Appendix 1

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AY279930 AY279827. Westneat and Alfaro (2005); Read et al. (2006);. Macropharyngodon kuiteri. □ □ □. DQ164134 DQ164169 DQ164152. Read et al.
Appendix 1 TEXT SUPPLEMENTAL RESULTS: Description of phylogenetic trees from Appendix 2 (Fig S1-8) with a comparison between maximum likelihood and Bayesian support values

SUPPLEMENTAL DISCUSSION: Discussion of several methodological considerations concerning affect of incomplete taxon sampling, underparameterization and the uses of LTT plot to infer changing tempo of lineages accumulation.

TABLES Table S1. Information on taxa sampled in each family, accession number for GenBank sequences, and primary publication source. Table S2. Information on gene regions included in family datasets Table S3. Ages estimated under both unpartitioned and partition model analyses, with ages estimated from previous studies for each family where available. Table S4. Results from Moment’s Estimation for additional reef fish families and gastropod genera. Table S5. Estimated net diversification rates for reef fish families and their % reef occupancy.

Supplemental Results PHYLOGENETIC RECONSTRUCTION Within the Labridae all major tribes had high support from both ML and BI analyses. There was also agreement between both methods for several lineages containing taxa from the paraphyletic genera Coris and Halichoeres (Table S3). There was disagreement between ML and BI for the relationship between the cheilines, labrines and scariness (Fig S1-2, Appendix 2). The best ML tree reported a closer relationship between cheilines and labrines, while the maximum clade credibility tree of the Bayesian analyses showed a closer relationship between cheilines and scarines. While there was low bootstrap support for the branching order between these three tribes, Bayesian posterior probability displayed high support for a sister group relationship between cheilines and scarines (Fig S1-2, Appendix 2). Overall the tree is consistent with most previous studies (Table S3) but with increased taxon sampling clarifying some resolution of some unresolved lineages, particularly within the Julidine tribe (Fig S2, Appendix 2). Highest support was observed within the Chaetodontidae with all major lineages having both 90-100 percent bootstrap support and 0.9-1.0 posterior probabilities (Fig S3-4, Appendix 2). All ten genera are monophyletic (Fig S4, Appendix 2). Lowest support values for both bootstrap and posterior probabilities were observed in the Chaetodon clade IV lineage. This phylogeny is highly congruent with previous studies (Table S3; Fig S4, Appendix 2). Within the Pomcentridae there was high Bayesian posterior support for the major tribes of the Stegastinae, Lepidozyginae, Chrominae, Abudefdufinae, and Pomacentrinae (Fig. S5, Appendix 2). The same topology was reflected by moderate to high ML bootstrap support (Fig S6, Appendix 2). Several genera received high

support in both analyses as monphyletic clades (e.g. Amphiprion, Pomacentrus, Neopomacentrus, Dischistodus). In general, Bayesian posterior probabilities gave higher support for reported lineages than ML bootstrap values. The topology is in strong agreement with a recent published phylogeny for the family (Fig S6, Appendix 2) Within the Apogonidae, both ML and BI methods support the placement of Siphamia and Pseudamia outside of the crown Apogonidinae, (Fig S7-8, Appendix 2). Bayesian posterior probabilities show high support (0.9-1.0) for a basal split in the Apogonidinae with the Rhabdamia et al, and Phaeoptyx et al. lineages, and a major lineage containing several sub-groups of Apogon (Fig. S8, Appendix 2). Other lineage relationships supported by Bayesian analyses were Zoramia & Ostorhinchus 1/Apogon & Archamia/ Ostorhinchus 3. The branching order between major lineages was not highly supported by ML bootstrapping, however, several crown lineages received moderate to high bootstrap support (Fig. S7, Appendix 2) and are congruent with BI posterior probabilities (Fig. S8, Appendix 2). While some nodes were not highly supported, the overall topology is congruent with previous studies (Fig. S8, Appendix). Genetic distance observed between sequences reported as the same taxa, and the separation between taxa reported as the same genera (eg. Zoramia) highlights difficulties in identification of apogonid species the need for taxonomic revision of this family.

Supplemental discussion METHODOLOGICAL CONSIDERATIONS Model Selection The phylogenetic reconstructions and age estimations presented here may be constrained by both model selection and incomplete taxon sampling. All family datasets underwent full Bayesian inference estimation of topology, branch lengths and age estimation under both, an unpartition, and a partitioned by gene model scheme. However, only the partitioned model analyses of the Chaetodontidae and the Pomacentridae reached convergence in both parameter and tree space. Model underparameterization can lead to bias in age estimation and subsequently in the estimation of diversification rates, which may result in the erroneous observation of decreasing rates of diversification over time based on the γ-statistic of Pybus and Harvey (2000) (see Revell et al. 2005). Fortunately, none of the four families exhibited decreasing rates over time (CR, MCCR, Table 4). Furthermore, model parameters for both unpartitioned and partitioned analyses included invariant sites and allowed for rate heterogeneity within general time reversible models (Table S2, Appendix 1), all of which can reduce the potential of bias in the γ-statistic (Revell et al. 2005). In addition, comparisons between unpartition and partitioned model analyses revealed little difference in topology or 95% HPD intervals of age estimates. Incomplete and biased taxon sampling Regarding taxon sampling, bias may occur from both overall incomplete sampling of the families, and from the biased (non-random) sampling within clades (Cusimano and Renner 2010). Both these factors will affect the estimation of

lineages ages and often result in an observed slowdown in rates of diversification towards the present. While the datasets for each of the four focal families are the largest to date they do not have complete taxon sampling. For both the Labridae (~50% sampled) and Chaetodontidae (75% sampled), comparison with previously published age estimated of studies with lower taxon sampling (Cowman et al. 2009, 18%; Bellwood et al. 2010, 44%) revealed little difference in overall topology or age estimates (Table S3). Regarding the Pomacentridae, as this is the first instance were ages have been estimated of the entire family, so no inference can be made on the possible effects of taxon sampling for the group, however, all lineages and genera are sampled for this family. A study by McCafferty et al. (2002) estimated the crown age of the genus Dascyllus at 16MY (11.7-21 95% CI) which is congruent with the age estimated by this study; 13.6MY (10.3-17.1). Incomplete or non-random sampling may have biased the overall topology and age estimates for some lineages of the Apogonidae. While the CR and MCCR test did not reveal a significant slowdown in rates over time, there was an observed decrease in the rate during the Miocene. If this is a biased result from taxon sampling, increased sampling would inflate rates in this time period (Miocene) which would be congruent with the rate increase seen in the Labridae, Pomacentridae and the Chaetodontidae. This highlights the need for a rigorous systematic assessment of the family Apogonidae to further elucidate the observed patterns. Fortunately while addition of more taxa and sequence data will increase the precision of both age and rate estimates, even a reasonable approximation of lineage ages are sufficient to approach a theoretical minimum variance in speciation rate estimates (Wertheim and Sanderson 2010). LTT plots and diversification statistics

Often LTT plots are used to infer the evolutionary affects of some underlying ecological drivers in the past, such as adaptive radiations, or changing speciation/extinction rates, to explain the variation in rates of lineage accumulation. However, interpreting LTT plots based on branching times of a chronogram without complete taxon sampling can potentially be misleading. Undersampling of younger lineages will deflate rates at the tips of the trees. To account for this, in the present study, exploration of patterns and diversification models was restricted to the first 70% of the history of the Labridae, Pomacentridae and Apogonidae, and the first 90% of the Chaetodontidae. Susequent LTT plots and model comparisons revealed moderate support for congruent patterns between the four reef fish families. In each case an upturn in diversification rate in the late Eocene to early Oligocene follows either low (Apogonidae) or decreasing diversification rates (Labridae, Pomacentridae) in the Paleo-Eocene. This upturn is synchronous with the origin of the Chaetodontidae and the appearance of significantly more species rich lineages associated with coral reefs. The RC test identifies nodes where subtending lineages deviate from a constant rate of cladogenesis. While the RC test itself is susceptible to type 2 error, the nodes identified by this test were congruent with nodes found by the MEDUSA analyses with the exception of the Julidine node in the Labridae. This exception may be due to a limitation in the MEDUSA analysis where a rate shift can only be placed on the stem of a lineage where species richness can be assigned. The placement of a rate shift by the RC test within the Julidine lineage is supported by the presence of significantly more diverse lineages than expected (Table 3, Fig 1A). This highlights at least to some extent the utility of the RC test, which is largely superseded by the MEDUSA analysis. This may also explain the lack of a rate shift placement by the

MEDUSA analysis on the Chrominae lineage (Pomacentridae), while moments estimation identified the crown lineage as being significantly more diverse (Fig 2B, Table S3). However, all statistics (RC test, MEDUSA, moments estimator) show congruent evidence for shifts in the rate of cladogenesis within the Oligocene/Miocene, offering some confidence in the observed patterns.



AF517587 GQ341585 DQ197923

Achoerodus viridis











Anampses caeruleopunctatus











Anampses geographicus Anampses lineatus Anampses meleagrides Anampses neoguinaicus





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■ ■

■ ■ ■ ■

Anampses twistii Austrolabrus maculatus

■ ■

■ ■

Bodianus anthioides Bodianus mesothorax Bodianus oxycephalus Bodianus perditio Bodianus pulchellus Bodianus rufus Bodianus scrofa

FJ582831 DQ164139 DQ164157 DQ164174





AY279576 AY279679 FJ582847 AY279885 AY279782 AY850807AY850870 AY850745





AY279577 AY279680 AY279886 AY279783 FJ582899











■ ■ ■ ■





AY279574 AY279677 EF609278 AY279883 AY279780 AY279575 AY850746 AY279884 AY279781 AJ810125 DQ164173 DQ164156

■ ■

Accession Number

S7



Tmo4c4

CytB



Rag2

COI

Acantholabrus palloni

16s

Labridae

12s

Table S1. Sequence data for each of the four focal families. Black square indicate presence of gene region for that species. GenBank accession numbers and source publications are given.



AY279578 AY279681 AY279887 AY279784 FJ237626 DQ885066 FJ582902

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AY279579 AY850866 AY850741AY279888 AY279785 AF517582 GQ341586 DQ197931

Source Hanel et al (2002); Kazancouigla et al (2009); Read et al. (2006) Westneat and Alfaro (2005); Ward and Holmes (2007) Westneat and Alfaro (2005); Read et al. (2006); Barber and Bellwood (2005) Arnal et al. (2006); Read et al. (2006) Steinke et al. (2009) Read et al. (2006) Westneat and Alfaro (2005); Steinke et al. (2009) Barber and Bellwood (2005) Westneat and Alfaro (2005) Steinke et al. (2009) Westneat and Alfaro (2005) Zhang and Hanner (unpubl.) Read et al. (2006) Steinke et al. (2009) Westneat and Alfaro (2005); Barber and Bellwood (2005); Hanel et al (2002); Kazancouigla et al

■ ■ ■

Bodianus speciosus Bodianus tanyokidus Bodianus unimaculatus Bolbometopon muricatum





Calotomus carolinus





Calotomus spinidens





Centrolabrus caeruleus Centrolabrus exoletus

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■ ■

Centrolabrus trutta





Cetoscarus bicolor





Cheilinus chlorourus



Cheilinus fasciatus





Cheilinus oxycephalus



Cheilinus trilobatus Cheilinus undulatus







GQ341587 FJ237633 EF609299

























EU601178 AY081091 AY081126 EU601307 AY081108 EU601179 AY081092 FJ237667 EU601358 EU601308 AY081109



EU601180 EU601228 EU601359 EU601309 EU601265 AF414194 AY092034



EU601224 EU601260 GQ341588 EU601403 EU601353 EU601303 GQ341613 AY092046 AY092035 GQ341614







EU601181 AY081088 AY662758 AY081123 EU601310 AY081105 AJ810127 EF609321















■ ■

AY279580 AF517580 FJ583120AY279889 AY279786 AY279581 AY279684 FJ583124AY279890 AY279787 AJ810128









EU601220 AY279685 EF609322 EU601399 AY279891 AY279788

Cheilio inermis











Chlorurus bleekeri









AY279583 AY850867 AY850742 AY279892 AY279789 EU601182 EU601230 EU601361 EU601311 EU601267







(2009); Read et al. (2006) Kazancouigla et al (2009) Zhang and Hanner (unpubl.) Ward and Holmes (2007) Smith et al. (2008); Almada et al. (unpubl.); Smith et al. (2008); Almada et al. (unpubl.); Zhang and Hanner (unpubl.); Smith et al. (2008) Almada (unpubl.) Smith et al. (2008); Kazancouigla et al (2009); Almada et al. (unpubl.); Almada et al. (unpubl.); Kazancouigla et al (2009); Smith et al. (2008); Almada et al. (unpubl.); Sparks and Smith (2004); Arnal et al. (2006); Ward and Holmes (2007); Westneat and Alfaro (2005); Hanel et al (2002); Steinke et al. (2009); Westneat and Alfaro (2005); Steinke et al. (2009); Arnal et al. (2006) Smith et al. (2008); Westneat and Alfaro (2005); Ward and Holmes (2007); Smith et al. (2008) Westneat and Alfaro (2005); Barber and Bellwood (2005); Smith et al. (2008)

Chlorurus bowersi











Chlorurus capistratoides











Chlorurus japanensis











Chlorurus microrhinos











Chlorurus oedema











Chlorurus sordidus











Choerodon anchorago









Choerodon azurio





Choerodon cephalotes Choerodon fasciatus Choerodon oligacanthus Choerodon rubescens Choerodon schoenleinii Choerodon venustus Cirrhilabrus cyanopleura Cirrhilabrus exquisitus Cirrhilabrus flavidorsalis Cirrhilabrus lubbocki Cirrhilabrus rubrimarginatus Cirrhilabrus rubriventralis





EU601183 EU601231 EU601362 EU601312 EU601268 EU601184 EU601232 EU601363 EU601313 EU601269 EU601209 EU601250 EU601388 EU601338 EU601288 EU601185 EU601233 EU601364 EU601314 EU601270 EU601186 AY081090 AY081125 EU601315 AY081107 AY279584 AY279687 AY081124 AY279893 AY081106 AY279585 AY279688 AY279894 AY279791 AB121235 AB084421 FJ237706



EF609329







■ ■



AY081079 AY081097 AY081132 AY081114 AF121218

Smith et al. (2008) Smith et al. (2008) Smith et al. (2008) Smith et al. (2008) Smith et al. (2008); Almada et al. (unpubl.); Westneat and Alfaro (2005); Almada et al. (unpubl.) Westneat and Alfaro (2005) Mabuchi et al. (2004); Zhang and Hanner (unpubl.) Ward and Holmes (2007) Almada et al. (unpubl.)



AY279587 AY279690 FJ583238 AY279896 AY279793 FJ583239

Nelson et al. (unpubl.) Ward and Holmes (2007) Westneat and Alfaro (2005); Ward and Holmes (2007) Ward and Holmes (2007) Steinke et al. (2009) Steinke et al. (2009) Steinke et al. (2009) Westneat and Alfaro (2005); Steinke et al. (2009); Steinke et al. (2009)



FJ583241

Steinke et al. (2009)



■ ■



■ ■ ■ ■ ■

EF609330





AY279586 AY279689 EF609331 AY279895 AY279792 EF609332 FJ583215 FJ583221 FJ583223







FJ583245

Cirrhilabrus scottorum Clepticus parrae





Coris atlantica Coris aurilineata Coris aygula

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■ ■

■ ■ ■





Coris batuensis











Coris dorsomacula Coris flavovittata Coris formosa Coris gaimard

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■ ■





■ ■ ■ ■

Coris julis







Coris picta Coris pictoides Cryptotomus roseus

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■ ■ ■

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Ctenolabrus rupestris







Cymolutes praetextatus









Cymolutes torquatus









Diproctacanthus xanthurus









Epibulus insidiator













AY279588 AY279691 AY279897 AY279794 GQ341590 AY850839 AY850902 AY850777 AY279589 AY850894 AY850769 AY279898 AY279795 AY279591 AY850918 AY850793 AY279900 AY279797 AY850830 AY850893 AY850768 AY850832 AY850895 AY850770 FJ583260









AY279590 AY850889 AY850764 AY279899 AY279796 AJ810130 AY092044 GQ341591 AY328856 AY329669 AY850829 AY850892 AY850767 AY850840 AY850903 AY850778







EU601188 AY279695 AY081131 AY279901 AY081113 AJ810131 AF517586 GQ341592



AY279593 AY279696 AY279902 AY279799 AY279594 AY279697 AY279903 AY279800 AY279595 AY279698 AY279904 AY279801 EU601222 EU601259 EU885925 AY279905 AY279802

Steinke et al. (2009) Westneat and Alfaro (2005) Kazancouigla et al (2009) Barber and Bellwood (2005) Westneat and Alfaro (2005); Barber and Bellwood (2005); Westneat and Alfaro (2005); Barber and Bellwood (2005); Barber and Bellwood (2005) Barber and Bellwood (2005) Steinke et al. (2009) Westneat and Alfaro (2005); Barber and Bellwood (2005); Arnal et al. (2006); Almada et al. (unpubl.); Kazancouigla et al (2009); Bernardi et al. (2004) Barber and Bellwood (2005) Barber and Bellwood (2005) Smith et al. (2008); Westneat and Alfaro (2005); Almada et al. (unpubl.); Arnal et al. (2006); Hanel et al (2002); Kazancouigla et al (2009); Westneat and Alfaro (2005) Westneat and Alfaro (2005) Westneat and Alfaro (2005) Smith et al. (2008)

Eupetrichthys angustipes Gomphosus caeruleus Gomphosus varius

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■ ■

Haletta semifasciata





Halichoeres argus





Halichoeres bathyphilus Halichoeres binotopsis Halichoeres biocellatus Halichoeres bivittatus Halichoeres brasiliensis Halichoeres brownfieldi Halichoeres burekae Halichoeres chloropterus Halichoeres chrysus

AB121250



■ ■















■ ■

■ ■ ■ ■

■ ■ ■

■ ■ ■



AY279597 AY279700 FJ583460 AY328858 AY279906 AY279803 AY329641 AY279656 AY279759 AY279965 AY279862 AY279598 AY850910 AY850785 AY279907 AY279804 EF185124 AY850845 AY850908 AY850783 AY850852 AY850915 AY850790









■ ■

AY328984 AY328857 AY329640

AY279599 AY850880 AY850755 AY823568 AY279908 AY279805 EF488024 AY823577



AY850860 AY850923 AY850798



EF185121







AY850861 AY850924 FJ583490







AF285919 AY850916 AY850791

■ ■ ■

AY591379

Halichoeres cyanocephalus Halichoeres dispilus Halichoeres garnoti

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■ ■

■ ■

Halichoeres hartzfeldii











Halichoeres hortulanus











AY850813 AY850876 AY850751





AY850819 AY850882 AY850757 AY591375 EF488018 AY279600 AY850873 AY850748 AY279909 AY279806 AJ810133 AY850886 AY850761 AY279910 AY279807 EF488031

Mabuchi et al. (2004) Bernardi et al. (2004) Westneat and Alfaro (2005); Steinke et al. (2009); Bernardi et al. (2004) Westneat and Alfaro (2005) Westneat and Alfaro (2005); Barber and Bellwood (2005); Weaver & Rocha (unpubl.) Barber and Bellwood (2005) Barber and Bellwood (2005) Westneat and Alfaro (2005); Barber and Bellwood (2005); Rocha et al. (2005); Yaakub et al. (unpubl.) Rocha et al. (2005) Barber and Bellwood (2005) Weaver & Rocha (unpubl.) Barber and Bellwood (2005); Steinke et al. (2009); Tang (2001); Barber and Bellwood (2005); Rocha (2004) Barber and Bellwood (2005) Barber and Bellwood (2005); Rocha (2004); Yaakub et al. (unpubl.); Westneat and Alfaro (2005); Barber and Bellwood (2005); Arnal et al. (2006); Barber and Bellwood (2005); Westneat and Alfaro (2005); Yaakub et al. (unpubl.);

Halichoeres lapillus Halichoeres leucoxanthus Halichoeres leucurus Halichoeres maculipinna

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Halichoeres margaritaceus











Halichoeres marginatus











Halichoeres melanurus







Halichoeres melasmapomus Halichoeres miniatus

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■ ■

Halichoeres nebulosus Halichoeres nicholsi

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■ ■

■ ■

Halichoeres nigrescens







Halichoeres notospilus











Halichoeres ornatissimus Halichoeres papilionaceus

■ ■

■ ■

■ ■

AY279606 AY850884 AY850759 AY279915 AY279812 AY850851 AY850914 AY850789





Halichoeres pictus







Halichoeres podostigma







AY279609 AY850909 AY850784 AY279918 AY279815 AY850815 AY850878 AY850753 AY850753 EF488035 AY850856 AY850919 AY850794

DQ164143 DQ164178 DQ164160 DQ164144 DQ164179 DQ164161 AY850848 AY850911 AY850786



AY850811 AY850874 AY850749 AY591354 AJ810134 AY850921 AY850796 AY279911 AY279808 AJ810135 AY850906 AY850780 AY279912 AY279809





AY850844 AY850907 AY850782 AY208614 AY850850 AY850913 AY850788









AY279604 AY850920 AY850795 AY279913 AY279810 AY850859 AY850922 AY850797



AY279605 AY850879 AY850754 AY850754 AY279914 AY279811 EF488033 AY850854 AY850917 AY850792





Read et al. (2006) Read et al. (2006) Barber and Bellwood (2005) Barber and Bellwood (2005); Rocha (2004); Arnal et al. (2006); Barber and Bellwood (2005); Westneat and Alfaro (2005); Arnal et al. (2006); Barber and Bellwood (2005); Westneat and Alfaro (2005); Barber and Bellwood (2005); Quenouille et al. (2004); Barber and Bellwood (2005) Westneat and Alfaro (2005); Barber and Bellwood (2005); Barber and Bellwood (2005) Westneat and Alfaro (2005); Barber and Bellwood (2005); Yaakub et al. (unpubl.) Barber and Bellwood (2005); Barber and Bellwood (2005); Barber and Bellwood (2005); Westneat and Alfaro (2005); Westneat and Alfaro (2005); Barber and Bellwood (2005) Westneat and Alfaro (2005); Barber and Bellwood (2005); Barber and Bellwood (2005); Yaakub et al. (unpubl.); Barber and Bellwood (2005)

Halichoeres poeyi









Halichoeres prosopeion Halichoeres radiatus

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■ ■

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Halichoeres richmondi













AY850820 AY850883 AY850758 AY823581 EF488037 AY850838 AY850901 AY850776



AY279607 AY850881 AY850756 AY823575 AY279916 AY279813 EF488038 AY850849 AY850912 AY850787



Halichoeres sazimai Halichoeres scapularis







Halichoeres semicinctus









Halichoeres socialis Halichoeres solorensis

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Halichoeres tenuispinis Halichoeres trimaculatus Hemigymnus fasciatus

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Hemigymnus melapterus





Hipposcarus longiceps





Hologymnosus annulatus Hologymnosus doliatus

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Iniistius aneitensis







■ ■





AY279608 AY850887 AY850762 AY279917 AY279814 AY850822 AY850885 AY850760 AY328859 AY329642 AY850814 AY850877 AY850752 AY279610 AY850904 AY850779 AY279919 AY279816 AB121236 AY850825 AY850888 AY850763 AJ810136 FJ583533



■ ■ ■

FJ800096





AY279611 DQ076707 FJ237777 AY279920 AY279817





EU601189 AY081093 AY081128 EU601318 AY081110 AY850834 AY850897 AY850772









AY279612 AY850896 AY850771 AY279921 AY279818 AY279654 AY279757 AY279963 AY279860

Barber and Bellwood (2005); Rocha et al. (2005); Yaakub et al. (unpubl.); Barber and Bellwood (2005) Westneat and Alfaro (2005); Barber and Bellwood (2005); Rocha et al. (2005); Yaakub et al. (unpubl.) Barber and Bellwood (2005); Barber and Bellwood (2005); Barber and Bellwood (2005); Luiz et al. (2009) Westneat and Alfaro (2005); Barber and Bellwood (2005); Barber and Bellwood (2005); Bernardi et al. (2004) Barber and Bellwood (2005) Westneat and Alfaro (2005); Barber and Bellwood (2005); Mabuchi et al. (2004) Barber and Bellwood (2005) Arnal et al. (2006); Steinke et al. (2009); Westneat and Alfaro (2005); Read et al. (2006); Zhang and Hanner (unpubl.); Smith et al. (2008) Barber and Bellwood (2005) Westneat and Alfaro (2005); Barber and Bellwood (2005); Westneat and Alfaro (2005)

Labrichthys unilineatus





Labroides bicolor





Labroides dimidiatus





Labroides rubrolabiatus



Labropsis australis





























Labrus bergylta







Labrus merula









AY279613 AY850875 AY850750 AY279922 AY279819 AY279614 AY279717 AY279923 AY279820 AJ810139 AY279718 AY279924 AY279821 AY279616 AY279719 AY279925 AY279822 AY279617 AY279720 AY279926 AY279823 AF414201 AF517591 GQ341593 EU492297



AJ810141 AF517592 GQ341595



Labrus mixtus Labrus viridis







Lachnolaimus maximus











Lappanella fasciata Larabicus quadrilineatus





Leptojulis cyanopleura







Leptoscarus vaigiensis







Macropharyngodon bipartitus Macropharyngodon choati Macropharyngodon cyanoguttatus







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■ ■

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EU492296 AJ810142 AF517593 GQ341596























EU601225 EU601261 AY662760 EU601404 AY279927 AY662809 AF517589 GQ341597 GQ341615



AY279619 AY279722 AY279928 AY279825 AY279620 AY850872 AY850747 AY279929 AY279826 EU601190 AY081094 FJ583627 AY081129 EU601319 AY081111 DQ164130 DQ164165 DQ164148 EF488039 AY850836 AY850899 AY850774



DQ164132 DQ164167 DQ164150 EF488041

Westneat and Alfaro (2005); Barber and Bellwood (2005); Westneat and Alfaro (2005) Arnal et al. (2006); Westneat and Alfaro (2005); Westneat and Alfaro (2005) Westneat and Alfaro (2005) Almada (unpubl.); Hanel et al (2002); Kazancouigla et al (2009); Noren et al. (unpubl.); Arnal et al. (2006); Hanel et al (2002); Kazancouigla et al (2009); Noren et al. (unpubl.); Arnal et al. (2006); Kazancouigla et al (2009); Smith et al. (2008); Sparks and Smith (2004); Westneat and Alfaro (2005) Hanel et al (2002); Kazancouigla et al (2009); Kazancouigla et al (2009); Westneat and Alfaro (2005) Westneat and Alfaro (2005); Barber and Bellwood (2005); Smith et al. (2008); Almada et al. (unpubl.); Steinke et al. (2009); Read et al. (2006); Yaakub et al. (unpubl.); Barber and Bellwood (2005) Read et al. (2006); Yaakub et al. (unpubl.);

Macropharyngodon geoffroy Macropharyngodon kuiteri Macropharyngodon meleagris Macropharyngodon negrosensis Macropharyngodon ornatus Malapterus reticulatus











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■ ■

AY279621 DQ164168 DQ164151 AY279930 AY279827 DQ164134 DQ164169 DQ164152











AY279622 AY850900 AY850775 AY279931 AY279828 AY850835 AY850898 AY850773

■ ■

■ ■



DQ164137 DQ164172 DQ164155

Neoodax balteatus





Nicholsina denticulata







Nicholsina usta







Notolabrus fucicola Notolabrus gymnogenis



■ ■



Notolabrus parilus Notolabrus tetricus

■ ■





Novaculichthys taeniourus







Novaculoides macrolepidotus Odax acroptilus











AY279623 AY279726 AY279932 AY279829 AY279657 AY279760 AY279966 AY279863 U95761 U95762 DQ457021





EU601191 AY279727 EU601370 AY279933 AY081112 EU848435





AY279625 AY279728 EF609418 AY279934 AY279831 AB121240 AJ810143 AB121241 EF609419



















Odax cyanoallix









Odax cyanomelas









AY279627 AY279730 FJ583739 AY279936 AY279833 AY279626 AY279729 AY279935 AY279832 AY279658 AY279761 AY279967 AY279864 AY279659 AY279762 AY279968 AY279865 AY279660 AY279763 AY279969 AY279866

Westneat and Alfaro (2005); Read et al. (2006); Read et al. (2006) Westneat and Alfaro (2005); Barber and Bellwood (2005); Barber and Bellwood (2005) Read et al. (2006) Westneat and Alfaro (2005) Westneat and Alfaro (2005) Bernardi et al. (2000); Read et al. (2006); Smith et al. (2008); Westneat and Alfaro (2005); Almada et al. (unpubl.) Deagle (unpubl.) Westneat and Alfaro (2005); Ward and Holmes (2007); Mabuchi et al. (2004) Arnal et al. (2006); Mabuchi et al. (2004); Ward and Holmes (2007); Westneat and Alfaro (2005); Steinke et al. (2009); Westneat and Alfaro (2005) Westneat and Alfaro (2005) Westneat and Alfaro (2005) Westneat and Alfaro (2005)

Odax pullus









Ophthalmolepis lineolata









Oxycheilinus bimaculatus









Oxycheilinus celebicus









Oxycheilinus digramma









Oxycheilinus unifasciatus









Oxyjulis californica









Paracheilinus carpenteri Paracheilinus mccoskeri Pictilabrus laticlavius









■ ■ ■

FJ583820









■ ■ ■





■ ■

■ ■

■ ■ ■





Pseudodax moluccanus











Pseudojuloides atavai









Pseudojuloides cerasinus









Pseudocheilinus evanidus Pseudocheilinus hexataenia Pseudocheilinus octotaenia



Pseudocheilinus tetrataenia Pseudocoris heteroptera Pseudocoris yamashiroi

AY279661 AY279764 AY279970 AY279867 AY279628 AY279731 AY279937 AY279834 AY279629 AY279732 AY279938 AY279835 AY279630 AY279733 AY279939 AY279836 EU601221 EU601258 EF609423 EU601400 EU885922 EU601300 AY279631 AY279734 AY279940 AY279837 AY279632 AY279735 AY279941 AY279838 FJ583815 AJ810144 AY279736 AY279942 AY279839 FJ583965 FJ583971 AY279634 AY279737 FJ583972 AY279943 AY279840 FJ583973 AY850827 AY850890 AY850765



AY279635 AY850891 AY850766 AY279944 AY279841 EU601227 EU601262 FJ583993 AY081133 AY279945 AY081115 AY279637 AY279740 AY279946 AY279843 AY279638 AY279741 AY279947 AY279844

Westneat and Alfaro (2005) Westneat and Alfaro (2005) Westneat and Alfaro (2005) Westneat and Alfaro (2005) Smith et al. (2008); Ward and Holmes (2007) Westneat and Alfaro (2005) Westneat and Alfaro (2005) Steinke et al. (2009) Steinke et al. (2009) Arnal et al. (2006); Westneat and Alfaro (2005); Steinke et al. (2009) Steinke et al. (2009) Westneat and Alfaro (2005); Steinke et al. (2009) Steinke et al. (2009) Barber and Bellwood (2005) Westneat and Alfaro (2005); Barber and Bellwood (2005); Smith et al. (2008); Steinke et al. (2009); Almada et al. (unpubl.); Westneat and Alfaro (2005) Westneat and Alfaro (2005) Westneat and Alfaro (2005)

Pseudolabrus biserialis Pseudolabrus eoethinus Pseudolabrus fuentesi Pseudolabrus gayi

■ ■ ■ ■

■ ■

Pseudolabrus guentheri Pseudolabrus miles Pseudolabrus sieboldi Pteragogus amboinensis

■ ■ ■ ■

■ ■ ■ ■





Pteragogus cryptus









Scarus altipinnis











Scarus chameleon











Scarus coelestinus











Scarus dimidiatus











Scarus festivus











Scarus flavipectoralis











Scarus forsteni











Scarus frenatus













Scarus ghobban













Scarus globiceps











AB121242 AB121243 AB121244







AY279639 AY279742 AY279948 AY279845 AB121245 AB121246 AB121247



AY279640 AY279743 AY279949 AY279846 AY279641 AF517579 AY279950 AY279847 EU601192 EU601237 EU601371 EU601321 EU601273 EU601193 EU601238 FJ237917 EU601372 EU601322 EU601274 EU601194 AY081084 AY081119 EU601323 AY081101 EU601195 AY279745 EU601374 AY279951 AY279848 EU601196 EU601239 EU601375 EU601325 EU601276 EU601197 AY081086 AY081121 EU601326 EU601277 EU601198 EU601240 EU601377 EU601327 EU601278 EU601199 AY279746 FJ237918 AY081122 AY279952 AY081104 EU601200 EU601241 EF609452 EU601379 EU601329 EU601279 EU601201 EU601242 EU601380 EU601330

Mabuchi et al. (2004) Mabuchi et al. (2004) Mabuchi et al. (2004) Westneat and Alfaro (2005) Mabuchi et al. (2004) Mabuchi et al. (2004) Mabuchi et al. (2004) Westneat and Alfaro (2005) Westneat and Alfaro (2005); Hanel et al (2002); Smith et al. (2008) Smith et al. (2008); Smith et al. (2008); Zhang and Hanner (unpubl.); Smith et al. (2008); Almada et al. (unpubl.); Smith et al. (2008); Westneat and Alfaro (2005); Smith et al. (2008) Smith et al. (2008); Almada et al. (unpubl.); Smith et al. (2008) Smith et al. (2008); Westneat and Alfaro (2005); Zhang and Hanner (unpubl.); Almada et al. (unpubl.) Smith et al. (2008); Ward and Holmes (2007); Smith et al. (2008)

EU601280

Scarus guacamaia











Scarus hoefleri Scarus hypselopterus

■ ■

■ ■

EU601202 EU601243 AY081120 EU601331 AY081102 AY141393 AY141463







Scarus iseri











Scarus niger











Scarus oviceps











Scarus prasiognathos











Scarus psittacus











Scarus quoyi











Scarus rivulatus











Scarus rubroviolaceus











Scarus schlegeli











Scarus spinus











Scarus taeniopterus











Scarus tricolor











EU601204 EU601245 EU601383 EU601333 EU601283 EU601203 EU601244 FJ584082 EU601382 EU601332 EU601282 EU601205 EU601246 EU601384 EU601334 EU601284 EU601206 EU601247 EU601385 EU601335 EU601285 EU601207 EU601248 EU601386 EU601336 EU601286 EU601208 EU601249 EU601387 EU601337 EU601287 EU601210 EU601251 EU601389 EU601339 EU601289 EU601211 EU601252 EU601390 EU601340 EU601290 EU601212 EU601253 EU601391 EU601341 EU601291 EU601213 EU601254 EU601392 EU601342 EU601292 EU601214 EU601255 EU601393 EU601343 EU601293 EU601215 EU601256 EU601394 EU601344 EU601294 EU601216 EU601257 EU601395 EU601345 EU601295 FJ584085

Scarus vetula Semicossyphus pulcher







■ ■







EU601226 AY920487 GU440521 EU601405 AY279953 AY279850

Smith et al. (2008); Almada et al. (unpubl.); Chen et al. (2003); Smith et al. (2008) Smith et al. (2008) Smith et al. (2008) Smith et al. (2008) Smith et al. (2008) Smith et al. (2008) Smith et al. (2008) Smith et al. (2008) Smith et al. (2008) Smith et al. (2008) Smith et al. (2008) Smith et al. (2008) Smith et al. (2008) Steinke et al. (2009) Smith et al. (2008); Byrne et al. (unpubl.); Hastings and Burton (unpubl.); Westneat and Alfaro (2005)

Siphonognathus argyrophanes Sparisoma amplum Sparisoma atomarium









■ ■

Sparisoma aurofrenatum











■ ■

EU601217 AY081082 EU601396 EU601346 AY081099 DQ457034





EU601218 AY279748 EU601397 AY279954 AY081100 U95777 AF517578 GQ341598 DQ457026

Sparisoma axillare Sparisoma chrysopterum





Sparisoma cretense





Sparisoma frondosum Sparisoma radians





Sparisoma rubripinne





Sparisoma strigatum Sparisoma tuiupiranga Sparisoma viride





Stethojulis albovittata Stethojulis balteata Stethojulis bandanensis

■ ■ ■

■ ■

Stethojulis trilineata





Suezichthys gracilis











AY279662 AY279765 AY279971 AY279868 DQ457024 U95767 U95768 DQ457029



■ ■

DQ457032



AF114483 U95774 GQ341599 EF456024

■ ■ ■

DQ457027

U95771 U95772 DQ457028

DQ457030





■ ■





AJ810146 AY850869 AY850744 AY279955 AY279852







AY279647 AY850868 AY850743 AY279956 AY279853 AB121238

EU601219 AY081081 EU601398 EU601348 AY081098 AJ810145 DQ164146 DQ164181 DQ164163

Westneat and Alfaro (2005) Read et al. (2006) Bernardi et al. (2000); Read et al. (2006); Smith et al. (2008); Almada et al. (unpubl.); Read et al. (2006) Smith et al. (2008); Westneat and Alfaro (2005); Almada et al. (unpubl.) Bernardi et al. (2000); Hanel et al (2002); Kazancouigla et al (2009); Read et al. (2006); Read et al. (2006) Bernardi et al. (2000); Read et al. (2006); Nelson et al. (unpubl.); Bernardi et al. (2000); Kazancouigla et al (2009); Gonzalez-Sevilla et al. (unpubl.) Read et al. (2006) Read et al. (2006) Smith et al. (2008); Almada et al. (unpubl.); Arnal et al. (2006) Read et al. (2006) Arnal et al. (2006); Barber and Bellwood (2005); Westneat and Alfaro (2005) Westneat and Alfaro (2005); Barber and Bellwood (2005); Mabuchi et al. (2004)

Symphodus bailloni









Symphodus cinereus













Symphodus doderleini

AY092052 AY092037 GQ341601 GQ341616 AJ810147 AY092036 GQ341603 GQ341618 AF517602 GQ341606

Symphodus mediterraneus







Symphodus melanocercus







Symphodus melops









Symphodus ocellatus Symphodus roissali

■ ■

■ ■

AY092049 AY092038 GQ341604 GQ341621 AJ810150 AF517603





AJ810151 AY092039 GQ341605 GQ341622

Symphodus rostratus









AF414198 AY092040 GQ341608 GQ341617

Symphodus tinca









AJ810152 AF517596 GQ341602 GQ341619

Tautoga onitis







Tautogolabrus adspersus









■ ■ ■ ■

Thalassoma amblycephalum Thalassoma ascensionis Thalassoma ballieui Thalassoma bifasciatum Thalassoma cupido







AJ810148 AF517601 GQ341607 GQ341620 AJ810149 AF517595 GQ341600



■ ■ ■ ■ ■





AY279648 AF517588 GQ341609 EU601402 AY279957 AY662810





AY279649 AF517585 GQ341610 AY279958 AY279855 AY328987 AY328860 AY329643





■ ■ ■ ■ ■

AY328988 AY328861 AY329644 AY328989 AY328862 AY329645 AJ810153 AY279753 AY328863 AY279959 AY279856 AY329646 AY328991 AY328864 AY329647

Almada et al. (unpubl.); Kazancouigla et al (2009); Arnal et al. (2006); Almada et al. (unpubl.); Kazancouigla et al (2009); Hanel et al (2002); Kazancouigla et al (2009); Arnal et al. (2006); Hanel et al (2002); Kazancouigla et al (2009); Arnal et al. (2006); Hanel et al (2002); Kazancouigla et al (2009); Almada et al. (unpubl.); Kazancouigla et al (2009); Arnal et al. (2006); Hanel et al (2002); Arnal et al. (2006); Almada et al. (unpubl.); Kazancouigla et al (2009); Almada (unpubl.); Almada et al. (unpubl.); Kazancouigla et al (2009); Arnal et al. (2006); Hanel et al (2002); Kazancouigla et al (2009); Westneat and Alfaro (2005); Hanel et al (2002); Kazancouigla et al (2009); Smith et al. (2008); Sparks and Smith (2004) Westneat and Alfaro (2005); Hanel et al (2002); Kazancouigla et al (2009); Bernardi et al. (2004); Bernardi et al. (2004); Bernardi et al. (2004); Arnal et al. (2006); Westneat and Alfaro (2005); Bernardi et al. (2004); Bernardi et al. (2004);

Thalassoma duperrey







Thalassoma genivittatum







Thalassoma grammaticum Thalassoma hardwicke

■ ■

■ ■

■ ■







AY328994 DQ443874 AY328865 AY329648 AY328992 DQ443875 AY328866 DQ443833 AY328993 AY328867 AY329650 AY850802 AY850865 DQ443843 AY328868 DQ443830 AY328996 AY328869 AY329652

Thalassoma hebraicum Thalassoma jansenii

■ ■

■ ■

■ ■

Thalassoma loxum Thalassoma lucasanum Thalassoma lunare



■ ■ ■



■ ■ ■

■ ■ ■

Thalassoma lutescens











AY850800 AY850863 DQ443877 AY328874 AY329657

■ ■ ■

■ ■ ■

AY329002 AY328875 AY329658



■ ■ ■

■ ■

■ ■

■ ■

AY329005 AY328878 AY329661



■ ■ ■

■ ■ ■

Thalassoma newtoni Thalassoma noronhanum Thalassoma pavo Thalassoma purpureum Thalassoma quinquevittatum Thalassoma robertsoni Thalassoma rueppellii Thalassoma sanctaehelenae



■ ■ ■





AY328997 DQ443873 AY328870 DQ443815 AY328998 AY328871 AY329654 AY328999 AY328872 AY329655 AJ810154 AY850862 DQ443879 AY328873 AY279960 AY279857 DQ443837

AY329003 AY328876 AY329659 AF517583 GQ341611 DQ198011 AY329660

AY850801 AY850864 DQ443855 AY328879 DQ443805 AY329007 AY328880 AY329663 AY329008 AY328881 AY329664 AY329009 AY328882 AY329665

Bernardi et al. (2004); Read et al. (2006); Bernardi et al. (2004); Read et al. (2006); Bernardi et al. (2004); Barber and Bellwood (2005); Read et al. (2006); Bernardi et al. (2004); Bernardi et al. (2004); Read et al. (2006); Bernardi et al. (2004); Bernardi et al. (2004); Arnal et al. (2006); Barber and Bellwood (2005); Read et al. (2006); Bernardi et al. (2004); Westneat and Alfaro (2005) Barber and Bellwood (2005); Barber and Bellwood (2005); Read et al. (2006); Bernardi et al. (2004); Bernardi et al. (2004); Bernardi et al. (2004); Hanel et al (2002); Kazancouigla et al (2009); Read et al. (2006); Bernardi et al. (2004); Bernardi et al. (2004); Barber and Bellwood (2005); Read et al. (2006); Bernardi et al. (2004); Bernardi et al. (2004); Bernardi et al. (2004); Bernardi et al. (2004);

Xiphocheilus typus





Xyrichtys martinicensis





■ ■ ■

■ ■ ■ ■











AY329010 AY328883 AY329666 AY329011 AY328884 AY329667 AY329012 AY328885

GU225071 U92004

Chaetodontidae









TMO-4c4



12s





16s

Xyrichtys splendens

ND3



Rag2



S7

Xyrichtys novacula

AY279652 AY279755 AY279961 AY279858 AY279653 AY279756 AY279962 AY279859 AY279655 AY279758 AY279964 AY279861 GQ341612 EF439246

Cytb



■ ■ ■ ■

ETS2

Thalassoma septemfasciata Thalassoma trilobatum Thalassoma virens Wetmorella nigropinnata

Accession

Chaetodon argentatus









FJ167793, FJ167730, FJ167682, AY530830, AY530860 EF617068, EF616986, EF616820, EF616904, EF617151 EF617107, EF617024, EF616859, EF616942, EF617190 FJ167794, FJ167731, U23582

Chaetodon aureofasciatus









FJ167795, FJ167732, FJ167683

Amphichaetodon howensis Amphichaetodon melbae











Chaetodon adiergastos













Chaetodon auriga Chaetodon auripes Chaetodon austriacus













EF617108, EF617025, FJ167733, FJ167684, EF616860, EF616943, EF617191, FJ167796, U23584









EF617074, EF616992, EF616826,

■ ■



Bernardi et al. (2004); Bernardi et al. (2004); Bernardi et al. (2004); Westneat and Alfaro (2005) Westneat and Alfaro (2005) Westneat and Alfaro (2005) Kazancouigla et al (2009); GonzalezSevilla et al. (unpubl.) Valdez-Moreno et al. (unpubl.); Hare et al. (unpubl.) Source Bellwood et al. (2010, 2004) Fessler and Westneat (2007) Fessler and Westneat (2007) Bellwood et al. (2010), McMillan (1995) Bellwood et al. (2010), Fessler and Westneat (2007) Bellwood et al. (2010), Fessler and Westneat (2007) Bellwood et al. (2010), McMillan (1995) Fessler and Westneat (2007)

EF616910, EF617157

Chaetodon baronessa









Chaetodon bennetti









Chaetodon blackburnii Chaetodon burgessi

■ ■



Chaetodon capistratus







Chaetodon citrinellus







Chaetodon collare









■ ■ ■



Chaetodon falcula



Chaetodon fasciatus

Chaetodon decussatus Chaetodon dolosus Chaetodon ephippium

Chaetodon flavirostris Chaetodon fremblii



Chaetodon guentheri









































■ ■

■ ■ ■

FJ167802, EF617088, EF617006, FJ167738, FJ167689, EF616840, EF616924, EF617171 AF108587

■ ■

EF617103, EF616855, EF616938, EF617186



















■ ■





■ ■















■ ■









■ ■



■ ■



Chaetodon guttatissimus Chaetodon hoefleri Chaetodon humeralis



■ ■

■ ■

FJ167797, EF617122, EF617039, FJ167734, FJ167685, EF616874, EF616957, EF617205 FJ167798, EF617075, EF616993, FJ167735, FJ167686, EF616827, EF616911, EF617158 FJ167799, FJ167736, FJ167687 EF617099, EF617017, EF616851, EF616934, EF617182 FJ167800, EF617078, EF616996, FJ167737, FJ167688, EF616830, EF616914, EF617161 FJ167801, EF617115, EF617032, AF108585, EF616867, EF616950, EF617198,

FJ167803, EF617090, EF617008, FJ167739, FJ167690, EF616842, EF616926, EF617173 EF617083, EF617001, EF616835, EF616919, EF617166 EF617105, EF617022, EF616857, EF616940, EF617188 AF108589, AF108514 FJ167804, EF617089, EF617007, FJ167740, FJ167691, EF616841, EF616925, EF617172 EF617116, EF617033, EF616868, EF616951, EF617199 AF108590, AF108515 EF617072, EF616990, EF616824, EF616908, EF617155 FJ167805, FJ167741, FJ167692

Bellwood et al. (2010), Fessler and Westneat (2007) Bellwood et al. (2010), Fessler and Westneat (2007) Bellwood et al. (2010) Fessler and Westneat (2007) Bellwood et al. (2010), Fessler and Westneat (2007) Bellwood et al. (2010), Fessler and Westneat (2007), Nelson et al (unpubl.) Bellwood et al. (2010), Fessler and Westneat (2007) Nelson et al. (unpubl.) Fessler and Westneat (2007) Bellwood et al. (2010), Fessler and Westneat (2007) Fessler and Westneat (2007) Fessler and Westneat (2007) Nelson et al. (unpubl.) Bellwood et al. (2010), Fessler and Westneat (2007) Fessler and Westneat (2007) Nelson et al. (unpubl.) Fessler and Westneat (2007) Bellwood et al. (2010)

Chaetodon interruptus Chaetodon kleinii

■ ■

Chaetodon larvatus









■ ■

FJ167806, FJ167742, FJ167693









FJ167807, EF617073, EF616991, FJ167743, AF108591, EF616825, EF616909, EF617156









EF617095, EF617013, AF108592, EF616847, EF616930, EF617178, , FJ167808, EF617104, EF617021, FJ167744, AF108593, EF616856, EF616939, EF617187

Chaetodon lineolatus

















Chaetodon lunula

















Chaetodon lunulatus Chaetodon madagaskariensis Chaetodon melannotus





■ ■



Chaetodon mertensii









■ ■

FJ167809, EF617109, EF617026, FJ167745, AF108594, EF616861, EF616944, EF617192 FJ167810, FJ167746, FJ167694 U23601





















■ ■



FJ167812, EF617101, EF617019, FJ167748, AF108597, EF616853, EF616936, EF617184 FJ167813, EF617082, EF617000, FJ167749, FJ167696, EF616834, EF616918, EF617165 FJ167814, EF617086, EF617004, FJ167750, FJ167697, EF616838, EF616922, EF617169 FJ167815, EF617098, EF617016, FJ167751, FJ167698, EF616850, EF616933, EF617181 EF617111, EF617028, AF108598, EF616863, EF616946, EF617194 EF617117, EF617034, FJ167752, AF108599,

Chaetodon mesoleucos Chaetodon meyeri









■ ■

Chaetodon miliaris

















Chaetodon multicinctus

















Chaetodon ocellatus















Chaetodon ocellicaudus













Chaetodon octofasciatus













FJ167811, EF617110, EF617027, FJ167747, FJ167695, EF616862, EF616945, EF617193 EF617123, EF617040, U23604 EF616875, EF616958, EF617206 AF108596

Bellwood et al. (2010) Bellwood et al. (2010), Fessler and Westneat (2007), Nelson et al (unpubl.) Fessler and Westneat (2007), Nelson et al. (unpubl.) Bellwood et al. (2010), Fessler and Westneat (2007), Nelson et al (unpubl.) Bellwood et al. (2010), Fessler and Westneat (2007), Nelson et al (unpubl.) Fessler and Westneat (2007) McMillan et al. (1995) Bellwood et al. (2010), Fessler and Westneat (2007) Fessler and Westneat (2007), McMillan et al. (1995) Nelson et al. (unpubl.) Bellwood et al. (2010), Fessler and Westneat (2007), Nelson et al (unpubl.) Bellwood et al. (2010), Fessler and Westneat (2007) Bellwood et al. (2010), Fessler and Westneat (2007) Bellwood et al. (2010), Fessler and Westneat (2007) Fessler and Westneat (2007), Nelson et al. (unpubl.) Fessler and Westneat (2007), Nelson

EF616869, EF616952, EF617200





Chaetodon oxycephalus



Chaetodon paucifasciatus Chaetodon pelewensis

Chaetodon ornatissimus

Chaetodon plebeius Chaetodon punctatofasciatus Chaetodon quadrimaculatus







Chaetodon rafflesii

































































































Chaetodon rainfordi

















Chaetodon reticulatus

















Chaetodon robustus















Chaetodon sanctaehelenae Chaetodon sedentarius

■ ■





■ ■







Chaetodon selene











Chaetodon semeion











FJ167816, EF617118, EF617035, AF108600, EF616870, EF616953, EF617201 EF617093, EF617011, AF108601, EF616845, EF616929, EF617176 EF617102, EF617020, EF616854, EF616937, EF617185 EF617097, EF617015, EF616849, EF616932, EF617180 FJ167817, EF617094, EF617012, FJ167753, AF108602, EF616846, EF617177 EF617096, EF617014, AF108603, EF616848, EF616931, EF617179 FJ167818, EF617087, EF617005, FJ167754, EF616839, EF616923, EF617170 EF617112, EF617029, AF108604, EF616864, EF616947, EF617195 FJ167819, EF617100, EF617018, FJ167755, FJ167699, EF616852, EF616935, EF617183 FJ167820, EF617080, EF616998, FJ167756, FJ167700, EF616832, EF616916, EF617163 FJ167821, EF617085, EF617003, FJ167757, FJ167701, EF616837, EF616921, EF617168 FJ167822, FJ167758, FJ167702 FJ167823, EF617076, EF616994, FJ167759, FJ167703, EF616828, EF616912, EF617159 EF617113, EF617030, EF616865, EF616948, EF617196 EF617077, EF616995, EF616829, EF616913, EF617160

et al. (unpubl.) Fessler and Westneat (2007), Nelson et al. (unpubl.) Fessler and Westneat (2007), Nelson et al. (unpubl.) Fessler and Westneat (2007) Fessler and Westneat (2007) Bellwood et al. (2010), Fessler and Westneat (2007), Nelson et al (unpubl.) Fessler and Westneat (2007), Nelson et al. (unpubl.) Bellwood et al. (2010), Fessler and Westneat (2007) Bellwood et al. (2010), Fessler and Westneat (2007), Nelson et al (unpubl.) Bellwood et al. (2010), Fessler and Westneat (2007) Bellwood et al. (2010), Fessler and Westneat (2007) Bellwood et al. (2010), Fessler and Westneat (2007) Bellwood et al. (2010) Bellwood et al. (2010), Fessler and Westneat (2007) Fessler and Westneat (2007) Fessler and Westneat (2007)

Chaetodon semilarvatus













Chaetodon speculum



























Chaetodon striatus



Chaetodon tinkeri Chaetodon trichrous Chaetodon tricinctus Chaetodon trifascialis

■ ■ ■



Chaetodon trifasciatus



Chaetodon ulietensis Chaetodon unimaculatus

■ ■

■ ■



■ ■





























Chaetodon vagabundus



Chaetodon xanthurus Chaetodon zanzibarensis Chelmon marginalis



Chelmon muelleri



Chelmon rostratus



Chelmonops curiosus Chelmonops truncatus

■ ■

AJ748303, AJ748312 FJ167826, FJ167762, FJ167706

















































































■ ■









■ ■

EF617084, EF617002, EF616836, EF616920, EF617167 EF617081, EF616999, AF108606, EF616833, EF616917, EF617164 FJ167824, EF617079, EF616997, FJ167760, FJ167704, EF616831, EF616915, EF617162 FJ167825, FJ167761, FJ167705



FJ167827, EF617091, EF617009, FJ167763, FJ167707, EF616843, EF616927, EF617174 FJ167828, EF617119, EF617036, FJ167764, FJ167708, EF616871, EF616954, EF617202 FJ167829, EF617092, EF617010, FJ167765, FJ167709, EF616844, EF616928, EF617175 FJ167830, EF617120, EF617037, FJ167766, EF616872, EF616955, EF617203 EF617114, EF617031, AF108610, EF616866, EF616949, EF617197 EF617121, EF617038, AF108611, EF616873, EF616956, EF617204 EF617106, EF617023, EF616858, EF616941, EF617189 FJ167831, EF617125, EF617042, FJ167767, FJ167711, EF616877, EF616960, EF617208 FJ167832, EF617124, EF617041, FJ167768, FJ167712, EF616876, EF616959, EF617207 FJ167833, EF617126, EF617043, FJ167769, AF108612, EF616878, EF616961, EF617209 FJ167834, FJ167770, FJ167713 FJ167835, FJ167771, FJ167714

Fessler and Westneat (2007) Fessler and Westneat (2007), Nelson et al. (unpubl.) Bellwood et al. (2010), Fessler and Westneat (2007) Fessler and Westneat (2007) Littlewood et al. (unpubl.) Bellwood et al. (2010) Bellwood et al. (2010), Fessler and Westneat (2007) Bellwood et al. (2010), Fessler and Westneat (2007) Bellwood et al. (2010), Fessler and Westneat (2007) Bellwood et al. (2010), Fessler and Westneat (2007) Fessler and Westneat (2007), Nelson et al. (unpubl.) Fessler and Westneat (2007), Nelson et al. (unpubl.) Fessler and Westneat (2007), Nelson et al. (unpubl.) Bellwood et al. (2010), Fessler and Westneat (2007) Bellwood et al. (2010), Fessler and Westneat (2007) Bellwood et al. (2010), Fessler and Westneat (2007) Fessler and Westneat (2007) Fessler and Westneat (2007)

Coradion altivelis



Coradion chrysozonus



Coradion melanopus

















Forcipiger flavissimus









Forcipiger longirostris









Hemitaurichthys polylepis









Hemitaurichthys thompsoni



Hemitaurichthys zoster







FJ167836, FJ167772, AF108613







FJ167837, EF617128, EF617045, FJ167773, AF108614, EF616880, EF616963, EF617211

























EF617127, EF617044, EF616879, EF616962, EF617210 FJ167838, EF617129, EF617046, FJ167774, AF108615, EF616881, EF616964, EF617212 FJ167839, EF617130, EF617047, FJ167775, FJ167715, EF616882, EF616965, EF617213 FJ167840, EF617070, EF616988, FJ167776, AF108616, EF616822, EF616906, EF617153

■ ■



FJ167841, FJ167777, FJ167716,















Heniochus acuminatus











Heniochus chrysostomus











Heniochus diphreutes











Heniochus monoceros













■ ■









Heniochus pleurotaenia Heniochus singularis Heniochus varius



■ ■









■ ■

EF617131, EF617048, AF108617, EF616883, EF616966, EF617214 FJ167842, EF617071, EF616989, FJ167778, AF108618, EF616823, EF616907, EF617154 FJ167843, EF617132, EF617049, FJ167779, FJ167717, EF616884 EF617136, EF617053, EF616888, EF616970, EF617218 EF617134, EF617051, EF616886, EF616968, EF617216 AF108620 FJ167844, EF617133, EF617050, FJ167780, FJ167718, EF616885, EF616967, EF617215 EF617135, EF617052, AF108621, EF616887, EF616969, EF617217

Fessler and Westneat (2007), Nelson et al. (unpubl.) Bellwood et al. (2010), Fessler and Westneat (2007), Nelson et al (unpubl.) Fessler and Westneat (2007) Bellwood et al. (2010), Fessler and Westneat (2007) Bellwood et al. (2010), Fessler and Westneat (2007) Bellwood et al. (2010), Fessler and Westneat (2007), Nelson et al (unpubl.) Bellwood et al. (2010), Nelson et al. (unpubl.) Fessler and Westneat (2007), Nelson et al. (unpubl.) Bellwood et al. (2010), Fessler and Westneat (2007), Nelson et al (unpubl.) Bellwood et al. (2010), Fessler and Westneat (2007) Fessler and Westneat (2007) Fessler and Westneat (2007) Nelson et al. (unpubl.) Bellwood et al. (2010), Fessler and Westneat (2007) Fessler and Westneat (2007), Nelson et al. (unpubl.)

Johnrandallia nigrirostris



Parachaetodon ocellatus



Prognathodes aculeatus



Prognathodes aya Prognathodes marcellae

























FJ167845, EF617054, FJ167781, FJ167719, EF616889, EF616971 FJ167847, FJ167783, AF108622, AF108547

■ ■











16s

BMP-4

ND3

RAG1

RAG2

ATP 8/6

Cyt B

Abudefduf abdominalis Abudefduf bengalensis





12s

Pomacentridae















■ ■

■ ■

■ ■

■ ■



■ ■

Abudefduf concolor Abudefduf declivifrons Abudefduf hoefleri













Abudefduf lorenzi Abudefduf luridus













Abudefduf margariteus Abudefduf notatus









■ ■



■ ■

■ ■

Abudefduf saxatilis

















Abudefduf septemfasciatus

















FJ167852, EF617137, EF617055, FJ167788, FJ167725, EF616890, EF616972, EF617219 EF617069, EF616987, EF616821, EF616905, EF617152 FJ167853, FJ167789, FJ167726

Bellwood et al. (2010), Fessler and Westneat (2007) Bellwood et al. (2010), Nelson et al. (unpubl.) Bellwood et al. (2010), Fessler and Westneat (2007) Fessler and Westneat (2007) Fessler and Westneat (2007)

Accession number

Source

AY208403, AY208546 FJ616289, FJ616397, FJ616505, FJ616617, FJ616729, FJ616836, AY208404, AY208547 AY208405, AY208548 AY208406, AY208549 FJ616290, FJ616398, FJ616506, FJ616618, FJ616730, FJ616837 AY208407, AY208550 FJ616291, FJ616399, FJ616507, FJ616619, FJ616731, FJ616838 AY208408, AY208551, AY208618 FJ616292, FJ616400, FJ616508, FJ616620, FJ616732, FJ616839, AY208409, AY208552 FJ616293, FJ616401, FJ616509, FJ616621, FJ616733, FJ616840, AY208410, AY208553, AY208624 FJ616294, FJ616402, FJ616510, FJ616622, FJ616734, FJ616841, AY208411, AY208554, AY208619

Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004) Quenouille et al. (2004) Quenouille et al. (2004) Cooper et al. (2009) Quenouille et al. (2004) Cooper et al. (2009) Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004)

Abudefduf sexfasciatus

















Abudefduf sordidus



















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Abudefduf sparoides Abudefduf taurus









■ ■

Abudefduf troschelii Abudefduf vaigiensis





Abudefduf whitleyi

















Acanthochromis polyacanthus

















Altrichthys curatus Amblyglyphidodon aureus

■ ■

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■ ■





■ ■





Amblyglyphidodon curacao

















Amblyglyphidodon leucogaster

















Amblypomacentrus clarus













Amphiprion akallopisos Amphiprion akindynos Amphiprion allardi





■ ■

■ ■







FJ616295, FJ616403, FJ616511, FJ616623, FJ616735, FJ616842, AY208412, AY208555, AY208620 FJ616296, FJ616404, FJ616512, FJ616624, FJ616736, FJ616843, AY208413, AY208556, AY208621 AY208415, AY208558 FJ616297, FJ616405, FJ616513, FJ616625, FJ616737, FJ616844, AY208416, AY208559, AY208622 AY208417, AY208560, AY208623 AP006016, AF436880, AY208418, AY208561 FJ616298, FJ616406, FJ616514, FJ616626, FJ616738, FJ616845, AY208419, AY208562 FJ616299, FJ616407, FJ616515, FJ616627, FJ616739, FJ616846, AY208368, AY208369, AY208521, AY208625 FJ616300, FJ616408, FJ616740, FJ616847 FJ616301, FJ616409, FJ616516, FJ616628, FJ616741, FJ616848, AY208420, AY208421, AY208563, AY208627 FJ616302, FJ616410, FJ616517, FJ616629, FJ616742, FJ616849, AY208423, AY208422, AY208564 FJ616303, FJ616411, FJ616518, FJ616630, FJ616743, FJ616850, AY208424, AY208425, AY208565, AY208626 FJ616304, FJ616412, FJ616519, FJ616631, FJ616744, FJ616851 AY208344, AY208345, AY208508 DQ343905, DQ343945, AY208346, AY208347, AY208509, AY208628 AY208348, AY208349, AY208510,

Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004) Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004) Quenouille et al. (2004) Mabuchi et al. (2007);Jang-Liaw et al. (2002); Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009) Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009) Quenouille et al. (2004) Santini and Polacco (2006); Quenouille et al. (2004) Quenouille et al. (2004)

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Amphiprion bicinctus Amphiprion chagosensis Amphiprion chrysogaster Amphiprion chrysopterus



■ ■

■ ■ ■ ■





Amphiprion clarkii













Amphiprion frenatus















Amphiprion latezonatus Amphiprion leucokranos Amphiprion mccullochi Amphiprion melanopus



■ ■ ■ ■











■ ■ ■

Amphiprion nigripes Amphiprion ocellaris













■ ■

■ ■

Amphiprion omanensis Amphiprion percula

■ ■



■ ■

Amphiprion perideraion

















Amphiprion polymnus





Amphiprion rubrocinctus Amphiprion sandaracinos

■ ■

■ ■

Amphiprion sebae









■ ■



AY208629 DQ343906, DQ343946 DQ343907, DQ343947 AY208350, AY208351, AY208511 DQ343908, DQ343948, AY208352, AY208353, AY208512 FJ616305, FJ616413, FJ616520, FJ616632, FJ616745, FJ616852, AY208354, AY208355, AY208513 FJ616306, FJ616414, FJ616521, FJ616633, FJ616746, FJ616853, AF097930 DQ343912 DQ343913, DQ343953 DQ343914, DQ343954 FJ616307, FJ616415, FJ616522, FJ616634, FJ616747, FJ616854, AY208356, AY208357, AY208514 AY208358, AY208515 FJ616308, FJ616416, FJ616523, FJ616635, FJ616748, FJ616855, AY208359, AY208360, AY208516, AY208631 AY208361, AY208362, AY208517 AF285924, DQ343918, DQ343958 FJ616309, FJ616417, FJ616524, FJ616636, FJ616749, FJ616856, AY208363, AY208364, AY208518, AY208630 AF097928, AY666170 DQ343920, DQ343961 FJ616310, FJ616418, FJ616525, FJ616637, FJ616750, FJ616857, AF097929 AY208365, AY208366, AY208519

Santini and Polacco (2006) Santini and Polacco (2006) Quenouille et al. (2004) Santini and Polacco (2006); Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009); Elliott et al. (1999) Santini and Polacco (2006) Santini and Polacco (2006) Santini and Polacco (2006) Cooper et al. (2009); Quenouille et al. (2004) Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004) Quenouille et al. (2004) Tang (2001); Santini and Polacco (2006) Cooper et al. (2009); Quenouille et al. (2004) Elliott et al. (1999); Sparks and Smith (2004) Santini and Polacco (2006) Cooper et al. (2009); Elliott et al. (1999) Quenouille et al. (2004)

Azurina hirundo













Cheiloprion labiatus















Chromis agilis Chromis alpha











■ ■



Chromis alta Chromis amboinensis













Chromis analis















Chromis atrilobata Chromis atripectoralis







■ ■









Chromis atripes Chromis caudalis Chromis chromis Chromis chrysura





Chromis cyanea Chromis flavomaculata





Chromis fumea





Chromis iomelas









■ ■

















■ ■

■ ■

■ ■

■ ■

■ ■

■ ■



FJ616312, FJ616420, FJ616527, FJ616639, FJ616752, FJ616859 AY208370, AY208371, AY208522, AY208641 FJ616313, FJ616421, FJ616528, FJ616640, FJ616753, FJ616860 AY958642 FJ616314, FJ616422, FJ616529, FJ616641, FJ616754, FJ616861, AY208372, AY208373, AY208523 FJ616315, FJ616423, FJ616530, FJ616642, FJ616755, FJ616862 EF489729, AY208374, AY208375, AY208524, AY208637 FJ616316, FJ616424, FJ616531, FJ616643, FJ616756, FJ616863 AY208377, AY208378, AY208526, AY208633 AY289557 FJ616317, FJ616425, FJ616532, FJ616644, FJ616757, FJ616864, AY208379, AY208380, AY208527, AY208640 AY208381, AY208382 AY208528 AF285925, AF285947, AY208383, AY208384, AY208529, AY208639 AY208385, AY208386 AY208530 AF081224, AY365121, EU267219

FJ616311, FJ616419, FJ616526, FJ616638, FJ616751, FJ616858 AF285926, AF285948, AY208387, AY208388, AY208531

Cooper et al. (2009) Quenouille et al. (2004) Cooper et al. (2009) Byrne et al. (unpublished); Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009) Domingues et al. (unpublished); Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004) Quenouille et al. (2004) Johns and Somero (2004) Cooper et al. (2009); Quenouille et al. (2004) Quenouille et al. (2004) Tang (2001); Quenouille et al. (2004) Quenouille et al. (2004) Jang-Liaw et al. (2002); Hwang et al. (unpublished); Park and Koh (unpublished) Cooper et al. (2009) Tang (2001); Quenouille et al. (2004)



Chromis limbata



EF489738, EF392576 FJ616318, FJ616426, FJ616533, FJ616645, FJ616758, FJ616865 FJ616319, FJ616427, FJ616534, FJ616646, FJ616759, FJ616866 AY208393, AY208394, AY208534, AY208638 EU267220 FJ616320, FJ616428, FJ616535, FJ616647, FJ616760, FJ616867 FJ616321, FJ616429, FJ616536, FJ616648, FJ616761, FJ616868 FJ616322, FJ616430, FJ616537, FJ616649, FJ616762, FJ616869, AY289559 FJ616323, FJ616431, FJ616538, FJ616650, FJ616763, FJ616870, AY208395, AY208396, AY208535, AY208634 FJ616324, FJ616432, FJ616539, FJ616651, FJ616764, FJ616871 FJ616325, FJ616433, FJ616540, FJ616652, FJ616765, FJ616872, AY208397, AY208398, AY208536, AY208635 FJ616326, FJ616434, FJ616541, FJ616653, FJ616766, FJ616873, AY208399, AY208400, AY208537, AY208642 FJ616327, FJ616435, FJ616542, FJ616654, FJ616767, FJ616874 AY208401, AY208402, AY208538 FJ616328, FJ616436, FJ616543, FJ616655, FJ616768, FJ616875 AY208426, AY208427, AY208566, AY208645 FJ616329, FJ616437, FJ616544, FJ616656, FJ616769, FJ616876

Chromis margaritifer

















Chromis multilineata























Chromis nitida



Chromis notata Chromis opercularis













Chromis ovatiformis













Chromis punctipinnis













Chromis retrofasciata













Chromis ternatensis













Chromis viridis

















Chromis weberi

















Chromis xanthochira













Chromis xanthopterygia Chromis xanthura























■ ■











Chrysiptera annulata Chrysiptera brownriggii







Domingues et al. (unpublished); Gonzalez-Sevilla et al. (unpublished) Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004) Quenouille et al. (2004) Park and Koh (unpublished) Cooper et al. (2009) Cooper et al. (2009) Cooper et al. (2009); Johns and Somero (2004) Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009) Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009) Quenouille et al. (2004) Cooper et al. (2009) Quenouille et al. (2004) Cooper et al. (2009)

Chrysiptera cyanea









Chrysiptera galba Chrysiptera glauca





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■ ■

■ ■









Chrysiptera hemicyanea Chrysiptera kuiteri



Chrysiptera leucopoma



Chrysiptera oxycephala













Chrysiptera rex

















Chrysiptera rollandi

















Chrysiptera springeri













Chrysiptera talboti













Chrysiptera taupou Chrysiptera unimaculata













Dascyllus carneus











Dascyllus albisella Dascyllus aruanus





■ ■





■ ■























FJ616330, FJ616438, FJ616545, FJ616657, FJ616770, FJ616877, AY208435, AY208436, AY208571, AY208648 AY208430, AY208431, AY208568 AY208432, AY208433, AY208569, AY208647 AY208434, AY208570, AY208644 FJ616336, FJ616444, FJ616551, FJ616663, FJ616776, FJ616883 AF081226, AY208648, AY208436, AY208571 FJ616331, FJ616439, FJ616546, FJ616658, FJ616771, FJ616878 FJ616332, FJ616440, FJ616547, FJ616659, FJ616772, FJ616879, AY208437, AY208438, AY208572 FJ616333, FJ616441, FJ616548, FJ616660, FJ616773, FJ616880, AY208439, AY208440, AY208573, AY208646 FJ616334, FJ616442, FJ616549, FJ616661, FJ616774, FJ616881 FJ616335, FJ616443, FJ616550, FJ616662, FJ616775, FJ616882, AY208441, AY208442, AY208574 AY208443, AY208444, AY208575 FJ616337, FJ616445, FJ616552, FJ616664, FJ616777, FJ616884 AF119405, AF489743, AF119396 FJ616338, FJ616446, FJ616553, FJ616665, FJ616778, FJ616885, AF489764, AY208539, AY208649, AF119404, AF489770, AY208540, AY208652

Cooper et al. (2009); Quenouille et al. (2004) Quenouille et al. (2004) Quenouille et al. (2004) Quenouille et al. (2004) Cooper et al. (2009) Jang-Liaw et al. (2002); Quenouille et al. (2004) Cooper et al. (2009) Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009) Cooper et al. (2009); Quenouille et al. (2004) Quenouille et al. (2004) Cooper et al. (2009) Bernardi and Crane (unpublished); McCafferty et al. (2002) Cooper et al. (2009); McCafferty et al. (2002) Bernardi and Crane (unpublished); McCafferty et al. (2002)

Dascyllus flavicaudus









AF119407, AY208650, AF489778, AY208541

Dascyllus marginatus









AF119403, AY208651, AF489784, AY208542 FJ616339, FJ616447, FJ616554, FJ616666, FJ616779, FJ616886, AF489788, AY208543, AY208653 FJ616340, FJ616448, FJ616555, FJ616667, FJ616780, FJ616887, AF489739, AY208544, AY208654 AF489808, FJ616341, FJ616449, FJ616556, FJ616668, FJ616781, FJ616888, AF489820, AY208545, AY208655 FJ616342, FJ616450, FJ616557, FJ616669, FJ616782, FJ616889 FJ616343, FJ616451, FJ616558, FJ616670, FJ616783, FJ616890, AY208445, AY208576, AY208656 FJ616344, FJ616452, FJ616559, FJ616671, FJ616784, FJ616891 FJ616345, FJ616453, FJ616560, FJ616672, FJ616785, FJ616892 FJ616346, FJ616454, FJ616561, FJ616673, FJ616786, FJ616893 FJ616347, FJ616455, FJ616562, FJ616674, FJ616787, FJ616894, AY208446, AY208447, AY208577 FJ616348, FJ616456, FJ616563, FJ616675, FJ616788, FJ616895 FJ616349, FJ616457, FJ616564, FJ616676, FJ616789, FJ616896 FJ616350, FJ616458, FJ616565, FJ616677,

Dascyllus melanurus

















Dascyllus reticulatus

















■ ■



Dascyllus strasburgi Dascyllus trimaculatus













Dischistodus chrysopoecilus













Dischistodus melanotus













Dischistodus perspicillatus













Dischistodus prosopotaenia













Dischistodus pseudochrysopoeci Hemiglyphidodon plagiometopon

























Hypsypops rubicundus













Lepidozygus tapeinosoma













Mecaenichthys immaculatus





















Bernardi and Crane (unpublished); Quenouille et al. (2004); McCafferty et al. (2002) Bernardi and Crane (unpublished); Quenouille et al. (2004); McCafferty et al. (2002) Cooper et al. (2009); Quenouille et al. (2004); McCafferty et al. (2002) Cooper et al. (2009); Quenouille et al. (2004); McCafferty et al. (2002) McCafferty et al. (2002) Cooper et al. (2009); Quenouille et al. (2004); McCafferty et al. (2002) Cooper et al. (2009) Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009) Cooper et al. (2009) Cooper et al. (2009) Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009) Cooper et al. (2009) Cooper et al. (2009)

Microspathodon chrysurus













Microspathodon dorsalis













Neoglyphidodon melas

















Neoglyphidodon nigroris

















Neoglyphidodon oxyodon

















Neoglyphidodon polyacanthus Neoglyphidodon thoracotaeniatu Neopomacentrus azysron

































Neopomacentrus cyanomos



■ ■

Neopomacentrus filamentosus Neopomacentrus miryae Neopomacentrus nemurus Neopomacentrus sindensis Neopomacentrus taeniurus







Nexilosus latifrons Parma microlepis

■ ■

■ ■

■ ■

Parma oligolepis























■ ■ ■

■ ■ ■















FJ616790, FJ616897 AY208448, AY208449, AY208578, AY208657 FJ616352, FJ616460, FJ616567, FJ616679, FJ616792, FJ616899 FJ616353, FJ616461, FJ616568, FJ616680, FJ616793, FJ616900, AY208450, AY208579 FJ616354, FJ616462, FJ616569, FJ616681, FJ616794, FJ616901, AY208451, AY208452, AY208580, AY208658 FJ616355, FJ616463, FJ616570, FJ616682, FJ616795, FJ616902, AY208453, AY208581, AY208659 AF285931, AF285953, AY208454, AY208582 FJ616356, FJ616464, FJ616571, FJ616683, FJ616796, FJ616903 FJ616357, FJ616465, FJ616572, FJ616684, FJ616797, FJ616904 AY098626, AY098631, AY208455, AY208583 AY208456, AY208457, AY208584, AY20866 AY208458, AY208459, AY208585 AY208460, AY208461, AY208586 AY208462, AY208463, AY208587, AY208660 FJ616358, FJ616466, FJ616573, FJ616685, FJ616798, FJ616905 FJ616359, FJ616467, FJ616906 FJ616360, FJ616468, FJ616574, FJ616686, FJ616799, FJ616907 AF285932, AF285954, AY208464, AY208588, AY208662

Quenouille et al. (2004) Cooper et al. (2009) Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004) Quenouille et al. (2004); Tang (2001) Cooper et al. (2009) Cooper et al. (2009) Quenouille et al. (2004); Tang (2001) Quenouille et al. (2004) Quenouille et al. (2004) Quenouille et al. (2004) Quenouille et al. (2004) Cooper et al. (2009) Cooper et al. (2009) Cooper et al. (2009) Quenouille et al. (2004); Tang (2001)

Plectroglyphidodon dickii













Plectroglyphidodon lacrymatus Plectroglyphidodon leucozonus





































Pomacentrus adelus Pomacentrus albicaudatus













Pomacentrus alexanderae













Pomacentrus amboinensis













Pomacentrus auriventris Pomacentrus australis



Pomacentrus bankanensis











Pomacentrus brachialis









Pomacentrus burroughi







Pomacentrus chrysurus





Pomacentrus coelestis



Pomacentrus grammorhynchus









































































FJ616361, FJ616469, FJ616575, FJ616687, FJ616800, FJ616908, AY208465, AY208466, AY208589, AY208663 FJ616362, FJ616470, FJ616576, FJ616688, FJ616801, FJ616909 FJ616363, FJ616471, FJ616577, FJ616689, FJ616802, FJ616910, AY208467, AY208468, AY208590 AY208469, AY208470, AY208591, AY208664 FJ616364, FJ616472, FJ616578, FJ616690, FJ616803, FJ616911 FJ616365, FJ616473, FJ616579, FJ616691, FJ616804, FJ616912 FJ616366, FJ616474, FJ616580, FJ616692, FJ616805, FJ616913 AF081235 AY208471, AY208472, AY208592, AY208668 FJ616367, FJ616475, FJ616581, FJ616693, FJ616806, FJ616914, AY208473, AY208593, AY208665 FJ616368, FJ616476, FJ616582, FJ616694, FJ616807, FJ616915, AY208474, AY208475, AY208594 FJ616369, FJ616477, FJ616583, FJ616695, FJ616808, FJ616916 FJ616370, FJ616478, FJ616584, FJ616696, FJ616809, FJ616917, AY208476, AY208595 FJ616371, FJ616479, FJ616585, FJ616697, FJ616810, FJ616918, AY208478, AY208477, AY208596 FJ616372, FJ616480, FJ616586, FJ616698, FJ616811, FJ616919, AY208479, AY208480, AY208597

Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009) Cooper et al. (2009); Quenouille et al. (2004) Quenouille et al. (2004) Cooper et al. (2009) Cooper et al. (2009) Cooper et al. (2009) Jang-Liaw et al. (2002) Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009) Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004)

Pomacentrus lepidogenys















■ ■ ■ ■ ■ ■

Pomacentrus leptus Pomacentrus milleri Pomacentrus moluccensis













■ ■ ■

Pomacentrus nagasakiensis Pomacentrus nigromanus













■ ■

Pomacentrus nigromarginatus Pomacentrus pavo

















Pomacentrus philippinus





■ ■















Pomacentrus reidi







Pomacentrus smithi







Pomacentrus stigma













Pomacentrus trilineatus Pomacentrus vaiuli













Pomachromis fuscidorsalis Pomachromis richardsoni













Premnas biaculeatus













■ ■

■ ■









FJ616373, FJ616481, FJ616587, FJ616699, FJ616812, FJ616920, AY208481, AY208482, AY208598 AY208483, AY208484, AY208599 AY208485, AY208600 FJ616374, FJ616482, FJ616588, FJ616700, FJ616813, FJ616921, AY208486, AY208487, AY208601, AY208669 AY208489, AY208488, AY208602 FJ616375, FJ616483, FJ616589, FJ616701, FJ616814, FJ616922, AY208490, AY208491, AY208603, AY208671 FJ616376, FJ616484, FJ616590, FJ616702, FJ616815, FJ616923 EF095577, EF095605, AY208492, AY208493, AY208604, AY208666 FJ616377, FJ616485, FJ616591, FJ616703, FJ616816, FJ616924 AY208496, AY208497, AY208606, AY208672 AY208498, AY208499, AY208607, AY208670 FJ616378, FJ616486, FJ616592, FJ616704, FJ616817, FJ616925 AY208500, AY208608 FJ616379, FJ616487, FJ616593, FJ616705, FJ616818, FJ616926, AY208501, AY208502, AY208609 AY208503, AY208610 FJ616380, FJ616488, FJ616594, FJ616706, FJ616819, FJ616927 FJ616381, FJ616489, FJ616595, FJ616707, FJ616820, FJ616928, AY208367, AY208520, AY208632

Cooper et al. (2009); Quenouille et al. (2004) Quenouille et al. (2004) Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004) Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004) Cooper et al. (2009) Chen et al. (2007); Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004) Quenouille et al. (2004) Quenouille et al. (2004) Cooper et al. (2009) Quenouille et al. (2004) Cooper et al. (2009); Quenouille et al. (2004) Quenouille et al. (2004) Cooper et al. (2009) Cooper et al. (2009); Quenouille et al. (2004)

Pristotis obtusirostris













Similiparma hermani













Stegastes adustus Stegastes altus Stegastes apicalis

■ ■ ■

■ ■









Stegastes diencaeus













Stegastes fasciolatus













Stegastes imbricatus













Stegastes leucostictus













Stegastes lividus Stegastes nigricans

■ ■











Stegastes obreptus













Stegastes partitus













■ ■





Apogonidae

CO1

ND1

ND2

■ ■





16s

■ ■



12s

Stegastes planifrons Stegastes variabilis Teixeirichthys jordani

Apogon amboinensis Apogon angustatus

■ ■

■ ■







Apogon apogonoides





FJ616382, FJ616490, FJ616596, FJ616708, FJ616821, FJ616929 FJ616383, FJ616491, FJ616597, FJ616709, FJ616822, FJ616930 AF285937, AF285959 AF081243 FJ616384, FJ616492, FJ616598, FJ616710, FJ616823, FJ616931 FJ616385, FJ616493, FJ616599, FJ616711, FJ616824, FJ616932 FJ616386, FJ616494, FJ616600, FJ616712, FJ616825, FJ616933 FJ616387, FJ616495, FJ616601, FJ616713, FJ616826, FJ616934 FJ616388, FJ616496, FJ616602, FJ616714, FJ616827, FJ616935 AF081245 FJ616389, FJ616497, FJ616603, FJ616715, FJ616828, FJ616936 FJ616390, FJ616498, FJ616604, FJ616716, FJ616829, FJ616937 FJ616391, FJ616499, FJ616605, FJ616717, FJ616830, FJ616938 AY208504, AY208611, AY208673 AF285938, AF285960 FJ616392, FJ616500, FJ616606, FJ616718, FJ616831, FJ616939

Accession Number AB206138 AB206139, FJ346747–FJ346748, FJ346706– FJ346707, FJ346790–FJ346791. AB206140

Cooper et al. (2009) Cooper et al. (2009) Tang (2001) Jang-Liaw et al. (2002) Cooper et al. (2009) Cooper et al. (2009) Cooper et al. (2009) Cooper et al. (2009) Cooper et al. (2009) Jang-Liaw et al. (2002) Cooper et al. (2009) Cooper et al. (2009) Cooper et al. (2009) Quenouille et al. (2004) Tang (2001) Cooper et al. (2009) Source Mabuchi et al. (2006) Mabuchi et al. (2006): Thacker and Roje (2009) Mabuchi et al. (2006)

■ ■

DQ533157 AB206141 FJ346757–FJ346758, FJ346714–FJ346715, FJ346800–FJ346801 AB206142 AB206143 AB206144 AB206145, FJ346749, FJ346708, FJ346792

Apogon atradorsatus Apogon aureus Apogon aurolineatus



Apogon carinatus Apogon cathetogramma Apogon compressus Apogon cookii

■ ■ ■ ■

■ ■ ■ ■

Apogon crassiceps Apogon cyanosoma Apogon doederleini

■ ■ ■

■ ■ ■

Apogon ellioti Apogon endekataenia Apogon erythrinus

■ ■ ■

■ ■ ■



Apogon exostigma











AB206131, FJ346742, FJ346702, FJ346785

Apogon flagelliferus Apogon fraenatus Apogon fuscus Apogon guamensis Apogon holotaenia







■ ■ ■

■ ■ ■







Apogon ishigakiensis Apogon kallopterus

■ ■

■ ■







Apogon kiensis Apogon lateralis Apogon lineatus Apogon maculatus



■ ■





■ ■



FJ346756, FJ346713, FJ346799 AB206132 AB206129 AB206150 FJ346745–FJ346746, FJ346705, FJ346788– FJ346789 AB206151 AB206133, FJ346750–FJ346751, FJ346709– FJ346710, FJ346793–FJ346794 AB206152 FJ346752–FJ346753, FJ346795–FJ346796 AB206153 EU380982-EU380983, EU381004-























AB206127 AB206146 AB206147, EU380981, EU381003, EU381023 AB206148 AB206149 AB206128, EF607315

Smith and Wheeler (2006) Mabuchi et al. (2006) Thacker and Roje (2009) Mabuchi et al. (2006) Mabuchi et al. (2006) Mabuchi et al. (2006) Mabuchi et al. (2006): Thacker and Roje (2009) Mabuchi et al. (2006) Mabuchi et al. (2006) Mabuchi et al. (2006): Thacker (2009) Mabuchi et al. (2006) Mabuchi et al. (2006) Mabuchi et al. (2006): Zhang (unpublished) Mabuchi et al. (2006): Thacker and Roje (2009) Thacker and Roje (2009) Mabuchi et al. (2006) Mabuchi et al. (2006) Mabuchi et al. (2006) Thacker and Roje (2009) Mabuchi et al. (2006) Mabuchi et al. (2006): Thacker and Roje (2009) Mabuchi et al. (2006) Thacker and Roje (2009) Mabuchi et al. (2006) Thacker (2009)

Apogon melas Apogon niger Apogon nigrofasciatus Apogon norfolcensis Apogon notatus Apogon novemfasciatus Apogon properuptus (dotted) Apogon properuptus (lined) Apogon quadrifasciatus Apogon quadrisquamatus Apogon rhodopterus Apogon sangiensis Apogon savayensis Apogon selas Apogon semilineatus Apogon semiornatus Apogon taeniatus Apogon taeniophorus (lined) Apogon taeniophorus (spotted) Apogon trimaculatus Apogon ventrifasciatus Archamia biguttata Archamia fucata

■ ■ ■

■ ■ ■







■ ■ ■ ■

■ ■ ■

■ ■

■ ■

■ ■ ■ ■ ■ ■

■ ■ ■ ■ ■ ■



EU381005, EU381025 AB206154 AB206155 AB206156, FJ346743, FJ346703, FJ346786 FJ237583 AB206157 AB206158 AB206159 AB206160 AB206161, EU148589, EF607317

Mabuchi et al. (2006) Mabuchi et al. (2006) Mabuchi et al. (2006): Thacker and Roje (2009) Lakra et al. (unpublished) Mabuchi et al. (2006) Mabuchi et al. (2006) Mabuchi et al. (2006)



FJ346744, FJ346704, FJ346787 AB206134 AB206162 AB206163 AB206164 AB206165 AB206130 EF607321 AB206167

Mabuchi et al. (2006) Mabuchi et al. (2006): Lakre (unpublished): Zhang (unpublished) Thacker and Roje (2009) Mabuchi et al. (2006) Mabuchi et al. (2006) Mabuchi et al. (2006) Mabuchi et al. (2006) Mabuchi et al. (2006) Mabuchi et al. (2006) Zhang (unpublished) Mabuchi et al. (2006)





AB206168

Mabuchi et al. (2006)









AB206135, FJ346754–FJ346755, FJ346711– FJ346712, FJ346797–FJ346798 AB206169 FJ346739–FJ346740, FJ346699–FJ346670, FJ346782–FJ346783 EU380979–EU380980, EU381001EU381002, EU381021-EU381022

Mabuchi et al. (2006): Thacker and Roje (2009) Mabuchi et al. (2006) Thacker and Roje (2009)

■ ■

























Thacker (2009)

Astroapogon alutus Astroapogon puncticulatus Cercamia eremia

■ ■ ■





Cheilodipterus artus Cheilodipterus isostigmus Cheilodipterus macrodon Fowleria aurita Fowleria isostigma



■ ■ ■ ■

■ ■ ■ ■ ■

■ ■ ■ ■ ■





■ ■

■ ■

Glossamia aprion Gymnoapogon urospilotus

■ ■

■ ■

■ ■

Phaeoptyx conklini Phaeoptyx pigmentaria Phaeoptyx xenus Pseudamia gelatinosa

■ ■ ■ ■









Pterapogon kauderni







Rhabdamia cypselura







Siphamia sp. Siphamia versicolor Sphaeramia nematoptera Sphaeramia orbicularis Zoramia fragilis Zoramia gilberti Zoramia leptacanthus

■ ■ ■ ■ ■



Fowleria marmorata Fowleria variegata







■ ■

■ ■









FJ609908 FJ346779, FJ346822 FJ346771, FJ346729–FJ346730, FJ346813– FJ346814 FJ346764–FJ346765, FJ346722–FJ346723 FJ346766, FJ346724, FJ346808 FJ346763, FJ346721, FJ346807 FJ346759, FJ346716, FJ346802 AB206125, FJ346760, FJ346717, FJ346803 FJ346761–FJ346762, FJ346720, FJ346806 AB206126, FJ346718–FJ346719, FJ346804– FJ346805 FJ346770, FJ346728, FJ346812 FJ346774–FJ346775, FJ346733–FJ346734, FJ346817–FJ346818 FJ346769, FJ346727, FJ346811 FJ609875 FJ609934 FJ346776–FJ346778, FJ346735–FJ346737, FJ346819–FJ346821 FJ346767–FJ346768, FJ346725–FJ346726, FJ346809–FJ346810 FJ346772–FJ346773, FJ346731–FJ346732, FJ346815–FJ346816 FJ346781, FJ346824 DQ790844, DQ790846, FJ584123, FJ346780, FJ346738, FJ346823 FJ346741, FJ346701, FJ346784 AB206137 AB206136

Baldwin et al (2009) Thacker and Roje (2009) Thacker and Roje (2009) Thacker and Roje (2009) Thacker and Roje (2009) Thacker and Roje (2009) Thacker and Roje (2009) Mabuchi et al. (2006): Thacker and Roje (2009) Thacker and Roje (2009) Mabuchi et al. (2006): Thacker and Roje (2009) Thacker and Roje (2009) Thacker and Roje (2009) Thacker and Roje (2009) Baldwin et al (2009) Baldwin et al (2009) Thacker and Roje (2009) Thacker and Roje (2009) Thacker and Roje (2009) Thacker and Roje (2009) Kaeding et al. (2007) Steinke et al. (2009) Thacker and Roje (2009) Thacker and Roje (2009) Mabuchi et al. (2006) Mabuchi et al. (2006)

 

Table S2. Information on gene region used in all four focal families. ‘% Data’ is the proportion of taxa from the entire data set that were represented by that gene. Model parameters were chosen based on results from jModelTest based on both AIC and BIC (i.e. both methods returned the same model within 95% CI.

Family Labridae

Chaetodontidae

Pomacentridae

Gene

BP

Type

% Data

Model

12s

857

mtDNA

76.4

TVMef+I+G

16s

538

mtDNA

83.0

TPM3uf+I+G

COI

654

mtDNA

55.1

TIM2+I+G

Cyt B

868

mtDNA

41.3

GTR+I+G

RAG 2

828

nDNA

46.4

TPM2uf+I+G

TMO4c4

457

nDNA

46.4

TrNef+I+G

S7 II

877

nDNA

18.0

TrNef+I+G

12s

925

mtDNA

88.4

SYM+I+G

16s

605

mtDNA

73.7

SYM+I+G

Cyt B

675

mtDNA

60.0

TrN+I+G

ND3

395

mtDNA

73.7

GTR+I+G

RAG2

801

nDNA

75.8

SYM+G

ETS 2

648

nDNA

58.9

TrN+G

TMO4c4

511

nDNA

72.6

TPM1uf+I+G

S7 II

663

nDNA

58.9

HKY+I+G

12s

961

mtDNA

69.4

TVMef+I+G

Apogonidae

16s

565

mtDNA

75.8

K80+I+G

ATP6/8

842

mtDNA

56.5

TVM+G

Cyt B

1141

mtDNA

64.5

TIM2+I+G

ND3

351

mtDNA

54.8

TIM+I+G

BMP 4

553

nDNA

55.9

TVM+G

RAG1

904

nDNA

68.3

TPM2uf+G

RAG2

802

nDNA

55.9

SYM+I+G

12s

455

mtDNA

45.4

TVM+I+G

16s

976

mtDNA

46.4

GTR+I+G

COI

1530

mtDNA

55.7

TPM3uf+I+G

ND1

975

mtDNA

47.4

GTR+I+G

ND2

1065

mtDNA

49.5

TIM3+I+G

Table S3. Mean age estimates of major lineages of the families Labridae, Chaetodontidae, Pomacentridae and Apogonidae, under both unpartitioned and partitioned models run in BEAST. Previously published age estimated and their sources are shown for comparison where available. * Denotes stem age of lineage. ^ The age estimates for labrid lineages of Kazancioglu et al (2009) are taken from an appendix and it is not know what error this interval represents. Family/Lineage

Total

Unpartitioned

Partitioned

Previously reported

Sp.

Mean

95% HPD

Mean

95% HPD

Mean (HPD)

Source

Labridae

608

59.9

54.4-66.7

60.2

55-66.1

55-68^

Kazancioglu et al. 2009

Hypsengyines

95

53.1

50.6-56.3

52.7

50.6-55.4

43(32-56)

Alfaro et al. 2009

57.3*

51.1-64.4*

58.4*

52-64.8*

53-64*^

Kazancioglu et al. 2009

Scarine/Cheilines/Labrines Labrines

23

23.4

17-30.1

20.9

16.2-26.1

13(6-20)

Alfaro et al. 2009

Cheilines

28

22.9

16.8-29.4

24.1

18.9-29.2

17(11-23)

Alfaro et al. 2009

Scarines

97

29

23.4-35

27.7

23.3-32.2

26-28^

Kazancioglu et al. 2009

Pseudocheilines

78

42.9

34.6-51.3

44.1

36.9-51.4

37(26-49)

Alfaro et al. 2009

Novaculines

38

43.8

20.3-34.8

30.9

24.4-36.7

24(16-33)

Cowman et al. 2009

Pseudolabrines

24

14.8

10.5-19.4

15.4

11.2-20.0

19.4 (28.4-11.1)

Cowman et al. 2009

Julidines

247

33.9

28.4-39.6

33.9

28.5-38.5

35(36-39)^

Kazancioglu et al. 2009

Labrichthyines

14

19.6

13.7-25.4

21.7

15.9-27.6

23.1 (30.4-15.9)

Cowman et al. 2009

Thalassoma/Gomphosus

30

15.8

12.5-19.6

13.6

10.1-17.3

8-15^

Kazancioglu et al. 2009

Macropharygodon

11

17.2

12.5-22.1

15.5

18.3-19.8

22

Read et al. 2006

Halichoeres IP

50

21.9

18-25.8

21.2

17.9-24.7

22(17-29)

Alfaro et al. 2009

Halichoeres NW

27

15.3

11.4-18.9

13

9.9-16.2

12(7-17)

Alfaro et al. 2009

Scarus

53

10.4

8-13

9

8.7-13.7

6(4-9)

Alfaro et al. 2009

Chlorurus

17

5.8

3.8-7.9

4.9

3-6

4(2-5)

Alfaro et al. 2009

Pomacentridae

384

62.9

50.8-88.1

55.3

50.6-65.2

53(50-59)

Santini et al. 2009

Stegastinae

67

54.9

38.9-79.5

47.1

38.3-58

NA

Lepidozyginae

1

61.4*

48.7-87.1

54.8*

49.8-65.3

NA

Chrominae

109

39.1

26.8-57.1

38

27.3-40.1

NA

Dascyllus

10

17.8

11.2-27.6

13.6

10.3-17.1

16 (11.7-21)

Abudefdufinae

19

31.4

20.4-47

24.8

18.5-32.5

NA

Pomacentrinae

187

45.1

33.9-64.4

38.2

32.9-45.4

NA

7

24.4

14.2-38.2

21

15.1-27.3

NA

Dischistodus

McCafferty et al. 2002

Chrysptera I

6

33.7

23-49.5

30.5

24.8-37.1

NA

Chrysptera II

26

25.3

22.7-47.3

21.5

17-26.7

NA

Chrysptera III

5

27.4

15.1-43.3

23.6

15.6-31.7

NA

Pomacentrus

72

28.1

19.6-40.7

30.9

16-27

NA

Neopomacentrus

19

34.39

25-50.1

28.1

22.9-34.4

NA

Amphiprionae

29

24.1

14.4-38

15.3

10.6-22.6

NA

Chaetodontidae

127

31.6

30.2-34.1

32.1

30.5-34.3

36.72

Fessler & Westneat 2007

Bannerfish

25

26.1

21.3-30.6

25.8

21.9-29.3

33.49

Fessler & Westneat 2007

Amphichaetodon*

2

26.1/5.1

21.3-30.6/1.9-

25.8/4.8

21.9-29.3/2-8.5

27.8

Fessler & Westneat 2007

8.7 Chelmon

3

3.2

1.7-5

3.1

1.4-5.1

3.7 (2.25.9)

Bellwood et al. 2010

Chelmonops

2

2

0.6-3.7

2.1

0.5-4.2

1 (0.37-2)

Bellwood et al. 2010

Coradion

3

4.2

2.5-6.1

3.2

2.1-4.4

2.7 (1.3-4.8)

Bellwood et al. 2010

Heniochus

8

9

6.4-11.7

7

6.2-10

9.0 (5.9-12.6)

Bellwood et al. 2010

Hemitaurichthys

4

2.4

0.9-4.3

2.4

0.7-4.6

3.05 (1.4-5.3)

Bellwood et al. 2010

Forcipiger

2

6.7

3.6-10.1

5.4

3.4-7.4

4.6 (2.1-8.05)

Bellwood et al. 2010

Chaetodon crown

91

18.8

15.5-21.8

16.3

14.0-18.7

19.67

Fessler & Westneat 2007

Clade 1

3

18.8*/8.1

15.5-21.8*/4-

16.3*/7.1

14.0-18.7*/4.6-

19.67*/9.75

Fessler & Westneat 2007

12.2

9.7

Clade 2

36

12.6

9.7-15.7

11

8.9-13.2

14.04

Fessler & Westneat 2007

Clade 3

21

14.6

11.9-17.4

12.7

10.8-14.7

14.51

Fessler & Westneat 2007

Clade 4

31

12.3

9.9-14.9

10.6

8.8-12.4

13.96

Fessler & Westneat 2007

Prognathodes

11

23.1*/8.7

19.3-26.9*

20.1*/7.1

17.2-23*/4.3-

23.93*

Fessler & Westneat 2007

/4.0-13.1

10.3

Apogonidae

345

63.2

51.0-81.1

56.4

50.5-62.7

NA

Pseudamia

12

63.2

51.0-81.1

56.4

50.5-62.7

NA

Siphamia

10

53.2

39.3-70.8

49.1

39.5-57.6

NA

47.4

39.3-70.8

39.4

29.8-48.2

~32

Crown Apogonidinae Phaeoptyx et al.

9

31

20.8-42.7

27

-

NA

Rhabdamia et al.

10

26.2

13.0-40.3

35.4

24.3-44.4

NA

Gymnoapogon et al.

11

20.4

-

16

-

NA

Sphaeramia

2

31

-

26.2

-

NA

Mabuchi 2006

Fowleria

10

29.4

19.6-40.5

21.7

15.6-29.4

~14

Mabuchi 2006

Pristiapogon

6

24.6

4.7-18.2

20.5

13.9-30.6

~29

Mabuchi 2006

Pristicon

3

10.6

1.1-21.9

12.9

1.5-25.7

~15

Mabuchi 2006

Apogon & Archamia

56

19.6

12.4-27.9

22.4

15.7-28.9

NA

Zoramia & Ostorhinchus 1

7

17.6

11-25.5

15.1

-

~21

Mabuchi 2006

Ostorhinchus 2 (barred)

41

16.9

10.4-28.2

21.5

-

~27

Mabuchi 2006

Ostorhinchus 3 (striped)

79

23.9

16.22-33

24.9

18.3-31.1

~27.5

Mabuchi 2006

Cheilodipterus &

32

19.6

11.6-28.8

19.23

13.3-25.3

NA

Glossamia

Table S4. Departure of lineages from the global rate of diversification within additional families of reef fishes and marine gastropod genera, taken from the literature (Bellwood et al. 2004; Alfaro et al. 2007; Williams and Duda 2010). Italicized P-values highlight significantly higher species richness in subtending clades than expected under the global rate of cladogenesis. ε is the extinction rate, rG is the estimated global speciation rate conditional on the extinction rate for each family. An asterisk indicates probabilities calculated using clade stem age. Conus Clade “X” is named from Williams and Duda (2010).

Family/Clade

Ages Species ε = 0

Pomacanthidae (rG)

38

88

0.0996 0.0993 0.0986 0.0972 0.0952 0.0923 0.0883 0.0825 0.0739 0.0584

Pomacanthus

33.7

13

0.9363 0.8989 0.8719 0.8527 0.8395 0.8311 0.8264 0.7201 0.8273 0.8342

Chaetodontoplus*

36.4

13

0.7231 0.7446 0.7632 0.7796 0.7941 0.8072 0.8190 0.7176 0.8404 0.8510

Pygoplites*

23

1

1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000

Holocanthus*

23

8

0.4738 0.5066 0.5383 0.5692 0.5999 0.6309 0.6629 0.5819 0.7359 0.7845

Centropyge (Xiphypops)

13.9

19

0.0391 0.0488 0.0597 0.0719 0.0858 0.1024 0.1234 0.0799 0.1976 0.2838

Centropyge*

24.8

11

0.4131 0.4474 0.4805 0.5129 0.5451 0.5775 0.6111 0.5127 0.6878 0.7392

Paracentropyge*

23

3

0.8078 0.8234 0.8378 0.8513 0.8642 0.8767 0.8892 0.8567 0.9161 0.9330

Genicanthus*

13.9

10

0.0746 0.0928 0.1142 0.1395 0.1696 0.2061 0.2511 0.2049 0.3858 0.5010

Apolemichthys*

24.8

9

0.4930 0.5254 0.5564 0.5862 0.6154 0.6446 0.6744 0.5860 0.7412 0.7853

ε = 0.1 ε = 0.2 ε = 0.3 ε = 0.4 ε = 0.5 ε = 0.6 ε = 0.7 ε = 0.8 ε = 0.9

Tetraodonitformes (rG) 68.5

430

0.0772 0.0770 0.0766 0.0758 0.0747 0.0731 0.0708 0.0676 0.0626 0.0536

Balistidae

22.9

43

0.0083 0.0122 0.0173 0.0241 0.0332 0.0454 0.0629 0.0898 0.1370 0.2408

Diodontidae

10.9

22

0.0002 0.0004 0.0008 0.0015 0.0029 0.0055 0.0106 0.0213 0.0464 0.1231

Monacanthidae

24.6

108

0.0000 0.0000 0.0000 0.0000 0.0001 0.0002 0.0005 0.0016 0.0057 0.0261

Ostraciidae

20.8

25

0.0288 0.0373 0.0474 0.0595 0.0744 0.0932 0.1184 0.1552 0.2160 0.3388

Tetraodonitdae

38.3

185

0.0008 0.0015 0.0025 0.0041 0.0065 0.0101 0.0155 0.0245 0.0414 0.0839

Turbo (rG)

61.5

75

0.0589 0.0588 0.0583 0.0575 0.0562 0.0544 0.0520 0.0485 0.0432 0.0338

Marmarostoma

23.7

25

0.0097 0.0138 0.0189 0.0254 0.0336 0.0441 0.0583 0.2400 0.1596 0.1797

Echinolittorina (rG)

38.5

60

0.0883 0.0881 0.0873 0.0860 0.0840 0.0813 0.0774 0.0718 0.0635 0.0488

Granulittorina

21

31

0.0399 0.0498 0.0603 0.0713 0.0831 0.0964 0.1123 0.1333 0.1645 0.2216

Conus (rG)

62

500

0.0891 0.0889 0.0884 0.0875 0.0863 0.0844 0.0819 0.0783 0.0727 0.0626

Clade “X”

23.4

273

0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0005

Table S5. Estimated net diversification rates (rG) at low and high extinction, and proportion of coral reef affiliated member taxa of each reef fish family. The families of the Tetraodontiformes were reexamined using ages from Alfaro et al. (2007). Family

% Reef ε=0

ε=0.9

Labridae

51.21

0.0902 0.0640

Pomacentridae

68.14

0.0856 0.0589

Apogonidae

52.46

0.0815 0.0556

Chaetodontidae 70.00

0.1274 0.0788

Balistidae

84.00

0.1257 0.0654

Diodontidae

64.00

0.2085 0.0938

Monacanthidae 53.00

0.1635 0.0987

Ostraciidae

76.00

0.1232 0.0571

Tetraodontidae

28.00

0.1170 0.0753

Molidae

0.00

0.0359 0.0109

Triacanthidae

0.00

0.0535 0.0177

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