title: Connectivité et endémisme d'espèces marines dans le sud-ouest de l'océan Indien : le cas des Aglaopheniidae
text: D ive r s i f i ca t ionra tesh i f t s. D ep a r tu r e sf r omac on s t an tr a t e o fd i v e r s i f i c a t i on (nu l lh yp o th e s i s )w e r ean a l y s edu s in gth ec on s t an t r a t et e s t. W ec omp a r edth e cv a lu eo fth eo r i g in a l ph y l o g en yt oth e d i s t r ibu t i ono fv a lu e so fth er and omph y l o g en i e s.T ot e s tth e s e c onda s sump t i ono fth ec on s t an tr a t et e s t,w eu s edth er e l a t i v e c l ad o g en e s i s(RC )t e s tw i thaB on f e r r on ic o r r e c t i onimp l em en t ed e i g e rp a c k a g e[ 6 5 ].Th i st e s tc a l cu l a t e sth ep r ob ab i l i t yth a ta th eg p a r t i cu l a rl in e a g ee x i s t in ga tat im et w i l lh a v end e s c end an t s und e rac on s t an tr a t eb i r th -d e a th m od e la tth ep r e s en tt im e.Th e nu l lh yp o th e s i so fth i st e s ti sth a ta l lan c i en tb r an ch e sh a v eth e s am ep r op o r t i on o fe x t an tsp e c i e s[ 6 6 ].I ta l l ow sid en t i f y in g b r an ch e sp r odu c in gm o r ed e s c end an tth anth eo th e r sa tth es am e t im ein t e r v a l. Wh enu s in gph y l o g en i e sw i than on -nu l le x t in c t i onr a t e[ 6 7 ], th ep ow e ro fth ecs t a t i s t i cf o rd e t e c t in gch an g e sind i v e r s i f i c a t i on ab l eS 2 ). r a t e si sl ow e rth anl i k e l ih o od m e th od s( e. g. ,DA ICRC)(T Th e DA ICRC t e s ts t a t i s t i cin c lud edinth el a s e rp a c k a g e[ 6 8 ] c omp a r e sd a t af i t st or a t e c on s t an td i v e r s i f i c a t i on m od e l s(Yu l e andb i r th -d e a th,A IC nds e v e r a lr a t e v a r i ab l em od e l s(Yu l e 2 RC)a r a t e,Yu l e 3 r a t e,l o g i s t i cd en s i t y -d ep end en tDDLande xp on en t i a l d en s i t y -d ep end en t DDX,A ICRV)w i thl i k e l ih o odr a t i ot e s t sand A ICs c o r e s. Und e r DDL m od e l,th esp e c i a t i onr a t es l ow sin r e l a t i ont oal o g i s t i cg r ow thd ep end in gon :th ein i t i a lsp e c i a t i on r a t e,th enumb e ro fl in e a g e sa tasp e c i f i cp o in
  
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  op a r am e t e r sa l l ow sc on t r o l l in gth ep o s s ib i l i t yth a tr e c en t e v o lu t i onand in c omp l e t es amp l in gm a yh id ed i v e r s i f i c a t i onph a s e s du r in gth ee a r l ys t a g e so fth eph y l o g en y.Th es amp l in gp a r am e t e r r ep r e s en t sth ep r op o r t i on o fe x t an tl in e a g e sp r e s en tinth e ph y l o g en y( th i sp a r am e t e rs e tt o1ind i c a t e sth a ta l ll in e a g e sh a v e b e ens amp l ed ). Th i s m e th od n e ed sth esp e c i f i c a t i on o fth e b ound a r i e so fth ep e r i ods tud i ed(h e r ef r om3 4t o3 M a,c o v e r in g O l i g o c en e,M i o c en eandP l i o c en e ),th eg r id(h e r e1 M a )andth e numb e ro fsh i f t st oin c lud e. One a chp o in to fth eg r id,ash i f ti s in s e r t edandr a t e sa r ee s t im a t ed. S l id ing w indow ana ly s i s. In o rd e rt oe xp l o r ep o t en t i a l bu r s t so fd i v e r s i f i c a t i onth r ou ght im e,w ep e r f o rm edas l id in g w ind owan a l y s i s[ 7 1 ].A s sum in gth a ta l ln on s amp l edl in e a g e s w e r ef o rm eddu r in gth eP l e i s t o c en e ( e. g.2. 6M at oP r e s en t ),w es e t aw ind owo f5 M aw id eandas t epo f1 M a,andc a l cu l a t eda d i v e r s i f i c a t i onr a t ef o re a chs t ep u s in gth ech r on o g r amf r om BEASTf r om5 6t o2. 6M a.In[ 7 2 ],th ed i v e r s i f i c a t i onr a t e i sg i v en a s– ln(Nb/N t )/ Dt, wh e r e Nbi sth enumb e ro fl in e a g e sa tth e b e g inn in go fth ep e r i od,N tth enumb e ro fl in e a g e sa tth eendo f th ep e r i odandDtth el en g tho fth ep e r i odin m i l l i ony e a r s. s im i l a rt oth ec a r r y in gc ap a c i t y. 5f o r t a x a l a r g eph y l o g en i e s(n =100 ).W ea s s e s s edth ec r i t i c a lv a lu e so f t a x a th eDA ICRC t e s tb ys imu l a t in g1000ph y lo g en i e so f74t a x aund e r th epu r eb i r th m od e l(T ab l eS3 ). W eu s edth eT r e eP a rp a c k a g e2.5[70 ]toh i gh l i gh tch an g e sin d i v e r s i f i c a t i onr a t e s( sp e c i a t ion e x t in c t ion ),i. e.th es l op eo fth e LTT,th r ou ght im eb yad ju s t in gth es t a r t in gt im eo fth ean a l y s i s andt a k in gin t oa c c oun tin comp l e t es amp l in g.Th econ t r o lo fth e s e Re su l t s Mo le cu l a rD a t ing Ou rph y l o g en e t i can a l y s i sw a sfu l l yc on s i s t en tw i thth ep r e v i ou s pub l i sh edph y l o g en yo fN e r i t a[ 4 0 ].N on ewc l ad e sw i th inN e r i t a sp e c i e sw e r ed i s c o v e r ed.Th et r e eg en e r a t edw i thanun c o r r e l a t ed r e l a x edl o gn o rm a lm o l e cu l a rc l o c kf o rb o th m a r k e r sind i c a t e s d i v e r g en c et im e s (F i gu r e2 ).Th er e l a x edm o l e cu l a rc l o c ke s t im a t ed th
  
  a tth eg enu sN e r i t ao r i g in a t ed5 5. 7M aa g o( 9 5% HPD :5 3. 7t o 5 7. 6M a ).E v enth ou ghs om en od e sa r ep o o r l ysupp o r t ed,th e m a j o r i t yo fn od e sa g e sw e r ee s t im a t edw i thh i ghc on f id en c e. Ou r ch r on o g r am,u s in gtw oind ep end en tm o l e cu l a rc l o c k s,d a t eda l l d i v e r s i f i c a t i one v en t sm o r er e c en t l yth anp r e v i ou sf ind in g s,th ou gh w i thth es am et op o l o g yandc on f id en c eo fn od e s.E s t im a t eda g e so f N e r i t asp e c i e sp r e s en tinth eSW IOr e g i ona r ea l ly oun g e rth an 2 0M a :N.a t e r r im a app e a r ed1 7. 2 6M a( 9 5% HPD :1 2. 7 6t o 2 2. 7 1M a ) ;N.m a g d a l e n a e1 7. 9M a( 9 5% HPD :1 1. 2 7t o2 3. 8M a ) ; N.q u a d r i c o l o r3. 5 9M a( 9 5% HPD :2. 4t o4. 9 9M a ) ;N.t e x t i l i s 1 5. 8 6M a( 9 5% HPD :1 3. 9 9t o1 7. 6 5M a ) ;N.um l a a s i a n a5. 3 9M a (n o9 5% HPDg i v enb yBEAST ).F o rsp e c i e sw i thInd o -P a c i f i c r an g e,ind i v idu a l sc o l l e c t edinth eSW IOsh owd i v e r g en tand.p o l i t a) :N. s t r on g l ysupp o r t ed m on oph y l e t i cc l ad e s( e x c ep tN a l b i c i l l aSW IOd i v e r g edf r omth eIAAc l ad e3. 6 4M a( 9 5% HPD : 2. 1 8t o5. 6 3M a ) ;N.p o l i t a3. 7 3M a(n o9 5% HPDg i v enb y BEAST ) ;N. l i t t e r a t a1. 1 3M a (n o9 5%HPDg i v enb yBEAST ) ;tw o N.u n d a t ac l ad e s2. 6 7M a(n o9 5% HPDg i v enb yBEAST ). F igu re4.S l id ing -w indowana ly s i so fthene td ive r s i f i ca t ionra te sNe r i tath roughgeo log i ca lpe r iod s.O l igo :O l igo cene ; o fthegenu P :P l io c en e. do i :10.1371 / jou rn a l.pone.0095040.g00 4 P LO SON E| www.p lo son e.o rg 7 Ap r i l2014|Vo lume9|I s sue4|e95040 E vo lu t ion a r yD yn am i c so ftheG enu sN e r i ta s in c eth e i rd i v e r s i t yin c r e a s edr ap id l ydu r in gth i sp e r i od(F i gu r e4 ). C on t r a s t in g l y,th eN.u n d a t ac omp l e x( o r i g in a t in gf r omth eIAA ) p r e s en t sah i gh e rp r ob ab i l i t yo fd i v e r s i f i c a t i ona ssh ownb yth eRC t e s t(p=0. 0 0 7 6,a=0. 0 5 ).O r i g in a t in gdu r in gm id -P l i o c en e,th i s c l ad eh a sd i v e r s i f i eds in c eth i sp e r i odin1 1r obu s tg en e t i cc l ad e s :2 inth e SW IOand9inth eIAA. Th ed e t e c t i ono fd i f f e r en t g e o g r aph i c a l l yr e s t r i c t edl in e a g e sw i th insp e c i e sw i thInd o -P a c i f i c d i s t r ibu t i on s,l i k eN.a l b i c i l l ao rN.u n d a t a,su g g e s t sth a td i sp e r s a l o c cu r sa tr e l a t i v e l ysm a l lg e o g r aph i cs c a l e s,d e sp i t eah i ghd i sp e r s a l p o t en t i a ldu et ol on g l i v edp l an k t o t r oph i cl a r v a e.Th esp a t i a land t emp o r a lh e t e r o g en e i t yo fth eIAAr e g i on m a yenh an c esp e c i e s d i v e r s i f i c a t i ona tsm a l lg e o g r aph i cs c a l e sb yc on s t an t l ym od i f y in g c onn e c t i v i t yb e tw e enp opu l a t i on sf o rsp e c i e sw i thb en th i cadu l t and p l an k t on i cl a r v a ls t a g e s wh i cha r ed ep end en t on o c e an cu r r en t sanda v a i l ab l eh ab i t a t sf o rs e t t l em en t[ 8 5, 8 6 ]. E vo lu t iono fL in e age sandT reeSh ape Th ech r on o g r amob t a in edw i thBEASTsu g g e s t edimb a l an c ein th ed i v e r s i f i c a t i ono fN e r i t aa si ti smo r eimb a l an c edth ane xp e c t ed und e rth eYu l em od e l (b=21.07,95%con f id en c e in t e r v a l :21. 4 3 t o20. 5 6 ).Th eRCt e s th i gh l i gh t edanin c r e a s eind i v e r s i f i c a t i on r a t es t a r t in ga t 13.15 M a(95% HPD : 11.39to 1 5. 8 3M a, p=0. 0 0 7 6,a=0. 0 5 )andrunn in ga l la lon gth eph y lo g en yt oth e N.u n d a t asp e c i e sc omp l e x. S tud i e so fd i v e r s i f i c a t ionr a t esh i f t sth rou ght im es e l e c t edth e Yu l e 3 r a t em od e la sth eb e s tf i tmod e lfo rth ewho l eN e r i t a,bu td id n o tr e j e c tth e Yu l e mod e l(c=0.63 ;c r i t i c a lv a lu e c=1. 9 6, a=0. 0 5 ). Th eT r e eP a ran a l y s e sd e t e c t edar edu c t iono fd i v e r s i f i c a t i onr a t e s s i tu a t eda t2 4M a,d e c r e a s in gf rom0.058to0.00013(T ab l e2 ). Th eLTTp l o ti scon s i s t en tw i thth eT r e eP a ran a l y s e s,sh ow in ga f a s t e ra c cumu l a t i ono fl in e a g e sdu r in gth eO l i go c en eandal a t e r s l owd own(F i gu r e3,T ab l e3 ). How e v e r,th eLTTp l o tr em a in s w i th inth e9 5%c on f id en c ein t e r v a lo fnu l ld i s t r ibu t ion so fLTT p l o t sund e rth eYu l e mod e l. Th es l id in g -w indowan a l y s i si sa l socon s i s t en tw i thp r e v i ou s r e su l t s,sh ow in gth a tth ed i v e r s i f i c a t ionr a t ew a sh i gh e rdu r in gth e O l i g o c en e.I td e c r e a s ed du r in gth e M io c en e andr em a in ed r e l a t i v e l yc on s t an tfo r10 M a(F i gu r e4 )tof in a l l yin c r e a s ea g a in du r in gm o r er e c en tg eo lo g i c a lt im e s. D i s cu s s ion B iog eog r aph y :G
  
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