Structure Analysis of Mitochondrial DNA Control Region Sequences and its Applications for the Study of Population Genetic Diversity of Acanthogobius ommaturus

Song, Chenyu; Sun, Zhicheng; Gao, Tianxiang; Song, Na

doi:10.1134/s1063074020040082

Cited by 15 publications

(7 citation statements)

References 25 publications

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“…Finally, our study also recovered the diversity information of mitochondrial and nuclear data that in contrast with previous studies that also shed light on the current status of the species. With the two mitochondrial markers, the genetic diversity recovered was lower (i.e., mtCox1 Hd = 0.28 and mtCytb Hd = 0.62) than previously reported for the species [18,72], and also in comparison with other euryhaline species [73,74]; for mtCox1, Hap3 was present in 80% of the samples analyzed. Similarly, in the nuclear data, the heterozygosity values obtained in our study were lower than those previously reported for 5 of our 11 microsatellite loci [25].…”

Section: Implications For Species Conservationcontrasting

confidence: 68%

Molecular Characterization of the Common Snook, Centropomus undecimalis (Bloch, 1792) in the Usumacinta Basin

et al. 2021

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The common snook is one of the most abundant and economically important species in the Usumacinta basin in the Gulf of Mexico, which has led to overfishing, threatening their populations. The main goal of the present study was to assess the genetic diversity and structure of the common snook along the Usumacinta River in order to understand the population dynamics and conservation status of the species. We characterized two mitochondrial markers (mtCox1 and mtCytb) and 11 microsatellites in the Usumacinta basin, which was divided into three zones: rainforest, floodplain and river delta. The mitochondrial data showed very low diversity, showing some haplotypic diversity differences between the rainforest and delta zones. In contrast, we consistently recovered two genetic clusters in the Usumacinta River basin with the nuclear data in both the DAPC and STRUCTURE analyses. These results were consistent with the AMOVA analyses, which showed significant differences among the genetic clusters previously recovered by DAPC and STRUCTURE. In terms of diversity distribution, the floodplain zone corresponded to the most diverse zone according to the mitochondrial and nuclear data, suggesting that this is a transition zone in the basin. Our results support the relevance of the molecular characterization and monitoring of the fishery resources at the Usumacinta River to better understand their connectivity, which could help in their conservation and management.

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Section: Implications For Species Conservationcontrasting

confidence: 68%

Molecular Characterization of the Common Snook, Centropomus undecimalis (Bloch, 1792) in the Usumacinta Basin

et al. 2021

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“…It has become one of the most commonly used molecular markers in population genetics due to its characteristics of codominant inheritance and a high variability ( Gupta, Varshney & Sharma, 1999 ; Zane, Bargelloni & Patarnello, 2002 ; Parida et al, 2009 ; Askari, 2013 ; Song et al, 2017 ). For instance, in contrast to works that did not find significant genetic differentiation based on other markers, Song (2020) detected genetic differentiation in Acanthogobius ommaturus between Zhoushan and other localities using 14 microsatellite loci. Beacham et al (2010) also detected significant genetic differentiation in Oncorhynchus keta from Pacific Coast Honshu based on 14 microsatellite loci, which was not found by mitochondrial DNA markers and allozyme loci.…”

Section: Discussioncontrasting

confidence: 93%

“…Lin et al (2009) also found that there was a big spawning ground of L. polyactis in the coastal waters of Zhoushan, which could also be the reason for the genetic differentiation. The special geographical environment of the coastal waters of Zhoushan has resulted in the complex population structure of many species ( Song, 2020 ). Also, the freshwater of Yangtze River has a wide influence on the East China Sea, including the Yangtze River Estuary fishing ground, Zhoushan fishing ground, etc ( Ni et al, 2014 ; Zhang & Hu, 2005 ).…”

Section: Discussionmentioning

confidence: 99%

Genetic structure of the small yellow croaker (Larimichthys polyactis) across the Yellow Sea and the East China Sea by microsatellite DNA variation: implications for the division of management units

Zheng

Yan

et al. 2022

PeerJ

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The small yellow croaker, Larimichthys polyactis, is a commercial fish of the order Perciformes that mainly inhabit estuaries and coastal waters.In recent years, the resources and catch of L. polyactis have undergone huge fluctuations. To detect genetic variations caused by the fluctuation of resources, genetic diversity of L. polyactis in the coastal waters of China were analyzed in this study using microsatellite DNA marker. The results revealed high genetic diversity of this species. The STRUCTURE, DAPC and FST results all indicated that there was no genetic structure consistent with the distribution pattern. Overall, our main findings are in agreement with previous studies, indicating that L. polyactis showed high genetic diversity and low genetic differentiation. Our results for high genetic connectivity among L. polyactis localities provide insights into the development of management strategies, that is, to manage this species as a single management unit.

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“…High haplotype diversity ( h = 0.989) and low nucleotide diversity (0.005) were found in T. nanhaiensis populations based on the mitochondrial cyt b gene. High haplotype diversity was similar to the haplotype diversity of most marine fishes on the coastlines of mainland China, suggesting large effective population sizes over time [e.g., Pampus argenteus 25 ( h = 0.736); Terapon jarbua 26 ( h = 0.857); Acanthogobius ommaturus 27 ( h = 0.923); Scatophagus argus 28 ( h = 0.870)]. The nucleotide diversity of T. nanhaiensis was higher than the nucleotide diversity of L. savala 8 but lower than the nucleotide diversity of T. japonicas in the family Trichiuridae along the coastlines of mainland China 18 .…”

Section: Discussionmentioning

confidence: 76%

Genetic pattern and demographic history of cutlassfish (Trichiurus nanhaiensis) in South China Sea by the influence of Pleistocene climatic oscillations

Yan

et al. 2022

Sci Rep

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Trichiurus nanhaiensis is one of the most important commercial fish species in the South China Sea. This study aimed to investigate the level of genetic variation and population genetic structure of T. nanhaiensis in the South China Sea for the first time, using 281 individuals collected from seven locations along the coast of mainland China, Taiwan, and Hainan Island. A high level of haplotype diversity and low nucleotide diversity were detected in the mitochondrial DNA cyt b gene and nuDNA RYR 3 gene. The overall expected heterozygosity (He = 0.693) among the seven populations ranged from 0.681 to 0.706 in microsatellite DNA data, which revealed high levels of genetic diversity. Significant genetic differentiation was found in Taidong populations in Taiwan, revealing the prevention of gene flow caused by the Kuroshio Current. Two major lineages based on the cyt b gene suggested that the Taiwan Strait acted as a geographic barrier for T. nanhaiensis during the glacier periods in the late Pleistocene. The Bayesian skyline plot also revealed that population demographic expansion of T. nanhaiensis was estimated to have occurred in 0.1 Mya. Our results indicated that all populations of T. nanhaiensis had experienced a recent genetic bottleneck following recent expansion based on ABC analysis.

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Structure Analysis of Mitochondrial DNA Control Region Sequences and its Applications for the Study of Population Genetic Diversity of Acanthogobius ommaturus

Cited by 15 publications

References 25 publications

Molecular Characterization of the Common Snook, Centropomus undecimalis (Bloch, 1792) in the Usumacinta Basin

Molecular Characterization of the Common Snook, Centropomus undecimalis (Bloch, 1792) in the Usumacinta Basin

Genetic structure of the small yellow croaker (Larimichthys polyactis) across the Yellow Sea and the East China Sea by microsatellite DNA variation: implications for the division of management units

Genetic pattern and demographic history of cutlassfish (Trichiurus nanhaiensis) in South China Sea by the influence of Pleistocene climatic oscillations

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