Toba, Japan
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Yoshida M.A.,Japan Society for the Promotion of Science | Yoshida M.A.,National Institute of Genetics | Yoshida M.A.,University of Florida | Ogura A.,Nagahama Institute of Bio-Science and Technology | And 6 more authors.
Integrative and Comparative Biology | Year: 2015

Coleoid cephalopods show remarkable evolutionary convergence with vertebrates in their neural organization, including (1) eyes and visual system with optic lobes, (2) specialized parts of the brain controlling learning and memory, such as vertical lobes, and (3) unique vasculature supporting such complexity of the central nervous system. We performed deep sequencing of eye transcriptomes of pygmy squids (Idiosepius paradoxus) and chambered nautiluses (Nautilus pompilius) to decipher the molecular basis of convergent evolution in cephalopods. RNA-seq was complemented by in situ hybridization to localize the expression of selected genes. We found three types of genomic innovations in the evolution of complex brains: (1) recruitment of novel genes into morphogenetic pathways, (2) recombination of various coding and regulatory regions of different genes, often called "evolutionary tinkering" or "co-option", and (3) duplication and divergence of genes. Massive recruitment of novel genes occurred in the evolution of the "camera" eye from nautilus' "pinhole" eye. We also showed that the type-2 co-option of transcription factors played important roles in the evolution of the lens and visual neurons. In summary, the cephalopod convergent morphological evolution of the camera eyes was driven by a mosaic of all types of gene recruitments. In addition, our analysis revealed unexpected variations of squids' opsins, retinochromes, and arrestins, providing more detailed information, valuable for further research on intra-ocular and extra-ocular photoreception of the cephalopods. © 2015 The Author.


PubMed | Toba Aquarium, University of Florida, Japan Agency for Marine - Earth Science and Technology, National Institute of Genetics and Nagahama Institute of Bio-Science and Technology
Type: Journal Article | Journal: Integrative and comparative biology | Year: 2015

Coleoid cephalopods show remarkable evolutionary convergence with vertebrates in their neural organization, including (1) eyes and visual system with optic lobes, (2) specialized parts of the brain controlling learning and memory, such as vertical lobes, and (3) unique vasculature supporting such complexity of the central nervous system. We performed deep sequencing of eye transcriptomes of pygmy squids (Idiosepius paradoxus) and chambered nautiluses (Nautilus pompilius) to decipher the molecular basis of convergent evolution in cephalopods. RNA-seq was complemented by in situ hybridization to localize the expression of selected genes. We found three types of genomic innovations in the evolution of complex brains: (1) recruitment of novel genes into morphogenetic pathways, (2) recombination of various coding and regulatory regions of different genes, often called evolutionary tinkering or co-option, and (3) duplication and divergence of genes. Massive recruitment of novel genes occurred in the evolution of the camera eye from nautilus pinhole eye. We also showed that the type-2 co-option of transcription factors played important roles in the evolution of the lens and visual neurons. In summary, the cephalopod convergent morphological evolution of the camera eyes was driven by a mosaic of all types of gene recruitments. In addition, our analysis revealed unexpected variations of squids opsins, retinochromes, and arrestins, providing more detailed information, valuable for further research on intra-ocular and extra-ocular photoreception of the cephalopods.


Tandavanitj N.,University of Ryukyus | Tandavanitj N.,Chulalongkorn University | Mitani S.,Toba Aquarium | Toda M.,University of Ryukyus
Current Herpetology | Year: 2013

The two laticaudine sea kraits, Laticauda laticaudata and L. semifasciata, are distributed in the tropical waters of the western Pacific and the northernmost limit of their breeding populations is considered to be the Northern Ryukyus, Japan. These two species, however, have been occasionally reported from the main islands of Japan, which are located further north. To determine the origins of such individuals, we examined partial sequences of the mitochondrial cytochrome b gene of one specimen of L. laticaudata from Yamaguchi and two specimens of L. semifasciata from Oita and Mie. Comparisons of the sequences with published data for apparently stable populations in the Ryukyu-Taiwan region revealed that sequence of the Yamaguchi specimen was identical with a haplotype previously detected from a broad range of the Ryukyu-Taiwan region and we could not specify its origin. Sequences of the Mie and Oita specimens were identical with, or very close to, haplotypes detected only from the Central Ryukyus and the Southern Ryukyus-Taiwan region, respectively. These results indicate that they were drifters from the Central Ryukyus and further south, corroborating the unconfirmed belief that sea kraits found on the main islands were accidentally transported by the Kuroshio Current from the south. Considering that both species exhibit certain degree of genetic differentiation among island groups in the Ryukyu-Taiwan region, the putative transportations by the Kuroshio seldom contribute to effective gene flow among local populations. The Kuroshio probably poses threats to their survival as the current may carry individuals out of their habitats and distributional range. © 2013 by The Herpetological Society of Japan.


Yoshida M.-A.,Ochanomizu University | Ishikura Y.,Kyoto University | Moritaki T.,Toba Aquarium | Shoguchi E.,Okinawa Institute of Science and Technology | And 4 more authors.
Gene | Year: 2011

Comparative genome structure analysis allows us to identify novel genes, repetitive sequences and gene duplications. To explore lineage-specific genomic changes of the molluscs that is good model for development of nervous system in invertebrate, we conducted comparative genome structure analyses of three molluscs, pygmy squid, nautilus and scallops using partial genome shotgun sequencing. Most effective elements on the genome structural changes are repetitive elements (REs) causing expansion of genome size and whole genome duplication producing large amount of novel functional genes. Therefore, we investigated variation and proportion of REs and whole genome duplication. We, first, identified variations of REs in the three molluscan genomes by homology-based and de novo RE detection. Proportion of REs were 9.2%, 4.0%, and 3.8% in the pygmy squid, nautilus and scallop, respectively. We, then, estimated genome size of the species as 2.1, 4.2 and 1.8. Gb, respectively, with 2× coverage frequency and DNA sequencing theory. We also performed a gene duplication assay based on coding genes, and found that large-scale duplication events occurred after divergence from the limpet Lottia, an out-group of the three molluscan species. Comparison of all the results suggested that RE expansion did not relate to the increase in genome size of nautilus. Despite close relationships to nautilus, the squid has the largest portion of REs and smaller genome size than nautilus. We also identified lineage-specific RE and gene-family expansions, possibly relate to acquisition of the most complicated eye and brain systems in the three species. © 2011 Elsevier B.V.


Yoshida Y.M.,Kyoto University | Morisaka T.,Kyoto University | Morisaka T.,Tokai University | Sakai M.,Tokai University | And 8 more authors.
Behavioural Processes | Year: 2014

Commerson's dolphin (. Cephalorhynchus commersonii), one of the smallest dolphin species, has been reported to produce only narrow-band high-frequency (NBHF) clicks and no whistles. To clarify their sound repertoire and examine the function of each type, we analysed the sounds and behaviour of captive Commerson's dolphins in Toba Aquarium, Japan. All recorded sounds were NBHF clicks with peak frequency >110. kHz. The recorded click-trains were categorised into four types based on the changing pattern of their Inter-click intervals (ICI): Decreasing type, with continuously decreasing ICI during the last part of the train; Increasing type, with continuously increasing ICI during the last part; Fluctuating type, with fluctuating ICI; and Burst-pulse type, with very short and constant ICI. The frequency of the Decreasing type increased when approaching an object newly introduced to the tank, suggesting that the sound is used for echolocation on approach. The Burst-pulse type suddenly increased in front of the object and was often oriented towards it, suggesting that it was used for echolocation in close proximity to the object. In contrast, the Increasing type was rarely recorded during approach, but increased when a dolphin approached another dolphin. The Increasing and Burst-pulse types also increased when dolphins began social behaviours. These results suggest that some NBHF clicks have functions other than echolocation, such as communication. © 2014 Elsevier B.V.


Sakai M.,Kyoto University | Sakai M.,Chiyoda Corporation | Morisaka T.,Kyoto University | Iwasaki M.,Tokyo Institute of Technology | And 5 more authors.
Journal of Ethology | Year: 2013

Mother-calf interactions and the behaviors of mothers during separation from their calves were examined in four Commerson's dolphin (Cephalorhynchus commersonii) mother-calf pairs. Four infants were observed: 56.8 h over 30 days from birth to 263 days of age, 36.9 h over 20 days from birth to 149 days of age, 10.4 h over 3 days from birth to 2 days of age, and 15.0 h over 3 days from birth to 2 days of age. All four pairs shared common characteristics in the rate and frequencies of mother-calf interactions and the behaviors of mothers during the first week of life. After the first week, individual differences in changes in the frequency of each behavior were observed. The three behaviors considered representative of maternal care (parallel swimming, synchronous breathing, and body-to-body contact) were frequently performed in the first week; thereafter, the frequencies declined. Separate behaviors of mothers were infrequent during the first week and increased with an increase in infants' age. Bumping by infants increased with time, suggesting an increase in soliciting by calves and conflict between mothers and calves. The frequency of flipper-to-body rubbing also changed but in a complex manner, probably because the calves needed to learn how to perform this behavior from their mothers and because initiator and recipient of this behavior can be changed quickly. © 2013 Japan Ethological Society and Springer Japan.

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