Researcher Database

Hitoshi Araki
Research Faculty of Agriculture Fundamental AgriScience Research Agrobiology and Bioresources

Researcher Profile and Settings


  • Research Faculty of Agriculture Fundamental AgriScience Research Agrobiology and Bioresources

Job Title

  • Professor


J-Global ID

Research Interests

  • Adaptation   fish   gene   anthoropogenic changes   Evolution   

Research Areas

  • Life sciences / Biodiversity and systematics
  • Life sciences / Ecology and environmental science
  • Life sciences / Evolutionary biology

Academic & Professional Experience

  • 2013/04 - Today Hokkaido University Research Faculty of Agriculture, Devision of Environmental Resources Professor
  • 2008/01 - 2013/03 Eawag, Swiss Federal Institute of Aquatic Science and Technology Department of Fish Ecology and Evolution Group leader
  • 2004/07 - 2007/12 Oregon State University Department of Zoology Postdoctoral research associate
  • 2001/04 - 2004/06 University of Chicago Department of Ecology and Evolution Postdoctoral fellow


  • 1997/04 - 2001/03  Kyushu University  Graduate School of Medical Science
  • 1995/04 - 1997/03  Kyushu University  Graduate School of Science
  • 1991/04 - 1995/03  Kyushu University  Faculty of Science  Department of Biology

Research Activities

Published Papers

  • Hiroki Mizumoto, Takashi Mitsuzuka, Hitoshi Araki
    For protecting endangered species, precise understanding of their distribution is crucial. However, it is often very difficult to estimate at a large scale with conventional methods (e.g., casting nets or electrofishing for aquatic species) because of their low densities in the wild. Sakhalin taimen (Parahucho perryi) is one of the largest and most critically endangered freshwater salmonid fishes in the world. In this study, we applied an environmental DNA (eDNA) detection system for this species to 120 rivers in Hokkaido, the second largest main island of Japan. We successfully detected eDNA from Sakhalin taimen in seven rivers (5.8%). Although these rivers were widely distributed across the island, > 95% of the total amounts of eDNA were detected from region-A and -I, indicating that local populations in the other regions of Hokkaido are very small and on the brink of extinction. In addition, principal component analyses based on the eDNA-based estimation of Sakhalin taimen distribution and GIS revealed their distribution determinants including limited topographic relief of watershed as well as presence of wetlands and lagoons. Our results suggest that eDNA-based detection systems are an efficient means of monitoring the population status of endangered freshwater species at large scales.
  • Tetsu Yatsuyanagi, Hitoshi Araki
    PLOS ONE 15 (10) 1932-6203 2020/10 
    Migratory organisms have their own life histories that efficiently link multiple ecosystems. Therefore, comprehensive understanding of migration ecologies of these organisms is essential for both species conservation and ecosystem management. However, monitoring migration at fine spatiotemporal scales, especially in open marine systems, often requires huge costs and effort. Recently, environmental DNA (eDNA) techniques that utilize DNA released from living organisms into their environment became available for monitoring wild animals without direct handling. In this study, we conducted an eDNA survey for understanding marine migration of an endemic fish species, Shishamo smelt (Spirinchus lanceolatus). We examined 1) seasonal habitat changes in coastal regions and 2) environmental factors potentially driving the migration of this species. The eDNA concentrations along a 100 km-long coastline exhibited spatiotemporal variation, suggesting that this species shifts their habitat away from nearshore areas between spring and summer. We also found a significantly negative association between the eDNA concentration and sea surface temperature. That finding suggests that the offshore migration of this species is associated with increased sea surface temperature. This study reveals new aspects of S. lanceolatus life history in coastal regions. Together with our previous eDNA study on the freshwater migration of S. lanceolatus, this study illustrates the potential of eDNA techniques for understanding the whole life history of this migratory species.
  • Toshifumi Minamoto, Masaki Miya, Tetsuya Sado, Satoquo Seino, Hideyuki Doi, Michio Kondoh, Keigo Nakamura, Teruhiko Takahara, Satoshi Yamamoto, Hiroki Yamanaka, Hitoshi Araki, Wataru Iwasaki, Akihide Kasai, Reiji Masuda, Kimiko Uchii
    Environmental DNA 2637-4943 2020/08/10 [Refereed][Not invited]
  • Tetsu Yatsuyanagi, Ryotaro Ishida, Masayuki K. Sakata, Takashi Kanbe, Hiroki Mizumoto, Yumi Kobayashi, Shoko Kamada, Satoko Namba, Hisaya Nii, Toshifumi Minamoto, Hitoshi Araki
    Environmental DNA 2 (2) 130 - 139 2637-4943 2020/04 [Refereed][Not invited]
  • Kouta Miyamoto, Hitoshi Araki
    HYDROBIOLOGIA 840 (1) 103 - 112 0018-8158 2019/09 [Refereed][Not invited]
    Both climate change and dam operations are affecting water levels in river systems worldwide and their influence can be especially drastic in upper streams, where juvenile salmonids hatch and grow. However, efficient means of mitigating such influence on salmonid populations have not been developed, at least not in a practical manner throughout the world. In this study, we investigated effects of declining water levels and structural complexity on populations of age-0 white-spotted charr (Salvelinus leucomaenis) in tank and pond experiments. Survival of the charr was lower in the shallow tanks (15 cm water depth) than in the deeper ones. Similarly, more fish survived in the tanks with artificial structures (cobbles with Ringlong tape) compared to those without them. The grey heron (Ardea cinerea) was the most frequently observed predator during the tank experiment, and settlement of fish in the shallow ponds increased when artificial structures were provided. These results suggest that declining water levels and the loss of structural complexity may lead to a decrease in populations of white-spotted charr by increasing predation risk and interference competition.
  • Kentaro Morita, Genki Sahashi, Masaki Miya, Shouko Kamada, Takashi Kanbe, Hitoshi Araki
    HYDROBIOLOGIA 840 (1) 207 - 213 0018-8158 2019/09 [Refereed][Not invited]
    Habitat fragmentation caused by damming can greatly reduce the population viability of aquatic organisms, with smaller fragmented populations at higher risk of extinction due to increased demographic, genetic, and environmental stochasticity. However, empirical evidence demonstrating that smaller natural populations are more vulnerable to extinction is limited. We studied the vulnerability to extinction of white-spotted charr (Salvelinus leucomaenis) populations in 30 dammed-off streams in Oshima Peninsula, southwestern Hokkaido Island, Japan, by comparing the incidence of charr populations in streams between 1999 and 2014. Using electrofishing and environmental DNA surveys, we identified three localized extinctions, with the probability of extinction increasing with decreasing watershed area (our surrogate for habitat size). We also found a new population in one dammed-off stream in which white-spotted charr were previously unknown, after installation of a fish ladder, indicating the capacity of white-spotted charr to recolonize reconnected habitat in a short period. Our results suggest that localized extinction of white-spotted charr in small dammed-off streams is ongoing, but that appropriate fish migration corridors can reduce localized extinction risk and increase the probability of species persistence.
  • Yuki Minegishi, Marty Kwok-Shing Wong, Takashi Kanbe, Hitoshi Araki, Tomomi Kashiwabara, Minoru Ijichi, Kazuhiro Kogure, Susumu Hyodo
    PLOS ONE 14 (9) e0222052  1932-6203 2019/09 [Refereed][Not invited]
    To understand the ecology of juvenile chum salmon during early marine life after their downstream migration, we developed a quantitative PCR-based environmental DNA (eDNA) method specific for chum salmon and investigated the spatiotemporal distribution of eDNA in Otsuchi Bay, Iwate, Japan. Indoor aquarium experiments demonstrated the following characteristics of chum salmon eDNA: (1) the eDNA shedding and degradation were time- and water temperature-dependent and the bacterial abundance could contribute to the eDNA decay, (2) fecal discharge may not be the main source of eDNA, and (3) a strong positive Pearson correlation was found between the number of juveniles and the eDNA amounts. As we discovered strong PCR inhibition from the seawater samples of the bay, we optimized the eDNA assay protocol for natural seawater samples by adding a further purification step and modification of PCR mixture. The intensive eDNA analysis in the spring of 2017 and 2018 indicated that juvenile chum salmon initially inhabited in shallow waters in the shorefront area and then spread over the bay from January to June. The eDNA data also pointed out that outmigration of juvenile chum salmon to open ocean temporarily suspended in April, possibly being associated with the dynamics of the Oyashio Current as suggested by a previous observation. The eDNA method thus enables us large-scale and comprehensive surveys without affecting populations to understand the spatiotemporal dynamics of juvenile chum salmon.
  • 気候変動下における日本系サケの持続可能な保全管理のあり方とその研究課題
    帰山雅秀, 荒木仁志, 宮下和士, 永田光博, 佐々木義隆, 浦和茂彦
    海洋と生物 40 (5) 459 - 466 2018/10 [Not refereed][Not invited]
  • 環境変動下におけるサケの持続可能な資源管理:国際サーモン年に向けたプロローグ
    浦和茂彦, 荒木仁志, 宮下和士, 永田光博, 佐々木義隆, 帰山雅秀
    海洋と生物 40 (4) 315 - 318 2018/08 [Not refereed][Not invited]
  • Marco Castellani, Mikko Heino, John Gilbey, Hitoshi Araki, Terje Svasand, Kevin A. Glover
    EVOLUTIONARY APPLICATIONS 11 (6) 1010 - 1025 1752-4571 2018/07 [Refereed][Not invited]
    Genetic interaction between domesticated escapees and wild conspecifics represents a persistent challenge to an environmentally sustainable Atlantic salmon aquaculture industry. We used a recently developed eco-genetic model (IBSEM) to investigate potential changes in a wild salmon population subject to spawning intrusion from domesticated escapees. At low intrusion levels (5%-10% escapees), phenotypic and demographic characteristics of the recipient wild population only displayed weak changes over 50 years and only at high intrusion levels (30%-50% escapees) were clear changes visible in this period. Our modeling also revealed that genetic changes in phenotypic and demographic characteristics were greater in situations where strayers originating from a neighboring wild population were domestication-admixed and changed in parallel with the focal wild population, as opposed to nonadmixed. While recovery in the phenotypic and demographic characteristics was observed in many instances after domesticated salmon intrusion was halted, in the most extreme intrusion scenario, the population went extinct. Based upon results from these simulations, together with existing knowledge, we suggest that a combination of reduced spawning success of domesticated escapees, natural selection purging maladapted phenotypes/genotypes from the wild population, and phenotypic plasticity, buffer the rate and magnitude of change in phenotypic and demographic characteristics of wild populations subject to spawning intrusion of domesticated escapees. The results of our simulations also suggest that under specific conditions, natural straying among wild populations may buffer genetic changes in phenotypic and demographic characteristics resulting from introgression of domesticated escapees and that variation in straying in time and space may contribute to observed differences in domestication-driven introgression among native populations.
  • Hiroki Mizumoto, Hirokazu Urabe, Takashi Kanbe, Michio Fukushima, Hitoshi Araki
    LIMNOLOGY 19 (2) 219 - 227 1439-8621 2018/04 [Refereed][Not invited]
    For field ecologists, detecting a target species in the wild is a severe bottleneck to understanding its distribution and population status. Recently, environmental DNA (eDNA) techniques have been developed as a noninvasive monitoring tool for aquatic organisms. While applications of eDNA techniques for biomass estimation have been proposed, little is known about an applicable size range of the organisms, which might affect relationships between biomass and eDNA concentration. Here, we investigated eDNA from Sakhalin taimen (Parahucho perryi), a giant salmonid species of northern Japan. This species is critically endangered and difficult to detect in the wild by conventional sampling methods. Using quantitative real-time PCR, we tested correlations between eDNA concentration and fish density using fish with a wide range of ages and body sizes in aquarium experiments. We found that our new primers and probe were truly species-specific, and that the eDNA concentration was significantly correlated with fish density and body size (p < 0.001). Furthermore, based on our calculation, the eDNA concentrations were rather constant among aquaria with fish in different age and size groups when their total weight was adjusted. These results suggest that eDNA concentrations can be an indicator of biomass of Sakhalin taimen, although further research is needed for its application in natural environments.
  • Kouta Miyamoto, Theodore E. Squires, Hitoshi Araki
    MARINE AND FRESHWATER RESEARCH 69 (3) 446 - 454 1323-1650 2018 [Refereed][Not invited]
    Predation after release is one of the major concerns of hatchery fish conservation and propagation. However, the relationships between the size of hatchery fish, the predator species and their behaviours in natural environments are largely unknown. To understand these relationships, we conducted predation experiments in outdoor tanks and a seminatural stream with exposure to local predators. Masu salmon (Oncorhynchus masou) of two different size classes were used as experimental prey fish in the present study. Camera trap data showed that grey herons (Ardea cinerea) were the primary predator in the experimental system, and that most herons used shallow areas in the morning or evening while feeding. Increasing the density of stocked salmon led to increases in the number of occurrences of grey heron. More importantly, predation by grey herons resulted in a significantly lower survival rate of larger salmon compared with smaller salmon. The results indicate that it is important to understand local predators, adjust the optimum body size of hatchery fish at release and choose the appropriate stocking site and time of day for maximising the effectiveness of fish stocking.
  • Shigehiko Urawa, Hitoshi Araki, Kazushi Miyashita, Mitsuhiro Nagata, Yoshitaka Sasaki, Masahide Kaeriyama
    NIPPON SUISAN GAKKAISHI 84 (5) 921 - 921 0021-5392 2018 [Refereed][Not invited]
  • Hitoshi Araki, Takashi Kanbe, Hiroki Mizumoto, Shoko Kamada, Shunpei Sato
    NIPPON SUISAN GAKKAISHI 84 (5) 936 - 936 0021-5392 2018 [Refereed][Not invited]
  • Kevin A. Glover, Monica F. Solberg, Phil McGinnity, Kjetil Hindar, Eric Verspoor, Mark W. Coulson, Michael M. Hansen, Hitoshi Araki, Oystein Skaala, Terje Svasand
    FISH AND FISHERIES 18 (5) 890 - 927 1467-2960 2017/09 [Refereed][Not invited]
    Atlantic salmon (Salmo salar) is one of the best researched fishes, and its aquaculture plays a global role in the blue revolution. However, since the 1970s, tens of millions of farmed salmon have escaped into the wild. We review current knowledge of genetic interactions and identify the unanswered questions. Native salmon populations are typically genetically distinct from each other and potentially locally adapted. Farmed salmon represent a limited number of wild source populations that have been exposed to 12 generations of domestication. Consequently, farmed and wild salmon differ in many traits including molecular-genetic polymorphisms, growth, morphology, life history, behaviour, physiology and gene transcription. Field experiments have demonstrated that the offspring of farmed salmon display lower lifetime fitness in the wild than wild salmon and that following introgression, there is a reduced production of genetically wild salmon and, potentially, of total salmon production. It is a formidable task to estimate introgression of farmed salmon in wild populations where they are not exotic. New methods have revealed introgression in half of similar to 150 Norwegian populations, with point estimates as high as 47%, and an unweighted average of 6.4% across 109 populations. Outside Norway, introgression remains unquantified, and in all regions, biological changes and the mechanisms driving population-specific impacts remain poorly documented. Nevertheless, existing knowledge shows that the long-term consequences of introgression is expected to lead to changes in life-history traits, reduced population productivity and decreased resilience to future challenges. Only a major reduction in the number of escapees and/or sterility of farmed salmon can eliminate further impacts.
  • Kouta Miyamoto, Hitoshi Araki
    FISHERIES SCIENCE 83 (2) 245 - 250 0919-9268 2017/03 [Refereed][Not invited]
    Predation after release is one of the major concerns of hatchery fish propagation. However, size-specific interaction between predator and prey on the survival of hatchery-released salmonid fish is largely unknown. To understand the size-selective predation risk, 24-h predation experiments were conducted on masu salmon Oncorhynchus masou in tanks. Four ranges of fork length (FL) were examined for masu salmon as a prey, in combination with three ranges of FL for white-spotted charr Salvelinus leucomaenis as a predator. The results show that not only predator and prey sizes, but also interaction between prey size and predator size, strongly affected the survival rate of masu salmon. Predation on masu salmon with the FL exceeding 40% of the FL of white-spotted charr was rare in the experiment. A logistic regression suggests that 37% relative FL of masu salmon to white-spotted charr results in the 50% survival of masu salmon. Our results suggest that adjusting relative size of hatchery fish to the size of local fish predators at the time of hatchery release will have a significant impact on the survival of hatchery fish in the wild. From this perspective, site-specific, adaptive management might be important to improve the effectiveness of hatchery fish propagation.
  • Makiko Mimura, Tetsukazu Yahara, Daniel P. Faith, Ella Vazquez-Dominguez, Robert I. Colautti, Hitoshi Araki, Firouzeh Javadi, Juan Nunez-Farfan, Akira S. Mori, Shiliang Zhou, Peter M. Hollingsworth, Linda E. Neaves, Yuya Fukano, Gideon F. Smith, Yo-Ichiro Sato, Hidenori Tachida, Andrew P. Hendry
    EVOLUTIONARY APPLICATIONS 10 (2) 121 - 139 1752-4571 2017/02 [Refereed][Not invited]
    Intraspecific variation is a major component of biodiversity, yet it has received relatively little attention from governmental and nongovernmental organizations, especially with regard to conservation plans and the management of wild species. This omission is ill-advised because phenotypic and genetic variations within and among populations can have dramatic effects on ecological and evolutionary processes, including responses to environmental change, the maintenance of species diversity, and ecological stability and resilience. At the same time, environmental changes associated with many human activities, such as land use and climate change, have dramatic and often negative impacts on intraspecific variation. We argue for the need for local, regional, and global programs to monitor intraspecific genetic variation. We suggest that such monitoring should include two main strategies: (i) intensive monitoring of multiple types of genetic variation in selected species and (ii) broad-brush modeling for representative species for predicting changes in variation as a function of changes in population size and range extent. Overall, we call for collaborative efforts to initiate the urgently needed monitoring of intraspecific variation.
  • Martin M. Turcotte, Hitoshi Araki, Daniel S. Karp, Katja Poveda, Susan R. Whitehead
    PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 372 (1712) 0962-8436 2017/01 [Refereed][Not invited]
    Agriculture is a dominant evolutionary force that drives the evolution of both domesticated and wild species. However, the various mechanisms of agriculture-induced evolution and their socio-ecological consequences are not often synthetically discussed. Here, we explore how agricultural practices and evolutionary changes in domesticated species cause evolution in wild species. We do so by examining three processes by which agriculture drives evolution. First, differences in the traits of domesticated species, compared with their wild ancestors, alter the selective environment and create opportunities for wild species to specialize. Second, selection caused by agricultural practices, including both those meant to maximize productivity and those meant to control pest species, can lead to pest adaptation. Third, agriculture can cause nonselective changes in patterns of gene flow in wild species. We review evidence for these processes and then discuss their ecological and sociological impacts. We finish by identifying important knowledge gaps and future directions related to the eco-evolutionary impacts of agriculture including their extent, how to prevent the detrimental evolution of wild species, and finally, how to use evolution to minimize the ecological impacts of agriculture.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.
  • Satoshi Yamamoto, Reiji Masuda, Yukuto Sato, Tetsuya Sado, Hitoshi Araki, Michio Kondoh, Toshifumi Minamoto, Masaki Miya
    SCIENTIFIC REPORTS 7 40368  2045-2322 2017/01 [Refereed][Not invited]
    Environmental DNA (eDNA) metabarcoding has emerged as a potentially powerful tool to assess aquatic community structures. However, the method has hitherto lacked field tests that evaluate its effectiveness and practical properties as a biodiversity monitoring tool. Here, we evaluated the ability of eDNA metabarcoding to reveal fish community structures in species-rich coastal waters. High-performance fish-universal primers and systematic spatial water sampling at 47 stations covering similar to 11 km(2) revealed the fish community structure at a species resolution. The eDNA metabarcoding based on a 6-h collection of water samples detected 128 fish species, of which 62.5% (40 species) were also observed by underwater visual censuses conducted over a 14-year period. This method also detected other local fishes (>= 23 species) that were not observed by the visual censuses. These eDNA metabarcoding features will enhance marine ecosystem-related research, and the method will potentially become a standard tool for surveying fish communities.
  • Satoshi Yamamoto, Kenji Minami, Keiichi Fukaya, Kohji Takahashi, Hideki Sawada, Hiroaki Murakami, Satsuki Tsuji, Hiroki Hashizume, Shou Kubonaga, Tomoya Horiuchi, Masamichi Hongo, Jo Nishida, Yuta Okugawa, Ayaka Fujiwara, Miho Fukuda, Shunsuke Hidaka, Keita W. Suzuki, Masaki Miya, Hitoshi Araki, Hiroki Yamanaka, Atsushi Maruyama, Kazushi Miyashita, Reiji Masuda, Toshifumi Minamoto, Michio Kondoh
    PLOS ONE 11 (4) e0153291  1932-6203 2016/04 [Refereed][Not invited]
  • Satoshi Yamamoto, Kenji Minami, Keiichi Fukaya, Kohji Takahashi, Hideki Sawada, Hiroaki Murakami, Satsuki Tsuji, Hiroki Hashizume, Shou Kubonaga, Tomoya Horiuchi, Masamichi Hongo, Jo Nishida, Yuta Okugawa, Ayaka Fujiwara, Miho Fukuda, Shunsuke Hidaka, Keita W. Suzuki, Masaki Miya, Hitoshi Araki, Hiroki Yamanaka, Atsushi Maruyama, Kazushi Miyashita, Reiji Masuda, Toshifumi Minamoto, Michio Kondoh
    PLOS ONE 11 (3) 1932-6203 2016/03 [Refereed][Not invited]
    Recent studies in streams and ponds have demonstrated that the distribution and biomass of aquatic organisms can be estimated by detection and quantification of environmental DNA (eDNA). In more open systems such as seas, it is not evident whether eDNA can represent the distribution and biomass of aquatic organisms because various environmental factors (e.g., water flow) are expected to affect eDNA distribution and concentration. To test the relationships between the distribution of fish and eDNA, we conducted a grid survey in Maizuru Bay, Sea of Japan, and sampled surface and bottom waters while monitoring biomass of the Japanese jack mackerel (Trachurus japonicus) using echo sounder technology. A linear model showed a high R-2 value (0.665) without outlier data points, and the association between estimated eDNA concentrations from the surface water samples and echo intensity was significantly positive, suggesting that the estimated spatial variation in eDNA concentration can reflect the local biomass of the jack mackerel. We also found that a best-fit model included echo intensity obtained within 10-150 m from water sampling sites, indicating that the estimated eDNA concentration most likely reflects fish biomass within 150 m in the bay. Although eDNA from a wholesale fish market partially affected eDNA concentration, we conclude that eDNA generally provides a 'snapshot' of fish distribution and biomass in a large area. Further studies in which dynamics of eDNA under field conditions (e.g., patterns of release, degradation, and diffusion of eDNA) are taken into account will provide a better estimate of fish distribution and biomass based on eDNA.
  • Tomotaka Matsumoto, Katsuhiko Mineta, Naoki Osada, Hitoshi Araki
    FRONTIERS IN GENETICS 6 (NOV) 1664-8021 2015/11 [Refereed][Not invited]
    Recent studies suggest the existence of a stochasticity in gene expression (SGE) in many organisms, and its non-negligible effect on their phenotype and fitness. To date, however, how SGE affects the key parameters of population genetics are not well understood. SGE can increase the phenotypic variation and act as a load for individuals, if they are at the adaptive optimum in a stable environment. On the other hand, part of the phenotypic variation caused by SGE might become advantageous if individuals at the adaptive optimum become genetically less adaptive, for example due to an environmental change. Furthermore, SGE of unimportant genes might have little or no fitness consequences. Thus, SGE can be advantageous, disadvantageous, or selectively neutral depending on its context. In addition, there might be a genetic basis that regulates magnitude of SGE, which is often referred to as "modifier genes," but little is known about the conditions under which such an SGE-modifier gene evolves. In the present study, we conducted individual-based computer simulations to examine these conditions in a diploid model. In the simulations, we considered a single locus that determines organismal fitness for simplicity, and that SGE on the locus creates fitness variation in a stochastic manner. We also considered another locus that modifies the magnitude of SGE. Our results suggested that SGE was always deleterious in stable environments and increased the fixation probability of deleterious mutations in this model. Even under frequently changing environmental conditions, only very strong natural selection made SGE adaptive. These results suggest that the evolution of SGE-modifier genes requires strict balance among the strength of natural selection, magnitude of SGE, and frequency of environmental changes. However, the degree of dominance affected the condition under which SGE becomes advantageous, indicating a better opportunity for the evolution of SGE in different genetic models.
  • Marco Castellani, Mikko Heino, John Gilbey, Hitoshi Araki, Terje Svasand, Kevin A. Glover
    PLOS ONE 10 (9) 1932-6203 2015/09 [Refereed][Not invited]
    Ecology and genetics can influence the fate of individuals and populations in multiple ways. However, to date, few studies consider them when modelling the evolutionary trajectory of populations faced with admixture with non-local populations. For the Atlantic salmon, a model incorporating these elements is urgently needed because many populations are challenged with gene-flow from non-local and domesticated conspecifics. We developed an Individual-Based Salmon Eco-genetic Model (IBSEM) to simulate the demographic and population genetic change of an Atlantic salmon population through its entire life-cycle. Processes such as growth, mortality, and maturation are simulated through stochastic procedures, which take into account environmental variables as well as the genotype of the individuals. IBSEM is based upon detailed empirical data from salmon biology, and parameterized to reproduce the environmental conditions and the characteristics of a wild population inhabiting a Norwegian river. Simulations demonstrated that the model consistently and reliably reproduces the characteristics of the population. Moreover, in absence of farmed escapees, the modelled populations reach an evolutionary equilibrium that is similar to our definition of a 'wild' genotype. We assessed the sensitivity of the model in the face of assumptions made on the fitness differences between farm and wild salmon, and evaluated the role of straying as a buffering mechanism against the intrusion of farm genes into wild populations. These results demonstrate that IBSEM is able to capture the evolutionary forces shaping the life history of wild salmon and is therefore able to model the response of populations under environmental and genetic stressors.
  • M. Miya, Y. Sato, T. Fukunaga, T. Sado, J. Y. Poulsen, K. Sato, T. Minamoto, S. Yamamoto, H. Yamanaka, H. Araki, M. Kondoh, W. Iwasaki
    ROYAL SOCIETY OPEN SCIENCE 2 (7) 150088  2054-5703 2015/07 [Refereed][Not invited]
    We developed a set of universal PCR primers (MiFish-U/E) for metabarcoding environmental DNA (eDNA) from fishes. Primers were designed using aligned whole mitochondrial genome (mitogenome) sequences from 880 species, supplemented by partial mitogenome sequences from 160 elasmobranchs (sharks and rays). The primers target a hypervariable region of the 12S rRNA gene (163-185 bp), which contains sufficient information to identify fishes to taxonomic family, genus and species except for some closely related congeners. To test versatility of the primers across a diverse range of fishes, we sampled eDNA from four tanks in the Okinawa Churaumi Aquarium with known species compositions, prepared dual-indexed libraries and performed paired-end sequencing of the region using high-throughput next-generation sequencing technologies. Out of the 180 marine fish species contained in the four tanks with reference sequences in a custom database, we detected 168 species (93.3%) distributed across 59 families and 123 genera. These fishes are not only taxonomically diverse, ranging from sharks and rays to higher teleosts, but are also greatly varied in their ecology, including both pelagic and benthic species living in shallow coastal to deep waters. We also sampled natural seawaters around coral reefs near the aquarium and detected 93 fish species using this approach. Of the 93 species, 64 were not detected in the four aquarium tanks, rendering the total number of species detected to 232 (from 70 families and 152 genera). The metabarcoding approach presented here is non-invasive, more efficient, more cost-effective and more sensitive than the traditional survey methods. It has the potential to serve as an alternative (or complementary) tool for biodiversity monitoring that revolutionizes natural resource management and ecological studies of fish communities on larger spatial and temporal scales.
  • M. Miya, Y. Sato, T. Fukunaga, T. Sado, J. Y. Poulsen, K. Sato, T. Minamoto, S. Yamamoto, H. Yamanaka, H. Araki, M. Kondoh, W. Iwasaki
    ROYAL SOCIETY OPEN SCIENCE 2 (7) 0831-2796 2015/07 [Refereed][Not invited]
    We developed a set of universal PCR primers (MiFish-U/E) for metabarcoding environmental DNA (eDNA) from fishes. Primers were designed using aligned whole mitochondrial genome (mitogenome) sequences from 880 species, supplemented by partial mitogenome sequences from 160 elasmobranchs (sharks and rays). The primers target a hypervariable region of the 12S rRNA gene (163-185 bp), which contains sufficient information to identify fishes to taxonomic family, genus and species except for some closely related congeners. To test versatility of the primers across a diverse range of fishes, we sampled eDNA from four tanks in the Okinawa Churaumi Aquarium with known species compositions, prepared dual-indexed libraries and performed paired-end sequencing of the region using high-throughput next-generation sequencing technologies. Out of the 180 marine fish species contained in the four tanks with reference sequences in a custom database, we detected 168 species (93.3%) distributed across 59 families and 123 genera. These fishes are not only taxonomically diverse, ranging from sharks and rays to higher teleosts, but are also greatly varied in their ecology, including both pelagic and benthic species living in shallow coastal to deep waters. We also sampled natural seawaters around coral reefs near the aquarium and detected 93 fish species using this approach. Of the 93 species, 64 were not detected in the four aquarium tanks, rendering the total number of species detected to 232 (from 70 families and 152 genera). The metabarcoding approach presented here is non-invasive, more efficient, more cost-effective and more sensitive than the traditional survey methods. It has the potential to serve as an alternative (or complementary) tool for biodiversity monitoring that revolutionizes natural resource management and ecological studies of fish communities on larger spatial and temporal scales.
  • Katsuhiko Mineta, Tomotaka Matsumoto, Naoki Osada, Hitoshi Araki
    GENE 562 (1) 16 - 21 0378-1119 2015/05 [Refereed][Not invited]
    The role of stochasticity in evolutionary genetics has long been debated. To date, however, the potential roles of non-genetic traits in evolutionary processes have been largely neglected. In molecular biology, growing evidence suggests that stochasticity in gene expression (SGE) is common and that SGE has major impacts on phenotypes and fitness. Here, we provide a general overview of the potential effects of SGE on population genetic parameters, arguing that SGE can indeed have a profound effect on evolutionary processes. Our analyses suggest that SGE potentially alters the fate of mutations by influencing effective population size and fixation probability. In addition, a genetic control of SGE magnitude could evolve under certain conditions, if the fitness of the less-fit individual increases due to SGE and environmental fluctuation. Although empirical evidence for our arguments is yet to come, methodological developments for precisely measuring SGE in living organisms will further advance our understanding of SGE-driven evolution. (C) 2015 Elsevier B.V. All rights reserved.
  • Long Wang, Weina Si, Yongfang Yao, Dacheng Tian, Hitoshi Araki, Sihai Yang
    PLOS ONE 7 (12) 1932-6203 2012/12 [Refereed][Not invited]
    Pseudogenes (Psi s), including processed and non-processed Psi s, are ubiquitous genetic elements derived from originally functional genes in all studied genomes within the three kingdoms of life. However, systematic surveys of non-processed Psi s utilizing genomic information from multiple samples within a species are still rare. Here a systematic comparative analysis was conducted of Psi s within 80 fully re-sequenced Arabidopsis thaliana accessions, and 7546 genes, representing similar to 28% of the genomic annotated open reading frames (ORFs), were found with disruptive mutations in at least one accession. The distribution of these Psi s on chromosomes showed a significantly negative correlation between Psi s/ORFs and their local gene densities, suggesting a higher proportion of Psi s in gene desert regions, e. g. near centromeres. On the other hand, compared with the non-Psi loci, even the intact coding sequences (CDSs) in the Psi loci were found to have shorter CDS length, fewer exon number and lower GC content. In addition, a significant functional bias against the null hypothesis was detected in the Psi s mainly involved in responses to environmental stimuli and biotic stress as reported, suggesting that they are likely important for adaptive evolution to rapidly changing environments by pseudogenization to accumulate successive mutations.
  • Akiko Satake, Hitoshi Araki
    THEORETICAL ECOLOGY 5 (2) 283 - 296 1874-1738 2012/05 [Refereed][Not invited]
    Releasing captive-bred fish into natural environments (stocking) is common in fisheries worldwide. Although stocking is believed to have a positive effect on fish abundance over the short term, little is known about the long-term consequences of recurrent stocking and its influence on natural populations. In fact, there are growing concerns that genetically maladapted captive-bred fish can eventually reduce the abundance of natural population. In this study, we develop a simple model to quantitatively investigate the condition under which recurrent stocking has long-term effects on the natural population. Using a population dynamics model that takes into account a density-dependent recruitment, a gene responsible for the fitness difference between wild and captive-bred fish, and hybridization between them, we show that there is little or no contribution of recurrent stocking to the stock enhancement without a replacement of the wild gene pool by the captive-bred gene pool. The model further predicted that stocking of an intermediate level causes a reduction, rather than enhancement, of population size over the long term. The population decline due to stocking was attributed to the fitness disadvantage of captive-bred fish and strong overcompensation at recruitment stage. These results suggest that it would be difficult to simultaneously attain population size recovery and conservation of the local gene pool when captive-bred fish have fitness disadvantage in the wild, although caution is needed when applying the predictions from the simplified model to a specific species or population.
  • Etienne Bezault, Patricia Balaresque, Aboubacar Toguyeni, Yves Fermon, Hitoshi Araki, Jean-Francois Baroiller, Xavier Rognon
    BMC GENETICS 12 102  1471-2156 2011/12 [Refereed][Not invited]
    Background: Reconstructing the evolutionary history of a species is challenging. It often depends not only on the past biogeographic and climatic events but also the contemporary and ecological factors, such as current connectivity and habitat heterogeneity. In fact, these factors might interact with each other and shape the current species distribution. However, to what extent the current population genetic structure reflects the past and the contemporary factors is largely unknown. Here we investigated spatio-temporal genetic structures of Nile tilapia (Oreochromis niloticus) populations, across their natural distribution in Africa. While its large biogeographic distribution can cause genetic differentiation at the paleo-biogeographic scales, its restricted dispersal capacity might induce a strong genetic structure at micro-geographic scales.Results: Using nine microsatellite loci and 350 samples from ten natural populations, we found the highest genetic differentiation among the three ichthyofaunal provinces and regions (Ethiopian, Nilotic and Sudano-Sahelian) (R-ST = 0.38 - 0.69). This result suggests the predominant effect of paleo-geographic events at macro-geographic scale. In addition, intermediate divergences were found between rivers and lakes within the regions, presumably reflecting relatively recent interruptions of gene flow between hydrographic basins (R-ST = 0.24 - 0.32). The lowest differentiations were observed among connected populations within a basin (R-ST = 0.015 in the Volta basin). Comparison of temporal sample series revealed subtle changes in the gene pools in a few generations (F = 0 - 0.053). The estimated effective population sizes were 23 - 143 and the estimated migration rate was moderate (m similar to 0.094 - 0.097) in the Volta populations.Conclusions: This study revealed clear hierarchical patterns of the population genetic structuring of O. niloticus in Africa. The effects of paleo-geographic and climatic events were predominant at macro-geographic scale, and the significant effect of geographic connectivity was detected at micro-geographic scale. The estimated effective population size, the moderate level of dispersal and the rapid temporal change in genetic composition might reflect a potential effect of life history strategy on population dynamics. This hypothesis deserves further investigation. The dynamic pattern revealed at micro-geographic and temporal scales appears important from a genetic resource management as well as from a biodiversity conservation point of view.
  • Tingting Gu, Shengjun Tan, Xiaoxi Gou, Hitoshi Araki, Dacheng Tian
    GENETICS 186 (3) 1077 - U490 0016-6731 2010/11 [Refereed][Not invited]
    Protein is an essential component for life, and its synthesis is mediated by codons in any organisms on earth. While some codons encode the same amino acid, their usage is often highly biased. There are many factors that can cause the bias, but a potential effect of mononucleotide repeats, which are known to be highly mutable, on codon usage and codon pair preference is largely unknown. In this study we performed a genomic survey on the relationship between mononucleotide repeats and codon pair bias in 53 bacteria, 68 archaea, and 13 eukaryotes. By distinguishing the codon pair bias from the codon usage bias, four general patterns were revealed: strong avoidance of five or six mononucleotide repeats in codon pairs; lower observed/expected (o/e) ratio for codon pairs with C or G repeats (C/G pairs) than that with A or T repeats (A/T pairs); a negative correlation between genomic GC contents and the o/e ratios, particularly for C/G pairs; and avoidance of C/G pairs in highly conserved genes. These results support natural selection against long mononucleotide repeats, which could induce frameshift mutations in coding sequences. The fact that these patterns are found in all kingdoms of life suggests that this is a general phenomenon in living organisms. Thus, long mononucleotide repeats may play an important role in base composition and genetic stability of a gene and gene functions.
  • Jia-Xing Yue, Jinpeng Li, Dan Wang, Hitoshi Araki, Dacheng Tian, Sihai Yang
    BMC PLANT BIOLOGY 10 1471-2229 2010/11 [Refereed][Not invited]
    Background: Rates of molecular evolution vary widely among species. While significant deviations from molecular clock have been found in many taxa, effects of life histories on molecular evolution are not fully understood. In plants, annual/perennial life history traits have long been suspected to influence the evolutionary rates at the molecular level. To date, however, the number of genes investigated on this subject is limited and the conclusions are mixed. To evaluate the possible heterogeneity in evolutionary rates between annual and perennial plants at the genomic level, we investigated 85 nuclear housekeeping genes, 10 non-housekeeping families, and 34 chloroplast genes using the genomic data from model plants including Arabidopsis thaliana and Medicago truncatula for annuals and grape (Vitis vinifera) and popular (Populus trichocarpa) for perennials.Results: According to the cross-comparisons among the four species, 74-82% of the nuclear genes and 71-97% of the chloroplast genes suggested higher rates of molecular evolution in the two annuals than those in the two perennials. The significant heterogeneity in evolutionary rate between annuals and perennials was consistently found both in nonsynonymous sites and synonymous sites. While a linear correlation of evolutionary rates in orthologous genes between species was observed in nonsynonymous sites, the correlation was weak or invisible in synonymous sites. This tendency was clearer in nuclear genes than in chloroplast genes, in which the overall evolutionary rate was small. The slope of the regression line was consistently lower than unity, further confirming the higher evolutionary rate in annuals at the genomic level.Conclusions: The higher evolutionary rate in annuals than in perennials appears to be a universal phenomenon both in nuclear and chloroplast genomes in the four dicot model plants we investigated. Therefore, such heterogeneity in evolutionary rate should result from factors that have genome-wide influence, most likely those associated with annual/perennial life history. Although we acknowledge current limitations of this kind of study, mainly due to a small sample size available and a distant taxonomic relationship of the model organisms, our results indicate that the genome-wide survey is a promising approach toward further understanding of the mechanism determining the molecular evolutionary rate at the genomic level.
  • Michael S. Blouin, Virginie Thuillier, Becky Cooper, Vindhya Amarasinghe, Laura Cluzel, Hitoshi Araki, Christoph Grunau
    CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES 67 (2) 217 - 224 0706-652X 2010/02 [Refereed][Not invited]
    When salmonid fish that have been raised in hatcheries spawn in the wild, they often produce fewer surviving adult offspring than wild fish. Recent data from steelhead (Oncorhynchus mykiss) in the Hood River (Oregon, USA) show that even one or two generations of hatchery culture can result in dramatic declines in fitness. Although intense domestication selection could cause such declines, it is worth considering alternative explanations. One possibility is heritable epigenetic changes induced by the hatchery environment. Here, we show, using methylation-sensitive amplified fragment length polymorphism, that hatchery and wild adult steelhead from the Hood River do not appear to differ substantially in overall levels of genomic methylation. Thus, although altered methylation of specific DNA sites or other epigenetic processes could still be important, the hatchery environment does not appear to cause a global hypo- or hypermethylation of the genome or create a large number of sites that are differentially methylated.
  • Wei-Kuang Wang, Chuan-Wen Ho, Kuo-Hsiang Hung, Kuo-Hsiung Wang, Chi-Chun Huang, Hitoshi Araki, Chi-Chuan Hwang, Tsai-Wen Hsu, Naoki Osada, Tzen-Yuh Chiang
    NEW PHYTOLOGIST 188 (2) 488 - 500 0028-646X 2010 [Refereed][Not invited]
    P>Outcrossing Arabidopsis species that diverged from their inbreeding relative Arabidopsis thaliana 5 million yr ago and display a biogeographical pattern of interspecific sympatry vs intraspecific allopatry provides an ideal model for studying impacts of gene introgression and polyploidization on species diversification.Flow cytometry analyses detected ploidy polymorphisms of 2x and 4x in Arabidopsis lyrata ssp. kamchatica of Taiwan. Genomic divergence between species/subspecies was estimated based on 98 randomly chosen nuclear genes. Multilocus analyses revealed a mosaic genome in diploid A. l. kamchatica composed of Arabidopsis halleri-like and A. lyrata-like alleles.Coalescent analyses suggest that the segregation of ancestral polymorphisms alone cannot explain the high inconsistency between gene trees across loci, and that gene introgression via diploid A. l. kamchatica likely distorts the molecular phylogenies of Arabidopsis species. However, not all genes migrated across species freely. Gene ontology analyses suggested that some nonmigrating genes were constrained by natural selection.High levels of estimated ancestral polymorphisms between A. halleri and A. lyrata suggest that gene flow between these species has not completely ceased since their initial isolation. Polymorphism data of extant populations also imply recent gene flow between the species. Our study reveals that interspecific gene flow affects the genome evolution in Arabidopsis.
  • Hitoshi Araki, Corinne Schmid
    AQUACULTURE 308 (SUPPL.1) S2 - S11 0044-8486 2010 [Refereed][Not invited]
    Hatchery fish stocking for stock enhancement has been operated at a massive and global scale. However, the use of hatchery fish as a means of stock enhancement is highly controversial, and little is known about its effects on wild stock and consequences for stock enhancement. Here we review the scientific literature on this subject in order to address a fundamental - question is hatchery stocking a help or harm for wild stock and stock enhancement? We summarized 266 peer-reviewed papers that were published in the last 50 years, which describe empirical case studies on ecology and genetics of hatchery stocks and their effects on stock enhancement. Specifically, we asked whether hatchery stock and wild stock differed in fitness and the level of genetic variation, and whether stocking affected population abundance. Seventy studies contained comparisons between hatchery and wild stocks, out of which 23 studies showed significantly negative effects of hatchery rearing on the fitness of stocked fish, and 28 studies showed reduced genetic variation in hatchery populations. None of these studies suggested a positive genetic effect on the fitness of hatchery-reared individuals after release. These results suggest that negative effects of hatchery rearing are not just a concern but undeniably present in many aquaculture species. In a few cases, however, no obvious effect of hatchery rearing was observed, and a positive contribution of hatchery stock to the abundance of fish populations was indicated. These examples suggest that there is a chance to improve hatchery practices and mitigate the negative effects on wild stocks, although scientific data supporting the positive effect on stock enhancement are largely missing at this moment. Technically, microsatellite-based parentage assignments have been proven as a useful tool for the evaluation of reproductive fitness in natural settings, which is a key for stock enhancement by hatchery-based stocking. We discuss implications of these results, as well as their limitations and future directions. (C) 2010 Elsevier B.V. All rights reserved.
  • Hitoshi Araki, Becky Cooper, Michael S. Blouin
    BIOLOGY LETTERS 5 (5) 621 - 624 1744-9561 2009/10 [Refereed][Not invited]
    Supplementation of wild populations with captive-bred organisms is a common practice for conservation of threatened wild populations. Yet it is largely unknown whether such programmes actually help population size recovery. While a negative genetic effect of captive breeding that decreases fitness of captive-bred organisms has been detected, there is no direct evidence for a carry-over effect of captive breeding in their wild-born descendants, which would drag down the fitness of the wild population in subsequent generations. In this study, we use genetic parentage assignments to reconstruct a pedigree and estimate reproductive fitness of the wild-born descendants of captive-bred parents in a supplemented population of steelhead trout (Oncorhynchus mykiss). The estimated fitness varied among years, but overall relative reproductive fitness was only 37 per cent in wild-born fish from two captive-bred parents and 87 per cent in those from one captive-bred and one wild parent (relative to those from two wild parents). Our results suggest a significant carry-over effect of captive breeding, which has negative influence on the size of the wild population in the generation after supplementation. In this population, the population fitness could have been 8 per cent higher if there was no carry-over effect during the study period.
  • Liucun Zhu, Qiang Wang, Ping Tang, Hitoshi Araki, Dacheng Tian
    MOLECULAR BIOLOGY AND EVOLUTION 26 (10) 2353 - 2361 0737-4038 2009/10 [Refereed][Not invited]
    Spontaneous mutations are not randomly distributed throughout a genome. Although mutation hotspots are found on genomes of a variety of species, mechanisms that generate the hotspots are not well understood. In eukaryotes, strong association between a regional nucleotide Substitution rate and insertions/deletions (indels) was reported in a previous study, and the "indel-induced mutation" hypothesis was proposed. However, it is unknown whether the association exists even in prokaryote genomes. In this study, we conducted a systematic survey for the association in 262 complete genomes from 73 bacterial species. In these bacteria, the level of nucleotide diversity was negatively correlated with the distance from the closest indel, which is consistent with the eukaryote data. The same pattern was observed even after excluding noncoding sequences, indicating that the difference in functional constraints among genomic regions is not a primary cause of the correlation. In addition, the increase of nucleotide substitution rate was detected disproportionally on a lineage carrying a derived indel mutation, confirming the indel-nucleotide diversity association in the bacterial genomes. In some cases, the level of nucleotide diversity was more than 100 times higher in regions close to indels than in distant regions. Although further understanding of the molecular mechanism is required to test the hypothesis, these results suggest that the same mechanism for the indel-nucleotide diversity associations might exist in eukaryotes and prokaryotes and play an important role in molecular evolution.
  • Jianchang Du, Tingting Gu, Hao Tian, Hitoshi Araki, Yong-Hua Yang, Dacheng Tian
    GENE 426 (1-2) 1 - 6 0378-1119 2008/12 [Refereed][Not invited]
    While information for single nucleotide polymorphism is accumulating in many organisms, little is known about the magnitude and the occurrence of nucleotide dimorphism or higher order structural polymorphisms (grouped nucleotide polymorphisms or GNPs). To address these questions, we systematically investigated the genetic variations of 996 loci in 96 Arabidopsis accessions. Our data suggest that GNP loci are highly frequent in the genomes (40.4% of 996 loci), and that 66.7% of genetic variation in 996 loci is attributed to GNPs. The frequency distribution and the linkage analysis of GNP loci demonstrate that GNPs occurred randomly, locally, ceaselessly and independently in general, although they are particularly abundant in the region near centromeres. The age distribution of GNP loci shows that the majority of these loci are under a transient phase of neutral evolution. The characteristics of GNPs imply that a molecular isolation exists in GNP loci, and most likely the indels caused isolation, which could explain how GNPs are generated and maintained. (c) 2008 Elsevier B.V. All rights reserved.
  • Wen Zhang, Xiaoqin Sun, Huizhong Yuan, Hitoshi Araki, Jue Wang, Dacheng Tian
    MOLECULAR GENETICS AND GENOMICS 280 (4) 351 - 361 1617-4615 2008/10 [Refereed][Not invited]
    Little is known about variation of nucleotide insertion/deletions (indels) within species. In Arabidopsis thaliana, we investigated indel polymorphism patterns between two genome sequences and among 96 accessions at 1215 loci. Our study identified patterns in the variation of indel density, size, GC content and distribution, and a correlation between indels and substitutions. We found that the GC content in indel sequences was lower than that in non-indel sequences and that indels typically occur in regions with lower GC content. Patterns of indel frequency distribution among populations were more consistent with neutral expectation than substitution patterns. We also found that the local level of substitutions is positively correlated with indel density and negatively correlated with their distance to the closed indel, suggesting that indels play an important role in nucleotide variation.
  • Dacheng Tian, Qiang Wang, Pengfei Zhang, Hitoshi Araki, Sihai Yang, Martin Kreitman, Thomas Nagylaki, Richard Hudson, Joy Bergelson, Jian-Qun Chen
    NATURE 455 (7209) 105 - U70 0028-0836 2008/09 [Refereed][Not invited]
    Mutation hotspots are commonly observed in genomic sequences and certain human disease loci(1-7), but general mechanisms for their formation remain elusive(7-11). Here we investigate the distribution of single- nucleotide changes around insertions/ deletions ( indels) in six independent genome comparisons, including primates, rodents, fruitfly, rice and yeast. In each of these genomic comparisons, nucleotide divergence ( D) is substantially elevated surrounding indels and decreases monotonically to near-background levels over several hundred bases. D is significantly correlated with both size and abundance of nearby indels. In comparisons of closely related species, derived nucleotide substitutions surrounding indels occur in significantly greater numbers in the lineage containing the indel than in the one containing the ancestral ( non- indel) allele; the same holds within species for single- nucleotide mutations surrounding polymorphic indels. We propose that heterozygosity for an indel is mutagenic to surrounding sequences, and use yeast genome- wide polymorphism data to estimate the increase in mutation rate. The consistency of these patterns within and between species suggests that indel- associated substitution is a general mutational mechanism.
  • Hitoshi Araki, Barry A. Berejikian, Michael J. Ford, Michael S. Blouin
    EVOLUTIONARY APPLICATIONS 1 (2) 342 - 355 1752-4571 2008/05 [Refereed][Not invited]
    Accumulating data indicate that hatchery fish have lower fitness in natural environments than wild fish. This fitness decline can occur very quickly, sometimes following only one or two generations of captive rearing. In this review, we summarize existing data on the fitness of hatchery fish in the wild, and we investigate the conditions under which rapid fitness declines can occur. The summary of studies to date suggests: nonlocal hatchery stocks consistently reproduce very poorly in the wild; hatchery stocks that use wild, local fish for captive propagation generally perform better than nonlocal stocks, but often worse than wild fish. However, the data above are from a limited number of studies and species, and more studies are needed before one can generalize further. We used a simple quantitative genetic model to evaluate whether domestication selection is a sufficient explanation for some observed rapid fitness declines. We show that if selection acts on a single trait, such rapid effects can be explained only when selection is very strong, both in captivity and in the wild, and when the heritability of the trait under selection is high. If selection acts on multiple traits throughout the life cycle, rapid fitness declines are plausible.
  • Hitoshi Araki, Flideki Innan, Martin Kreitman, Joy Bergelson
    GENETICS 177 (2) 1031 - 1041 0016-6731 2007/10 [Refereed][Not invited]
    The bacterial pathogen Pseudomonas viridiflava possesses two pathogenicity islands (PAIs) that share many gene homologs, but are structurally and phenotypically differentiated (T-PAI and S-PAI). These PAIs are paralogous, but only one is present in each isolate. While this dual presence/absence polymorphism has been shown to be maintained by balancing selection, little is known about the molecular evolution of individual genes on the PAIs. Here we investigate genetic variation of 12 PAI gene loci (7 on T-PAI and 5 on SPAI) in 96 worldwide isolates of R viridiflava. These genes include avirulence genes (hopPsyA and avrE), their putative chaperones (shcA and avrF), and genes encoding the type III outer proteins (hrpA, hrpZ, and hrpW). Average nucleotide diversities in these genes (pi = 0.004-0.020) were close to those in the genetic background. Large numbers of recombination events were found within PAIs and a sign of positive selection was detected in avrE. These results suggest that the PAI genes are evolving relatively freely from each other on the PAIs, rather than as a single unit tinder balancing selection. Evolutionarily stable PAIs may be preferable in this species because preexisting genetic variation enables P. viridiflava to respond rapidly to natural selection.
  • Hitoshi Araki, Becky Cooper, Michael S. Blouin
    SCIENCE 318 (5847) 100 - 103 0036-8075 2007/10 [Refereed][Not invited]
    Captive breeding is used to supplement populations of many species that are declining in the wild. The suitability of and long-term species survival from such programs remain largely untested, however. We measured lifetime reproductive success of the first two generations of steelhead trout that were reared in captivity and bred in the wild after they were released. By reconstructing a three-generation pedigree with microsatellite markers, we show that genetic effects of domestication reduce subsequent reproductive capabilities by similar to 40% per captive-reared generation when fish are moved to natural environments. These results suggest that even a few generations of domestication may have negative effects on natural reproduction in the wild and that the repeated use of captive-reared parents to supplement wild populations should be carefully reconsidered.
  • Undral Orgil, Hitoshi Araki, Samantha Tangchaiburana, Robert Berkey, Shunyuan Xiao
    Genetics 176 (4) 2317 - 2333 0016-6731 2007/08 [Refereed][Not invited]
    The RPW8 locus of Arabidopsis thaliana confers broad-spectrum resistance to powdery mildew pathogens. In many A. thaliana accessions, this locus contains two homologous genes, RPW8.1 and RPW8.2. In some susceptible accessions, however, these two genes are replaced by HR4, a homolog of RPW8.1. Here, we show that RPW8.2 from A. lyrata conferred powdery mildew resistance in A. thaliana, suggesting that RPW8.2 might have gained the resistance function before the speciation of A. thaliana and A. lyrata. To investigate how RPW8 has been maintained in A. thaliana, we examined the nucleotide sequence polymorphisms in RPW8 from 51 A. thaliana accessions, related disease reaction phenotypes to the evolutionary history of RPW8.1 and RPW8.2, and identified mutations that confer phenotypic variations. The average nucleotide diversities were high at RPW8.1 and RPW8.2, showing no sign of selective sweep. Moreover, we found that expression of RPW8 incurs fitness benefits and costs on A. thaliana in the presence and absence of the pathogens, respectively. Our results suggest that polymorphisms at the RPW8 locus in A. thaliana may have been maintained by complex selective forces, including those from the fitness benefits and costs both associated with RPW8. Copyright © 2007 by the Genetics Society of America.
  • Sihai Yang, Ke Jiang, Hitoshi Araki, Jing Ding, Yong-Hua Yang, Dacheng Tian
    GENE 394 (1-2) 87 - 95 0378-1119 2007/06 [Refereed][Not invited]
    High levels of inter-specific diversity are expected due to genetic isolation, the reproductive or geographical barriers, which lead to the accumulation of nucleotide variation. However, high levels of genetic variation are repeatedly observed even within species, notably at loci of the human major histocompatability complex and of plant resistance genes. Are molecular isolations responsible for the high intra-specific variation? To address this issue, we performed a genome-wide survey of the relationship between the possible factors that could cause genetic isolation, and the level of polymorphism, based on two rice genome comparisons. Here, we show that the levels of polymorphism in rice genes are positively correlated with the proportions of non-alignable flanking sequences, and that the correlation is observed even in single-copy genes. The physical locations of the genes were also investigated, and a strong association between the asymmetric architecture of genomes and the levels of polymorphism was revealed. These results suggest that the flank heterogeneity and the asymmetric architecture between genomes serve as isolation mechanisms at the molecular level that result in accumulation of higher genetic variation. This mechanism is of fundamental importance to understand natural genetic variation within species. (C) 2007 Elsevier B.V. All rights reserved.
  • Jing Ding, Hitoshi Araki, Qiang Wang, Pengfei Zhang, Sihai Yang, Jian-Qun Chen, Dacheng Tian
    BMC GENOMICS 8 1471-2164 2007/06 [Refereed][Not invited]
    Background: Individuals in the same species are assumed to share the same genomic set. However, it is not unusual to find an orthologous gene only in small subset of the species, and recent genomic studies suggest that structural rearrangements are very frequent between genomes in the same species. Two recently sequenced rice genomes Oryza sativa L. var. Nipponbare and O. sativa L. var. 93-11 provide an opportunity to systematically investigate the extent of the gene repertoire polymorphism, even though the genomic data of 93-11 derived from whole-short-gun sequencing is not yet as complete as that of Nipponbare.Results: We compared gene contents and the genomic locations between two rice genomes. Our conservative estimates suggest that at least 10% of the genes in the genomes were either under presence/absence polymorphism (5.2%) or asymmetrically located between genomes (4.7%). The proportion of these "asymmetric genes" varied largely among gene groups, in which disease resistance (R) genes and the RLK kinase gene group had 11.6 and 7.8 times higher proportion of asymmetric genes than housekeeping genes ( Myb and MADS). The significant difference in the proportion of asymmetric genes among gene groups suggests that natural selection is responsible for maintaining genomic asymmetry. On the other hand, the nucleotide diversity in 17 R genes under presence/absence polymorphism was generally low ( average nucleotide diversity = 0.0051).Conclusion: The genomic symmetry was disrupted by 10% of asymmetric genes, which could cause genetic variation through more unequal crossing over, because these genes had no allelic counterparts to pair and then they were free to pair with homologues at non-allelic loci, during meiosis in heterozygotes. It might be a consequence of diversifying selection that increased the structural divergence among genomes, and of purifying selection that decreased nucleotide divergence in each R gene locus.
  • Hitoshi Araki, Robin S. Waples, Michael S. Blouin
    MOLECULAR ECOLOGY 16 (11) 2261 - 2271 0962-1083 2007/06 [Refereed][Not invited]
    Indirect genetic methods are frequently used to estimate the effective population size (N-e) or effective number of breeders (N-b) in natural populations. Although assumptions behind these methods are often violated, there have been few attempts to evaluate how accurate these estimates really are in practice. Here we investigate the influence of natural selection following a population admixture on the temporal method for estimating N-e. Our analytical and simulation results suggest that N-e is often underestimated in this method when subpopulations differ substantially in allele frequencies and in reproductive success. The underestimation is exacerbated when true N-e and the fraction of the low-fitness group are large. As an empirical example, we compared N-b estimated in natural populations of steelhead trout (Oncorhynchus mykiss) using the temporal method (N-b[temp]) with estimates based on direct demographic methods (N-b[demo]) and the linkage disequilibrium method (N-b[LD]). While N-b[LD] was generally in close agreement with N-b[demo], N-b[temp] was much lower in sample sets that were dominated by nonlocal hatchery fish with low reproductive success, as predicted by the analytical results. This bias in the temporal method, which arises when genes associated with a particular group of parents are selected against in the offspring sample, has not been widely appreciated before. Such situations may be particularly common when artificial propagation or translocations are used for conservation. The linkage disequilibrium method, which requires data from only one sample, is robust to this type of bias, although it can be affected by other factors.
  • Jing Ding, Houlong Cheng, Xinqing Jin, Hitoshi Araki, Yonghua Yang, Dacheng Tian
    GENETICA 129 (3) 235 - 242 0016-6707 2007/03 [Refereed][Not invited]
    Heterogeneities in evolutionary pattern among different loci are commonly observed. To see whether the heterogeneity can also be observed among allelic groups in a single locus, we investigated the coding sequence and the flanking regions of Rpp13, a disease resistance gene in up to 60 accession lines from worldwide populations in Arabidopsis thaliana. An extraordinarily high level of polymorphism (pi=0.098) and four distinct clades were found in the leucine-rich repeat (LRR) region in this gene. No obvious geographic relationship with the clades was observed, and such clades were not observed in the other regions in and around this gene. The average genetic diversity among the clades ranged from 10 to 14.6% in the LRR. The levels of polymorphism within each clade varied largely, and significant heterogeneity in evolutionary rates among clades was detected. A statistically significant departure from neutrality was also detected by Fu & Li's tests. These results suggest that both directional and diversifying selection are working on this locus, and that natural selection can cause heterogeneity in evolutionary rate, even among allele groups in a locus.
  • Hitoshi Araki, Robin S. Waples, William R. Ardren, Becky Cooper, Michael S. Blouin
    MOLECULAR ECOLOGY 16 (5) 953 - 966 0962-1083 2007/03 [Refereed][Not invited]
    The effective population size is influenced by many biological factors in natural populations. To evaluate their relative importance, we estimated the effective number of breeders per year (N-b) and effective population size per generation (N-e) in anadromous steelhead trout (Oncorhynchus mykiss) in the Hood River, Oregon (USA). Using demographic data and genetic parentage analysis on an almost complete sample of all adults that returned to the river over 15 years (> 15 000 individuals), we estimated N-b for 13 run years and N-e for three entire generations. The results are as follows: (i) the ratio of N-e to the estimated census population size (N) was 0.17-0.40, with large variance in reproductive success among individuals being the primary cause of the reduction in N-e/N; (ii) fish from a traditional hatchery program (H-trad: nonlocal, multiple generations in a hatchery) had negative effects on N-b, not only by reducing mean reproductive success but also by increasing variance in reproductive success among breeding parents, whereas no sign of such effects was found in fish from supplementation hatchery programs (H-supp: local, single generation in a hatchery); and (iii) N-b was relatively stable among run years, despite the widely fluctuating annual run sizes of anadromous adults. We found high levels of reproductive contribution of nonanadromous parents to anadromous offspring when anadromous run size is small, suggesting a genetic compensation between life-history forms (anadromous and nonanadromous). This is the first study showing that reproductive interaction between different life-history forms can buffer the genetic impact of fluctuating census size on N-e.
  • Hitoshi Araki, William R. Ardren, Erik Olsen, Becky Cooper, Michael S. Blouin
    CONSERVATION BIOLOGY 21 (1) 181 - 190 0888-8892 2007/02 [Refereed][Not invited]
    Population supplementation programs that release captive-bred offspring into the wild to boost the size of endangered populations are now in Place for many species. The use of hatcheries for supplementing salmonid populations has become particularly popular Nevertheless, whether such programs actually increase the size of wild populations remains unclear, and predictions that supplementation fish drag down the fitness of wild fish remain untested. To address these issues, we performed DNA-based parentage analyses on almost complete samples of anadromous steelhead (Oncorhynchus mykiss) in the Hood River in Oregon (U.S.A.). Steelhead from a supplementation hatchery (reared in a supplementation hatchery and then allowed to spawn naturally in the wild) had reproductive success indistinguishable from that of wild fish. In contrast, fish from a traditional hatchery (nonlocal origin, multiple generations in hatcheries) breeding in the same river showed significantly lower fitness than wild fish. In addition, crosses between wild fish and supplementation fish were as reproductively successful as those between wild parents. Thus, there was no sign that supplementation fish drag down the fitness of wild fish by breeding with them for a single generation. On the other band, crosses between hatchery fish of either type (traditional or supplementation) were less fit than expected, suggesting a possible interaction effect These are the first data to show that a supplementation program with native brood stock can provide a single-generation boost to the size of a natural steelhead population without obvious short-term fitness costs. The long-term effects of population supplementation remain untested.
  • Hitoshi Araki, Dacheng Tian, Erica M. Goss, Katrin Jakob, Solveig S. Halldorsdottir, Martin Kreitman, Joy Bergelson
    Proceedings of the National Academy of Sciences of the United States of America 103 (15) 5887 - 5892 0027-8424 2006/04 [Refereed][Not invited]
    The contribution of arms race dynamics to plant-pathogen coevolution has been called into question by the presence of balanced polymorphisms in resistance genes of Arabidopsis thaliana, but less is known about the pathogen side of the interaction. Here we investigate structural polymorphism in pathogenicity islands (PAIs) in Pseudomonas viridiflava, a prevalent bacterial pathogen of A. thaliana. PAIs encode the type III secretion system along with its effectors and are essential for pathogen recognition in plants. P. viridiflava harbors two structurally distinct and highly diverged PAI paralogs (T- and S-PAI) that are integrated in different chromosome locations in the P. viridiflava genome. Both PAIs are segregating as presence/absence polymorphisms such that only one PAI ([T-PAI, ∇S-PAI] and [∇T-PAI, S-PAI]) is present in any individual cell. A worldwide population survey identified no isolate with neither or both PAI. T-PAI and S-PAI genotypes exhibit virulence differences and a host-specificity tradeoff. Orthologs of each PAI can be found in conserved syntenic locations in other Pseudomonas species, indicating vertical phylogenetic transmission in this genus. Molecular evolutionary analysis of PAI sequences also argues against "recent" horizontal transfer. Spikes in nucleotide divergence in flanking regions of PAI and ∇-PAI alleles suggest that the dual PAI polymorphism has been maintained in this species under some form of balancing selection. Virulence differences and host specificities are hypothesized to be responsible for the maintenance of the dual PAI system in this bacterial pathogen. © 2006 by The National Academy of Sciences of the USA.
  • Jingdan Shen, Hitoshi Araki, Lingling Chen, Jian Qun Chen, Dacheng Tian
    Genetics 172 (2) 1243 - 1250 0016-6731 2006/02 [Refereed][Not invited]
    While the presence/absence polymorphism is commonly observed in disease resistance (R-) genes in Arabidopsis, only a few R-genes under the presence/absence polymorphism (R-P/A) have been investigated. To understand the mechanism of the molecular evolution of R-P/A, we investigated genetic variation of nine R-P/A in A. thaliana from worldwide populations. The number of possessed R-genes varied widely among accessions (two to nine, on average 4.3 ± 1.6/accession). No pair of accessions shared the same haplotype, and no clear geographic differentiation was observed with respect to the pattern of presence/absence of the R-genes investigated. Presence allele frequencies also varied among loci (25-70%), and no linkage disequilibrium was detected among them. Although the LRR region in regular R-genes is known to be highly polymorphic and has a high Ka/Ks ratio in A. thaliana, nucleotide sequences of this region in the R-P/A showed a relatively low level of genetic variation (π = 0.0002-0.016) and low Ka/Ks (0.03-0.70, <1). In contrast, the nucleotide diversities around the deletion junction of R-P/A were constantly high between presence and absence accessions for the R-genes (Dxy = 0.031-0.103). Our results suggest that R-P/A loci evolved differently from other R-gene loci and that balancing selection plays an important role in molecular evolution of R-P/A. Copyright © 2006 by the Genetics Society of America.
  • Hitoshi Araki, Michael S. Blouin
    Molecular Ecology 14 (13) 4097 - 4109 0962-1083 2005/11 [Refereed][Not invited]
    Parentage assignment is widely applied to studies on mating systems, population dynamics and natural selection. However, little is known about the consequence of assignment errors, especially when some parents are not sampled. We investigated the effects of two types of error in parentage assignment, failing to assign a true parent (type A) and assigning an untrue parent (type B), on an estimate of the relative reproductive success (RRS) of two groups of parents. Employing a mathematical approach, we found that (i) when all parents are sampled, minimizing either type A or type B error insures the minimum bias on RRS, and (ii) when a large number of parents is not sampled, type B error substantially biases the estimated RRS towards one. Interestingly, however, (iii) when all parents were sampled and both error rates were moderately high, type A error biased the estimated RRS even more than type B error. We propose new methods to obtain an unbiased estimate of RRS and the number of offspring whose parents are not sampled (zWz), by correcting the error effects. Applying them to genotypic data from steelhead trout (Oncorhynchus mykiss), we illustrated how to estimate and control the assignment errors. In the data, we observed up to a 30% assignment error and a strong trade-off between the two types of error, depending on the stringency of the assignment decision criterion. We show that our methods can efficiently estimate an unbiased RRS and zWz regardless of assignment method, and how to maximize the statistical power to detect a difference in reproductive success between groups. © 2005 Blackwell Publishing Ltd.
  • H. Araki, S. Yoshizumi, N. Inomata, T. Yamazaki
    Journal of Heredity 96 (4) 388 - 395 0022-1503 2005/07 [Refereed][Not invited]
    In natural populations of Drosophila melanogaster, an amylase isozyme with the lowest α-amylase activity (AMY1,1) is predominant. To evaluate the selective significance of AMY1,1 and its regulatory factor(s), we examined selection experiments in laboratory populations on two distinct food environments. After 300 generations, AMY1,1 became predominant (89%) in a glucose (a product of AMY)-rich environment, while an isozyme with higher α-amylase activity, AMY1,6, became predominant (83%) in a starch (substrate)-rich environment. We found that the identical alleles of the amylase (Amy) gene, which encodes each of AMY 1,1 and AMY1,6, were shared between the two populations in the different food environments, employing the nucleotide sequencing of the duplicated Amy genes. Nevertheless, AMY1,6 homozygotes selected in the starch-rich environment had a twofold higher AMY enzyme activity than those selected in the glucose-rich environment, suggesting a coadaptation of the coding region and its regulatory factor(s) on the genetic background. Such a difference in AMY enzyme activity was not detected between AMY1,1 homozygotes, suggesting that the effect of the genetic background is epistatic. Our results indicate that natural selection is working on the Amy gene system as a whole for flies to adapt to the various food environments of local populations. © The American Genetic Association. 2005. All rights reserved.
  • T. Zhou, Y. Wang, J. Q. Chen, H. Araki, Z. Jing, K. Jiang, J. Shen, D. Tian
    Molecular Genetics and Genomics 271 (4) 402 - 415 1617-4615 2004/05 [Refereed][Not invited]
    A complete set of candidate disease resistance (R) genes encoding nucleotide-binding sites (NBSs) was identified in the genome sequence of japonica rice (Oryza sativa L. var. Nipponbare). These putative R genes were characterized with respect to structural diversity, phylogenetic relationships and chromosomal distribution, and compared with those in Arabidopsis thaliana. We found 535 NBS-coding sequences, including 480 non-TIR (Toll/IL-1 receptor) NBS-LRR (Leucine Rich Repeat) genes. TIR NBS-LRR genes, which are common in A. thaliana, have not been identified in the rice genome. The number of non-TIR NBS-LRR genes in rice is 8.7 times higher than that in A. thaliana, and they account for about 1% of all of predicted ORFs in the rice genome. Some 76% of the NBS genes were located in 44 gene clusters or in 57 tandem arrays, and 16 apparent gene duplications were detected in these regions. Phylogenetic analyses based both NBS and N-terminal regions classified the genes into about 200 groups, but no deep clades were detected, in contrast to the two distinct clusters found in A. thaliana. The structural and genetic diversity that exists among NBS-LRR proteins in rice is remarkable, and suggests that diversifying selection has played an important role in the evolution of R genes in this agronomically important species. (Supplemental material is available online at http:// © Springer-Verlag 2004.
  • Katrin Jakob, Erica M. Goss, Hitoshi Araki, Tam Van, Martin Kreitman, Joy Bergelson
    Molecular Plant-Microbe Interactions 15 (12) 1195 - 1203 0894-0282 2002/12/01 [Refereed][Not invited]
    We report the isolation and identification of two natural pathogens of Arabidopsis thaliana, Pseudomonas viridiflava and Pseudomonas syringae, in the midwestern United States. P. viridiflava was found in six of seven surveyed Arabidopsis thaliana populations. We confirmed the presence in the isolates of the critical pathogenicity genes hrpS and hrpL. The pathogenicity of these isolates was verified by estimating in planta bacterial growth rates and by testing for disease symptoms and hypersensitive responses to A. thaliana. Infection of 21 A. thaliana ecotypes with six locally collected P. viridiflava isolates and with one P. syringae isolate showed both compatible (disease) and incompatible (resistance) responses. Significant variation in response to infection was evident among Arabidopsis ecotypes, both in terms of symptom development and in planta bacterial growth. The ability to grow and cause disease symptoms on particular ecotypes also varied for some P. viridiflava isolates. We believe that these pathogens will provide a powerful system for exploring coevolution in natural plant-pathogen interactions.
  • Dacheng Tian, Hitoshi Araki, Eli Stahl, Joy Bergelson, Martin Kreitman
    Proceedings of the National Academy of Sciences of the United States of America 99 (17) 11525 - 11530 0027-8424 2002/08/20 [Refereed][Not invited]
    Natural selection and genetic linkage cause DNA segments to have genealogical histories resembling those of the selected sites. When a polymorphism maintained by selection is old, it will have an island of enhanced sequence variability surrounding it, which represents a detectable "signature of selection." We investigate the structure of single-nucleotide polymorphisms (SNPs) in a 20-kb interval containing the Arabidopsis thaliana disease resistance gene RPS5, a locus containing common alleles for the presencej presence/absence of the entire locus. The alleles are considerably diverged at surrounding sites, indicative of an old polymorphism maintained by selection. The island of "enhanced" variability extends several kilobases to either side of the RPS5 deletion junction, and these SNPs are in nearly complete linkage disequilibrium with the RPS5 insertion/deletion. At a distance of 10 kb to either side of the locus, however, we find low levels of polymorphism and the absence of linkage disequilibrium between individual SNPs and RPS5 alleles. Our results show that the interval of enhanced variability surrounding this balanced polymorphism in Arabidopsis is large enough to be readily detected, but small enough to span the focal gene and few others. For this species it should be possible to identify the complete set of genes with long-lived polymorphisms, a potentially important subset of genes segregating for functional variants.
  • Hitoshi Araki, Nobuyuki Inomata, Tsuneyuki Yamazaki
    Genetics 157 (2) 667 - 677 0016-6731 2001 [Refereed][Not invited]
    In this study, we randomly sampled Drosophila melanogaster from Japanese and Kenyan natural populations. We sequenced duplicated (proximal and distal) Amy gene regions to test whether the patterns of polymorphism were consistent with neutral molecular evolution. Fst between the two geographically distant populations, estimated from Amy gene regions, was 0.084, smaller than reported values for other loci, comparing African and Asian populations. Furthermore, little genetic differentiation was found at a microsatellite locus (DROYANETSB) in these samples (Gst′ = -0.018). The results of several tests (Tajima's, Fu and Li's, and Wall's tests) were not significantly different from neutrality. However, a significantly higher level of fixed replacement substitutions was detected by a modified McDonald and Kreitman test for both populations. This indicates that positive selection occurred during or immediately after the speciation of D. melanogaster. Sliding-window analysis showed that the proximal region 1, a part of the proximal 5′ flanking region, was conserved between D. melanogaster and its sibling species, D. simulans. An HKA test was significant when the proximal region 1 was compared with the 5′ flanking region of Alcohol dehydrogenase (Adh), indicating a severe selective constraint on the Amy proximal region 1. These results suggest that natural selection has played an important role in the molecular evolution of Amy gene regions in D. melanogaster.
  • Hitoshi Araki, Hidenori Tachida
    Genetics 147 (2) 907 - 914 0016-6731 1997/10 [Refereed][Not invited]
    Variances of evolutionary rates among lineages in some proteins are larger than those expected from simple Poisson processes. This phenomenon is called overdispersion of the molecular clock. If population size N is constant, the overdispersion is observed only in a limited range of 2Nσ under the nearly neutral mutation model, where σ represents the standard deviation of selection coefficients of new mutants. In this paper, we investigated effects of changing population size on the evolutionary rate by computer simulations assuming the nearly neutral mutation model. The size was changed cyclically between two numbers, N1 and N2 (N1 > N2), in the simulations. The overdispersion is observed if 2N2σ is less than two and the state of reduced size (bottleneck state) continues for more than ~0.1/u generations, where u is the mutation rate. The overdispersion results mainly because the average fitnesses of only a portion of populations go down when the population size is reduced and only in these populations subsequent advantageous substitutions occur after the population size becomes large. Since the fitness reduction after the bottleneck is stochastic, acceleration of the evolutionary rate does not necessarily occur uniformly among loci. From these results, we argue that the nearly neutral mutation model is a candidate mechanism to explain the overdispersed molecular clock.


Awards & Honors

  • 2007 Society of Evolutionary Studies, Japan Awards for encouragement of young scientist
    受賞者: Hitoshi Araki

Research Grants & Projects

  • 環境DNAを用いたサケ科魚類および回遊性魚類の種内多型解析手法の開発
    日本学術振興会:科学研究費助成事業 基盤研究(B)
    Date (from‐to) : 2020/04 -2023/03 
    Author : 荒木 仁志
  • Monitoring of fauna of the Northern Territory, with a special attention to the sika deer and the European mink
    Japan Society for the Promotion of Science:Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)
    Date (from‐to) : 2020/04 -2023/03 
    Author : 大舘 智志, 荒木 仁志, 河合 久仁子
  • Understanding genetic diversity, population structure and natural distribution of a critically endangered salmonid species (Sakhalin taimen) using environmental DNA
    Japan Society for the Promotion of Science:Grants-in-Aid for Scientific Research Grant-in-Aid for JSPS Fellows
    Date (from‐to) : 2017/11 -2020/03 
    Author : 荒木 仁志, CAMPBELL MATTHEW
    本研究は日本最大の淡水魚で絶滅危惧種であるイトウの生態に関する新たな知見を得るため、昨今進展目覚ましい環境DNAを用いた手法を核DNAの種内多型に応用する技術開発を目標としている。現在環境DNA技術は主に細胞内小器官の一つであるミトコンドリアのDNAを基に解析されているが、ミトコンドリアDNAは一般に種内多型に乏しく、同一種内でおこる変異の多くを反映していない。そこで、環境水中の核DNA情報をより高密度で集積することにより、「一すくいの水から希少種・野外集団の遺伝的多様性評価」へとつなげるのが本研究プロジェクトの狙いである。この技術開発が実現すれば、イトウに限らず希少種を捕獲したり傷つけたりすることなく彼らの遺伝的多様性を評価できるばかりか、過去のボトルネック、集団間の遺伝的交流といった歴史についても推定が可能となることが期待される。 これにはRAD-seqと呼ばれる手法を用い、本解析に適したゲノムスケールでの核DNAマーカー探索を行う必要があるため、H29年度はこの解析を実施するためのサンプル収集と予備的な解析を実施した。共同研究者であるマシュー・キャンベル(JSPS外国人特別研究員)の着任がH29年10月末であったことから、昨年度は5カ月間という限られた期間ではあったが、研究協力者らの協力の下、約30個体のイトウ組織サンプルからのDNA抽出が実現し、これらのサンプルを基にRAD-seq法による核DNAマーカー開発の準備が整いつつある。
  • 環境DNAを用いた回遊性魚類分布推定と河川工作物の影響評価
    日本学術振興会:科学研究費助成事業 基盤研究(B)
    Date (from‐to) : 2017/04 -2020/03 
    Author : 荒木 仁志, 福島 路生
    本研究プロジェクトは、生態学分野において発展目覚ましい「環境DNA」を用いて、地域特異性の高い回遊性魚類の生物分布や季節性、河川工作物の影響を客観的かつ網羅的に解明することを目的としている。河川工作物には大規模なダムから大小さまざまな堰堤・カルバートなど様々なものがあり、また新たに魚道を新設した場所など、その形態は多岐にわたる。これら個別の状況を体系立てて整理し、環境DNAメタバーコーディングと呼ばれる手法により、工作物上下の魚類相を明らかにするのが目下の目標となっている。 H30年度はH29年度に引き続き国立環境研究所の協力の下、胆振・日高地方をはじめ北海道内約100河川(二年合計では250河川)において本解析に供する河川水サンプルの収集を行った。これらのサンプルは申請者(荒木)の所属する北海道大学農学部において継続して解析中だが、初年度に調査を行った道北・道東地方の河川水からは回遊魚であるサケやサクラマス、カラフトマスはもちろんのこと、絶滅危惧種イトウや希少種エゾホトケを含む多数の魚種由来の環境DNA検出が見られている。 これらの研究成果は日本生態学会(神戸大会)や環境DNA学会(東京)で発表したほか、環境アセスメント協会や魚道研究会、猿払イトウ保全協議会シンポジウムでの招待講演等でも発表を行い、専門家・一般市民を交えての情報交換を行った。 最終年度となるH31年度にはこれらの結果をもとに河川工作物上下比較による各魚種の遡上阻害の有無を評価する予定だが、サケ、イトウ、サクラマス、シシャモについては種特異的な環境DNA定量プライマー開発に基づく生物量推定も進めており、上記サンプルの一部を用いて定性的のみならず定量的な評価を可能にする。
  • Japan Society for the Promotion of Science:Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
    Date (from‐to) : 2014/04 -2017/03 
    Author : SAITOH Takashi
    The relationship between mtDNA and ncDNA diversity was analyzed in order to test a theoretical prediction that mtDNA diversity should be much lower than ncDNA diversity. In contrast to this prediction, mtDNA diversity was higher than ncDNA diversity in many mammalian and avian populations. This was attributed to higher mutation rate in mtDNA, while high variation of the diversities was interpreted as a result of population fluctuation. The relationship between mtDNA and ncDNA diversity differed between mammalian and avian populations: mtDNA diversity was higher in mammals than in birds. This difference could be explained by different dispersal tendency. Male-biased dispersal prevails in mammals, where female-biased dispersal is common in birds. These results supported my hypothesis that sub-population structure plays an important role in maintaining genetic diversity.
  • Japan Society for the Promotion of Science:Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
    Date (from‐to) : 2014/04 -2017/03 
    Author : Araki Hitoshi, SATO Shunpei, KOIZUMI Itsuro, O' MALLEY Kathleen
    Salmon is very popular in Japan. While majority of fish in a market is hatchery-reared, ecology of wild salmon is largely unknown. In this study, we investigated genetic basis of wild chum salmon, which returned to their mother rivers at different timings. We found that in some rivers in Japan, early-run population and late-run population are clearly distinct both in timing and the population genetic structure. In addition, the population genetic structure in a river where hatchery fish have been imported was similar to that in its source, despite the fact that the river holds large amount of wild population at this point of time. These results suggest that salmon populations with different run timings are genetically differentiated even within a same river, and that they should be managed differently.
  • Japan Society for the Promotion of Science:Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Exploratory Research
    Date (from‐to) : 2014/04 -2017/03 
    Author : ARAKI Hitoshi, KONDO Michio, DOI Hideyuki, SATO Shunpei
    Monitoring and biomass estimation of wild organisms are of central importance in conservation biology. However, aquatic organisms are difficult to monitor because of their difficulties in catch and visual observations in the wild. In this study, we aimed to establish a new molecular method for monitoring and biomass estimation of salmonid species in the wild. We use environmental DNA, which is defined as DNA from environmental media (e.g., water for fish), in order to identify and estimate the amount of wild organisms nearby. Results from our rearing experiments, together with our trials in rivers and the ocean, suggest that environmental DNA we detected indeed reflects the presence/absence and spatio-temporal variation in salmonid species.
  • シロイヌナズナの抵抗性遺伝子と病原体抗原遺伝子の共進化に関する研究
    日本学術振興会:科学研究費助成事業 特別研究員奨励費
    Date (from‐to) : 2002 -2004 
    Author : 荒木 仁志
    シロイヌナズナで見つかっている病原体認識遺伝子、R遺伝子は、LRRと呼ばれるシグナル伝達に関わると思われる領域を持ち、バクテリアの持つAvr遺伝子の産物を特異的に認識して免疫反応を引き起こす。しかしながら、R遺伝子、Avr遺伝子の分子進化上の対応関係については未だ明らかにされていない。本研究は、シロイヌナズナのR遺伝子の一つ、RPS5の種内変異を解析すると共に、自然界における主要な病原体と思われるPseudomonas viridiflavaのAvr遺伝子を同定し、種内変異を基にR遺伝子との共進化のパターンについて解析を行うことにより、植物の抵抗性遺伝子とバクテリアの抗原遺伝子の間の相互作用、植物の免疫システムの獲得プロセスを解明することを目的としている。 本年度は、昨年度より研究代表者が共同研究者であるシカゴ大学生態進化学講座のメンバーと共に携わってきたRPS5の種内変異の解析を行い、この遺伝子が、これまで一般に受け入れられていた「軍拡競争仮説」の予測に反して分子進化上、長期にわたって「病原体抵抗性・非抵抗性」の種内多型を選択的に維持していることを示した。また、自家受精型であるこのシロイヌナズナにおいて、上記の遺伝子で選択的種内多型を維持したことがゲノム上の隣接する遺伝子に与える影響を、周辺部位のDNA多型から推定したところ、その影響の範囲がおよそ10KB以内であったことも示した。さらに、バクテリアの一種、Pseudomonas viridiflava及びPseudomonas syringaeがシロイヌナズナに寄生する天然の寄生バクテリアであることを示すに当たって、寄生に不可欠なプロセスに関与する複数の遺伝子がこれらのバクテリアに存在することを示した.。
  • キイロショウジョウバエのアミラーゼ遺伝子におけるエサ環境と適応度に関する研究
    日本学術振興会:科学研究費助成事業 特別研究員奨励費
    Date (from‐to) : 1999 -2000 
    Author : 荒木 仁志

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