DNA Taxonomy, Molecular Phylogeny and Population Genetics of Cartilaginous Fishes and Teleost Fishes

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: 15 September 2024 | Viewed by 2522

Special Issue Editors

Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
Interests: environmental DNA; coral reef fish; fish mitogenome; fish phylogeny
Chinese Academy of Sciences Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
Interests: molecular phylogeny; population genetics; sharks and rays conservation in Northwest Pacific; fish life history

Special Issue Information

Dear Colleagues,

During the past decade, the remarkable increase in cartilaginous and teleost fishes genome sequencing has revolutionized molecular phylogeny and population genetics, with the outcome of stimulating insights into fish conservation biology. The IUCN Red List states that 30% of chondrichthyans are threatened by extinction, and overfishing is considered the main threat to their existence. Genetic approaches play an essential role in shark conservation; there has been some progress, but a great deal of work still lies ahead. Cartilaginous fish genomic sequences can be compared with other Osteichthyes to trace species’ evolutionary history and origin as well as phylogenetic relationships. Understanding the heritability of conservation biology requires a more comprehensive assessment of fish genetic variation. This Special Issue of Genes on “DNA Taxonomy, Molecular Phylogeny and Population Genetics of Cartilaginous Fishes and Teleost Fishes” aims to provide an overview of recent developments in this field of research, including critical perspectives on current and upcoming challenges.

Dr. Xiao Chen
Dr. Jie Zhang
Guest Editors

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Keywords

  • cartilaginous fish
  • teleost fish
  • molecular evolution
  • phylogeny
  • population genetics
  • genome sequencing
  • DNA taxonomy and DNA barcoding

Published Papers (3 papers)

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Research

13 pages, 4924 KiB  
Article
Complete Mitochondrial Genome of Four Peristediidae Fish Species: Genome Characterization and Phylogenetic Analysis
by Xianhui Liao, Yijia Shih, Chenghao Jia and Tianxiang Gao
Genes 2024, 15(5), 557; https://doi.org/10.3390/genes15050557 - 27 Apr 2024
Viewed by 484
Abstract
The systematic revision of the family Peristediidae remains an unresolved issue due to their diverse and unique morphology. Despite the popularity of using mitochondrial genome research to comprehensively understand phylogenetic relationships in fish, genetic data for peristediid fish need to be included. Therefore, [...] Read more.
The systematic revision of the family Peristediidae remains an unresolved issue due to their diverse and unique morphology. Despite the popularity of using mitochondrial genome research to comprehensively understand phylogenetic relationships in fish, genetic data for peristediid fish need to be included. Therefore, this study aims to investigate the mitochondrial genomic characteristics and intra-family phylogenetic relationships of Peristediidae by utilizing mitochondrial genome analysis. Therefore, this study aims to investigate the phylogenetic relationship of Peristediidae by utilizing mitochondrial genome analysis. The mitochondrial genome of four species of Peristediidae (Peristedion liorhynchus, Satyrichthys welchi, Satyrichthys rieffeli, and Scalicus amiscus) collected in the East China Sea was studied. The mitochondrial gene sequence lengths of four fish species were 16,533 bp, 16,526 bp, 16,527 bp, and 16,526 bp, respectively. They had the same mitochondrial structure and were all composed of 37 genes and one control region. Most PCGs used ATG as the start codon, and a few used GTG as the start codon. An incomplete stop codon (TA/T) occurred. The AT-skew and GC-skew values of 13 PCGs from four species were negative, and the GC-skew amplitude was greater than that of AT-skew. All cases of D-arm were found in tRNA-Ser (GCT). The Ka/Ks ratio analysis indicated that 13 PCGs were suffering purifying selection. Based on 12 PCGs (excluding ND6) sequences, a phylogenetic tree was constructed using Bayesian inference (BI) and maximum likelihood (ML) methods, providing a further supplement to the scientific classification of Peristediidae fish. According to the results of divergence time, the four species of fish had apparent divergence in the Early Cenozoic, which indicates that the geological events at that time caused the climax of species divergence and evolution. Full article
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15 pages, 7025 KiB  
Article
Population Genomics of Commercial Fish Sebastes schlegelii of the Bohai and Yellow Seas (China) Using a Large SNP Panel from GBS
by Beiyan Zhu, Tianxiang Gao, Yan He, Yinquan Qu and Xiumei Zhang
Genes 2024, 15(5), 534; https://doi.org/10.3390/genes15050534 - 24 Apr 2024
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Abstract
Sebastes schlegelii is one of the most commercially important marine fish in the northwestern Pacific. However, little information about the genome-wide genetic characteristics is available for S. schlegelii individuals from the Bohai and Yellow Seas. In this study, a total of 157,778, 174,480, [...] Read more.
Sebastes schlegelii is one of the most commercially important marine fish in the northwestern Pacific. However, little information about the genome-wide genetic characteristics is available for S. schlegelii individuals from the Bohai and Yellow Seas. In this study, a total of 157,778, 174,480, and 188,756 single-nucleotide polymorphisms from Dalian (DL), Yantai (YT), and Qingdao (QD) coastal waters of China were, respectively, identified. Sixty samples (twenty samples per population) were clustered together, indicating shallow structures and close relationships with each other. The observed heterozygosity, expected heterozygosity, polymorphism information content, and nucleotide diversity ranged from 0.14316 to 0.17684, from 0.14035 to 0.17145, from 0.20672 to 0.24678, and from 7.63 × 10−6 to 8.77 × 10−6, respectively, indicating the slight difference in genetic diversity among S. schlegelii populations, and their general genetic diversity was lower compared to other marine fishes. The population divergence showed relatively low levels (from 0.01356 to 0.01678) between S. schlegelii populations. Dispersing along drifting seaweeds, as well as the ocean current that flows along the western and northern coasts of the Yellow Sea and southward along the eastern coast of China might be the major reasons for the weak genetic differentiation. These results form the basis of the population genetic characteristics of S. schlegelii based on GBS (Genotyping by Sequencing). In addition to basic population genetic information, our results provid a theoretical basis for further studies aimed at protecting and utilizing S. schlegelii resources. Full article
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14 pages, 2729 KiB  
Article
Evolution of the Critically Endangered Green Sawfish Pristis zijsron (Rhinopristiformes, Pristidae), Inferred from the Whole Mitochondrial Genome
by Chen Wang, Peiyuan Ye, Richard Pillans, Xiao Chen, Junjie Wang and Pierre Feutry
Genes 2023, 14(11), 2052; https://doi.org/10.3390/genes14112052 - 8 Nov 2023
Viewed by 1048
Abstract
The green sawfish Pristis zijsron (Bleeker, 1851), a species of sawfish in the family Pristidae (Rhinopristiformes), mainly inhabits the Indo-West Pacific region. In this study, the complete mitochondrial genome of the critically endangered green sawfish is first described. The length of the genome [...] Read more.
The green sawfish Pristis zijsron (Bleeker, 1851), a species of sawfish in the family Pristidae (Rhinopristiformes), mainly inhabits the Indo-West Pacific region. In this study, the complete mitochondrial genome of the critically endangered green sawfish is first described. The length of the genome is 16,804 bp, with a nucleotide composition of 32.0% A, 24.8% C, 13.1% G, and 30.0% T. It contains 37 genes in the typical gene order of fish. Two start (GTG and ATG) and two stop (TAG and TAA/T-) codons are found in the thirteen protein-coding genes. The 22 tRNA genes range from 67 bp (tRNA-Ser) to 75 bp (tRNA-Leu). The ratio of nonsynonymous substitution (Ka) and synonymous substitution (Ks) indicates that the family Pristidae are suffering a purifying selection. The reconstruction of Bayesian inference and the maximum likelihood phylogenetic tree show the same topological structure, and the family Pristidae is a monophyletic group with strong posterior probability. Pristis zijsron and P. pectinata form a sister group in the terminal clade. And the divergence time of Rhinopristiformes show that P. zijsron and P. pectinata diverged as two separate species in about Paleogene 31.53 Mya. Complete mitochondrial genomes of all five sawfishes have been published and phylogenetic relationships have been analyzed. The results of our study will provide base molecular information for subsequent research (e.g., distribution, conservation, phylogenetics, etc.) on this endangered group. Full article
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Genetic signature of river capture imprinted in several Schizopygopsis fishes from the eastern Tibetan Plateau
Authors: -
Affiliation: -

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