BACKGROUND
labrid fishes comprise roughly  <dig> species and inhabit tropical and temperate marine habitats around the world.
they are an ecologically dominant component of major reef systems  <cit>  and display a staggering degree of trophic and morphological diversity  <cit> .
members exploit nearly all known feeding niches available to fishes including algae, fish, zooplankton, ectoparasites, crabs, polychaetes, mollusks, amphipods, and echinoderms  <cit> , range in size from a few grams to over  <dig> kg, and exhibit high diversity in cranial and axial morphology  <cit> .
recently, the parrotfishes , which constitute one of the major groups of reef herbivores and bioeroders  <cit> , have been recognized as a subclade of labrids  <cit> .
one classic explanation for both the species richness and the ecomorphological diversity of labrids is that this clade has evolved a key innovation in the form of modified pharyngeal jaws that has fueled their subsequent radiation  <cit> .
percomorph fishes possess two sets of jaws: oral jaws which function in prey capture and manipulation, and pharyngeal jaws which usually aid in processing food and moving it to the esophagus.
like cichlids, which are also widely recognized for their exceptional functional diversity and species richness, labrids exhibit a highly modified condition of the pharyngeal jaw apparatus  referred to as pharyngognathy  <cit> .
pharyngognathy involves united left and right lower jaw elements , a muscular sling connecting the neurocranium to the united fifth ceratobranchials, and a mobile diarthrotic articulation of the upper pharyngeal jaws with the neurocranium  <cit> .
one of the most species-rich groups of labrids, the parrotfishes, exhibit further modifications of the pja that are associated with forceful grinding  <cit> .
these include a laterally expanded fourth epibranchial, laterally compressed upper pharyngeal jaws , an anterior muscular sling through novel attachments of the transversalis ventralis muscle , a well developed sliding joints between the pharyngobranchial, neurocranium and epibranchial that permit extensive anterior-posterior motion of the upper jaw, and a posterior to anterior progression of ordered tooth tows on the lower pharyngeal jaws.
these modifications are thought to enable trophic diversification by allowing the pharyngeal jaws to take on enhanced functions in prey processing, freeing the oral jaws to become specialized for prey capture  <cit> .
the labroid pharyngeal jaw condition has been proposed to be a key innovation  <cit>  that underlies putative adaptive radiation in cichlids  <cit>  and labrids  <cit> .
recent studies have examined the role of the pharyngeal jaws in shaping cichlid morphological diversification and cladogenesis  <cit> .
however, the hypothesis that pharyngeal jaws have influenced labrid diversity has never been explicitly tested .
similarly, although structural and functional innovations of the scarine pharyngeal jaw to allow the processing of algae and coral skeletons are thought to underlie the ecological radiation of this clade in reef and seagrass habitats  <cit> , the influence of this trait upon parrotfish diversification patterns has never been studied.
in schluter's framework of ecological adaptive radiation, key innovations are one mechanism that provides ecological opportunity  <cit> .
these traits are hypothesized to trigger adaptive radiations by enabling a lineage that evolves the innovation to exploit a range of previously unavailable niches.
the filling of niche space is expected to proceed rapidly.
one of the central predictions of a key innovation hypothesis in this framework then is concordance between the acquisition of the key innovation and a shift in lineage diversification rate  <cit> .
here we evaluate this aspect of the key innovation hypothesis by testing whether the evolution of modified pharyngeal jaws has accelerated lineage diversification within labrid fishes.
the current lack of knowledge of phylogenetic relationships among major percomorph groups prevents a sister group comparison between labrids and their outgroup.
however labrids remain an especially good group to address this question because the nested radiation of parrotfishes within them provides the opportunity to examine both ancient and recent signatures of pharyngeal jaw innovation on patterns of diversification.
we assembled the largest time-calibrated phylogeny of labrids to date and used comparative methods to assess the impact of the pharyngeal jaw modifications on diversification rate.
we asked three general questions:
<dig>  did pharyngeal jaw innovation trigger rapid lineage diversification as part of an adaptive radiation?
if specialized pharyngeal jaws enabled labrids or parrotfishes to adaptively radiate along ecological axes, we would expect to see a pattern where diversification after the acquisition of the trait was rapid  and then slowed through time   <cit> .
we tested for this pattern, which has recently been identified as one of the ten key signatures of adaptive radiations  <cit> , in two ways: first using the mccr test of pybus and harvey  <cit>  which tests for a slowing of diversification rates through time and second, by directly comparing the fit of density dependent models of cladogenesis to models where diversification is not a function of clade richness  <cit> .
we applied these methods to both the entire timetree to test for this signature of adaptive radiation in the initial diversification of labrids, and within parrotfishes, to test for adaptive radiation following the evolution of pharyngeal jaws modified for grinding.
<dig>  are diversification rate shifts within labrids and scarids temporally concordant with the pharyngeal jaw innovations?
if pja innovations have been primarily responsible for diversification within labrids and parrotfishes, we can make three further predictions.
first, since key innovations are thought to trigger increased diversification, we would expect the overall rate of labrid diversification to be high compared to other percomorph fishes.
second, if the pja is the main cause of labrid species richness, any additional diversification rate increases should be restricted to relatively small subclades.
if a large fraction of labrid richness occurs in young, fast-evolving subclades temporally removed from the labrid root, then the pja is a weak explanation for standing labrid diversity even if the pja played some role in initially establishing the clade in diverse environments.
third, if the pharyngeal mill in parrotfishes were a key innovation that triggered a further adaptive radiation, we would expect to see diversification rates increase at or near the origin of this clade.
<dig>  does the character state of the pharyngeal jaws predict diversification rate?
key innovation hypotheses predict that lineages with the innovation should diversify more quickly than lineages that lack the trait  <cit> .
we used bisse  <cit> , a recently developed comparative method, to test whether labrid lineages with a modified pharyngeal mill  have diversified more quickly than those with the labroid pja.
the sister group of labrids is currently not known  <cit> .
this lack of phylogenetic resolution prevented us from testing whether the labroid pja itself was associated with faster rates of diversification than the generalized percomorph condition.
RESULTS
divergence time analysis
our beast analysis produced a well-resolved phylogeny of  <dig> labrid species that was in good agreement with previous work   <cit> .
a recent divergence time study of labrids treated the crown age as fixed at  <dig> my  <cit> .
our analysis recovered an almost identical crown age of labrids even though we assigned far more liberal constraints to this node  .
our estimate of the split between scarines and cheilines + labrines  is consistent with both the cr  and pl  estimates of smith et al  <cit> .
in contrast, our estimates for the age of crown scarines  excludes both streelman et al.
's  <cit>  age of  <dig> my and smith et al.
's  <cit>  estimate of  <dig> my.
the rest of our estimates within parrotfishes including the age of the seagrass clade, reef clade, scarus + chlorurus and crown ages of those genera are slightly older than those smith et al.,  <cit>  though in almost all cases their mean is captured in our 95% credible interval.
nodes in bold were fossil-calibrated .
diversification analysis
a lineage through time plot revealed that the log number of lineages appeared to accumulate at a roughly constant rate in the early history of labrids.
this pattern is expected for lineages where diversification rate has been constant  <cit> , suggesting that diversification in early labrid history was not initially fast .
this interpretation was supported by the mccr test for labrids which failed to reject the hypothesis of a constant diversification rate .
although the exponential density dependent model fit the labrid data best, the 95% credible set of models based on the calculation of akaike weights  <cit>  did not exclude the pure-birth model.
a lineage through time plot for scarines revealed fewer lineages in their early history than expected under a constant rates model.
this result was reinforced by a nonsignificant mccr test , suggesting that explosive scarine diversification did not accompany the evolution of modified pharyngeal jaws.
an exponential model of density-dependent diversification fit the scarines best but the 95% credible interval did not exclude the pure birth model .
akaike weights  <cit>  indicate the relative strength of support  for four candidate models: pb = pure birth, ddx = density dependent , ddl = density dependent , ld = linear decline.
best model indicated in bold.
medusa , a recently developed comparative method that integrates taxonomic and phylogenetic information, allows exceptionally radiating clades to be identified on an incompletely sampled phylogeny  <cit> .
medusa analysis revealed that the background rate of labrid diversification,  is somewhat higher than the average rate of diversification of percomorph  and ostariophysan  fishes as well as most major tetrapod lineages  <cit>  .
we found evidence for two significant rate shifts within labrids, though neither of these corresponded to the predictions generated by the pja key-innovation hypothesis .
the first corresponded to the origin of a clade comprising scarus and chlorurus .
the net diversification rate of the stem s-c lineage is only modestly higher than the background rate of labrid diversification due to a long branch leading from the split with hipposcarus to the crown group .
however rates within the crown s-c clade  were approximately  <dig>  times greater than the net diversification rate of other labrids.
the second rate shift occurred on the branch leading to most of the julidine diversity including the indo-pacific halichoeres, the new world halichoeres, and the labrichthyinae.
the rate within this lineage was approximately twice that of labrids diversifying at the background rate and roughly equal to the rate of diversification within the crown s-c clade .
we fit diversification models to both of the fast-evolving clades identified by medusa analysis to explore whether their patterns were consistent with adaptive radiation.
the scarines did not strongly favor a density dependent model , suggesting that their early diversification was not explosive.
this result was reinforced by a convex lineage through time plot, indicating fewer than expected species in their early history.
in contrast, the fast evolving julidines showed some evidence for adaptive radiation both by model fitting which strongly favored density dependent models , and a concave lineage through time plot  indicating more species than expected in their early history.
clade number refers to rate shifts identified in fig.
<dig>  r is the net diversification rate, ε is the extinction fraction .
aic and Δaic show improvement of aic score over a constant rates birth-death model as clades are allowed to change rates.
background shows background rates of other labrid clades under the two-rate model.
we tested for a correlation between diversification rate and the presence of a parrotfish pharyngeal mill using bisse  <cit> .
our results found strong support in favor of a model where pharyngeal mill-equipped lineages diversified ~4x faster than lineages with the typical labrid pharyngeal jaw apparatus .
however we were concerned with the possibility of a trickle-down effect from the s-c clade given that our medusa analysis found a rate increase for this group.
to investigate this further, we reran bisse with the s-c clade excluded and found no support for a two-rate model .
furthermore, the speciation estimates in this unsupported two-rate model were nearly identical  suggesting that diversification rates in parrotfish genera besides scarus and chlorurus are similar to rates in other labrids.
parameter estimates of the constrained  and unconstrained models for the pharyngeal jaw modifications found in all scaridae .
the s-c clade comprises the most sexually dichromatic, haremic, and territorial of parrotfishes  <cit>  and it has been suggested that sexual selection has played a dominant role in their diversification  <cit> .
to test whether extreme sexual dichromatism was a better explanation of diversification rates than a pharyngeal mill, we performed another bisse analysis with the parrotfishes in the s-c clade coded as  <dig> and the rest of the phylogeny as state  <dig>  a comparison of likelihood scores favored the extreme dichromatic model over the pharyngeal mill .
discussion
did the evolution of the labrid pharyngeal jaw trigger rapid lineage diversification?
a common element of many key innovation hypotheses is that the trait is linked to rapid diversification  <cit>  and adaptive radiation  <cit> .
although we found the labridae as a whole to have diversified rapidly compared to other percomorphs, we also found no evidence for a pulse of cladogenesis coincident with the origin of the clade followed by declining rates as predicted by models of adaptive radiation  <cit> .
instead, we found that cladogenesis in the early history of labrids proceeded in a fairly log-linear manner consistent with a model where net diversification rates were constant.
thus, we find no direct support for the hypothesis that the pja triggered rapid lineage diversification as part of an adaptive radiation .
high rates of extinction have been shown to erase the signature of adaptive radiation  <cit>  and so one possibility is that background extinction within labrids has masked pja-facilitated diversification.
however other marine fish clades of roughly similar ages with less trophic diversity and species richness do retain the signature of exceptionally rapid initial diversification  <cit> .
thus we are skeptical that exceptionally high extinction rates have masked the signal of explosive lineage diversification in labrids.
further evaluation of extinction rates across labrid history is hampered by their poor fossil record.
in any case, our analyses cast doubt on the pja-key innovation as a strong general explanation of labrid species richness because over 40% of non-scarine labrid diversity can be attributed to the julidine rate shift, an event which occurred ~ <dig> my after the origin of the labrid pja.
our findings are similar to those from recent studies of cichlid diversity.
although the pharyngeal jaw has been suggested to underpin species richness in this family as well  <cit> , recent phylogenetic analyses have found that the major diversification rate shift which lead to the origin of most of the diversity of east african haplochromines  occurred within the last  <dig>  my, well after the evolution of the pja  <cit> .
instead, diversification patterns appear to be strongly correlated with the evolution of specific behavioral and sexual characters  <cit>  such as mouth brooding and egg spots on the anal fins  <cit> .
is the parrotfish pharyngeal mill a key innovation that explains scarine biodiversity?
we similarly found weak evidence in favor of the pharyngeal mill key innovation hypothesis.
the mccr test did not support the hypothesis that early parrotfish diversification had slowed through time and fitting of diversification models did not favor density dependent models .
once again it is possible that high extinction rates have masked this signature although we regard this as less likely since scarines are considerably younger than crown labrids.
although we did find a significant increase in the rate of scarine diversification relative to other labrids, this rate increase was restricted to a clade comprising two very young genera of parrotfishes rather than at or near the root of the entire clade.
the strongest evidence supporting the idea that a pharyngeal mill has contributed to scarine biodiversity comes from our bisse analysis which found a high correlation between the possession of a pharyngeal mill and the diversification rate.
however we suggest that this result is driven by trickledown effects of the rate increase on scarus + chlorurus.
this was supported by our bisse reanalysis which showed that the diversification rate in other scarines was very similar to the average labrid diversification rate.
we suggest that the most likely cause of diversification in the s-c clade is the evolution of extreme male breeding coloration and reproductive behaviors through sexual selection  <cit> .
other contributing biogeographic factors are considered in smith et al.,  <cit>  and include pliocene/pleistocene fluctuations in sea level and the closing of the isthmus of panama.
what explains the rate shifts in julidines?
the julidines have been recognized as one of the largest of all coral reef fish radiations  <cit> .
for the first time we show that this radiation was exceptionally fast, with a net diversification rate of  <dig>  species/my.
recently alfaro et al.
<cit>  found evidence of rapid diversification of reef-associated tetraodontiform families during the late oligocene and early miocene.
the mean age estimate of the julidine rate increase  falls at the end of the oligocene, suggesting that similar factors may underlie the diversification of julidines and possibly other major reef-associated fish clades.
these include the closing of the tethys and the collision of the australia new guinea plate with se eurasia  <cit> .
do trophic key innovations drive species diversification?
the key innovation hypothesis has been invoked to explain both the species richness and phenotypic diversity of labrids  <cit> .
although these two aspects of a radiating clade are often conflated, it is important to point out that diversification and phenotypic evolution need not be strongly linked  <cit> .
our results show that pharyngeal jaw innovations provide weak explanations for the major patterns of species richness observed at relevant levels of labrid and scarine phylogeny.
however it is currently not known if the labrid pja or the pharyngeal mill of parrotfishes could have acted as a key innovation to spur rates of functional evolution as it has in cichlids  <cit> .
the wealth of studies on labrid functional evolution suggests that this might be true.
multiple studies have established that labrids are functionally  <cit>  and trophically diverse  <cit> , that their functional diversity is partitioned unevenly across extant clades  <cit> , and that they display complex patterns of functional evolution over their history  <cit> .
similarly, it is possible that the parrotfish pharyngeal mill is associated with a greater than expected amount of functional and morphological diversity observed in scarines relative to other labrid clades  <cit> .
increasingly sophisticated methods exist for answering questions about patterns and rates of morphological evolution  <cit>  but have yet to be applied to test key innovation hypotheses.
our results add to a growing body of work on diversification patterns in fish clades with modified pharyngeal jaws  <cit> .
together these studies cast doubt on the hypothesis that the pharyngeal jaw innovation itself is directly responsible for observed patterns of species richness in fishes.
it is possible that pharyngeal jaw innovations influence diversification rates by allowing clades to establish ecological 'footholds' in novel environments  <cit>  or in ways that are context-dependent  <cit> .
however, these formulations of key innovation hypotheses are difficult to test with the suite of comparative methods currently available to evolutionary biologists  <cit> .
in contrast, predictions about the influence of pharyngeal jaw modifications on evolution of other trophic characters are more direct and lend themselves to hypothesis testing  <cit> .
we suggest that pharyngeal jaw innovations do not constitute a general explanation for patterns of labrid or scarine diversity but that the hypothesis that this trait represents a key innovation might still be useful in explaining patterns of morphological and functional evolution within these clades.
CONCLUSIONS
labrids diversified rapidly relative to other percomorphs.
however there is no evidence that pharyngeal jaw innovations triggered explosive lineage diversification within either labrids or scarines.
even if pharyngeal jaw evolution triggered adaptive radiation with accelerated cladogenesis, over half of labrid richness can be attributed to two more recent diversification events where key innovations are not suspected as causes: one within the julidines and one within the most dichromatic of parrotfishes, scarus and chlorurus.
the similarity of these results to similar studies of diversification patterns in cichlids suggests that the pharyngeal jaws-as-key-innovations hypothesis should not be invoked as a general explanation for the species diversity in either family though it may have utility in explaining patterns of ecomorphological diversity.

 labrid fishes comprise roughly species and inhabit tropical and temperate marine habitats around the world. they are an ecologically dominant component of major reef systems and display a staggering degree of trophic and morphological diversity. members exploit nearly all known feeding niches available to fishes including algae, fish, zooplankton, ectoparasites, crabs, polychaetes, mollusks, amphipods, and echinoderms, range in size from a few grams to over kg, and exhibit high diversity in cranial and axial morphology. recently, the parrotfishes, which constitute one of the major groups of reef herbivores and bioeroders, have been recognized as a subclade of labrids. one classic explanation for both the species richness and the ecomorphological diversity of labrids is that this clade has evolved a key innovation in the form of modified pharyngeal jaws that has fueled their subsequent radiation. percomorph fishes possess two sets of jaws: oral jaws which function in prey capture and manipulation, and pharyngeal jaws which usually aid in processing food and moving it to the esophagus. like cichlids, which are also widely recognized for their exceptional functional diversity and species richness, labrids exhibit a highly modified condition of the pharyngeal jaw apparatus referred to as pharyngognathy. pharyngognathy involves united left and right lower jaw elements, a muscular sling connecting the neurocranium to the united fifth ceratobranchials, and a mobile diarthrotic articulation of the upper pharyngeal jaws with the neurocranium. one of the most species-rich groups of labrids, the parrotfishes, exhibit further modifications of the pja that are associated with forceful grinding. these include a laterally expanded fourth epibranchial, laterally compressed upper pharyngeal jaws, an anterior muscular sling through novel attachments of the transversalis ventralis muscle, a well developed sliding joints between the pharyngobranchial, neurocranium and epibranchial that permit extensive anterior-posterior motion of the upper jaw, and a posterior to anterior progression of ordered tooth tows on the lower pharyngeal jaws. these modifications are thought to enable trophic diversification by allowing the pharyngeal jaws to take on enhanced functions in prey processing, freeing the oral jaws to become specialized for prey capture. the labroid pharyngeal jaw condition has been proposed to be a key innovation that underlies putative adaptive radiation in cichlids and labrids. recent studies have examined the role of the pharyngeal jaws in shaping cichlid morphological diversification and cladogenesis. however, the hypothesis that pharyngeal jaws have influenced labrid diversity has never been explicitly tested. similarly, although structural and functional innovations of the scarine pharyngeal jaw to allow the processing of algae and coral skeletons are thought to underlie the ecological radiation of this clade in reef and seagrass habitats, the influence of this trait upon parrotfish diversification patterns has never been studied. in schluter's framework of ecological adaptive radiation, key innovations are one mechanism that provides ecological opportunity. these traits are hypothesized to trigger adaptive radiations by enabling a lineage that evolves the innovation to exploit a range of previously unavailable niches. the filling of niche space is expected to proceed rapidly. one of the central predictions of a key innovation hypothesis in this framework then is concordance between the acquisition of the key innovation and a shift in lineage diversification rate. here we evaluate this aspect of the key innovation hypothesis by testing whether the evolution of modified pharyngeal jaws has accelerated lineage diversification within labrid fishes. the current lack of knowledge of phylogenetic relationships among major percomorph groups prevents a sister group comparison between labrids and their outgroup. however labrids remain an especially good group to address this question because the nested radiation of parrotfishes within them provides the opportunity to examine both ancient and recent signatures of pharyngeal jaw innovation on patterns of diversification. we assembled the largest time-calibrated phylogeny of labrids to date and used comparative methods to assess the impact of the pharyngeal jaw modifications on diversification rate. we asked three general questions: did pharyngeal jaw innovation trigger rapid lineage diversification as part of an adaptive radiation? if specialized pharyngeal jaws enabled labrids or parrotfishes to adaptively radiate along ecological axes, we would expect to see a pattern where diversification after the acquisition of the trait was rapid and then slowed through time. we tested for this pattern, which has recently been identified as one of the ten key signatures of adaptive radiations, in two ways: first using the mccr test of pybus and harvey which tests for a slowing of diversification rates through time and second, by directly comparing the fit of density dependent models of cladogenesis to models where diversification is not a function of clade richness. we applied these methods to both the entire timetree to test for this signature of adaptive radiation in the initial diversification of labrids, and within parrotfishes, to test for adaptive radiation following the evolution of pharyngeal jaws modified for grinding. are diversification rate shifts within labrids and scarids temporally concordant with the pharyngeal jaw innovations? if pja innovations have been primarily responsible for diversification within labrids and parrotfishes, we can make three further predictions. first, since key innovations are thought to trigger increased diversification, we would expect the overall rate of labrid diversification to be high compared to other percomorph fishes. second, if the pja is the main cause of labrid species richness, any additional diversification rate increases should be restricted to relatively small subclades. if a large fraction of labrid richness occurs in young, fast-evolving subclades temporally removed from the labrid root, then the pja is a weak explanation for standing labrid diversity even if the pja played some role in initially establishing the clade in diverse environments. third, if the pharyngeal mill in parrotfishes were a key innovation that triggered a further adaptive radiation, we would expect to see diversification rates increase at or near the origin of this clade. does the character state of the pharyngeal jaws predict diversification rate? key innovation hypotheses predict that lineages with the innovation should diversify more quickly than lineages that lack the trait. we used bisse, a recently developed comparative method, to test whether labrid lineages with a modified pharyngeal mill have diversified more quickly than those with the labroid pja. the sister group of labrids is currently not known. this lack of phylogenetic resolution prevented us from testing whether the labroid pja itself was associated with faster rates of diversification than the generalized percomorph condition.  divergence time analysis our beast analysis produced a well-resolved phylogeny of labrid species that was in good agreement with previous work. a recent divergence time study of labrids treated the crown age as fixed at my. our analysis recovered an almost identical crown age of labrids even though we assigned far more liberal constraints to this node. our estimate of the split between scarines and cheilines + labrines is consistent with both the cr and pl estimates of smith et al. in contrast, our estimates for the age of crown scarines excludes both streelman et al.'s age of my and smith et al.'s estimate of my. the rest of our estimates within parrotfishes including the age of the seagrass clade, reef clade, scarus + chlorurus and crown ages of those genera are slightly older than those smith et al., though in almost all cases their mean is captured in our 95% credible interval. nodes in bold were fossil-calibrated. diversification analysis a lineage through time plot revealed that the log number of lineages appeared to accumulate at a roughly constant rate in the early history of labrids. this pattern is expected for lineages where diversification rate has been constant, suggesting that diversification in early labrid history was not initially fast. this interpretation was supported by the mccr test for labrids which failed to reject the hypothesis of a constant diversification rate. although the exponential density dependent model fit the labrid data best, the 95% credible set of models based on the calculation of akaike weights did not exclude the pure-birth model. a lineage through time plot for scarines revealed fewer lineages in their early history than expected under a constant rates model. this result was reinforced by a nonsignificant mccr test, suggesting that explosive scarine diversification did not accompany the evolution of modified pharyngeal jaws. an exponential model of density-dependent diversification fit the scarines best but the 95% credible interval did not exclude the pure birth model. akaike weights indicate the relative strength of support for four candidate models: pb = pure birth, ddx = density dependent, ddl = density dependent, ld = linear decline. best model indicated in bold. medusa, a recently developed comparative method that integrates taxonomic and phylogenetic information, allows exceptionally radiating clades to be identified on an incompletely sampled phylogeny. medusa analysis revealed that the background rate of labrid diversification, is somewhat higher than the average rate of diversification of percomorph and ostariophysan fishes as well as most major tetrapod lineages. we found evidence for two significant rate shifts within labrids, though neither of these corresponded to the predictions generated by the pja key-innovation hypothesis. the first corresponded to the origin of a clade comprising scarus and chlorurus. the net diversification rate of the stem s-c lineage is only modestly higher than the background rate of labrid diversification due to a long branch leading from the split with hipposcarus to the crown group. however rates within the crown s-c clade were approximately times greater than the net diversification rate of other labrids. the second rate shift occurred on the branch leading to most of the julidine diversity including the indo-pacific halichoeres, the new world halichoeres, and the labrichthyinae. the rate within this lineage was approximately twice that of labrids diversifying at the background rate and roughly equal to the rate of diversification within the crown s-c clade. we fit diversification models to both of the fast-evolving clades identified by medusa analysis to explore whether their patterns were consistent with adaptive radiation. the scarines did not strongly favor a density dependent model, suggesting that their early diversification was not explosive. this result was reinforced by a convex lineage through time plot, indicating fewer than expected species in their early history. in contrast, the fast evolving julidines showed some evidence for adaptive radiation both by model fitting which strongly favored density dependent models, and a concave lineage through time plot indicating more species than expected in their early history. clade number refers to rate shifts identified in fig. r is the net diversification rate, ε is the extinction fraction. aic and Δaic show improvement of aic score over a constant rates birth-death model as clades are allowed to change rates. background shows background rates of other labrid clades under the two-rate model. we tested for a correlation between diversification rate and the presence of a parrotfish pharyngeal mill using bisse. our results found strong support in favor of a model where pharyngeal mill-equipped lineages diversified ~4x faster than lineages with the typical labrid pharyngeal jaw apparatus. however we were concerned with the possibility of a trickle-down effect from the s-c clade given that our medusa analysis found a rate increase for this group. to investigate this further, we reran bisse with the s-c clade excluded and found no support for a two-rate model. furthermore, the speciation estimates in this unsupported two-rate model were nearly identical suggesting that diversification rates in parrotfish genera besides scarus and chlorurus are similar to rates in other labrids. parameter estimates of the constrained and unconstrained models for the pharyngeal jaw modifications found in all scaridae. the s-c clade comprises the most sexually dichromatic, haremic, and territorial of parrotfishes and it has been suggested that sexual selection has played a dominant role in their diversification. to test whether extreme sexual dichromatism was a better explanation of diversification rates than a pharyngeal mill, we performed another bisse analysis with the parrotfishes in the s-c clade coded as and the rest of the phylogeny as state a comparison of likelihood scores favored the extreme dichromatic model over the pharyngeal mill. discussion did the evolution of the labrid pharyngeal jaw trigger rapid lineage diversification? a common element of many key innovation hypotheses is that the trait is linked to rapid diversification and adaptive radiation. although we found the labridae as a whole to have diversified rapidly compared to other percomorphs, we also found no evidence for a pulse of cladogenesis coincident with the origin of the clade followed by declining rates as predicted by models of adaptive radiation. instead, we found that cladogenesis in the early history of labrids proceeded in a fairly log-linear manner consistent with a model where net diversification rates were constant. thus, we find no direct support for the hypothesis that the pja triggered rapid lineage diversification as part of an adaptive radiation. high rates of extinction have been shown to erase the signature of adaptive radiation and so one possibility is that background extinction within labrids has masked pja-facilitated diversification. however other marine fish clades of roughly similar ages with less trophic diversity and species richness do retain the signature of exceptionally rapid initial diversification. thus we are skeptical that exceptionally high extinction rates have masked the signal of explosive lineage diversification in labrids. further evaluation of extinction rates across labrid history is hampered by their poor fossil record. in any case, our analyses cast doubt on the pja-key innovation as a strong general explanation of labrid species richness because over 40% of non-scarine labrid diversity can be attributed to the julidine rate shift, an event which occurred ~ my after the origin of the labrid pja. our findings are similar to those from recent studies of cichlid diversity. although the pharyngeal jaw has been suggested to underpin species richness in this family as well, recent phylogenetic analyses have found that the major diversification rate shift which lead to the origin of most of the diversity of east african haplochromines occurred within the last my, well after the evolution of the pja. instead, diversification patterns appear to be strongly correlated with the evolution of specific behavioral and sexual characters such as mouth brooding and egg spots on the anal fins. is the parrotfish pharyngeal mill a key innovation that explains scarine biodiversity? we similarly found weak evidence in favor of the pharyngeal mill key innovation hypothesis. the mccr test did not support the hypothesis that early parrotfish diversification had slowed through time and fitting of diversification models did not favor density dependent models. once again it is possible that high extinction rates have masked this signature although we regard this as less likely since scarines are considerably younger than crown labrids. although we did find a significant increase in the rate of scarine diversification relative to other labrids, this rate increase was restricted to a clade comprising two very young genera of parrotfishes rather than at or near the root of the entire clade. the strongest evidence supporting the idea that a pharyngeal mill has contributed to scarine biodiversity comes from our bisse analysis which found a high correlation between the possession of a pharyngeal mill and the diversification rate. however we suggest that this result is driven by trickledown effects of the rate increase on scarus + chlorurus. this was supported by our bisse reanalysis which showed that the diversification rate in other scarines was very similar to the average labrid diversification rate. we suggest that the most likely cause of diversification in the s-c clade is the evolution of extreme male breeding coloration and reproductive behaviors through sexual selection. other contributing biogeographic factors are considered in smith et al., and include pliocene/pleistocene fluctuations in sea level and the closing of the isthmus of panama. what explains the rate shifts in julidines? the julidines have been recognized as one of the largest of all coral reef fish radiations. for the first time we show that this radiation was exceptionally fast, with a net diversification rate of species/my. recently alfaro et al. found evidence of rapid diversification of reef-associated tetraodontiform families during the late oligocene and early miocene. the mean age estimate of the julidine rate increase falls at the end of the oligocene, suggesting that similar factors may underlie the diversification of julidines and possibly other major reef-associated fish clades. these include the closing of the tethys and the collision of the australia new guinea plate with se eurasia. do trophic key innovations drive species diversification? the key innovation hypothesis has been invoked to explain both the species richness and phenotypic diversity of labrids. although these two aspects of a radiating clade are often conflated, it is important to point out that diversification and phenotypic evolution need not be strongly linked. our results show that pharyngeal jaw innovations provide weak explanations for the major patterns of species richness observed at relevant levels of labrid and scarine phylogeny. however it is currently not known if the labrid pja or the pharyngeal mill of parrotfishes could have acted as a key innovation to spur rates of functional evolution as it has in cichlids. the wealth of studies on labrid functional evolution suggests that this might be true. multiple studies have established that labrids are functionally and trophically diverse, that their functional diversity is partitioned unevenly across extant clades, and that they display complex patterns of functional evolution over their history. similarly, it is possible that the parrotfish pharyngeal mill is associated with a greater than expected amount of functional and morphological diversity observed in scarines relative to other labrid clades. increasingly sophisticated methods exist for answering questions about patterns and rates of morphological evolution but have yet to be applied to test key innovation hypotheses. our results add to a growing body of work on diversification patterns in fish clades with modified pharyngeal jaws. together these studies cast doubt on the hypothesis that the pharyngeal jaw innovation itself is directly responsible for observed patterns of species richness in fishes. it is possible that pharyngeal jaw innovations influence diversification rates by allowing clades to establish ecological'footholds' in novel environments or in ways that are context-dependent. however, these formulations of key innovation hypotheses are difficult to test with the suite of comparative methods currently available to evolutionary biologists. in contrast, predictions about the influence of pharyngeal jaw modifications on evolution of other trophic characters are more direct and lend themselves to hypothesis testing. we suggest that pharyngeal jaw innovations do not constitute a general explanation for patterns of labrid or scarine diversity but that the hypothesis that this trait represents a key innovation might still be useful in explaining patterns of morphological and functional evolution within these clades.  labrids diversified rapidly relative to other percomorphs. however there is no evidence that pharyngeal jaw innovations triggered explosive lineage diversification within either labrids or scarines. even if pharyngeal jaw evolution triggered adaptive radiation with accelerated cladogenesis, over half of labrid richness can be attributed to two more recent diversification events where key innovations are not suspected as causes: one within the julidines and one within the most dichromatic of parrotfishes, scarus and chlorurus. the similarity of these results to similar studies of diversification patterns in cichlids suggests that the pharyngeal jaws-as-key-innovations hypothesis should not be invoked as a general explanation for the species diversity in either family though it may have utility in explaining patterns of ecomorphological diversity. 
much of modern labrid diversity stems from two recent rapid diversification events; one within julidine fishes and the other with the origin of the most species-rich clade of reef-associated parrotfishes. a secondary pharyngeal jaw innovation was correlated with rapid diversification within the parrotfishes. we suggest that pharyngeal jaws might have played a more important role in enabling morphological evolution of the feeding apparatus in labrids and scarines rather than in accelerating lineage diversification. however one of the central predictions of this hypothesis, that the acquisition of a modified pharyngeal jaw apparatus will be positively correlated with explosive lineage diversification, has never been tested. the pja-innovation hypothesis also fails to explain the most dominant aspect of labrid lineage diversification, the radiation of the julidines. major modifications to the pharyngeal jaw apparatus are widely regarded as a recurring evolutionary key innovation that has enabled adaptive radiation in many species-rich clades of percomorph fishes. however diversification rate shifts within parrotfishes are more strongly correlated with the evolution of extreme dichromatism than with pharyngeal jaw modifications. the temporal lag between pharyngeal jaw modifications and changes in diversification rates casts doubt on the key innovation hypothesis as a simple explanation for much of the richness seen in labrids and scarines. we applied comparative methods to a new time-calibrated phylogeny of labrid fishes to test whether diversification rates shifted at two scales where major pharyngeal jaw innovations have evolved: across all of labridae and within the subclade of parrotfishes. although the possession of a secondarily modified pja was correlated with increased diversification rates, this pattern is better explained by the evolution of extreme dichromatism within scarus and chlorurus. diversification patterns within early labrids did not reflect rapid initial radiation.
 major modifications to the pharyngeal jaw apparatus are widely regarded as a recurring evolutionary key innovation that has enabled adaptive radiation in many species-rich clades of percomorph fishes. however one of the central predictions of this hypothesis, that the acquisition of a modified pharyngeal jaw apparatus will be positively correlated with explosive lineage diversification, has never been tested. we applied comparative methods to a new time-calibrated phylogeny of labrid fishes to test whether diversification rates shifted at two scales where major pharyngeal jaw innovations have evolved: across all of labridae and within the subclade of parrotfishes.  diversification patterns within early labrids did not reflect rapid initial radiation. much of modern labrid diversity stems from two recent rapid diversification events; one within julidine fishes and the other with the origin of the most species-rich clade of reef-associated parrotfishes. a secondary pharyngeal jaw innovation was correlated with rapid diversification within the parrotfishes. however diversification rate shifts within parrotfishes are more strongly correlated with the evolution of extreme dichromatism than with pharyngeal jaw modifications.  the temporal lag between pharyngeal jaw modifications and changes in diversification rates casts doubt on the key innovation hypothesis as a simple explanation for much of the richness seen in labrids and scarines. although the possession of a secondarily modified pja was correlated with increased diversification rates, this pattern is better explained by the evolution of extreme dichromatism within scarus and chlorurus. the pja-innovation hypothesis also fails to explain the most dominant aspect of labrid lineage diversification, the radiation of the julidines. we suggest that pharyngeal jaws might have played a more important role in enabling morphological evolution of the feeding apparatus in labrids and scarines rather than in accelerating lineage diversification. 