|Junko Kusumi||Last modified date：2023.09.26|
Professor / Biodiversity Science / Department of Environmental Changes / Faculty of Social and Cultural Studies
|Junko Kusumi||Last modified date：2023.09.26|
|1.||Akiko Satake, Kayoko Ohta, Noriko Takeda‐Kamiya, Kiminori Toyooka, Junko Kusumi, Seasonal gene expression signatures of delayed fertilization in Fagaceae, Molecular Ecology, 10.1111/mec.17079, 2023.07, 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..|
|2.||Ilham V Utama, Ixchel F Mandagi, Sjamsu A Lawelle, Kawilarang W A Masengi, Keiichi Watanabe, Naomi Sawada, Atsushi J Nagano, Junko Kusumi, Kazunori Yamahira, Deeply divergent freshwater fish species within a single river system in central Sulawesi., Molecular phylogenetics and evolution, 10.1016/j.ympev.2022.107519, 173, 107519-107519, 2022.05, 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..|
|3.||Zhi-Hui Su, Ayako Sasaki, Junko Kusumi, Po-An Chou, Hsy-Yu Tzeng, Hong-Qing Li, Hui Yu, Pollinator sharing, copollination, and speciation by host shifting among six closely related dioecious fig species, Communications Biology, 10.1038/s42003-022-03223-0, 5, 1, 2022.04,
The obligate pollination mutualism between figs (
|4.||Kazunori Yamahira, Daniel F. Mokodongan, Maki Konishi, Ixchel F. Mandagi, Kawilarang W. A. Masengi, Sjamsu A. Lawelle, Junko Kusumi, Nobuyuki Inomata, Discovery of a genetically distinct lineage in medaka species within Lake Towuti in central Sulawesi, ICHTHYOLOGICAL RESEARCH, 10.1007/s10228-021-00856-9, 2022.01, 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..|
|5.||Ixchel F. M, agi, Ryo Kakioka, Javier Montenegro, Hirozumi Kobayashi, Kawilarang W. A. Masengi, Nobuyuki Inomata, Atsushi J. Nagano, Atsushi Toyoda, Satoshi Ansai, Masatoshi Matsunami, Ryosuke Kimura, Jun Kitano, Junko Kusumi, Kazunori Yamahira, Species divergence and repeated ancient hybridization in a Sulawesian lake system, Journal of Evolutionary Biology, 10.1111/jeb.13932, 2021.09.|
|6.||Mizuki Horoiwa, Ixchel F. Mandagi, Nobu Sutra, Javier Montenegro, Fadly Y. Tantu, Kawilarang W. A. Masengi, Atsushi J. Nagano, Junko Kusumi, Nina Yasuda, Kazunori Yamahira, Mitochondrial introgression by ancient admixture between two distant lacustrine fishes in Sulawesi Island, PLOS ONE, 10.1371/journal.pone.0245316, 16, 6, e0245316-e0245316, 2021.06, 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
|7.||Moeko Hirata, Chika Mitsuyuki, Etsuko Moritsuka, Phourin Chhang, Shuichiro Tagane, Hironori Toyama, Heng Sokh, Sukid Rueangruea, Somran Suddee, Yoshihisa Suyama, Tetsukazu Yahara, Kousuke M Teshima, Hidenori Tachida, Junko Kusumi, Evaluating the genetic diversity in two tropical leguminous trees, Dalbergia cochinchinensis and D. nigrescens, in lowland forests in Cambodia and Thailand using MIG-seq., Genes & genetic systems, 10.1266/ggs.20-00026, 96, 1, 41-53, 2021.03, 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..|
|8.||Ryo Miyokawa, Hiroyuki J Kanaya, Taichi Q Itoh, Yoshitaka Kobayakawa, Junko Kusumi, Immature symbiotic system between horizontally transmitted green algae and brown hydra., Scientific reports, 10.1038/s41598-021-82489-6, 11, 1, 2921-2921, 2021.02, Some strains of brown hydra (Hydra vulgaris) are able to harbor the green algae Chlorococcum in their endodermal epithelial cells as symbionts. However, the relationship between brown hydra and chlorococcum is considered to be incipient symbiosis because most artificially introduced symbionts are not stable and because symbiotic H. vulgaris strains are rare in the wild. In this study, we compared the gene expression levels of the newly established symbiotic hydra (strain 105G), the native symbiotic strain (J7), and their non-symbiotic polyps to determine what changes would occur at the early stage of the evolution of symbiosis. We found that both the 105G and J7 strains showed comparable expression patterns, exhibiting upregulation of lysosomal enzymes and downregulation of genes related to nematocyte development and function. Meanwhile, genes involved in translation and the respiratory chain were upregulated only in strain 105G. Furthermore, treatment with rapamycin, which inhibits translation activity, induced the degeneration of the symbiotic strains (105G and J7). This effect was severe in strain 105G. Our results suggested that evolving the ability to balance the cellular metabolism between the host and the symbiont is a key requirement for adapting to endosymbiosis with chlorococcum..|
|9.||Hiroyuki J Kanaya, Sungeon Park, Ji-Hyung Kim, Junko Kusumi, Sofian Krenenou, Etsuko Sawatari, Aya Sato, Jongbin Lee, Hyunwoo Bang, Yoshitaka Kobayakawa, Chunghun Lim, Taichi Q Itoh, A sleep-like state in Hydra unravels conserved sleep mechanisms during the evolutionary development of the central nervous system, Science Advances, 10.1126/sciadv.abb9415, 6, 41, 2020.10, 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..|
|10.||Hitomi Yagi, Jie Xu, Natsuki Moriguchi, Ryutaro Miyagi, Etsuko Moritsuka, Eri Sato, Kyoko Sugai, Suzuki Setsuko, Takeshi Torimaru, Shin ichi Yamamoto, Aya Takahashi, Koichiro Tamura, Hidenori Tachida, Kosuke M. Teshima, Junko Kusumi, Population genetic analysis of two species of Distylium
D. racemosum growing in East Asian evergreen broad-leaved forests and D. lepidotum endemic to the Ogasawara (Bonin) Islands, Tree Genetics and Genomes, 10.1007/s11295-019-1386-x, 15, 6, 2019.12, 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 FST-outlier approach..
|11.||Nobu Sutra, Junko Kusumi, Javier Montenegro, Hirozumi Kobayashi, Shingo Fujimoto, Kawilarang W.A. Masengi, Atsushi J. Nagano, Atsushi Toyoda, Masatoshi Matsunami, Ryosuke Kimura, Kazunori Yamahira, Evidence for sympatric speciation in a Wallacean ancient lake, Evolution, 10.1111/evo.13821, 2019.08, 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..|
|12.||Junko Kusumi, Motoshi Ichinose, Masaru Iizuka, Effects of gene duplication, epistasis, recombination and gene conversion on the fixation time of compensatory mutations, Journal of Theoretical Biology, 10.1016/j.jtbi.2019.02.001, 467, 134-141, 2019.04, Gene duplication is one of the major mechanisms of molecular evolution. Gene duplication enables copies of a gene to accumulate mutations through functional redundancy. If a gene encodes a specific protein that interacts with other proteins, RNA, or DNA, the relaxation of selective constraints caused by gene duplication might contribute to the fixation of compensatory mutations that occur at the interacting sites. In this study, we investigate the effect of gene duplication, epistasis among the duplicated copies and gene conversion on the fixation time of compensatory mutations by extending the original model of compensatory evolution proposed by Kimura in 1985. Our simulation results reveal that the time to fixation of compensatory mutations can be decreased remarkably by gene duplication if one of the duplicated loci can completely mask the deleterious effects of a mutation that occurs at the other locus. Conversely, the fixation time can be increased by gene duplication if such functional compensation is weak. We also show that the combination of the degree of functional compensation and the rate of gene conversion between duplicate loci have contrasting effects on the time to fixation of compensatory mutations..|
|13.||Natsuki Moriguchi, Kentaro Uchiyama, Ryutaro Miyagi, Etsuko Moritsuka, Aya Takahashi, Koichiro Tamura, Yoshihiko Tsumura, Kosuke M. Teshima, Hidenori Tachida, Junko Kusumi, Inferring the demographic history of Japanese cedar, Cryptomeria japonica, using amplicon sequencing, Heredity, 10.1038/s41437-019-0198-y, 2019.01, The evolution of a species depends on multiple forces, such as demography and natural selection. To understand the trajectory and driving forces of evolution of a target species, it is first necessary to uncover that species’ population history, such as past and present population sizes, subdivision and gene flow, by using appropriate genetic markers. Cryptomeria japonica is a long-lived monoecious conifer species that is distributed in Japan. There are two main lines (omote-sugi and ura-sugi), which are distinguished by apparent differences in morphological traits that may have contributed to their local adaptation. The evolution of these morphological traits seems to be related to past climatic changes in East Asia, but no precise estimate is available for the divergence time of these two lines and the subsequent population dynamics in this species. Here, we analyzed the nucleotide variations at 120 nuclear genes in 94 individuals by using amplicon sequencing in combination with high-throughput sequencing technologies. Our analysis indicated that the population on Yakushima Island, the southern distribution limit of C. japonica in Japan, diverged from the other populations 0.85 million years ago (MYA). The divergence time of the other populations on mainland Japan was estimated to be 0.32 MYA suggesting that the divergence of omote-sugi and ura-sugi might have occurred before the last glacial maximum. Although we found modest levels of gene flow between the present populations, the long-term isolation and environmental heterogeneity caused by climatic changes might have contributed to the differentiation of the lines and their local adaptation..|
|14.||Ryo Miyokawa, Takuya Tsuda, Hiroyuki J. Kanaya, Junko Kusumi, Hidenori Tachida, Yoshitaka Kobayakawa, Horizontal Transmission of Symbiotic Green Algae Between Hydra Strains, Biological Bulletin, 10.1086/699705, 235, 2, 113-122, 2018.10, 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..|
|15.||Tatsuya Ide, Junko Kusumi, Kazuki Miura, Yoshihisa Abe, Gall Inducers Arose from Inquilines
Phylogenetic Position of a Gall-Inducing Species and Its Relatives in the Inquiline Tribe Synergini (Hymenoptera: Cynipidae), Annals of the Entomological Society of America, 10.1093/aesa/sax065, 111, 1, 6-12, 2018.01, 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..
|16.||Haruki Yamamoto, Junko Kusumi, Hisanori Yamakawa, Yuichi Fujita, The Effect of Two Amino acid Residue Substitutions via RNA Editing on Dark-operative Protochlorophyllide Oxidoreductase in the Black Pine Chloroplasts, Scientific Reports, 10.1038/s41598-017-02630-2, 7, 1, 2017.12, 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..|
|17.||Hidenori Nishihara, Roscoe Stanyon, Junko Kusumi, Hirohisa Hirai, Akihiko Koga, Evolutionary Origin of OwlRep, a Megasatellite DNA Associated with Adaptation of Owl Monkeys to Nocturnal Lifestyle, Genome Biology and Evolution, 10.1093/gbe/evx281, 10, 1, 157-165, 2017.12, 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..|
|18.||Yuka Ikezaki, Yoshihisa Suyama, Beth A. Middleton, Yoshihiko Tsumura, Kosuke Teshima, Hidenori Tachida, Junko Kusumi, Inferences of population structure and demographic history for Taxodium distichum, a coniferous tree in North America, based on amplicon sequencing analysis, American journal of Botany, 10.3732/ajb.1600046, 103, 11, 2016.12, 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..
|19.||Nakatada Wachi, Junko Kusumi, Hsy-Yu Tzeng, Zhi-Hui Su, Genome-wide sequence data suggest the possibility of pollinator sharing by host shift in dioecious figs (Moraceae, Ficus), MOLECULAR ECOLOGY, 10.1111/mec.13876, 25, 22, 5732-5746, 2016.11, 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..|
|20.||Junko Kusumi, Motoshi Ichinose, Masasuke Takefu, Robert Piskol, Wolfgang Stephan, Masaru Iizuka, A model of compensatory molecular evolution involving multiple sites in RNA molecules, Journal of Theoretical Biology, doi:10.1016/j.jtbi.2015.10.008, 388, 96-107, 2016.01, 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..|
|21.||Junko Kusumi, Yoshihiko Tsumura, Hidenori Tachida, Evolutionary rate variation in two conifer species, Taxodium distichum (L.) Rich. var. distichum (baldcypress) and Cryptomeria japonica (Thunb. ex L.f.) D. Don (Sugi, Japanese cedar), Genes & Genetic Systems, http://doi.org/10.1266/ggs.14-00079, 90, 305-315, 2015.12, 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..|
|22.||Baosheng Wang, Marjan Khalili Mahani, Wei Lun Ng, Junko Kusumi, Hai Hong Phi, Nobuyuki Inomata, Xiao-Ru Wang, ALFRED EDWARD SZMIDT, Extremely low nucleotide polymorphism in Pinus krempfii Lecomte, a unique flat needle pine endemic to Vietnam, Ecology and Evolution, 10.1002/ece3.1091, 2014.05, 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..|
|23.||Junko Kusumi, Zhi-Hui Su, Isolation and characterization of 15 polymorphic microsatellite markers for the fig-pollinating wasp, Blastophaga nipponica (Hymenoptera: Agaonidae), Applied Entomology and Zoology, 10.1007/s13355-014-0267-x, 2014.04, 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..|
|24.||Miyuki Takeda, Junko Kusumi, Shinji Mizoiri, Mitsuto Aibara, Semvua Isa Mzighani, Tetsu Sato, Yohey Terai, Norihiro Okada, Hidenori Tachida, Genetic Structure of Pelagic and Littoral Cichlid Fishes from Lake Victoria, PLOS ONE, 10.1371/journal.pone.0074088, 8, 9, 2013.09, 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..|
|25.||Motoshi Ichinose, Masaru Iizuka, Junko Kusumi, Masasuke Takefu, Models of compensatory molecular evolution: Effects of back mutation, JOURNAL OF THEORETICAL BIOLOGY, 10.1016/j.jtbi.2013.01.011, 323, 1-10, 2013.01, 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..|
|26.||Ayako Tanaka & Masato Ohtani & Yoshihisa Suyama &
Nobuyuki Inomata & Yoshihiko Tsumura &
Beth A. Middleton & Hidenori Tachida & Junko Kusumi, Population genetic structure of a widespread coniferous tree, Taxodium distichum [L.] Rich. (Cupressaceae), in the Mississippi River Alluvial Valley and Florida, Tree Genetics & Genomes, 2012.03, 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..
|27.||Junko Kusumi; Hiroshi Azuma; Hsy-Yu Tzeng; Lien-Siang Chou; Yan-Qiong Peng;
Keiko Nakamura; Zhi-Hui Su, Phylogenetic analyses suggest a hybrid origin of the figs (Moraceae: Ficus) that are endemic to
the Ogasawara (Bonin) Islands, Japan, Molecular Phylogenetics and Evolution, http://dx.doi.org/10.1016/j.bbr.2011.03.031, 63, １, 168-179, 2012.01, 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..
|28.||Junko Kusumi, Zidong, Li, Tomoyuki Kado, Yoshihiko Tsumura, Beth A. Middleton and Hidenori Tachida, Multilocus patterns of nucleotide polymorphism and demographic change in Taxodium distichum (Cupressaceae) in the lower Mississippi River alluvial valley, American journal of botany, 10.3732/ajb.1000082, 97, 11, 1848-1857, 2010.11.|
|29.||Akihiko Koga, Atsuko Shimada, Toshiya Kuroki, Hiroshi Hori, Junko Kusumi, Yoriko Kyono-Hamaguchi and Satoshi Hamaguchi, The Tol1 transposable element of the medaka fish moves in human and mouse cells, Journal of Human genetics, 10.1007/s10038-007-0161-2, 52, 628-635, 2007.07.|
|30.||Junko Kusumi、Aya Sato、Hidenori Tachida, Relaxation of Functional Constraint on Light-Independent Protochlorophyllide Oxidoreductase in Thuja, Molecular Biology and Evolution, 10.1093/molbev/msj097, 23, 5, 941-948, Relaxation of Functional Constraint on Light-Independent Protochlorophyllide Oxidoreductase in Thuja, 2006.05.|
|31.||Junko Kusumi and Hidenori Tachida, Compositional properties of green-plant plastid genomes., Journal of Molecular evolution, 10.1007/s00239-004-0086-8, 60, 4, 417-425, 2005.04.|
|32.||Junko Kusumi, Yoshihiko Tsumura, Hiroshi Yoshimaru and Hidenori Tachida, Molecular evolution of nuclear genes in Cupressaceae, a group of conifer trees., Molecular biology and evolution, 19, 5, 736-747, 2002.10.|
|33.||Junko Kusumi, Yoshihiko Tsumura, Hiroshi Yoshimaru and Hidenori Tachida, Phylogenetic relationships in Taxodiaceae and Cupressaceae sensu stricto based on matK gene, chlL gene, trnL-trnF IGS region, and trnL intron sequences., American Journal of Botany, 10.2307/2656874, 87, 10, 1480-1488, 2000.10.|
|34.||Junko Kusumi, Koh Iba, Characterization of a nonsense mutation in FAD7, the gene which encodes ω-3 desaturase in Arabidopsis thaliana, Journal of Plant Research, 111, 1101, 87-91, 1998.03, 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..|