Complete mitochondrial genome of the endangered freshwater fish <i>Microphysogobio rapidus</i> (Cypriniformes, Cyprinidae) from Korea

Kim, Kang-Rae; Bang, In-Chul

doi:10.1080/23802359.2019.1704642

Cited by 3 publications

(2 citation statements)

References 4 publications

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“…The following supporting information can be downloaded at: , Figure S1: Time tree of Huigobio and its close relatives based on 13 protein-coding genes of mitochondrial genomes; Table S1: Reviews of the genetic diversity of freshwater fishes endemic to southern China revealed by mitochondrial genes; Table S2: Reviews of the phylogeographical patterns of freshwater fishes endemic to southern China revealed by mitochondrial genes; Table S3: Primers and annealing temperature used in PCR amplification of mitochondrial genomes; Table S4: Sampling localities and source of mitochondrial genome for Huigobio and outgroup taxa; Table S5: Comparisons among six models of biogeography analyses in ancestral area reconstruction of H. chenhsienensis . References [ 11 , 13 , 14 , 15 , 16 , 17 , 18 , 26 , 27 , 37 , 65 , 72 , 73 , 74 , 75 , 76 , 77 , 78 , 79 , 80 , 81 , 82 , 83 , 84 , 85 , 86 , 87 , 88 , 89 , 90 , 91 , 92 , 93 , 94 , 95 , 96 , 97 , 98 , 99 , 100 , 101 , 102 , 103 , 104 , 105 , 106 ] are cited in the supplementary materials.…”

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Phylogeographical Analysis of the Freshwater Gudgeon Huigobio chenhsienensis (Cypriniformes: Gobionidae) in Southern China

Yang

2022

Life

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The freshwater gudgeon Huigobio chenhsienensis (Cypriniformes: Gobionidae) is a small fish endemic to southern China. In this study, we used mitochondrial cytochrome b gene (Cytb), from wide-ranging samplings of H. chenhsienensis from the Ou River (the central of southern China) to the Yangtze River Basin (the northernmost part of southern China) to explore genetic variations and the evolutionary history of H. chenhsienensis in southern China. In total, 66 haplotypes were identified from Cytb sequences of 142 H. chenhsienensis individuals, which could be divided into lineages A, B, and C with divergence times of ~4.24 Ma and ~3.03 Ma. Lineage A was distributed in the lower reaches of the Yangtze River, the Oujiang River, and the Jiao River, lineage B was distributed in the Qiantang River and the Cao’e River, whereas lineage C was restricted to the Poyang Lake drainage from the middle reaches of the Yangtze River. Lineage A could be subdivided into sub-lineages A-I, A-II, A-III, and A-IV, with divergence times of 1.30, 0.97, and 0.44 Ma. Lineage C could be subdivided into sub-lineages C-I and C-II, with a divergence time of 0.85 Ma. Our findings indicate that climate change during the Pliocene and Pleistocene eras, as well as the limited dispersal ability of H. chenhsienensis, have been major drivers for shaping the phylogeographical patterns of H. chenhsienensis.

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Phylogeographical Analysis of the Freshwater Gudgeon Huigobio chenhsienensis (Cypriniformes: Gobionidae) in Southern China

Yang

2022

Life

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“…Obtaining such data will be crucial for the development of a systematic conservation strategy, which is urgently required to safeguard the future of this species. Despite a few molecular phylogenetic studies, the lack of efficient molecular markers and comprehensive population genetic studies has hindered the comprehensive evaluation of the genetic diversity and genetic structure of this species [8,[12][13][14][15][16]. DNA fingerprinting analysis, including the utilization of microsatellite markers, is a widely used molecular method for evaluating genetic variability in natural populations, including endangered fish species [17,18].…”

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confidence: 99%

The Impact of Weir Construction in Korea’s Nakdong River on the Population Genetic Variability of the Endangered Fish Species, Rapid Small Gudgeon (Microphysogobio rapidus)

Hong

Kim

et al. 2023

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Microphysogobio rapidus, an endemic cyprinid fish species found exclusively in Korea, has been identified in only two tributaries of the Nakdong River. The species predominantly occupies the near-gravel bottom waters within shallow sections of the middle and lower reaches of the river, characterized by swift currents. M. rapidus is currently recognized as a critically endangered species due to its distinct habitat preference, as well as the negative impacts of stream dam development and water environment pollution. In this study, we used 10 microsatellite markers to examine the genetic diversity of M. rapidus in the upper Nam (UN), lower Nam (LN), and Deokcheon Rivers (DC) in Korea, with a specific focus on assessment of the impact of dam development. Fish sampled from the UN and LN showed a greater average number of alleles and allelic richness (A = 18.3–18.4, AR = 13.8) compared to those from DC (A = 11.8, AR = 11.5). The observed heterozygosity among the fish examined ranged from HO = 0.748 (LN) to 0.766 (DC). All three fish groups exhibited a significant departure from Hardy–Weinberg equilibrium (HWE) (p < 0.05). Despite having the largest effective population size (Ne = 175 and 157, respectively), the fish sampled from UN and LN showed the highest inbreeding coefficients (FIS = 0.056–0.053, respectively), which were highly significant (p < 0.01). In contrast, the fish sampled from DC exhibited the smallest effective population size (Ne = 61) and showed an inbreeding coefficient close to zero (p > 0.05). BOTTLENECK analysis and estimated M-ratio values (0.341–0.372) revealed indications of past population size reduction in all fish groups examined. No significant genetic differentiation (FST < 0.05) was detected using the DAPC, STRUCTURE, and AMOVA among the fish studied. However, pairwise comparisons of FST between fish sampled from the Nam and Deokcheon Rivers revealed significant values (p < 0.001) ranging from 0.013 to 0.014. In addition, the closest genetic distance (0.026) was observed between UN and LN, while the greatest distance (0.087) was found between UN and DC. Analysis of gene flow rates among the fish examined indicated asymmetrical gene exchange within the Nam River, which was 31.51% in the downstream direction (from UN to LN), with a minimal gene flow rate (0.41%) in the upstream (from LN to UN) direction. The opposite trend was recorded between DC and LN, with a higher gene flow rate (29.74%) in the upstream direction compared to the downstream direction (0.12%). Our study highlighted the importance of implementing long-term conservation efforts focused on maintaining river integrity by removing water barriers such as weirs that impede fish migration and implementing active protection measures, such as aquaculture breeding and reasonable stocking practices, to preserve M. rapidus in the study area.

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Pleistocene Landscape Dynamics Drives Lineage Divergence of a Temperate Freshwater Fish Gobio rivuloides in Coastal Drainages of Northern China

Ni,

Chen,

Deng

et al. 2023

Genes

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Understanding historical processes underlying lineage distribution patterns is a primary goal of phylogeography. We selected Gobio rivuloides (Cypriniformes: Gobionidae) as a model to improve our knowledge about how intraspecific genetic divergence of freshwater fishes arises in coastal drainages of northern China via statistical analysis using cytochrome b gene. The time-calibrated phylogeny of G. rivuloides showed the divergence of two major lineages (I and II) at ~0.98 Ma (million years ago). Lineage I can be divided into two sub-lineages (I-A and I-B) with a divergence time of ~0.83 Ma. Sub-lineage I-A inhabits the Amur River, and sub-lineage I-B lives in the Luan River and Liao River. Lineage II is distributed in the Yellow River and Hai River, with close genetic relationships between the two drainages, and can be split into two sub-lineages (II-C and II-D) with a divergence time of ~0.60 Ma. Our findings indicate that the splitting of lineages and sub-lineages could be attributed to geographic isolation caused by the formation of the Bohai Sea, river capture, and the episodic hydrologic closing of a paleolake during the late Lower–Middle Pleistocene. It is also the first report we know of displaying a clear phylogeographic break for freshwater fishes across coastal drainages in northern China.

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Complete mitochondrial genome of the endangered freshwater fish Microphysogobio rapidus (Cypriniformes, Cyprinidae) from Korea

Cited by 3 publications

References 4 publications

Phylogeographical Analysis of the Freshwater Gudgeon Huigobio chenhsienensis (Cypriniformes: Gobionidae) in Southern China

Phylogeographical Analysis of the Freshwater Gudgeon Huigobio chenhsienensis (Cypriniformes: Gobionidae) in Southern China

The Impact of Weir Construction in Korea’s Nakdong River on the Population Genetic Variability of the Endangered Fish Species, Rapid Small Gudgeon (Microphysogobio rapidus)

Pleistocene Landscape Dynamics Drives Lineage Divergence of a Temperate Freshwater Fish Gobio rivuloides in Coastal Drainages of Northern China

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