Table 1. Information on the six sub-regions investigated in this study in the Ryukyu Islands (RYS).

Sub-region	Yakutane	Tokara	Amami	Okinawa	Miyako	Yaeyama	RYS total	Reference(s)
Major islands	Yakushima, Tanegashima, Kuchinoerabu, others	Nakanoshima, Suwanose, Kuchinoshima, Taira, Takara, Kodakara, Akuseki, others	Amami-Oshima, Kikai, Tokunoshima, Okinoerabu, Yoron, others	Okinawa Main Island, Kume, Izena, Iheya, Kerama Islands, Ikei Islands, Aguni, Ie, Sesoko, Kouri, others	Miyako, Ikema, Tarama, others	Ishigaki, Iriomote, Taketomi, others	198 islands (not including <0.01 km2)	NA
Notable marine research stations & institutes	Yakushima Umigane-kan	None	Kagoshima University Amami Station, Seikai National Fisheries Research Institute Amami Station, Kikai Coral Reef Research Institute (from 2014), Kagoshima U. Fac. Fisheries Yoron Station	Akajima Marine Science Laboratory (closed 2017), Okinawa Institute of Science and Technology (from 2011), Okinawa National College of Technology, University of the Ryukyus Tropical Biosphere Research Center Sesoko Station, University of the Ryukyus Main Campus, Itoman Pref. Exp. Center, Meio University	Miyakojima City Museum	University of the Ryukyus Iriomote Field Station, Ishigaki Pref. Exp. Station, Ishigaki MoE Parks Station, Kuroshima Sea Turtle Station		Various institution homepages
OBIS cover (# squares)	27	14	36	50	11	26	164	OBIS
Land area (km2)	1,030	101.35	1,231.47	1,418.59	226.5	587.16	4,595.07	Geospatial Information Authority of Japan (2017)
Population	41,870	768	107,238	1,341,553	52,456	54,092	1,597,977	Kagoshima Prefecture (2017), Okinawa Prefecture (2018)
Population density (/km2)	40.7	7.6	87.1	945.7	231.6	92.1	347.8	NA
Geological formation	Volcanic, sedimentary, granite uplift	Volcanic, coral reefs	Volcanic, sedimentary, uplift, coral reefs	Volcanic, sedimentary, uplift, coral reefs	Volcanic, coral reefs	Volcanic, sedimentary, uplift, coral reefs	N/A	Kayanne, Hongo & Yamano (2004), Fujita et al. (2015)
Annual average SST (°C)	24.3		24.5	25.0	25.8	25.2	N/A	Hasegawa & Yamano (2004), Kajiwara & Matsumoto (2004), Nakai & Nojima (2004), Nakai & Oki (2004),Sakai (2004), Shimoike (2004), Yokochi (2004a)
Reef perimeter (km)	Local coral reef flats only	19	420.3	382.2	121.6	268.4	1,211.5	Hasegawa & Yamano (2004), Kajiwara & Matsumoto (2004), Nakai & Nojima (2004), Nakai & Oki (2004),Sakai (2004), Shimoike (2004), Yokochi (2004a)
Coral community area (ha)	118		5,951.2	6,980	1,957.1	19,231.5	34,237.8	Hasegawa & Yamano (2004), Kajiwara & Matsumoto (2004), Nakai & Nojima (2004), Nakai & Oki (2004),Sakai (2004), Shimoike (2004), Yokochi (2004a)
Fishing activities	Recreational, commercial	Recreational, some commercial	Recreational, commercial	Recreational, commercial	Recreational, commercial	Recreational, commercial	N/A	Hasegawa & Yamano (2004), Kajiwara & Matsumoto (2004), Nakai & Nojima (2004), Nakai & Oki (2004),Sakai (2004), Shimoike (2004), Yokochi (2004a)
Agricultural activities	Sugarcane, rice, sweet potatoes, vegetables, other fruits, flowers, tobacco, others	Minimal	Sugarcane, pineapple, potatoes, vegetables, other fruits, flowers, tobacco, others	Sugarcane, vegetables, pineapple, other fruits, flowers, tobacco, others	Sugarcane, vegetables, other fruits, flowers, tobacco, others	Sugarcane, vegetables, pineapple, other fruits, flowers, tobacco, others	N/A	Kagoshima, Okinawa prefectural homepages
Other activities/issues	Local tourism	Minimal	Local tourism	Extensive tourism, red soil runoff, landfill, military bases local pollution & eutrophication	Extensive tourism	Extensive tourism, red soil runoff, landfill	N/A	Nakano (2004a), Kagoshima, Okinawa prefectural homepages
COTS outbreaks	None	None	1970s onwards	1970s onwards	1957–59, 1970s–1980s, 2004∼	1970s–1980s, 2007∼	N/A	Yokochi (2004b), Ministry of Environment
Water quality notes	Oligotrophic oceanic	Oligotrophic oceanic	Oligotrophic oceanic with turbid bays	Oligotrophic oceanic with turbid bays, local pollution & eutrophication	Oligotrophic oceanic with turbid bays	Oligotrophic oceanic with turbid bays	N/A	Hasegawa & Yamano (2004), Kajiwara & Matsumoto (2004), Nakai & Nojima (2004), Nakai & Oki (2004),Sakai (2004), Shimoike (2004), Yokochi (2004a)
Recent years of level 2 bleaching events	1998, 2001, 2016–7	1998	1998, 2016–7	1998, 2001, 2016–7	1998, 2001, 2016–7	1998, 2001, 2010, 2016–7	N/A	Nakano (2004b), NOAA, Ministry of Environment
National parks	Yakushima	None	Amamigunto	Yanbaru, Keramashoto	None	Iriomote-Ishigaki	5 parks	Hasegawa & Yamano (2004), Kajiwara & Matsumoto (2004), Nakai & Nojima (2004), Nakai & Oki (2004),Sakai (2004), Shimoike (2004), Yokochi (2004a), Ministry of Environment
Number of coral species	151	>151	200	340	302	363	N/A	Nishihira & Veron (1995), Nishihira (2004)