Tunas are migratory fishes in offshore habitats and top predators with unique features. Despite their ecological importance and high market values, the open-ocean lifestyle of tuna, in which effective sensing systems such as color vision are required for capture of prey, has been poorly understood. To elucidate the genetic and evolutionary basis of optic adaptation of tuna, we determined the genome sequence of the Pacific bluefin tuna (Thunnus orientalis), using next-generation sequencing technology. A total of 26,433 protein-coding genes were predicted from 16,802 assembled scaffolds. From these, we identified five common fish visual pigment genes: red-sensitive (middle/long-wavelength sensitive; M/LWS), UV-sensitive (short-wavelength sensitive 1; SWS1), blue-sensitive (SWS2), rhodopsin (RH1), and green-sensitive (RH2) opsin genes. Sequence comparison revealed that tuna's RH1 gene has an amino acid substitution that causes a short-wave shift in the absorption spectrum (i.e., blue shift). Pacific bluefin tuna has at least five RH2 paralogs, the most among studied fishes; four of the proteins encoded may be tuned to blue light at the amino acid level. Moreover, phylogenetic analysis suggested that gene conversions have occurred in each of the SWS2 and RH2 loci in a short period. Thus, Pacific bluefin tuna has undergone evolutionary changes in three genes (RH1, RH2, and SWS2), which may have contributed to detecting blue-green contrast and measuring the distance to prey in the blue-pelagic ocean. These findings provide basic information on behavioral traits of predatory fish and, thereby, could help to improve the technology to culture such fish in captivity for resource management.tuna genome | visual system | animal opsin

So far, the dietary requirements of the ten amino acids arginine, histidine, isoleucine, leucine, ly sine, methionine, phenylalanine, threonine, tryptophan and valine have been proved in fish and the quantitative requirements have been determined in several fishes. However, each essential amino acid re quirement determined by different laboratories does not correspond with each other, not only among species but also even within species, because of the differences of experimental conditions. Therefore, some researchers have applied a new method based on the idea that there shoud be a correlation be tween whole body amino acid pattern and the dietary amino acid requirement: i.e., only one amino acid requirement is determined by growth data and the other nine are estimated as being propotional to the whole body amino acid pattern. There would be little difference in the patterns of requirement by this new method among species, because body amino acid patterns are almost identical among species. On the other hand, when the A/E ratios of amino acid requirements based on growth assay are compared, close similarities were noted between carp and catla in the family Cyprinidae, and among chinook salmon, chum salmon and coho salmon in the family Salmonidae, suggesting the existence of specificity in requirements among fish species or family.

Teleost fish develop seven pharyngeal arches (mandible, hyoid and five gill arches) which give rise to the jaw and gills, and skeletal cell populations which originate from the cranial neural crest. The anterior border of expression of the Deformed (Dfd) group is located in the hindbrain and pharyngeal region. To investigate pharyngeal skeletal formation in the teleost fish, we cloned the cDNA coding Hoxd-4 from a cDNA library for flounder (Paralichthys olivaceus) embryos, and analyzed gene expression pattern during embryogenesis and the effects of retinoic acid (RA) on this gene expression. Between the 21-somite and prim-5 stages, Hoxd-4 was expressed in the central nervous system from rhombomere 7 to the spinal cord, and in the pharyngeal region posterior from gill arch 2. Its expression then became restricted to cartilage precursor cells of gill arches 2-5. When embryos in the early shield stage were exposed to RA at concentrations above 10(-7) M, the anterior border of Hoxd-4 expression shifted anteriorly in a dose-dependent manner, both in the central nervous system and pharyngeal region. We propose that, during gill skeleton formation, Hoxd-4 functions in the specification of regional identity between gill arches 1 and 2, and that their identity is affected by treatment with RA.

During the development of pharyngeal cartilages, signal molecules, including sonic hedgehog (shh) and various growth factors, as well as Hox genes are expressed in the pharyngeal area. To elucidate whether shh and Hoxd-4 function in pharyngeal cartilage formation in teleost jaw and gill primordia, spatial and temporal patterns of shh expression in flounder (Paralichthys olivaceus) embryonic pharynx were examined. The effects of retinoic acid (RA) on shh and Hoxd-4 expression and the patterning of pharyngeal cartilages were analyzed. At the prim-5 stage, when cartilage precursor cells aggregate in the pharyngeal primordia, pharyngeal endoderm expressed shh in two domains, in portions of the mandibular and hyoid primordia and in the gill primordia. After a further 40 h, shh domains expanded at the posterior edge of the endoderm of each mandibular, hyoid and gill primordium, concurrent with the growth of the primordia. A new shh expression domain appeared at the endodermal border of the mouth. Retinoic acid treatment depressed shh and Hoxd-4 expression, and also reduced the amount of expansion of the shh expression domains. Pharyngeal cartilages that formed in these embryos were malformed; their growth direction was shifted posteriorly and size was reduced. This provides the possibility that shh and Hoxd-4 regulate the growth and direction of pharyngeal cartilage precursor cells and that RA disturbs their expression, causing skeletal malformation.

We used mitochondrial DNA sequences to determine the phylogenetic placement of southern smelts (Retropinnidae), a group of diadromous fishes endemic to New Zealand and Australia. Our genetic data strongly support a sister group relationship between retropinnids and northern hemisphere smelts (Osmeridae), a relationship that seems consistent with the similar appearance and life history strategies of these two groups. Our analysis indicates that Retropinnidae and Osmeridae together represent the sister group to the southern hemisphere galaxiid fishes (Galaxiidae). However, this finding conflicts with several recent osteological analyses, which supported a sister relationship for Retropinnidae and Galaxiidae, giving a monophyletic southern hemisphere assemblage (Galaxioidea). We review cases of incongruence and discuss factors that might explain significant disagreement between molecular and morphological data matrices. We suggest that repeated evolutionary simplification may have undermined the accuracy of morphological hypotheses of osmeroid relationships. Although equally weighted parsimony analysis of morphological data rejects the molecular hypothesis (Osmeridae + Retropinnidae), implementation of a range of weighting schemes suggests that incongruence is nonsignificant under asymmetric character transformation models. We propose that a simple "equal transformation cost" parsimony analysis may be biologically unrealistic, especially when reductive homoplasy is widespread; as is increasingly being accepted, complex character states are more readily lost than gained. Therefore, we recommend that morphological systematists routinely implement a range of character transformation models to assess the sensitivity of their phylogenetic reconstructions. We discuss the antitropical biogeography of osmeroid fishes in the context of vicariance and transequatorial dispersal.