Language：English   Publishing type：Research paper (scientific journal)  

PREMISE OF THE STUDY: Studies of natural genetic variation can elucidate the genetic basis of phenotypic variation and the past population structure of species. Our study species, Taxodium distichum, is a unique conifer that inhabits the ood plains and swamps of North America. Morphological and eco- logical di erences in two varieties, T. distichum var. distichum (bald cypress) and T. distichum var. imbricarium (pond cypress), are well known, but little is known about the level of genetic di erentiation between the varieties and the demographic history of local populations.
METHODS: We analyzed nucleotide polymorphisms at 47 nuclear loci from 96 individuals collected from the Mississippi River Alluvial Valley (MRAV), and Gulf Coastal populations in Texas, Louisiana, and Florida using high-throughput DNA sequencing. Standard population genetic statistics were calculated, and demographic parameters were estimated using a composite-likelihood approach.
KEY RESULTS: Taxodium distichum in North America can be divided into at least three genetic groups, bald cypress in the MRAV and Texas, bald cypress in Florida, and pond cypress in Florida. The levels of genetic di erentiation among the groups were low but signi cant. Several loci showed the signatures of positive selection, which might be responsible for local adaptation or varietal di erentiation.
CONCLUSIONS: Bald cypress was genetically di erentiated into two geographical groups, and the boundary was located between the MRAV and Florida. This di erentiation could be explained by population expansion from east to west. Despite the overlap of the two varieties’ ranges, they were genetically di erentiated in Florida. The estimated demographic parameters suggested that pond cypress split from bald cypress during the late Miocene.

DOI： 10.3732/ajb.1600046

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With the advance of sequencing technologies, large-scale data of expressed sequence tags and full-length cDNA sequences have been reported for several conifer species. Comparative analyses of evolutionary rates among diverse taxa provide insights into taxon-specific molecular evolutionary features and into the origin of variation in evolutionary rates within genomes and between species. Here, we estimated evolutionary rates in two conifer species, Taxodium distichum and Cryptomeria japonica, to illuminate the molecular evolutionary features of these species, using hundreds of genes and employing Chamaecyparis obtusa as an outgroup. Our results show that the mutation rates based on synonymous substitution rates (dS) of T. distichum and C. japonica are approximately 0.67×10-9 and 0.59×10-9/site/year, respectively, which are 15-25 times lower than those of annual angiosperms. We found a significant positive correlation between dS and GC3. This implies that a local mutation bias, such as context dependency of the mutation bias, exists within the genomes of T. distichum and C. japonica, and/or that selection acts on synonymous sites in these species. In addition, the means of the ratios of synonymous to nonsynonymous substitution rate in the two species are almost the same, suggesting that the average intensity of functional constraint is constant between the lineages. Finally, we tested the possibility of positive selection based on the site model, and detected one candidate gene for positive selection.

DOI： http://doi.org/10.1266/ggs.14-00079

Language：English   Publishing type：Research paper (scientific journal)  

We developed microsatellite markers for the fig-pollinating wasp Blastophaga nipponica Grandi using a dual-suppression-PCR technique. Twenty-one candidates of microsatellite loci were obtained, of which 15 yielded scorable patterns. The degree of polymorphism for the 15 loci was further characterized using summary statistics describing the genetic variation in 60 individuals from three natural populations in Japan. All 15 loci were polymorphic and yielded 2–27 alleles per locus. Overall observed heterozygosity (HO) and expected heterozygosity(HE) were 0.465 and 0.631, respectively. As expected,based on the inbreeding tendency of this species, the mean inbreeding coefficient (FIS) was high (= 0.255). These markers will contribute to studies on the population structure of this species.

DOI： 10.1007/s13355-014-0267-x

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Compensatory mutations are individually deleterious but appropriate combinations of mutants are harmless. For several models of compensatory molecular evolution, we consider the effects of back mutation. It is shown that the effects of back mutation on the rate of compensatory molecular evolution are weak. Further we estimate the values of selection parameter of deleterious single mutants for the models of compensatory molecular evolution both with and without back mutation using sequence data of folded RNA molecules and compare them with previous results.

DOI： 10.1016/j.jtbi.2013.01.011

Language：English   Publishing type：Research paper (scientific journal)  

Studies of genetic variation can elucidate the structure
of present and past populations aswell as the genetic basis
of the phenotypic variability of species. Taxodium distichum is
a coniferous tree dominant in lowland river flood plains and
swamps of the southeastern USA which exhibits morphological
variability and adaption to stressful habitats. This study
provides a survey of the Mississippi River Alluvial Valley
(MAV) and Florida to elucidate their population structure and
the extent of genetic differentiation between the two regions
and sympatric varieties, including bald cypress (var. distichum)
and pond cypress (var. imbricatum). We determined
the genotypes of 12 simple sequence repeat loci totaling 444
adult individuals from 18 natural populations. Bayesian clustering
analysis revealed high levels of differentiation between
the MAV and the Florida regions. Within the MAV region,
there was a significant correlation between genetic and geographical
distances. In addition, we found that there was
almost no genetic differentiation between the varieties. Most
genetic variation was found within individuals (76.73 %),
1.67 % among individuals within population, 15.36 % among
populations within the regions, and 9.23 % between regions
within the variety. Our results suggest that (1) the populations
of theMAVand the Florida regions are divided into two major
genetic groups, which might originate from different glacial
refugia, and (2) the patterns of genetic differentiation and
phenotypic differentiation were not parallel in this species.

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The Ogasawara Islands are oceanic islands and harbor a unique endemic flora. There are
three fig species (Ficus boninsimae, F. nishimurae and F. iidaiana) endemic to the Ogasawara Islands,
and these species have been considered to be closely related to Ficus erecta, and to have diverged
within the islands. However, this hypothesis remains uncertain. To investigate this issue, we assessed
the phylogenetic relationships of the Ogasawara figs and their close relatives occurring in Japan,
Taiwan and South China based on six plastid genome regions, nuclear ITS region and two nuclear
genes. The plastid genome-based tree indicated a close relationship between the Ogasawara figs and F.
erecta, whereas some of the nuclear gene-based trees suggested this relationship was not so close. In
addition, the phylogenetic analyses of the pollinating wasps associated with these fig species based on
the nuclear 28S rRNA and mitochondrial cytB genes suggested that the fig-pollinating wasps of F.
erecta are not sister to those of the Ogasawara figs. These results suggest the occurrence of an early
hybridization event(s) in the lineage leading to the Ogasawara figs.

DOI： http://dx.doi.org/10.1016/j.bbr.2011.03.031

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DOI： 10.3732/ajb.1000082

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DOI： 10.1093/molbev/msj097

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DOI： 10.1007/s00239-004-0086-8

Language：English   Publishing type：Research paper (scientific journal)  

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

Abstract

Background

This study explored chromosome number variation, phylogenetic divergence, and mechanisms underlying speciation in East Asian thistle Cirsium Mill. sect. Onotrophe (Cass.) DC. subsect. Nipponocirsium Kitam. (Compositae). The study focused on the newly identified species from Taiwan: Cirsium pengii Y.H. Tseng, P.C. Liao & Chih Y. Chang. Utilizing phylotranscriptomic data to reconstruct evolutionary relationships between the Taiwanese and Japanese taxa of Cirsium subsect. Nipponocirsium as well as their divergence times and chromosomal characteristics. Additionally, the chromosome number, morphology, and pollen morphology of the unknown Cirsium taxon are compared with other known subsect. Nipponocirsium taxa from Taiwan.

Results

Phylotranscriptomic analysis reveals a division within subsect. Nipponocirsium into Japanese and Taiwanese clades. In the Taiwanese clade, C. pengii is basal, while C. tatakaense remains monophyletic with other Taiwanese species despite higher genetic diversity. The prevalent chromosome number in this subsection is tetraploid (2n = 4x = 68), common in Japanese taxa, while Taiwanese members have 2n = 4x = 64. Notably, C. pengii has a diploid number (2n = 32), indicating descending dysploidy followed by polyploidization in Taiwan. This polyploidization, driven by glaciations, likely shaped the evolution of Nipponocirsium. Divergence time estimates suggest the separation of Japanese and Taiwanese clades around 0.74 million years ago (Myr) during glacial periods. Cirsium pengii diverged around 0.47 Myr, while tetraploid species C. kawakamii and C. tatakaense diverged around 0.35 Myr. These species likely evolved in separate refugia, with distinct species boundaries confirmed through species delimitation analysis, karyotype, morphology, and pollen morphology comparisons.

Conclusions

These findings enhance our understanding of chromosomal evolution and speciation within subsect. Nipponocirsium and underscore the importance of integrating transcriptomic data in phylogenetic studies. This study provides a comprehensive framework for further investigations into the genetic diversity and adaptive mechanisms of this ecologically vital group.

DOI： 10.1186/s40529-025-00454-2

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Other Link： https://link.springer.com/article/10.1186/s40529-025-00454-2/fulltext.html

Publishing type：Research paper (scientific journal)   Publisher：Wiley  

ABSTRACT

Because riverine fishes can disperse along linear river corridors and even between tributaries, allopatric divergence within river systems is limited to large rivers. Within small rivers, such as island rivers, allopatric divergence rarely occurs, and no cases of secondary contact have been reported to date.

Two congeneric riverine ricefishes, Oryzias dopingdopingensis and O. landangiensis, are found in the Doping‐doping and Cerekang Rivers, respectively, on Sulawesi Island, which are connected via estuarine waters. These two species are suggested to have diverged in allopatry within this single river system.

Phylogenetic and population genetic structure analyses using genome‐wide single nucleotide polymorphisms revealed that Oryzias individuals recently discovered from the downstream Cerekang River are phylogenetically distinct not only from O. dopingdopingensis in the Doping‐doping River but also from O. landangiensis in the upstream Cerekang River. Species tree analysis and demographic model inference revealed that the downstream Cerekang Oryzias diverged from upstream Cerekang Oryzias in allopatry approximately 57,000 generations ago, and they came into secondary contact with each other approximately 22,000 generations ago. Thereafter, the upstream Cerekang population split into two populations, O. landangiensis and O. dopingdopingensis, approximately 14,000 generations ago.

We are not aware of any freshwater fish groups that may have experienced both allopatric divergence and secondary contact within such a small single river system. The allopatric divergence and secondary contact within the Cerekang–Doping‐doping River system can be explained by assuming that a lake once existed in this region, where many tectonic lakes have formed and disappeared because of the collision and/or juxtaposition of tectonic subdivisions since the Pliocene/Pleistocene.

Gene flow from O. landangiensis to the downstream Cerekang Oryzias is also evident. Although the secondary contact between the upstream and downstream Cerekang populations was estimated to have occurred more than 40,000 years ago, they are still not completely homogenised within the linear corridor of the Cerekang River. This stagnation of homogenisation can be explained by their weak dispersal ability, which may reflect past adaptation to lacustrine environments.

DOI： 10.1111/fwb.70004

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Biology Letters  

Heteroplasmy, the presence of multiple mitochondrial DNA (mtDNA) haplotypes within cells of an individual, is caused by mutation or paternal leakage. However, heteroplasmy is usually resolved to homoplasmy within a few generations because of germ-line bottlenecks; therefore, instances of heteroplasmy are limited in nature. Here, we report heteroplasmy in the ricefish species Oryzias matanensis, endemic to Lake Matano, an ancient lake in Sulawesi Island, in which one individual was known to have many heterozygous sites in the mitochondrial NADH dehydrogenase subunit 2 (ND2) gene. In this study, we cloned the ND2 gene for some additional individuals with heterozygous sites and demonstrated that they are truly heteroplasmic. Phylogenetic analysis revealed that the extra haplotype within the heteroplasmic O. matanensis individuals clustered with haplotypes of O. marmoratus, a congeneric species inhabiting adjacent lakes. This indicated that the heteroplasmy originated from paternal leakage due to interspecific hybridization. The extra haplotype was unique and contained two non-synonymous substitutions. These findings demonstrate that this hybridization-driven heteroplasmy was maintained across generations for a long time to the extent that the extra mitochondria evolved within the new host.

DOI： 10.1098/rsbl.2023.0385

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Abstract

Because speciation might have been promoted by ancient introgression from an extinct lineage, it is important to detect the existence of ‘ghost introgression’ in focal taxa and examine its contribution to their diversification. In this study, we examined possible ghost introgression and its contributions to the diversification of ricefishes of the genus Adrianichthys in Lake Poso, an ancient lake on Sulawesi Island, in which some extinctions are known to have occurred. Population‐genomic analysis revealed that two extant Adrianichthys species, A. oophorus and A. poptae are reproductively isolated from each other. Comparisons of demographic models demonstrated that introgression from a ghost population, which diverged from the common ancestor of A. oophorus and A. poptae, is essential for reconstructing the demographic history of Adrianichthys. The best model estimated that the divergence of the ghost population greatly predated the divergence between A. oophorus and A. poptae, and that the ghost population secondarily contacted the two extant species within Lake Poso more recently. Genome scans and simulations detected a greatly divergent locus, which cannot be explained without ghost introgression. This locus was also completely segregated between A. oophorus and A. poptae. These findings suggest that variants that came from a ghost population have contributed to the divergence between A. oophorus and A. poptae, but the large time‐lag between their divergence and ghost introgression indicates that the contribution of introgression may be restricted.

DOI： 10.1111/jeb.14223

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier {BV}  

Repeated colonizations and resultant hybridization may increase lineage diversity on an island if introgression occurs only in a portion of the indigenous island lineage. Therefore, to precisely understand how island biodiversity was shaped, it is essential to reconstruct the history of secondary colonization and resultant hybridization both in time and space. In this study, we reconstructed the history of multiple colonizations of the Oryzias woworae species group, a freshwater fish group of the family Adrianichthyidae, from Sulawesi Island to its southeast satellite island, Muna Island. Phylogenetic and species tree analyses using genome-wide single-nucleotide polymorphisms revealed that all local populations on Muna Island were monophyletic, but that there were several genetically distinct lineages within the island. Population structure and phylogenetic network analyses demonstrated that colonization of this island occurred more than once, and that secondary colonization and resultant introgressive hybridization occurred only in one local population on the island. The spatially heterogeneous introgression induced by the multiple colonizations were also supported by differential admixture analyses. In addition, the differential admixture analyses detected reverse colonization from Muna Island to the Sulawesi mainland. Coalescence-based demographic inference estimated that these mutual colonizations occurred during the middle to late Quaternary period, during which sea level repeatedly declined; this indicates that the colonizations occurred via land bridges. We conclude that these mutual colonizations between Muna Island and the Sulawesi mainland, and the resultant spatially heterogeneous introgression shaped the current biodiversity of this species group in this area.

DOI： 10.1016/j.ympev.2023.107804

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Molecular Ecology  

In the family Fagaceae, fertilization is delayed by several weeks to 1 year after pollination, leading to 1- or 2-year fruiting species depending on whether fruiting occurs in the same or the next year after flowering. To investigate physiological responses underlying the regulation of delayed fertilization, we monitored seasonal changes in genome-wide gene expression in tissues including leaves and buds over 2 years under natural conditions in one- (Quercus glauca) and 2-year fruiting species (Lithocarpus edulis). Genes associated with metabolic changes in response to winter cold, photosynthesis and cell proliferation, which are essential for survival and growth, showed highly conserved seasonal expression profiles between species. However, seasonal expression profiles diverged between species in genes associated with pollination, an important process contributing to the origin and maintenance of the reproductive barrier between plant species. By comparing seasonal progression of ovule development and gene expression in pistillate flowers, we revealed that ovules started developing after winter in the 2-year fruiting species, which could be linked to the activation of genes involved in fertilization and female gametophyte development after winter. These findings suggest that the 2-year fruiting species may have evolved a requirement of winter cold to prevent fertilization before winter and facilitate fertilization and embryo development in the following spring when temperature rises. This study offers new possibilities to explore the evolution of reproductive strategies in Fagaceae.

DOI： 10.1111/mec.17079

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Molecular Phylogenetics and Evolution  

Sulawesi is a biodiversity hotspot for ricefishes (Adrianichthyidae), with many species endemic to the central part of this island in single ancient lakes or lake systems. Frequent vicariance by lake fragmentation since the Pliocene may be largely responsible for diversification in this family. In this study, we demonstrate that not only lacustrine species but also riverine species in this area are also deeply divergent even within a single river system. A mitochondrial phylogeny revealed that a ricefish population newly discovered from Cerekang River is sister to Oryzias dopingdopingensis Mandagi, Mokodongan, Tanaka, & Yamahira, another riverine species endemic to Doping-doping River. However, the Cerekang Oryzias was genetically isolated from O. dopingdopingensis, despite that Cerekang River and Doping-doping River share a connection across estuarine waters. This separation was supported by phylogenomic trees and population genetic structure analyses based on genome-wide single nucleotide polymorphisms. Coalescent-based demographic inference demonstrated that the ancestral population of these two riverine ricefishes had experienced a substantial population decrease and subsequently diverged into two sub-populations. Because the Cerekang Oryzias was also morphologically distinguished from O. dopingdopingensis, we described it as a new species, O. landangiensis. We infer that O. landangiensis and O. dopingdopingensis are of lake-origin and are relic species which were left in these rivers after the lake disappeared, and that they have lost their dispersal ability when inhabiting the ancient lake. The lost dispersal ability possibly contributed to the formation of the biodiversity hotspot for this fish group on this island.

DOI： 10.1016/j.ympev.2022.107519

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media {LLC}  

<jats:title>Abstract</jats:title><jats:p>The obligate pollination mutualism between figs (<jats:italic>Ficus</jats:italic>, Moraceae) and pollinator wasps (Agaonidae, Hymenoptera) is a classic example of cospeciation. However, examples of phylogenetic incongruencies between figs and their pollinators suggest that pollinators may speciate by host shifting. To investigate the mechanism of speciation by host shifting, we examined the phylogenetic relationships and population genetic structures of six closely related fig species and their pollinators from southern China and Taiwan-Ryukyu islands using various molecular markers. The results revealed 1) an extraordinary case of pollinator sharing, in which five distinct fig species share a single pollinator species in southern China; 2) two types of copollination, namely, sympatric copollination by pollinator duplication or pollinator migration, and allopatric copollination by host migration and new pollinator acquisition; 3) fig species from southern China have colonized Taiwan repeatedly and one of these events has been followed by host shifting, reestablishment of host specificity, and pollinator speciation, in order. Based on our results, we propose a model for pollinator speciation by host shifting in which the reestablishment of host-specificity plays a central role in the speciation process. These findings provide important insights into understanding the mechanisms underlying pollinator speciation and host specificity in obligate pollination mutualism.</jats:p>

DOI： 10.1038/s42003-022-03223-0

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER JAPAN KK  

Oryzias marmoratus and Oryzias profundicola in Lake Towuti in Sulawesi are considered to have experienced ancient admixture with a lineage phylogenetically close to the extant O. marmoratus in Lake Lantoa. However, the admixture may be ongoing because these lakes are currently connected to each other by rivers. In this study, we examined population genetic structures of O. marmoratus and O. profundicola in Lake Towuti and adjacent lakes. Mitochondrial and microsatellite analyses revealed that O. marmoratus and O. profundicola in Lake Towuti are generally clearly separated from O. marmoratus in Lake Lantoa. However, we found one O. marmoratus individual in Lake Towuti shared a mitochondrial haplotype and a large fraction of ancestry with the Lantoa O. marmoratus. The discovery of this Lantoa-type individual in Lake Towuti suggests that either dispersal of individuals from Lake Lantoa to Lake Towuti is ongoing, or that there is another unknown population within Lake Towuti that originated from ancient admixture.

DOI： 10.1007/s10228-021-00856-9

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An increasing volume of empirical studies demonstrated that hybridization between distant lineages may have promoted speciation in various taxa. However, the timing, extent and direction of introgressive hybridization remain unknown in many cases. Here, we report a possible case in which repeated hybridization promoted divergence of Oryzias ricefishes (Adrianichthyidae) on Sulawesi, an island of Wallacea. Four Oryzias species are endemic to the Malili Lake system in central Sulawesi, which is composed of five tectonic lakes; of these, one lake is inhabited by two species. Morphological and population genomic analyses of genome-wide single-nucleotide polymorphisms revealed that these two sympatric species are phylogenetically sister to but substantially reproductively isolated from each other. Analyses of admixture and comparison of demographic models revealed that the two sympatric species experienced several substantial introgressions from outgroup populations that probably occurred soon after they had secondary contact with each other in the lake. However, the ratio of migrants from the outgroups was estimated to be different between the two species, which is consistent with the hypothesis that these introgressions aided their divergence or prevented them from forming a hybrid swarm. Repeated lake fragmentations and fusions may have promoted diversification of this freshwater fish species complex that is endemic to this ancient lake system.

DOI： 10.1111/jeb.13932

Language：English   Publishing type：Research paper (scientific journal)  

Long-lived organisms are exposed to the risk of accumulating mutations due to DNA damage. Previous studies in animals have revealed the positive relationship between the copy number of DNA repair genes and longevity. However, the role of DNA repair in the lifespan of plants remains poorly understood. Using the recent accumulation of the complete genome sequences of diverse plant species, we performed systematic comparative analyses of the copy number variations of DNA repair genes in 61 plant species with different lifespans. Among 121 DNA repair gene families, PARP gene family was identified as a unique gene that exhibits significant expansion in trees compared to annual and perennial herbs. Among three paralogs of plant PARPs, PARP 1 showed a close association with growth rate. PARPs catalyze poly(ADP-ribosyl)ation and play pivotal roles in DNA repair and antipathogen defense. Our study suggests the conserved role of PARPs in longevity between plants and animals.

DOI： 10.1016/j.isci.2021.102779

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Sulawesi, an island located in a biogeographical transition zone between Indomalaya and Australasia, is famous for its high levels of endemism. Ricefishes (family Adrianichthyidae) are an example of taxa that have uniquely diversified on this island. It was demonstrated that habitat fragmentation due to the Pliocene juxtaposition among tectonic subdivisions of this island was the primary factor that promoted their divergence; however, it is also equally probable that habitat fusions and resultant admixtures between phylogenetically distant species may have frequently occurred. Previous studies revealed that some individuals of <italic>Oryzias sarasinorum</italic> endemic to a tectonic lake in central Sulawesi have mitochondrial haplotypes that are similar to the haplotypes of <italic>O</italic>. <italic>eversi</italic>, which is a phylogenetically related but geologically distant (ca. 190 km apart) adrianichthyid endemic to a small fountain. In this study, we tested if this reflects ancient admixture of <italic>O</italic>. <italic>eversi</italic> and <italic>O</italic>. <italic>sarasinorum</italic>. Population genomic analyses of genome-wide single-nucleotide polymorphisms revealed that <italic>O</italic>. <italic>eversi</italic> and <italic>O</italic>. <italic>sarasinorum</italic> are substantially reproductively isolated from each other. Comparison of demographic models revealed that the models assuming ancient admixture from <italic>O</italic>. <italic>eversi</italic> to <italic>O</italic>. <italic>sarasinorum</italic> was more supported than the models assuming no admixture; this supported the idea that the <italic>O</italic>. <italic>eversi</italic>-like mitochondrial haplotype in <italic>O</italic>. <italic>sarasinorum</italic> was introgressed from <italic>O</italic>. <italic>eversi</italic>. This study is the first to demonstrate ancient admixture of lacustrine or pond organisms in Sulawesi beyond 100 km. The complex geological history of this island enabled such island-wide admixture of lacustrine organisms, which usually experience limited migration.

DOI： 10.1371/journal.pone.0245316

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It is vital to measure the levels of genetic diversity and differentiation between populations in a species to understand the current genetic structure and evolution of the species. Here, MIG-seq (multiplexed inter-simple sequence repeat genotyping by sequencing) was employed to assess the genetic variation in two tropical leguminous tree species, Dalbergia cochinchinensis and D. nigrescens, in Cambodia and Thailand. Sequence data for 255-618 loci, each with an approximate length of 100 bp, were obtained, and the nucleotide diversity, Tajima's D and FST were computed. The estimates calculated from the data obtained by MIG-seq were compared to those obtained by Sanger sequencing of nine nuclear coding genes in D. cochinchinensis in our previous study. The nucleotide diversity at the MIG-seq loci was slightly higher than that at silent sites in the coding loci, whereas the FST values at the MIG-seq loci were generally lower than those at the coding loci, although the differences were not significant. Moreover, nucleotide diversities within populations of the two species were similar to each other, at approximately 0.005. Three and four population clusters were genetically recognized in D. cochinchinensis and D. nigrescens, respectively. Although the populations were differentiated from each other, the levels of differentiation among them, as measured by FST, were higher in D. cochinchinensis than in D. nigrescens. This indicates higher levels of gene flow between the populations in the latter species. We recommend using MIG-seq for quick surveys of genetic variation because it is cost-effective and results in smaller variance in the estimates of population genetic parameters.

DOI： 10.1266/ggs.20-00026

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Sleep behaviors are observed even in nematodes and arthropods, yet little is known about how sleep-regulatory mechanisms have emerged during evolution. Here, we report a sleep-like state in the cnidarian Hydra vulgaris with a primitive nervous organization. Hydra sleep was shaped by homeostasis and necessary for cell proliferation, but it lacked free-running circadian rhythms. Instead, we detected 4-hour rhythms that might be generated by ultradian oscillators underlying Hydra sleep. Microarray analysis in sleep-deprived Hydra revealed sleep-dependent expression of 212 genes, including cGMP-dependent protein kinase 1 (PRKG1) and ornithine aminotransferase. Sleep-promoting effects of melatonin, GABA, and PRKG1 were conserved in Hydra However, arousing dopamine unexpectedly induced Hydra sleep. Opposing effects of ornithine metabolism on sleep were also evident between Hydra and Drosophila, suggesting the evolutionary switch of their sleep-regulatory functions. Thus, sleep-relevant physiology and sleep-regulatory components may have already been acquired at molecular levels in a brain-less metazoan phylum and reprogrammed accordingly.

DOI： 10.1126/sciadv.abb9415

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Although the genetic structures of populations in several model organisms have been studied even at the genomic level, quite a few ecologically important or evolutionary interesting species, such as endemic species on oceanic islands, exist whose genetic variations have not yet been studied. Genetic studies of those species may add new insights to our knowledge of evolution, especially when accompanied with ecological and geological knowledge of the species. In this study, we analyzed the genetic variation of two related species of Hamamelidaceae, Distylium racemosum and Distylium lepidotum, living in different habitats and possessing distinctive morphological characteristics. Distylium racemosum is one of the dominant trees of broad-leaved evergreen forests in Japan, and D. lepidotum is a dominant shrub in dry scrub endemic to the Ogasawara Islands. We analyzed the nucleotide variation at 112 protein-coding loci in 95 samples for the two Distylium species and inferred population structure and demographic history on the basis of these data. Our results showed that the samples from two Distylium species were genetically clustered into the following three groups: D. racemosum, D. lepidotum in the Chichijima Island, and D. lepidotum in the Hahajima Island. Furthermore, D. racemosum appears to have diverged first approximately 10 million years ago (MYA), and, then, the split of two populations of D. lepidotum occurred around 1 MYA. Additionally, we detected a few candidate loci that may contribute to adaptation of the species or local populations by exploring the pattern of the variation within and between species using the F_ST-outlier approach.

DOI： 10.1007/s11295-019-1386-x

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Sympatric speciation has been demonstrated in few empirical case studies, despite intense searches, because of difficulties in testing the criteria for this mode of speciation. Here, we report a possible case of sympatric speciation in ricefishes of the genus Oryzias on Sulawesi, an island of Wallacea. Three species of Oryzias are known to be endemic to Lake Poso, an ancient tectonic lake in central Sulawesi. Phylogenetic analyses using RAD-seq-derived single nucleotide polymorphisms (SNPs) revealed that these species are monophyletic. We also found that the three species are morphologically distinguishable and clearly separated by population-structure analyses based on the SNPs, suggesting that they are reproductively isolated from each other. A mitochondrial DNA chronogram suggested that their speciation events occurred after formation of the tectonic lake, and existence of a historical allopatric phase was not supported by coalescent-based demographic inference. Demographic inference also suggested introgressive hybridization from an outgroup population. However, differential admixture among the sympatric species was not supported by any statistical tests. These results all concur with criteria necessary to demonstrate sympatric speciation. Ricefishes in this Wallacean lake provide a promising new model system for the study of sympatric speciation.

DOI： 10.1111/evo.13821

Language：English   Publishing type：Research paper (scientific journal)  

Some hydra strains belonging to the vulgaris group show a symbiotic relationship with green algae Chlorococcum sp. The symbiotic green algae can escape from the host polyps and can form swimming zoospores (which have two flagella) in culture solution. We observed that co-culture with the symbiotic polyps caused horizontal transmission of the symbionts into some non-symbiotic hydra strains that have no symbionts in nature and that belong not only to the vulgaris group but also to other hydra species groups. Although most of the horizontal transmission has ended in transient symbioses, a newly formed symbiosis between the symbiotic Chlorococcum sp. and strain 105 of Hydra vulgaris (Hydra magnipapillata) has been sustained for more than five years and has caused morphological and behavioral changes in the host polyps. We named this strain 105G. The asexual proliferation rate by budding increased under light conditions, although the feeding activity decreased and the polyp size was reduced in strain 105G. This new symbiosis between Chlorococcum sp. and strain 105G of H. vulgaris provides us with an intriguing research system for investigating the origin of symbiosis.

DOI： 10.1086/699705

Language：English   Publishing type：Research paper (scientific journal)  

It has long been assumed that members of the cynipid tribe Synergini (sensu stricto) are all inquilines, that is, gallers of galls: The larvae can modify the galls of other species but cannot initiate gall formation on their own. Surprisingly, Abe et al. recently showed that one member of the tribe, Synergus itoensis Abe, Ide et Wachi, is a true gall inducer: It produces small galls inside acorns without the help of other species. Here, we present a comprehensive phylogenetic analysis of the Synergini to determine whether S. itoensis acquired this ability recently or if it represents a survivor of ancient gall inducers from which inquiline Synergini evolved. We studied 71 species belonging to five genera, covering all the Palearctic inquiline genera associated with oaks and one outgroup, Rhoophilus loewi Mayr, which is an inquiline in Lepidoptera galls on Searsia (formerly Rhus) (Anacardiaceae). We obtained partial sequences of cytochrome c oxidase subunit I and 28S ribosomal RNA (1.1 kbp of data). The results show that S. itoensis is most closely related to two undescribed species, which have also been reared from acorns. Their life history is unknown but the molecular phylogenetic data and the similarity in gall and adult morphology suggest that they are also gall inducers. The three species are deeply nested within lineages known to be inquilines, strongly suggesting that they acquired the ability to induce galls recently. Based on the molecular phylogenetic data and morphological features, Synergus yukawai (Wachi, Ide et Abe) is transferred back to Saphonecrus (Saphonecrus yukawaicomb. rev.), where it was originally described.

DOI： 10.1093/aesa/sax065

Language：English   Publishing type：Research paper (scientific journal)  

Dark-operative protochlorophyllide oxidoreductase (DPOR) is a key enzyme to produce chlorophyll in the dark. Among photosynthetic eukaryotes, all three subunits chlL, chlN, and chlB are encoded by plastid genomes. In some gymnosperms, two codons of chlB mRNA are changed by RNA editing to codons encoding evolutionarily conserved amino acid residues. However, the effect of these substitutions on DPOR activity remains unknown. We first prepared cyanobacterial ChlB variants with amino acid substitution(s) to mimic ChlB translated from pre-edited mRNA. Their activities were evaluated by measuring chlorophyll content of dark-grown transformants of a chlB-lacking mutant of the cyanobacterium Leptolyngbya boryana that was complemented with pre-edited mimic chlB variants. The chlorophyll content of the transformant cells expressing the ChlB variant from the fully pre-edited mRNA was only one-fourth of the control cells. Co-purification experiments of ChlB with Strep-ChlN suggested that a stable complex with ChlN is greatly impaired in the substituted ChlB variant. We then confirmed that RNA editing efficiency was markedly greater in the dark than in the light in cotyledons of the black pine Pinus thunbergii. These results indicate that RNA editing on chlB mRNA is important to maintain appropriate DPOR activity in black pine chloroplasts.

DOI： 10.1038/s41598-017-02630-2

Language：English   Publishing type：Research paper (scientific journal)  

Rod cells of many nocturnal mammals have a "non-standard" nuclear architecture, which is called the inverted nuclear architecture. Heterochromatin localizes to the central region of the nucleus. This leads to an efficient light transmission to the outer segments of photoreceptors. Rod cells of diurnal mammals have the conventional nuclear architecture. Owl monkeys (genus Aotus) is the only taxon of simian primates that has a nocturnal or cathemeral lifestyle, and this adaptation is widely thought to be secondary. Their rod cells were shown to exhibit an intermediate chromatin distribution: a spherical heterochromatin block was found in the central region of the nucleus although it was less complete than that of typical nocturnal mammals. We recently demonstrated that the primary DNA component of this heterochromatin block was OwlRep, a megasatellite DNA consisting of 187-bp-long repeat units. However, the origin of OwlRep was not known. Here we show that OwlRep was derived from HSAT6, a simple repeat sequence found in the centromere regions of human chromosomes. HSAT6 occurs widely in primates, suggesting that it was already present in the last common ancestor of extant primates. Notably, Strepsirrhini and Tarsiformes apparently carry a single HSAT6 copy, while many species of Simiiformes contain multiple copies. Comparison of nucleotide sequences of these copies revealed the entire process of the OwlRep formation. HSAT6, with or without flanking sequences, was segmentally duplicated in New World monkeys. Then, in the owl monkey linage after its divergence from other New World monkeys, a copy of HSAT6 was tandemly amplified, eventually forming a megasatellite DNA.

DOI： 10.1093/gbe/evx281

Language：English   Publishing type：Research paper (scientific journal)  

The obligate mutualism of figs and fig-pollinating wasps has been one of the classic models used for testing theories of co-evolution and cospeciation due to the high species-specificity of these relationships. To investigate the species-specificity between figs and fig pollinators and to further understand the speciation process in obligate mutualisms, we examined the genetic differentiation and phylogenetic relationships of four closely related fig-pollinating wasp species (Blastophaga nipponica, Blastophaga taiwanensis, Blastophaga tannoensis and Blastophaga yeni) in Japan and Taiwan using genome-wide sequence data, including mitochondrial DNA sequences. In addition, population structure was analysed for the fig wasps and their host species using microsatellite data. The results suggest that the three Taiwanese fig wasp species are a single panmictic population that pollinates three dioecious fig species, which are sympatrically distributed, have large differences in morphology and ecology and are also genetically differentiated. Our results illustrate the first case of pollinator sharing by host shift in the subgenus Ficus. On the other hand, there are strict genetic codivergences between allopatric populations of the two host-pollinator pairs. The possible processes that produce these pollinator-sharing events are discussed based on the level and pattern of genetic differentiation in these figs and fig wasps.

DOI： 10.1111/mec.13876

Language：English   Publishing type：Research paper (scientific journal)  

Consider two sites under compensatory fitness interaction, such as a Watson-Crick base pair in an RNA helix or two interacting residues in a protein. A mutation at any one of these two sites may reduce the fitness of an individual. However, fitness may be restored by the occurrence of a second mutation at the other site. Kimura modeled this process using a two-locus haploid fitness scheme with two alleles at each locus. He predicted that compensatory evolution following this model is very rare unless selection against the deleterious single mutations is weak and linkage between the interacting sites is tight. Here we investigate the question whether the rate of compensatory evolution increases if we take the context of the two directly interacting sites into account. By "context", we mean the effect of neighboring sites in an RNA helix. Interaction between the focal pair of sites under consideration and the context may lead to so-called indirect compensation. Thus, extending Kimura's classical model of compensatory evolution, we study the effects of both direct and indirect compensation on the rate of compensatory evolution. It is shown that the effects of indirect compensation are very strong. We find that recombination does not slow down the rate of compensatory evolution as predicted by the classical model. Instead, compensatory substitutions may be relatively frequent, even if linkage between the focal interacting sites is loose, selection against deleterious mutations is strong, and mutation rate is low. We compare our theoretical results with data on RNA secondary structures from vertebrate introns. (C) 2015 Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.jtbi.2015.10.008

Language：English   Publishing type：Research paper (scientific journal)  

Pinus krempfii Lecomte is a morphologically and ecologically unique pine, endemic to Vietnam. It is regarded as vulnerable species with distribution limited to just two provinces: Khanh Hoa and Lam Dong. Although a few phylogenetic studies have included this species, almost nothing is known about its genetic features. In particular, there are no studies addressing the levels and patterns of genetic variation in natural populations of P. krempfii. In this study, we sampled 57 individuals from six natural populations of P. krempfii and analyzed their sequence variation in ten nuclear gene regions (approximately 9 kb) and 14 mitochondrial (mt) DNA regions (approximately 10 kb). We also analyzed variation at seven chloroplast (cp) microsatellite (SSR) loci. We found very low haplotype and nucleotide diversity at nuclear loci compared with other pine species. Furthermore, all investigated populations were monomorphic across all mitochondrial DNA (mtDNA) regions included in our study, which are polymorphic in other pine species. Population differentiation at nuclear loci was low (5.2%) but significant. However, structure analysis of nuclear loci did not detect genetically differentiated groups of populations. Approximate Bayesian computation (ABC) using nuclear sequence data and mismatch distribution analysis for cpSSR loci suggested recent expansion of the species. The implications of these findings for the management and conservation of P. krempfii genetic resources were discussed.

DOI： 10.1002/ece3.1091

Language：English  

The approximately 700 species of cichlids found in Lake Victoria in East Africa are thought to have evolved over a short period of time, and they represent one of the largest known examples of adaptive radiation. To understand the processes that are driving this spectacular radiation, we must determine the present genetic structure of these species and elucidate how this structure relates to the ecological conditions that caused their adaptation. We analyzed the genetic structure of two pelagic and seven littoral species sampled from the southeast area of Lake Victoria using sequences from the mtDNA control region and 12 microsatellite loci as markers. Using a Bayesian model-based clustering method to analyze the microsatellite data, we separated these nine species into four groups: one group composed of pelagic species and another three groups composed mainly of rocky-shore species. Furthermore, we found significant levels of genetic variation between species within each group at both marker loci using analysis of molecular variance (AMOVA), although the nine species often shared mtDNA haplotypes. We also found significant levels of genetic variation between populations within species. These results suggest that initial groupings, some of which appear to have been related to habitat differences, as well as divergence between species within groups took place among the cichlid species of Lake Victoria.

DOI： 10.1371/journal.pone.0074088

Language：English   Publishing type：Research paper (scientific journal)  

Premise of the Study: Studies of the geographic patterns of genetic variation can give important insights into the past population structure of species. Our study species, Taxodium distichum L. (bald-cypress), prefers riparian and wetland habitats and is widely distributed in southeastern North America and Mexico. We compared the genetic variation of T. distichum with that of its close relative, Cryptomeria japonica, which is endemic to Japan.
Methods: Nucleotide polymorphisms of T. distichum in the lower Mississippi River alluvial valley, USA, were examined at 10 nuclear loci.
Key Results: The average nucleotide diversity at silent sites, pi(sil), across the 10 loci in T. distichum was higher than that of C. japonica (pi(sil) = 0.00732 and 0.00322, respectively). In T. distichum, Tajima's D values were each negative at 9 out of 10 loci, which suggests a recent population expansion. Maximum-likelihood and Bayesian estimations of the exponential population growth rate (g) of T. distichum populations indicated that this species had expanded approximately at the rate of 1.7-1.0 x 10(-6) per year in the past.
Conclusions: Taxodium distichum had significantly higher nucleotide variation than C. japonica, and its patterns of polymorphism contrasted strikingly with those of the latter, which previously has been inferred to have experienced a reduction in population size.

DOI： 10.3732/ajb.1000082

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1007/s10038-007-0161-2

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.2307/2656874

Language：English  

Characterization of a nonsense mutation in FAD7, the gene which encodes ω-3 desaturase in Arabidopsis thaliana
The Arabidopsis fad7-1 mutant is deficient in the activity of plastid ω-3 desaturase as a direct consequence of being devoid of FAD7 mRNA. Comparison of the genomic sequence from the fad7-1 mutant line (JB101) with the wild-type sequence revealed that the only single-base pair transition occurred within the FAD7 gene-coding region. Transgenic study and northern analysis both indicated that the absence of FAD7 mRNA in the fad7-1 mutant was not caused by any disability regarding transcriptional regulation, but by the destabilization of the mRNA.

Event date： 2013.9

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：慶應義塾大学 日吉キャンパス   Country：Japan  

ヌマスギは北米南東部に広く分布する針葉樹で、二種類の変種bald cypressとpond cypressが存在する。本研究ではミシシッピ川沿岸部、フロリダ、テキサスの2変種を含む12集団96個体を用い、48核遺伝子座の配列を次世代シーケンサー（454 GS FLX）により決定した。quality controlの結果から、総read数の76.3&#37;のreadを用い、重複遺伝子と思われる遺伝子を除いた37遺伝子の解析を行った。その結果、平均π(total)の値は0.00427であった。固定指数（Fst）は、生育地域間で0.0391、変種間で0.0376であり共に分化の程度は低いことを示した。

Event date： 2013.3

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：岡山 岡山大学   Country：Japan  

裸子植物の芽生えは、葉緑体DNAにコードされる暗所作動型プロトクロロフィリド還元酵素（DPOR）の活性により暗所においてもクロロフィルを合成し、緑化することができる。いくつかの裸子植物ではDPORのサブユニットをコードする遺伝子の1つchlBにおいてRNA編集による転写後修飾を受けることが報告されている。RNA編集による塩基置換を介したChlBのアミノ酸置換は、DPORの機能発現に重要な意味をもつと推察されているが、その実験的根拠は得られていない。本研究では、明所もしくは暗所で生育したクロマツPinus thunbergiiの実生における、DPORの３つのサブユニット遺伝子chlL, chlN, chlBの発現量、chlBのmRNAにおけるRNA編集の効率の解析を行った。その結果、暗所においてDPOR遺伝子の発現量、およびchlBのRNA編集効率が明所に比べ有意に高いことが確認された。また、RNA編集前のアミノ酸配列をもつ変異ChlBはDPORの触媒コンポーネントNB蛋白質（ChlNとChlBのヘテロ4量体）を形成しないことが明らかとなった。この結果は、RNA編集によるアミノ酸置換はNB蛋白質の形成を介し、DPORの活性を制御していることを示唆している。クロマツの実生では環境の光条件に応答したchlBのRNA編集の効率変化によりDPOR活性を制御し緑化を調節していると考えられる。

Event date： 2012.9 - 2013.9

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：九州大学 百年講堂   Country：Japan  

SSRマーカーを用いた解析により、北米南東部に分布する針葉樹ヌマスギの２変種bald cypressとpond cypressの間の遺伝的分化の程度は低く、むしろ主要分布域であるミシシッピ川沿岸部とフロリダ地域の間に有意な分化が認められている。本研究では、両地域の２変種のサンプル（13集団、135個体）を用い、５核遺伝子座の配列を決定し解析した。その結果、AMT遺伝子座では変種間に高い固定指数（Fst）が検出された。AMTでのFst値が変種間の分化によるものかを検討するため中立モデルを使って検定したところ、観測値のＰ値は0.0495となり、AMT遺伝子が変種間分化に寄与している可能性が示唆された。

Event date： 2012.9

Language：Others   Presentation type：Oral presentation (general)  

Venue：九州大学   Country：Japan  

イチジク属植物とイチジクコバチ類の送粉共生系は種特異性が高く、相互に依存した繁殖システムを持つ。従って、それぞれの分散や地域集団間の遺伝子流動の程度は互いに影響しあうことが予想される。本研究では、日本と台湾のイヌビワ、イヌビワコバチを用い、SSR多型及びオルガネラゲノムの塩基配列多型解析を行い、両者の遺伝的集団構造を比較した。SSRの解析では、イヌビワとイヌビワコバチの集団構造がほぼ一致しており、両者の２集団間のFstの値に有意な正の相関があることが示された。一方、ミトコンドリア塩基配列多型から推定されたイヌビワコバチの遺伝的分化のパターンは、SSR多型の結果とは一部矛盾する結果が得られた。

Event date： 2011.3

Language：Others   Presentation type：Oral presentation (general)  

Country：Japan  

Event date： 2009.9

Language：Others   Presentation type：Oral presentation (general)  

Venue：信州大学・松本   Country：Japan  

Event date： 2025.3

Language：English   Presentation type：Oral presentation (general)  

Venue：札幌、札幌コンベンションセンター   Country：Japan  

Event date： 2024.12

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：福岡　伊都キャンパス   Country：Japan  

Event date： 2023.12

Language：Japanese  

Venue：オンライン開催   Country：Japan  

researchmap

Event date： 2023.12

Language：Japanese  

Venue：オンライン開催   Country：Japan  

researchmap

Event date： 2023.9

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：佐賀大学農学部   Country：Japan  

Event date： 2023.9

Language：English   Presentation type：Oral presentation (general)  

Venue：佐賀大学農学部   Country：Japan  

Event date： 2023.9

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：山形大学小白川キャンパス   Country：Japan  

Event date： 2022.9 - 2022.5

Language：Japanese   Presentation type：Symposium, workshop panel (public)  

Venue：オンライン   Country：Japan  

Event date： 2019.12

Language：Japanese  

Country：Japan  

Event date： 2019.11 - 2019.12

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：九州大学 伊都キャンパス   Country：Japan  

Event date： 2019.9

Language：English   Presentation type：Oral presentation (general)  

Venue：Evangelische Akademie Tutzing   Country：Germany  

Event date： 2019.3

Language：Japanese  

Venue：神戸   Country：Japan  

Event date： 2018.12

Language：Japanese  

Country：Japan  

Event date： 2018.9

Language：Japanese  

Venue：奈良先端科学技術大学院大学   Country：Japan  

Event date： 2018.9

Language：Japanese  

Venue：北海道大学   Country：Japan  

Event date： 2018.8

Language：Japanese  

Venue：東京大学駒場キャンパス   Country：Japan  

Event date： 2017.11

Language：Japanese  

Venue：ふじのくに地球環境史ミュージアム （静岡市）   Country：Japan  

従来、北部九州には日本本土に分布する日本亜種 D.t.pilifer(以下ホンド系統群)が分布 していると考えられてきたが、ミトコンドリア DNA の CO 領域の解析から北部九州の一部 地域に対馬、壱岐、五島列島のそれぞれに分布する対馬亜種 D.t.castanicolor、壱岐亜種 D. t. tatsutai、五島列島亜種 D. t. karasuyamai に相当する個体群(以下ツシマ系統群)の一 部が侵入している可能性があることが示唆された。後者の 3 亜種は互いに形態が似ており、 分類学的問題も指摘されている。こうした現状にあって本研究では、北部九州におけるこれ ら二系統群間の遺伝子浸透の有無およびツシマ系統群の侵入状況を明らかにすることを目 的とし、遺伝的集団構造の解析を行った。その結果北部九州のヒラタクワガタを対象にした ミトコンドリア DNA の COI 領域を用いた解析では、ツシマ系統群とホンド系統群に分か れることがわかり、先行研究の結果と一致した。また核遺伝子のマイクロサテライト多型を 用いた帰属性解析では対馬、壱岐・五島列島、北部九州、南部九州の大きく 4 つのグルー プに分けられる可能性があることが示され、北部九州にはツシマ系統群のうち、地理的に近 い壱岐・五島列島亜種の個体群の一部が分布していると考えられた。

Event date： 2017.9

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：岡山大学   Country：Japan  

東南アジアに生息するマルオカブトガニ(マルオ)とミナミカブトガニ(ミナミ)は、ほぼ同所的に生息し、類似した生息環境や生活環を持つ一方で、マルオはマングローブ林を産卵地として利用するなど種固有の生態的特徴を有する。これら2種について、6地域(マレー半島西岸・北、南スマトラ・西、東ジャワ・東カリマンタン)、計201個体を用い、mtDNA AT-rich領域および核ゲノムの非コード領域の塩基配列を決定した。その結果、マルオでは地域間に明瞭な遺伝的分化が示されたが、ミナミでは遺伝的分化は示されなかった。これら2種の集団構造の違いは、産卵地および分散能力の違いが強く影響している可能性が示唆された。

Event date： 2017.9

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：岡山大学   Country：Japan  

日本で普通に見られるHydra vulgarisというヒドラには、クロロコッカム属の緑藻と共生関係にある系統が存在し、ヒドラポリプ間で共生緑藻が水平伝播することが確認されている。水平伝播により共生関係を構築したヒドラは、体長が小さくなり、増殖率が大きくなる変化が起きる。
本研究では、水平伝播における共生メカニズムを調べるために、“105”系統の共生緑藻を持っていない野生状態のヒドラと、水平伝播によって新たに共生体を獲得した105系統のヒドラ（105G系統）のRNA-seqを用いて、発現変動遺伝子の検出を行った。その結果、オプシン関連の遺伝子に発現変動が見られた。

Event date： 2017.9

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：岡山大学   Country：Japan  

東南アジアの熱帯低地林に生育するマメ科樹木のDalbergia cochinchinensisとD. nigrescensの集団遺伝学的解析を行った。カンボジア及びタイの集団から合計97個体をサンプルし、MIG-seq法によりゲノム中の約800箇所の塩基配列を決定した。主成分分析の結果D. nigrescensのタイ集団はカンボジア集団から強く分化していること、カンボジア集団の集団内分化の程度はD. nigrescensよりD. cochinchinensisの方が高いことがわかった。なお塩基多様度は両種で同程度であったが、タンパク質翻訳領域10遺伝子座を用いた先行研究よりも高い値を示した。分布パターンの異なるこれら二種ではこのように遺伝的変異パターンが異なることを明らかにした。

Event date： 2015.12

Language：English   Presentation type：Oral presentation (general)  

Venue：San Francisco, California   Country：United States  

Finless porpoise, Neophocaena asiaeorientalis sunameri, is distributed from the Taiwan Strait to Japanese waters. It inhibits in shallow waters close to shore and has been under considerable human impacts through habitat destruction and/or bycatch, and recent decline of the population size was reported in Japanese waters. In parallel to measuring the levels of genetic diversity in neutral markers, we also investigated a functional genetic marker under selection, the major histocompatibility complex (MHC), to obtain the information of demographics and adaptation processes within/among populations in Japan. MHC plays a key role in the initiation of immune response, and it is one of the most important genetic systems for infectious disease resistance in vertebrates. The decline of population size will lead the loss of diversity of MHC genes, ultimately reducing the ability of immune function to suppress an infection. Therefore, the assessment of MHC genes is greatly important in conservation genetics. Here, we analyzed two loci of MHC genes, DRB locus for 102 individuals and DQB locus for 88 individuals from five populations in Japanese waters. We found that there were totally six alleles at MHC DRB locus of which frequencies differed among local populations. Eight alleles were found in DQB locus and one of them was reported from Chinese waters. DRB locus had lower heterozygosity (HO=0.11) compared to DQB locus (HO=0.68). The patterns of population differentiation of each MHC locus were not identical and were differed from one of the microsatellite loci, a neutral genetic marker. Both loci showed a sign of positive selection (dN/dS>1). These results suggest that regional adaptations on each MHC locus, which correspond to different selection pressures from different pathogens, occurred among Japanese populations.

Event date： 2015.9

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：東北大学川内北キャンパス（宮城県仙台市）   Country：Japan  

スギは日本列島に広く分布する針葉樹で、それぞれ日本海側と太平洋側に分布するウラスギ・オモテスギの2系統が存在する。これらは遺伝的に分化しており、系統内でも地理的な分化があることが示されている。本研究では、スギの2系統を含む4集団（鯵ヶ沢・美女平・下和田・屋久島）計96個体を用い、約140核遺伝子座の配列を次世代シーケンサーで決定した。このうち30遺伝子座は近縁種ヌマスギで既に多型解析が行われている。得られた60kbpの配列データから約2,000個の多型サイトを検出した。塩基多様度πtotalは全座位の平均で0.0036、集団分化の程度を表すFSTの平均は0.06であった。特に屋久島集団は他集団から分化している傾向にあった。

Event date： 2015.9

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：静岡県三島市   Country：Japan  

スギは日本列島に広く分布する針葉樹であり、日本海側と太平洋側に分布するウラスギ・オモテスギの2変種が存在する。先行研究によりこれらの変種内には地理的な分化があることが示されている。本研究では、スギの2変種を含む4集団（鯵ヶ沢・美女平・下和田・屋久島）計96個体を用い、約140核遺伝子座の配列をIllumina MiSeqを用いて決定した。得られた60kbpの配列データから約2,000個の多型サイトを検出した。主成分分析では第一主成分で屋久島集団が他集団から分離し、屋久島集団の強い分化を示唆する先行研究の結果と一致した。また第三主成分ではウラスギとオモテスギが分離し、変種間の遺伝的分化を確認した。

Event date： 2015.3

Language：Japanese  

Venue：鹿児島大学 郡元キャンパス   Country：Japan  

スナメリは沿岸性の小型鯨類であり、日本沿岸個体群に関しては分布の不連続性や頭骨形態の差異、さらにmtDNA CR領域、マイクロサテライト解析により5つの地域個体群(仙台湾～東京湾、伊勢・三河湾、瀬戸内海～玄界灘、大村湾、有明海・橘湾)の存在が示唆されている。地域個体群の動態には地域固有の環境要因が関わっているため、保護管理ユニットを設定し、保全に向けた施策を考えていく上では機能的な遺伝子の解析が求められる。この点、免疫に関与するMHC遺伝子領域は非常に多型性に富み、その遺伝的多様性を把握することは、地域個体群の持続可能性を考える上で有用である。日本沿岸個体群のクラスⅡDQB遺伝子の解析では、大村湾と有明海•橘湾を除いた個体群間で有意な遺伝的分化と高い平均ヘテロ接合度が報告されている(Hayashi et al. 2006)。しかしながら、MHC遺伝子領域には多数の遺伝子が存在しており、その多様性の解明には複数の遺伝子の変異量の把握が求められる。そこで本研究では、クラスⅡDQB遺伝子に加え、クラスⅡDRB遺伝子の多型解析を行った。DRB遺伝子に関して88個体を解析した結果、5種類のアリルを識別し、非常に低い平均ヘテロ接合度(Ho=0.244)が検出された。一方でDQB遺伝子に関して86個体を解析した結果、8種類のアリルを識別し、高い平均へテロ接合度(Ho=0.669)が検出された。遺伝子間で検出された多型パターンの違いは、遺伝子間の淘汰圧の違い等を示唆すると考えられ、網羅的なMHC遺伝子の多型解析の必要性が示された。

Event date： 2014.9

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：広島大学 教育学部   Country：Japan  

1300種以上からなるタマバチ科の多くの種はゴール形成者であるが、約200種が所属するヤドカリタマバチ族は、自らゴールを形成せず他者が形成したゴールに寄生する同居者として、ゴール形成者から派生したとされている。本族は形態学的特徴に基づいて他の族と識別されてきたが、2011年にヤドカリタマバチ族の形態を有しながら、ゴール形成能力を有する種、アラカシミヤドカリタマバチが発見された。そこで本種の系統学的位置を検討するため、ミトコンドリアDNAのCOI、cytb領域および核DNAの28SrRNA領域の部分塩基配列に基づき系統解析を行った。その結果、本種がヤドカリタマバチ族のSynergusとSaphonecrusからなる１つのクレードに含まれることが支持され、本族において喪失したゴール形成能力が本種を含む系統において再獲得されたという可能性が示唆された。また、クヌギ、ウバメガシの堅果のゴールから発見された本族の未記載種2種が、アラカシミヤドカリタマバチの姉妹群として支持された。これにより、これら2種もゴール形成能力を有している可能性が高まった。

Event date： 2014.5

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：東京大学本郷キャンパス   Country：Japan  

イチジク属（Ficus：クワ科）植物は、熱帯を中心におよそ750種分布している。日本はイチジク属の分布域の北限にあたり、琉球列島を中心に16種が生息している。イチジク属植物は花嚢とよばれる袋状の閉じた花序をつけ、その内側に多数の花を咲かせる。送粉者であるイチジクコバチは、花嚢に入ったあと、授粉と同時に花に産卵し、ふ化した幼虫は子房を食べて成長する。次世代のコバチが花嚢内で羽化・交配し、雌成虫が花粉を持って他の花嚢へと移動することでライフサイクルを完成する。このようにイチジク属植物とイチジクコバチは、繁殖を互いに強く依存し合い、「1種対1種」という種特異性の高い絶対的共生関係を構築している。
この「1種対1種」関係を維持しながら種分化するとしたら、同調した種分化や系統分化が起こることが予想される。これまでの分子系統学的解析の結果は、高次分類群間ではおおむねこの仮説を支持しているものの、種間レベルでは系統関係の不一致のほかに、植物の雑種形成や送粉コバチの隠蔽種など多くの不明瞭な点が指摘されている。本研究は東アジアに広く分布しているイヌビワ (Ficus erecta)とその送粉コバチであるイヌビワコバチ(Blastophaga nipponica) を対象に、分子系統解析と集団遺伝解析の手法を用いて、両者の種内の遺伝的多様性と地域的集団間の分化を調べ、種内における同調的分化を検証した。
イヌビワとイヌビワコバチは、中国南部から台湾、琉球列島、日本列島の関東にかけて分布しており、済州島にも生息している。本研究は、日本の５地域（伊豆、関西、九州、沖縄、八重山）と台湾で材料の採集を行った。各植物個体の葉および花嚢を採集し、葉の一部からDNAを抽出した。イヌビワコバチは、植物１個体あたり、1～４個の花嚢から採取した。同じ親由来の個体が重複するのを避けるため、花嚢１つあたり１匹の雌を用いることとし、１個体ごとにDNAを抽出した。
まず葉緑体DNA 6 領域（rps16イントロン、trnGイントロン、petBイントロン、trnLイントロン、trnL-trnFスペーサー、atpB-rbcLスペーサー）およそ 3500 塩基を用いて集団のハプロタイプの分布について解析を行った。その結果から、日本産のイヌビワは南方から北進して分布域を拡大し、本州に到達したあと、比較的短期間で広がったと考えられた。また、台湾産のイヌビワは日本産のものより多様性に富んでいること、両者の間にある程度分化が起きていることが判明した。
イヌビワの葉緑体DNA塩基配列の種内変異が少ないため、より多型性の高いマイクロサテライトマーカー (9個) を用いて集団遺伝解析を行った。その結果、５つの遺伝的集団が確認され、それらは地域的集団と一致することが判明した。また、集団間の遺伝的分化の程度を示す統計量（FST）を計算したところ、地域集団間の遺伝的分化が有意にあることが示された。さらに、地域集団間のFSTとその地理的距離にも有意な相関が見られ、イヌビワの遺伝子流動（花粉や種子の移動）は地理的距離が大きいほど制限される度合いが強いことが考えられた。
一方、イヌビワコバチの集団間の遺伝的分化程度を解析したところ、イヌビワと同様に集団間の遺伝的分化が起きていることがわかった。特に台湾集団と日本の集団との間では、遺伝的分化が高い。イヌビワとイヌビワコバチの集団の遺伝構成、集団間分化の程度を比較すると、イヌビワの方がより地域集団に分化しやすい傾向があることが示唆された。また、イヌビワとイヌビワコバチは集団間で互いに類似した遺伝的分化が起きており、相関も見られた。この結果から、イヌビワとイヌビワコバチの地域集団間の分化や遺伝子流動は相互に影響しあっている可能性があると考えられる。

Event date： 2014.3

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：高知市 高知市文化プラザ「かるぽーと」   Country：Japan  

タマバチ科の多くの種はゴールを形成するが、ヤドカリタマバチ族は自らゴールを作らず、他者が形成したゴールに住み込み寄生（同居）をおこなう。例外的に、アラカシミヤドカリタマバチSynergus itoensisはアラカシの堅果に自らゴールを形成する。野外調査によって、これと酷似したゴールがクヌギ、ウバメガシから発見され、それぞれから本族の未記載種が得られた。ゴールの特徴および他に形成者と思われる種の脱出が認められなかったことから、これらの種もゴール形成をおこなうことが予測された。アラカシミヤドカリタマバチの系統学的位置およびクヌギ、ウバメガシの未記載種2種との系統学的関係を推定するため、ミトコンドリアDNA（COI+cytb領域）の塩基配列（973bp）に基づき、ヨーロッパおよびアジアの種を含めた系統樹を構築した。その結果、アラカシミヤドカリタマバチはSynergusとSaphonecrusからなる1つのクレードに含まれた。このクレード内で、上記未記載種2種は本種と1つのクレードを形成した。本種によるゴール形成は住み込み寄生をおこなうヤドカリタマバチ族内で再獲得された性質である可能性が考えられた。ゴール形成をおこなうことが疑われた未記載種2種は本種と近縁であることが示唆された。また、得られたヤドカリタマバチ族の分子系統樹において、分布域や同居する寄主による明確なクレードは見られなかった。

Event date： 2013.12

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：愛知 豊橋市自然史博物館   Country：Japan  

オオクワガタ日本亜種（Dorcus hopei binodulosus）およびその近縁タクサを対象に、マイクロサテライトマーカーによるDNA多型解析と幾何学的形態測定学的手法を用いて抽出した形態形質情報に基づいてオオクワガタ日本亜種およびその近縁タクサの分化の様相を把握することを試みた。

Event date： 2013.6

Language：English   Presentation type：Oral presentation (general)  

Venue：Jeju,   Country：Korea, Republic of  

To clarify fine-scale population genetic structure, levels of genetic diversity, and population history of the finless porpoise, Neophocaena phocaenoides, in Japanese waters, we analysed 10 microsatellite (MS-DNA) loci and mtDNA control region sequence (853bp) for 120 individuals from five localities; the Sendai Bay-Tokyo Bay, the Ise Bay-Mikawa Bay, the Inland Sea-Genai Nada, the Omura Bay and the Ariake Sound-Tachibana Bay. Analyses of MS-DNA and mtDNA revealed a significant population genetic structure that corresponds to the locality. This result is compatible with previous studies based on ecological, morphological and molecular data, therefore, we concluded that there are (at least) five local populations in Japanese waters. All Japanese populations had lower levels of heterozygosity (HO = 0.45-0.55) than those found in Chinese populations. Considering from significant population genetic structure and low genetic diversity, five local populations should be treated as different management units in the design and implications of conservation programs. In addition, levels of genetic differentiation among the local populations based on mtDNA data (FST) are higher than those based on MS-DNA data (RST) and the test of isolation by distance is significant only in MS-DNA, suggesting the existence of male-mediated gene flow of this species. The phylogenetic analysis of the Chinese and the Japanese finless porpoises indicated that the population of Japanese finless porpoises has two diverged haplotypes. Major haplotype cluster is constructed from all of Japanese populations, but the other is mainly constructed from the Ariake Sound-Tachibana Bay population. This may suggest that there are at least two distinct origins of Japanese finless porpoises.

Event date： 2013.3

Language：Japanese  

Venue：静岡 静岡県コンベンションアーツセンター   Country：Japan  

スナメリNeophocaena phocaenoidesは沿岸性の小型鯨類であり、日本沿岸個体群に関しては、分布の不連続性、頭骨形態の差異、および
mtDNAコントロール領域(345bp)の解析により少なくとも5つの地域集団(仙台湾～東京湾、伊勢・三河湾、瀬戸内海～玄界灘、大村湾、有明海～橘湾)の存在が示唆されている。本研究では両系遺伝するマイクロサテライトDNA(MS-DNA)10座位と、mtDNAコントロール領域のより長い配列(853bp)を用いた解析を行うことで、雌雄の遺伝情報に基づいた日本沿岸個体群の遺伝的構造の解明とその形成史の解明を目指した。

Event date： 2012.9 - 2012.10

Language：Others   Presentation type：Oral presentation (general)  

Venue：玉川大学（町田市）   Country：Japan  

オオクワガタ日本集団は人為的影響による野外個体群の減少に加え、逸出した外国産近縁タクサとの交雑による遺伝子浸透も懸念されている。こうした現状にあって、日本集団を含む近縁タクサ間を識別する遺伝的指標の確立や、各タクサ内の遺伝的分化の様相の把握、保全のための進化的重要単位（ESU）の検出は重要な課題である。しかし、既往のミトコンドリアDNA解析の結果では、タクサ間の識別が不明瞭な上に（五箇, 2004）、母系マーカーであるため交雑の検証も不確実であった。そこで本研究では多型性が高く、両系で交雑の検出にも応用しうるSSRマーカーを新規に7座位開発し、日本集団を含むD. hopeiと近縁なD. grandisの2種全5亜種を解析した。その結果、5つの遺伝的グループの存在が示唆され、これらはD. h. binodulosus （日本）、D. h. binodu- losus （北朝鮮・中国北部）、D. h. hopei （中国）、D. g. formosanus （台湾）、D. g. grandis＋D. g. moriyai （ベトナム～インド）に対応した。SSRマーカーによる解析結果は従来不明瞭だったタクサ間の識別に加え、同亜種とみなされている日本と北朝鮮・中国北部の集団は区別可能で、日本集団がESUとして位置づけられることを示唆している。

Event date： 2012.9

Language：Japanese  

Venue：独立行政法人水産大学校（下関市）   Country：Japan  

Event date： 2012.3

Language：Others   Presentation type：Oral presentation (general)  

Venue：京都産業大学   Country：Japan  

クロロフィル（Chl）生合成系には進化的起源の異なる2つのプロトクロロフィリド還元酵素が存在し、このうち暗所作動型酵素（DPOR）が暗所でのChl生合成能を決定づけている。DPORはL-蛋白質（ChlL）とNB-蛋白質（ChlN-ChlB）という各々ニトロゲナーゼのFe-蛋白質とMoFe-蛋白質と類似した2つのコンポーネントから構成される。被子植物を除く真核光合成生物においてDPORは葉緑体DNAにコードされ、クロマツやカラマツなどの針葉樹ではchlNとchlBがmRNAの段階でRNA editingによってアミノ酸置換を伴う塩基置換が導入される。本研究では、ラン藻Leptolyngbya boryanaのDPORを用いてRNA-editingによるアミノ酸置換の影響を検討した。L. boryanaのchlB欠損株においてediting前と後のそれぞれのアミノ酸配列を持つNB-蛋白質を発現させ、暗所で生育させた細胞のChl含量によりDPOR活性を評価した。その結果、editing後のNB-蛋白質を発現する形質転換体においてのみ有意にChl含量が増加した。さらにラン藻粗抽出液での活性測定もこの結果を支持していた。これらの結果は暗所における緑化がRNA editingによるNB-蛋白質の活性調節を介して制御されていることを示唆している。

Event date： 2012.3

Language：Japanese  

Venue：東京 東京海洋大学   Country：Japan  

Event date： 2011.12

Language：Others   Presentation type：Oral presentation (general)  

Venue：鹿児島大学   Country：Japan  

日本産オオクワガタDorcus hopei binodulosusは北海道南部から九州・対馬の主として里山に分布しているが、人為的影響のため各地で野外個体群の減少が著しい。一方、飼育・流通個体の数は極めて多く、入手も容易であるため、すでに国内他地域産や近縁タクサの飼育個体の逸出・放虫が生じており、交雑による遺伝子浸透も懸念されている。こうした現状にあって、日本産オオクワガタの遺伝的多様性や地域個体群間の遺伝的分化の様相を把握し、保全のための進化的重要単位を検出することは極めて重要な課題である。しかし、本種に関しては一般的に他種では有効なミトコンドリアDNAのCOＩ・II領域には遺伝的変異が少なく地域性が検出できないことが示唆されている(五箇, 2004)。そこで、本研究では塩基の反復配列数の違いを利用した遺伝マーカーであり、多型性が高い上、両系マーカーであるため交雑の検出にも応用しうるマイクロサテライトマーカーを用いた解析を試みた。残念なことに、クワガタムシ科ではマイクロサテライトに関する既往の研究例がなく、新たなマーカーの開発を進める必要があった。マーカーの開発にはdual-Suppression PCR法を用い、1次スクリーニングの結果、6カ所のマイクロサテライトが見つかり、このうち2座位でマーカーとして利用できうる多型が認められた。これらのマーカーを用い、日本産オオクワガタ、中国産オオクワガタD.h.hopei、グランディスオオクワガタD.grandis (2亜種)の2種4亜種で解析を行ったところ、指標となりうる多型が見つかった。

Event date： 2011.3

Language：Others   Presentation type：Oral presentation (general)  

Venue：東北大学 仙台市   Country：Japan  

Language：Others  

Country：Japan  

Clock and sleep in a cnidarian, Hydra.

Language：English  

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Type：Academic society, research group, etc. 

Type：Competition, symposium, etc. 

Number of participants：40

Type：Peer review 

Number of peer-reviewed articles in foreign language journals：5

Type：Peer review 

Number of peer-reviewed articles in foreign language journals：3

Type：Competition, symposium, etc. 

Type：Competition, symposium, etc.