Transitions in Sex Determination and Sex Chromosomes Across

Home , Sex, Sex chromosome

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Running title: Transitions in vertebrate sex determination Email: [email protected] Ecology andUnive Evolution, Institute Peichel, of L. Catherine Correspondence: BC,Vancouver, Canada; This article by article rightsprotected This reserved. is All copyright. 10.1111/mec.14540 doi: lead to differences between this version the Versionand of Record. Please cite this article as pa typesetting, copyediting, through the been publication for accepted hasbeen article This 4 1 Matthew W. Pennell species vertebrate across chromosomes sex and determination sex in Transitions Article type : Issue Special DR. CATHERINE PEICHELL. (Orcid : ID 0000-0002-7731-8944) Institute ofEcologyInstitute and UniversityEvolution, of Bern, Bern, S Department Zoologyof and Biodiversity Research Centre, Univers 1 , Judith E. Mank E. , Judith 2 Department of Genetics, Evolution and Environment, University 3 Department of Organismal Biology, of Sweden; University, Uppsala Organismal Department Biology, 2,3 , Catherine L. Peichel L. Catherine , gination and proofreading process, which which may process, and proofreading gination and undergone full and review buthas peer full undergone not 4

rsity rsity Switzerland of Bern, Bern, witzerland ity of Britishity of Columbia, provided byBernOpenRepositoryandInformationSystem(BORIS) brought toyouby CORE Accepted Article This article by article rightsprotected This reserved. is All copyright. reptilessquamate amphibians, Keywords: sex determination, sexchromosome, phylogenetic compa questions the about evolution long-standing of sexualreproduct evolution of vertebrate sex determination in a phylogenetic con higher rates in fish. Together, these results provide the most squamates, and while amphibians to similartransitions rates in we transitions male between systems in find fish. that Finally, determinationfrom sex environmental heteromorphic homom versus homomorphic and heteromorphic sex chromosomes in both fish and chromosomes “evolutionary are an trap”. Rather, we find similar However, a ourmore stable. data the than in reverse rates squamates fish, both and suggesting t sex genetic sex determination environmental to from transitions tohermaphroditismsexes occur a irreve thatis of separate sexes evolution the noevidence find amphibians. fish, reptiles, and squamate Cont ofteleost clades r indetermination the evolution in sex the systems of patterns mechanisms.determination o Tree Weusedtherecently assembled trends andunclear, convergent in ifthere are itis th unknown mechanisms.diversity ofsex determination underlying cause The reproduction of theprevalence across sexual Despite eukaryotes Abstract re not consistent with re consistent the hypo not t higherrates than the reverse comprehensive view to date of the rsible, as transitions from separate and female heterogamety andfemale occur at rary theoretical predictions, to we rary e directionality of turnover in sex in turnover of e directionality emarkably diverse vertebrate hat genetic sex determination is determination geneticsex hat male heterogamety occur at text, providing newinsight into ion. thesis heteromorphicthesis that sex in fish. also We that find transition rates between between rates transition determination occur higher at , there is a remarkable is remarkable there a , s this remainof diversity f toassess Sex f database rative methods, fish, amphibians, and to to and amphibians, orphic chromosome sex Accepted Article This article by article rightsprotected This reserved. is All copyright. revealed no consistent trends in the rates of transition betwee 2013; Käfer al., 2014, et 2017; Renner, 2014). Indeed, recent a transitionsto hermaphroditism from dioecy that commonly might considered wasonce irreversible tobe sexes (Bull Charnov, 1 & 94%of Ricklefs,in species 1995;& (Renner Renner, 2014).Alth 2008) flowering is common in but quite plants, some with o form Hermaphroditism 5% species found in is ofanimal only (Jarne & individuals in different gonochorism sexes animals (called a in (hermaphrodit within sameindividual the both sexes of presence me determination in sex transitions most of fundamental the One transitionsdetermination amongsex on mechanistic constraints occur aat higherrate than othe sex determination among mechanis Perrin, 2014).& Furthermore, is aboutlittle known themechani 1983; hypotheses (Bull, these test critically empiricaldata to determination system whywe might in sex expect transitions and theore of body extensive an is there Although occur. mechanisms extensive diversity begs the que are determination present al., (Bachtrog sex et 2014; Tree The in aclade vertebrates, whichmechanisms in encapsulated is nea al.,et Bachtrog 2014; Beukeboom Perrin, & 2014). This diversit enormousan diversity in mechanisms the a sex usedtodetermine phenotypes conserved taxa. are broadly across vast of array a D majority reproduce of The eukaryotes vast sexually, an male and Introduction rs provide can into whether the stion of both how and why trans why and how both of stion ms. identifyin As firststep, a Bachtrog al., et 2014; Beukeboom study inflowering plants n hermaphroditism and dioecy nd dioecy in plants). of Sex Consortium, 2014). This re are evolutionary or y of sex-determinationof y 985), recent work has suggested espite this conservation, there there is conservation, this espite ough theough transition separate to g whether particular transitions sms that underlie transitions underlie smstransitions that rly all all known mechanisms of rly itions among sex determination d female reproductive d female Auld, 2006; Eppley & Jesson, systems. tical work predicting when f hermaphroditism observed chanisms is between the chanismsthe between is ism) and the presence oftwo presence ism) the and s, we have lacked sufficient sufficient s, lacked wehave cross (Bull, eukaryotes 1983; occur (Barrett, in plants Accepted Article This article by article rightsprotected This reserved. is All copyright. in other suitablehave not tested been groups, such as fish. 2015;al., Sabath, Itescu et 2016).al., However, the rates of squamate reptilesto GSD fromESD in (Pokorn oftransition rate GSD between rates differences in hypothesis,transition with no a analysis systems. GSD bias toward expect A recent found might restoreeq systems that by to prone and replacement invasion be to i might resilient more GSD be balanced mechanisms thatrestore 2018). al., s Sexdetermining et 1987;PenHeins, et al., 2010), particularly during periods of more stableassumed ESD, tobe than which result can highly in 1983). In addition, locus because GSD single resultsroughly in is environments orin inunpredictable GSD favored environments females and males (Charnov Bull,& 1977; Warner Shine, & 2008). favored to thought environmental when be variation has adiffer (GSD). determination sex genetic have mammals, and birds known all as development,are usedto determine sex. Many other species of fish, reptilesand amphibians, as well environmentalsex determination (ESD), in which environmentalcues, such astemperature during of Tree mechanisms (The Consortium,Sex 2014). across a is gonochoristicEven there vertebrate species, still transition rates. hermaphroditism gonochorism and excellent c in fish it makes an gonochorism have not yet been investigated in any group of anim al.,(Goldberg 2017).et However, the rates oftransition betwe ystems with unbalanced sexrati nvasion by new sex determining sex by new determining nvasion sex ratios(Fisher, 1930). The Many fish and non-avian reptiles have transitions between GSD and ESD GSD and ESD between transitions large diversity diversity of sexdetermination large environmental instability (Jensen (Jensen instability environmental en en hermaphroditism and even sex ratios, it has been even ratios,sex it hasbeen os are prone os areprone to invasions by ESDand inturtles, a higher but skewed sexratios (Conover & a Kratochvíl, Gamble 2009; & et refore, the balanced sex ratioin the balanced refore, ential effect on the fitness of of effect the fitness on ential mixed support thisfor mechanisms, while ESD might might ESD while mechanisms, ual sex ratios. As aresult, we lade to investigate these these toinvestigate lade als. The prevalenceals. The of both By contrast, the evolution of with low variability (Bull, The evolution of ESD isof ESD evolution The Accepted Article This article by article rightsprotected This reserved. is All copyright. investigation. further requires 2009; et Kratochvíl,al., Gamble & (Pokorná in squamates found transitions. to empiricalLimited support fortheevolutionary thecounterintuitive idea more that older, to leading degenerat 2013, al., 2014).et chrom acuteassex Thelatter more be will accumulation on the deleteriousof mutations the non-recombinin (van Doorn ofsexually antagonistic acombination selection to chrom sex that suggestions theoretical atoddswithis somewhat on either genes the Y or 1983; (Bull, W Bull Charnov, & 1977; P chromosomes rare accumulation will due tothe be of recessive m that transition trap, and evolutionary are an established, once clades. vertebrate This suggestionhas tothe led that highly h al., Gamble et see 2017), given therapid chromosomesex turnov al., 2006;et 2013). Vicoso etal., cladesThese exhibit a surp 2014; Cortez et al., 2014), birds 2014; (Zhou etal., e Bellott the the in found notably most are chromosomes sex Heteromorphic sex Y chromosomes, and distinct X female and heterozygosity to al., et Bachtrog 2013; etal., Wright 2016). In these cases,ma progressed hasoften difference heteromorphic to chromosome sex assmall can as nucleotide asingle females (Kamiya be variant locus. Insingle-locusdetermination GSD systems, the genetic d male resultingi the or female insystems either where control, Although GSD can polygenic (Moore Roberts,be 2013),& itis mo t al., 2017), and snakes (Matsubara rising degree ofconservation degree rising (but le le heterozygosity progresses to eteromorphic chromosomes, sex osome divergence progresses, trap was previouslyhypothesis s heteromorphicfrom sex s heterozygous at the sex- the at s heterozygous et al., 2012),et however this e systems morepronee systems would be ifference between males and malesand between ifference & Kirkpatrick,& 2007,2010) and okorná okorná Kratochvíl, 2009).& This 2015), thisbut hypothesis Z Z Wsexand chromosomes. osomes might due quickly cycle er exhibited erother by exhibited re often under single locus utations and loss of essential andloss essential utations of g or WchromosomeY (Blaser s (Charlesworth etal., 2005; rian mammals et al., (Bellott Accepted Article This article by article rightsprotected This reserved. is All copyright. 173 amphibians and 487 squamate reptiles, and as such constitut inform includes dataset complete The systems. determination sex groups (fish, reptiles;vertebrate amphibians, squamate Figure Consortium, 2014)andthe diversi advantage therecently of wetake assembled Tree d of Sex Here, direction of transitions and any in between male the biases are amphibians (Evans al., et Additional2012). work is clearly nee found supportanother no transition adifference in for rates b ZWfrom toXYsystemstransitions more theare commonthan reve conducted producedhave been mixed results.While aprevious st However, empirical this of limited hypothesistests been have a from transitions to systemsinthese in XY groupsZW Doorn (van etal., 2010)and amphibiansSer (Ogata al., 2008),et s itwas shown to dominantbeen tothe be ancestral chromosomeY in spec system (van Doorn Kirkpatrick,& 2010; al.,Veller et Be 2017). system sex-determination epistati shouldnew drift, then the be sexually an by driven are systems and XY ZW between transitions Doorn & Kirkpatrick, 2010; Bachtrog et al., 2011; Veller et al. (BullCharnov,antagonistic 1977;& selection Werren Beukeboo & se genes, sex-determination of effects pleiotropic on selection proposedsystems have been ofevolutio result avariety from to heteromorphic species. sexchromosomes in that present Transiti heterogamety and female as asZW,XY heterogamety regardless of of S heterogametic(The sex Tree species withIn there GSD, is further variation whether in the ex ex Consortium, 2014). Here, we ty of sex-determination sex-determination system of ty uggested that there could be a bias thata be could there uggested , 2017). 2017). , Theory suggests if that male or the female is the the is female the or male lection on sex ratio, and sexually sexually and ratio, sex on lection etween XY and ZW systems across cause cause W chromosomesnew have ded todetermine whetherded there female heterogamety. female 1) to examine transitions among among 1) toexamine transitions nd nd the few studies that have cally dominant to the dominant cally tothe ancestral nary forces, including drift, atabase (The Tree of Sex & Kirkpatrick,& 2010). will refer to species to refer will male with es the broadest and most ons between XY and ZW s found in threes found in major udy in found in amphibians that udy ationon 705 speciesfish, of tagonistic selection or even or tagonisticeven by selection m, 1998; 2001;Jaenike, van whether are there ies of fish (Kallman, 1984;ies offish(Kallman, rse (Hillis& Green, 1990), Accepted Article of character evolution,of solong algorithmthe is it such notto that conservative is guaranteed imputation data Unlike algorithm). detailsthe on 2016 for full spec equivalent’ with ‘phylogenetically dataset our in included the toswap in species (https://github.com/traitecoevo/phyndr), algorithm al., developed et (Pennell thes speciesin thedataset.In species and in the tree between al. 2015; Rovatsos et et al., 2014,2015, 2016). In many cases, (Koubovádataset et 2014;al. Pokorná, 2014; Rens etal., Pokor etal., 2017).(Gamble However, studiesother recent in squamat This article by article rightsprotected This reserved. is All copyright. discovered recently XY of systems in twospecies ( Sexdatasetweusedis of same origas in The Tree the the that Eastman et al.,2013). All treeswere ultrametric with branch l reptiles (Pyron et al., 2013, Pyron & Burbrink, 2014), and amph from speciesremoved theoriginal;placed erroneously M. Alfaro published phylogenielarge-scale matched data from We (The database Tree the ofSex of Tree Sex Data Methods systems in fish, amphibians squamates and (Table 1). heteromorphicvs. sex chromosomes ESD fish; (5) and in and a XY homomorphic and heteromorphic sex chromosomes in amphi fish and fis in GSD and ESD (2) fish; in hermaphroditism and gonochorism o tocomparerates the data these used We context. phylogenetic comprehensive analysis sex determination evolutio ofvertebrate

as taxonomyas the is phylogenetic s ofray-finned fishes (Rabosky

2016), implemented inthe 2016), implemented ‘phyndr’R package Boa imperator we had congeneric matches matches congeneric had we e cases,we used arecently introduce any biases into analyses analyses into biases any introduce inal publication with addition the approaches (see approaches Rabosky,2015), engths in units of millions of years. ies that were (see Pennell et al., etal., (see Pennell ies that were ally informative. thereSince ally may ná, Rovatsosná, 2014; etal., Gamble ibians (Pyron Wiens,& 2011; es are included in this esnot are et et 2013,al., with 11 , pers. comm), squamate f transition (1) f transition between: , Consortium, 2014)torecently phylogeny which werenot n conducted to date in a h and h and squamates; (3) Python bivittatus nd ZW sex determination determination sex ZW nd bians; (4) homomorphic ) of snakes Accepted Article This article by article rightsprotected This reserved. is All copyright. relativ the evaluate to order In clade. this in hermaphroditism transition in rates of betw totestdifferences for it possible The prevalence of hermaphroditism in fish (Devlin & Nagahama, 2 hermaphroditism and gonochorism between Transitions https://github.com/mwpennell/vert_trans. toreproduce results allCode and at isanalyses available ourway topresent this isthemostaccurate results. theIn absence of a reliable procedure for estimating Bayes Fac of distribution the which to extent the examined and posterior for computed thereof) differences rates, we lack intransition results individualanalyses fromall the weresummarized togeth related datasetsorde across wasrun analysis trait/tree in ten for 50,000 generations 10,000 and thefirst removed samples as 2012). all(FitzJohn, For rates,broad exponentialpri weset a Markov chain Monte Carlo (MCMC) p model e aMarkov fit trait of states and asdiscrete characters addressed fivedifferentWe questions in our analyses. each For analyses of Overview essentially identicalgave results. in include selected one these anof to eachrandomly oftheten for Furthermore, artifacts. in multipl which were species there our that analys toensure combinations and trait tree different swaps, wer equivalent manyphylogenetically combinations of be rocedure implemented in the R

All analyses were were conducted analyses All Rin v3.3.1. een gonochorism and and gonochorism een

or (mean of 0.1). chains Weranall volution volution (Pagel, using1994) a differences in rates across the differences r mitigateto sampling error, and e transition rates between e transition rates between alyses. The alternative datasets datasets alternative The alyses. es wererobust tosampling e e records in the dataset, we tors MKfor models in R, we think differences overlapped with zero. overlapped differences analysis, we coded the coded we analysis, er. Toexamine support the (or burn-in. As above,each burn-in. stated an each analysis across ten each acrossanalysis ten an 002; Mank al., 2006)et makes package ‘diversitree’ Accepted Article This article by article rightsprotected This reserved. is All copyright. heteromorphic) sexchromosomes 2) or not; and whether they were 1)whethertheycoded species fortwovariables: had cytogeneti (Maddisoncorrelations 2015).& FitzJohn, Restricting analy the etal., 2015; 2016),(Gamble precluding Gamble, the estimation the due data to rarity conclusive of evidence for homomorphic s weconsidered analysis, this For sex chromosomes heteromorphic and homomorphic between Transitions average). thetree on matched to were 389GSDthere records (279matched tothe tree on average) thetree on average)to and 61 E Figure 1).(Supplemental fish, there For were 310 GSD records i ambiguously codedspecies thisexcluded, and not didqualitativ environmental the alsoWe sex determination. repeated as having some had degree environmentalof both genetic and sex determina Species were coded oneas orthehaving other form ofsexdeter Markov model fit a two-state similar gonochorism/hermaph the to ordertra toinvestigate In these in clades. of both repeatedly fishand squamates, ESthis analysis, wefocusedon asboth For GSD and ESD between Transitions 309 and records ofhermaphroditism (165matched on tothetree records ofgonochorism (178.8of which treeon a matchedtothe fi our In gonochorism. of category single a into sexes separate gonochorism hermaphroditism, and Markov mode wefitatwostate both fish and amphibians. We d We amphibians. and fish both SD records SD t the matchedto (22

nsitions between GSD and ESD, we sh dataset, there were 371 D and GSD have evolved evolved have GSD and D of meaningful of meaningful character sisto gonochoristic we species, n the database n the (156.8 matched ely affectour results ree on ree squamates, For average). on mination. For any species that species that any mination. For ex chromosomesex this in group cally visible (i.e. id analyze the squamate not verage across the ten runs) analysis these with and 49 ESD records (22 average). average). roditism above. analysis tion, wecoded species these l, collapsing all species with male male female or

Accepted Article

This article by article rightsprotected This reserved. is All copyright. homomorphic GSD to ESD versus th three the Forsimplicity,states. report weonly the comparison and Markov estimated model state 64.8species, heteromorphic ESD 16.4 species and species, pera matching tree, tothe After we ended upwith ESD. species with 137 in resulted species withhomomorphic GSD, 125 species with analysis.previous had GSD andSpecies some that both level of were orfemale heterogame whether they between male distinguish ESD, being homomorphic or GSD, heteromorphic GSD. For species w otherclades. For in parameters the thisestimate analysis, we only were to able We perform this fish, analysis on aswewere sex chromosomes vs.heteromorphic ESD homomorphic and between Transitions 25.9,matched counts: 18.3, 14,12.8, and 21). homomorphic, 16 heteromorphic,ZW and39unknown homomorphic re For amphibians, these numbers are 37 XY homomorphic, 29 XY hete 11 unknown homomorphic tree-matched records (average counts: 53 83XYhomomorphic,in 97XY heteromorphic, 51ZW homomorphic, 2 were excluded. Across determination sex also with polygenic fis 1983;(Bull, Maddison & Leduc-Robert, 2013; Blackmon & Demuth, evolutionary the as we expect dynamics differentfrom be to tho record) wherethe Y (or W)sexchromosome has completely l been Weremoved speciesheterogametic. (fi thefew fromthedatasets the sixthe (i.e., forward and rev e transition ratefrom heteromo coded gonochoristic speciesas of the transition rate from transition rate the of not able to meaningfully meaningfully to able not ESD were included.not This erse) transition rates between an averagean of 76.7 homomorphic nalysis. Wethen fitasimple3- nalysis. h, this coding scheme resulted coding this h, se oftrue systems XYorZW sh: 15records; amphibians: 1 heteromorphic GSD, and 52 52 and GSD, heteromorphic ost (i.e., XO andost (i.e., ZO systems) XO 2014). fishThree species rphic GSD to ESD. tic, in contrast to the ith GSD, didnot we ith GSD, romorphic, 18ZW .2, 47, 23.4, 17.1, and 5.6). 9 ZW heteromorphic, and cords tree- (average Accepted Article hig times 2.4 is hermaphroditism to gonochorism from transition occur ahigherrateat than transitions to gonochorism (Figure However, 94.9% ofthe posterior distribution supports that tran approximately 179 gonochoristic 165hermaphroditic and species hermaphroditicdatasets, =309)species ther ten (n (acrossthe ourIn fish there dataset, roughly equalwere numbers gonoch of Transition rates from gonochorism to hermaphroditism are higher than the reverse Results ratesX transition between and estimated model Markov net state (average tree-matchedcounts: 46.2 28 inXY, the ZW) amphibian tree-matched counts: 88 160 an inXY, the squamate dataset, ZW) 110.5 matched counts: fishXY, an dataset, 47ZW) in116 XY the ZW systems XYand Therewere (seebelow). both 204 and 92 ZWXY rates transition between homomorphic andheteromorphic chro sex heteromorphic sexchromosomes. This assumption is wi consistent sexnovel chromosome did depend onnot whether a species ho had This article by article rightsprotected This reserved. is All copyright. heterogametic (ZW) andassu female single-locus WecodedgonochoristicGSD. speci species with all and amphibian this analysis, dataset weusedfish,For squamate systems determination sex XY and ZW between Transitions med for simplicity that the p the simplicity med that for

2; Table 1). ofThe rate median e were on average onaverage e were es as being either or male (XY) es as being d 231 ZW systems (average sitions hermaphroditism to s. We again considered only only considered s.again We oristic (n 371)and = robability of an invasion by a her than the reverse. dataset. We fit a simple, two Wedataset. asimple, fit d 67 XY and 32 ZW systems systems ZW 32 and XY 67 d Y and ZW systems. matched to the tree). tree). tothe matched th our finding that the the that our finding th momorphic or or momorphic mosomes similar in are systems (average systems (average tree- Accepted Article This article by article rightsprotected This reserved. is All copyright. fish. atleastin ESD, chromosomesheteromorphic sex does presence the of that suggest rate from heteromorphictransition chromosomessex ESD (Figu to transition between the difference rate from homomorphic sex chr Ho 3). 2, Figures (Supplemental zero than greater significantly ratestransition The fromeitherhomomorphic heteromorphicor s chromosomes sex vs. heteromorphic homomorphic from ESD to transition ratesof Similar heteromorphic shown). sexchromosomes not (data amphibians, XY systemsboth and ZW show oftransisimilar rates having occurred at higher 30% and rates suggests reversethe (F hete thefrom distributionsupports transition posterior the of heteromorphic sexchromosomes; the fish both amphibianin d and rates in the difference did detect asignificant of tran We not homo between transition ratesof Similar reverse in squamates. toGSD ESD is from the than higher times reverse six fish, in a posterior distribution; squamates:the ofthe 100% posterior di fishin (F both than opposite and squamates the transition rate support is for transitions theconclusion strong There fro that Transition rates from ESD to GSD are higher than the reverse morphic and heteromorphic sex chromosomes sex morphic and heteromorphic sitions between sitions homomorphicbetween and nd 17.3 timesnd the than higher m ESD to m ESD to GSD occur higher at a romorphic tohomomorphic as wever, there iswever, there significant no igure 3; Table fish:1; 98.4%of stribution). The transition rate rate transition The stribution). igure 4; Table 1).In fish and tions fromhomomorphic to omosomes toESD versus the ex chromosomes toESDex are re 5; Table 1). These data atasets approximately 70% not to transitions preclude not

Accepted Article This article by article rightsprotected This reserved. is All copyright. etal., 2014,Käfer 2017; Renner, i studies recent with consistent street”, “one-way evolutionary the in reverse fish. than Thus, weconclude the that evolution 1985), wefind transitions that from gonochorism hermaphrodi to hypothesiscontrast to the In se of separate theevolution that The evolution of separate sexes is not always irreversible mechanisms, determination sexchromosomes,sex particularly for mechanisms,determination ofour analyses, and the thecaveats theoretical provided have predictions into the insight new abou Here, traits. these fundamental in mostvariation extensive the in mechanismsdifferent determination among ofsex transitions Tree of (TheUsing of the Sex database Tree Consortium, Sex 201 Discussion 6;systems (Figure Table 1). in is the rate significant of t there difference amphibians, no ( this data describe not adequately model may our that suggests aretwo configuration produce ratesdifferent that there the of systems. distributionXY the posterior bimodal However, of prob 77.9% the squamates, of posterior distribution supports ahighe oftransition rate higher the systems reversfrom to than ZW XY the fish 99.9% distribution theposterior In dataset, suppor of clades among differ and ZW systems XY between transition of Rates 2014;Goldberg 2017).et al., ransition between ZW and XY

our resultis Nonetheless, perhaps xes is irreversible (Bull & & Charnov, (Bull xesirreversible is of separate sexes is not always an an always sexes separate not is of ts the isthat there conclusion a same distribution at the tips and tipsand the samedistribution at n flowering plants (Barrett, 2013; (Barrett, plants n flowering wediscuss results these how e (Figure 6; 1).Table In t transitions in sex sex in t transitions Figure 6; Table 1). In r rate oftransition from ZW to implications of the evolution of implications theevolution of of abilities likely reflects that that reflects likely abilities 4), wecompared of rates the three vertebrate clades with clades vertebrate three tism occur at higher rates rates higher at occur tism speciation.

Accepted Article hermaphroditism. ecological or life pred historypotential conditions thatmight in plant sexes separate hermaphroditism and between transitions This article by article rightsprotected This reserved. is All copyright. 2017). al., et Goldberg 2014; Renner, 2017; 2014, al., et Käfer 2013; (Barrett, dioecy and hermaphroditism between transition of rates the in differences no are there and times, many occurred has ancestor ahermaphroditic from sexes separate of evolution the as plants, flowering in present to be appear a gonochoristic ancestor might preclude a reversion to separate sexes. Such a constraint does not from hermaphroditism of evolution the underlie that mechanisms developmental and genetic the then reef fish. and plants (Rennerin Ricklefs, & Renner,1995; 2014), these factor factors that select against gonochorism in reef environments. G (see dataset relativeover-sampli a led to aquarium have may trade, the also it is thatand worth noting colorsthe bright ofmany reef-fish Hermaphroditism common is particularly in reef-dwelling fish (G dataset. current possibilitiesthe with test these formally to gonochoristic orextinction lineages rates are higher hermafor 1; (Figure Table database it Although 1). is spec possible that However, areactually there fewer hermaphroditic speciesg than counter-intuitive, as thatthereshouldmor it would suggest be Future work work is evolutionaryFuture and toidentifythe needed genetic Caveats of our analyses Alternatively, if gonochorism is the ancestral state in fish (still to be formally tested), tested), (stillformally to be in fish state isthe ancestral if gonochorism Alternatively,

). Nonetheless, also may there extrinsicbe orintrinsic es, which make them popular in ispose lineages to these iation arehigheriation forrates e hermaphroditic fish. in lineages s might be shared between s beshared plants might between phroditic lineages, we are unable ng of these lineages in our our in lineages ofthese ng iven the relative rarity of dioecy rarity the iven of relative onochoristic our species in hislelin, 1969; Smith, 1975), s and fish, as as well the mechanisms underlying underlying mechanisms Accepted Article This article by article rightsprotected This reserved. is All copyright. with disting did this consistent not analyses hypothesis, these Charnov,& 1977; Pokorná Kratochvíl, & 2009).Although previous of eith to thedegeneration due determination mechanisms ofsex heteromorphic sexchromosomes, acts as evolutionary an trap tha heteromorphic sexchromosomes ha mammals, birds someincluding and that groups, observation The trap evolutionary always an not are chromosomes sex Heteromorphic across systems many are shedneeded furtherto light mechani on mechanisms a that determination and onsex sources ofselection in long-lived resu species.even GSD to invasion These by prone to lead skewsmajor et to shown 2018), (Jensen sex-bias al., in 2016). However, broader climatic suchshifts, ashuman-induced crocodylians tuatara, and which exhibit are ESD, only long also have longer average lifespans than turtles with other and GSD, short-lived species (Bull & Bulmer, 1989; 2 Valenzuela & Lance, tobiased inthe environment couldthat lead variation seasonal of turtles (Sabath,lifespan 2016). al., Itescu et Such longer- rates and ESD in GSD transition difference between turtles, in 2009; Gamble Kratochvíl, 2015; al., Sabath,et Itescual., 2 et that transitions found from to GSD more ESD are common the than resultssquamates. withprevious consistent arealso Our studie transitionsthat fromESD to GSD prone toinvasionsbe therefore GSD torestore sexby balanced Consistent with hypothesis species mightthe that with ESD have GSD than is stable less ESD occur at higher rates the than s led to the suggestion GS that tothe suggestion s led lived species are less affected by by affected less lived species are 016). However, there 016). However, is no uish with between GSD suggesting that ESD may be possibly due due possibly to the longer -lived (Sabath, Itescu et al., reverse in both fish and fish in and reverse both lineages of reptiles including sex ratiosand sex in extinction s in squamates, which have also also which have s in squamates, ratios (Fisher, 1930),wefind lts highlight that there are many 004). Indeed, turtles with ESD unequal sex ratios and and ratios sex unequal climate change, have been been have change, climate er the er the Y or 1983;W (Bull, Bull studiesdditional comparative sms transitions. drivingthese have evolutionarily stable t prevents transitions to other other to transitions prevents t analyses in squamates are are squamates in analyses D, particularly reverse (Pokorna &

Accepted Article This article by article rightsprotected This reserved. is All copyright. which facilitated needed, be will on by newmethodsthat rely n squamates (e.g. Rovatsos et al., 2014, 2016; Gamble et al., 201 have been effortsthis goal towards recently Excellent systems. ofs analyses molecular toawait detailed will need hypothesis, aspos chromosomes versus with of degeneration, low high levels 2015;al., Gamble, 2016). Testing whether there are differences ofreveal the extent found chromosome degeneration on asex (Ro the both of number homomorphic heteromorphic and th systems and However, available. cytogenetic methodshavelow and resolution of SexConsortium,(The Tree 2014). For the vast majority ofsp on thepresencechromosomes cytogenetically of ismostly based inwhich adataset these classific the on we performed analyses However, these results should be precludes trapthat evolutionary sex chromosomes suggestthese heteromorphic data that together, ancient sexchromosomesthat toautosomes havereverted (Vicoso stud recent a with consistent are data Our fish. in chromosomes fr ESD ratestransitions to of different significantly than not ratesanalysis, we found that ESDof transitions to from homomo homomorphic and heteromorphic sex chromosomes in either fish or first differences the hypothesis. analysis, In we no t found in 2016). performedwe Thus, analyses totest twocomplementary th systems with homomorphic sex chromosomese (Gamble insquamates 2009; Gamble Kratochvíl, 2015). al., Thiset dueto is in part homomorphic sexchromosomes GSD with and heteromorphic chrosex transitions to other systems. systems. other to transitions considered as preliminary. It om heteromorphic sex the difficulty identifyingthe ofreliably ransition rate between between rate ransition 5),are butmuch data more

ex chromosomesex across many made in some groups of is important to emphasize that is toemphasize that important ecies, this is the only data ecies, only data this the is of heteromorphic sex ation in transition rates between sex sex between rates transition in ext-generation sequencing sequencing ext-generation y in rphicchromosomes sex were distinct sexchromosomes ited by the evolutionary trapthe evolutionary by ited will greatly underestimate underestimate greatly will ss &Peichel, 2008;Gamble et might not always might an not always be e evolutionary trap trap evolutionary e & Bachtrog, & 2013). Taken Drosophila amphibians. In the second second the In amphibians. erefore do not necessarily erefore not do t al. 2015;t al. Gamble, mosomes & (Pokorná demonstrating Accepted Article This article by article rightsprotected This reserved. is All copyright. Importantly, resul ofthese none different updated phylogeny,methodologies. and larger dataset, systems XY Green, (Hillis 1990). & to However, ourstudyboth a (2012), al. Evans et although an earlier studyin amphibians fo systems insquamates ZW amphibians. or Our results amphibian in theBy wefound in than nodifferences reverse. contrast, rates heterogametic male systems. (XY) fish, transitions In ZW t from foundtransition clade-specific rates We in patterns fe between clades among differ systems ZW XY and between rates Transition promote turnoveractually chromosomes sex ofdegenerate (Blaser 2016). Such analyses also loa will testsofwhether high enable todetect sex approaches chromosomes (VicosoBachtrog, & 2013; segregate. segregate. Furthermore, bothW-l are be fewsystems becausecould there very in which types both systems in which Y chromosome anew isancestral to an dominant amphibians (Kallman, 1984; et al., 2008; Ogata Ser 2010 al., et chromosomes Y sex determination in multi-factorial sy ancestral c W new that findings empirical and 2017), al., et Veller 2010; sex chromosomenew is dominant theancestralto sex chromosome on both theoretical transiti wasprediction that based findings systems should occur higher in at theserates groups (van Doorn relationships between W and W relationshipsbetween hypoand alternative Y-chromosomes. One (Bachtrog al.,et 2014), suggestin ts support the prediction that ts supportthepredictionthat g that there shouldg neces not inked and Y-linked sex determin sex inked and Y-linked hromosomes are to dominant sarily be a bias in the dominance ). Toour knowledge, are there no occur mostreadilywhen ons the transition rates between XY and transitions from XY to fromZW to transitions XY und evidencefor bias ZW from a ds of deleterious mutations might might mutations deleterious ds of male heterogametic male and (ZW) o XY systemso XY occur higher at nd Evans nd (2012)used et al. a

Kirkpatrick,& 2010). This stems found instems found fish and ofsex chromosomes ation loci are often dominant dominant often are loci ation Gamble, 2016; Muyle etal., s are consistent with those of Wchromosome, this but et al., 2013, etal., 2014). thesis to explain the the toexplain thesis (van Doorn & Kirkpatrick, Kirkpatrick, & Doorn (van Accepted Article This article by article rightsprotected This reserved. is All copyright. induce spuriousthan ones. aconservative asthisapproach, assumptionlikely iswill tend a the acrossassumption all this rate-homogeneity maintained we modellinear formulation (FitzJohn, 2012). Therefore, s for the extendedsome of ou tothemulti-statebeen caseweconsider in Drummond & Suchard, 2010; Beaulieu al., et 2013; King & Lee, 20 methods exist positionat toestimateseveral the phylogenetic traitsAlthough transition highly areoften rates between varia could were differ assumed tobethe same withinfish but rates ea within rates transitions homogeneous assume to necessary was of a number are there scales, phylogenetic across large systems Because we were making inferences about the evolutionary dynami analyses our of Caveats hypotheses.explore these further an provide vertebrates in systems and XY ZW between transitions cytoplasmic sexratio distorters (Beukeboom Perrin, & 2014). Th chromosome onsex-rati aY protect against female mutations can systems toXY befavored hypothesis might b transitions is that is in stronger fish in generally selection amphibians than ors beneficial in (Rice,males 1986; Bachtrog al., et 2011). Howeve locu XY if sex-determination systems promote transitions to the of ZW prevalence transitionsfish to XY sex in is stronger that quamates. A second alternative alternative A second quamates. ual selection in mightselection males ual to obscure toobscure true differences rather ble (e.g., Beaulieu et al., 2013) and r, it is not known whether r, whether itis known sexual not ake ake and coherence,of consistency which change (e.g., they between fish and squamates). squamates). and fish between ecause dominantecause masculinizing caveatstoour analyses. First, it s toloci are is linked that r analyses, particular to the tothe particular ranalyses, e presence ofnumerous nalyses. As a result, ours is As ours aresult, nalyses. o biases caused by caused by biases o 15), such methodshave not excellent opportunity to excellentto opportunity ch westudied that (i.e., clade cs of sex determination sexdetermination cs of Accepted Article This article by article rightsprotected This reserved. is All copyright. with homomorphic chromosomes sex underrepresented in ourda are this to could i lead example, estimates.dataset, erroneous For ifsome 1994). dispropo taxonomicHowever, groupsor states are estimates of transition our diversity, existing ofthe system) However, ifourdataset represents (at a wi sample random least tha less comprise similarly datasets amphibian and squamate The hermaphroditism) wehave680records for fishbony aclade from our datas in largest example, For is our dataset sparse. Third, associations found spurious. we to have areunlikely be partsof inphylogeny different timesthe such that r be we can transitions the of we each from 1, Asapparent Figure dataset. evolutionaof independent ofestimates number robustness as the pseudoreplication. th However, phylogenetic testfor diagnostic etal., 2017).Uyeda There tothisis solution clear no problem only from resulted afew evolutionary (Readevents Nee, 1995; & wherein pseudoreplication, strongevolutionaryapparently assoc ofevolutionsuch models make may as our one this pron analysis that can processmodel adequately describe the of chromosomald ofmorerefined theabsence size on of data sexrelative ch the or WchromosomeY is diminished. severely However this simplifi content gene t chromosomes identical in size and sex nearly are in continuum fact in ofsexa chromosome divergence, rangingfr chromosomes, weassumed thatall ho between oftransitions in our analysis particular, In cases. we all coded states, discrete characters even Second, as having heteromorphic chromosomes were rates will be unbiased (Pagel, will be (Pagel, unbiased rates momorphic and heteromorphic sex sex heteromorphic and momorphic , is anynor there reliable et (gonochorismet vs. romosomes or a phylogenetic t is quite plausible that species that t is plausible quite easonably confident the considered hasoccurredconsidered multiple though thisinsome artificial is ere is a general increase in the the in increase general a is ere o those o those in which thesex-limited om systemswhich thetwo in th regard to th regard their sexual Maddison & 2015;FitzJohn, e to phylogenetic e iations between characters characters between iations rtionately represented in our ry transitions increases in a cation is necessary in the the in necessary is cation n 5% of extant species. ofmore than 27,000 species. ifferentiation. Discrete Discrete ifferentiation. tabase; asdiscussed alike, even alike, though there Accepted Article to studying are developed, studying diversification state-dependent itw to developed. yet has been problem such background rates (Rabosky variation in Goldberg, & 2015). work recent has thatshown related BiSSE (and methods) are susc unre tobemany arelikely inspeciation rates differences that diversification (FitzJohn rates al., 2009). et Second, data our This article by article rightsprotected This reserved. is All copyright. as in these clades; such species above, in the number our speciesof datasetstate included is s f wechose below). However, speciation toignore and extinction systems rates to sexual maylead in the at differences which ne thepotential there bias. Indeed, for mitigating are theoretica to simultaneously model developed the evolutionof t traitsand extinction) and of family models Maddison(e.g., et 2007;al., being Abiased. ofrates number methods,most the*SSE notably diversification when rates such association an actually exists pointed out,to consider aneloquently association failing betw influence macroevolutionary rate sex the system of that assumption make the ouranalyses Fourth, As such, readers this in caveat we encourage tokeep important our 2014), et al., the in database issampling (FitzJohn still ofsuch sampling effect on evolutionarymitigatebiases the inf variety for database a reasons. the some of While methods have cytogenetic data. mostly Likewise, some taxonomic groups arefa aremoreabove, these challenging torecognize than heteromorph , we would have no essentially When more data When more available data become s of speciation or extinction. s ofspeciationor extinction. too low to apply these methods these here. low toapply too spans large taxonomic groups,such l predictions that differences in that l predictions differences FitzJohn, 2012) been have can lead to estimates of transition lated to the traits of interest; traitsthe to ofinterest; lated mall relative tothe number of power to detect any differences in differences power todetectany erence fromdiscrete characters een a character and character a een and But as Maddison (2006) as But Maddison w species form (see extinct orgo ould be torevisit ould interesting be very he diversification process, process, he diversification thus mind. or tworeasons. First, aswe been developed to developedassess to and been (State-dependent speciation determination does not does not determination No general solution to this r more likely to be included in includedr more in tobe likely eptible to being misled by ic chromosomessex with and/or novel approaches Accepted Article This article by article rightsprotected This reserved. is All copyright. vertebrates. that presencethe of heteromorphicevidence sexchromosomes inf or squamates 2008; birds Janes, (Organ Sabath, & Itescu etal. found no association between diversification rates and the pres thosein turtles crocodyliansto and (Philips &Edmands, 2012). diversification net intervals birds, whichin have heteromorphi heteromorphic sexchromosomes are rare absent.or However, thes which heteromorphic sexchromosomes are common, than turtlesin reptiles; speciation rate occ in that found speciation for they EdmandsPhilips (2012) & this tested hypothesis diver using net with more heteromorphic or larger sexchromosomes (Turelli Be & in species found sexchromosomeswith inthose than sex without hypothesis found. has been example, higher For levels intrin of Edmands, & Philips 2001; (Rieseberg, incompatibilities zygotic heteromorphic sexchromosomes might part facilitate speciation, hy the to led have patterns These 2008). Presgraves, 1989; Orr, a in inviability and sterility hybrid post-zygotic of evolution heteromorphic provide that evidence effect, chromosomessex pla In particular, implications forspeciation. two empiricalpatte evolution ofsexThe particularly determination, sex chromosome speciation? influence mechanisms sex determination of evolution the Does systems. ofsexual distribution understand the this work to ofspeciation i role andextinction nimals (Haldane, 1922; Coyne and urs more rapidly in squamates, urs more in squamates, in rapidly rns, Haldane’s Rule and the large-X Rule and the rns, Haldane’s 2016). Thus, there is strong not n phylogeneticn shapingthe sic post-zygotic isolation are are isolation post-zygotic sic c sexchromosomes, aresimilar pothesis that the presence of presence of the pothesis that Indeed, other have analyses 2012). Limited this support for ence of turtles, ence ESD or GSD in sification intervals as a proxy icularly theicularly evolution of post- s, also has important important has also s, chromosomes, in species and y an y an role important in the luences speciation rates in rates in luences speciation gun, 1997; 2014). Lima, e results were equivocal as equivocal e results were crocodylians,and which in Accepted Article This article by article rightsprotected This reserved. is All copyright. (R01GM116853). National a US was funded by Award. Merit C.L.P. Wolfson Society the from European Research Council (grant agreements 260233 and Fellowship,Postdoctoral anand NSERC Discovery Grant. J.E.M. g 0905606). M.W.P. was funded by aNSERC Postdoctoral Fellowship, Evolutionary Synthesis Center (NESCent) through a S US National manuscript. the ofcomments on Tree SexConsortiumThe wasfund Nicole Valenzuela for collection of the vertebrate dataset and members thank all We of Tree of the Sex Consortium, particularl Acknowledgements Consortium, 2014),will provide a rich reseresource for future inv present inplants asthe and aswell diversity vertebrates, determination mechanisms thediversity sex of that characterize mechanismsdetermination is totheprocessofspeciation mostly 2016). Thus, the relative importance ofsex chromosome turnover et 2013; (Leslie al., rates McDaniel et al., 2013; Villareal & however,plants; association consistent se wasfound no between et al., here 2009). (FitzJohn assembled for vertebrates few s A using methodsspeciation such as BiSSE requires d more complete role ofsex the testing chromosome turnover ortransitions in s chromosome turnover hasthis in case(Ki facilitated speciation both behavioral in isolation hybridand sterility between male chromosomeautosome an and aneo-sex chromosome created system chromosomes (Demuth, 2014). Indeed, in stickleback fish, afusi speciation is that mightIt also rates reflect possible instead Renner, 2013; Sabath, Goldberg et al., the rates ofturnover the in sex ertebrates (The Tree ertebratesof Sex (The Tree Sally Otto forSally discussion Otto and tudies have been in conducted tudies have arch toaddressarch this question. species, suggesting that sex that sex species, suggesting ex determination mechanismsin tano et al., al., 2009).et tano However, on between anexisting Y ratefully acknowledges support y Jun Kitano, Nicolas Perrin and and Perrin Nicolas Kitano, y Jun we have highlighted here in Institutes of Health grant grant of Institutes Health unclear. Additional studies to xual systemdiversificationand xual cience Foundation grant (EF- grant Foundation cience or transitions in sex in ortransitions sex atasets than we have wehave than atasets an Izaak anIzaak Killam Memorial ed by the National the ed National by 680951) aRoyal and that harbors loci involved involved loci harbors that Accepted Article

irreversible? S. Barrett, C. (2013).H. The plant reproductive evolution of s angiosperms. of evolution the character: morphological binary a of evolution Beaulieu, J. M., O’Meara, B. C., & Donoghue, M. (2013).J. Iden why somanydetermination: ways ofdoingit? Kitano, J., Mayrose, I., Ming, R., Perrin, N., Ross, L., Valenz Bachtrog, Mank,D., E.,J. Peichel, C. L., Kirkpatrick, M., Ott This article by article rightsprotected This reserved. is All copyright. sex (2011). Areall chromosomes equal? created Bachtrog, Kirkpatrick,D., M., Mank, E., McDaniel,J. S. Pi F., chromosome degeneration. Bachtrog, (2013). Y-chromosomeD. evolution: emerging insights References (https://github.com/mwpennell/vert_trans). on and produceanalyses, run data, figures areavailable clean been has this analysis in used data phylogenetic and trait All Data Accessibility paper.C.L.P. wrotethe M.W.P., J.E.M. and C.L.P. designed the study; M.W.P. conducted Author Contributions Proceedings of Royalthe Society B: Biological Sciences Systematic Biology Nature Reviews Genetics , 62 , 725-737. PLoS Biology Trends in Genetics , 14 , 113-124. uela, N., & Vamosi, J. C.(2014). Sex o, o, S. P., Ashman, T-L., Hahn, M. W., res, J. C., Rice, W.R., Valenzuela, & N. , tifying hidden rate changes in the 12 ystems: how often are transitions transitions are often how ystems: previously published. Scripts to to Scripts published. previously GitHub GitHub the analysis; M.W.P., J.E.M. and plant habitat in Campanulid Campanulid in habitat plant , e1001899. into processes Y- into of , , 280 27 , 350-357. , 20130913. Accepted Article This article by article rightsprotected This reserved. is All copyright. deleterious load.induced by mutation Blaser, O., Grossen, C., Neuenschwander, S., Perrin,& N. (2013 regulators. sensitive Page, C.(2017).D. Avian W mammalian and chromosomesY converg Koutseva, N., Graves, T., Kremitzki, C., Warren, W. C., Clark, Bellott, D. W., Skaletsky, H., Cho, T-J., Brown, L., Locke, D., regulators. dosage-sensitive widely-expressed Warren, W. C.,Gibbs, R. A., Wilson, R.K., & Page, D. (2014 C. Lewis, L., Buhay, C., Wang, Q., Watt, J., Holder, M., Lee, S., Zaghul, S., Graves, T., Rock, S., Kremitzki, C., Fulton, R. S., Bellott, D. W., Hughes, J. F., Skaletsky, H., Brown, G.,L. Pyn Bull, J. J., & Bulmer, M. G.(198 Bull, J. J. (1983). model. Blaser, O., Neuenschwander, S., & Perrin, N.(2014). chromoSex chromosome Y explaining hypothesis. Y loss withthefragile Blackmon, H., & Demuth, J. P.(2014). Estimating mode tempo and Press.University Beukeboom, L., & Perrin, N. (2014).

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Explaining distribution the of ion alternative sex-determining of ng a binary character’s effect on character’s abinary on ng effect Paroedura ge tophylogeneticge correlation sex chromosome fusions Altmanová, M.,Altmanová, & Kratochvíl, & L. ra, C.,Agata, K., & Matsuda, Y. kes, kes, birds, andmammals and ders Salticidae). (Araneae: y are associated with are associated with y tionary stable? stable? tionary , diversification character and 5 , 4743. , 87 (Squamata: (Squamata: , 83-93. Chromosome Chromosome Accepted Article 156 sex evolutionary chromosomesreptiles: trap? an are M., Pokorná, Kratochvíl,& (2009). L. Phylogeny ofsex-determin heteromorphic sexchromosomes? Philips, Edmands,B. C., & S. (2012). Does the speciation clock ofphylogeneticoverlap comparative and data. Pennell, M. W., FitzJohn, R. G.,&Cornwell, W. (2016).K. A si systems. in sex-determining divergence population I.,Pen, T., Uller, Feldmeyer, B., Harts, A., G. 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PLoS Biology PLoS , 7 , 12087. Nature , 11 , e1001643. , 451 , 566-568. BMC Evolutionary Biology , 29 , 233-261. . Gilbert,D., M. T. P., &Zhang, G. g, (2013).D. Comparative sex and dioecy in hornworts, the the hornworts, in dioecy and to make a sex chromosome. make asex to temperature-dependent sex- x ratios, and genetic conflict. conflict. ratios, genetic and x rata, and lack of dosage of global rata, and lack ross bird taxa. taxa. bird ross , 13 , 239. Science , Nature Nature 346 , Accepted Article This article by article rightsprotected This reserved. is All copyright. random. differentslightly taxonomic purposes for the coverage; this of acrossanalyses actual weestimatedparameters in the that Note hadsomedegreeSpecies that ESDwereclassifiedof assuch, re having environmental sex determination (ESD, green), or being h heteromorphic red), (dark hom ZW coded either as being XY heteromorphic (dark blue),homomorp XY dete 1.The distribution ofsex Figure Figures

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Accepted Article occur a higher rateat than the reverse. supports transitions that distribution conclusion the from gono fish. in hermaphroditism and gonochorism the reverse in fish. Figure 2. Transitions from gonochorism to hermaphroditism occur at a higher rate than This article by article rightsprotected This reserved. is All copyright. Posterior density Transitions to gonochorism to Transitions occur ahigher rate at .0 .0 0.005 0.000 0.005 Posterior distribution of the difference in transition rates in be ofthe difference Posteriordistribution Difference in transition rates my rates in transition Difference

Across the 10 datasets, 94.9% 10datasets, Across oftheposterior the Transitions to hermaphroditism occur ahigher rate at -1 chorism to hermaphroditism hermaphroditism to chorism

tween Accepted Article reverse. toGSD ESD from is, average, on around 6(fish) 17.3 and (squam than rate higher thereverse. posterioracross Indeed, the dist that insquamates supports distribution transiti the conclusion 10datasets, 98.4% distribution theposterior fish of the an in (ESD) determination sex environmental distribution of the difference in transition rates between gene determination occur ata higherrate thanreverse the inandfishsquamates. Figure 3. Transitions from environmental sex determination to genetic sex This article by article rightsprotected This reserved. is All copyright.

Posterior density 0.10 occur at a higher rate higher a at occur Transitions to ESD to Transitions Difference in rates my transition .500 .50.10 0.05 0.00 0.05 occur at a higher rate higher a at occur Transitions to Transitions GSD -1

for fish (left panel) and for (right and panel) squamates fish (left Acrosspanel). 0.02 occur at a higher rate ahigher at occur Transitions to Transitions ESD Difference in transition rates inDifference transition rates my d 100% ofthe posterior ribution, the rate of transition the oftransition rate ribution, tic sexdeterminationand (GSD) ons toons ESD from GSD occur a at .100 .10.02 0.01 0.00 0.01 ates) times thanates) higher the occur at a higher rate higher a at occur Transitions to GSD Transitions Posterior Posterior -1

Accepted Article heteromorphic tohomomorphic sex 69.7% and of the posterior in distribution amphibians supporta amphibians (right Acrossand the10datasets, panel). 69.9%of rates homomorphictransition between heteromorphicand chro sex sex chromosomes in either fish or amphibians. Figure 4. No differences in transition rates between homomorphic and heteromorphic significant. This article by article rightsprotected This reserved. is All copyright.

Posterior density Transitions to heteromorphic to heteromorphic Transitions sex chromosomes occur ata higher rate 0.2 Difference in transition rates my rates in transition Difference . . . 0.2 0.1 0.0 0.1 Transitions to homomorphic homomorphic to Transitions sex chromosomes occur at a higher rate higher a at -1 chromosomes the than reverse, Posterior distribution of the difference in in difference the of distribution Posterior Transitions to heteromorphic heteromorphic to Transitions sex occur chromosomes 0.2 at a higher rate a higher at Difference in transition rates my rates in transition Difference the posterior in fish distribution . . . 0.2 0.1 0.0 0.1 higher rate higher rate of from transitions mosomes in fish (left panel) mosomes fishpanel) in (left but these results are not Transitions to homomorphic homomorphic to Transitions sex occur chromosomes at a higher rate at a higher -1

Accepted Article zero (Supple than greater are significantly ESD and chromosomes and chromosomes ESD heteromorphicbetween between and sex rates poster The significant. ESD,chromosomes this not is to but sex distribution theposterior supports43.7% of ahigher oft rate heteromorphic Across sexchromosomes ESD. and 10 a the datasets rates in transition difference homomorphic between sex chromoso versus heteromorphic sex ch Figure 5.Nodifference in transition ra This article by article rightsprotected This reserved. is All copyright. Posterior density ESD evolves at a higher rate rate atahigher ESD evolves from homomorphic sex sex homomorphic from chromosomes . . 0.1 0.0 0.1 Difference in transition rates my rates in transition Difference romosomes tofish. ESDin te from homomorphicte se ESD evolves at a higher rate ESDrate ata evolves higher from heteromorphic sex sex heteromorphic from chromosomes -1 Posterior distribution of Posterior distribution of the ransitions fromheteromorphic ior distributions of the transition transition the of distributions ior mental Figures 2 and 3). 3). and 2 Figures mental mes and ESD, ESD, and mes and nd the entire analyses, analyses, entire the nd x chromosomesx toESD

homomorphic sex Accepted Article reverse. the than systems inamphibians distribution ahigher rate transitionsof suggest squam in distribution posterior the of 77.9% only clades: other significan not is there However, fish. in systems determination supports rat thereis that distribution higher conclusion the a and amphibians(middle (right panel), panel). Across the10dat and rates systems in transition difference ZW XY between than thereverse in fish, but not in squamates or amphibians. Figure 6. This article by article rightsprotected This reserved. is All copyright.

Posterior density determination systems occur occur determination systems 0.10 Transitions to ZW sex toZW sex Transitions at a higher rate at a higher

Difference in transition rates my rates transition in Difference Transitions from ZW to XY sex determination systems occur at a higher rate rate at a higher occur systems determination sex ZW XY to from Transitions .500 .50.10 0.05 0.00 0.05 determination systems occur occur systems determination Transitions to XY sex toXY Transitions at a higher rate at a higher -1 determination systems occur occur systems determination Transitions to ZW sex to sex Transitions ZW at a higher atrate ahigher .0 .0 0.004 0.000 0.004 Difference intransition rates my determination systems occur determination systems Transitions to XY sex toXY sex Transitions at a higher rate at ahigher -1

for fish (left panel), squamates squamates for fishpanel), (left e of transitions from ZW to XY sex from ZW to XY fromZW toXY sex determination t supportforthis in conclusion ates and 56.0%ates posterior and ofthe asets, 99.9% posteriorasets, of the 0.06 Posterior the distribution of determination systems occur occur systems determination Transitions to ZW sex toZW sex Transitions at a higher rate at a higher Difference ratesin transition my .300 .30.06 0.03 0.00 0.03 determination systems occur occur determination systems Transitions to XY sex toXY Transitions at a higher rate at a higher -1

Accepted Article This article by article rightsprotected This reserved. is All copyright. 1 Table Fish ESD: 61 (22) GSD: 310 (156.8) N/A 0.984 ESD to GSD GSD to ESD 0.984 to GSD ESD 1.0 Homomorphic: Fish 137 N/A N/A (156.8) 310 GSD: (279) 389 GSD: Homomorphic: Fish (22) 61 3. ESD: Transitionsbetween homomorphicand heteromorphic sexchromosomes (22) 49 ESD: 145 Squamates Fish Gonochorism: Fish 1. Transitionsbetween gonochorismhermaphroditismand 371 #species 1: State Clade Amphibians XY: 67 (46.2) ZW: 32 (28) N/A 0.560 ZW to XY XY to ZW 0.560 XY to ZW 0.999 XY to ZW 0.779 N/A N/A N/A (28) 32 ZW: (160) 231 ZW: (47) 92 ZW: (46.2) 67 XY: (110.5) 204 XY: Amphibians (88) 116 XY: Squamates Fish 5. Transitions between XY and ZW sex determination systems systems determination sex ZW and XY between Transitions 5. Amphibians Homomorphic: 94 2. Transitions between ESD and GSD 4. Transitions between homomorphicvs. heteromorphic sex chromosomes and ESD . Summary ofanalysis Summary (76.7) (76.7) (82.2) (178.8) species) tree-matched in # dataset (avg (60.9) (60.9)

(64.8) Heteromorphic: 125 (64.1) Heteromorphic: 126 309 (165) Hermaphroditism: species) tree-matched # (avg dataset in State #2: species (31.1) Heteromorphic: 45 N/A 0.699 0.699 N/A heteromorphic 0.949 N/A species) tree-matched gonochorism # (avg dataset in species # 3: State to S:5 1.) 0.437 heteromorphic ESD: 52 (16.4) N/A 0.697 0.697 N/A heteromorphic hermaphroditism transition rate higher Prob. of to ESD to homomorphic to homomorphic to homomorphic