Yuichi Nakajima

Yuichi Nakajima
National Institute for Environmental Studies · Center for Climate Change Adaptation

Ph.D. (Science)

About

38
Publications
6,301
Reads
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488
Citations
Additional affiliations
April 2021 - March 2022
Nagahama Institute of Bio-Science and Technology
Position
  • Project Associate Professor
February 2019 - March 2021
Okinawa Institute of Science and Technology
Position
  • Staff Scientist
August 2013 - January 2019
Okinawa Institute of Science and Technology
Position
  • Postdoctoral Scholar
Education
April 2006 - March 2009

Publications

Publications (38)
Article
In this study, we used a population genetic approach with microsatellite markers to attempt to clarify the species boundary of Acropora corals. Species in this taxon are usually difficult to distinguish with the usual molecular phylogenetic approach. We used Acropora sp. 1 and Acropora digitifera as the target species to shed light on the species b...
Article
Information on genetic diversity and differentiation of seagrass populations is essential for the conservation of coastal ecosystems. However, little is known about the seagrasses in the Indo-West Pacific Ocean, where the world's highest diversity of seagrasses occurs. The influence of sea currents on these populations is also unknown. We estimated...
Article
Full-text available
Population connectivity resulting from larval dispersal is essential for the maintenance or recovery of populations in marine ecosystems, including coral reefs. Studies of species diversity and genetic connectivity within species are essential for the conservation of corals and coral reef ecosystems. We analyzed mitochondrial DNA sequence types and...
Article
Full-text available
The elucidation of species diversity and connectivity is essential for conserving coral reef communities and for understanding the characteristics of coral populations. To assess the species diversity, intraspecific genetic diversity, and genetic differentiation among populations of the brooding coral Seriatopora spp., we conducted phylogenetic and...
Article
The farming of insects for food has many advantages, since insects are readily available, can be grown in small areas, are efficient at the conversion of food to biomass, and have a minimal contribution to environmental degradation. We review the prospects for farming insects using data obtained from next-generation genome-wide DNA sequencing to gu...
Preprint
Full-text available
Many marine species have a pelagic larval phase that undergo dispersal among habitats. Studies on marine larval dispersal have revealed a large variation in the spatial scale of dispersal, and accumulated evidence has shown that seascape patchiness is the major determinant for variation in self-recruitment. However, few studies have investigated th...
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Studies of mangrove population connectivity have focused primarily on global to regional scales and have suggested potential for long-distance connectivity, with archipelagos serving as stepping stones for trans-oceanic dispersal. However, the contribution of propagule dispersal to connectivity is still largely unknown, especially at local-scale. I...
Preprint
Understanding the structure and connectivity of coral populations is fundamental for developing marine conservation policies, especially in patchy environments such as archipelagos. The Nansei Islands, extending more than 1,000 km in southwestern Japan, are characterized by high levels of biodiversity and endemism, supported by coral reefs, althoug...
Article
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In this era of global climate change, understanding fundamental mechanisms of coral community maintenance and persistence in temperate non-reefal areas is a high marine conservation priority. To identify mechanisms of community maintenance and persistence via larval supply, we monitored coral settlement over 12 years and investigated the genetic po...
Article
Stony corals (Scleractinia) form the basis for some of the most diverse ecosytems on Earth, but we have much to learn about their evolutionary history and systematic relationships. In order to improve our understanding of species in corals we here investigated phylogenetic relationships between morphologically defined species and genetic lineages i...
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Coral-algae symbiosis represents the trophic and structural basis of coral reef ecosystems. However, despite global threats to coral reefs and the dependence of coral health and stress resistance upon such mutualisms, little is known about the community ecology of endosymbiotic Symbiodiniaceae. Concepts and methods from metacommunity ecology may be...
Article
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Okinawa Island is located near the center of the Nansei Islands (∼24–31°N), at a relatively high latitude for coral reefs. Nevertheless, more than 80 coral genera (over 400 species) are abundant in the Nansei Islands. Since March, 2017, scleractinian corals have been held in an outdoor tank at the OIST Marine Science Station at Seragaki, Onna with...
Article
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Populations of marine organisms on coral reef islands (CRI) are connected in space and time by seawater that transports propagules of plants, animals, and algae. Yet, despite this reality, it is often assumed that routine replenishment of populations of marine organisms on CRI is supported by locally-sourced propagules (hereafter, larvae). Followin...
Article
Due to increasing anthropogenic impacts on deep-sea hydrothermal vent ecosystems, it is essential to understand population structure and maintenance through larval recruitment and recovery of vent faunas after disturbances. In this study, we quantified vent animal recruitment in the Okinawa Trough, in the western Pacific Ocean. This is the first st...
Article
Full-text available
Seagrasses are marine angiosperms and play an essential ecological role in coastal ecosystems; however, seagrass meadows are threatened locally by anthropogenic disturbances. Understanding the dispersal patterns of seagrasses is essential for appropriate ecosystem management and establishment of marine protected areas (MPAs) in coastal ecosystems....
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Population genetics of the coral genus Pocillopora have been more intensively studied than those of any other reef-building taxon. However, recent investigations have revealed that the current morphological classification is inadequate to represent genetic lineages. In this study, we isolated and characterized novel microsatellite loci from morphol...
Article
Recent genetic research has begun to reveal population structures of deep-sea, hydrothermal vent species, but detailed assessments of genetic diversity and connectivity in hydrothermal vent populations, based on multiple genetic loci, are still scarce, especially in the Northwest Pacific. Accordingly, we isolated 38 novel polymorphic microsatellite...
Article
Tricholoma matsutake is an economically valuable fungus in Japan. Its fruit bodies occur in colonies established in natural pine forests. We traced colony establishment processes of T. matsutake in 2001 and 2010 by using microsatellite markers. T. matsutake genets persisted at least for a decade. Comparing colonies found in 2001 and 2010, five nove...
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To establish effective locations and sizes of potential protected areas for reef ecosystems, detailed information about source and sink relationships between populations is critical, especially in archipelagic regions. Therefore, we assessed population structure and genetic diversity of Acropora tenuis, one of the dominant stony coral species in th...
Article
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Cymodocea rotundata is an ecologically important tropical pioneer seagrass species distributed in the Indo-Pacific region. The population genetic diversity and structure of this species were analysed at 46 sites spanning the Philippines, Ryukyu Islands (northern limit) and Hainan Island, by using microsatellite simple sequence repeat (SSR) markers....
Article
While mitochondrial (mt) genomes are used extensively for comparative and evolutionary genomics, few mt genomes of deep-sea species, including hydrothermal vent species, have been determined. The Genus Lepetodrilus is a major deep-sea gastropod taxon that occurs in various deep-sea ecosystems. Using next-generation sequencing, we determined nearly...
Article
Hydrothermal vent fields in the western Pacific Ocean are mostly distributed along spreading centers in submarine basins behind convergent plate boundaries. Larval dispersal resulting from deep-ocean circulations is one of the major factors influencing gene flow, diversity, and distributions of vent animals. By combining a biophysical model and dee...
Article
Full-text available
Persistence of populations at their distributional ranges relies on local population dynamics and the fitness of species with low dispersal potential. We analyzed the population genetic diversity and structure of a tropical seagrass species, Cymodocea serrulata, at 34 sites spanning Philippine (diversity hotspot) and Ryukyu Islands (northern limit...
Article
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Recently, seagrasses have been declining along coastlines worldwide. We genetically analyzed 1058 ramets of Syringodium isoetifolium collected from 21 populations in the Philippines and 9 in the Ryukyu Islands using nine microsatellite markers, to provide a baseline of genetic information on seagrasses in the western North Pacific region under the...
Article
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The reef-building, scleractinian coral, Galaxea fascicularis, is classified into soft and hard types, based on nematocyst morphology. This character is correlated with the length of the mitochondrial non-coding region (mt-Long: soft colony type, and nematocysts with wide capsules and long shafts; mt-Short: hard colony type, and nematocysts with thi...
Article
Cymodocea serrulata is a tropical seagrass species distributed widely in the Indo-Pacific region. We developed 16 novel microsatellite (simple sequence repeat) markers for C. serrulata using next-generation sequencing for use in genetic studies. The applicability of these markers was attested by genotyping of 40 individuals collected from a natural...
Article
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Barnacles of the genus Neoverruca are abundant near deep-sea hydrothermal vents of the northwestern Pacific Ocean, and are useful for understanding processes of population formation and maintenance of deep-sea vent faunas. Using next-generation sequencing, we isolated 12 polymorphic microsatellite loci from Neoverruca sp., collected in the Okinawa...
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Full-text available
The genus Acropora (Scleractinia, Acroporidae) is one of the most widespread coral genera, comprising the largest number of extant species among scleractinian (reef-building) corals. Molecular phylogenetic studies have suggested that A. tenuis belongs to the most basal clade (clade I) while A. digitifera belongs to a derived clade (clade IV). In or...
Article
Full-text available
Genetic diversity and population genetic structure are key components of seagrass resilience and contribute to an understanding of its conservation and management. We isolated 29 polymorphic microsatellite (SSR) markers from a widely distributed pioneer seagrass, Cymodocea rotundata, by two methods; next generation sequencing and compound SSR marke...
Article
Nine microsatellite markers of a tropical seagrass species, Syringodium isoetifolium, were developed to investigate genetic diversity and genetic connectivity. The number of alleles detected per locus ranged from two to 16, and the observed and expected heterozygosities ranged from 0.00 to 1.00 and 0.12 to 0.91, respectively. The markers described...
Article
Knowledge of genetic connectivity is useful for understanding of the recovery potential of coral populations after various disturbances, such as coral mass bleaching. Population genetic studies in corals are mostly restricted to Australian and Caribbean species; studies in the northern Pacific are relatively limited. Using microsatellite markers, t...
Article
Nine microsatellite markers of a widely-distributed seagrass, Thalassia hemprichii, were developed to investigate genetic diversity and genetic connectivity. The number of alleles detected per locus ranged from 3 to 26, and the expected and observed heterozygosities ranged from 0.00 to 1.00 and 0.00 to 0.87, respectively. The markers described here...
Article
Using the dual-suppression polymerase chain reaction technique, 12 novel polymorphic nuclear microsatellite DNA markers were isolated from the tropical seagrass Enhalus acoroides. The isolated markers provided the polymorphisms of 2-13 alleles per locus in 3 populations located in Japan, China, and the Philippines. The values of the expected hetero...
Article
Full-text available
Recently, reef-building coral populations have been decreasing worldwide due to various disturbances. Population genetic studies are helpful for estimating the genetic connectivity among populations of marine sessile organisms with metapopulation structures such as corals. Moreover, the relationship between latitude and genetic diversity is informa...
Article
We performed fertilization experiments with Acropora digitifera, which is one of the dominant scleractinian corals in the Ryukyu Archipelago, Japan, to determine optimal conditions for in vitro manipulations. Our result suggests that conspecific fertilization is essentially complete within 30 min under the experimental conditions used in usual fert...
Article
Full-text available
Worldwide decline has been observed in coral populations due to environmental changes at both regional and global levels. Since corals have a typical metapopulation structure, the recovery of severely disturbed local populations depends on larval recruitment from outside the disturbed region. Therefore, the connectivity among local populations may...
Article
Full-text available
The development of microsatellite markers specific to corals (especially those of the genus Acropora) is difficult for various reasons (e.g. the small genome size and low number of microsatellite loci within the genome). Therefore, we developed a novel microsatellite marker and also attempted to apply those developed from other coral species to inv...

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