Takushi Kishida

Having transitioned from a terrestrial lifestyle to an aquatic one over evolutionary time, cetaceans are prime subjects for the study of reduced olfaction. Here, we investigated the size of the cribriform plate in extant Artiodactyla and fossil whales. We also investigated the number of olfactory receptor (OR) genes encoded in artiodactyl genomes and found that the size of the cribriform plate is positively correlated with the number of OR genes among extant species. We extended this finding to fossil whales and estimated that a loss of genes occurred during the early/middle Eocene, before cetaceans became obligately aquatic. Extant toothed whales have reduced olfaction, but two Miocene toothed whales are predicted to have as many or more OR genes than extant baleen whales. Therefore, some fossil toothed whales might have had some olfaction. For their body size, extant baleen whales have cribriform plates that are similar in size to that of the dromedary camel, which is consistent with the growing evidence that baleen whales have retained some olfaction. As the first quantitative, morphological analysis of cetacean olfaction across the land-to-water transition, our study facilitates further study of olfactory neuroanatomy and the link between olfactory phenotype and genotype.

Flowering cherries (genus Cerasus) are iconic trees in Japan, celebrated for their cultural and ecological significance. Despite their prominence, high-quality genomic resources for wild Cerasus species have been limited. Here, we report chromosome-level genome assemblies of two representative Japanese cherries: Cerasus itosakura, a progenitor of the widely cultivated C. ×yedoensis “Somei-yoshino,” and Cerasus jamasakura, a traditional popular wild species endemic to Japan. Using deep PacBio long-read and Illumina short-read sequencing, combined with reference-guided scaffolding based on near-complete C. speciosa genome, we generated assemblies of 259.1 Mbp (C. itosakura) and 312.6 Mbp (C. jamasakura), with both >98% BUSCO completeness. Consistent with their natural histories, C. itosakura showed low heterozygosity, while C. jamasakura displayed high genomic diversity. Comparative genomic analyses revealed structural variations, including large chromosomal inversions. Notably, the availability of both the previously published C. speciosa genome and our new C. itosakura genome enabled the reconstruction of proxy haplotypes for both parental lineages of “Somei-yoshino.” Comparison with the phased genome of “Somei-yoshino” revealed genomic discrepancies, suggesting that the cultivar may have arisen from genetically distinct or admixed individuals, and may also reflect intraspecific diversity. Our results offer genomic foundations for evolutionary and breeding studies in Cerasus and Prunus.

The barnacle genus Platylepas contains obligate epibionts of marine vertebrates, but the taxonomic status and evolutionary history of the sea-snake specialist, P. ophiophila , have remained unclear. Here, we reassess species boundaries and host associations in Platylepas using shell-morphological comparisons and sequence data from mitochondrial COI and nuclear H3 genes from specimens collected from sea turtles, sea snakes, and a dugong. Our results show that P. ophiophila is a valid species, phylogenetically and morphologically distinct from the widespread turtle barnacles P. decorata and P. hexastylos . Furthermore, we report the first record of P. ophiophila from a sirenian host ( Dugong dugon ), a discovery that necessitates the re-examination of historical records of barnacles on sirenians worldwide. Our phylogeny places P. decorata , a turtle epibiont, as the earliest diverging lineage within the genus. This is consistent with the hypothesis that the ancestor of Platylepas was associated with sea turtles, a conclusion supported by the ichnofossil record. The subsequent divergence of the P. ophiophila clade may represent an important host-use transition: an ancient host shift from sea turtles to the taxonomically disparate but ecologically linked inhabitants—sea snakes and sirenians—of seagrass ecosystems. This study clarifies species limits within Platylepas and provides a framework for discussing host associations and potential host shifts in light of existing molecular and fossil evidence.

Flowering cherries (genus Cerasus ) are iconic trees in Japan, celebrated for their cultural and ecological significance. Despite their prominence, high-quality genomic resources for wild Cerasus species have been limited. Here, we report chromosome-level genome assemblies of two representative Japanese cherries: Cerasus itosakura , a progenitor of the widely cultivated C. × yedoensis ‘Somei-yoshino’, and Cerasus jamasakura , a traditional popular wild species endemic to Japan. Using deep PacBio long-read and Illumina short-read sequencing, combined with reference-guided scaffolding based on near-complete C. speciosa genome, we generated assemblies of 259.1 Mbp ( C. itosakura ) and 312.6 Mbp ( C. jamasakura ), with both >98% BUSCO completeness. Consistent with their natural histories, C. itosakura showed low heterozygosity, while C. jamasakura displayed high genomic diversity. Comparative genomic analyses revealed structural variations, including large chromosomal inversions. Notably, the availability of both the previously published C. speciosa genome and our new C. itosakura genome enabled the reconstruction of proxy haplotypes for both parental lineages of ‘Somei-yoshino’. Comparison with the phased genome of ‘Somei-yoshino’ revealed genomic discrepancies, suggesting that the cultivar may have arisen from genetically distinct or admixed individuals, and may also reflect intraspecific diversity. Our results offer genomic foundations for evolutionary and breeding studies in Cerasus and Prunus .

The Tsushima leopard cat (Prionailurus bengalensis euptilurus), an endangered feline endemic to Tsushima Island, Japan, faces critical threats due to its small and isolated population. Understanding its demographic history and genetic differentiation from continental populations is essential for conservation planning. In this study, we performed whole-genome sequencing of four Tsushima individuals and applied demographic inference methods, including pairwise sequentially Markovian coalescent (PSMC) and Sequentially Markovian Coalescent (SMC++), to reconstruct the historical effective population size (Ne) and estimate divergence times. PSMC revealed a population expansion between 200,000 and 100,000 years ago, followed by a long-term decline. SMC++ inferred a continuous decline and estimated that the divergence from the Korean leopard cat population occurred approximately 30,000–20,000 years ago. Genetic diversity analysis showed that the Tsushima population has significantly lower heterozygosity and higher inbreeding levels than continental populations. Genetic clustering based on genome-wide SNPs indicated that the Tsushima population is genetically closest to the Korean population, forming a northern cluster distinct from southern populations, such as Borneo and the Malay Peninsula. These findings provide valuable insights into the evolutionary history and genetic status of the Tsushima leopard cat and contribute critical data for the design of future conservation strategies targeting this unique insular lineage.

Understanding the mechanisms of speciation in the open ocean, where few obvious geographic barriers exist, is an important question in ecology. Marine amniotes are an ideal model for studying speciation in the ocean because monophyly is ensured in many groups with evident time points when they have begun their life in the sea. Among such marine amniotes, sea snakes of the genus Hydrophis exhibit an extremely high species diversity. Here, we performed genome‐wide analyses of 16 Hydrophis individuals belonging to 14 species to understand how Hydrophis sea snakes have diversified and speciated. Demographic data suggest that most Hydrophis sea snakes speciated almost simultaneously around 1 million years ago, and little inter‐species admixture after speciation is inferred except for a group of genetically closely related species. Strict reproductive isolation is observed even between geographically distant conspecific local populations. The high species diversity of Hydrophis sea snakes may be owing mainly to such recent rapid speciation events and strict reproductive isolation.

The genus Andrias includes the largest extant salamanders, and is comprised of one Japanese species A. japonicus and four Chinese species. The fossil record of the giant salamander is incomplete and modern giant salamanders are not differentiated osteologically among species, making it difficult to identify bones at the species level. In this study, we re-examined a fossil series of giant salamander discovered from a cave on Shikoku Island, Japan. We obtained ancient DNA from the fossil and confirmed that the partial sequence of mitochondrial DNA was identical to that of extant A. japonicus. These remains were dated to the Late Pleistocene, however, the result of carbon-14 dating in this study estimated the age as more recent, approximately 3,500–4,100 years ago. Currently, there is a small population of A. japonicus in Shikoku, but it is far removed from the fossil discovery area. Our findings suggest that wild A. japonicus in western Shikoku may have been extirpated very recently.

The Oshima cherry (Cerasus speciosa), which is endemic to Japan, has significant cultural and horticultural value. In this study, we present a near complete telomere-to-telomere genome assembly for C. speciosa, derived from the old growth “Sakurakkabu” tree on Izu Oshima Island. Using Illumina short-read, PacBio long-read, and Hi-C sequencing, we constructed a 269.3 Mbp genome assembly with a contig N50 of 32.0 Mbp. We examined the distribution of repetitive sequences in the assembled genome and identified regions that appeared to be centromeric. Detailed structural analysis of these putative centromeric regions revealed that the centromeric regions of C. speciosa comprised repetitive sequences with monomer lengths of 166 or 167 bp. Comparative genomic analysis with Prunus sensu lato genome revealed structural variations and conserved syntenic regions. This high-quality reference genome provides a crucial tool for studying the genetic diversity and evolutionary history of Cerasus species, facilitating advancements in horticultural research and the preservation of this iconic species.

Despite numerous studies on the rise and fall of terrestrial megafauna in the late Quaternary, knowledge about marine megafauna from this period remains limited. In this study, we performed radiocarbon dating and partial mitochondrial DNA sequencing from the skeletal remains of three species of small odontocetes (Pacific white-sided dolphins, Dall’s porpoises and harbour porpoises) excavated from prehistoric archaeological sites around the Japanese shore dating back to 8500–1000 years ago (ya). Pacific white-sided dolphins that habituated the eastern coast of Hokkaido around 2000 ya belonged to different maternal groups than those from over 5000 ya and today. Furthermore, the species composition excavated from eastern Hokkaido sites varies between 5000 and 2000 ya. These findings suggest two significant population turnovers of small odontocetes on the east coast of Hokkaido, a transitional zone between the coastal area of East Asia and the offshore North Pacific. Notably, the first turnover, occurring between 5000 and 2000 ya, represents the oldest evidence of local population turnovers of marine megafauna during the late Quaternary.