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To understand marine biodiversity in Japanese waters, we have compiled information on the marine biota in Japanese waters, including the number of described species (species richness), the history of marine biology research in Japan, the state of knowledge, the number of endemic species, the number of identified but undescribed species, the number of known introduced species, and the number of taxonomic experts and identification guides, with consideration of the general ocean environmental background, such as the physical and geological settings. A total of 33,629 species have been reported to occur in Japanese waters. The state of knowledge was extremely variable, with taxa containing many inconspicuous, smaller species tending to be less well known. The total number of identified but undescribed species was at least 121,913. The total number of described species combined with the number of identified but undescribed species reached 155,542. This is the best estimate of the total number of species in Japanese waters and indicates that more than 70% of Japan's marine biodiversity remains un-described. The number of species reported as introduced into Japanese waters was 39. This is the first attempt to estimate species richness for all marine species in Japanese waters. Although its marine biota can be considered relatively well known, at least within the Asian-Pacific region, considering the vast number of different marine environments such as coral reefs, ocean trenches, ice-bound waters, methane seeps, and hydrothermal vents, much work remains to be done. We expect global change to have a tremendous impact on marine biodiversity and ecosystems. Japan is in a particularly suitable geographic situation and has a lot of facilities for conducting marine science research. Japan has an important responsibility to contribute to our understanding of life in the oceans.
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Marine Biodiversity in Japanese Waters
Katsunori Fujikura
*, Dhugal Lindsay
, Hiroshi Kitazato
, Shuhei Nishida
, Yoshihisa Shirayama
1Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa, Japan, 2Atmosphere and Ocean Research Institute,
University of Tokyo, Kashiwa, Chiba, Japan, 3Seto Marine Biological Laboratory, Kyoto University, Shirahama, Wakayama, Japan
To understand marine biodiversity in Japanese waters, we have
compiled information on the marine biota in Japanese waters,
including the number of described species (species richness), the
history of marine biology research in Japan, the state of knowledge,
the number of endemic species, the number of identified but
undescribed species, the number of known introduced species, and
the number of taxonomic experts and identification guides, with
consideration of the general ocean environmental background,
such as the physical and geological settings. A total of 33,629
species have been reported to occur in Japanese waters. The state
of knowledge was extremely variable, with taxa containing many
inconspicuous, smaller species tending to be less well known. The
total number of identified but undescribed species was at least
121,913. The total number of described species combined with the
number of identified but undescribed species reached 155,542.
This is the best estimate of the total number of species in Japanese
waters and indicates that more than 70% of Japan’s marine
biodiversity remains un-described. The number of species reported
as introduced into Japanese waters was 39. This is the first attempt
to estimate species richness for all marine species in Japanese
waters. Although its marine biota can be considered relatively well
known, at least within the Asian-Pacific region, considering the
vast number of different marine environments such as coral reefs,
ocean trenches, ice-bound waters, methane seeps, and hydrother-
mal vents, much work remains to be done. We expect global
change to have a tremendous impact on marine biodiversity and
ecosystems. Japan is in a particularly suitable geographic situation
and has a lot of facilities for conducting marine science research.
Japan has an important responsibility to contribute to our
understanding of life in the oceans.
Understanding the biodiversity and function of marine ecosys-
tems, and how they respond to global change and human activities,
is essential to maintaining sustainable human life in harmony with
nature, because humans are directly or indirectly dependent on
marine life. However, the resources to identify and inventory
marine biodiversity have not increased commensurately with this
demand [1]. To contribute to our understanding of marine
ecosystems, a global network called the Census of Marine Life
(Census) was implemented in 2000 ( The
purpose of the Census is to assess and explain the diversity,
distribution, and abundance of marine life. To strengthen support
for marine biodiversity research at the country or regional scale, the
Census formed National and Regional Implementation Committees
(NRICs) in 12 countries or regions. The role of the NRICs is to
identify research and data priorities for marine biodiversity. The
work reported here contributes to the Japan NRICs efforts.
Japan has a rich marine species diversity because of a combination
of various historical and environmental (geological and physical
oceanographic) factors [2]. Traditionally, the marine biota has
constituted an important food resource in Japan owing to the
overpopulation of the country. According to the Food and
Agriculture Organization of the United Nations statistics, Japan’s
average per capita consumption of fishery products was 66.9 kg per
year for 2001–2003, approximately four times the world average.
Many Japanese people understand the importance of the marine
biota, and marine biology, including taxonomy, ecology, and
physiology, is more well studied in Japan than in many other nations.
Japan is surrounded by the sea, and marine ecosystem services
are expected to be affected by global climate change and human
impacts on the ocean. Thus, to understand marine biodiversity in
Japanese waters, we have compiled related marine biodiversity
information in Japan, including species richness indicators—such
as the number of described species (NDS), the number of endemic
species (NES), the number of identified but undescribed species
(NUS), the number of known introduced species (NIS), history of
marine biology, state of knowledge, list of taxonomic experts and
identification guides with consideration of the oceanic environ-
mental background (see Tables 1 and 2 for a list of abbreviations
used in this study).
General description of Japanese waters
Topographical and geological characteristics. Japan is an
island arc located on the western Pacific side of the Northern
Hemisphere and has no common land border with any other
country. The Japanese archipelago is located between approxi-
mately 20u309Nto45u309N and 123uE to 150uE, and
encompasses several climatic regimes from north to south, such as
the subboreal zone, cool temperate zone, middle temperate zone,
warm temperate zone, subtropical zone, and tropical zone. Japan’s
Exclusive Economic Zone (EEZ) extends from approximately 17uN
to 48uN, and from approximately 122uE to 158uE. The land area
of Japan is small at 3.78610
, but the EEZ is large at
, or approximately 11 times the area of the land, and
ranks as sixth largest in the world. The maximum water depth in
Japanese waters is 9,780 m in the Izu-Ogasawara (Bonin) Trench.
Japan is a nation composed of numerous islands. Hokkaido,
Honshu, Shikoku and Kyushu islands form a line from north to
south. There are some other groups of islands including the
Chishima (Kurile) Islands off the northeast of Hokkaido, the Izu-
Ogasawara (Bonin) Island chain stretching south of Honshu, and
Citation: Fujikura K, Lindsay D, Kitazato H, Nishida S, Shirayama Y (2010) Marine
Biodiversity in Japanese Waters. PLoS ONE 5(8): e11836. doi:10.1371/journal.
Editor: Joel M. Schnur, George Mason University, United States of America
Received February 9, 2010; Accepted May 12, 2010; Published August 2, 2010
Copyright: ß2010 Fujikura et al. This is an open-access article distributed
under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the
original author and source are credited.
Funding: This work was funded as part of a grant from the Alfred P. Sloan
Foundation and the Japan Agency for Marine-Earth Science and Technology. The
funders had no role in study design, data collection and analysis, decision to
publish, or preparation of the manuscript.
Competing Interests: The authors have declared that no competing interests
* E-mail:
PLoS ONE | 1 August 2010 | Volume 5 | Issue 8 | e11836
the Ryukyu Islands stretching south of Kyushu. The Japanese
archipelago is situated between the North Pacific Ocean and
several marginal seas, such as the Sea of Okhotsk to the north, the
Sea of Japan to the west, and the East China Sea to the southwest
(Figure 1). The length of the coastline is approximately 30,000 km.
Sea floor depth within Japan’s EEZ expressed as percentages of
the total seafloor area claimed as territory by Japan is shown in
Figure 2.
Topographic and geological characteristics of coastal areas and
the deeper seafloor have been reported in many studies [3,4].
There are varied topographies such as bays, beaches, inland seas,
mud flats, and rocky shores along the coastlines. Land reclamation
areas also are common in and around city areas. The major bays
are Uchiura Bay in Hokkaido, Ise Bay, Mikawa Bay, Mutsu Bay,
Sagami Bay, Suruga Bay, and Tokyo Bay on the Pacific side of
Honshu, Toyama Bay and Wakasa Bay on the Sea of Japan side of
Honshu, Tosa Bay in Shikoku Island, and Ariake Bay and
Kagoshima Bay in Kyushu Island. Mud flats larger than one
hectare in area number approximately 30, of which the largest is
in Ariake Bay. The most distinctive inland sea is the Seto Inland
Sea between Honshu, Shikoku, and Kyushu. This Inland Sea has
an area of approximately 20,000 km
and contains 720 small
Four tectonic plates, namely, the Eurasian, North American,
Pacific, and Philippine plates, converge in Japanese territory
(Figure 1). The Pacific Plate is moving from the East Pacific
Rise. A part of this plate subducts beneath the North American
Plate in the Japan and Kurile trenches. Another part of this
plate subducts beneath the Philippine Plate in the Izu-
Ogasawara (Bonin) Trench. The northern part of the Philippine
Plate subducts beneath the North American Plate. The
northwestern part of the Philippine Plate subducts beneath the
Eurasian Plate in the Nankai Trough and the Nansei-shoto
(Ryukyu) Trench. In these plate subduction areas, island arc-
trench systems are well developed. Usually, these systems are
composed of active volcanoes and trenches. Sagami and Suruga
troughs also belong to this system. Many submarine volcanoes
are situated in the Okinawa Trough and on the west side of the
Izu-Ogasawara (Bonin) Trench, namely, the Shichito-Iwojima
Ridge. On the whole, sea bottom topography in Japanese waters
is characterized by depression forms, such as trenches and
Physical and chemical characteristics. The Kuroshio and
Tsushima Currents are the major warm currents in Japanese
waters, and the Oyashio Current is the major cold current
(Figure 3). The Kuroshio is the largest current in the Pacific [5].
This current begins in the East China Sea and runs along the
Pacific coast of Japan. The current is about 200 km wide and its
influence can be recognized to as deep as 700 m. The speed in the
center of the current axis is 150–250 cm sec
. Transport volume
is estimated at 5610
ton sec
. The Tsushima Current splits
from the Kuroshio Current and flows from off Kyushu into the
Sea of Japan. The Oyashio Current flows southward through
Japanese waters from off Hokkaido along the Pacific coast. The
speed of this current is 20 cm sec
and the transportation ability
Table 1. Terminology abbreviations used in this study.
Acronym Word or Phrase
AUV Autonomous Underwater Vehicle
EEZ Exclusive economic zone
ENS Expected number of species
HOV Human occupied vehicle
ND No data
NDS Number of described species
NDSo Number of species recorded in Japanese waters in OBIS
NES Number of endemic species
NIS Number of known introduced species
NUS Number of identified but undescribed species
PES Percentage of endemic species
PRO Percentage of species recorded in Japanese waters in OBIS
ROV Remotely Operated Vehicle
tNDS Total number of described species
Table 2. Abbreviations for institutions and organizations.
Acronym Word or Phrase
AMSL Akajima Marine Science Laboratory
AIST Advanced Industrial Science and Technology
BIK Biological Institute on Kuroshio
BISMaL Biological Information System for Marine Life
CoML Census of Marine Life
GBIF Global Biodiversity Information Facility
HJC Hakodate Junior College
IODP Integrated Ocean Drilling Program
ISU Ishinomaki Senshu University
JAMSTEC Japan Agency for Marine-Earth Science and Technology
JMA Japan Meteorological Agency
JODC Japan Oceanographic Data Center
JSNFRI Japan Sea National Fisheries Research Institute
KMNH Kitakyushu Museum of Natural History and Human History
KMPC Kushimoto Marine Park Center
LBM Lake Biwa Museum
NHMIC Natural History Museum and Institute, Chiba
NIES National Institute for Environmental Studies
NIPR National Institute of Polar Research
NITE National Institute of Technology and Evaluation
NMNS National Museum of Nature and Science, Tokyo,
NRICs National and Regional Implementation Committees
NRIFS National Research Institute of Fisheries Science
OBIS Ocean Biogeographic Information System
OMNH Osaka Museum of Natural History
ORI Ocean Research Institute, the University of Tokyo
SFL Sugamo Foraminiferal Research Laboratory
SNF Seikai National Fisheries Research Institute
TAT Tokyo University of Agriculture and Technology
TNFRI Tohoku National Fisheries Research Institute
TSM Toyama Science Museum
TUMSAT Tokyo University of Marine Science and Technology
UBC University of British Columbia
YNU Yokohama National University
Marine Biodiversity in Japan
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of the Oyashio Current is smaller than that of the Kuroshio
Generally, the distribution of sea surface water temperature in
Japan follows the seasons and is characterized by spring, summer,
autumn, and winter patterns. Figure 4 shows the sea surface
temperature patterns for each season; summer is warmest and
winter is coldest. The vertical temperature profile in the Sea of
Japan differs sharply from that on the Pacific side (Figure 5).
Temperatures in the Sea of Japan are much lower than in the
Pacific. Climate regimes in Japanese waters are classified into six
categories between the subboreal and tropical zones (Figure 3).
The northernmost regions, such as the Sea of Okhotsk and the
Pacific east of Hokkaido belong to the subboreal zone, while the
southernmost areas such as the Ryukyu and Izu-Ogasawara
(Bonin) island regions belong to the tropical zone. On a large scale,
biogeographically, Japan belongs to the Indo-western Pacific
Various ecosystems in Japanese waters are associated with each
type of environment. For example, unique biological communities
occur above and below drift ice on the sea surface in coastal areas
in the Sea of Okhotsk off northern Hokkaido in winter.
Contrastingly, coral reefs are common in the Ryukyu and Izu-
Ogasawara (Bonin) island areas. Deep-sea organisms are found in
bathyal, abyssal, and hadal zones such as in trenches and troughs
and in the water column above them. Chemosynthesis-based
communities, including hydrothermal vent and methane seep
communities, are distributed along plate convergence areas
because of the accompanying tectonic activity [6,7]. Many seeps
have been found in the Japan Trench, Nankai Trough, Ryukyu
Trench, Sagami and Suruga bays, and the Sea of Japan. Several
vent communities have been found in the Izu-Ogasawara (Bonin)
Island area and in the Okinawa Trough.
Brief history of research in Japan. From 1616 to 1858,
Japan had a foreign relations policy prohibiting the entry of
Figure 1. Ocean bottom topography around Japan. White and red lines indicate plate boundaries and Japan’s Exclusive Economic Zone (EEZ),
Figure 2. Areal ratio of each 1,000 m depth zone in Japan’s
Exclusive Economic Zone (EEZ). Modified from http://www.sof.or.
Marine Biodiversity in Japan
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foreigners into Japan proper. During this period, biological
inventories were produced in the form of species lists for use in
natural medicines and seasonal keywords (kigo) for Haiku poetry.
However, the Dutch, who at the time were the only nationality
with permission to trade with Japan, brought many marine
organisms back to Holland, and these were then used by European
researchers for the production of marine biological monographs.
After 1858, several scientists were invited from Germany and the
United States to lecture on natural history at Japanese universities.
During this time, they conducted advanced investigations of the
marine fauna of Japan. Before World War II, several museums
and institutes were established and the foundations for marine
biological research were laid (Table S1).
The fauna of Sagami Bay and the ocean off the Boso Peninsula
were investigated in 1875 as part of a pioneering cruise by the
HMS Challenger (1872–76). Scientists of the Challenger purchased
many marine organisms at the fish market for their biological
samples. Also, scientists from the United States investigated
Sagami and Suruga bays using the HMS Albatross in 1906. The
first human-occupied vehicle (HOV) designed specifically for
studies on marine biology was named the Nishimura-shiki Mame
Sensui-tei ichi-go and was developed in 1929 in Japan. This
vehicle had sampling gear, a diesel engine, lights, two view ports,
and an underwater telephone system. After 1955, large-scale
investigations on marine fauna have been conducted using many
different research vessels in collaboration with international
projects. The former Emperor Hirohito actively studied the
taxonomy of marine animals, and he and his colleagues published
several monographs on the Arthropoda, Ascidia, Cnidaria,
Echinodermata, Mollusca, and Porifera [8–18].
Species richness estimation
Three species richness indices—including the number of
described species (NDS), the number of endemic species (NES),
and the number of identified but undescribed species (NUS), as
well as the number of known introduced species (NIS)—were
estimated for each taxonomic order of organisms occurring in
Japanese waters. In cases where it was impossible to classify species
to order, these indicators were estimated at the superorder,
infraorder, suborder, or family level. Additionally, the number of
taxonomic experts and identification guides such as monographs,
illustrated books, related scientific papers, or URLs for identifica-
tion of species were identified and counted. In cases where many
experts exist for each taxon, only two experts’ names were shown.
Figure 3. Schematic diagram of surface currents and climate regimes around Japan. Red and yellow arrows indicate warm (Kuroshio and
Tsushima) and cold (Oyashio) currents, respectively.
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Identification guides were chosen for their ability to satisfy the
basic requirements of students and scientists studying and working
on marine biology [1].
For each taxon, an attempt was made to estimate the status of
knowledge under a five-stage classification system based on the
following definitions:
5: Very well known. Satisfies all of the following requirements:
(1) more than 80% or more than 100 species occurring in Japanese
waters have been described in the scientific literature, (2)
identification guides including monographs, illustrated books, or
related scientific papers have been published within the last 20
years, and (3) more than one taxonomic expert exists in Japan.
4: Well known. (1) More than 70% or more than 10 species
occurring in Japanese waters have been described in the scientific
literature, (2) identification guides including monographs, illus-
trated books or related scientific papers have been published, and
(3) one or more taxonomic experts exist in Japan.
3: Poorly known. (1) More than 50% or fewer than 10 species
occurring in Japanese waters have been described in the scientific
literature, (2) at least one publication aiding identification has been
published in the past, and (3) no taxonomic experts active in
2: Very poorly known. Falls under at least one of the following
categories: (1) less than 50% or only a few species occurring in
Japanese waters have been described or, 2) no taxonomic expert
and or identification guide exists anywhere in the world.
1: Unknown. Falls under at least one of the following categories:
(1) no described species have been identified from Japanese waters
or, (2) no published information exists.
Many experts on the taxonomy or ecology of marine organisms
collaborated in the gathering of this species richness data (Table
The total number of described species (tNDS) was calculated by
combining the NDS for all taxa. Also, the total combined number
of both described and undescribed species in each phylum or
division was calculated by combining the NDS with the NUS in all
orders, superorders, infraorders, suborders, or families within the
phylum or division. The NUS values were estimated based on the
contributor’s own samples or according to their experience and
knowledge. We also calculated the expected number of species
(ENS) by combining the NDS and the NUS.
Endemic species were defined as those that have only been
reported from Japanese waters. The percentages of NES versus
NDS were calculated as the percentage of endemic species (PES)
Figure 4. Sea surface temperature maps in each season around Japan.
Marine Biodiversity in Japan
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according to the following equation: PES = (NES/NDS)6100.
Known introduced species were defined as those that have been
introduced into Japanese waters from outside their native
distributional range by human activity. We not only estimated
the NIS but also recorded the species names, presumed primary
mechanism of transport to Japan, and the presumed origin of the
introduced species.
Unfortunately, Japan does not yet have a national marine
species inventory for all marine organisms that occur in Japanese
waters. Thus, where there were no active experts for a taxon,
indicators were estimated using published scientific papers, or
databases such as the Japanese Biota Species Number Survey
( and others. Marine
biological studies have been carried out not only in the tidal zones
but also in the open ocean and in deep-sea regions using an array
of research vessels. Active ocean research vessels larger than 500
tons are shown in Table 3.
Comparisons between NDS and the number of species
recorded from Japanese waters in OBIS
The Ocean Biogeographic Information System (OBIS: http://, the Census of Marine Life’s main repository for
biogeographical information, is a useful database bringing together
an array of information on marine species occurrence and
distribution data throughout the world ocean. We referred to
the number of species recorded in Japanese waters in OBIS
(NDSo) for each taxon, using the advanced search function of
OBIS on 6 June 2009. The search was done within a polygon, the
boundaries of which corresponded to Japan’s EEZ, as claimed by
Japan on the same date. The percentages of the NDS versus the
NDSo were calculated as the percentage of species recorded in
Japanese waters in OBIS (PRO) according to the following
equation: PRO = (NDSo/NDS)6100.
Species richness in Japanese waters
Summarized data concerning species richness including the NDS
and NIS, and information on state of knowledge estimates, taxonomic
experts, and identification guides were compiled in Table 4. More
detailed data on species richness in each lower taxa (order or family
levels) including the NDS, NES, NUS, ENS, NIS, and information
on taxonomic experts, identification guides, and state of knowledge
estimates for each taxon are shown in Table S3. The tNDS in
Japanese waters reached 33,629. Among 79 phyla or divisions, 66
phyla or divisions contained more than one species. In 13 phyla or
divisions, there was no information allowing the computation of NDS
and NUS (Table S4). The phyla belonging to the Eukarya contain
many conspicuous, often larger species, had members living in
shallow water, and generally had a tendency to exhibit higher
reported species richness. The phylum Mollusca had the highest
reported value of 8,658 for the NDS. The second and third highest
NDS were within the Arthropoda and Chordata, respectively. The
10 phyla with the highest totals for the NDS comprised about 85
percent of the tNDS (Figure 6). Contrastingly, phyla containing many
inconspicuous, smaller species had a small NDS (Table S4).
The total NES was at least 1,872 (Table S5). Three classes—
Foraminifera, Actinopterygii and Gastropoda—contained 383,
358, and 286 endemic species, respectively. Two orders—Mysida
and Gorgonacea (this is currently placed within Alcyonacea by
many authors)—also had a high NES and relatively high PES,
approximately 50%. Several taxa, such as Platycopioida within the
Arthropoda, Nematomorpha, and Loricifera had an outstanding
PES, but the NDS values for these taxa were very low, usually 1 or
2. In spite of a relatively high NDS, Phyllodocida within the
Annelida and the Haptophyta had a very low NES. Totals of NUS
and ENS were estimated at 121,913 and 155,542, respectively
(Table S4). The total ENS is our best estimate of the total number
of species currently occurring in Japanese waters. Nematoda had
an exceptional NUS of 115,010, in spite of the fact that the NDS
was only 70 (Table S4). This signifies that almost all species within
the Nematoda are currently undescribed. Relatively well known
taxa, such as the Chordata, Crustacea, and Mollusca still
contained many undescribed species (Tables S3, S4). For example,
Nudibranchia of the Gastropoda, Amphipoda and Isopoda of the
Crustacea, and Gobiidae of the Chordata had more than 200
undescribed species. The state of knowledge varied greatly among
the lower taxa, even for conspicuous organisms.
The total NIS was 39, including 11 Mollusca, 10 each of the
Annelida and Arthropoda, 3 Chordata, 2 Myxozoa, and 1 of each
of the Chlorophyta, Cnidaria, and Heterokontophyta (Table S6).
The main presumed primary mechanism of transport is thought to
be through hull fouling or in ballast water brought by ships, as well
as through import as fisheries resources. On the other hand, the
Japanese Association of Benthology has indicated recently that
more than 40 of Japan’s native species have dispersed to other
nations as introduced species.
State of knowledge
Twelve phyla—Acanthocephala, Amoebozoa, Blastocladiomy-
cota, Chytridiomycota, Cycliophora, Glomeromycota, Heliozoa,
Figure 5. Vertical structure of temperature and salinity
between Sagami Bay on the Pacific side and the Sea of Japan.
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Microsporidia, Oomycota, Opalozoa, Percolozoa, and Thau-
marchaeota—were classified as Status 1 (Table S3). Many of these
unknown phyla are characterized as parasites and belong to either
the Fungi or Protista. Taxa containing many species targeted by
fisheries and with large and conspicuous species had a tendency to
be better known (Tables S3, S4). However, some unknown lower
taxa were recognized even within conspicuous phyla such as
Annelida, Cnidaria, Mollusca, and Porifera.
Comparisons between NDS and the number of species in
Japanese waters recorded in OBIS
Three phyla—the Nematoda, Phoronida, and Priapulida—had
a PRO of almost 100% (Table 5). This means that in the present
study the NDS corresponded to the NDSo, although we do not
know whether the species contained are identical or not. Taxa
having high NDS values, such as the Arthropoda, Chordata,
Echinodermata, Heterokontophyta, and Mollusca, had low PRO
values. The PRO of Annelida was moderate. The total NDSo was
only 2,820. This is a very low number in spite of the very high
tNDS of 33,629 in Japanese waters.
According to OBIS, the total number of marine species
described from the global ocean is estimated at about 230,000.
The tNDS in Japanese waters is 33,629 (Table 4) and this
approaches 14.6% of all marine species. The total area of Japanese
waters is 4.48610
and this is only 1.2% of the area of the
global ocean, which is 360610
in area. Also, the total
volume of Japanese waters is 12610
, or 0.9% of the global
ocean, which is 1,370610
in volume. Thus, Japan’s marine
species richness is high considering the small area and volume of
Japanese waters. The reason why such high diversity occurs is
undoubtedly the varied environments existing in Japanese waters
[19] including various topographical, geological, physical and
chemical characteristics (see ‘‘General description of Japanese
waters’’). Japan’s high reported species richness is also biased by
investigative effort. More so than in many other countries, marine
biologists in Japan have accumulated much taxonomic and
ecological data concerning marine species, because the Japanese
people have traditionally relied on marine fishery resources. Thus,
Japanese marine species diversity seems relatively high compared
with that of other areas.
In 2002, the Japanese Biota Species Number Survey Project,
including all the terrestrial and marine species in Japan, was
conducted by the Union of Japanese Societies for Systematic
Biology ( Japan’s to-
tal number of all species on land and in its waters was estimated at
about 90,000 species by this survey [20]. The taxon with the
highest reported species richness was the Insecta, with about
Table 3. Ocean research vessels (more than 500 gross tons) for marine biology in Japan.
Name of research vessel Gross tonnage Institution/Affiliation
Main mission
Bosei-maru 2,174 Tokai University Multi-purpose missions
Chikyu 57,087 JAMSTEC Drilling
Hakuho-maru 3,991 JAMSTEC Multi-purpose missions
Hokko-maru 568 NRIFS Fisheries science
Kairei 4,628 JAMSTEC Support of remotely operated vehicle
Kaiyo 3,350 JAMSTEC Multi-purpose missions
Kaiyo-maru 2,942 NRIFS Fisheries science
Keifu-maru 1,882 JMA Oceanography
Keiten-maru 860 Kagoshima University Fisheries science, Oceanography
Koyo-maru 2,703 NRIFS Fisheries science, Oceanography
Mirai 8,687 JAMSTEC Multi-purpose missions
Nagasaki-maru 842 Nagasaki University Fisheries science, Oceanography
Natsushima 1,739 JAMSTEC Support of remotely operated vehicle
Oshoro-maru 1,792 Hokkaido University Fisheries science, Oceanography
Ryofu-maru 1,380 JMA Oceanography
Shinyo-maru 649 TUMSAT Fisheries science, Oceanography
Shirase 12,500 NIPR Antarctic Expedition
Shoyo-maru 2,494 NRIFS Fisheries science
Shunyo-maru 1,228 NRIFS Fisheries science
Soyo-maru 1,234 NRIFS Fisheries science
Tansei-maru 610 JAMSTEC Multi-purpose missions
Tenyo-maru 1,020 NRIFS Fisheries science
Umitaka-maru 1,886 TUMSAT Fisheries science, Oceanography
Wakataka-maru 692 NRIFS Fisheries science
Yoko-maru 608 NRIFS Fisheries science
Yokosuka 4,439 JAMSTEC Support of human occupied vehicle
Each abbreviation is shown in Table 2.
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30,000 species, and this comprised fully one-third of all of Japan’s
reported species. The present tNDS in Japanese waters (33,629) is
also about one-third of all of Japan’s reported species. The areal
ratio of Japanese land (3.78610
) versus its waters (EEZ+
territorial, 4.47610
) is approximately 1:12. Thus, the
richness of marine species per unit area is 7.5610
, lower than the 2.4 species/km
reported for land species,
though the number of phyla is greater. Taxonomic and ecological
studies are more advanced on land than in the sea because of
logistic problems associated with research at sea, particularly
concerning the deep-sea. For example, more than 500 novel
species have been described over the last three decades in deep-sea
hydrothermal vent areas [21]. In other words, marine species
richness has a high potential to be underestimated, and species
richness values potentially increase more rapidly per unit of
investigative effort.
In 1981, the NDS values for several representative taxa
occurring in Japanese waters were estimated by Nishimura [19].
In the 28 years since that publication, NDS values for Amphipoda,
Asteroidea, Cephalopoda, Hydrozoa, Pisces, Polyplacophora, and
Pycnogonida have increased considerably owing to taxonomic and
ecological studies (Table 6). However, NDS values for Calcarea,
Echinoidea, Scyphozoa, and Sipuncula have remained the same
or have decreased. Recently, several researchers have become
active in Japan working on the Calcarea, Echinoidea, and
Scyphozoa, so their NDS values are expected to increase in the
near future. However, the number of taxonomic experts studying
the Sipuncula is too few—only a single researcher within Japan.
In Japanese waters, the NES is not great (Table S5), being only
5.6% of the tNDS. Because most marine species spend a part of or
their whole life cycle within the pelagic zone, the number of
endemic species in general in the oceans is few. An exception to
this rule is the many endemic species that have been reported from
unique habitats such as submarine caves, deep-sea hydrothermal
vents, methane seeps, sunken wood, and whale falls [7,22,23].
Additionally, the strong ocean currents in Japanese waters
(Figure 3) obviously allow marine organisms to disperse over a
wide distributional range. For example, the Kuroshio Current
transports marine organisms from the equatorial Pacific into
Japanese waters, while the Oyashio Current transports them from
Table 4. Taxonomic classification of species reported in the Japan’s exclusive economic zone (EEZ).
Taxonomic group NDS
State of
No. experts
No. identification
Domain Archaea 9 1–3 ND 10 .10
Domain Bacteria (including
843 3–5 ND 10 .10
Domain Eukarya
Kingdom Chromista Phaeophyta (Phaeophyceae) 304 3, 4 1 2 .3
Other Chromista 943 3–5 ND 2 .3
Kingdom Plantae Chlorophyta 248 3, 4 1 2 .3
Rhodophyta 898 3–5 0 2 .3
Angiospermae 44 4 0 2 .3
Other Plantae 5 3, 4 ND 2 .3
Kingdom Protista (Protozoa) Dinomastigota (Dinoflagellata) 470 3–5 0 4 .1
Foraminifera 2,321 3–5 0 5 6
Other Protista 1,410 1–5 0 16 .50
Kingdom Fungi 367 1–4 0 2 3
Kingdom Animalia Porifera 745 1–5 0 1 14
Cnidaria 1,876 1–5 1 16 .10
Platyhelminthes 188 1–5 0 2 1
Mollusca 8,658 1–5 11 10 .10
Annelida 1,076 1–5 10 7 4
Crustacea 6,232 2–5 10 .20 .10
Bryozoa 300 5 0 2 .1
Echinodermata 1,052 3–5 0 6 2
Urochordata (Tunicata) 384 4, 5 2 4 .3
Other invertebrates 1,314 1–5 2 .10 .10
Vertebrata (Pisces) 3,790 3–5 1 15 .50
Other vertebrates 152 3–5 0 4 .50
Sub-Total Eukarya 32,777 39
Total Regional Diversity
33,629 39
Number of described species.
State of knowledge definitions: see Methods.
Number of known introduced species.
Total regional diversity including all taxonomic groups as reported in Table S3.
Marine Biodiversity in Japan
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the northeast Pacific [2]. Decapoda and Echinoidea in Japanese
waters tend toward a high degree of endemism according to one
paleontological study [19]. However, the PES of Decapoda in the
present study is only 1.1% and is therefore not in agreement with
this previous study.
NUS values were estimated for only 30 of the 93 phyla (Table
S4). Total NUS in Japanese waters—121,913—is obviously an
underestimate because we could not estimate NUS for many taxa
containing predominantly inconspicuous, smaller species. The
NUS is approximately four times the tNDS. In the Nematoda,
incredibly high species diversity and the existence of numerous
undescribed species have been suggested by previous investigations
[24,25]. The present study also suggests an exceptional NUS in the
Nematoda within Japanese waters. In spite of this high species
richness in the Nematoda, the number of taxonomic experts in this
group is far too few in Japan. Taxa showing a smaller NUS than
NDS suggest that they are relatively well known taxonomically,
although the existence of cryptic species is still possible because of
a lack of good morphological characteristics in some taxa.
Examples of the above taxa include the Annelida, Arthropoda,
Chordata, Cnidaria, Granuloreticulosa, Mollusca, and Radiozoa.
According to our study, the percentage of NUS versus NDS is
low in the Rotifera, Cercozoa, Chordata, and Cyanobacteria, at
0.3%, 2.8%, 7.5%, and 9.1%, respectively. At a glance, this would
suggest that the Cercozoa and Cyanobacteria are well known
taxonomically. This assessment is probably erroneous, however,
because a concentrated sampling effort has been lacking, and too
few samples of these taxa have been studied.
In spite of the fact that Chordata is the most taxonomically well
known taxon in Japanese waters, a high number of undescribed
species was estimated. In particular, the family Gobiidae within
the Actinopterygii contains 216 undescribed species, versus 316
described species. The high ratio of NUS to NDS in the Gobiidae
is probably due to (1) difficulty of sample collection, (2) lack of
good morphological characteristics enabling ready species identi-
fication, and (3) lack of funding for taxonomic studies [26]. These
reasons are common to many groups with a high NUS-to-NDS
Another factor that needs to be borne in mind is that there may
be a higher reported ratio of NUS to NDS when a taxonomic
expert is actively working on a group, than when this is not the
case. For example, before 1999 a total of 28 siphonophore species
were reported from Japanese waters according to local taxonomic
treatises [27], and many of these were reported under obsolete
scientific names. Since 1999, it has become apparent that at least
65 species of siphonophore species occur [28,29], and that at least
9 of these are undescribed, sometimes at the genus or even family
level [28].
As maritime trade has increased, so have introductions of
invasive species into foreign waters throughout the world.
Introduced species can have severe impacts on local marine
ecosystems and on fisheries, shipping and power stations [30–33].
At least 39 recently introduced species occur in Japanese waters
(Table S6). Concrete examples include the gastropod Nassarius
sinarus, which detrimentally affects mariculture [33], and the
gastropod Euspira fortunei, which has also had an impact on the
native bivalve Ruditapes philippinarum [34]. Mytilopsis sallei, Mytilus
galloprovincialis, Perna viridis in the Mollusca, Hydroides elegans and
Hydroides dianthus in the Annelida, and Balanus amphitrite and Balanus
eburneus in the Arthropoda have had a highly detrimental effect on
oyster aquaculture. These species attach to the hulls of ships and to
the intake pipes of power plants. Balanus amphitrite, Balanus glandula,
and Carcinus aestuarii of the Arthropoda, and Mytilus galloprovinciali
of the Mollusca also have invaded several areas and excluded
Figure 6. Percent ratio of the number of described species (NDS) in respective phyla. The ratio means NDS versus the total number of
described species (tNDS) in all phyla ranked from top to 10th.
Marine Biodiversity in Japan
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native species. Caulerpa taxifolia of the Chlorophyta, called the
‘‘Killer Algae,’’ has spread from the Indian Ocean to areas off the
coasts of Australia, into the Mediterranean, and along the coasts of
the United States, affecting many native marine ecosystems. This
species was also recently introduced into Japanese waters.
Transport within the ballast water of large ships is one of the
major mechanisms responsible for the dispersal of nonnative
marine organisms around the world. Japan is one of the largest
nations for maritime trade, and ships traveling either to or from
Japan account for about 10% of the total ballast water around the
world [32]. This indicates that Japan has a high potential for
causing the introduction of invasive species to other regions. To
mitigate or avoid introductions of invasive species, the Invasive
Alien Species Act was promulgated in Japan in 2004.
State of knowledge
Taxa containing many conspicuous, larger species have a
tendency to be well known taxonomically and ecologically. On the
other hand, many taxa of which our knowledge is only of
elementary status (State of Knowledge 1) are recognized to occur
in Japanese waters (Table S3). Those less well known taxa include
the Acanthocephala, Amoebozoa, Apicomplexa, Cycliophora,
Heliozoa, Oomycota, Opalozoa, and Percolozoa. Except for the
Acanthocephala, the remaining taxa predominantly contain small
species. Difficulties in sample collection and morphological
identification due to the organisms being so small, as well as the
lack of taxonomic expertise in Japan (and indeed around the
world), are the major reasons for our lack of knowledge about
these taxa. To solve the problems arising from difficulties in
identification based on morphology, modern molecular and
microscopic techniques can be a useful tool. Recently, Eukarya
were indicated to be classifiable into six major supergroups based
on their molecular phylogeny [35,36] (Figure 7). Amoebozoa is
one of the supergroups, although in the case of Heliozoa, it is as
yet unclear to which group it belongs. Each supergroup contains
many small species, commonly called protists. Small species,
including these protists, seem to exhibit a much higher species
diversity than large species [36]. Thus, to understand diversity and
evolution in the Eukarya, it is important to gather more taxonomic
and systematic information on taxa containing many small species.
The present study has revealed that our state of knowledge
concerning the taxonomy and ecology of many taxa in Japanese
waters ranges from fairly well known to almost totally unknown.
To more easily compare the state of knowledge for each taxon, we
classify their state of knowledge into three categories—known,
mostly unknown, unknown—for each phylum or division based on
the following definitions; Known: almost all orders, superorders,
infraorders, suborders, or families were estimated to have a status
of either 5 or 4. Unknown: almost all orders, superorders,
infraorders, suborders, or families were estimated to have a status
of 1. Mostly Unknown: neither known nor unknown. The relative
numbers of taxa belonging to each category were 22 known, 42
mostly unknown, and 14 unknown (Table 7). Japan therefore has a
high percentage of mostly unknown or unknown taxa. It is
necessary to encourage the development of taxonomists who
specialize in these taxa in Japan.
Databases concerning marine life in Japan
OBIS is a powerful tool and data source for marine
biogeographical and other studies. Unfortunately, the total PRO
is quite low at only 8.4%. Potentially, several databases concerning
the diversity or distribution of marine organisms exist in Japan.
Some of them are listed as follows;
NAlgae resource database:
NBiological Information System for Marine Life (BISMaL):
NCMarZ-Asia Database:
NDatabase for aquatic-vertebrate science: http://research.
NIllustrated Guide of Marine Mammals: http://svrsh1.kahaku.
NJapan Collection of Microorganisms: http://www.jcm.riken.
NJapanese Biota Species Number Survey: http://research2.
NJapan Oceanographic Data Center (JODC): http://www.jodc.
NNaGISA Database:
NNITE Biological Resource Center: http://www.nbrc.nite.go.
NOne Hundred Seaweeds of Japan: http://research.kahaku.go.
Table 5. Number of species recorded in Japanese waters in
OBIS (NDSo) and the percentage of the species recorded in
Japanese waters in OBIS (PRO).
Phylum/Division NDS
NDSo PRO (%)
Nematoda 70 71 101
Phoronida 2 2 100
Priapulida 2 2 100
Cryptophyta 8 5 63
Annelida 1,076 529 49
Dinomastigota 470 187 40
Sipuncula 47 17 36
Ectoprocta/Bryozoa 300 85 28
Cyanobacteria 11 2 18
Hemichordata 11 2 18
Chlorophyta 248 42 17
Heterokontophyta 1,207 191 16
Arthropoda 6,393 663 10
Cnidaria 1,860 181 10
Echiura 21 2 10
Echinodermata 1,052 97 9
Chaetognatha 36 3 8
Chordata 4,330 242 6
Brachiopoda 73 4 5
Mollusca 8,658 415 5
Rhodophyta 898 39 4
Ctenophora 41 1 2
Ciliophora 530 12 2
Porifera 745 12 2
Haptophyta 304 3 1
Granuloreticulosa 2,321 11 0
Total 2,820
Number of described species.
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NProtist Information Server:
Of these, NaGISA, CMarZ-Asia and the JODC databases
directly or indirectly link to OBIS. The BISMaL adopts a common
Darwin Core schema to link to OBIS and the Global Biodiversity
Information Facility. Most other databases are operated in the
Japanese language and have different data schema, so it is not easy
to link them to OBIS. To encourage linkages between Japan’s
databases and OBIS, we need to establish a regional OBIS node in
Japan in the near future.
We expect rapid changes in the marine biota in Japanese waters:
(1) declining wild fish catches, (2) increasing aquaculture, (3) changes
in harvesting of specific species, (4) changes in harvested areas, (5)
food web changes, (6) shifts in diversity at population, species, and
genetic levels, (7) species extinction, population extirpation, (8)
changes in species distribution: contraction, expansion, and range
shifts, (9) changed traffic patterns of animal migrations, (10)
introduction of exotic species, (11) changes in nutrient cycles, (12)
changes in habitat provision, (13) changes in surface primary
productivity and carbon fluxes to the seafloor, and so on. However,
our knowledge is still too elementary for proper understanding of
the roles played by marine life in ecosystem services and
functioning. There are numerous unexplored areas, even in
Japanese waters, especially in the deep sea. Japan is a so-called
maritime nation and is in a particularly suitable geographic situation
for marine biological investigations. In particular, deep-sea troughs
Table 6. Comparison of number of described species in selected taxa between present study and a previous study of Nishimura
(1981) [19].
of previous
study [19]
NDS of present
study Increase of NDS
Phylum Class Order
Chordata Pisces 2700 3790 1090
Cnidaria Hydrozoa 315 523 208
Chordata Ascidiacea 281 313 32
Echinodermata Ophiuroidea ca. 260 308 48
Echinodermata Echinoidea 192 161 231
Echinodermata Asteroidea 167 280 113
Platyhelminthes Polycladida Polycladida 149 150 1
Porifera Calcarea 130 130 0
Mollusca Cephalopoda 125 204 79
Arthropoda Pycnogonida 67 153 86
Sipuncula 58 47 211
Arthropoda Crustacea Amphipoda 57 544 487
Mollusca Polyplacophora 56 129 73
Brachiopoda 55 73 18
Arthropoda Crustacea Stomatopoda 41 56 15
Cnidaria Scyphozoa 38 37 21
Echiura 17 21 4
Number of described species.
Difference between NDS reported in Nishimura (1981) [19] and NDS of the present study.
Figure 7. Supergroups of eukaryotes based on molecular data,
after six supergroups of eukaryotes [36].
Marine Biodiversity in Japan
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and trenches are concentrated in Japanese waters. To investigate
these deep-sea areas, several tools such as autonomous underwater
vehicles (AUVs), HOVs, remotely operated vehicles (ROVs), and
other research vessels have been developed and deployed by Japan.
Additionally, the ocean drilling ship Chikyu, under the Integrated
Ocean Drilling Program (IODP), also started operations in 2007.
One of the targets of the IODP is to investigate the deep biosphere
below the seafloor, the diversity of which remains unknown. Japan,
as a maritime nation, has an important responsibility to contribute
to our understanding of life in the oceans.
Finally, this study provides the baseline data for biodiversity
studies in Japanese waters. This is an important contribution not
only for science but also for the general public including NGO,
NPO and policy-making stakeholders. Therefore, we have
attached alternative language (Japanese) versions (Alternative
Language Article S1 and S2).
Supporting Information
Table S1 Brief history of marine biological activities in Japan.
Found at: doi:10.1371/journal.pone.0011836.s001 (0.04 MB
Table S2 Contributors for species diversity estimation.
Found at: doi:10.1371/journal.pone.0011836.s002 (0.03 MB
Table S3 List of species diversity including the number of
described species (NDS), the number of endemic species (NES),
the number of undescribed species (NUS), expected number of
species (ENS), the number of introduced species (NIS), the number
of taxonomic experts, the number of identification guides, and
state of knowledge in each taxon in Japanese waters.
Found at: doi:10.1371/journal.pone.0011836.s003 (0.25 MB
Table S4 Number of described species (NDS), number of
identified but undescribed species (NUS) and expected number
of species (ENS) in each phylum or division in Japanese waters.
Found at: doi:10.1371/journal.pone.0011836.s004 (0.03 MB
Table S5 Number of endemic species (NES) and the percentage
of endemic species in Japanese waters.
Found at: doi:10.1371/journal.pone.0011836.s005 (0.03 MB
Table S6 List of species introduced into Japanese waters, their
presumed primary mechanism of transportation and origin.
Found at: doi:10.1371/journal.pone.0011836.s006 (0.02 MB
Alternative Language Article S1 Alternative Language Japa-
nese Article S1, part 1 of 2
Found at: doi:10.1371/journal.pone.0011836.s007 (7.55 MB
Alternative Language Article S2 Alternative Language Japa-
nese Article S2, part 2 of 2
Found at: doi:10.1371/journal.pone.0011836.s008 (5.80 MB
Table 7. Current taxonomic status, Known, Mostly unknown and Unknown, for each Phylum or Division.
Taxonomic status
Known Mostly unknown Unknown
Acoelomorpha Acidobacteria Hemichordata Acanthocephala
Bacteroides Actinobacteria Heterokontophyta Amoebozoa
Cercozoa Annelida Kinorhyncha Apicomplexa
Chaetognatha Aquificae Loricifera Blastocladiomycota
Chlorophyta Arthropoda Metamonada Chytridiomycota
Choanozoa Ascomycota Nematoda Cycliophora
Chordata Basidiomycota Nematomorpha Glomeromycota
Ctenophora Brachiopoda Nemertea Heliozoa
Cyanobacteria Ciliophora Nitrospirae Microsporidia
Dicyemida Cnidaria Orthonecta Oomycota
Echinodermata Crenarchaeota Phoronida Opalozoa
Ectoprocta/Bryozoa Cryptophyta Placozoa Percolozoa
Firmicutes Deferribacteres Platyhelminthes Priapulida
Granuloreticulosa Deinococci Porifera Thaumarchaeota
Haptophyta Dinomastigota Proteobacteria
Labyrinthulomycota Echiura Sipuncula
Magnoliopsida Entoprocta Tardigrade
Mollusca Euglenophyta Thermotogae
Myxozoa Euryarchaeota Verrucomicrobia
Radiozoa Gastrotricha Zygomycota
Rhodophyta Glaucophyta
Rotifera Gnathostomulida
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We are grateful to the many contributors of data to Table S2 for supplying
taxonomic information, the Census of Marine Life for leading this work,
Michele DuRand, Patricia Miloslavich, Dale Langford, and Charles
Griffiths for providing constructive criticism on the first draft of this
manuscript, Yasuo Furushima for drawing the figures, and Tadashi
Maruyama, who advised and supported this project.
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... The wIPWP is the large body of water in the western Pacific denoted by sea-surface temperatures >28 • C (Sosdian and Lear, 2020). Western Indo-Pacific biodiversity is known to be high also in adjacent mid-latitude areas, such as the Ryukyu Islands (Fujikura et al., 2010), for example in larger benthic foraminifera, bivalves, ostracods and coastal fishes (Hohenegger, 1994(Hohenegger, , 2006Tittensor et al., 2010;Jablonski et al., 2013;Yasuhara et al., 2016). ...
... The northwestern Pacific Ocean has high species richness, which may be attributed to the high topographic complexity that includes large semi-enclosed seas, several islands, and deep-sea trenches (Fujikura et al. 2010, Brandt et al. 2019. Such topographic complexity is also expected to result in high species diversity and genetic variation in deep-sea fish species. ...
The numbers of deep-sea fish species and their genetic diversities are poorly understood because of taxonomic confusion and the lack of robust diagnostic features. However, DNA barcoding using mitochondrial DNA sequences may offer an effective approach to identifying cryptic species and characterizing their genetic diversities. To validate the genetic differentiation identified by DNA mitochondrial barcoding, it is necessary to show that these reflect variations present in nuclear genomic markers. Here, we performed DNA barcoding using cytochrome c oxidase subunit I (COI) sequences and also carried out multiplexed intersimple sequence repeat genotyping by sequencing (MIG-seq) for mesopelagic and demersal fish species from the continental shelf and upper slope of the northwestern Pacific Ocean. We obtained the COI sequences of 115 species from 48 families; the species were identified using the Barcode of Life Data System. Phylogenetic analyses using COI sequences showed high levels of intraspecific genetic differentiation (Kimura 2-parameter distances >2%) in 20 of 115 species, suggesting many cryptic species or intraspecific genetic differentiation previously unknown in these species. We performed phylogenetic and population genetic analyses using multiple single-nucleotide polymorphism loci obtained by MIG-seq of 3 species that showed high levels of intraspecific genetic differentiation in COI sequences. The nuclear markers confirmed the genetic differentiation in all 3 species identified by the COI sequences. The high concordance between these different genetic markers indicates the effectiveness of DNA barcoding for identifying cryptic deep-sea species and characterizing genetic differentiation in these species.
... Due to both warm and cold currents surrounding the archipelago, a high diversity of marine taxa were, and remain, present. Along the coast, fish and shellfish are abundant (3,700 and 9,000 species, respectively), and they have been historically a major protein source (Fujikura et al. 2010; JBOSC (Japan Biodiversity Outlook Science Committee, The Ministry of the Environment) 2010). Many of the species present have been found on Jōmon sites (Table S4 and S5). ...
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One of the most entrenched binary oppositions in archaeology and anthropology has been the agriculturalist vs hunter-gatherer-fisher dichotomy fuelling a debate that this paper tackles from the bottom-up by seeking to reconstruct full past diets. The Japanese prehistoric Jōmon cultures survived without fully-developed agriculture for more than 10,000 years. Here we compile a comprehensive, holistic database of archaeobotanical and archaeozoological records from the two ends of the archipelago, the northernmost prefecture of Hokkaido and the southernmost island-chain of Ryukyu. The results suggest Jōmon diets varied far more geographically than they did over time, and likely cultivated taxa were important in both regions. This provides the basis for examining how fisher-hunter-gatherer diets can fulfil nutritional requirements from varied environments and were resilient in the face of environmental change.
... In addition, the Pacific Ocean side of northern and eastern Japan can be strongly influenced by the Oyashio Current, which is a cold current (e.g., [22,35]). With their diverse marine environments, seas around Japan are an important place for maintaining biodiversity [15]. ...
Ecosystems composed of reef-building corals play an essential role in maintaining biodiversity and as a place for tourism and fisheries. Where there is a gap between the distribution, use, management, regulation, and future concerns/interests of corals, the value of coral communities may not be properly received, and the resource may be degraded under future environmental change. We organized records of coral occurrence in each prefecture in Japan. We assessed coral use and management status based on administrative documents. Moreover, we compiled information on how laws regulate coral harvesting. Concerns for future changes were extracted from climate change adaptation plans. Text analysis of several administrative documents showed that the frequency of occurrence of coral-related keywords varied greatly among prefectures and documents. Comparing the information on coral distribution areas and the status of use, management, and regulation organized in this study for each prefecture revealed significant gaps in some prefectures, suggesting that management and regulation should be reviewed following the distribution status. With the projected increase in the magnitude of bleaching and expansion of coral distribution areas as water temperatures rise due to global warming, one of the strengths of this study is the identification of the current status and issues of the gap between distribution and use, management, and regulation. In areas where the spatial gradient of the environment/ecosystem is considerable or where significant changes in the environment/ecosystem are expected in the future, it is essential to establish a utilization and management system that reflects the characteristics of these areas.
The transitional coral ecosystem of Taiwan features tropical and temperate scleractinian coral species and suboptimal environmental conditions. As the largest continental island in the region, Taiwan is proposed as a stepping-stone for range expansion to higher latitudes of East Asia. In this chapter, we synthesize the literature and highlight the importance of the transitional role of Taiwanese coral ecosystem in sustaining its high-latitudinal counterparts in this era of changing climate. The boundary line separating tropical coral reefs and subtropical non-reefal coral communities stretches from south Penghu towards the Sandiao Cape in northeastern Taiwan. Between 1948 and 2020, the average seawater warming trend around Taiwan was 1.58 °C. This trend was not homogeneous; the region with non-reefal coral communities experienced a higher warming rate owing to gradually increasing winter sea surface temperatures. However, studies on the effect of typhoons, ocean acidification, and bioerosion on this transitional coral ecosystem are limited. To comprehensively understand how coral ecosystems in Taiwan respond to climate change, we recommended four research directions: (1) biodiversity formation, (2) the role of Kuroshio Current in reef formation and in connecting coral ecosystems of East Asia, (3) long-term ecological research of these coral ecosystems, and (4) the conservation and governance of transitional coral ecosystems using novel socio-ecological paradigms.KeywordsMarginal reefsBiogeographyPoleward migrationCold domeUpwelling
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Background Zooplankton plays an important role in the marine ecosystem. A high level of taxonomic expertise is necessary for accurate species identification based on morphological characteristics. As an alternative method to morphological classification, we focused on a molecular approach using 18S and 28S ribosomal RNA (rRNA) gene sequences. This study investigates how the accuracy of species identification by metabarcoding improves when taxonomically verified sequences of dominant zooplankton species are added to the public database. The improvement was tested by using natural zooplankton samples. Methods rRNA gene sequences were obtained from dominant zooplankton species from six sea areas around Japan and registered in the public database for improving the accuracy of taxonomic classifications. Two reference databases with and without newly registered sequences were created. Comparison of detected OTUs associated with single species between the two references was done using field-collected zooplankton samples from the Sea of Okhotsk for metabarcoding analysis to verify whether or not the newly registered sequences improved the accuracy of taxonomic classifications. Results A total of 166 sequences in 96 species based on the 18S marker and 165 sequences in 95 species based on the 28S marker belonging to Arthropoda (mostly Copepoda) and Chaetognatha were registered in the public database. The newly registered sequences were mainly composed of small non-calanoid copepods, such as species belonging to Oithona and Oncaea . Based on the metabarcoding analysis of field samples, a total of 18 out of 92 OTUs were identified at the species level based on newly registered sequences in the data obtained by the 18S marker. Based on the 28S marker, 42 out of 89 OTUs were classified at the species level based on taxonomically verified sequences. Thanks to the newly registered sequences, the number of OTUs associated with a single species based on the 18S marker increased by 16% in total and by 10% per sample. Based on the 28S marker, the number of OTUs associated with a single species increased by 39% in total and by 15% per sample. The improved accuracy of species identification was confirmed by comparing different sequences obtained from the same species. The newly registered sequences had higher similarity values (mean >0.003) than the pre-existing sequences based on both rRNA genes. These OTUs were identified at the species level based on sequences not only present in the Sea of Okhotsk but also in other areas. Discussion The results of the registration of new taxonomically verified sequences and the subsequent comparison of databases based on metabarcoding data of natural zooplankton samples clearly showed an increase in accuracy in species identification. Continuous registration of sequence data covering various environmental conditions is necessary for further improvement of metabarcoding analysis of zooplankton for monitoring marine ecosystems.
Shiretoko was inscribed as a Natural World Heritage site in 2005. It has an outstanding universal value as a connection between the terrestrial and marine ecosystems. However, coastal fisheries are operated throughout the area, and it was required that the protection of the area was strengthened during the nomination process. World Heritage areas are protected by the national laws of each country and are not under international control. Japanese coastal fisheries are based on comanagement of fisheries cooperative associations (FCA) aiming at sustainable fisheries. The fishers expanded the seasonal fishing-ban areas of walleye pollock (Gadus chalcogrammus), and Shiretoko became a World Heritage Site. In this way, Shiretoko became a case of a new world heritage, where the protection of nature was not guaranteed by the government but rather the initiative of the local stakeholders to protect it. Unlike other chapters, this chapter does not include explanation of mathematical techniques for ecological risk management. We discuss the importance of comanagement and decision-making by the local stakeholders in ecological risk management.
Underwater images (UWIs) require higher compression ratio than terrestrial images due to the limited bandwidth of underwater wireless acoustic channel. In many studies such as marine species, the foreground objects (FGOs) in UWIs need to be observed in detail, while the background only needs to be viewed in general. However, existing image compression methods achieve limited compression ratio and reconstruction quality, which cannot fulfill these practical applications since they do not consider the unique underwater physical priors. To overcome the limitation, we propose an underwater physical prior-based extreme compression network (PPECN) for UWIs compression, which includes an underwater physical prior-guided FGOs autoencoder (UPGAE) and a FGOs-assisted background generator (FG-BGGAN). Specifically, we design an underwater physical prior guidance structure that simulates the data flow in the underwater physical imaging process to adaptively adjust the distribution of received Gaussian features in the UPGAE to be more consistent with real UWIs. During the adjustment, some basic UWI properties can be reconstructed, which can improve the reconstruction quality and implicitly reduce bits through the end-to-end training. Furthermore, the background is generated from simple semantic map under the constraint of the perceptual consistency between background and FGOs, significantly saving coding bits and improving the perceptual quality of the generated background. Extensive experimental results on four underwater image datasets verify that, compared with state-of-the-art compression methods, our PPECN achieves both impressive improvement in the perceptual quality of the whole image and significant gain in the pixel fidelity of the FGOs at the similar low bitrate.
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To investigate the invasion history and recent geographic distribution of marine organisms introduced to Japan or transferred domestically to non-native regions, a questionnaire survey on their occurrence in the field, including both published and unpublished records, was conducted in 2002-2003. A total of 105 taxa was reported by 94 respondents. According to three criteria, viz. known or unknown geographic origin, established invasion history, and presumed dispersal mechanisms associated with human activities, 42 taxa were designated as non-indigenous species introduced to Japan through human activities, 26 taxa as indigenous species that are distributed both in Japan and other countries but are introduced from abroad to Japan for fisheries or as fish bait, 20 taxa as cryptogenic species which are not demonstrably native or introduced, two taxa as non-indigenous species that have extended their range to Japan through natural dispersion, and one taxon as an indigenous species. The remaining 14 taxa were considered to have been transferred domestically to new areas. Analysis of the years of first record of 42 non-indigenous species suggests that the rate of invasion has increased over the past century, with seven or eight species being introduced per decade after 1960. Data on temporal change in geographic distribution revealed that many non-indigenous species have become widespread recently, from the Pacific coasts of central Japan to the coasts of the Sea of Japan or northward. However, the species listed in the present study are not exhaustive, and more extensive investigations covering all taxa and all presumed dispersal mechanisms are urgently needed before consideration of legislative management of introduced marine organisms.
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The clam Ruditapes philippinarum is a commercially important fishery resource in Japan. Because the amount of production has been decreasing gradually in Japan, the clam has been imported from China and Korea in recent years to provide seed for aquaculture and also for recreational shellfish gathering. The object of this study is to confirm whether alien species are being introduced together with the clam and to obtain information on their distribution in Japanese waters. Three species of mollusk-eating moon snail, Euspira fortunei, Glossaulax didyma, and Glossaulax reiniana, were collected from sacks filled with R. philippinarum imported from China. Seven other gastropod species, nine species of bivalves including Meretrix pethechialis, the purse crab Phiiyra pisum, and a brachiopod, Lingula unguis, were also collected from the sacks. Almost all the unintentionally introduced animals were living and were directly released with commercially introduced clams into Mangoku-ura Inlet, Miyagi Prefecture, by a fishermen's cooperative. Although the snail Euspira fortunei is not indigenous to the eastern and northern coasts of Japan, relatively large populations of it occur in the clam production areas of Lake Hamana (Shizuoka), the estuary of the Obitsu River (Chiba), and Mangoku-ura Inlet. I believe that a population of this invasive snail has already been established at least in Mangoku-ura Inlet and is becoming a new, strong predator of the clam stocks. Prevention of further spread and estimation of the rate of predation are important to the clam culture. Among the 22 alien species recorded in this survey, seven were also found in the native communities. The effect of the alien population on the preexisting population is also important problem to be solved.
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There is an increasing public concern about the introduction of marine organisms, and shipping is perceived to be responsible for many unwanted introductions into Japanese waters. A total of 25 unintentionally introduced marine species has been reported in Japanese waters, comprising Annelida (two spp.), Mollusca (10 spp.), Arthropoda (nine spp.), and Chordata (two spp.) among animal taxa, and Phaeophyta (one sp.) and Chlorophyta (one sp.) among marine algae. It is estimated that 68% of these introduced species were introduced via visiting ships. Two main mechanisms, ballast water and hull fouling, are considered responsible for the dispersal of marine organisms worldwide via shipping. The relative importance of these mechanisms for the dispersal of marine organisms differs among nations and regions as a consequence of their trading patterns. Since large amounts of ballast water are discharged at ports exporting dry bulk commodities, ballast water can be considered a relatively important mechanism for introductions in such places (e.g., Australia or San Francisco Bay), whereas hull fouling might be more important in regions that import bulk commodities (e.g., Hawaii or Japan). This study estimates that hull fouling is responsible for 44% of the introduced marine species in Japan. The importance of sea chests as an alternative mechanism for transporting marine organisms around the world has only recently been recognized, and a mechanism may have been responsible for introducing the clam Mercenaria mercenaria, spider crab Pyromaia tuberculata, green crab Carcinus aestuarii, and blue crab Callinectes sapidus to Japan. To prevent the introduction of unwanted marine organisms into Japan by hull fouling, not only are advances in effective and nontoxic anti-fouling paint technology required, but also increases in the frequency of vessel dockings to inspect and clean the hulls. Furthermore, since large volumes of ballast water are exported from the Japanese coasts to many overseas regions, the Japanese government should establish regulations and develon treetment technology to minimize the unintentional export of marine organisms via ballast water.
This paper discusses the diversity, common features, and geographic distrbution of submarine cave bivalves collected with SCUBA from a number of islands around the Philippine Sea (Okinawa, Miyako, Yonaguni, Daito, Bonin, Bohol and Cebu of the Philippines, Palau, and Guam). Common significant characteristics of cave bivalves are: (1) unique taxonomic assemblage, (2) reduced adult size, (3) many deep-water genera, (4) occurrence of several "cavity-dwelling" shallow-water genera on the exposed wall and sediment surface, (5) frequent paedomorphosis by progenesis, (6) relative abundance of non-planktotrophic species, (7) low fecundity and dominance of brooding, and (8) archaic life mode reminiscent of a fauna before the "Mesozoic marine revolution" (rarity of sedentary species and deep burrowers). These features must be related to one another and are generally regarded as due to a common adaptive strategy toward the oligotrophic condition and low predation pressure of cave habitats. It is still mysterious how cave bivalves, even brooding species, have become so extensively distributed in the western Pacific region. Although there is no positive evidence, rafting is a possible mechanism of transoceanic dispersal for minute epibyssate bivalves.
We observed coarse-scale (1-100 km) distributions of hydromedusae in two locations in Japanese waters, the Osaka Bay-Kii Channel area and the Tokyo Bay-Sagami Bay area in early summer. Hydromedusan assemblages, defined by cluster analysis, were divided into several groups in both areas. Distributions of the assemblages were fitted to those of water masses defined by T-S diagrams. The fitness shows that physical processes influenced the coarse-scale distributions of hydromedusae. In the semi-enclosed inlet waters (Osaka Bay and Tokyo Bay), species numbers were low. In the coastal waters (northern parts of Kii Channel and Sagami Bay), high abundance of Muggiaea atlantica and occurrence of specific meroplankters were recognized. Assemblages in the southern part of the Kii Channel and central Sagami Bay, which are boundary areas between both coastal and oceanic waters, showed high number of species because coastal and oceanic species occurred in these regions. Species belonging to the oceanic assemblage were distributed in southern part of Sagami Bay and were comprised of many siphonophores and some trachymedusae without meroplankters. Because the same distribution pattern of hydromedusan assemblages was recognized in both the study areas, it is considered that assemblages of hydromedusae are useful as indicators of water masses. Meroplankters, which occurred in the coastal waters (northern parts of Kii Channel and Sagami Bay), have characteristic life cycles such as asexual reproduction by immature medusae or high productivity where medusae are formed from hydroids. It is likely that such biological factors as well as physical factors influence the horizontal distribution of hydromedusae.
Recent investigations in marine biodiversity have given cause to rethink some basic assumptions about marine biodiversity. Only c160 000 marine species have been described. This contrasts with the possibly one million described species of insects. Estimates for the total insect diversity range from about 5 × 106 up to 2 × 108. Compared with these figures marine biodiversity would appear trivial, <1.3% of the world's metazoans being marine. But such a comparison is hugely misleading as it makes no sense to compare the number of described marine species with the estimated total terrestrial diversity. When a methodology similar to that used for terrestrial global biodiversity estimates is used, a global macrofauna diversity of 1 × 107 species can be calculated. The biodiversity of the small marine metazoa, the meiofauna, may be an order of magnitude higher. Recent investigations into local diversity patterns have highlighted the importance of non-equilibrium patch dynamics in species diversity. A spatial-temporal mosaic of unique small-scale patches, operating against a low disturbance, low nutrient background prevents competitive exclusion and allows a high regional species pool in environments such as the deep sea and tropical rainforests. -from Author
Numerous alien species have been reported in Japanese waters in recent years, but identifications of these species are difficult in most cases. In the Ariake Inland Sea, two new alien gastropods were found in 2000. One of them is Nassarius (Zeuxis) sinarus (Philippi, 1851) from China. This carnivorous species has recently increased explosively in number and has become a pest, eating fish caught in traps. This problem has spread rapidly over wide regions of the Ariake Inland Sea, with goby fisheries using traps in the central and western parts of Saga Prefecture suffering most. Unfortunately, this species was initially misidentified as the endangered species Mitrella martensi (Lischke, 1871). The other alien gastropod species is Stenothyra sp. from Korea. It is an undescribed species in spite of being an alien and had never before been reported from Korea. This case shows that alien species include not only ones that are abundant in their original distribution range, but also unrecognized ones. Several other taxonomic problems posed by alien species are reviewed. Most alien species in Japan have at first been misidentified and/or confused with other species. One of the most important measures to prevent such confusion is the adequate preparation of specimens. Because alien species often appear suddenly, we can not know their origin immediately. If enough specimens are preserved, exact identification may be made through subsequent study. In this connection, alpha-taxonomy will become ever more significant from now on. Comprehensive revisional works for many taxa will be needed in order to identify the alien species.