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DNA Taxonomy, Molecular Phylogeny and Population Genetics of Cartilaginous Fishes...
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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: closed (15 September 2024) | Viewed by 7458

Special Issue Editor

Dr. Xiao Chen

E-Mail Website
Guest Editor
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
Special Issues, Collections and Topics in MDPI journals

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
Guest Editor

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Keywords

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

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Published Papers (6 papers)

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Research

20 pages, 6103 KiB  
Article
Variation in the Local Grey Mullet Populations (Mugil cephalus) on the Western Pacific Fringe
by Chien-Hsien Kuo, Sin-Che Lee, Shin-Yi Du, Chao-Shen Huang and Hung-Du Lin
Genes 2024, 15(10), 1280; https://doi.org/10.3390/genes15101280 - 29 Sep 2024
Viewed by 780
Abstract
Background: Understanding population genetic structures is crucial for planning and implementing conservation programmes to preserve species’ adaptive and evolutionary potential and thus ensure their long-term persistence. The grey mullet (Mugil cephalus) is a globally distributed coastal fish. Its populations in [...] Read more.
Background: Understanding population genetic structures is crucial for planning and implementing conservation programmes to preserve species’ adaptive and evolutionary potential and thus ensure their long-term persistence. The grey mullet (Mugil cephalus) is a globally distributed coastal fish. Its populations in waters surrounding Taiwan on the western Pacific fringe are divided into at least two stocks (migratory and residential), but questions remain regarding their genetic divergence and gene flow. Methods and Results: To cast more light on this, allozyme variations at 21 presumptive gene loci of 1217 adult grey mullets from 15 localities in Japan, Taiwan and mainland China, and four gene loci from 1470 juveniles from three localities in Taiwan were used to investigate patterns of genetic variation. The mean expected heterozygosity (He) was 0.128—ranging from 0.031 (Matsu) to 0.442 (Kaoping)—and the mean observed heterozygosity (Ho) was 0.086—ranging from 0.017 (Kaohsiung) to 0.215 (Kaoping). Both AMOVA and the high overall mean FST of 0.252 indicated enormous genetic differentiation among populations and the positive mean value of FIS was 0.328, indicating a deficiency of heterozygotes. PCoA indicated that the samples of M. cephalus could be split into three groups and STRUCTURE analysis showed that all individuals were grouped into three genetic clusters. The results of mutation-drift equilibrium tests did not suggest that the populations experienced any recent genetic bottleneck. The results from all localities in the present investigation showed significant change in the GPI-A genotype frequencies with latitudes—e.g., increases in GPI-A*135/135 homozygote frequencies and GPI-A*100/100 frequencies were highly correlated with latitudinal cline. All migratory populations with the GPI-A genotype were almost exclusively the GPI-A*100/100 homozygote. During the life history of M. cephalus, the GPI-A*100/135 heterozygote frequency significantly decreases with age. Conclusions: Based on these data, we suggest that each GPI-A genotype represents trait combinations of higher fitness in some portions of the environment. Furthermore, the genotypic frequencies change in accordance with life stages, suggesting that selection occurs throughout the life span. Full article
(This article belongs to the Special Issue DNA Taxonomy, Molecular Phylogeny and Population Genetics of Cartilaginous Fishes and Teleost Fishes)
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17 pages, 2046 KiB  
Article
Genetic Signature of River Capture Imprinted in Schizopygopsis Fish from the Eastern Tibetan Plateau
by Lijun He, Yonghong Bi, David Weese, Jie Wu, Shasha Xu, Huimin Ren, Fenfen Zhang, Xueqing Liu, Lei Chen and Jing Zhang
Genes 2024, 15(9), 1148; https://doi.org/10.3390/genes15091148 - 31 Aug 2024
Viewed by 860
Abstract
Some East Asian rivers experienced repeated rearrangements due to Indian–Asian Plates’ collisions and an uplift of the Tibetan Plateau. For the upper Changjiang (Yangtze/Jinsha River), its ancient south-flowing course and subsequent capture by the middle Changjiang at the First Bend (FB) remained controversial. [...] Read more.
Some East Asian rivers experienced repeated rearrangements due to Indian–Asian Plates’ collisions and an uplift of the Tibetan Plateau. For the upper Changjiang (Yangtze/Jinsha River), its ancient south-flowing course and subsequent capture by the middle Changjiang at the First Bend (FB) remained controversial. The DNA of freshwater fishes possess novel evolutionary signals of these tectonic events. In this study, mtDNA Cyt b sequences of endemic Schizopygopsis fish belonging to a highly specialized grade of the Schizothoracinae from the eastern Tibetan Plateau were used to infer the palaeo-drainages connectivity history of the upper Changjiang system. Through phylogenetic reconstruction, a new clade D of Schizopygopsis with three genetic clusters and subclusters (DI, DII, DIIIa, and DIIIb) were identified from the upper Yalong, Changjiang, and Yellow Rivers; the Shuiluo River; the FB-upper Changjiang; and the Litang River; respectively. Ancient drainage connections and capture signals were indicated based on these cladogenesis events and ancestral origin inference: (1) the upper Yalong River likely acted as a dispersal origin of Schizopygopsis fish to the adjacent upper Yellow and Changjiang Rivers at ca. 0.34 Ma; (2) the Litang River seemed to have directly drained into the upper Changjiang/Yangtze/Jinsha River before its capture by the Yalong River at ca. 0.90 Ma; (3) the Shuiluo River likely flowed south along a course parallel to the upper Changjiang before their connection through Hutiao Gorge; (4) a palaeo-lake across the contemporary Shuiluo, Litang, and Yalong Rivers was inferred to have served as an ancestral origin of clade D of Schizopygopsis at 1.56 Ma. Therefore, this study sheds light on disentangling ambiguous palaeo-drainage history through integrating biological and geological evidence. Full article
(This article belongs to the Special Issue DNA Taxonomy, Molecular Phylogeny and Population Genetics of Cartilaginous Fishes and Teleost Fishes)
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17 pages, 3167 KiB  
Article
Biodiversity of Demersal Fish Communities in the Cosmonaut Sea Revealed by DNA Barcoding Analyses
by Hai Li, Xing Miao, Rui Wang, Yuzhuo Liao, Yilin Wen, Ran Zhang and Longshan Lin
Genes 2024, 15(6), 691; https://doi.org/10.3390/genes15060691 - 26 May 2024
Viewed by 1037
Abstract
The Cosmonaut Sea is one of the least accessed regions in the Southern Ocean, and our knowledge about the fish biodiversity in the region is sparse. In this study, we provided a description of demersal fish diversity in the Cosmonaut Sea by analysing [...] Read more.
The Cosmonaut Sea is one of the least accessed regions in the Southern Ocean, and our knowledge about the fish biodiversity in the region is sparse. In this study, we provided a description of demersal fish diversity in the Cosmonaut Sea by analysing cytochrome oxidase I (COI) barcodes of 98 fish samples that were hauled by trawling during the 37th and 38th Chinese National Antarctic Research Expedition (CHINARE) cruises. Twenty-four species representing 19 genera and 11 families, namely, Artedidraconidae, Bathydraconidae, Bathylagidae, Channichthyidae, Liparidae, Macrouridae, Muraenolepididae, Myctophidae, Nototheniidae, Paralepididae and Zoarcidae, were discriminated and identified, which were largely identical to local fish occurrence records and the general pattern of demersal fish communities at high Antarctic shelf areas. The validity of a barcoding gap failed to be detected and confirmed across all species due to the indicative signals of two potential cryptic species. Nevertheless, DNA barcoding still demonstrated to be a very efficient and sound method for the discrimination and classification of Antarctic fishes. In the future, various sampling strategies that cover all geographic sections and depth strata of the Cosmonaut Sea are encouraged to enhance our understanding of local fish communities, within which DNA barcoding can play an important role in either molecular taxonomy or the establishment of a dedicated local reference database for eDNA metabarcoding analyses. Full article
(This article belongs to the Special Issue DNA Taxonomy, Molecular Phylogeny and Population Genetics of Cartilaginous Fishes and Teleost Fishes)
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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
Cited by 1 | Viewed by 1262
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
(This article belongs to the Special Issue DNA Taxonomy, Molecular Phylogeny and Population Genetics of Cartilaginous Fishes and Teleost Fishes)
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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
Viewed by 1145
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
(This article belongs to the Special Issue DNA Taxonomy, Molecular Phylogeny and Population Genetics of Cartilaginous Fishes and Teleost Fishes)
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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 1558
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
(This article belongs to the Special Issue DNA Taxonomy, Molecular Phylogeny and Population Genetics of Cartilaginous Fishes and Teleost Fishes)
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