View metadata,citationandsimilarpapersatcore.ac.uk This article isprotected rights by All copyright. reserved. 10.1111/nph.15654 doi: lead been and throughtypesetting, proofreadingwhich may thecopyediting, process, pagination This article undergone has for and buthas accepted been not review publication fullpeer Beverley Glover: J. Pablo Vargas: Pau Carnicero: Ana Juan: LuisJosé Blanco Mario Fernández ORCID Accepted: Received: Article type : 6 2 5 7 Macroevolutionary dynamics of of dynamics Macroevolutionary Centre for Middle Eastern Plants, Roy Plants, Eastern Middle for Centre Mario Fernández Departamento de Biodiversidad y Conservación, Real Jardín Botánico (RJB Botánico Real Jardín y Conservación, Biodiversidad de Departamento Departament de Biologia Animal, Biologia de Departament Accepted(I Barcelona de Institut Botànic Article 4 *Correspondence: Mario Fernández Mario *Correspondence: Departamento de Ciencias Ambientales y Recursos Naturales (dCARN) & Instituto de la Biodiversidad Biodiversidad la de &Instituto (dCARN) Naturales yRecursos Ambientales Ciencias de Departamento 1 to differences version between this and theofPleasecite article Version Record. this as Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA,UK CB2 Cambridge Street, Downing Cambridge, University of Sciences, Plant Department of

27 June 2018 27 June http://orcid.org/0000 1 3 1 December2018 INRA, Centre Nouvelle Centre INRA, https://orcid.org/0000 https://orcid.org/0000 Forrest

- - (CIBIO), Universidad de Alicante, P.O. Box 99, 03080 Alicante, Spain Alicante, 03080 99, Box P.O. Alicante, de Universidad (CIBIO), - Pastor: Mazuecos:

- Regular Regular Mazuecos https://orcid.org/0000 6 ,

Marisa Alarcón https://orcid.org/0000 Article BB 1,2 https://orcid.org/0000

Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma Autònoma Universitat Biociències, de Facultat i Ecologia, Vegetal Biologia - de Barcelona, 08193 Bellaterra, Spain Bellaterra, 08193 Barcelona, de CSIC - , LuisJosé Blanco - 0002 Aquitaine al Botanic Garden Edinburgh, 20a Edinburgh, Garden Botanic al - Mazuecos. Mazuecos. - - ICUB), Passeig del Migdia s/n, Parc de Montjuïc, 08038 Barcelona, Barcelona, Montjuïc,08038 de Parc s/n, Migdia del Passeig ICUB), 0003 - - 2929 0002 innovation 7 - Madrid, Spain Madrid, , Poitiers, UR4 (URP3F), 86600 Lusignan, France 86600 (URP3F), UR4 Poitiers, - - 0002 Pablo Vargas 4502 - - 8345 3818 E Spain - UK mail: mail:

- nectar spurs, spurs, nectar - 0002 -

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Inverleith Row, Edinburgh EH3 5LR, EH3 Edinburgh Row, Inverleith -

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keyevolutionary 4 provided byRepositorioInstitucionaldelaUniversidadAlicante , Pau Carnicero . Tel.: +34 914203017 +34 Tel.:

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CORE This article isprotected rights by All copyright. reserved. animal include innovations key considered increas and/or fitness clade clade. resulting increased an to linked causally is that trait individual an in change by given definition the to biodiversity inn evolutionary Key Introduction nectar spur, words: Key     Summary Accepted Article e eeae te ot opeesv pyoey f niriee o ae and date to Antirrhineae of phylogeny the comprehensive reconstructed most the generated We number of species on focus special with tested, was diversification 300 and genera 29 contains which (Plantaginaceae), Antirrhineae tribe the in spurs nectar of shifts. dynamics pollinator of means by angiosperms divers promoting innovation key a considered widely are spurs nectar Floral abiotic factors. diversificati but Antirrhineae, the of dynamics diversification in role a played spurs Nectar was within examined speciation and length spur in changes between association The uncertainty. taxonomic trait using investigated consistent with a fitting length, spur of evolution rates diversification increased with D associated loosely analyses are Diversification spurs spurs. nectar that nectar revealed of acquisitions independent four inferred We tce rt sit wr dlyd ih epc t te custo o te trait the of acquisition the to respect with delayed were shifts rate etected

speciation. (Erwin, 1992; Heard & Hauser, 1995; Hunter, 1998; Rabosky, 2014) Rabosky, 1998; Hunter, 1995; Hauser, & Heard 1992; (Erwin,

can only be fully explained by the complex interaction of multiple biotic and biotic multiple of interaction complex the by explained fully be only can Antirrhineae, Antirrhineae, This effect may result from the invasion of new adaptive zones, zones, adaptive new of invasion the from result may effect This

a scenario of pollinator - . 0 species 400

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propensity for reproductive isolation. isolation. reproductive for propensity

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( 70 speciational - , 0 spurred 80%

shifts drivingshifts diversification diversification, flower, flower, diversification,

pollination, floral zygomorphy and nectar spurs spurs nectar and zygomorphy floral pollination, - independent methods, and accounting for for accounting and methods, independent model, was inferred in inferred was model, W

considered ivsiae te macroevolutionary the investigated e , a key innovation is an evolutionary evolutionary an is innovation key a , ) Linaria . The effect of nectar spurs on on spurs nectar of effect The .

the , as

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Linaria .

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This article isprotected rights by All copyright. reserved. Igea approaches 2016) O'Meara, & (Beaulieu models complex more of development the to led this positives false of rate F m 2016) O'Meara, & Beaulieu increasingly comparisons clade sister classical the include only and innovations key identify to Methods importance mechanisms. ofthese Muchhala & Armbruster cause conversely promotes extinction reduce proposed: been have explanations species clade and specialisation spurs o n between relationship led has shifts rate diversification of location al. sister their than diversity cl species higher significantly exhibit usually clades spurred and 2015) isolation reproductive spurs nectar nectar. A Puzey genus the on research term innov key plant a of example textbook a constitute to come have spurs Dodd (Hodges,1997; hr uhr hv age ta a that argued have authors ther or example or ades, suggesting a consistent positive effect on diversification rates diversification on effect positive consistent a suggesting ades, ethods , 2006) , Accepted Articlen ectar spur ectar

et al. ) .

et al. on speciation is only one possible explanation for the association between floral floral between association the for explanation possible one only is speciation on Indeed, nectar spurs have evolved independently in numerous angiosperm families, families, angiosperm numerous in independently evolved have spurs nectar Indeed, By enhancing pollinator specificity, pollination effi pollination specificity, pollinator enhancing By

dealing with diversification rates diversification with dealing

, 2017) . tighter

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is needed to to needed is may facilitate the transition to a new adaptive new a to transition the facilitate may , sophisticated

Rabosky and Goldberg (2015) Goldberg and Rabosky is

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et al. and thus speciation thus and iiihn te eaie fet o itrpcfc pollination interspecific of effects negative the diminishing ectar spurs and diversification and spurs ectar in in pcaiain y rmtn caatr displacement character promoting by specialisation , 2009) , h nblt fsse ru oprsn o rcsl ipit the pinpoint precisely to comparisons group sister of inability the provide commonly used tests to detect to tests used commonly

, 1999; Sargent, 2004; Kay 1999; Sargent, , mo . Aquilegia oee, m However, del . .

I diversity

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i cer ht a that clear is t Empirical evidence is still needed to determine the relative relative the determine to needed still is evidence Empirical

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(Hodges & Arnold, 1995; Whittall & Hodges, 2007; Hodges, & Whittall 1995; Arnold, & (Hodges

(Fulton & Hodges, 1999; Shivanna, 2014; Minelli, Minelli, 2014; Shivanna, 1999; Hodges, & (Fulton (Armbruster & Muchhala, 2009) Muchhala, & (Armbruster

investigate their macroevolutionary dynamics not not dynamics macroevolutionary their investigate toooia controversy ethodological (Rabosky & Goldberg, 2015; Moore 2015; Goldberg, & (Rabosky fet f pcaie flo specialised of effect

some authors some reported ;

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(Donoghue & Sanderson, 2015) Sanderson, & (Donoghue Soisi Gyr 1993) Guyer, & (Slowinski et al. et model inadequacies model

dynamics diversification analyse to trait space to , 2006) , ciency and reproductive success, success, reproductive and ciency

cast doubt on a on doubt cast -

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This article isprotected rights by All copyright. reserved. regions: (ptDNA) and DNA transcribed twoplastid spacers (ITS) Antirrhineae 2007) Gatesy, & super a adopted we data, sequence available of use full make To sampling Taxonomic methodsMaterials and in increases significant to significantlywith speciation events. associated linked consistently are tribe diver the of evolution the during tested: were hypotheses Two innovation. the in In study, this suitable study test systemto length inspur displaysremarkable variation genus spurred the Antirrhineae, the In evol true, speciation ultimately and isolation premating to lead shift” to linked variable the of mechanisms specific distribution by speciation phylogenetic the also but matters, that innovation by out pointed As background poten spurs of of unrelated diversity species of 80% al. et tra floral specialised their by characterised and in their spurs, species The clude

Accepted Articletrait the , 2015; Guzmán 2015; , sification rates; and and rates; sification nprgn ad eaie ( relatives and snapdragons tially scenario trib Antirrhinum majus Antirrhinum 300 utionary changes in spur length would length spur in changes utionary (Fior lineages . Unlike previously studied systems like systems studied previously Unlike .

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400 species classified into into classified species 400 ( our objective was to niriee ih h aim the with Antirrhineae Supporting Information Supporting , differences in spur length would influence pollinator influence would length spur in differences ,

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most diverse, with diverse, most (Whittall & Hodges, 2007) Hodges, & (Whittall to be associated be to , 2015) , i i nt ut h peec o a of presence the just not is it , model the including Plantaginaceae), olutinary dynamics. dynamics. olutinary

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This article isprotected rights by All copyright. reserved. rates. ondiversification trait singlebinaryeffect a of BiSSE et trait detect to methods Three of twotypes: trait rates diversification spurs nectar that hypothesis the test to methods of range a applied We Diversification rate species notrecognised byeach treatment trees Phylogenetic considered not were subspecies genera monotypic after followed, was included were literature recent in described species distinct as considered Nanorrhinum literature recent literature available on based taxon definedthreealternative 2009) Bernal, & Sáez 2009; Güemes, Antirrhineae the for revisions Some ( of revision taxonomic 2017) genera monotypic new genera the in (particularly Chaenorhinum species new many described have taxonomists Antirrhineae tribe the analyses rate diversification a in recognised are that species of number The treatments Taxonomic Nanorrhinum

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This article isprotected rights by All copyright. reserved. m were models four the under reconstructions choice, model rates diversification speciation model( andextinction (3) fullbinary a (CID character a (1) tested: were models state including the interest of trait the to addition in rates diversification BiSSE HiSSE A simul 1000 of function add.species.to.genus the (using the of clades corresponding the to species unsampled adding randomly g incomplete by sampling 2017) Goldberg, & Rabosky (https://github.com/macroevolution/fisse; FiSSE th describe issues the of some to robust considered but BiSSE, as aim same the with test ( FiSSE on MLunder values parameter the model. fullBiSSE discarded were values. ML on based priors model values AIC by assessed values parameter ML states. (λ) rates transition asymmetrical and includ were treatment taxonomic clade sampling, incomplete for account package

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This article isprotected rights by All copyright. reserved. as suggested for selection divergent by Quaternary endemics narrow related differentiation 2009) Sargent, & al. et Fernández2013a; Blanco 2011; Vargas, & Mazuecos Asia and World New the in regions unoccupied previously by provided e in least at diversification, influence Guzmán 1988; (Sutton, occlusion of levels different with corolla, personate the interactingwit observed be can rates developmental 2016) Theißen, & Melzer 2015; Sanderson, & (Donoghue additional robustness, developmental interest additional pattern this for explanation As also for other traits spurs nectarfor a of evolution recently several for obtained rates higher and early for estimated rates diversification low with depicted is pattern were nested withinspurr of base the at increase subtle possible a for (except 5 delayed of pattern a depicted also clades spurred four increasingly cological Accepted Articlec). Indeed, detected r Indeed,detected , 2018) , to trigger diversification trigger to nrni and intrinsic opportunities climatic cycles climatic . higher rates for spurred than for spurless lineages spurless for than spurred for rates higher

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This article isprotected rights by All copyright. reserved. Accepted RM.Arnold 1982. 2009. N. Muchhala ArmbrusterWS, 2014. WS. Armbruster Santin ME, Alfaro 2005. B. Oxelman HM, Meudt DC, Albach References M.F. M.F. data; collected P.V. ArticleM.F. Author Contributions of Education, reference Sport, Culture and BEST/2014/264) IJCI reference fellowship Cierva la de Juan Cambridge) College, (Trinity Grant Research Trust Newton Isaac an 624396), reference Intra Curie Marie B BC,BCN, Elisens photographs; providing analyses diversification and Igea Javier Otero, Ana thank We Acknowl - - M. wrote the paper with feedback paper M. wrotefrom the allauthors. M.F. research; the designed B.J.G. and M. , American Midland Naturalist diversity: effect, cause, orcorrelation? divergence, fitness trade the United America States of vertebrates. jawed in diversity 2009. LJ. Harmon American Journal ofBotany

Jaime Güemes Jaime edgements

and - 2015

RSA -

uoen Fellowship European Pollination, predation and seed setin and predation seed Pollination, - i F, Brock C, Alamillo H, Dornburg A, Rabosky DL, Carnevale G, Carnevale DL, Rabosky A, Dornburg H, Alamillo C, Brock F, i

23459)

herbaria for providing plant materials providingplant for herbaria ,

S.M.M. Hamdi for providing information on Iranian speci Iranian on information providing for Hamdi S.M.M. ; Jorge Alfredo Reyes Betancort Reyes Alfredo Jorge -

ahw oln fr ehia support; technical for Dorling Mathew . nlsd aa M.F. data; analysed M.

and a Generalitat Valenciana postdoctora Valenciana Generalitat a and Floral specialization and angiosperm diversity: phenotypic phenotypic diversity: angiosperm and specialization Floral species explain turnover high plus radiations exceptional Nine

to M.F. to - offs and accuracy. pollination realized

92 1

107 - 06 M.

: 297 rceig f h ainl cdm f cecs of Sciences of Academy National the of Proceedings Associations between floral specializa floral between Associations : 13410

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aal ui d Casas de Rubio Rafael (Spanish Ministry of Economy and Competitivity, and Economy of Ministry (Spanish LINARIA - 315. - Evolutionary Ecology 369.

- 13414. Piecing together the "new" Plantaginaceae. Plantaginaceae. "new" the together Piecing

- . J.L.B. M.,

- - . PV an P.V. M., SPECIATION , Isabel Liberal Isabel ,

Linaria vulgaris Linaria . .

- This work was supported bythe supported was work This P., A.J., P.C., A.F., M.A. and and M.A. A.F., P.C., A.J., P., d B.J.G. interpreted results; results; interpreted B.J.G. d

(FP7 for useful discussion on on discussion useful for

23 l grant grant l

: 159 AoB Plants Cecilia Martínez for for Martínez Cecilia and the MA the and - PEOP

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This article isprotected rights by All copyright. reserved. AcceptedGarcia L, Sáez P, Carnicero Copsey M, Couchman H, Tavares D, Field A, Whibley II, Mohorianu P, Xu D, Bradley 2011. BJ. Glover RM, Bateman PJ, Rudall S, Dodsworth MS, Box Rambau MA, Suchard D, Xie CH, Wu T, Vaughan D, Kühnert J, Heled R, Bouckaert Bouchenak Blanco ArticleBlanco Blanco C Benedí 2010. PS. Soltis DE, Soltis CD, Bell 2016. BC. O'Meara JM, Beaulieu JM,JM, AlcántaraBastida Re - - - meet in a Mediterranean genus: the biogeographic history of of history biogeographic the genus: Mediterranean (Plantaginaceae). a in meet 2017. selection onregulatory RNAs. al. small et M Li R, Carpenter L, 68 Linaria analysis. 2014. AJ. Drummond A, complexityevolutionaryradiations. oftriggering and incomplete lineage sortinginMediterranean 5651 in speciation geographical versus expansion lo range Quaternary: the during plants Mediterranean in strategies of Biology radiation recent a in variation floral explain Madrid: CSIC, eds. J, Güemes E, Rico C, revisited. dependent extinction. and speciation contrastingradiations. Aquilegia Pastor JL, Vargas P, Pfeil BE. 2012. BE. Pfeil P, Vargas JL, Pastor 2013. P. Vargas JL, Pastor 20 P. Vargas JM, Gómez IM, Liberal D, Romero C, Ornosa JL, Pastor , Güemes J 2009. GüemesJ , : 703 ‐ - 5668. hlai , nti R, ig , cwr O Lne H. 2015. HP. Linder O, Schwery Y, Xing RE, Onstein Y, Khelladi -

28 714. KNOX genes suggests a role in petal in role a suggests genes KNOX PLoS Computational Biology Computational PLoS : the biogeographical and ecological patterns of two simultaneous but but simultaneous two of patterns ecological and biogeographical the : American JournalAmerican ofBotany : 851

167 - 863. Taxon - 198.

Chaenorhinum

- Plant Systematics andEvolution Plant Jacas N, Galbany N, Jacas

66 y PJ, Vargas P,PJ,Herrera 2010. CM. Vargas y

: 393 BEAST 2: a software platform for Bayesian evolutionary evolutionary Bayesian for platform software a 2: BEAST Flora iberica XIII (Plantaginaceae XIII iberica Flora

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: 1296 Evolution of flower color pattern through through pattern color flower of Evolution Coalescent simulations reveal hybridization hybridization reveal simulations Coalescent : e1003537. - Casals M. 2017. M. Casals Rchb. In: Castroviejo S, Herrero A, Benedí Benedí HerreroA, S, In:Castroviejo Rchb.

358 - - s 1303. pur development. pur : 92 : Linari New Phytologist

ersification shifts in models of trait of models in shifts ersification Linaria 5 Linaria

- 928.

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Different speciation types speciation Different . Journal of Evolutionary Evolutionary of Journal

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207 Characterization of of Characterization Scrophulariaceae) The Plant Journal Plant The

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This article isprotected rights by All copyright. reserved. AcceptedFernández Fernández Fernández Fernández Fernández A. Hudson E, Coen A, Hannah A, Bangham R, Kennaway J, Bowers Y, Wilson X, Feng 2016. JC. Svenning WL, Eiserhardt S, Faurby Article1992. DH. Erwin 1963. PI. Dorofeev 2015. MJ. Sanderson MJ, Donoghue 1999. MW. Chase J, Silvertown ME, Dodd 2007. J. Gatesy A, Queiroz De 2012. D. Posada R, Doallo GL, Taboada D, Darriba Fernández E, Cullen oncin bten uoe n Arc i bfd odlxs ( toadflaxes bifid in Africa and Versicolores Europe between connections genotyping of robustness and power radiations: sequencing. plant recent Resolving &Ecology E evolutionaryconsequences. ( ( toadflaxes bifid in Versicolores rates diversification influences morphology 2009. o opinion 6 SSSR. diversification. species diversity variation &Evolution heuristics and parallel comput of Botany of clade Li : 133 naria naria - - - - - aucs , lvr J 2017. BJ. Glover M, Mazuecos Blanco M, Mazuecos Blanco M, Mazuecos Mazuecos M, Vargas P. 2011. P. Vargas M, Mazuecos 2018. BJ. Glover P, Vargas L, Sáez B, Vigalondo G, Mellers M, Mazuecos

Evolution ofallometryEvolution in -

147. Linaria Linaria Mill.) based on nuclear internal transcribed spacer sequences: systematic and systematic sequences: spacer transcribed internal nuclear on based Mill.) n diversification analyses.

122

A preliminary classification of evolutionary radiations. radiations. evolutionary of classification preliminary A

Systematic Biology Systematic ). ).

22 volution Tretichnye flory flory Tretichnye : 801 Annals of Botany Annals of PLOS ONE - : 34 New Phytologist Mazuecos M, Glover BJ. 2018. BJ. Glover M, Mazuecos reflects changes in cell division rather than in cell expansion. expansion. cell in than rather division cell in changes reflects - - 809. 41.

1 : 0110.

The supermatrix approach to systematics. to approach supermatrix The

amongangiosperm families. 6 - Pastor JL, Vargas P. 2013b. P. Vargas JL, Pastor : e22234. International JournalSciences ofPlant - Pas

ing.

Antirrhinum 67 112

207 o J, óe J, ags . 2013a. P. Vargas JM, Gómez JL, tor ofune snoain ad eaprn i plant in depauperons and synnovation, Confluence, Nature Methods Nature : 250 Methods inEcology andEvolutionMethods : 1705 : 260

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7 : 234 Linaria Linaria Linaria : 4 - 744. - 13.

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Nature Nature Annals sect. sect. sect. - by -

This article isprotected rights by All copyright. reserved. 1995. DL. Hauser SB, Heard 2017. P. Vargas JM, Gómez B, Guzmán 2015. P. Vargas JM, Gómez B, Guzmán 2017. JF. Mota J, Güemes 2009. J Güemes 1997. J. Güemes 1989. A. Grafen 2008. B. Igić EE, Goldberg Thulin B, Bremer M, Ghebrehiwet 2000. M. Ghebrehiwet 1999. SA. Hodges M, Fulton Fi 2012. RG. FitzJohn 2013. C. Varotto L, Ometto SA, Hodges R, Viola B, Oxelman M, Li S, Fior

Accepted Article 2009. SP. Otto WP, Maddison RG, tzJohn mechanisms. toAntirrhineaevisitors relatives)? (snapdragons and and Syste (Antirrhineae). relatives and snapdragons from Spain. Almería, Sierra Gádor, de 166. eds. Jardín Botánico de Society ofLondon. 2727 and morphological Systematics andEvolution on based (Scrophulariaceae) Nanorrhinum pu 611. phylogenies. resolved incompletely from rates extinction MethodsEvolution inEcology and 198 next reconstruction Spatiotemporal bescens : 579 ‐

- lr ieia II (Plantaginaceae XIII iberica Flora 2741 eeain eunig f ail eovn cDA regions. cpDNA evolving rapidly of sequencing generation - matics 592.

. Antirrhinum Antirrhinum

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Proceedings of the Royal Sciences SocietyProceedings B: Biological The phylogenetic regression. regression. phylogenetic The

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(Scrophulariaceae). Diversitree: comparative phylogenetic analyses of diversification in R. R. in diversification of analyses phylogenetic comparative Diversitree:

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aooy pyoey n boegah of biogeography and phylogeny Taxonomy, Gadoria

On phylogenetic tests of irreversible evolution. irreversible of tests phylogenetic On L. In: Castroviejo S, Herrero A, Benedí C, Rico E, Güemes J, Güemes E, Rico C, Benedí A, Herrero S, Castroviejo In: L. -

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10 Nordic Journal ofBotany Nordic

. 2000. M. : 151 3 f the of - - 493. : 1084 239.

Is floral morphology a good predictor of floral floral of predictor good a morphology floral Is

Phytotaxa es n eouin f cldd ools in corollas occluded of evolution and Bees -

173.

– - siaig trait Estimating Philosophical Transactions of the Royal Royal the of Transactions Philosophical esetvs n ln Eooy Evolution Ecology, Plant in Perspectives 1092.

Scrophulariaceae)

Aquilegia Aquilegia hlgn o te rb Antirrhineae tribe the of Phylogeny

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qiei formosa Aquilegia : 119 Plant Biology : 201 ndh - Systematic Biology Systematic - 157. ai rdain through radiation rapid 221. - F sequence data. data. sequence F

dependent speciation and and speciation dependent 20 : a new genus, endemic endemic genus, new a : : 655

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This article isprotected rights by All copyright. reserved. Accepted 2014. RG. FitzJohn WP, Maddison 2007 TH. Oakley A, Singh AØ, Mooers S, Blay C, Lee Stones A, Wilson R, Moir M, Kearse Huffo JY, Yang C, Voelckel KM, Kay 2009. RD. Sargent KM, Kay 2008. H. Toh K, Katoh 2008. P. Kampstra Article2009. VSFT. Merckx EF, Smets S, Huysmans EB, Knox SB, Janssens 2017. AJ. Tanentzap AST, Papadopulos EF, Miller J, Igea 1998. JP. Hunter 1995. ML. Arnold SA, Hodges 1997. SA. Hodges 2003. DA. Baum EM, Kramer LC, Hileman tests for categorical character Bioinformatics phylogenies. on evolution character continuous of models comparing data. sequence of analysis and organization the for platform software desktop extendable 2012. al. et C Duran S, Markowitz A, Cooper evolution flowers of eds. SCH, Barrett LD, Harder In: diversification. species and characters Systematics genetics. and geography, ecology, program. Software, CodeJournal ofStatistical Snippets change. Impatiens e2002792. a across diversification speciescorrelate with evolution Evolution innovation? Sciences Sciences morphologies. floral of evolution the Bioinformatics Molecular PhylogeneticsandEvolution

158 100 Briefing

13

(Balsaminaceae) during Pliocene and Pleistocene: result of a global climate climate global a of result Pleistocene: and Pliocene during (Balsaminaceae)

Key innovations and the ecology of macroevolution. of ecology the and innovations Key

40 Proceedings ofthe Royal Sciences Society B: Biological : 31

: 81 : 12814 F Beanplot: A boxplot alternative for visual comparison of distributions. distributions. of comparison visual for alternative boxplot A Beanplot: loral nectar spurs and diversification. diversification. and spurs nectar loral : 637

2006 - - 36. 88.

s inBioinformatics Recent developments in the MAFFT multiple sequence alignment alignment sequence multiple MAFFT the in developments Recent - . Oxford: University Oxford Press,

: 183 -

656.

28 12819.

: 1647 The role of animal pollination in plant speciation: integrating speciation: plant in pollination animal of role The

- 186. key a spurs nectar floral are diversification: plant Spurring

s. - 1649.

Systematic Biology Systematic

The unsolved challenge to phylogenetic correlation correlation phylogenetic to challenge unsolved The -

aa S Cen M Surc S B S, Sturrock M, Cheung S, Havas d M Ksa D Hde S 2006. SA Hodges DD, Kaska KM, rd

9 nul eiw f clg, vlto, and Evolution, Ecology, of Review Annual : 286

Differential regulation of symmetry genes and and genes symmetry of regulation Differential rceig o te ainl cdm of Academy National the of Proceedings - 298.

28

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nentoa Junl f Plant of Journal International 311 ngiosperms. - 824.

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Trends in Ecology & Ecology in Trends

Rapid radiation of of radiation Rapid PLOS Biology PLOS

262 : 3 Evolutionary Evolutionary Ecology and and Ecology 43 xo S, uxton - 348.

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: This article isprotected rights by All copyright. reserved. Accepted 2014. DL. Rabosky 2010. DL. Rabosky Mah EM, Kramer SA, Hodges SJ, Gerbode JR, Puzey 2004. DA. Baum RK, Oyama Orme 2012 D 2016. JC. Vamosi E, Ogutcen 2017. JC. Vamosi DB, King J, Theriault E, Ogutcen LC, Hileman CR, Hardy LD, Article Harder WS, Armbruster SD, Smith BC, O'Meara 2016. JP. Huelsenbeck B, Rannala MR, May S, Höhna BR, Moore 2015. A. Minelli 2016. G. Theißen R, Melzer 2001. HD. Mai 2011 DR Maddison WP, Maddison dependence onphylogenetictrees. Evolution Proceedings Society ofthe Royal B: Sciences Biological in diversity length (Veronicaceae). URL document] [WWW American Journal ofBotany l and duplications Ecology,in Plant Evolution andSystematics modes. pollination and shifts range of contribution the (Plantaginaceae): Royal Sciences SocietyBiological B: diversity. angiosperm extant shape interactions trait floral and Sm S, Magallón A, Litt L, Hufford mixtures. macroevolutionary of Proceedings Academy ofthe National ofSciences analysis Bayesian of performance and theory the developmental biology. dive Paläobiologie. und Abteilung B Fundstellen III: Teil Lausitz. der in Folge URL document] [WWW rsity. . The . The

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- - This article isprotected rights by All copyright. reserved. RW.2011. Scotland AcceptedSchäferhof 2018. S. Magallón H, Sauquet 2004. RD. Sargent Sánchez 2009. M Bernal L, Sáez Liu LargetB, S, Höhna A, Darling DL, P,Ayres Markder van M,F,Teslenko Ronquist 2013 LJ. Revell Article2012. LJ. Revell 2014 AJ Drummond D, Xie MA, Suchard A, Rambaut 2014. M. Assadi I, Mehregan SMM, Hamdi T, Nejadsatari A, Rahmani An M, Grundler DL, Rabosky 2017. EE. Goldberg DL, Rabosky 2015. EE. Goldberg DL, Rabosky chloroplast sequences. 2010. New Phytologist the Royal Biological Sciences Society B: Botany Annals of with study experimental an flowers: complex CSIC, eds. J, Güemes space. model largeBiology a across choice 2012. model and JP. inference phylogenetic Huelsenbeck MA, Suchard L, MethodsEvolution inEcology and things). URL European JournalBiology ofExperimental of analysis phylogenetic trees. 2014. binarycharacter onlineage rates. diversification dependent speciation. - Lafuente AM. 2007. AM. Lafuente f B, Fleischmann A, Fischer E, Albach DC, Borsch T, Heubl G, Müller KF. KF. Müller G, Heubl T, Borsch DC, Albach E, Fischer A, Fleischmann B, f http://tree.bio.ed.ac.uk/software/tracer/

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Accepted Blanco LM, Valente P, argas Article s P, Rosselló JA, Oyama R, Güemes J. 2004. J. Güemes R, Oyama JA, Rosselló P, s Fernández independent three Old. and the Evolution and (Scrophulariaceae) World New Antirrhineae the from lineages tribe evolutionary the in genera Antirrhinum tongued bees. ( snapdragons of corolla and traits reproductive diversity, species lineages: geographical isolation. Mediterranean of origin nuclear DNApolymorphisms. Antirrhinum 69 extinction. and speciation plant flowering of patterns genome whole follow often rates duplications. diversification increased diversification: 2015. LJ. Harmon EB, Sessa and speciation random of extinction. model a on based method improved an diversification: eds. KR, Shivanna JM, Mérillon KG, Ramawat In: pollinators. potential of restriction and breeding systemsofthe species. ( toadflaxes related - oaus G Mateu JG, Moragues : 685 ReproductiveBiology ofPlants - 706.

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Srpuaica) pcain ic te loee ae o patd and plastid on based Pliocene the since speciation (Scrophulariaceae) New Phytologist Biotic pollination: how plants achieve conflicting demands of attraction of demands conflicting achieve plants how pollination: Biotic : 151 Plant Biology Plant - Mazuecos M, Heleno R. 2018. R. Heleno M, Mazuecos - specialized? specialized? - 172. Linaria Plant Biology Plant - 2010. J. Arroyo FJ, Sanchez Antirrhinum - nrs . 2007. I. Andrés -

Pastor JL, Liberal I, Guzmán B, Cano E, Forrest A, A, Forrest E, Cano B, Guzmán I, Liberal JL, Pastor

, Plantaginaceae) and their correspondence with the the with correspondence their and Plantaginaceae) , 19 Testing whether certain traits have caused amplified amplified caused have traits certain whether Testing

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This article isprotected rights by All copyright. reserved. Accepted 2016. G. Heubl S, Zarre N, Yousefi Article 2015. EM. Kramer C, Levy JR, Puzey S, Collani L, Yant 1995. M. Nei S, Kumar Z, Yang 2011. A. Hudson Y, Wilson 2007. SA. Hodges JB, Whittall 2003. JW. Kadereit KB, Hagen von niriee, ih ou o tx i te lr Iaia region. Iranica Flora Botany the in taxa on focus with Antirrhineae), genera B: Sciences Biological the of elaboration dimensional amino acid sequences. 1032 hybridizations. repeated survived combinations phenotype columbine flowers. ecological key versus innovation. opportunity flora. Madrean the and snapdragons phylogenetics: molecular using palaeofloras - 1043. Journal ofBiogeogra

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This article isprotected rights by All copyright. reserved. Accepted Article

This article isprotected rights by All copyright. reserved. Accepted Article

This article isprotected rights by All copyright. reserved. Accepted Article

This article isprotected rights by All copyright. reserved. Accepted Article

This article isprotected rights by All copyright. reserved. Accepted Article