BackgroundCarassius auratus is a primary freshwater fish with bisexual diploid and unisexual gynogenetic triploid lineages. It is distributed widely in Eurasia and is especially common in East Asia. Although several genetic studies have been conducted on C. auratus, they have not provided clear phylogenetic and evolutionary descriptions of this fish, probably due to selection bias in sampling sites and the DNA regions analysed. As the first step in clarifying the evolutionary entity of the world's Carassius fishes, we attempted to clarify the phylogeny of C. auratus populations distributed in East Asia.ResultsWe conducted a detailed analysis of a large dataset of mitochondrial gene sequences [CR, 323 bp, 672 sequences (528 sequenced + 144 downloaded); CR + ND4 + ND5 + cyt b, 4669 bp in total, 53 sequences] obtained from C. auratus in East Asia. Our phylogeographic analysis revealed two superlineages, one distributed mainly among the Japanese main islands and the other in various regions in and around the Eurasian continent, including the Ryukyus and Taiwan. The two superlineages include seven lineages with high regional specificity that are composed of endemic populations indigenous to each region. The divergence time of the seven lineages was estimated to be 0.2 million years ago (Mya) by a fossil-based method and 1.0-1.9 Mya by the molecular clock method. The antiquity and endemism of these lineages suggest that they are native to their respective regions, although some seem to have been affected by the artificial introduction of C. auratus belonging to other lineages. Triploids of C. auratus did not form a monophyletic lineage but were clustered mostly with sympatric diploids.ConclusionsThe results of the present study revealed the existence of two superlineages of C. auratus in East Asia that include seven lineages endemic to each of the seven regions examined. The lack of substantial genetic separation between triploids and diploids indicates that triploids are not composed of a single independent lineage. The ancient origins and evolutionary uniqueness of the seven lineages warrant their conservation. An overall phylogenetic framework obtained from the present study will be of use for estimating the phylogenetic relationships of Carassius fishes on the Eurasian continent.

The genetic constitution and phylogenetic relationships among the proposed species and subspecies of the crucian carp complex in Japan (Carassius cuvieri, C. auratus subspp. 1 and 2, C. a. grandoculis, C. a. buergeri, and C. a. langsdorfii) were investigated based on analyses of the partial nucleotide sequences of the mitochondrial DNA control region and amplified fragment length polymorphisms of nuclear DNA. Our results demonstrate that C. cuvieri and C. auratus are different entities. However, although several distinct lineages were observed for C. auratus, none corresponded to the proposed subspecies. Moreover, the five subspecies of C. auratus were not necessarily separated genetically from each other. Triploid fish, which are currently classified as a single subspecies (C. a. langsdorfii) but are sometimes treated as an independent species, fell into various clades along with diploid individuals of other subspecies that have the same or similar mitochondrial haplotypes. This suggests that gynogenetic triploid crucian carps distributed throughout the Japanese Archipelago have polyphyletic maternal origins. Our results indicate that Japanese crucian carps are a much more complex assemblage than previously believed.

Asexual vertebrates are rare and at risk of extinction due to their restricted adaptability through the loss of genetic recombination. We explore the mechanisms behind the generation and maintenance of genetic diversity in triploid asexual (gynogenetic) Carassius auratus fish, which is widespread in East Asian fresh waters and exhibits one of the most extensive distribution among asexual vertebrates despite its dependence on host sperm. Our analyses of genetic composition using dozens of genetic markers and genome-wide transcriptome sequencing uncover admixed genetic composition of Japanese asexual triploid Carassius consisting of both the diverged Japanese and Eurasian alleles, suggesting the involvement of Eurasian lineages in its origin. However, coexisting sexual diploid relatives and asexual triploids in Japan show regional genetic similarity in both mitochondrial and nuclear markers. These results are attributed to a unique unidirectional gene flow from diploids to sympatric triploids, with the involvement of occasional sexual reproduction. Additionally, the asexual triploid shows a weaker population structure than the sexual diploid, and multiple triploid lineages coexist in most Japanese rivers. The generated diversity via repeated interploidy gene flow as well as an increased establishment of immigrants is assumed to offset the cost of asexual reproduction and might contribute to the successful broad distribution of this asexual vertebrate.

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