A ddRAD-based population genetics and phylogenetics of an endangered freshwater fish from Japan

Takahashi, Tetsumi; Nagano, Atsushi J.; Kawaguchi, Lina; Onikura, Norio; Nakajima, Jun; Miyake, Teruki; Suzuki, Noriyasu; Kanoh, Yoshihiko; Tsuruta, Tetsuya; Tanimoto, Takuya; Yasui, Yukio; Oshima, Noriyuki; Kawamura, Kazuo

doi:10.1007/s10592-020-01275-5

Cited by 8 publications

(7 citation statements)

References 35 publications

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“…Recently, the RAD-seq technique, including GBS, 2b-RAD and dd-RAD, has been widely used in genetic studies of aquatic species, such as red swamp crayfish [ 16 ], black bass ( Micropterus spp. ) [ 17 ], Rhodeus ocellatus kurumeus [ 18 ] and Nujiang catfish ( Creteuchiloglanis macropterus ) [ 11 ]. In this study, we used the RAD-seq method to unravel the population dynamics and population structure of T. yarkandensis in the Tarim River basin.…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Population Differentiation of Kashgarian Loach (Triplophysa yarkandensis) in Xinjiang Tarim River Basin

Zhou

Zhao

et al. 2021

Biology

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The distribution of Triplophysa yarkandensis is restricted to Xinjiang’s Tarim River basin. We collected 119 T. yarkandensis samples from nine geographic populations in the Tarim River basin and utilized the RAD-seq method for SNP genotyping. In this study, a total of 164.81 Gb bases were generated with the Illumina platform, and 129,873 candidate SNPs were obtained with the Stacks pipeline for population genetic analyses. High levels of genetic diversity were detected among nine populations. The AMOVA results showed that the majority of genetic variations originated from among populations (FST = 0.67), and the pairwise FST values ranged from 0.4579 to 0.8736, indicating high levels of genetic differentiation among these populations. The discriminate analysis of principal components (DAPCs) and neighbor joining (NJ) tree revealed that the nine populations could be separated into two clusters (i.e., south and north populations), and modest genetic differentiation between south and north populations was observed, while the individuals from several populations were not clustered together by geographical location. The evidence of two genetic boundaries between south and north populations (except TTM) was supported by barrier analysis. The Bayesian skyline plotting indicated that T. yarkandensis populations in the Tarim River basin had not experienced genetic bottlenecks, and the effective population size remained stable. This study first clarified the genetic diversity and differentiation of T. yarkandensis populations in the Tarim River basin, and it provided valuable molecular data for conservation and management of natural populations.

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Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Population Differentiation of Kashgarian Loach (Triplophysa yarkandensis) in Xinjiang Tarim River Basin

Zhou

Zhao

et al. 2021

Biology

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“…The current genetic structure of East Asian freshwater snails in Japan was presumably affected by past mtDNA introgressions that were facilitated by ancient rivers in the Seto Inland Sea [ 16 ]. Furthermore, Takahashi et al (2020) showed genetic differentiation of the Japanese rosy bitterling, Rhodeus ocellatus kurumeus , between Honshu-Shikoku and Kyushu lineages using the Double Digest RAD-seq technique; they suggested the effect of ancient rivers on the lineage differentiation [ 17 ]. These previous studies, considered with the present study, supported the presence of the ancient river, thereby suggesting that the ancient river hypothesis is correct.…”

Section: Discussionmentioning

confidence: 99%

“…Previous biogeographic studies of a plant ( Rhododendron ripense ; [ 15 ]), snails ( Semisulcospira spp. ; [ 16 ]), and fish (Japanese rosy bittering Rhodeus ocellatus kurumeus ; [ 17 ]) in the main Japanese islands (Honshu, Shikoku, and Kyushu) suggested the influence of ancient rivers on the current population genetic structures of these species. To our knowledge, there have been no reports regarding the relationships between ancient rivers and the phylogeography of organisms inhabiting the islands in the Seto Inland Sea; the formation of this phylogeography was presumably directly influenced by ancient rivers.…”

Section: Introductionmentioning

confidence: 99%

Ancient rivers shaped the current genetic diversity of the wood mouse (Apodemus speciosus) on the islands of the Seto Inland Sea, Japan

Sato

Yasuda

2022

Zoological Lett

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The current distributions of organisms have been shaped by both current and past geographical barriers. However, it remains unclear how past geographical factors—currently cryptic on the sea floor—affected the current distributions of terrestrial animals. Here, we examined the effects of currently cryptic ancient rivers on current genetic differentiation of the large Japanese wood mouse, Apodemus speciosus, which inhabits islands in the Seto Inland Sea, Japan. Genome-wide polymorphisms were identified by GRAS-Di (Genotyping by Random Amplicon Sequencing, Direct) analysis of 92 A. speciosus individuals. Maximum-likelihood analysis was performed with 94,142 single nucleotide polymorphisms (SNPs) identified by GRAS-Di analyses. Ancient rivers were visualized by Geographic Information System (GIS) channel analysis. Maximum-likelihood analysis showed strong support for the monophyly of each population in the islands in the Seto Inland Sea; it also showed close relationships between Innoshima-Ikuchijima, Ohmishima-Hakatajima-Oshima, Ohmishima-Hakatajima, Ohsakikamijima-Ohsakishimojima, Kamikamagarijima-Shimokamagarijima, and Kurahashijima-Etajima islands. The principal component analyses of the SNPs also supported these relationships. Furthermore, individuals from islands located on the east and west sides of the main stream of the ancient river were clustered on each side with strong support. These phylogenetic relationships were completely congruent with the paleogeographic relationships inferred from ancient rivers. In conclusion, the findings demonstrated that the current distribution of genetically distinct island lineages was shaped by ancient rivers that are currently submerged beneath the Seto Inland Sea, Japan.

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“…In these species, genetic divergence between Japanese and Chinese lineages is estimated to be the early-middle Pliocene (Sakai et al, 1998;Tsao et al, 2016), when the Second Setouchi Basin ran westward through the northern part of Kyushu, having a connection with the paleo-Yellow River on the Asian continent, which flowed into the East China Sea (Ichihara, 2001;Nishimura, 1980). It has been suggested that these species dispersed from China to Japan through this large paleo-drainage system, rather than through the Korean Peninsula (Sakai et al, 1998;Takahashi et al, 2020).…”

Section: Differences In the Colonization Process Of Bitterling In East Asiamentioning

confidence: 99%

“…Recent phylogeographic analyses have demonstrated that the genetic structure of primary freshwater fishes in Japan has been shaped chiefly by geological and topographical events, coupled with climatic changes since the Late Miocene (Watanabe et al, 2017). The current genetic structure of aquatic animals in western Japan, including freshwater fishes (Takahashi et al, 2020;Yoshikawa et al, 2008), is particularly believed to be related to the existence of the Second Setouchi Basin, extending from the Kinki region to northern Kyushu, from the Pliocene to the Pleistocene (Ichihara, 2001). Although phylogeographic patterns shared by co-distributed species could be attributed to these historical events, interspecific differences in genetic structure might also be related to ecological and historical factors, including the dispersal abilities of particular species and local extinction events (Tominaga et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversification of the Kanehira bitterling Acheilognathus rhombeus inferred from mitochondrial DNA, with comments on the phylogenetic relationship with its sister species Acheilognathus barbatulus

Miyake

Nakajima

Umemura

et al. 2021

Journal of Fish Biology

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The Kanehira bitterling, Acheilognathus rhombeus, is a freshwater fish, discontinuously distributed in western Japan and the Korean Peninsula. Unusually among bitterling it is an autumn-spawning species and shows developmental diapause.Consequently, the characterization of its evolutionary history is significant not only in the context of the fish assemblage of East Asia, but also for understanding life-history evolution. This study aimed to investigate the phylogeography of A. rhombeus and its sister species Acheilognathus barbatulus, distributed in China, using a mitochondrial analysis of the ND1 gene from 311 samples collected from 50 localities in Japan and continental Asia. Phylogenetic analysis revealed that A. barbatulus is included in A. rhombeus and genetically closer to Japanese A. rhombeus than to Korean A. rhombeus. Divergence of Korean A. rhombeus and A. barbatulus from Japanese A. rhombeus was estimated to be from the late Pliocene (3.44 Mya) and the early Pleistocene (1.98 Mya), respectively. Each event closely coincided with the time of the Japan Sea opening. Japanese A. rhombeus comprised seven lineages: three in Honshu and four in Kyushu. One lineage in central Kyushu was genetically closer to the Honshu lineages than to other lineages in northern Kyushu. Divergence of Japanese lineages was estimated to be from the early to middle Pleistocene (0.55-0.93 Mya), during a period of geological and paleoclimatic change, including volcanic activity. Population expansion in the late Pleistocene (<0.10 Ma) was suggested in many of the lineages, which accords with other freshwater fishes. Biogeographically the ancestral A. rhombeus/ A. barbatulus was likely to have repeatedly colonized Japan from the continent through land bridges in the late Pliocene and the early Pleistocene. However, the close genetic relationship between Japanese A. rhombeus and A. barbatulus suggests another possibility, with the second colonization occurring in reverse, from Japan to China. The small genetic distance between them indicates that the colonization occurred later than colonization events of other freshwater fishes, including other bitterling species.

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A ddRAD-based population genetics and phylogenetics of an endangered freshwater fish from Japan

Cited by 8 publications

References 35 publications

Genetic Diversity and Population Differentiation of Kashgarian Loach (Triplophysa yarkandensis) in Xinjiang Tarim River Basin

Genetic Diversity and Population Differentiation of Kashgarian Loach (Triplophysa yarkandensis) in Xinjiang Tarim River Basin

Ancient rivers shaped the current genetic diversity of the wood mouse (Apodemus speciosus) on the islands of the Seto Inland Sea, Japan

Genetic diversification of the Kanehira bitterling Acheilognathus rhombeus inferred from mitochondrial DNA, with comments on the phylogenetic relationship with its sister species Acheilognathus barbatulus

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