chain rcrtctio¡¡. J Clin Chcnr Clin lliochcrlr 28:5-13 Martin AP, Kcssing BD' Pulunrbi SR (1990) Accuracy of estinrating

gcnctic (listxnccs betwecn species ltonr short sct¡tlcnces of ¡nitoctx¡ndrill DNA. Mol Biol Evol 7:4t15-488 Martíncz MA, Dopazo J, llcrnrindcz J, Matcu MG, Sobrino F, Donringo E, Knowlcs NJ ( 1992) Evolution o[ thc capsicl ¡:rotein gencs ol lix)t-iltt(l-tlloulh tliscasc virus: irntigcrric varialion witltottt accutt¡t¡(r(r:35-57luti0D 0l'rrUclcolitlc sUltstituti0ns t¡vcr six «lccirtlcs. .l Virol 35(r-5

Nci M (l9tJ7) M«rteculrt cvolutionary gcnctics' Colunrbiit Univcrsity Pt'css, Ncw York Nicoh N. l-llyrrsc N, lw:rbc N, Ktrnra K-1, Miyllt'l'(1994) I'hylogcncric l.clillioIshi¡ts 0l' thc kingdonrs Anintirli¡r. l)lllltlilc. rrnd Ftrngi

inl'crrctl lirrrn 23 clil'l'crcnt ¡rrotcin s¡rocics' Mol

lliol ljvol ll:762-

7(rS

Ou C-Y, Cicsiolski CA, Mycrs C, llrrntlct Cl. I-tro C-(" Ko¡{tor l}'l'M' Mullirrs Jl, Scltt¡cttclttla¡l C, lJcrkolttrltn IlL, Ecotlotltotl AN' W¡ltc JJ, l:uttlrtrn LJ, Sltltcn CA' Maclnnes KA, Curratr JW' Jal'l'c I'lW (1992) Molccular c¡riclcrtriology ol' I{lV trltltstnissiotr in it dc¡rtal l)rilc(icc. Scicncc 25(r: I l(r5-l l7 I tlico-l-lcssc R, ['rrllansch MA' Nottay BK, Kcw OM (l9tJ7) Ceogmphic

r t3ri

tlistribution ol' rviltl poliovirus tyPc I Bcno(yl)cs. Virology I 60:3 I l322 Rottrigo MJ, Dopuz.o J (1995) liv«rltrtionilry lrnrrlysis ol' picorttavirtts lirnrily. J Mol llvol 40:3(r2-37 I Itzhetsky A, Nei M (1993) Thcoreticll lbunthrtion ol' (lre nrininrt¡nlL'volution nrc(ho(l ol' phylogcnctic inlc¡cltcr:. Mttl Biol llvol l0: 1073-109-5

llzhctsky A. Nci M (1994) Utlhittsc(l cstilllillcs ol'tl¡c ¡ttllrtlrcr ol'¡tt¡cleotitle substitutions whcn subst¡ttttion rlltc vill'ics anrong tlil'l'crent sites. J Mol Evol 38:295-299 S¡riki RK. Ccllirntl Dl-1. Stol'ltl S. Sch¡rrf'SJ. llig,uchi R, IIor¡r G'l', Ivlullis Kll. l}'lich I-lA (l9Sti) l'rinrcr-tlircclctl cttz.ytturtic rrrrlplilic¡rt¡on ol'DNA with a tl¡ctnrostrrble DNA polynlcrilsc. Scicncc 239: 487-491

N, Intlnishi T (l9tig) llclltivc ot'l'icicncics «rl' thc lritchMitrgoliash, tn:txitnttttr-p:ltsinrony, ntitxitnunt-likclihotltl, rnininlurn-evolutiotl lttttl ncigltbour-.ioinirrg rncthtltls ol' phykrgcrrctic tree constfilction in obtlrirling lhc corrcct trcc. Mtrl Biol Evol (r: 5 l4-525 ,suitou N. Nci M (19S7) Tltc ncighhotrr-.ittittirrg rnclhotl: :t ¡tr:rv rrtclllrrtl

S¡ril«ru

liir rcconstnlctitrg plrylogcnclic trccs. Mol lliol llvol 4:4OG425

Sliiz JC, Sotrrirto l?, Do¡ritzo J ( 1993) Molcctrlitr c¡rid Írnd-moulh tlisease vints type O. J Cen Virol 74 Swul'l't»'tl Dl-, Olscn C., (199(» l)llylogcny ruconsl: l)M, Moritz C (ctls) Molccttl¡¡r syslcrn¡lt¡cs. Si Sundcrl:tnd. MA, p 4l I 'l'liinrrr F (1991) Dctcrnlin¡ttiotl ol' wintlow sizr: lirr sc(fucnccs. J Mol fivol 11:47(l-473 'l'iriirn:r l; (1993) Unbi¡sctt cstinr¡lion ol' cvolulion. twccn nuclcotidc scqucnccs. Mol Biol llvtrl l0:6 Tnteno Y. Takez¿rki N, Nei M (1994) Relativc ef flcic i nrt¡rrt-l ikclihtxrtl, nci ghbor-.ioirti ng arrtl lrl¡tx i¡trt¡trl' otts wlrctt sttbslilt¡litlll rttlc v¡tl'ics witll silc. Mol ll 277 Wurtcll RM, f-losscini H, Mor¡tn CJ Jr (1990) Dct

substilutions in DNA f'ragmcnts hy tcmpcrilturo plxrrcsis. Ntrclcic Acitts llcs lll:2699-2701 Wirlon¡tirn MS, Clil'lirnl 1'l'l (1971) On thc sirnilarity ' 'l-hcor Iliol 73:7f|9-t'l(X) Zh¡rrkikh A, l,¡ W-l'l (1992) .Strrlisticirl propcrlics ol'I tiort ol'¡rhykrgcrtclic vrrrilhility l'ro¡n ¡lttclctf ith: st tilx¡r wilh lt ntolcctttar clock. Mr¡l

tliol llvol 9:lll

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