Japanese Freshwater Fishes: Biogeography and Cryptic Diversity

Abstract

More than 300 species of freshwater fishes are present in Japan. Because their distribution is expected to reflect geological history consequent to their low dispersal ability, they are a suitable group for studying historical relationships between land and biota. The strictly freshwater fish fauna in the Japanese Archipelago is primarily separated into two groups: those in northeastern Hokkaido, and those in other southwestern areas. The latter is further divided into two endemic faunas in the eastern and western regions across the Fossa Magna area. Recent phylogenetic and phylogeographic studies, primarily using mitochondrial DNA markers, support the importance of the Fossa Magana area in isolating related forms or intraspecific populations since the Late Miocene–Pliocene. This isolation, however, is not a primary one in some species. In western Japan, which has a rich and endemic freshwater fish fauna, both similar and different phylogeographic patterns have been observed among species, which may reflect differences in distribution histories and ecological traits of species. Further analyses using nuclear DNA loci, or genomic data, are necessary to elucidate the true processes of distribution, demography, and adaptation. Currently, 181 species/subspecies that depend heavily on freshwater environments are recognized in the Japanese Archipelago, but at least 244 evolutionary units (i.e., deep lineages with a long, unique history) are included in its freshwater fish fauna. The introduction of nonindigenous species is the primary driver for the decrease in β-diversity among regions, but the effects of species transplanted from other regions within Japan (i.e., the mixture and loss of endemic evolutionary units) remain underevaluated. Evolutionarily distinct units of freshwater fishes are historical legacies and should be maximally protected and passed on to future generations.

Appendices

Appendices

1.1 Appendix 1

Data and methods for analyses of faunal patterns of Japanese freshwater fishes

1.1.1 Data

Regions

Freshwater fish assemblages from the four main islands of the Japanese Archipelago (Kyushu, Shikoku, Honshu, and Hokkaido) were analyzed (Watanabe 2012). Regions were divided into the following 27 areas based on straits, primary watersheds (Takahashi and Sakaguchi 1976), and other watersheds that separated fish faunas (Fig. 7.2):(1) Ky-SE (southeastern Kyushu), (2) Ky-SW (southwestern Kyushu), (3) Ky-NW (northwestern Kyushu), (4) Ky-NE (northeastern Kyushu), (5W) Sh-SW (southwestern Shikoku), (5E) Sh-SE (southeastern Shikoku), (6W) Sh-NW (northwestern Shikoku), (6E) Sh-NE (northeastern Shikoku), (7) Ch-SW (southwestern Chugoku Region), (8) Ch-SE (southeastern Chugoku Region; eastern Sanyo), (9) Ch-N (northern Chugoku Region; San’in), (10) Ki-M (middle Kinki Region), (11) Ki-N (northern Kinki Region), (12) Ki-S (southern Kinki Region), (13) Tk-I (Tokai Region around Ise Bay), (14) Tk-E (eastern Tokai Region), (15) Ho-W (western Hokuriku Region), (16) Ho-E (eastern Hokuriku Region), (17) Ka (Kanto Region), (18) To-P (Pacific side of Tohoku Region), (19) To-J (Japan Sea side of Tohoku Region), (20) Hk-WS (southern southwestern Hokkaido), (21) Hk-WN (northern southwestern Hokkaido), (22) Hk- MS (southern middle Hokkaido), (23) Hk-MN (northern middle Hokkaido), (24) Hk-ES (southern eastern Hokkaido), and (25) Hk-EN (northern eastern Hokkaido).

Fishes

Ninety-three forms (species, subspecies, and intraspecific monophyletic groups detected by genetic studies) of 32 genera in 8 families occurring in Japan were used in the analysis (primarily based on Nakabo 2000; Kawanabe et al. 2001). These forms included almost all primary freshwater fishes and some secondary taxa (sensu Myers 1949), excluding several species whose original distribution was uncertain, and any diadromous fishes and their sister forms (e.g., landlocked salmonids, sculpins, and gobies). Intraspecific monophyletic groups were defined as those that meet the conditions of categories I or II of Avise (2000); that is, regional allopatric populations associated with deeply separated gene (mostly mtDNA) lineages. Note that the classification (species identity, scientific names, and Japanese common names) is not updated from that used by Watanabe (2012). The presence/absence data for each fish form were obtained from papers, monographs, books, and other literature sources (see Watanabe 1998 for primary references).

1.1.2 Methods

The structures of the freshwater fish faunas were analyzed using parsimony analysis of endemicity (PAE) (Watanabe 2012) and a cluster analysis by unweighted pair-group method with arithmetic mean (UPGMA) based on the presence/absence matrix.

PAE

The calculation for PAE using the distribution data of 93 forms and 27 areas (see following table) was conducted using PAUP*4.0b10 (Swofford 2002). The strict consensus tree was calculated from the most parsimonious area cladograms, with changes in the distribution of each fish parsimoniously reconstructed on the consensus tree under the DELTRAN criterion (Wiley et al. 1991). Endemic areas were defined as the areas or “monophyletic” clades of areas in the consensus tree that were involved with one or more “autapomorphic” or “synapomorphic” (i.e., endemic) fish forms with CI = 1.0 (without homoplasy). The robustness of each clade was evaluated by bootstrap analysis (Felsenstein 1985) with 1000 replications.

UPGMA

The presence/absence data were summarized by calculating the pairwise Jaccard’s coefficient of percentage faunal similarity: $J=\left[a/\left(a+b+c\right)\right]\times 100\ \%$, where a is the number of fish forms shared between the two regions being compared, b is the number of fish forms found only in the first area, and c is the number of fish forms found only in the second area (Jaccard 1908). Based on the similarity matrix, UPGMA clustering was conducted using the NEIGHBOR program in PHYLIP 3.6 (Felsenstein 2005).

1.1.3 Data Source for Appendix 1

• Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

• Felsenstein J (2005) PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle. http://evolution.genetics.washington.edu/phylip.html. Accessed 8 Sept 2011

• Jaccard P (1908) Nouvelles rescherches sur la distribution florale. Bull Soc Vaud Sci Nat 44:223–270

• Kawanabe H, Mizuno N, Hosoya K (2001) Freshwater fishes of Japan, 3rd edn. Yama-Kei Publishers, Tokyo

• Myers GS (1949) Salt tolerance of fresh-water fish groups in relation to zoogeographical problems. Bijdr Dierkd 28:315–322

• Nakabo T (2000) Fishes of Japan with pictorial keys to the species, 2nd edn. Tokai University Press, Tokyo

• Swofford DL (2002) PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4b10. Sinauer, Sunderland

• Takahashi Y, Sakaguchi Y (1976) Rivers in Japan. Kagaku 46:488–499

• Watanabe K (1998) Parsimony analysis of the distribution pattern of Japanese primary freshwater fishes, and its application to the distribution of the bagrid catfishes. Ichthyol Res 45:259–270

• Watanabe K (2012) Faunal structure of Japanese freshwater fishes and its artificial disturbance. Environ Biol Fish 94:533–547

• Wiley EO, Siegel-Causey D, Brooks DR, Funk VA (1991) The compleat cladist: a primer of phylogenetic procedures. Museum of Natural History, University of Kansas, Lawrence

Distribution data for native strictly freshwater fishes in the Japanese Archipelago (presence = 1/absence = 0)
Taxon			Region
Code	Species/group	Japanese name	1	2	3	4	5W	5E	6W	6E	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24	25	OG
Cyprinidae
T01	Carassius cuvieri	Gengoro-buna	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T02	C. auratus grandoculis	Nigoro-buna	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T03	Tanakia tanago	Miyako-tanago	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
T04	T. lanceolata	Yari-tanago	0	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0
T05	T. limbata	Aburabote	0	1	1	1	0	0	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0
T06	Acheilognathus melanogaster	Tanago	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0
T07	A. tabira tabira	Shirohire-tabira	0	0	0	0	0	0	0	1	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
T08	A. tabira erythropterus	Akahire-tabira	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0
T09	A. tabira tohokuensis	Kitanoakahire-tabira	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0
T10	A. tabira jordani	Minamiakahiretabira	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
T11	A. tabira nakamurae	Seboshi-tabira	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T12	A. rhombeus	Kanehira	0	1	1	0	0	0	0	0	0	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T13	A. cyanostigma	Ichimonji-tanago	0	0	0	0	0	0	0	0	0	1	0	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0
T14	A. longipinnis	Itasenpara	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0
T15	A. typus	Zeni-tanago	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0
T16	Rhodeus ocellatus kurumeus	Nipponbara-tanago	0	1	1	1	0	0	0	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T17	R. atremius atremius	Kazetoge-tanago	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T18	R. atremius suigensis	Suigenzeni-tanago	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T19	Ischikauia steenackeri	Wataka	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T20	Hemigrammocypris rasborella	Kawabata-moroko	0	1	1	0	0	0	0	1	0	1	0	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0
T21	Opsariichthys uncirostris	Hasu	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T22	Zacco platypus	Oikawa	0	1	1	1	0	0	1	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0
T23	Z. temminckii	Kawamutsu	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0
T24	Z. sieboldii	Numamutsu	0	1	1	1	0	0	0	1	1	1	0	1	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0
T25	Aphyocypris chinensis	Hina-moroko	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T26	Rhynchocypris percnurus sachalinensis	Yachi-ugui	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0
T27	R. lagowskii (Japanese clade)	Aburahaya	0	0	0	0	0	0	0	0	0	1	0	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0
T28	R. oxycephalus (Japanese clade)	Takahaya	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0
T29	Pseudorasbora parva	Motsugo	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0
T30	P. pumila pumila	Shinai-motsugo	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0
T31	P. pumila subsp.	Ushi-motsugo	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
T32	Sarcocheilichthys biwaensis	Abura-higai	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T33	S. variegatus variegatus	Kawa-higai	0	1	1	0	0	0	0	0	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0
T34	S. variegatus microoculus	Biwa-higai	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T35	Pungtungia herzi	Mugitsuku	0	1	1	1	0	1	0	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0
T36	Gnathopogon elongatus	Tamoroko	0	0	0	1	1	0	1	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0
T37	G. caerulescens	Honmoroko	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T38	G. suwae	Suwamoroko	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
T39	Biwia zezera	Zezera	0	1	1	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
T40	Biwia sp.	Yodo-zezera	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T41	Pseudogobio esocinus	Kamatsuka	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0
T42	Abbottina rivularis	Tsuchifuki	0	1	1	0	0	0	0	0	0	1	0	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0
T43	Hemibarbus longirostris	Zunaganigoi	0	0	0	0	0	0	0	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0
T44	H. labeo	Kourai-nigoi	0	0	0	0	0	0	0	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0
T45	H. barbus	Nigoi	0	1	1	0	0	0	1	0	1	0	0	1	0	0	0	1	1	1	1	1	1	0	0	0	0	0	0	0
T46	Squalidus gracilis gracilis	Ito-moroko	0	1	1	1	0	0	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0
T47	S. japonica japonica	Deme-moroko	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
T48	S. chankaensis biwae	Sugo-moroko	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T49	S. chankaensis subsp.	Kourai-moroko	0	0	0	0	0	0	0	1	1	1	0	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0
Cobitidae
T50	Leptobotia curta	Ayumodoki	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T51	Misgurnus anguillicaudatus	Dojo	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0
T52	Niwaella delicata (Group G)	Ajime-dojo G	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
T53	Niwaella delicata (Group S)	Ajime-dojo S	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
T54	Cobitis takatsuensis	Ishi-dojo	0	0	1	1	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T55	C. shikokuensis	Hinaishi-dojo	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T56	C. biwae (Eastern)	Shima-dojo E	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0
T57	C. biwae (Kochi)	Shima-dojo K	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T58	C. biwae (Western)	Shima-dojo W	0	0	0	1	0	0	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0
T59	C. sp. Y86	Yamatoshima-dojo Y86	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T60	C. sp. Y90	Yamatoshima-dojo Y90	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T61	C. sp. Y94	Yamatoshima-dojo Y94	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T62	C. sp. 3 (Middle)	Sujishima-dojo M	0	0	1	1	0	0	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T63	C. sp. 2 subsp. 1 (Small-Sanyo)	Sujisima-dojo S-SY	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T64	C. sp. 2 subsp. 2 (Small-Tokai)	Sujisima-dojo S-T	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0
T65	C. sp. 2 subsp. 3 (Small-San’in)	Sujisima-dojo S-SI	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T66	C. sp. 2 subsp. 4 (Small-Kyushu)	Sujisima-dojo S-K	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T67	C. sp. 2 subsp. 5 (Small-L.Biwa)	Sujisima-dojo S-B	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T68	C. sp. 2 subsp. 6 (Small-R.Yodo)	Sujisima-dojo S-Y	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T69	C. sp. 1 (Large)	Sujisima-dojo L	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T70	Noemacheilus barbatulus toni	Fuku-dojo	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0
T71	Lefua nikkonis	Ezohotoke-dojo	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0
T72	L. echigonia (Hokuriku)	Hotoke-dojo Hokuriku	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0
T73	L. echigonia (Tohoku)	Hotoke-dojo Tohoku	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
T74	L. echigonia (Tokai)	Hotoke-dojo Tokai	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0
T75	L. echigonia (Kinki)	Hotoke-dojo Kinki	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
T76	L. echigonia (N-Kanto)	Hotoke-dojo N-Kanto	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0
T77	L. echigonia (S-Kanto)	Hotoke-dojo S-Kanto	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
T78	L. sp. (Kinki-Shikoku)	Nagarehotoke-dojo KS	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T79	L. sp. (Sanyo)	Nagarehotoke-dojo SY	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T80	L. sp. (Tokai)	Nagarehotoke-dojo TK	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
Bagridae
T81	Pseudobagrus nudiceps	Gigi	0	0	0	1	0	0	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T82	P. tokiensis	Gibachi	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0
T83	P. ichikawai	Neko-gigi	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
T84	P. aurantiacus	Ariake-gibachi	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Siluridae
T85	Silurus lithophilus	Iwatoko-namazu	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T86	S. biwaensis	Biwakooo-namazu	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T87	S. asotus	Namazu	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0
Amblycipitidae
T88	Liobagrus reini	Akaza	0	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0
Adrianichthyidae
T89	Oryzias latipes subsp.	Medaka N	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0
T90	O. latipes latipes	Medaka S	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0	0	1	1	0	0	0	0	0	0	0	0
Sinipercidae
T91	Coreoperca kawamebari	Oyanirami	0	1	1	1	0	0	0	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Odontobutiidae
T92	Odontobutis obscura	Donko	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0
T93	O. hikimius	Ishi-Donko	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

1. For region codes, see text and Fig. 7.2
2. The data shown are as used by Watanabe (2012); scientific names and Japanese common names have not been updated

1.2 Appendix 2

Total number of papers per 5 years using each type of molecular marker.

Data from the database GEDIMAP (http://gedimap.zool.kyoto-u.ac.jp), retrieved on 20 August 2015

1.3 Appendix 3

Comparisons of the levels of genetic divergence (as uncorrected p values for the mtDNA cytochrome b gene) among intraspecific deep lineages, subspecies, and closest species pairs

Code	Species	Details	Original source	Sequence region	Minimum	Maximum	Mean	Remark
Intraspecific
1	Tanakia lanceolata	4 lineages (LA1, LA2, LA3, LA4)	Hashiguchi et al. (2006)	Full	0.0292	0.0416	0.0357	1
2	Tanakia limbata	3 (LI1, LI2, LI3)	Hashiguchi et al. (2006)	Full	0.0378	0.0424	0.0397	1
3	Acheilognathus cyanostigma	3 (Clades 1, 2, 3)	Kitazima et al. (2015)	Full	0.0126	0.0171	0.0147	1
4	Rhodeus ocellatus kurumeus	3 (Osaka, Okayama, Kyushu)	Abe et al. (2013)	Full	0.0088	0.0167	0.0134	1
5	Hemigrammocypris rasborella	2 (Honshu+Shikoku, Kyushu)	Watanabe et al. (2014)	Full			0.1011	2
6	Sarcocheilichthys variegatus variegatus	2 (A+B+C+D, E)	Komiya et al. (2014)	3′-half			0.0317	1
7	Gnathopogon elongatus elongatus	3 (E1, E2, E3)	Kakioka et al. (2013)	Full	0.0471	0.0800	0.0682	1
8	Biwia zezera	4 (ISE, LBW, SNY, KYS)	Watanabe et al. (2010a, b)	Full	0.0102	0.0357	0.0236	1
9	Pseudogobio esocius	3 (Groups A, B, C)	Tominaga et al. (2016)	Full	0.0615	0.0855	0.0757	1
10	Lefua echigonia	5 of 8 (Tohoku, Echigo, North-Kanto, South-Kanto, Tokai–Kinki)	Saka et al. (2003)	Full	0.0785	0.1336	0.1098	1
11	Liobagrus reinii	2 (Groups 1, 2)	Nakagawa et al. (2016)	Full			0.0856	2
						n	11
						Average	0.0545
						SD	0.0349
						Minimum	0.0134
						Maximum	0.1098
Inter-subspecific
12	Acheilognathus tabira	5 subspp.	Kitamura et al. (2012)	Full	0.0317	0.0814	0.0630	1
13	Tribolodon brandtii	2 subspp.	Watanabe and Sakai et al. (unpublished data)	3′-half			0.0391	1
Interspecific
14	Acheilognathus typus–A. longipinnis		Kawamura et al. (2014)	Full			0.0710	1
15	Nipponocypris temminckii–N. sieboldii		Saitoh et al. (2006) and Miya et al. (2015)	Full			0.1105	1
16	Rhynchocypris lagowskii steindachneri–R. oxycephalus jouyi		Sasaki et al. (2008)	Full			0.1070	1
17	Pseudorasbora pumila–P. pugnax		Kakioka et al. (2013)	Full			0.0742	1
18	Gnathopogon elongatus–G. caerulescens		Kakioka et al. (2013)	Full			0.0335	2
19	Biwia zezera–B. yodoensis		Watanabe et al. (2010)	Full			0.0845	1
20	Cobitis spp. BIWAE complex		Kitagawa et al. (2003)	5′-half	0.0920	0.1420	0.1220	1
21	Lefua echigonia–L. sp.		Saka et al. (2003)	Full			0.1309	1
						n	10
						Average	0.0836
						SD	0.0336
						Minimum	0.0335
						Maximum	0.1309

1. Remark: 1 recalculated, 2 described in the original reference

1.3.1 Data Source for Appendix 3

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• Kawamura K, Ueda T, Arai R, Smith C (2014) Phylogenetic relationships of bitterling fishes (Teleostei: Cypriniformes: Acheilognathinae), inferred from mitochondrial cytochrome b sequences. Zool Sci 31:321–329

• Kitagawa T, Watanabe M, Kitagawa E, Yoshioka M, Kashiwagi M, Okazaki T (2003) Phylogeography and the maternal origin of the tetraploid form of the Japanese spined loach, Cobitis biwae, revealed by mitochondrial DNA analysis. Ichthyol Res 50:318–325

• Kitamura J, Nagata N, Nakajima J, Sota T (2012) Divergence of ovipositor length and egg shape in a brood parasitic bitterling fish through the use of different mussel hosts. J Evol Biol 25:566–573

• Kitazima J, Matsuda M, Mori S, Kokita T, Watanabe K (2015) Population structure and cryptic replacement of local populations in the endangered bitterling Acheilognathus cyanostigma. Ichthyol Res 62:122–130

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• Sasaki T, Kartavtsev YP, Chiba SN, Uematsu T, Sviridov VV, Hanzawa N (2007) Genetic divergence and phylogenetic independence of Far Eastern species in subfamily Leuciscinae (Pisces: Cyprinidae) inferred from mitochondrial DNA analyses. Genes Genet Syst 82:329–340

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• Watanabe K, Kawase S, Mukai T, Kakioka R, Miyazaki J-I, Hosoya K (2010) Population divergence of Biwia zezera (Cyprinidae: Gobioninae) and the discovery of a cryptic species, based on mitochondrial and nuclear DNA sequence analyses. Zool Sci 27:647–655

• Watanabe K, Mori S, Tanaka T, Kanagawa N, Itai T, Kitamura J, Suzuki N, Tominaga K, Kakioka R, Tabata R, Abe T, Tashiro Y, Hashimoto Y, Nakajima J, Onikura N (2014) Genetic population structure of Hemigrammocypris rasborella (Cyprinidae) inferred from mtDNA sequences. Ichthyol Res 61:352–360

1.4 Appendix 4

A list of species, subspecies, and distinct intraspecific deep lineages of freshwater fishes occurring in the Japanese Archipelago (not including the Ryukyu Islands).

Only species that largely spend their lives in freshwater or diadromous fishes that reproduce in freshwater are included. This list is NOT an effective publication under the International Code of Zoological Nomenclature.

Table 3

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• Mukai T, Shibukawa K, Shinozaki T, Sugiyama H, Chiba SN, Hanzawa N (2010) Preliminary review and conservation of Gymnogobius castaneus complex in Japan. Jpn J Ichthyol 57:173–176

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