to the surprise of the authors , their data led them to propose a clade that includes bats ( order chiroptera ) , carnivores such as cats and dogs ( order carnivora ) , horses and other odd-toed ungulates ( order perissodactyla ) and pangolins ( order pholidota ) as springing from a single evolutionary origin within the mammals .

the name pegasoferae was coined from the name of the mythological flying horse pegasus to refer to bats and horses , and the term ferae , encompassing carnivorans and pangolins .

according to this , the odd-toed ungulates ' closest living relatives are the carnivorans .

earlier theories of mammalian evolution would , for example , have aligned bats with the insectivores ( order eulipotyphla ) and horses with the even-toed ungulates ( order artiodactyla ) .

some subsequent molecular studies published shortly afterwards have failed to support it .

in particular , two recent studies , each combining genome-wide analyses of multiple taxa with testing of competing alternative phylogenetic hypotheses , concluded that pegasoferae is not a natural grouping .

pegasoferae

pegasoferae , an unexpected mammalian clade revealed by tracking ancient retroposon insertions . - pubmed - ncbi
pegasoferae is a proposed clade of mammals based on genomic research in molecular systematics by nishihara , hasegawa and okada ( 2006 ) .
this is a one - residue deletion in the second transmembrane helix of this shortwave imaging opsin considered under informative opsin indels . this is too phylogenetically narrow to illuminate pegasoferae .
this potentially informative retroposon insertion denoted int283 conflicts with pegasoferae topology . that is not a fatal flaw because a certain fraction of such events resolve anomalously via lineage - sorting after speciation .
pegasoferae is a proposed clade of mammals based on genomic research in molecular systematics by nishihara , hasegawa and okada ( 2006 ) . it includes bats , carnivorans , pangolins , and odd - toed ungulates .
nishihari et al located 4 retroposon insertion events that support pegasoferae . in the ensuing 2 - 3 years , it has become possible to reinvestigate these events with additional species utilizing bioinformatic methods on the 10 available laurasiathere genomes ( not all of which will completely cover a given event ) .
the one - residue indel appears cleanly restricted to pegasoferae . there are 5 laurasiatheres with it and 5 without it , which needs further buttressing by pcr ( adding more basal species has the effect of localizing the event farther back on the stem ) . the parental gene did not develop the indel in any bioinformatically accessible species .
it can always be asked whether this is the
same
l1ma9 in cetartiodactyls or merely a similar one from a separate insertion event of the active parental element . however pushing the putative event back to basal vicugna narrows the window for that . while this situation can be dismissed with an appeal to lineage - sorting ( importantly 4 events support pegasoferae versus this 1 conflict ) .
knowledge of the biological characteristics , physiology and behavior of the creature group pegasoferae . this group contains for instance bats , carnivorans ( the dog - and cat - like animals ) , and odd - toed ungulates such as horses and nosehorns . a higher skill increases taming and / or controlling chances , butchery yield , carcass cooking quality , and damage and defense for creatures in this group .
pegasoferae is a novel proposal using rare genomic events involving retroposon insertions to establish the phylogenetic ordering within laurasiatheres , grouping bats , perissodactyls and carnivores to the exclusion of the other hoofed mammalian group , artiodactyls . bats have been placed in many previous locations , notably in the euarchonta wing ( outgroup to primates ) . while that particular idea is clearly refuted by many lines of evidence , the proper placement of bats remains under discussion .
despite more intensive phylogenetic sampling , int391 continues to support pegasoferae as nishijimi et al originally stated . it should be noted that the mer - class retroposon , while not at issue here , exhibits the type of homoplasy that makes retroposons dicey as tree topology markers . introns are often susceptible to multiple insertions of similar retroposons as well as to complicated patterns of micro deletions that prevent their recognition even if they aren ' t fully deleted .
the last exon of rbp3 , like in many proteins , does not appear to be under a great deal of selective pressure . this surfaces in a certain amount of observed ' terminal wander ' as various mutations allow readthru of the original stop codon to the next one that occurs by chance downstream . here pegasoferae , relative to artiodactyls , all share a one bp indel within coding that causes an altogether novel amino acid sequence to terminate the protein .
this gene duplication might simply be restricted to this one genus ( or even this one species ) . alternatively it might have greater phylogenetic depth and be somewhat informative in resolving intra - bat taxonomy . this would require pcr of many additional bat species since no further genomic work is anticipated any time soon . it is not relevent to pegasoferae per se since bats are clearly monophyletic overall , even as the macro / micro distinction remains equivocal as a taxonomic character .
again , this presented a favorable annotation situation because the two flanking exons are well - conserved and the intonic distance is short at about 1500 bp . using new genomic data , the species density can be brought up 10 laurasiatheres , tiling traces in unassembled genomes as necessary . the conflict with pegasoferae holds up even sampling at this greater taxonomic sampling depth : an orthologous l1ma9 is also missing in microbat , shrew , hedgehog but present with correct orientation and correct fragment coordinates in vicugna , pig , and dolphin .
an example of int391 locus suggesting pegasoferae clade . ( a ) an electrophoretic profile of pcr products of locus int391 , in which l1 is present in horse , cat , and bat , but not other mammals . the larger size of the mouse pcr product is caused by species - specific insertions of another retrotransposon ( database position chr19 : 55196706–55197619 in mm7 ) . m , size markers ( øx174 / hincii digest ) . ( b ) an alignment of locus int391 sequences . thick and thin lines denote the l1 and the direct repeat sequences , respectively , that were generated during integration . the central region of the inserted l1 sequence is omitted .
the history here is quite complex when tetrapods outside laurasiatheres are included . ancestrally , the exon was clearly much shorter , terminating at consistent length just after module m4 ended in the rpb3 internal repeat structure from frog to marsupial divergence . in afrotheres , either the stop codon mutated or a frameshift occured , causing the protein to become longer . the new stop codon in hyrax represents the ancestral placental position . elephants retain a cryptic stop codon here but evolved an earlier one that is used today . this stop codon and some aspects of sequence was conserved in pegasoferae but not artiodactyls ( though by reinstituting the original trinucleotide ggg and former reading frame , residual ancestral sequence as well as the original distal stop codon can still be seen . shrew and hedgehog diverged by a different scheme and are unhelpful .
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molecular studies have reported divergence times of modern placental orders long before the cretaceous–tertiary boundary and far older than paleontological data . however , this discrepancy may not be real , but rather appear because of the violation of implicit assumptions in the estimation procedures , such as non - gradual change of evolutionary rate and failure to correct for convergent evolution .
new procedures for divergence - time estimation robust to abrupt changes in the rate of molecular evolution are described . we used a variant of the multidimensional vector space ( mvs ) procedure to take account of possible convergent evolution . numerical simulations of abrupt rate change and convergent evolution showed good performance of the new procedures in contrast to current methods . application to complete mitochondrial genomes identified marked rate accelerations and decelerations , which are not obtained with current methods . the root of placental mammals is estimated to be ∼18 million years more recent than when assuming a log brownian motion model . correcting the pairwise distances for convergent evolution using mvs lowers the age of the root about another 20 million years compared to using standard maximum likelihood tree branch lengths . these two procedures combined revise the root time of placental mammals from around 122 million years ago to close to 84 million years ago . as a result , the estimated distribution of molecular divergence times is broadly consistent with quantitative analysis of the north american fossil record and traditional morphological views .
by including the dual effects of abrupt rate change and directly accounting for convergent evolution at the molecular level , these estimates provide congruence between the molecular results , paleontological analyses and morphological expectations . the programs developed here are provided along with sample data that reproduce the results of this study and are especially applicable studies using genome - scale sequence lengths .
citation : kitazoe y , kishino h , waddell pj , nakajima n , okabayashi t , watabe t , et al . ( 2007 ) robust time estimation reconciles views of the antiquity of placental mammals . plos one 2 ( 4 ) : e384 . urltoken
copyright : © 2007 kitazoe et al . this is an open - access article distributed under the terms of the creative commons attribution license , which permits unrestricted use , distribution , and reproduction in any medium , provided the original author and source are credited .
funding : this work was supported by the technology agency ( jst ) and the japan society for the promotion of science ( jsps grant sr b - 16300086 to yk and hk ) . pjw acknowledges the jsps senior fellowship program and nih grant 5r01lm8626 for support .
despite great progress over the past decade , the evolutionary history of placental mammals remains controversial . while a consensus is emerging on the topology of the evolutionary tree [ 1 ] – [ 5 ] , although with occasional disagreement [ 6 ] – [ 8 ] , divergence times remain uncertain . the age of earlier nodes and in particular the root , remain especially uncertain in the absence of definitive placental fossils deeper into the cretaceous [ 4 ] – [ 6 ] , [ 9 ] . both paleontological and morphological studies suggest that the radiation of placental orders and super orders occurred close to the cretaceous–tertiary ( k–t ) boundary about 65 million years ago ( mya ) [ 9 ] , [ 10 ] .
in contrast , molecular studies have suggested markedly older origins for many superordinal groups and that some extant orders diversified before the k–t boundary . the root of living placental mammals has been reported to be in the range of 100–140 mya [ 4 ] , [ 11 ] – [ 15 ] even with application of rate - adjustment techniques [ 4 ] , [ 15 ] . the molecular consensus of an old root is becoming strong enough that it may become dogma without a close examination of the assumptions being made in such analyses . the true age of the orders and superorders has important implications for determining the overall paleoecology and biogeography of placental mammals during a period that included the breakup of continents and the extinction of terrestrial dinosaurs . reconciling the different paleontological and molecular divergence time estimates has important implications for basic methodologies that are central to evolutionary study .
the strength of molecular divergence time studies is their potential to draw information from very long aligned sequences of many species . it is widely assumed that a huge amount of sequence data and the approximate rate constancy of sequence evolution [ 16 ] make molecular estimates more reliable than those based solely on fossil data . such analyses on a genomic scale are generally anticipated to be decisive because they are expected to be free of stochastic noise [ 17 ] , [ 18 ] .
however , molecular studies acknowledge the problem of misspecification of the model of sequence change , which may result in seriously biased estimation . the relationships among placental orders do vary according to the data used and the taxa sampled [ 1 ] – [ 8 ] , [ 13 ] – [ 15 ] , [ 19 ] – [ 22 ] . most methods of phylogenetic inference rely strongly on probabilistic models of sequence evolution , and neither directly detect nor correct for convergent evolution [ 23 ] . when left uncorrected , such “homoplasy” may attract lineages and underestimate certain pairwise distances . this in turn distorts branch ( edge ) length estimates , which are of primary importance for divergence time estimation . while some methods will detect potential convergent evolution , for example hadamard conjugations and splitstree [ 24 ] , kitazoe et al . have developed multidimensional vector space ( mvs ) representation methods to both detect convergent evolution among estimated distances and to also correct for this bias [ 25 ] – [ 27 ] .
a further problem facing molecular dating is the evolutionary rate constancy , or lack of constancy , over long periods . since its proposal in 1965 [ 28 ] , the molecular clock hypothesis has been one of the most hotly debated subjects in evolutionary biology . it is now widely accepted that a molecular clock tends to hold well for closely related organisms , but breaks down with increasing evolutionary divergence . to adjust for the inevitable fluctuation of evolutionary rates , nonparametric [ 17 ] , [ 18 ] , local clock [ 29 ] , [ 30 ] , and hierarchical bayesian [ 31 ] methods have been developed . these methods are robust against stochastic fluctuations of evolutionary rates [ 31 ] – [ 33 ] . however , they may cause serious problems when pronounced transient changes of rate occur , because they overly smooth such rate changes . in this article , we show the magnitude of such problems using clear worked examples .
to improve the detection of , and robustness to , abrupt rate changes , we have developed a new procedure that minimizes the local variability of the inverse of the evolutionary rate . just as the effective size of fluctuating populations is represented by the harmonic mean over time , the mean evolutionary rate among lineages is expressed better by the harmonic mean . this approach is especially useful when branch lengths measured in the expected number of substitutions per site ( the products of rates and times ) are estimated accurately , and there are either rapid transient changes of rate ( hence large rate heterogeneity ) or a general bias towards a speed up or slow down in rates through time .
using this new procedure , an analysis of 69 mitochondrial protein sequences ( 3660 amino acid sites in total ) from placental mammals identified a rapid acceleration of evolutionary rate for the lineage directly leading to the common ancestor of supraprimates and an even more marked one for the lineage leading to laurasiatheria . this acceleration was followed closely by a strong deceleration , which persisted in nearly all lineages of laurasiatheria . in contrast , almost all lineages of afrotheria and xenarthra seem to have retained rates similar to that of the root . this view is in marked contrast to current rate - change penalty functions . the robustness of the new procedure is assessed using simulations that show the types of change that most concern biologists ; speedups or slowdowns through time , transient rate changes , and rate changes that are do not follow a normal or transformed normal distribution , as well as stochastic variation . a revised estimate of the origin of placental mammals is as young as 84 mya , which is much more recent than current estimates using molecular data . the inferred age of deeper splits in the placental tree are compared with the rate of occurrence of new species from the north american fossil record . these two sources of data are far more congruent than is suggested by using current , possibly strongly misleading , dating methods .
mitochondrial protein sequences are used widely in phylogenetic studies and have been particularly popular in studying placental mammals . a desirable feature of these data is relatively long sequences , good taxon sampling and very little missing data . following alignment , we retained 3660 amino acid sites present in all of 62 placental mammals plus seven outgroup taxa ( table s1 gives the accession numbers of protein sequences ) . in contrast , large nuclear protein datasets of mammals with diverse taxon sampling [ e . g . 3 ] , [ 4 ] show a large proportion of missing data . such missing heterogeneous data may lead to complex systematic errors in distance estimation [ 34 ] . this is particularly relevant since mvs analyses work best with low stochastic noise ( hence relatively long sequences ) , diverse taxon sampling with a considerable proportion of taxa showing minimal convergent evolution , and minimal bias of the input distances from sources such as missing data .
we adopted a standard two - step procedure to estimate divergence times . the first step is to estimate the phylogenetic tree with unconstrained branch lengths in units of expected numbers of substitutions per site . given the problems with convergent evolution in mitochondrial data [ 4 ] , [ 5 ] , [ 22 ] , [ 25 ] , we used the mvs procedure to correct the input distances for convergent evolution . a variant of the core set approach [ 27 ] to mvs was used in this instance ( materials and methods ) . fixing the topology to the tree obtained by mvs , which is very similar to trees obtained by previous authors using varied data sets [ 2 ] – [ 5 ] , branch lengths were reestimated using maximum likelihood ( ml ) in the program paml [ 35 ] . we used the jtt [ 36 ] + gamma model with α = 0 . 5 for these analyses . the second step uses the tree and its branch lengths , some fossil constrained nodes , and a penalty or cost function to dampen rate changes , to infer divergence times of all nodes and evolutionary rates along all branches .
three cost functions , f add , f log , and f ir , were applied to the mvs and ml trees . these functions penalize the fluctuation of rates , and do this on either a linear scale ( here called the add function ) , on the log rate ( log ) , or on the inverse rates ( ir ) , respectively ( see equations ( 1 ) , ( 2 ) , and ( 4 ) in materials and methods ) . the tree estimated by mvs and f add is denoted mvs - f add and so on ( while ml - f add indicates use of ml branch lengths ) .
to calibrate these trees , we used eight fossil constraints , all taken from previous studies ( see figure 1 caption ) [ 4 ] , [ 15 ] . the divergence times were estimated by then minimizing each cost function subject to these constraints ( see materials and methods ) . the ci was calculated using a likelihood interpretation ( see materials and methods ) of the cost function residual analogous to the method used in multidivtime [ 31 ] . this captures the error caused by deviations of the tree ' s branch lengths away from their expected values and includes the unpredictability of rate changes , which might mimic brownian motion , for example . it will also incorporate variability arising from ancestral polymorphism . polymorphism will cause fluctuations of the edge lengths of the tree when the analysis has multiple nodes constrained by fossil or other data [ c . f . 13 ] . generally , the time at the most recent common ancestor of sequences from different species is older than the time at speciation . the extent of this difference varies among internal nodes due to both the stochastic nature of the coalescent and factors governing its expected magnitude , such as population size . the cost function does not take account of this bias , but the ci does include the variance arising from ancestral polymorphism at internal nodes .
a and b show the mvs - f ir and ml - f log trees , respectively . the numbers 1–61 denote the ancestral nodes . the red numbers 1–8 indicate the internal nodes with fossil constraints which are as follows : 1 , 49–61 ; 2 , 52–58 ; 3 , 45–63 ; 4 , 43–60 ; 5 , < 63 ; 6 , > 12 ; 7 , 36–55 ; 8 , 54–65 ( all in mya ) [ see 4 ] , [ 15 ] . the colors of the branches denote inferred evolutionary rates ( in units of ×10 −9 / site per year ) as follows : black , < 0 . 2 ; dark blue , 0 . 2–0 . 3 ; light blue , 0 . 3–0 . 4 ; green , 0 . 4–0 . 5 ; brown , 0 . 5–0 . 6 ; yellow , 0 . 6–0 . 7 ; and red , > 0 . 7 .
the mvs - f ir analysis ( figure 1a ) estimated the age of the root at 84 . 2 mya with a 95 % confidence interval ( ci ) of 80 . 7–88 . 4 mya ( table 1 ) . this time is much more recent than the result of the ml - f l analysis ( figure 1b ) , i . e . , 122 . 2 ( 95 % ci , 112 . 2–144 . 7 ) mya . note that , ml - f l is giving results consistent with that reported in earlier studies [ 1 ] – [ 5 ] , [ 12 ] – [ 15 ] , indicating that the younger root for placentals returned using the function f ir ( see below ) is due to the method and not the data . the difference between the f log and the f ' log function in table 1 is explained in materials and methods . it is the f log method that most closely approximates the brownian motion assumed by multidivtime .
figure 1 shows the estimated ancestral rates across the tree , while figure 2 represents the inferred evolutionary rates going from the root to a terminal . the single instance of root to fin whale is shown in figure 2 , while figure s1 traces the evolutionary rates inferred by different methods along seven representative lineages . the mvs - f ir tree identified an abrupt acceleration of evolutionary rate near the common ancestor of both supraprimates and laurasiatheria , then a very strong acceleration in just the ancestral lineage of laurasiatheria ( figures 1a and 2a ) . this acceleration was followed closely by a strong deceleration along nearly all lineages of laurasiatheria . in contrast , almost all lineages of afrotheria and xenarthra have retained rates close to that of the root . there are also sporadic later accelerations , for example that among hedgehogs and moon rat ( figure 1a ) .
figures a and b , respectively , trace the estimated rates along edges on analyses using mvs and ml branch lengths . the root time of of the f add analysis in figure a and b was set at a large value ( 400 mya ) because the numerical calculation continues towards an infinite root time .
the cost function f ir detected an acceleration–deceleration pattern near the base of laurasiatheria using both the mvs and ml branch lengths ( the red lines of figure 2 ) , whereas the function f log showed a far more flat prediction of generally lower evolutionary rates that led to older root times ( the green lines of figure 2 ) . even more extreme , the cost function f add inferred gradually decreasing rates in all deep branches of the mvs and ml trees ( the blue lines of figure 2 ) , and the root time tended to infinity . table 1 summarizes the root time values estimated by various models ( all the node divergence times from these models are listed in table s2 ) .
table 1 also compares the inferred times with those obtained from r8s , a popular program for estimating absolute rates [ 17 ] , [ 18 ] . this program has two options of for its cost functions , f add and f′ log ( equation ( 3 ) in materials and methods ) . it also takes account of stochastic noise caused by the finite length of the sequences used to derive the branch lengths using a penalized - likelihood approach . the fitting to the estimated branch lengths is expressed by the log likelihood , while the weight for the cost function is estimated using cross validation . in our mitochondrial dataset , with its long sequences , the root time values changed little due to the cross validation effect ( the reason is explained in materials and methods ) . further , root divergence time estimates returned by r8s do not show confidence intervals in table 1 , since r8s only assesses the sampling variance of node times due to stochastic errors in branch lengths due to finite sequence length ( it does this via the bootstrap ) and does not include the effect of stochastic variation of evolutionary rate . this source of error remains as sequence lengths go to infinity , and will be dominant with long sequences .
figure 3 represents the chronological distribution of the internal node density for the mvs - f ir tree ( figure 1a ) compared with the rate of new species appearing in the well - studied north american fossil record . to avoid potential bias of divergence times in the molecular tree due to species sampling , the scaling constant was determined by a least - squares fit to the fossil data in the period 85–50 mya .
the blue squares show the rate of the appearance of new species based on the fossil record [ adapted from 3 ] . at present , such quantitative data are limited to the well - studied north american record . the red circles represent the chronological distribution of node density ( or splits ) on the mvs - f ir tree ( figure 1a ) . the green triangles represent split frequency on the ml - f log tree ( figure 1b ) . the node density is given by the number of nodes in an 8 myr sliding window . a scaling constant for the molecular frequencies was calculated via a least - squares fit to the fossil data in the period 85–50 mya .
the mvs - f ir analysis reconciles molecular with fossil data in two ways . first , the chronological distribution of the internal node density is clearly largely consistent with the rate of appearance of novel fossil species . this is despite the fact that the paleontological data assessed are limited to the well - studied north american record [ 10 ] . both the mvs - f ir tree and the fossil record suggest accelerating taxonomic diversity near the k–t boundary , rather than a longer slower buildup [ 2 ] – [ 5 ] , [ 12 ] – [ 15 ] . use of the less robust f log criterion seems to suggest a prolonged increase in diversity that agrees far less with the quantitative fossil record . this congruence with fossils does not automatically show that the combination of mvs and f ir is the best way to analyze this data , but it does reframe the discussion of the relationship between the fossil and molecular times into one where the molecular dates are being looked at far more critically .
second , and more indicatively , the cost function f ir resolves incongruence among the fossil constraints / inferred divergence times in different parts of the molecular tree . the best fossil constraints in laurasiatheria suggest much older times than constraints in other parts of the tree [ 4 ] , [ 37 ] . the mvs - f ir , mvs - f log , and mvs - f add trees with all constraints give the root as 84 . 2 , 105 . 0 , and ∞ mya , respectively ( table 1 ) . removing the whale–hippo constraint gives 82 . 4 , ∞ , and 91 . 2 mya ; removing the horse–rhino constraint gives , 82 . 8 , 105 . 0 , and ∞ mya ; and removing both sets of constraints gave 82 . 9 , 87 . 2 , and ∞ mya . thus , in this case only the f ir tree is insensitive to “constraint sampling” .
finally , there is a good fossil calibration for tarsier [ 4 ] that was withheld because it is not used in both references 4 and 15 . it suggests that human and tarsier split around 50–60 mya and the molecular trees suggest the human - loris split was not much earlier ( probably < 5 myr earlier ) . despite our use of whale–hippo and horse–rhino calibrations , the mvs - f ir tree ( figure 1 ) gives a human - loris split close to this age , in contrast to earlier studies [ 4 ] , [ 15 ] , [ 33 ] .
we highlight two distinct properties of the new function f ir with the help of evolutionary simulations and worked examples . the first property is its ability to detect a transient acceleration of evolutionary rate . such an effect might be caused by a burst of positive selection and / or a bottleneck in population size . the second is to assess the effects of both stochastic fluctuations and systematic bias on the robustness of estimated times . here , we model bias in the form of either a general slowdown or a general acceleration of evolutionary rate across the whole tree .
we first modeled a strong instantaneous acceleration as an analogue to what is inferred by f ir to have occurred ancestral branch leading to laurasiatheria . we simulated a 32 - taxon symmetric tree in which a molecular clock holds except for an abrupt elevation ( by a factor of 10 ) of evolutionary rate along a short internal branch ( the red line in figure 4a ) . this example is useful for demonstrating the efficacy of the f ir function and something similar appears on both the mvs - f ir and ml - f ir mitochondrial trees . the times at the internal nodes were set to 48 , 56 , 64 , and 72 mya , and the root time was set to 80 mya . on this weighted tree , the cost functions were minimized with two constrained node times , which corresponded to two fossil calibration points . only the f ir function accurately estimated the true divergence times and appeared robust against the abrupt change ( figure 4b ) . in contrast , the functions f log and f add inferred gradual rate changes ( figure 4e ) , which are erroneous and lead to overestimation of the root time along with that of many other nodes ( figures 4c and 4d ) . table 2 summarizes the root time values inferred by various models . table 2 includes the result of r8s with the cross - validation method .
a worked example of the effect of a transient elevation of evolutionary rate upon estimated divergence times .
in this worked example using a symmetric 32 - taxon tree ( figure a ) , a global molecular clock holds , except for a short - term increase in evolutionary rate along one branch ( the red line in figure a ) . the true root time was set to 80 mya , and the times at the internal nodes are 48 , 56 , 64 , and 72 mya . the deep internal branch ( the red line in figure a ) is given an evolutionary rate ten times that of the remaining edges . the various cost functions were minimized subject to two calibrated nodes ( the red numbers 1 and 2 in figure a ) , using the exact branch lengths of this example as input data . the cost functions f ir , f log , and f add inferred the weighted trees of figures b , c and d , respectively . figures e–g show the trace of evolutionary rates along the lineages from the root to taxa numbers 5 , 9 , and 25 of figure a , respectively . the inferred age of the root for each cost function is shown with an arrow . the function f ir recovered the original pattern of rate change , whereas the other two functions inferred far more gradual changes , which resulted in a substantial overestimation of the root time .
we next simulated stochastic rate fluctuations by themselves , plus either a prevailing slowing down or acceleration of rates through time . such simulations are distinct from a brownian - type process , and are used to gauge the general robustness of the functions . to impose rate fluctuations on the same basic tree as figure 4a , but without the abrupt rate change , the age of the root was set to 100 mya . we assumed infinite length of sequences and that the branch lengths are known without uncertainty . next a branch was randomly selected proportional to its duration in time and all its descendant branch lengths were multiplied by a factor ( chosen randomly ) from a uniform distribution of range 0 . 5–1 . 5 . a total of 25 such rate changes were placed on the tree to give the final branch lengths for that tree . these branch lengths were used as the input data and the various cost functions were minimized with on calibrated internal node , and then determined all node times . we repeated this procedure 600 times to obtain the mean and standard error of the root time . we also simulated the two other cases . the only difference was the range of the uniform distribution used . using a range of 1 . 0–1 . 75 the model is biased toward rate acceleration through time , while using and 0 . 25–1 induces a rate slow down through time ( a probable situation in the placentals generally ) . as table 3 shows , the function f ir gave reasonable estimates with a bias towards deceleration , whereas f add gave an infinite root time in 139 of 600 samples . these undefined root - time values were set arbitrarily to 200 mya before calculating the mean and standard error .
the mvs model was shown previously to recover the correct tree in a simulation with two strongly convergent lineages [ 26 ] that were grouped erroneously by standard methods ( including the neighbor joining ( nj ) [ 38 ] and ml [ 35 ] methods ) . here , we examined a different question ; this is how well the mvs method recovers the true branch lengths , which are of primary importance when estimating divergence times . we simulated the evolution of a sequence of 10 4 amino acid sites , following the tree depicted in figure 5 . the model of amino acid substitutions used was the jtt [ 36 ] . convergent evolution was then imposed on this data . this was done by sharing parts of the sequences among three ingroup clades plus the outgroup . the red lines in figure 5 indicate which lineages shared sequence and were therefore subject to a form of convergent evolution .
amino acid substitutions were evolved on the shown weighted tree using the jtt model [ 36 ] of amino acid substitutions . after this , 30 % of sites were swapped between the four lineages indicated by the red lines .
pairwise distances were then estimated from the terminal sequences obtained above using the same jtt model . a modified mvs core - set procedure [ 27 ] was able to recognize that the tree consisted of three groups of eight sequences which had additive distances within each group and the outgroup . the mvs procedure then converted the distances within the three ingroups into three sets of perfectly additive distances and sequentially combined them to form a single core set ( materials and methods ) . the final mvs tree was obtained by modifying the distances between this single ingroup core set and the outgroup following the rules described in materials and methods .
the branch lengths recovered by the mvs model reproduced the true values accurately ( figure 6 ) . the distribution around the diagonal line in figure 6 represents the stochastic fluctuation of the estimated distances ; that is , the magnitude of this fluctuation did not change after the simulation was rerun without convergent evolution . in contrast , the nj and ml trees returned branch lengths that were affected clearly by convergent evolution . the worst affected branch lengths were ancestral to the groups showing convergent evolution ( underestimated ) or else were leading to the sister groups of the groups affected by convergent evolution ( overestimated ) .
the tree topology inferred by these methods was identical to the tree that generated the data , so the estimated branch lengths are plotted against their true values . the blue numbers show the branch index , as used on figure 5 , of outliers . note , all the outliers are internal branches ancestral to the four lineages undergoing convergent evolution or are ancestral to the sister group to these lineages . branch lengths ancestral to the groups undergoing convergent evolution are underestimated by the ml and nj methods , whereas those ancestral to their sister taxa are overestimated .
we begin the discussion by examining why the current cost functions , f log and f add , overestimated the age of the root in the worked example with strong rate heterogeneity in the form of a short term highly elevated evolutionary rate . it is also important to examine the profile of the cost function around their minimal values for the age of the root . the functions f log and f add showed asymmetric behavior around the estimated root time , even in worked examples with a perfect molecular clock ( data not shown ) , whereas the f ir profile was symmetric and parabolic in shape . the asymmetry seen with f log and f add increased in response to a general bias towards deceleration of rates through time ( figure 7a ) . in particular , the function f add showed a monotonic decrease with respect to increasing age of the root , that is , its estimate tended to infinity . thus , asymmetric behavior of a cost function seems to be a symptom of unstable estimation of the age of the root . a similar strong asymmetry appeared in the profile of the current cost function with respect to the age of the root of the mitochondrial tree of placental mammals ( figure 7b ) , irrespective of whether mvs or ml branch lengths were used . comparing figures 7a and 7b suggests that bias due to decelerating evolutionary rates occurred in the evolutionary history of placental mammals , and is impacting the ability of current methods to estimate the correct age of the root .
this figure shows the profile of the cost function with respect to the age of the root estimated by three different cost functions . because the root age estimated by function f add was going to infinity , it was set to 200 mya for illustrative purposes . figure a is a single example from a tree simulated under the scenario of random auto - correlated changes of rate moving towards the tips , strongly biased towards a deceleration of evolutionary rates as time progresses ( from the set of simulations used for table 3 ) . the true age of the root was 100 mya . figure b shows the results using the mvs tree derived from the mitochondrial sequences of placental mammals . the dotted line indicates the 95 % confidence interval of the estimated age of the root using the sum - of - squares approach described in materials and methods .
other approaches to divergence time estimation are under active development . for example , drummond et al . [ 39 ] recently developed a set of bayesian procedures to jointly estimate divergence times , evolutionary rates , and the tree topology . the uncorrelated variable rate model they use , which assumes independence of evolutionary rates between branches , may also be able to identify instantaneous accelerations . however , the magnitude of rate acceleration may be underestimated because hierarchical bayes estimates can generally be regarded as shrinkage estimators [ 40 ] . an important future direction is to assess the performance of the various estimators in simulations where rate variability is a mixture of an autocorrelated process plus rare , but strong , instantaneous accelerations .
our refined approaches resolve apparent contradictions between the quantitative molecular and paleontological data of placental mammals . given such agreement , there is no need for ancillary hypotheses such as the long fuse model [ 2 ] , [ 5 ] , [ 9 ] , [ 12 ] – [ 15 ] , [ 41 ] to explain the lack of any positively identified fossils of modern placental mammals prior to about 75 million years ago . in addition , dates of markedly less than 100 mya for the root of placental mammals also bring into question earlier hypotheses that traditional continental drift models explain the geographic distribution of the four major groups of placental mammals [ 2 ] – [ 5 ] , [ 13 ] , [ 42 ] . we anticipate that the f ir cost function developed in this paper will provide an improved methodology for a wide range of molecular studies because its robustness to rapid fluctuations of rate is essential to understanding events such as adaptive evolution . for example , because acquisition of new molecular functions can be achieved in a few million years after gene duplications [ 40 ] , the duration of an inflated evolutionary rate may be surprisingly short , and , correspondingly , difficult to detect . we hope our new methods will be beneficial in such situations and will lead to a richer understanding of molecular evolution .
because the branch lengths of a phylogenetic tree are estimated from the data as the product of the evolutionary rate of a branch and its time duration , these two factors cannot be directly estimated separately . it has become standard to use loose constraints to accommodate uncertainty and it is often wise to exclude constraints if there is no firm basis for them . information on the age of some internal nodes may be fairly directly available from the fossil record . an example of this is the horse - rhino split [ 13 ] . if the molecular clock [ 16 ] governs the process of molecular evolution well , we can accurately estimate the times at other nodes given just a single reliable calibration point . however , the assumption of the molecular clock is often rejected by the fit of a clock - like tree to the data .
the most widely used assumption in order to model the evolutionary rate changes away form being constant ( or away from a clock ) is to introduce a stochastic process . for example , sanderson
that rate changes follow a random walk with independent increments randomly drawn from a normal distribution . likewise , thorne et al .
uses rates at the nodes , instead of average rates along branches , as the free parameters ) . this can be interpreted as an assumption that the log rate undergoes brownian motion . that is , independent increments of normal random variables , whose variances are proportional to the average time duration between the pair of branches ( that is , the average length in time of the two branches ) . recently , sanderson implemented the unweighted cost function
however , the estimated rates based on any of the above cost functions may overly smooth the change of evolutionary rates when a pronounced transient change of rate has occurred . in turn , biased estimates of evolutionary rates will lead to biased estimates of divergence times . here we propose a new cost function , which penalizes the local rate deviation from the harmonic mean . for simplicity , we ignore the stochastic variance of branch length
, which goes to zero with increasingly long sequences . denote the branch length and inverse rate of the
because f ir places a smaller penalty on abrupt rate changes than do previous models , it can confine an abrupt change close to where it occurred on the tree . in contrast , f add and f log a priori put stress upon the smoothness of evolutionary rate change from one branch to the next , and this may propagate the effect of an abrupt rate change over successive branches . in this article , the variable ( t n ) ( the divergence times ) were estimated by minimizing the cost functions ( equations 1–4 ) subject to the ( fossil ) constraints without introducing other modifiers such as cross validation .
at first glance , it seems most intuitive to use a penalty such as ( rate 1 −rate 2 ) 2 ; this has been the implicit assumption until now [ 31 ] and is the basis of published programs such as r8s and multidivtime [ 17 ] , [ 18 ] , [ 31 ] . it rests on the implicit expectation that any reasonable type of smoothing of changes in rate will give a similar answer . however , a simple linear form for the difference in rates is misleading , and this is illustrated by considering the general problem of estimating velocity ( rate ) given distance ( in our case branch length ) . going from point a to b at velocity v 1 , then back at velocity v 2 , the average velocity ( v av ) is equal not to the standard arithmetic mean , but to the harmonic mean , 1 / v av = ( 1 / v 1 + 1 / v 2 ) / 2 . further , going from point ( node ) a to b at velocity ( rate ) v 1 , and from point b to c at velocity v 2 , then the distances traveled ( d ab and d bc ) need no longer be equal so we must use weights . specifically , v av = ( d ab + d bc ) / ( t 1 + t 2 ) , where t 1 = d ab / v 1 and t 2 = d bc / v 2 . as a result , 1 / v av = ( d ab / v 1 + d bc / v 2 ) / ( d ab + d bc ) . this is the same form as the average quantity a n used to obtain f ir ( equation 4 ) . the use of the harmonic mean becomes important when v 1 differs greatly from v 2 .
the bayesian approach estimates the divergence times and evolutionary rates in the form of a posterior distribution , which is summarized approximately as p ( b | r , t ) exp ( −λf ) . here b , r , and t are the vectors of the estimated branch lengths , evolutionary rates , and divergence times , respectively , while f is the cost function . the value of λ expresses the weight for the penalty , and is called a hyperparameter . introducing the distribution for the hyperparameter is done via a so - called hyper - prior ; the hyperparameter is then estimated concurrently with the posterior distribution . the penalized likelihood approach maximizes log p ( b | r , t ) − λf . the weight for the penalty λ is estimated using cross - validation . when the sequences are long enough , for example concatenated mitochondrial protein sequences , it is often safe to assume that the branch lengths are estimated accurately , that is with minimal stochastic error ( but not necessarily without systematic error , something we address in this paper using mvs ) . accordingly , it is assumed that the products of rates and times are known exactly . thus in a situation of long , or very long sequences ( e . g . genomic alignments ) , the results returned by using just the penalty function will converge to those returned by either a bayesian or a penalized likelihood approach with the same type of cost function .
in the mvs method , the additivity of evolutionary distances is converted using the expected orthogonality among branch vectors in a multidimensional euclidean space [ 25 ] . if the estimated pairwise distances do not satisfy additivity , mvs provides an index to measure deviations from orthogonality without specifying a tree structure . this index enables one to diagnose whether a distance matrix is compatible with a tree and to modify the biased distances until they satisfy orthogonality , that is , with a zero value for the index . here , a revised core - set approach , that is , an extension of [ 27 ] , is applied to correct the observed pairwise distances for convergent evolution .
the first step of this approach is to divide the set of taxa into subgroups and to correct the distances between pairs in each subgroup . we decompose the taxa based on partitions with both strong biological support and high bootstrap support . the deviation from additivity of pairwise distances is much smaller within each subgroup than across the whole distance matrix . if an anomalously large deviation is observed associated with a single taxon within a subgroup , that taxon is removed temporarily from the analysis . when the only deviations between distances within a subset of taxa are judged to be due to stochastic noise , the pairwise distances are modified by solving the equation of motion ( a method using a many body kinetic equation in physics ) , which uses the index of the deviation from additivity as the potential energy [ 25 ] , [ 26 ] . the modified distance matrix within a subgroup is interpreted as the true additive distance matrix ( core set ) achieved by minimal modification of the original distances . generally , the modified distances are very close to the distances estimated by the nj method for just these taxa . then , the excluded taxa are deposited into this core set tree by solving the equation of motion with the same potential function . assuming that convergent evolution and long - branch attraction are the main source of deviation from additivity , we allow for only positive corrections of the biased distances between the core set and excluded taxa ( that is , distances can only get bigger ) .


carangoides is a genus of tropical to subtropical marine fishes in the jack family , carangidae .

they are small - to large-sized , deep-bodied fish characterised by a certain gill raker and jaw morphology , often appearing very similar to jacks in the genus caranx .

they inhabit the subtropical and tropical regions of the indian , pacific , and atlantic oceans , often occupying coastal areas , including reefs , bays , and estuaries , rarely venturing far offshore .

they are all predatory fishes , taking a variety of smaller fishes , crustaceans and cephalopods as prey .

the genus was first erected in 1851 by pieter bleeker for an unknown taxon and currently contains 21 species .

many make up significant proportions of various fisheries , although a number of ciguatera cases have been attributed to them .

carangoides

frédéric ducarme marked
file : carangoides ferdau , avec sa méduse thysanostoma loriferum . jpg
as trusted on the
carangoides ferdau
page .
species - specific conservation measures for carangoides coeruleopinnatus in the persian gulf are unknown .
jennifer hammock chose to hide data on
carangoides ferdau ( forsskål , 1775 )
.
jennifer hammock chose to hide data on
carangoides chrysophrys ( cuvier , 1833 )
.
hosts : longnose trevally carangoides chrysophrys and c . hedlandensis ( both carangidae , perciformes ) .
hosts : shadow trevally carangoides dinema and yellowspotted trevally c . fulvoguttatus ( both carangidae , perciformes ) .
carangoides coeruleopinnatus is incidentally taken by artisanal fisheries throughout its range ( smith - vaniz 1984 ) . carangoides coeruleopinnatus is caught mostly on hook and line ( carpenter et al . 1997 ) , but is also taken by gillnets and traps ( smith - vaniz 1984 ) . carangoides coeruleopinnatus is marketed fresh and dried salted .
, a group of fish commonly known as jacks and trevallies . carangoides falls into the jack and horse mackerel family
nick hope marked the arabic common name
bayad
from
carangoides ferdau ( forsskål , 1775 )
as untrusted .
carangoides coeruleopinnatus is not well - known in the persian gulf , therefore , carangoides coeruleopinnatus is listed as data deficient . distribution within the persian gulf is not well - known . studies that improve our knowledge regarding the geographic distribution and habitat preferences of carangoides coeruleopinnatus within the persian gulf as well as a reliable estimate of abundance are needed to make a proper conservation appraisal .
williams , f . ; venkataramani , v . k . ( 1980 ) .
notes on indo - pacific carangid fishes of the genus carangoides bleeker ii . the carangoides armatus group
. bulletin of marine science 28 ( 3 ) : 501–511 .
froese , rainer and pauly , daniel , eds . ( 2008 ) .
carangoides armatus
in fishbase . january 2008 version .
froese , rainer and pauly , daniel , eds . ( 2008 ) .
carangoides ciliarius
in fishbase . january 2008 version .
froese , rainer and pauly , daniel , eds . ( 2008 ) .
carangoides fulvoguttatus
in fishbase . october 2008 version .
bludger trevally , carangoides gymnostethus , at mornington island . source : rick stuart - smith / reef life survey . license : cc by attribution
ascaridoid larvae designated as “ raphidascaris larval type” were reported from carangoides chrysophrys from off new caledonia by shamsi et al . [ 64 ] .
carangoides coeruleopinnatus distribution within the persian gulf is not well - known . carangoides coeruleopinnatus has not been reported off iran , kuwait , and abu dhabi ( w . smith - vaniz , f . kaymaram , j . bishop , and s . hartmann pers . comm . 2013 ) .
nick hope marked the common name
sulphur cinquefoil
in an unknown language from
carangoides ferdau ( forsskål , 1775 )
as untrusted .
embed this arkive thumbnail link (
portlet
) by copying and pasting the code below . < a href =
urltoken
title =
arkive species - orange spotted trevally ( carangoides bajad )
> < img src =
urltoken
alt =
arkive species - orange spotted trevally ( carangoides bajad )
title =
arkive species - orange spotted trevally ( carangoides bajad )
border =
0
/ > < / a >
frédéric ducarme marked
file : carangoides ferdau , avec sa méduse thysanostoma loriferum . jpg
as trusted on the
thysanostoma loriferum ehrenberg 1835
page .
ascaridoid larvae from carangoides spp . a–c : hysterothylacium sp . third - stage larva from carangoides fulvoguttatus ( a : anterior end of body ; b : cephalic end ; c : tail ; all lateral views ) . d–f : raphidascaris ( ichthyascaris ) sp . third - stage larva from carangoides fulvoguttatus ( d : anterior end of body ; e : cephalic end ; f : tail ; all lateral views ) . g–i : raphidascaris ( ichthyascaris ) sp . fourth - stage larva from carangoides fulvoguttatus ( g : anterior end of body ; h : cephalic end ; i : tail ; all lateral views ) . j , k : terranova sp . third - stage larva from carangoides fulvoguttatus ( j : anterior end of body ; k : tail ; both lateral views ) .
nematode parasites of four species of carangoides ( osteichthyes : carangidae ) in new caledonian waters , with a description of philometra dispar n . sp . ( philometridae )
( of carangoides auroguttatus ( cuvier , 1833 ) ) randall , j . e . ( 1992 ) . red sea reef fishes . immel publishing . [ details ]
nématodes parasites de quatre espèces de carangoides ( osteichthyes : carangidae ) des eaux de nouvelle - calédonie , avec description de philometra dispar n . sp . ( philometridae )
three species of opisthomonorchiine monorchiids ( digenea ) in carangoides spp . ( perciformes : carangidae ) from off new caledonia , with a description of opisthomonorchis dinema n . sp
carangoides bleeker ( carangidae , perciformes ) is a genus comprising at present 21 species of marine fishes that inhabit the tropical and subtropical regions of the indian , pacific and atlantic oceans [ 14 ] . in 2009 and 2010 , during extensive studies of the parasites of marine fishes in new caledonian waters , specimens of four species of carangoides were examined . since no data on the parasites of carangoides spp . from off new caledonia were available , the newly obtained helminthological material has provided the first information from this zoogeographically interesting region .
carangoides coeruleopinnatus is commonly found over deeper coastal reefs ( smith - vaniz 1984 ) , sea grass beds ( satapoomin 2011 ) , and sand bottoms near reefs between 10 - 25 m in depth ( allen and erdmann 2012 ) . however , due to its rather sluggish nature , carangoides coeruleopinnatus is rarely found close to the shore ( smith - vaniz 1984 ) . carangoides coeruleopinnatus is generally solitary ( kuiter and tonozuka 2001 ) , though , known to occur in small groups ( allen and erdmann 2012 ) . the recorded maximum total length for c . coeruleopinnatus is 41 cm ( allen and erdmann 2012 ) .
( of carangoides hemigymnostethus bleeker , 1851 ) froese , r . & d . pauly ( editors ) . ( 2018 ) . fishbase . world wide web electronic publication . , available online at urltoken [ details ]
( of carangoides rectipinnus williams , 1958 ) froese , r . & d . pauly ( editors ) . ( 2018 ) . fishbase . world wide web electronic publication . , available online at urltoken [ details ]
( of carangoides rhomboides kotthaus , 1974 ) froese , r . & d . pauly ( editors ) . ( 2018 ) . fishbase . world wide web electronic publication . , available online at urltoken [ details ]
( of carangoides chrysophryoides bleeker , 1851 ) froese , r . & d . pauly ( editors ) . ( 2018 ) . fishbase . world wide web electronic publication . , available online at urltoken [ details ]
( of carangoides gymnostethoides bleeker , 1851 ) froese , r . & d . pauly ( editors ) . ( 2018 ) . fishbase . world wide web electronic publication . , available online at urltoken [ details ]
( of carangoides ferdan ( forsskål , 1775 ) ) froese , r . & d . pauly ( editors ) . ( 2018 ) . fishbase . world wide web electronic publication . , available online at urltoken [ details ]
( of carangoides auroguttatus ( cuvier , 1833 ) ) froese , r . & d . pauly ( editors ) . ( 2018 ) . fishbase . world wide web electronic publication . , available online at urltoken [ details ]
( of carangoides auroguttataus ( cuvier , 1833 ) ) froese , r . & d . pauly ( editors ) . ( 2018 ) . fishbase . world wide web electronic publication . , available online at urltoken [ details ]
( of carangoides chrysophyra ( cuvier , 1833 ) ) froese , r . & d . pauly ( editors ) . ( 2018 ) . fishbase . world wide web electronic publication . , available online at urltoken [ details ]
( of carangoides laticaudis ( alleyne & macleay , 1877 ) ) froese , r . & d . pauly ( editors ) . ( 2018 ) . fishbase . world wide web electronic publication . , available online at urltoken [ details ]
capillariidae gen . sp . , gravid female from carangoides dinema . a : anterior end of body . b : region of vulva , lateral view . c : stichocyte from middle part of stichosome . d : posterior end of body , lateral view . e : egg .
johnstonmawsonia sp . from carangoides fulvoguttatus , nongravid female . a : anterior end of body , lateral view . b : same , larger magnification . c : cephalic end , apical view . d : oesophageal portion of body , lateral view . e : tail , lateral view .
{ author1 , author2 . . . } , ( n . d . ) . carangoides armatus ( rüppell , 1830 ) . [ online ] india biodiversity portal , species page : { name of species field } available at : urltoken [ accessed date jul 10 , 2018 ] .
the finding of one female specimen of this species , reported as capillariidae gen . sp . 3 , in new caledonian waters was recorded by moravec & justine [ 40 ] ; however , the host reported as carangoides oblongus ( cuvier ) was in fact c . dinema [ 12 ] .
cite this article as : moravec f , gey d & justine j - l : nematode parasites of four species of carangoides ( osteichthyes : carangidae ) in new caledonian waters , with a description of philometra dispar n . sp . ( philometridae ) . parasite , 2016 , 23 , 40 .
philometra dispar n . sp . from carangoides dinema , male . a : anterior end of body , lateral view . b : cephalic end , apical view . c : caudal end , apical view . d : gubernaculum , lateral view . e , f : posterior end , lateral and ventral views .
all the above - mentioned forms are considered to represent one and the same species of raphidascaris railliet & henry , 1915 , which attains full maturity in carangoides spp . the presence of characteristic , anteriorly united lateral alae in fourth - stage larvae shows that this currently undescribed species belongs to the subgenus ichthyascaris wu , 1949 .
grandcourt , e . m . , al abdessalaam , t . z . , francis , f . and al shamsi , a . ( 2004 ) population biology and assessment of representatives of the family carangidae carangoides bajad and gnathanodon speciiosus ( forsskål , 1775 ) , in the southern arabian gulf . fisheries research , 69 : 331 - 341 .
johnstonmawsonia sp . from carangoides fulvoguttatus , scanning electron micrographs of nongravid female . a , b : cephalic end , apical and dorsoventral views , respectively ( arrows indicate sublabia ) . c : detail of mouth , apical view ( arrows indicate inner prostomal teeth ) . d : excretory pore , ventral view . abbreviations : a , amphid ; b , submedian cephalic papilla ; c , sublabium .
carangoides chrysophrys ( cuvier , 1833 ) : wickel & jamon ( 2010 ) [ statut pour mayotte ] wickel , j . & jamon , a . 2010 . inventaire taxonomique actualisé des poissons marins de l’île de mayotte et des bancs récifaux de geyser - zélée , canal de mozambique . liste révisée des espèces et élaboration d’une base de données fonctionnelle . rapport lagonia / apnee en collaboration avec l’aquarium de la réunion . 34 pp . + annexe .
a green to bluish - green trevally becoming silver below , with or without small golden to dark orange spots ( usually less than 30 ) scattered on the sides , olive green dorsal , anal , caudal and pelvic fins , and often white tips on the soft dorsal and anal fins . juveniles to 200 mm are silver to silvery - green with a few scattered golden spots on the side , and a dark line running obliquely through the eye that fades with age . this species is often misidentified as carangoides fulvoguttatus .
cucullanus bulbosus ( lane , 1916 ) from carangoides fulvoguttatus . a , b : anterior end of gravid female , dorsoventral and lateral views , respectively . c , d : cephalic end of gravid female , lateral and ventral views , respectively . e : cephalic end of male , lateral view . f : posterior end of male , lateral view . g : egg . h : caudal end of male , lateral view . i : cephalic end of male , apical view . j : tail of gravid female , lateral view . k : caudal end of male , ventral view .
all species of johnstonmawsonia were described to have no teeth in the prostom . the present specimen has no anterior prostomal teeth , but its prostom is provided with six minute , more posteriorly located denticles , which are visible only with the use of sem . however , it should be remarked that none of the johnstonmawsonia spp . has so far been studied by sem ( except for the poor quality sem micrograph of the cephalic end of j . porichthydis [ 68 ] ) . therefore , it is not currently clear whether the presence of small posterior prostomal denticles is a generic feature in johnstonmawsonia or it is only a character of an apparently undescribed congeneric species parasitising carangoides fulvoguttatus .
parukhin [ 51 – 53 ] reported p . carangi from 12 species of carangid fishes ( including two carangoides spp . ) from the western part of the indian ocean ( monar bay , arabian sea near oman , gulf of aden , red sea , off southeastern coast of africa ) , whereas p . decapteri was recorded from the north pacific ocean near japan [ 29 ] . although specimens of the present material may belong to one of these two species ( which , however , may be identical to each other ) , their poor original descriptions and principally the absence of a male in our material do not allow us to assign the new caledonian specimens to a species .
based on this material , digeneans [ 4 , 9 – 12 ] and trypanorhynch cestodes [ 8 ] have already been recorded . regarding the parasitic nematodes , moravec & justine [ 40 ] mentioned the finding of the unidentified capillariid female , capillariidae gen . sp . , from c . dinema bleeker ( erroneously reported as c . oblongus ( cuvier ) – see bray & justine [ 12 ] ) , and shamsi et al . [ 64 ] recorded four ascaridoid larval types , anisakis type i , raphidascaris type and terranova types i and ii , in five carangoides spp . results of the evaluation of nematodes collected from four species of congeneric hosts from off new caledonia are presented herein .
with a deep , flattened , streamlined body , the orange spotted trevally ( carangoides bajad ) is a powerful , fast - swimming predatory fish of the jack family ( carangidae ) ( 2 ) ( 3 ) . this carnivorous fish is also recognised by its deeply - forked tail fin , low dorsal fin with elongated rays , and naked patch on the middle of the belly ( 2 ) ( 3 ) . this beautiful fish is typically silvery - grey in colour with a scattering of conspicuous , bright orange - yellow spots along the sides ( 2 ) ( 4 ) ( 5 ) . it does , however , display the remarkable ability to change its colour to become almost entirely orange , although the spotting still shows through ( 4 ) .
philometra dispar n . sp . from carangoides dinema , scanning electron micrographs of male . a , b : cephalic end , dorsoventral and apical views , respectively . c , d : caudal end , lateral and apical views , respectively ( arrow indicates phasmid ) . e : caudal end , subdorsal view ( arrows indicate phasmids ) . f : deirid . g : anterior end of body , dorsoventral view ( arrow indicates location of deirid ) . abbreviations : a , amphid ; b , submedian pair of cephalic papillae of external circle ; c , submedian cephalic papilla of internal circle ; d , lateral cephalic papilla of internal circle ; e , caudal papillae in region of cloacal aperture ; f , caudal papilla of last postanal pair ; g , caudal mound ; o , oral aperture .
to date , 10 species of raphidascaris ( ichthyascaris ) are known as parasites of marine fishes [ 72 ] . of these , five species were reported from the south pacific ocean in the australian region : r . ( i . ) fisheri ( hooper , 1983 ) , r . ( i . ) gymnocraniae ( bruce , 1990 ) and r . ( i . ) sillagoides ( bruce , 1990 ) in australian waters and r . ( i . ) etelidis moravec & justine , 2012 and r . ( i . ) nemipteri moravec & justine , 2005 from off new caledonia [ 13 , 39 , 41 ] . however , none of the raphidascaris ( ichthyascaris ) spp . has so far been described from fishes of the family carangidae . therefore , it can be assumed that the nematodes parasitising carangoides spp . in new caledonian waters belong to a new species .
based on their morphology , the present hysterothylacium larvae from c . fulvoguttatus cannot be assigned to any of the congeneric larval types of shamsi et al . [ 63 , 64 ] , all of which were reported from non - carangid fishes . it is not clear whether the present hysterothylacium larvae may attain full maturity in c . fulvoguttatus , serving thus as the definitive host , or whether this fish is only utilised as the paratenic host . the only two species reported from carangid fishes are h . chorinemi ( parukhin , 1966 ) , recorded from atule mate ( cuvier ) , caranx sexfasciatus quoy & gaimard and scomberoides lysan ( forsskål ) ( all carangidae ) in the south china , arabian and red seas and off the southeastern coast of africa [ 50 , 53 ] , and h . carangis ( kalyankar , 1971 ) , described from carangoides malabaricus ( bloch & schneider ) off india [ 13 , 26 ] .
common names : pompano ( english ) , jack ( english ) , cocinero ( espanol ) , jurel ( espanol ) , palometa ( espanol ) , pámpano ( espanol ) carangoides otrynter ( jordan & gilbert , 1883 ) threadfin jack , thread pompano body deep , compressed ; head profile angular ; both jaws with a band of teeth , at least at the front ; gill rakers on first arch ( excluding rudiments ) 15 - 17 + 21 - 23 ; dorsal rays viii + i , 18 - 19 ; anal rays ii + i , 16 - 17 ; elongate and filamentous dorsal and anal lobes ; dorsal and anal fins not followed by finlets ; pectoral fins longer than head ; lateral line anteriorly with moderate arch , the curved part about equal to straight part ; straight rear part of lateral line with 0 - 15 scales , followed by 40 - 52 small scutes ( large , hard spiny scales ) ; a large isolated scaleless area covering front of breast and extending up onto base of pectoral fins . generally silvery to silver grey ; an elongate black spot in the upper of the operculum ; small dark blotches between bases of dorsal rays . size : grows to 60 cm . habitat : coastal pelagic . depth : 0 - 100 m . southern baja and the central gulf of california to ecuador , including the revillagigedos , galapagos and malpelo .
by the body length 5 . 1 mm , the present male resembles only that of p . selaris ( 5 . 3–5 . 5 mm ) , whereas the males of other three species are distinctly shorter ( 1 . 5–3 . 3 mm ) . moreover , both p . dispar sp . n . and p . selaris possess a dorsal reflexed barb at the tip of the gubernaculum , which is absent in other species . however , the new species differs from p . selaris in having conspicuously unequal spicules ( length ratio of spicules 1 : 1 . 28 vs . 1 : 1 . 03–1 . 04 ) , a different shape and structure of the gubernaculum ( presence vs . absence of a dorsal protuberance ) and a more posterior location of the oesophageal cell nucleus ; in addition , it was collected from a fish belonging to a different genus ( carangoides vs . selar ) . males of the remaining four philometrid species from carangids are not known and , consequently , cannot be compared with p . dispar ; however , these species can be separated based on the different genus of their type host and their geographical distribution . the allocation of the new species to philometra is provisional ; present philometrid genera are mostly based on the morphology of gravid and subgravid females , whereas males of some genera ( e . g . caranginema , philometra and philometroides ) are unidentifiable to genus [ 42 ] .
parasitological examination of marine perciform fishes belonging to four species of carangoides , i . e . c . chrysophrys , c . dinema , c . fulvoguttatus and c . hedlandensis ( carangidae ) , from off new caledonia revealed the presence of nematodes . the identification of carangids was confirmed by barcoding of the coi gene . the eight nematode species found were : capillariidae gen . sp . ( females ) , cucullanus bulbosus ( lane , 1916 ) ( male and females ) , hysterothylacium sp . third - stage larvae , raphidascaris ( ichthyascaris ) sp . ( female and larvae ) , terranova sp . third - stage larvae , philometra dispar n . sp . ( male ) , camallanus carangis olsen , 1954 ( females ) and johnstonmawsonia sp . ( female ) . the new species p . dispar from the abdominal cavity of c . dinema is mainly characterised by the body length ( 5 . 14 mm ) , the lengths of markedly unequal spicules ( 163 and 96 μm ) and gubernaculum ( 102 μm long ) provided with a dorsal protuberance and a small , reflexed dorsal barb on its posterior portion . the finding of c . bulbosus represents the first record of this parasite a century after its discovery ; the first study of this species by scanning electron microscopy ( sem ) enabled detailed redescription . the finding of johnstonmawsonia sp . in c . fulvoguttatus is the first record of a rhabdochonid nematode from a host belonging to the carangidae family . johnstonmawsonia africana moravec & puylaert , 1970 and j . campanae puylaert , 1973 are transferred to prosungulonema roytman , 1963 as p . africanum ( moravec & puylaert , 1970 ) comb . n . and p . campanae ( puylaert , 1973 ) n . comb .
l’examen parasitologique de poissons perciformes marins appartenant à quatre espèces de carangoides , c . chrysophrys , c . dinema , c . fulvoguttatus et c . hedlandensis ( carangidae ) de nouvelle - calédonie a révélé la présence de nématodes . l’identification des carangidés a été confirmée par barcoding du gène coi . les huit espèces de nématodes trouvées étaient : capillariidae gen . sp . ( femelles ) , cucullanus bulbosus ( lane , 1916 ) ( mâles et femelles ) , hysterothylacium sp . ( larves de troisième stade ) , raphidascaris ( ichthyascaris ) sp . ( femelles et larves ) , terranova sp . ( larves de troisième stade ) , philometra dispar n . sp . ( mâle ) , camallanus carangis olsen , 1954 ( femelles ) et johnstonmawsonia sp . ( femelle ) . la nouvelle espèce p . dispar , de la cavité abdominale de c . dinema , se caractérise principalement par la longueur du corps ( 5 . 14 mm ) , les longueurs des spicules sensiblement inégales ( 163 et 96 μm ) et un gubernaculum ( 102 μm de long ) montrant une protubérance dorsale et un petit ardillon dorsal orienté vers l’arrière sur sa partie postérieure . la trouvaille de c . bulbosus représente la première mention de ce parasite , un siècle après sa découverte ; la première étude de cette espèce par meb a permis une redescription détaillée de l’espèce . la découverte de johnstonmawsonia sp . chez c . fulvoguttatus est la première mention d’un nématode rhabdochonidae chez un hôte appartenant à la famille carangidae . johnstonmawsonia africana moravec & puylaert , 1970 et j . campanae puylaert , 1973 sont transférés vers prosungulonema roytman , 1963 comme p . africanum ( moravec & puylaert , 1970 ) n . comb . et p . campanae ( puylaert , 1973 ) n . comb .
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cfm script by eagbayani , 30 . 11 . 04 , , php script by cmilitante , 05 / 11 / 2010 , last modified by cmilitante , 14 / 03 / 2013
french , carangue , the name of a caribbean fish ; 1836 ( ref . 45335 )
marine ; brackish ; reef - associated ; depth range 1 - 60 m ( ref . 3197 ) . tropical ; 37°n - 35°s , 25°e - 127°w
indo - pacific : red sea and east africa ( to port elizabeth , south africa , ref . 3197 ) to the hawaiian islands .
maturity : l m ? range ? - ? cm max length : 70 . 0 cm tl male / unsexed ; ( ref . 3287 ) ; common length : 30 . 0 cm tl male / unsexed ; ( ref . 9137 ) ; max . published weight : 8 . 0 kg ( ref . 3287 )
dorsal spines ( total ) : 9 ; dorsal soft rays ( total ) : 26 - 34 ; anal spines : 3 ; anal soft rays : 21 - 26 .
adults are found in coastal waters adjacent to sandy beaches ; also found to depths of 60 m , often near reefs ( ref . 30573 ) . pelagic ( ref . 58302 ) . singly or in small groups ( ref . 48635 ) . they feed mainly on mollusks , benthic crustaceans , and occasionally on small fish ( ref . 90102 ) that are abundant in the lagoons . excellent food fish ( ref . 12484 ) , the flesh is rarely poisonous .
paxton , j . r . , d . f . hoese , g . r . allen and j . e . hanley , 1989 . pisces . petromyzontidae to carangidae . zoological catalogue of australia , vol . 7 . australian government publishing service , canberra , 665 p . ( ref . 7300 )
) : 24 . 7 - 29 . 1 , mean 28 . 1 ( based on 1490 cells ) .
phylogenetic diversity index ( ref . 82805 ) : pd 50 = 0 . 5000 [ uniqueness , from 0 . 5 = low to 2 . 0 = high ] .
bayesian length - weight : a = 0 . 02455 ( 0 . 01643 - 0 . 03666 ) , b = 2 . 94 ( 2 . 82 - 3 . 06 ) , in cm total length , based on lwr estimates for this species & genus - body shape ( ref . 93245 ) .
trophic level ( ref . 69278 ) : 4 . 3 ±0 . 5 se ; based on diet studies .
resilience ( ref . 69278 ) : medium , minimum population doubling time 1 . 4 - 4 . 4 years ( k = 0 . 21 ) .
vulnerability ( ref . 59153 ) : moderate vulnerability ( 44 of 100 ) .
maturity : l m ? range ? - ? cm max length : 25 . 0 cm tl male / unsexed ; ( ref . 11441 ) ; common length : 16 . 0 cm fl male / unsexed ; ( ref . 3287 )
smith - vaniz , w . f . , 1984 . carangidae . in w . fischer and g . bianchi ( eds . ) fao species identification sheets for fishery purposes . western indian ocean fishing area 51 . vol . 1 . [ pag . var . ] . fao , rome . ( ref . 3287 )
) : 24 . 9 - 29 . 2 , mean 28 . 3 ( based on 1476 cells ) .
bayesian length - weight : a = 0 . 01905 ( 0 . 00897 - 0 . 04049 ) , b = 2 . 94 ( 2 . 77 - 3 . 11 ) , in cm total length , based on lwr estimates for this genus - body shape ( ref . 93245 ) .
trophic level ( ref . 69278 ) : 3 . 9 ±0 . 5 se ; based on size and trophs of closest relatives
resilience ( ref . 69278 ) : high , minimum population doubling time less than 15 months ( preliminary k or fecundity . ) .
vulnerability ( ref . 59153 ) : low vulnerability ( 20 of 100 ) .
marine ; reef - associated ; depth range ? - 40 m ( ref . 86942 ) . tropical
indo - west pacific : seychelles south to durban , south africa and east to japan , the arafura sea ( ref . 9819 ) , australia , and samoa ( ref . 3197 ) .
maturity : l m ? range ? - ? cm max length : 32 . 0 cm tl male / unsexed ; ( ref . 3197 )
dorsal spines ( total ) : 9 ; dorsal soft rays ( total ) : 20 - 22 ; anal spines : 3 ; anal soft rays : 16 - 18 . greenish blue above , silvery grey below ; blackish blotch on upper opercular margin ; caudal fin yellowish ( ref . 3197 ) . adult males with 3 - 8 central dorsal and anal filamentous rays ; ll with 17 - 29 scutes .
adults inhabit coastal waters of the continental shelf ( ref . 5213 , 7300 ) .
) : 23 . 7 - 29 , mean 27 . 9 ( based on 1044 cells ) .
bayesian length - weight : a = 0 . 02951 ( 0 . 01854 - 0 . 04698 ) , b = 2 . 92 ( 2 . 79 - 3 . 05 ) , in cm total length , based on lwr estimates for this species & genus - body shape ( ref . 93245 ) .
trophic level ( ref . 69278 ) : 4 . 0 ±0 . 5 se ; based on size and trophs of closest relatives
vulnerability ( ref . 59153 ) : low vulnerability ( 15 of 100 ) .
marine ; reef - associated ; depth range 0 - 50 m ( ref . 9710 ) . subtropical ; 42°n - 25°s , 97°w - 7°e
western atlantic : massachusetts ( usa ) and bermuda , through the gulf of mexico and the caribbean to são paulo , brazil ( ref . 57756 ) . eastern central atlantic : st . paul ' s rocks ( ref . 13121 ) .
maturity : l m 45 . 0 , range 32 - ? cm max length : 100 . 0 cm tl male / unsexed ; ( ref . 5217 ) ; common length : 50 . 0 cm tl male / unsexed ; ( ref . 5217 ) ; max . published weight : 14 . 0 kg ( ref . 26340 )
dorsal spines ( total ) : 8 - 9 ; dorsal soft rays ( total ) : 25 - 28 ; anal spines : 2 - 3 ; anal soft rays : 22 - 25 . upper jaw does not reach to anterior margin of eye . juveniles have about 5 vertical dark bars on body .
adults prefer offshore reefs ( ref . 9710 ) and open marine waters ( ref . 26938 ) . juveniles often found near the shore on seagrass beds or often associated jellyfish or floating sargassum ( ref . 5217 ) . generally solitary but sometimes seen in small groups ( ref . 26235 ) . they feed on small fishes ( ref . 26235 ) . spawning occurs offshore from february to october ( ref . 26938 ) . flavor considered fair to good ( ref . 5521 ) .
cervigón , f . , 1993 . los peces marinos de venezuela . volume 2 . fundación científica los roques , caracas , venezuela . 497 p . ( ref . 9626 )
) : 22 . 8 - 28 , mean 26 . 4 ( based on 462 cells ) .
bayesian length - weight : a = 0 . 02138 ( 0 . 01368 - 0 . 03341 ) , b = 2 . 93 ( 2 . 80 - 3 . 06 ) , in cm total length , based on lwr estimates for this species & genus - body shape ( ref . 93245 ) .
trophic level ( ref . 69278 ) : 4 . 5 ±0 . 2 se ; based on diet studies .
resilience ( ref . 69278 ) : high , minimum population doubling time less than 15 months ( fec > 7 million eggs ) .
vulnerability ( ref . 59153 ) : moderate to high vulnerability ( 51 of 100 ) .
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marine ; reef - associated ; depth range 1 - 60 m ( ref . 86942 ) . tropical ; 30°n - 37°s , 19°e - 167°w
indo - west pacific : east africa to samoa ( ref . 592 ) and tonga ( ref . 53797 ) , north to japan , south to australia ( ref . 3197 ) and new caledonia ( ref . 9070 ) .
maturity : l m ? range ? - ? cm max length : 41 . 0 cm tl male / unsexed ; ( ref . 90102 ) ; common length : 30 . 0 cm tl male / unsexed ; ( ref . 5450 )
dorsal spines ( total ) : 9 ; dorsal soft rays ( total ) : 20 - 23 ; anal spines : 3 ; anal soft rays : 16 .
adults are found in deep coastal reefs and rarely inshore ( ref 3197 ) . they are usually in small groups over sand bottoms near reefs ( ref . 90102 ) .
) : 24 . 4 - 28 . 9 , mean 27 . 8 ( based on 782 cells ) .
bayesian length - weight : a = 0 . 02630 ( 0 . 01594 - 0 . 04341 ) , b = 2 . 91 ( 2 . 77 - 3 . 05 ) , in cm total length , based on lwr estimates for this species & genus - body shape ( ref . 93245 ) .
trophic level ( ref . 69278 ) : 4 . 4 ±0 . 7 se ; based on diet studies .
vulnerability ( ref . 59153 ) : low to moderate vulnerability ( 28 of 100 ) .
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robins , c . r . , g . c . ray , j . douglass and r . freund . 1986 . a field guide to atlantic coast fishes of north america . houghton mifflin co . boston . 354 p . [ details ]
froese , r . & d . pauly ( editors ) . ( 2018 ) . fishbase . world wide web electronic publication . , available online at urltoken [ details ]
intergovernmental oceanographic commission ( ioc ) of unesco . the ocean biogeographic information system ( obis ) , available online at urltoken [ details ]
description schools in open waters and lagoons and outer reef slopes . feeds mainly on crustaceans , molluscs and small fish that are . . .
description schools in open waters and lagoons and outer reef slopes . feeds mainly on crustaceans , molluscs and small fish that are abundant in the lagoons . the flesh is rarely poisonous . [ details ]
liu j . y . [ ruiyu ] ( ed . ) . ( 2008 ) . checklist of marine biota of china seas . china science press . 1267 pp . ( look up in imis ) [ details ] available for editors [ request ]
( of caranx ferdau ( forsskål , 1775 ) ) froese , r . & d . pauly ( editors ) . ( 2018 ) . fishbase . world wide web electronic publication . , available online at urltoken [ details ]
( of caranx gilberti jordan & seale , 1906 ) froese , r . & d . pauly ( editors ) . ( 2018 ) . fishbase . world wide web electronic publication . , available online at urltoken [ details ]
( of caranx hemigymnostethus ( bleeker , 1851 ) ) froese , r . & d . pauly ( editors ) . ( 2018 ) . fishbase . world wide web electronic publication . , available online at urltoken [ details ]
( of caranx laticaudis alleyne & macleay , 1877 ) froese , r . & d . pauly ( editors ) . ( 2018 ) . fishbase . world wide web electronic publication . , available online at urltoken [ details ]
( of scomber ferdau forsskål , 1775 ) froese , r . & d . pauly ( editors ) . ( 2018 ) . fishbase . world wide web electronic publication . , available online at urltoken [ details ]
( of ferdauia lindemanensis whitley , 1951 ) froese , r . & d . pauly ( editors ) . ( 2018 ) . fishbase . world wide web electronic publication . , available online at urltoken [ details ]
hong kong marine fish database . afcd . , available online at urltoken [ details ]
widespread in northern australia , from coral bay , western australia , to moreton bay , queensland . elsewhere the species occurs in the tropical , indo - west pacific from south africa to new caledonia , and north to the ryukyu islands , japan . adults usually inhabit deeper offshore reefs in depths to 100 m .
dorsal fin viii + i , 28 - 33 ; anal fin ll + i , 24 - 27 ; gill rakers 8 - 9 + 19 - 22 = 28 - 31 . naked area on breast extending up to , but not above , pectoral fin base ; head profile relatively steep in small juveniles ( less than 150 mm lcf ) becoming less steep with age , large adults elongate with very shallow head profile ( angle of head with the horizontal axis of the body 33 - 42° ) . curved portion of lateral line gently to moderately arched .
juveniles to 200 mm are silver to silvery - green with a few scattered golden spots on the side , and a dark line running obliquely through the eye , fading with age . larger individuals are green to bluish - green above , silver below , with or without gold to golden brown spots ( usually less than 30 ) scattered on the sides , olive green dorsal , anal , caudal and pelvic fins , and often white tips on the soft dorsal and anal fins .
caranx gymnostethus cuvier in cuvier & valenciennes 1833 , histoire naturelle des poissons 9 : 73 . type locality : seychelles .
blaber , s . j . m . , brewer , d . t . & harris , a . n . 1994 . distribution , biomass and community structure of demersal fishes of the gulf of carpentaria , australia .
bleeker , p . 1851 . over eenige nieuwe geslachten en soorten van makreelachtige visschen van den indischen archipel .
cuvier , g . l . in cuvier , g . l . & valenciennes , a . 1833 .
. paris : levrault vol . 9 512 pp . pls 246 - 279 .
gloerfelt - tarp , t . & kailola , p . j . 1984 .
. jakarta : dir . gen . fish . ( indonesia ) , german tech . coop . , aust . dev . ass . bur . 406 pp .
gunn , j . s . 1990 . a revision of selected genera of the family carangidae ( pisces ) from australian waters .
hutchins , j . b . 1994 . a survey of the nearshore reef fish fauna of western australia ' s west and south coasts — the leeuwin province .
johnson , j . w . 2010 . fishes of the moreton bay marine park and adjacent continental shelf waters , queensland , australia . pp . 299 - 353 in davie , p . j . f . & phillips , j . a . proceedings of the thirteenth international marine biological workshop , the marine fauna and flora of moreton bay .
reef and shore fishes of the south pacific . new caledonia to tahiti and the pitcairn islands
russell , b . c . 1983 . annotated checklist of the coral reef fishes in the capricorn - bunker group , great barrier reef , australia . great barrier reef marine park authority . special publication series 1 : 1 - 184 figs 1 - 2
smith - vaniz , w . f . 1999 . family carangidae . pp . 2659 - 2756 in carpenter , k . e . & niem , t . h . ( eds ) .
the living marine resources of the western central pacific . fao species identification guide for fisheries purposes
smith - vaniz , w . f . & williams , i . 2016 .
. ( errata version published in 2017 ) the iucn red list of threatened species 2016 : e . t20429774a115374026 . urltoken downloaded on 23 july 2017 .
whitley , g . p . 1947 . new sharks and fishes from western australia . part 3 .
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disclaimer : itis taxonomy is based on the latest scientific consensus available , and is provided as a general reference source for interested parties . however , it is not a legal authority for statutory or regulatory purposes . while every effort has been made to provide the most reliable and up - to - date information available , ultimate legal requirements with respect to species are contained in provisions of treaties to which the united states is a party , wildlife statutes , regulations , and any applicable notices that have been published in the federal register . for further information on u . s . legal requirements with respect to protected taxa , please contact the u . s . fish and wildlife service .
eschmeyer ( personal communication , feb - 2003 , and online catalog of fishes , 2003 ) notes that apparently no first first reviser has been identified , so he is acting in that capacity . since both spellings ( coeruleopinnatus and caeruleopinnatus ) appeared in the original publication , and both have been used in recent literature , the first spelling listed in the original publication ( coeruleopinnatus ) was chosen as the correct spelling
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thank you for taking the time to provide feedback on the iucn red list of threatened species website , we are grateful for your input .
justification : this species is widespread and relatively common throughout the indo - west pacific . this species is commercially harvested for human consumption , is sometimes taken as by - catch in trawl fisheries and is also a major baitfish species in parts of its range . however , there have been no observed or suspected declines in the population of this species due to exploitation , and there are no other known major threats . therefore , this species is listed as least concern .
this species occurs along the continental shores of the indian ocean from east africa to the southwestern red sea and persian gulf , east to fiji , north to the ryukyu islands , south to australia ( lieske and myers 1994 ) new caledonia and the chesterfield bank ( r . myers pers . comm . 2016 ) . insular coastal localities in the indian ocean include madagascar , comoros , the seychelles ( smith - vaniz 1984 ) , reunion and mauritius ( r . myers pers . comm . 2016 ) . the depth range for this species is 30 to 90 m ( smith - vaniz 1999 ) .
australia ; bahrain ; bangladesh ; brunei darussalam ; cambodia ; china ; comoros ; disputed territory ( paracel is . , spratly is . ) ; djibouti ; eritrea ; french southern territories ( mozambique channel is . ) ; india ( andaman is . , nicobar is . ) ; indonesia ; iran , islamic republic of ; iraq ; japan ; kenya ; kuwait ; madagascar ; malaysia ; mayotte ; mozambique ; myanmar ; new caledonia ; oman ; pakistan ; papua new guinea ; philippines ; qatar ; seychelles ; singapore ; somalia ; south africa ; sri lanka ; sudan ; taiwan , province of china ; tanzania , united republic of ; thailand ; timor - leste ; united arab emirates ; viet nam ; yemen
this species is relatively common throughout much of its range ( w . smith - vaniz pers . comm . 2015 ) .
this species is caught as bycatch in shrimp trawl fisheries throughout the persian gulf ( j . bishop , f . kaymaram , and s . hartmann pers . comm . 2013 ) . in iran , total landings are in negligible amounts ( less than 1 mt ) ( f . kaymaram pers . comm . 2013 ) . between 2001 and 2002 , paighambari and daliri ( 2012 ) sampled shrimp trawl fisheries by - catch composition in the bushehr province ( iranian waters ) . during the two fishing seasons , 31 . 896 and 28 . 970 kg of this species were collected as by - catch , which comprised of 0 . 192 and 0 . 22 % of the total catch , respectively . cpue was determined to be 0 . 307 and 0 . 186 kg / h , respectively ( paighambari and daliri 2012 ) . raeisi et al . ( 2011 ) conducted a study on the bycatch of the cutlassfish trawl fishery in the bushehr waters , persian gulf . this species occurred in 82 % of trawls with a mean biomass of 2 . 7 kg / h ( + / - 0 . 9 s . e . ) and a mean catch rate of 1 . 1 individuals / h ( + / - 0 . 24 s . e . ) . raeisi et al . ( 2011 ) reported this species contribution to the bycatch was 2 . 8 % in weight and 0 . 2 % in the number of individuals collected . between 2009 and 2010 , hosseini et al . ( 2012 ) conducted a study on the bycatch of the cutlassfish trawl fishery in bushehr and hormozgan waters ; in bushehr waters , this species occurred in 82 % of trawls , and in hormozgan waters , this species occurred in 20 % of trawls .
this species is abundant in omani waters , being caught regularly along the coast from the southern arabian sea to the gulf of oman and the persian gulf ( al - abdessalaam 1995 ) . a . govender ( pers . comm . 2013 ) determined the omani stock of this species was under - exploited with substantial room for development . however , instead an industrial fishery , a traditional fishery should be developed to reduce the risk of growth overfishing ( a . govender pers . comm . 2013 ) .
this species inhabits open waters of coastal reefs ( lieske and myers 1994 ) and occurs to depths of 90 m ( smith - vaniz 1999 ) . juveniles are found in inshore areas , including estuaries . the maximum recorded total length ( tl ) is 77 cm ( al - rasady et al . 2013 ) . al - rasady et al . ( 2013 ) estimated this species longevity to be 16 years . this species occurs to depths of 90 m , but most abundant between 30 and 60 m ( smith - vaniz 1999 ) . this species diet consists of small demersal fishes and epibenthic crustaceans ( smith - vaniz 1999 ) . this species is gonochoristic ( graham and castellanos 2005 ) , each individual is either male or female throughout its lifetime . males attain sexual maturity at 46 . 90 cm in length and 4 . 7 years of age and females attain sexual maturity at 42 . 08 cm and 4 . 1 years of age . a single peak in gonadosomatic index ( gsi ) , corresponding with a single spawning season , began in september and ended in february in the arabian sea ( al - rasady et al . 2012 ) .
this species is harvested as a food fish and is served fresh , as well as dried and salted ( smith - vaniz 1984 ) . it is collected using hook and line , gillnets , and traps ( smith - vaniz 1984 ) . this species is one of ~ 36 species that supports commercial carangid fisheries off india ( kasim 2003 ) . this species is also a major baitfish species in the west pacific ( blaber et al . 1993 ) .
this species is caught as bycatch in parts of its range ; however , there have not been any observed or suspected population declines to date as a result of commercial harvesting . other major threats are unknown .
there are no species - specific conservation efforts in place for this species ; however , its range overlaps with a number of marine protected areas ( iucn and unep 2014 ) .
this errata assessment has been created because the map was accidentally left out of the version published previously .
( errata version published in 2017 ) . the iucn red list of threatened species 2016 : e . t20257324a115371478 .
to make use of this information , please check the < terms of use > .
justification : this species is widespread and relatively common throughout the indo - west pacific . it is an important commercial species and is sometimes taken as bycatch in shrimp trawls ; however , significant global population declines have not been observed and are not suspected . this species is also relatively common in most parts of its range , and there are numerous marine protected areas throughout its range . it is therefore listed as least concern .
this species occurs in the indo - pacific from the red sea to the gulf of aden and the persian gulf and gulf of oman . it also is found in the gulf of thailand , throughout indonesia to the philippines , to new britain and the solomon islands in the south to okinawa , japan to the north ( smith - vaniz 1984 , 1999 ) . this species has recently been identified from fayu island ( r . myers pers . comm . 2016 ) . the depth range for this species is 2 to 70 m ( allen and erdmann 2012 ) .
australia ; bahrain ; brunei darussalam ; cambodia ; china ; disputed territory ( spratly is . ) ; djibouti ; egypt ; eritrea ; india ( andaman is . , nicobar is . ) ; indonesia ; iran , islamic republic of ; iraq ; israel ; japan ; jordan ; kuwait ; malaysia ; micronesia , federated states of ; myanmar ; oman ; pakistan ; palau ; papua new guinea ; philippines ; qatar ; saudi arabia ; singapore ; solomon islands ; somalia ; sudan ; taiwan , province of china ; thailand ; timor - leste ; united arab emirates ; viet nam ; yemen
this species is a coastal species that inhabits inshore coral and rocky reefs throughout its range ( grandcourt et al . 2004 ) . this species occurs in schools and is found to 50 m in depth ( al - abdessalaam 1995 ) . this species feeds on nekton , crustaceans and finfish ( blaber et al . 1990 , masuda and allen 1993 ) . grandcourt et al . ( 2004 ) estimated mean size at first maturity for female this species is 24 . 7 cm ( tl ) . this species spawns between may and september , with main spawning activity during june and september . gonado - somatic indices peak during may and august in females and july in males . growth rate for this species is fastest during the winter months ( november - april ) and slowest during the summer ( may - september ) ( grandcourt et al . 2004 ) . the maximum recorded fork length recorded for this species is 55 cm ( smith - vaniz 1984 ) .
this species is utilised throughout its range . it is a commercially important food fish and is sometimes taken as bycatch ( allen and robertson 1994 , carpenter et al . 1997 ) .
there are no known species - specific conservation measures for this species ; however , its range overlaps with a number of marine protected areas ( iucn and unep 2014 ) .
( errata version published in 2017 ) . the iucn red list of threatened species 2016 : e . t46080857a115391273 .
justification : this species is found throughout the western indian ocean to the west pacific . this species occurs to 25 m depth and inhabits seagrass beds , deep coastal reefs and shallow coral reefs . this species is incidentally taken by artisanal fisheries throughout its range and is sold fresh or dried salted ; however , there have been no observed or suspected population declines resulting from exploitation . there are no known major threats to this species . it is therefore listed as least concern .
this species occurs in coastal continental waters of the indian ocean ( randall 1995 ) ( including east africa , madagascar and réunion ) , the red sea and the persian gulf , east to tonga in the western pacific ( randall et al . 2003 ) , north to japan and taiwan ( chang 1985 ) and south to australia ( smith - vaniz 1986 ) and new caledonia ( wantiez 1993 ) . this species is also known from the seychelles ( smith and smith 1963 ) and the maldives ( randall and anderson 1993 ) and has been recorded from off southern kerala , india ( naomi et al . 2011 ) and has recently been identified from majuro island in the marshall islands ( r . myers pers . comm . 2016 ) . the depth range for this species is 10 to 25 m ( allen and erdmann 2012 ) .
australia ; bahrain ; bangladesh ; brunei darussalam ; cambodia ; china ; disputed territory ( paracel is . , spratly is . ) ; djibouti ; eritrea ; fiji ; french southern territories ( mozambique channel is . ) ; guam ; india ( andaman is . , nicobar is . ) ; indonesia ; iran , islamic republic of ; iraq ; japan ; kenya ; korea , republic of ; kuwait ; madagascar ; malaysia ; maldives ; marshall islands ; mauritius ; mozambique ; myanmar ; new caledonia ; northern mariana islands ; oman ; pakistan ; palau ; papua new guinea ; philippines ; qatar ; réunion ; samoa ; seychelles ; singapore ; solomon islands ; somalia ; south africa ; south sudan ; sri lanka ; taiwan , province of china ; tanzania , united republic of ; thailand ; timor - leste ; tokelau ; tonga ; united arab emirates ; vanuatu ; viet nam ; yemen
this species is considered to be common in coastal waters throughout the western indian ocean ( smith - vaniz 1984 ) .
this species is commonly found over deeper coastal reefs ( smith - vaniz 1984 ) , seagrass beds ( satapoomin 2011 ) , and coral reefs ( letourneur et al . 2004 ) ; however , due to its rather sluggish nature , this species is rarely found close to the shore ( smith - vaniz 1984 ) . this species is generally solitary ( kuiter and tonozuka 2001 ) . the maximum recorded total length ( tl ) for this species is 41 cm ( allen and erdmann 2012 ) .
this species is incidentally taken by artisanal fisheries throughout its range ( smith - vaniz 1984 ) . this species is caught mostly on hook and line ( carpenter et al . 1997 ) , but is also taken by gillnets and traps ( smith - vaniz 1984 ) . it is marketed fresh as well as dried and salted ( smith - vaniz 1984 ) .
this species is caught on hook - and - line by recreational anglers and is sometimes taken coincidentally by gill nets and traps in artisanal fisheries ( smith - vaniz 1984 , carpenter et al . 1997 ) ; however , there have not been any observed or suspected population declines resulting from these uses . there are no other known major threats to this species .