BACKGROUND
fishes of the families cichlidae and labridae  <cit>   represent good probable examples of vertebrate adaptive radiations  <cit> .
although the two families inhabit different aquatic environments , both families have radiated into several hundreds to over a thousand of species exhibiting various feeding modes .
in terms of species richness, cichlids exceed labrids   <cit> .
indeed, biomechanical studies of lower jaw shapes  <cit>  quantitatively demonstrated that the labrid functional diversity in lower jaw was well comparable to that of all ray-finned fishes.
the dramatic radiation of the cichlid and labrid fishes is widely believed to result from the "key innovation" of a unique pharyngeal jaw apparatus .
generalized percomorph fishes, from which the cichlids and labrids were derived, have upper and lower "pharyngeal jaws" within the throat, which function chiefly to transport food into the esophagus, whereas the "oral jaws" have a task of both collecting and manipulating  food.
in the cichlid and labrid fishes, the pharyngeal jaws and attached muscles  was modified into a derived condition with three major features: 1) the left and right lower jaw elements are fused into a single structure, 2) the lower jaw is suspended in a muscular sling that runs from the neurocranium to the posterior muscular arms of the lower jaw, and 3) the upper jaw elements have a diarthrotic articulation with the underside of the neurocranium   <cit> .
the unique condition of the pja is assumed to allow efficient manipulation  of food  <cit> .
liem  <cit>  has suggested that the evolution of the uniquely modified pja in cichlids and labrids freed the oral jaws from the task of food manipulation, allowing it to diversify into various food-collecting modes .
although this scenario is one of the most well-known examples of an evolutionary key innovation , it has never been evaluated adequately.
unfortunately, the key innovation hypothesis on the specialized pja has been proposed being coupled with a taxonomic hypothesis that has widely been accepted ever since: the family labridae and cichlidae have been classified into the suborder labroidei, together with pomacentridae and embiotocidae, based on the sharing of the specialized pja  <cit> .
according to stiassny & jensen  <cit> , the specialized pja has seven morphological features including the above three major ones.
none of them is, however, unique to labroid fishes, although there is no other group known to have them all  <cit> .
moreover, there is no independent, corroborative evidence for a monophyletic labroidei outside of the specialized pja  <cit> .
this situation has led some evolutionary biologists to doubt not only the taxonomic hypothesis but also the key innovation hypothesis .
the doubt about the latter hypothesis is a little rash, however, because appropriateness of the evolutionary hypothesis essentially does not depend on that of the appended taxonomic hypothesis.
a discussion of the specialized pja as a key innovation, however, hinges, first of all, upon a phylogenetic hypothesis independent of pharyngeal characters as below.
the widely-accepted taxonomic hypothesis  assumed that the evolution of the specialized pja occurred only once during the percomorph evolution, a situation that has prevented the famous evolutionary example from being examined from the aspect of historical repeatability.
the traditional taxonomic hypothesis based on the sharing of the specialized pja, however, needs reconsideration.
phylogeny independent of the pja may come to demonstrate multiple origins of the specialized pja followed by trophic radiations, which support the key innovation hypothesis at least from the aspect of the historical repeatability.
the hypothesis, however, must be tested statistically by comparing the diversity of the clades with the trait to that of the sister taxa without that trait  <cit>  when the true sister taxa are found in a future study.
for the first step of evaluating the key innovation hypothesis on the specialized pja, we examined labroid monophyly based on  <dig> whole mitochondrial genome sequences from a variety of the perciformes and related other ordinal taxa .
usefulness of whole mitochondrial genome sequences  for resolving higher-level phylogenetic relationships of teleost has been demonstrated in several studies .
although non-monophyly of the labroid families have been suggested in previous studies  <cit> , limited sequence data used in these studies  have precluded them from drawing definite conclusions, and no statistical test has been conducted for corroborating that hypothesis.
our analysis used the whole mitochondrial genome sequences , and confirmed the independent origins of the two diversified families by statistical tests using bayes factors.
RESULTS
the final dna alignment contains  <dig>  nucleotide sites for the  <dig> taxa listed in table  <dig>  of the sites,  <dig>  were variable and  <dig>  informative under the parsimony criterion.
partitioned bayesian analyses based on three differently-weighted datasets, # <dig>  # <dig> , and # <dig> , recovered nearly identical topologies.
figure  <dig> shows a 50% majority rule consensus tree of the  <dig>  pooled trees from two independent bayesian analyses for dataset # <dig>  it was fully bifurcated with the exception of an unresolved trichotomy denoted by an arrow, and most internal branches were supported by 100% posterior probabilities .
topological differences among results from the three datasets were shown only in the trichotomy and five internal branches denoted by arrowheads in fig.
<dig>
in the resultant trees, every family of the suborder labroidei  was monophyletic with 100% pps, and moreover, the family labridae  was phylogenetically distant from the remaining three labroid families forming clade b. monophyly of the labroidei comprised of all the four families was confidently rejected by a statistical test using bayes factor .
the family pseudochromidae , which was sometimes thought to be a possible sister to the labridae based on larval morphology  <cit> , was placed not close to the labridae , but more closely related to the clade b.
discussion
percomorpha phylogeny
overall relationships among the percomorph fishes examined here were quite similar to those obtained by unweighted and weighted maximum-parsimony analyses in miya et al.
<cit> , except for the newly added fishes, such as labroids.
although the phylogenies recovered many interesting inter-subordinal relationships that were not congruent with the traditional classification, sparse taxon sampling outside the labroidei precludes further discussions.
labroid phylogeny
the resultant trees and the statistical test with bayes factor demonstrated that the labridae and the remaining three labroid families including cichlidae have independent origins within the percomorpha.
based on molecular analyses, various relationships among the labroid families have been so far proposed  <cit> .
our analysis demonstrated entirely different relationships from the various ones with high statistical support, whereas none of the previous relationships was supported with high statistical value, probably owing to short sequences .
the present analyses were conducted based on the long nucleotide sequences more than six times the lengths of those so far used .
in spite of the high statistical supports, we must keep in mind that the sister relationships obtained here are highly tentative because of the sparse taxon sampling  compared to the tremendous taxonomic diversity of the percomorpha .
that is to say, although the present phylogeny demonstrated that the three labroid families, cichlidae, pomacentridae, and embiotocidae, formed a well-supported monophyletic group  without non-labroid taxa, there remains a possibility that some non-labroid taxa would break into the group when more extensive taxon sampling is conducted.
in the same way, there remains not a few possibilities that some yet-to-be-analyzed taxa  would become sister group of the "labroid" taxa.
to evaluate these possibilities, we need to conduct analyses with more extensive taxon sampling.
in doing so, we would be able to evaluate "key innovation" hypothesis in a more rigorous manner using statistical test  <cit> .
implications of the revised labroid phylogeny
the present result supports, from the aspect of historical repeatability, the famous  evolutionary hypothesis that the dramatic labroid radiations in trophic ecology are due to evolution of specialized pharyngeal jaw apparatus .
based on the present phylogeny, a single origin of the specialized pja in a common ancestor of the suborder labroidei is unlikely, because such an evolutionary scenario requires subsequent losses of the complex structures in a wide variety of percomorphs.
rather, it is plausible that the specialized pja has evolved twice independently in the percomorpha history, in a common ancestor of the labridae  and that of the cichlidae, pomacentridae, and embiotocidae .
interestingly, evolutionary radiations in jaw forms and head shape  have occurred within both of the lineages with specialized pja: one in the labridae, and the other in the cichlidae.
the independent occurrence of such evolutionary succession  appears to support the idea that the evolution of the specialized pja provided these lineages with the morphological "potential" for trophic radiations.
despite their specialized pja, the pomacentridae and embiotocidae seem not to have experienced clear trophic radiation.
this may reflect the context-dependence of a key trait's effect on diversification  <cit> .
there are many potential factors that could influence how a key trait affects diversification.
de queiroz  <cit>  categorized these factors roughly into three types:  other taxa,  other traits of the group itself, and  the physical environment.
evolutionary radiations in african great lake cichlids are supposedly facilitated by colonization of novel habitats  without other competitive taxa  <cit> .
the pomacentridae and embiotocidae, both of which inhabit coastal marine waters, may not have had such opportunity to colonize novel habitats without competitors.
evolution of the specialized "labroid" pja
it is interesting fact that the complex "labroid" pja evolved multiply in the percomorpha history .
is the acquisition of the "successful" pja not so difficult for percomorph fishes, like parallel evolution of trophic morphologies in african great lake cichlids  <cit> ?
according to stiassny & jensen  <cit> , typical labroid pja has seven features .
interestingly, none of them is unique to labroid fishes , though there is no other group known to have them all  <cit> .
in addition to it, it seems that such features can be accomplished by a very simple change in ontogenetic mechanism   <cit> .
the labroid pja is therefore considered to have been achieved through the unique combination of several commonplace and slight morphological modifications.
it will be worthwhile to study the molecular mechanisms underlying the morphological modifications, which would reveal molecular basis for the probable key innovations.
according to hulsey et al.
<cit> , more than ten genes have been so far recognized which putatively influence teleost pharyngeal jaw.
the present result will provide a new view point for functional morphology of the unique organ .
although many works on the trophic apparatus have been so far published , comparison between labrid and other labroid fishes  as evolutionary independent lineages has never been conducted.
careful comparisons, particularly based on more extensive phylogenies including labroid and non-labroid fishes possessing "partly" specialized pja , will shed light on overlooked evolutionary implications.
CONCLUSIONS
the phylogenetic analyses of whole mitochondrial dnas from various labroid and non-labroid "percomorph" fishes revealed that the labridae and the remaining three labroid families have diverged basally within percomorpha, indicating that the specified "labroid" pja evolved independently at least twice, once in labridae and once in the common ancestor of the remaining three labroid families .
because both of the evolution appear to be followed by trophic radiations, we consider that our result supports the idea that the evolution of the specialized pja provided these lineages with the morphological potential for their spectacular trophic radiations.
the present result will provide a new view point for functional morphology of the unique organ: although many works on the specialized pja have been so far published, comparison between labrid and other labroid fishes  as evolutionary independent lineages has never been conducted.
careful comparisons, particularly based on more extensive phylogenies, will shed light on overlooked evolutionary implications.

 fishes of the families cichlidae and labridae represent good probable examples of vertebrate adaptive radiations. although the two families inhabit different aquatic environments, both families have radiated into several hundreds to over a thousand of species exhibiting various feeding modes. in terms of species richness, cichlids exceed labrids. indeed, biomechanical studies of lower jaw shapes quantitatively demonstrated that the labrid functional diversity in lower jaw was well comparable to that of all ray-finned fishes. the dramatic radiation of the cichlid and labrid fishes is widely believed to result from the "key innovation" of a unique pharyngeal jaw apparatus. generalized percomorph fishes, from which the cichlids and labrids were derived, have upper and lower "pharyngeal jaws" within the throat, which function chiefly to transport food into the esophagus, whereas the "oral jaws" have a task of both collecting and manipulating food. in the cichlid and labrid fishes, the pharyngeal jaws and attached muscles was modified into a derived condition with three major features: 1) the left and right lower jaw elements are fused into a single structure, 2) the lower jaw is suspended in a muscular sling that runs from the neurocranium to the posterior muscular arms of the lower jaw, and 3) the upper jaw elements have a diarthrotic articulation with the underside of the neurocranium. the unique condition of the pja is assumed to allow efficient manipulation of food. liem has suggested that the evolution of the uniquely modified pja in cichlids and labrids freed the oral jaws from the task of food manipulation, allowing it to diversify into various food-collecting modes. although this scenario is one of the most well-known examples of an evolutionary key innovation, it has never been evaluated adequately. unfortunately, the key innovation hypothesis on the specialized pja has been proposed being coupled with a taxonomic hypothesis that has widely been accepted ever since: the family labridae and cichlidae have been classified into the suborder labroidei, together with pomacentridae and embiotocidae, based on the sharing of the specialized pja. according to stiassny & jensen, the specialized pja has seven morphological features including the above three major ones. none of them is, however, unique to labroid fishes, although there is no other group known to have them all. moreover, there is no independent, corroborative evidence for a monophyletic labroidei outside of the specialized pja. this situation has led some evolutionary biologists to doubt not only the taxonomic hypothesis but also the key innovation hypothesis. the doubt about the latter hypothesis is a little rash, however, because appropriateness of the evolutionary hypothesis essentially does not depend on that of the appended taxonomic hypothesis. a discussion of the specialized pja as a key innovation, however, hinges, first of all, upon a phylogenetic hypothesis independent of pharyngeal characters as below. the widely-accepted taxonomic hypothesis assumed that the evolution of the specialized pja occurred only once during the percomorph evolution, a situation that has prevented the famous evolutionary example from being examined from the aspect of historical repeatability. the traditional taxonomic hypothesis based on the sharing of the specialized pja, however, needs reconsideration. phylogeny independent of the pja may come to demonstrate multiple origins of the specialized pja followed by trophic radiations, which support the key innovation hypothesis at least from the aspect of the historical repeatability. the hypothesis, however, must be tested statistically by comparing the diversity of the clades with the trait to that of the sister taxa without that trait when the true sister taxa are found in a future study. for the first step of evaluating the key innovation hypothesis on the specialized pja, we examined labroid monophyly based on whole mitochondrial genome sequences from a variety of the perciformes and related other ordinal taxa. usefulness of whole mitochondrial genome sequences for resolving higher-level phylogenetic relationships of teleost has been demonstrated in several studies. although non-monophyly of the labroid families have been suggested in previous studies, limited sequence data used in these studies have precluded them from drawing definite conclusions, and no statistical test has been conducted for corroborating that hypothesis. our analysis used the whole mitochondrial genome sequences, and confirmed the independent origins of the two diversified families by statistical tests using bayes factors.  the final dna alignment contains nucleotide sites for the taxa listed in table of the sites, were variable and informative under the parsimony criterion. partitioned bayesian analyses based on three differently-weighted datasets, # #, and #, recovered nearly identical topologies. figure shows a 50% majority rule consensus tree of the pooled trees from two independent bayesian analyses for dataset # it was fully bifurcated with the exception of an unresolved trichotomy denoted by an arrow, and most internal branches were supported by 100% posterior probabilities. topological differences among results from the three datasets were shown only in the trichotomy and five internal branches denoted by arrowheads in fig. in the resultant trees, every family of the suborder labroidei was monophyletic with 100% pps, and moreover, the family labridae was phylogenetically distant from the remaining three labroid families forming clade b. monophyly of the labroidei comprised of all the four families was confidently rejected by a statistical test using bayes factor. the family pseudochromidae, which was sometimes thought to be a possible sister to the labridae based on larval morphology, was placed not close to the labridae, but more closely related to the clade b. discussion percomorpha phylogeny overall relationships among the percomorph fishes examined here were quite similar to those obtained by unweighted and weighted maximum-parsimony analyses in miya et al., except for the newly added fishes, such as labroids. although the phylogenies recovered many interesting inter-subordinal relationships that were not congruent with the traditional classification, sparse taxon sampling outside the labroidei precludes further discussions. labroid phylogeny the resultant trees and the statistical test with bayes factor demonstrated that the labridae and the remaining three labroid families including cichlidae have independent origins within the percomorpha. based on molecular analyses, various relationships among the labroid families have been so far proposed. our analysis demonstrated entirely different relationships from the various ones with high statistical support, whereas none of the previous relationships was supported with high statistical value, probably owing to short sequences. the present analyses were conducted based on the long nucleotide sequences more than six times the lengths of those so far used. in spite of the high statistical supports, we must keep in mind that the sister relationships obtained here are highly tentative because of the sparse taxon sampling compared to the tremendous taxonomic diversity of the percomorpha. that is to say, although the present phylogeny demonstrated that the three labroid families, cichlidae, pomacentridae, and embiotocidae, formed a well-supported monophyletic group without non-labroid taxa, there remains a possibility that some non-labroid taxa would break into the group when more extensive taxon sampling is conducted. in the same way, there remains not a few possibilities that some yet-to-be-analyzed taxa would become sister group of the "labroid" taxa. to evaluate these possibilities, we need to conduct analyses with more extensive taxon sampling. in doing so, we would be able to evaluate "key innovation" hypothesis in a more rigorous manner using statistical test. implications of the revised labroid phylogeny the present result supports, from the aspect of historical repeatability, the famous evolutionary hypothesis that the dramatic labroid radiations in trophic ecology are due to evolution of specialized pharyngeal jaw apparatus. based on the present phylogeny, a single origin of the specialized pja in a common ancestor of the suborder labroidei is unlikely, because such an evolutionary scenario requires subsequent losses of the complex structures in a wide variety of percomorphs. rather, it is plausible that the specialized pja has evolved twice independently in the percomorpha history, in a common ancestor of the labridae and that of the cichlidae, pomacentridae, and embiotocidae. interestingly, evolutionary radiations in jaw forms and head shape have occurred within both of the lineages with specialized pja: one in the labridae, and the other in the cichlidae. the independent occurrence of such evolutionary succession appears to support the idea that the evolution of the specialized pja provided these lineages with the morphological "potential" for trophic radiations. despite their specialized pja, the pomacentridae and embiotocidae seem not to have experienced clear trophic radiation. this may reflect the context-dependence of a key trait's effect on diversification. there are many potential factors that could influence how a key trait affects diversification. de queiroz categorized these factors roughly into three types: other taxa, other traits of the group itself, and the physical environment. evolutionary radiations in african great lake cichlids are supposedly facilitated by colonization of novel habitats without other competitive taxa. the pomacentridae and embiotocidae, both of which inhabit coastal marine waters, may not have had such opportunity to colonize novel habitats without competitors. evolution of the specialized "labroid" pja it is interesting fact that the complex "labroid" pja evolved multiply in the percomorpha history. is the acquisition of the "successful" pja not so difficult for percomorph fishes, like parallel evolution of trophic morphologies in african great lake cichlids? according to stiassny & jensen, typical labroid pja has seven features. interestingly, none of them is unique to labroid fishes, though there is no other group known to have them all. in addition to it, it seems that such features can be accomplished by a very simple change in ontogenetic mechanism. the labroid pja is therefore considered to have been achieved through the unique combination of several commonplace and slight morphological modifications. it will be worthwhile to study the molecular mechanisms underlying the morphological modifications, which would reveal molecular basis for the probable key innovations. according to hulsey et al., more than ten genes have been so far recognized which putatively influence teleost pharyngeal jaw. the present result will provide a new view point for functional morphology of the unique organ. although many works on the trophic apparatus have been so far published, comparison between labrid and other labroid fishes as evolutionary independent lineages has never been conducted. careful comparisons, particularly based on more extensive phylogenies including labroid and non-labroid fishes possessing "partly" specialized pja, will shed light on overlooked evolutionary implications.  the phylogenetic analyses of whole mitochondrial dnas from various labroid and non-labroid "percomorph" fishes revealed that the labridae and the remaining three labroid families have diverged basally within percomorpha, indicating that the specified "labroid" pja evolved independently at least twice, once in labridae and once in the common ancestor of the remaining three labroid families. because both of the evolution appear to be followed by trophic radiations, we consider that our result supports the idea that the evolution of the specialized pja provided these lineages with the morphological potential for their spectacular trophic radiations. the present result will provide a new view point for functional morphology of the unique organ: although many works on the specialized pja have been so far published, comparison between labrid and other labroid fishes as evolutionary independent lineages has never been conducted. careful comparisons, particularly based on more extensive phylogenies, will shed light on overlooked evolutionary implications. 
because the independent evolution of pharyngeal jaws appears to have been followed by trophic radiations, we consider that our result supports, from the aspect of historical repeatability, the idea that the evolution of the specialized pja provided these lineages with the morphological potential for their spectacular trophic radiations. the resultant phylogenies indicated that the labridae and the remaining three labroid families have diverged basally within the percomorpha, and monophyly of the suborder was confidently rejected by statistical tests using bayes factors. the resultant phylogenies indicated that the specified pja evolved independently at least twice, once in labridae and once in the common ancestor of the remaining three labroid families. fishes in the families cichlidae and labridae provide good probable examples of vertebrate adaptive radiations. we examined those based on whole mitochondrial genome sequences through partitioned bayesian analyses with concatenated sequences. their spectacular trophic radiations have been widely assumed to be due to structural key innovation in pharyngeal jaw apparatus, but this idea has never been tested based on a reliable phylogeny. the present result will provide a new framework for the study of functional morphology and genetic basis of their pja. for the first step of evaluating the hypothesis, we investigated the phylogenetic positions of the components of the suborder labroidei within the percomorpha, the most diversified crown clade of teleosts.
 fishes in the families cichlidae and labridae provide good probable examples of vertebrate adaptive radiations. their spectacular trophic radiations have been widely assumed to be due to structural key innovation in pharyngeal jaw apparatus, but this idea has never been tested based on a reliable phylogeny. for the first step of evaluating the hypothesis, we investigated the phylogenetic positions of the components of the suborder labroidei within the percomorpha, the most diversified crown clade of teleosts. we examined those based on whole mitochondrial genome sequences through partitioned bayesian analyses with concatenated sequences.  the resultant phylogenies indicated that the labridae and the remaining three labroid families have diverged basally within the percomorpha, and monophyly of the suborder was confidently rejected by statistical tests using bayes factors.  the resultant phylogenies indicated that the specified pja evolved independently at least twice, once in labridae and once in the common ancestor of the remaining three labroid families. because the independent evolution of pharyngeal jaws appears to have been followed by trophic radiations, we consider that our result supports, from the aspect of historical repeatability, the idea that the evolution of the specialized pja provided these lineages with the morphological potential for their spectacular trophic radiations. the present result will provide a new framework for the study of functional morphology and genetic basis of their pja. 