The University of Tokyo · Biochemistry, Genetics and Molecular Biology
Professor Shotaro Hirase's research lab specializes in evolutionary genomics and phylogeography, focusing on marine vertebrates and invertebrates to unravel the mechanisms of speciation, gene flow, and adaptive evolution. The lab employs population genomic approaches, including whole-genome and mitochondrial DNA analyses, to investigate evolutionary processes in marine organisms such as abalones and gobies, particularly in the context of historical biogeography and ecological speciation. A central theme is understanding how genetic diversity and introgression—especially from extinct or unsampled lineages—shape current biodiversity in the Northwest Pacific. The lab also explores the role of structural variants, such as GCNVs, in adaptive evolution.
Figures are computed from collected data and may differ slightly.
How early stages of speciation in free-spawning marine invertebrates proceed is poorly understood. The Western Pacific abalones, Haliotis discus, H. madaka, and H. gigantea, occur in sympatry with shared breeding season and are capable of producing viable F1 hybrids in spite of being ecologically differentiated. Population genomic analyses revealed that although the three species are genetically distinct, there is evidence for historical and ongoing gene flow among these species. Evidence from d
Reliably rooted phylogenetic trees play irreplaceable roles in clarifying diversification in the patterns of species and populations. However, such trees are often unavailable in phylogeographic studies, particularly when the focus is on rapidly expanded populations that exhibit star-like trees. A fundamental bottleneck is known as the random rooting effect, where a distant outgroup tends to root an unrooted tree "randomly." We investigated whether parallel mitochondrial genome (mitogenome) sequ
We examined the phylogeography of the common Japanese intertidal goby Chaenogobius annularis using the mitochondrial cytochrome b gene, the NADH dehydrogenase subunit 2 gene, and the surrounding transfer RNA from 195 specimens collected in 27 localities around the Japanese Archipelago and the Korean Peninsula, and reconstructed the historical processes of its current distribution. In total, 169 unique haplotypes were obtained, and phylogenetic trees showed 2 genetically distinct lineages: the Pa
The identification of GCNVs that were likely under parallel selection suggests that contribution of GCNVs should be considered in studies on adaptive evolution.
Abstract Elucidating the scale of gene flow among populations is an important challenge for understanding the ecological dynamics and local adaptation of marine organisms. We assessed whether gene flow is restricted even at a small spatial scale in the Japanese common intertidal goby Chaenogobius annularis , using highly polymorphic DNA markers, involving the mitochondrial DNA (mtDNA) control region and 15 microsatellite DNA (msDNA), because past ecological studies have suggested low dispersal a
Extinct lineages can leave legacies in the genomes of extant lineages through ancient introgressive hybridization. The patterns of genomic survival of these extinct lineages provide insight into the role of extinct lineages in current biodiversity. However, our understanding on the genomic landscape of introgression from extinct lineages remains limited due to challenges associated with locating the traces of unsampled 'ghost' extinct lineages without ancient genomes. Herein, we conducted popula
Hybridization between divergent lineages generates new allelic combinations. One mechanism that can hinder the formation of hybrid populations is mitonuclear incompatibility, that is, dysfunctional interactions between proteins encoded in the nuclear and mitochondrial genomes (mitogenomes) of diverged lineages. Theoretically, selective pressure due to mitonuclear incompatibility can affect genotypes in a hybrid population in which nuclear genomes and mitogenomes from divergent lineages admix. To
MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 499:217-231 (2014) - DOI: https://doi.org/10.3354/meps10641 Long-term vicariance and post-glacial expansion in the Japanese rocky intertidal goby Chaenogobius annularis Shotaro Hirase1,2,*, Minoru Ikeda1 1Integrative Aquatic Biology, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsum
The genetic basis of speciation in free-spawning marine invertebrates is poorly understood. Although gene copy number variations (GCNVs) and nucleotide variations possibly trigger the speciation of these organisms, empirical evidence for such a hypothesis is limited. In this study, we searched for genomic signatures of GCNVs that may contribute to the speciation of Western Pacific abalone species. Whole-genome sequencing data suggested the existence of significant amounts of GCNVs in closely rel
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