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Identification of coral spawn
source areas around Sekisei
Lagoon for recovery and poleward
habitat migration by using
a particle‑tracking model
Naoya Takeda1, Motohiko Kashima1*, Sachika Odani2, Yusuke Uchiyama2, Yuki Kamidaira3 &Satoshi Mitarai4
A massive coral bleaching event occurred in 2016 in the interior of Japan’s largest coral lagoon, theSekisei Lagoon, located in the Kuroshio upstream region in southwestern Japan. Recovery of thecoral lagoon will require the influx of coral spawn and larvae; therefore, it is important to identify andconserve source sites. A surface-particle-tracking simulation of coral spawn and larvae was used to
identify source areas of coral spawn outside of the Sekisei Lagoon for potential recovery of the interiorlagoon. The northern coastal zone of Iriomote Island, including Hatoma Island, was identified as amajor source area. Hatoma Island was also identified as a key source for the Kuroshio downstream
region and for aiding the poleward migration of coral habitat under ongoing global climate change,
making it one of the most important source areas in the Nansei Archipelago.
Corals are an integral part of the coral reef ecosystem and are also a major tourism resource in the Nansei
Archipelago, a string of islands in southwestern Japan located between Kyushu and Taiwan (Fig. 1). Coral reefs
around Okinawa Island, which is in the middle of the archipelago, were massively damaged by a coral bleaching
event in ­19981,2. Direct or inter-generational gene flows link coral populations across the Nansei ­Archipelago3,4.
The Sekisei Lagoon is the largest coral lagoon in Japan and is located in the Kuroshio upstream region (i.e.,the southern Nansei Archipelago). The lagoon is thought to help maintain coral reef ecosystems across the entirearchipelago by supplying coral spawn and larvae to downstream sites (i.e., relatively northern regions of the archipelago). However, corals in this lagoon were impacted considerably by a massive bleaching event in 2016, some
18 years after the 1998 event that hit Okinawa Island. Both bleaching events (1998 and 2016) occurred during theyears of GCBE (Global-scale Coral Bleaching Events)5. Diving surveys showed that of the 11 major coral species
in the lagoon, the rate of colony bleaching or death exceeded 98% in 10 ­species6. Coral reefs regenerate throughthe influx of coral spawn and larvae especially from upstream regions; this means that the recovery of corals in
the Sekisei Lagoon is a necessary first step toward the recovery of the entire Nansei Archipelago and for aiding
poleward migrations of coral habitat under the influence of ongoing global climate change.
Quantitative pathways of coral spawn and larvae dispersal through direct advection by ocean currents andassociated dispersal effects were investigated in our previous study, which used the Regional Oceanic Modeling
System (ROMS) coupled with a 3-D Lagrangian particle-tracking model to simulate coral spawn and larvae as
neutrally buoyant particles. Although the study showed that particles released off the Yaeyama Islands (i.e., theregion around the Sekisei Lagoon) may be advected more than 400 km northeast to reach Okinawa Island withina typical pelagic larval duration of 21 d
­ ays4, we were not able to identify specific source areas for the coral spawn
and larvae. Therefore, our current study aims to identify major source areas for (1) the interior Sekisei Lagoon,and (2) the entire Kuroshio downstream region, (and hence, for aiding the poleward coral habitat migration) byusing 3-D Lagrangian particle-tracking s­ imulations4.

1
Faculty of Humanities and Sciences, Kobe Gakuin University, Kobe, Japan. 2Department of Civil Engineering,
Kobe University, Kobe, Japan. 3Nuclear Science and Engineering Center, Japan Atomic Energy Agency, Tokai,
Japan. 4Marine Biology Unit, Okinawa Institute of Science and Technology, Onna, Japan. *email: kashima@human.kobegakuin.ac.jp

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Figure 1.  Model domains for ROMS-L1 (red) and ROMS-L2 (blue). Colors indicate bathymetry.

ROMS-L1

ROMS-L2

Computational period

1 Jan 2005–2 Nov 201527 Dec 2010–2 Nov 2015

Grid cells

768 × 768 (× 32 Layers)

1280 × 1280 (× 32 layers)

Horizontal grid resolution

3 km

1 km

Baroclinic time step

240 s

40 s

QuikSCAT-ECMWF (daily, until 31 Dec 2007)

Surface wind stress

JMA GPV-GSM (daily, 1 Jan 2008 and later)

Surface flux

NOAA COADS (monthly climatology)

SST and SSS to restore

JCOPE2 (20-days averaged)

JMA GPV-MSM (h)Yangtze River discharge

Monthly ­climatology11

Open boundary/initial conditions

JCOPE2 (daily)

ROMS-L1 (daily)

Temperature-salinity nudging

JCOPE2 (10-days averaged)

Not used

Tides

Not Used

TPXO 7.0

Topography

SIO SRTM30_Plus

Table 1.  Model parameters for ROMS-L1 and ROMS-L2 setting ­conditions4.

Figure 2.  Close-up of the model domain around Sekisei Lagoon. Circles indicate source and destination areas
separated into numbered groups. Groups 3, 10, and 14–18 are located in the interior and the remainder areoutside of the lagoon.
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Figure 3.  Connectivity matrices around the Sekisei Lagoon for each year during the period 2012–2015.
Numbers on the abscissa (source areas) and ordinate (destination areas) correspond to the groups shown in
Fig. 2. High probability densities (warm colors) indicate that numerous particles drifted from the source area tothe destination area. Red outlines show high-probability-density source areas outside of the lagoon (i.e., otherthan groups 3, 10, and 14–18) for Group 16.

Methods

We used submesoscale eddy-resolving synoptic ocean models based on the Regional Oceanic Modeling System(ROMS) in a double-nested configuration coupled with a 3-D Lagrangian particle-tracking model embedded in
the Japan Coastal Ocean Predictability Experiment 2 (JCOPE2)4. JCOPE2 is a numerical reanalysis product for
the northwestern Pacific Ocean assimilated with a vast amount of satellite and in situ ­data7. ROMS-L1 (Fig. 1,
red rectangle) has a spatial resolution of 3 km and a calculation period of 1 January 2005 to 2 November 2015.
ROMS-L2 (Fig. 1, blue rectangle) has a higher spatial resolution of 1 km and a shorter calculation period of 27
December 2010 to 2 November 2­ 0154 (Table 1).
To identify major source areas and common transport routes of coral spawn and larvae, about 29,000 virtualsurface Lagrangian particles were tracked between 145 areas that served as both potential source areas anddestination areas on land grids (Fig. 2) or on the boundaries of the ROMS-L2 model domain for at least 21 days
with a time step of 200 ­s8,9. Connectivity was calculated by using probability density functions (PDFs)10; areas
with the highest probability density were identified as major sources. Lagrangian particles were discharged at
20:00 on the first night after the full moon during a spring tide in May, which is when mass coral spawning is
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Figure 4.  Reachability of particles from outside of the lagoon. Groups 1, 2, and 6 are indicated by red ovals,
respectively. Orange ovals indicate the southern coast of Kohama Island (the western part of Group 16), which
was the highest-probability destination area in the interior lagoon.

most likely to occur, and continued each night for the next 7 days for simulations of the Sekisei Lagoon and thenext 14 days for simulations of the entire Kuroshio downstream region during the years 2012–2015.
Coastal areas around the Sekisei Lagoon (Iriomote Island, the Sekisei Lagoon, and Ishigaki Island) weredivided into 18 groups (Fig. 2). Groups 3, 10, and 14–18 are located in the interior and the remainder are outside of the lagoon. All areas were considered as potential sources and as potential destinations. By using PDFs,
we identified major source areas outside of the lagoon that could contribute to recovery of the interior lagoon.

Results

Identification of major source areas outside of the lagoon that could supply the interiorlagoon. Group 16, on the southern coast of Kohama Island (Fig. 2), was the highest-probability destination

area in the interior lagoon in each examined year (Figs. 3, 4). Relatively more particles drifted from the northerncoastal zone of Iriomote island, especially from the northern and northeastern coasts of Iriomote Island (Groups
1 and 2, respectively) and the coast of Hatoma Island (Group 6) (Fig. 4).
Two major routes toward Group 16 from Groups 1, 2, and 6 were revealed from the particle drift trajectories:
one passes southward through the Yonara Channel on the west side of Kohama Island, and the second passes
through the channel on the east side (Figs. 5, 6, 7). No particles drifted around Ishigaki or Iriomote islands toreach the interior lagoon.

Identification of major source areas around the Sekisei Lagoon for the Kuroshio downstream
region and for poleward coral habitat migration. We also sought to identify source areas aroundthe Sekisei Lagoon for reefs in the Kuroshio downstream region and hence for aiding poleward coral habitat
migration due to the influence of global climate change. To identify simulated particles that drifted from aroundthe Sekisei Lagoon to the Kuroshio downstream region (including Okinawa Island) or otherwise drifted in a
poleward direction, we focused on particles that were advected north of 26.5° N (hereafter referred to as longdistance particles [LDPs]). Many particles from the northern coasts of Iriomote and Ishigaki islands drifted to
the Kuroshio downstream region (Fig. 8), as did particles from the northern coast of Hatoma Island (Fig. 9). This
was not true for particles from southern coasts, such as the Urabishi reef (which suffered extensive damage fromthe 2016 bleaching event) (Figs. 9, 10).

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Figure 5.  Trajectories of particles discharged from the northern coast of Iriomote Island (Group 1) that reached
the southern coast of Kohama Island (Group 16) during the years 2012–2015 (a–d). Only 10% of the simulated
trajectories are shown for clarity. Red and green dots indicate particle discharge and destination points in sourceand destination areas, respectively.

Discussion and concluding remarks

Our results reveal the location of source areas outside of the lagoon that could export coral spawn and larvae
to the lagoon interior. This is an important process in the potential recovery of coral reefs in this area. Major
source areas were located around Hatoma Island and the northern and northeastern coasts of Iriomote Island.
Hatoma Island was also a major source area for simulated coral spawn and larvae arriving in the Kuroshio
downstream region. In fact, it was the most important source area for both the interior Sekisei Lagoon and
the Kuroshio downstream region. These results can be used to aid recovery of coral reefs in the entire coastalzone of the Sekisei Lagoon and the Kuroshio downstream region by informing the design of effective coral reef
conservation areas in this region and directing efforts to remove Acanthaster planci (crown-of-thorns starfish)
and transplant coral seedlings.
Previous research has highlighted the difficulty of tracking simulated coral spawn and larvae in complex
generalized zonal current systems such as the eastern equatorial Pacific, where the North Equatorial Current,
South Equatorial Current, and Northern Equatorial Countercurrent interact with prevailing easterlies under the
influence of ENSO v­ ariability12. In contrast, our study region features a relatively simple and strong poleward
western boundary current, the Kuroshio, which maintains a distinct surface current and never directs equatorward. Furthermore, the Kuroshio passes near the Coral Triangle in the further upstream region, which is known
as the center of global coral reef ­biodiversity13. Accordingly, poleward coral mass migrations can occur relatively
easily and can be tracked with relative simplicity in this region. The areas investigated in this study (the Sekisei
Lagoon and Nansei Archipelago) play a key role as stepping stone relay stations in poleward migration mostly
by the Kuroshio, thus the identification of coral spawn and larval sources in these areas is of crucial importance.
Given that global climate change is causing corals to migrate poleward, it is particularly important to conserve
coral populations in upstream regions, especially in the areas that serve as sources of coral spawn and larvae inwestern boundary current systems. It is not a coincidence that upstream source areas in the western boundaries

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Figure 6.  Same as Fig. 5, but from the northeastern coast of Iriomote Island (Group 2).

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Figure 7.  Same as Fig. 5, but from Hatoma Island (Group 6).

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Figure 8.  Probability density functions of reachability for particles discharged at 20:00 for 14 days beginning on
the night after the full moon during a spring tide in May during the years 2012–2015. Warm colors indicate highprobability densities. Advection time was 21 days in all cases, and discharge periods began on (a) 7 May 2012,(b) 24 May 2013, (c) 15 May 2014, and (d) 3 May 2015.

Figure 9.  Probability density functions of reachability for long-distance particles during the years 2012–2015.
The orange circles (marked (A,B)) show the northern coast of Hatoma Island and Urabishi reef, respectively.

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Figure 10.  Trajectories of particles discharged from (a) the northern coast of Hatoma Island and (b) Urabishi
reef during the years 2012–2015. Dates at the top of each map show the first particle discharge day in each year,
and red lines indicate the trajectory of a drifter buoy observed during 2006 that followed the Kuroshio C­ urrent4.

of subtropical gyres (i.e., where boundary currents direct poleward) around the world are located in warmer
climates (as is true of the source areas identified in this study). Other examples of similar source regions include
the Great Barrier Reef along the East Australian Current as well as reefs along the Gulf Stream, Agulhas Current,and Brazil Current. Identification and recovery of source areas in upstream regions of these western boundary
currents should help coral populations in subtropical gyres adapt to global climate change by facilitating theirpoleward migration.
Received: 29 May 2020; Accepted: 12 February 2021

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Acknowledgements

This study was conducted using the Regional Oceanic Modeling System and was financially supported by Grantsin-aid for Scientific Research (KAKENHI) from the Japan Society for the Promotion of Science (Grant Nos.
15H04049, 15KK0207, and 18H03798 at Kobe University and 17K00653 at Kobe Gakuin University).

Author contributions

M.K., N.T. and Y.U. wrote the main manuscript text. S.O., N.T., M.K. and Y.U. prepared figures. All authors
reviewed the manuscript.

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Competing interests

The authors declare no competing interests.

Additional information

Correspondence and requests for materials should be addressed to M.K.
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