Large-scale hybridization of Japanese populations of Hinamoroko, Aphyocypris chinensis, with A. kikuchii introduced from Taiwan

Abstract

Aphyocypris chinensis is a small cyprinid that is widely distributed in lowland areas of continental China, the Korean Peninsula, and the northwestern part of Kyushu, Japan. However, this species is severely threatened in Japan due to human impacts; thus, several facilities and citizen groups implemented captive breeding and reintroduction/reinforcement programs using several dozen founder fish collected from Tanushimaru, the location with the only known natural population, in the 1980s and 1990s. To determine the phylogenetic position and genetic authenticity of Japanese populations of A. chinensis, we conducted mtDNA and genome-wide SNP analyses using a total of 254 specimens from 31 wild and captive samples, including specimens of Chinese and Korean A. chinensis and the close relative A. kikuchii from Taiwan. The mtDNA divergence and phylogeny indicated that the haplotypes found exclusively in Japan were differentiated from the Chinese/Korean haplotypes (uncorrected p = 2.6% in the cytochrome b gene) to the same extent as they were from A. kikuchii haplotypes (p = 2.9%). Results from mtDNA sequences and 47-359 SNPs, obtained using the MIG-seq method with different parameter sets, revealed that the initial captive populations and an extinct wild population in Ukiha, adjacent to Tanushimaru, were genuine Japanese populations, whereas all extant captive and wild populations in Japan are hybrids between Japanese A. chinensis and A. kikuchii, or A. kikuchii itself. The details of the captive breeding and exchange programs, as well as evidence for the aquarium trade of A. kikuchii since the 1990s, strongly suggest that the mixture of A. kikuchii into Japanese populations occurred within the first several years of the establishment of captive populations in 1994. The present case of the highly probable extinction of genuine Japanese populations of A. chinensis emphasizes the importance of confirmation and management of the genetic authenticity of conservation-targeted species. Keywords Captive breeding • Endangered species • Ex situ conservation • Hybridization • MIG-seq • mtDNA cytochrome b JPN-1 (n=2) HFC16, KEE04 JPN-2 (4) LBM00,01, KEE04 JPN-3 (2) UK08 JPN-5 (1) UK07 JPN-4 (10) TNS08, CPR18, LBM09, KEE04 AB218688 TNS CK-1 (1) KOR07 CK-4 (2) KOR07 CK-6 (2) KOR07 CK-7 (1) KOR07 CK-8 (2) KOR07 CK-2 (2) CLN01 CK-3 (1) KOR07 CK-5 (1) KOR07 AF307452 CN KKC-1 (138) TNS08… JX184925 TW-Hualien KKC-2 (1) THL02 AP012123 Aquarium KKC-3 (1) THL02 CSC-2 (1) CSC02 CSC-1 (1) CSC02 AP011398 Yaoshanicus arcus AP011396 Nicholsicypris normalis JX311312 Pararasbora moltrechti 0.08

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