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Fishes
Special Issues
Molecular Ecology and Genetic Diversity of Fish
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Molecular Ecology and Genetic Diversity of Fish

A special issue of Fishes (ISSN 2410-3888). This special issue belongs to the section "Genetics and Biotechnology".

Deadline for manuscript submissions: closed (20 November 2023) | Viewed by 4502

Special Issue Editors

Dr. Jun Qiang

E-Mail Website
Guest Editor
Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
Interests: molecular biology; genetics; germplasm resources
Dr. Shengjie Li

E-Mail Website
Guest Editor
Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
Interests: genomes; aquaculture; genetic breeding
Dr. Jianjun Fu

E-Mail Website
Guest Editor
Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
Interests: molecular biology; genetics; germplasm resources
Dr. Yifan Tao

E-Mail Website
Guest Editor
Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
Interests: genetics; genomics; aquaculture; molecular ecology; omics
Dr. Yan Li

E-Mail Website
Guest Editor
Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
Interests: aquaculture breeding; environmental hazards; molecular ecology; omics; sustainability

Special Issue Information

Dear Colleagues,

Genomic approaches are increasingly applied across various disciplines. The interface of genetics and genomics with ecology and environmental sciences is "molecular ecology". Molecular ecology is a large interdisciplinary area of research, which comprises diverse fields, including population and evolutionary genetics, biodiversity, conservation biology, behavioural ecology, and species–habitat interactions. In addition, genetic diversity is the premise and guarantee of biological survival and development. Good genetic diversity indicates rich biological germplasm resources, which are conducive to making corresponding adaptations to some uncertain changes in the environment. Therefore, exploring the molecular basis and mechanism of the interaction between aquatic organisms and the environment, investigating the genetic diversity of aquatic organisms and understanding their germplasm resources are beneficial to the protection of aquatic ecological environments and aquatic biodiversity, which can also promote the sustainable development of fisheries and aquaculture. However, compared with mammals, an insufficient amount of research has been conducted on fish species. Therefore, I am pleased to invite you to contribute to the Special Issue “Molecular Ecology and Genetic Diversity of Fish” in the journal Fishes.

Dr. Jun Qiang
Dr. Shengjie Li
Dr. Jianjun Fu
Dr. Yifan Tao
Dr. Yan Li
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Fishes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • molecular ecology
  • genetic diversity
  • aquaculture
  • genomic
  • fish

Published Papers (4 papers)

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Research

14 pages, 956 KiB  
Article
Critically Small Contemporaneous Effective Population Sizes Estimated for Stocks of the African Bonytongue in Western Africa
by Luis A. Hurtado, Mariana Mateos, Isabel C. Caballero, Tofunmi E. Oladimeji, Alphonse Adite, Michael O. Awodiran, Kirk O. Winemiller and Matthew B. Hamilton
Fishes 2024, 9(6), 196; https://doi.org/10.3390/fishes9060196 (registering DOI) - 25 May 2024
Viewed by 135
Abstract
Inland capture fisheries play a critical role in supporting food security and livelihoods in Africa. Therefore, it is important to evaluate the genetic health of exploited fish populations. The African bonytongue, Heterotis niloticus, supports important commercial and subsistence fisheries in western Africa. [...] Read more.
Inland capture fisheries play a critical role in supporting food security and livelihoods in Africa. Therefore, it is important to evaluate the genetic health of exploited fish populations. The African bonytongue, Heterotis niloticus, supports important commercial and subsistence fisheries in western Africa. However, sharp declines in stocks have been reported. Herein, we estimate contemporary effective population sizes (Ne) of four Heterotis populations in Nigeria, three in Benin, and five in Cameroon using Linkage Disequilibrium methods. Ne estimates were used to assess genetic short-term (i.e., inbreeding depression) and long-term (i.e., loss of evolutionary potential) risks. Ne point estimates obtained with the best estimator (out of 16), as determined by computer simulations, were <50 (range = 5.1–36.2) for nine of the twelve populations examined, which is below the minimum recommended for avoiding the potential deleterious effects of inbreeding depression (original criterion Ne ≥ 50, revised to Ne ≥ 100); and well below the minimum recommended for populations to retain evolutionary potential (original criterion Ne ≥ 500; revised to Ne ≥ 1000). The lower bound of the confidence interval for two of the remaining populations was below the minimum recommended to retain evolutionary potential (with the point estimate of one of them also below this threshold), and for some methods, values were lower than the minimum recommended to avoid inbreeding depression. Accordingly, our results suggest that urgent conservation and management plans are needed to guarantee the persistence and sustainability of the H. niloticus populations examined. Full article
(This article belongs to the Special Issue Molecular Ecology and Genetic Diversity of Fish)
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21 pages, 1139 KiB  
Article
Population Genetic Differentiation of Walleye (Sander vitreus) across the Eastern Highlands of the United States
by Sheila C. Harris, George Palmer, Carol A. Stepien and Eric M. Hallerman
Fishes 2024, 9(1), 15; https://doi.org/10.3390/fishes9010015 - 29 Dec 2023
Viewed by 1434
Abstract
Walleye is an important sportfish across eastern North America, is commercially fished in the Laurentian Great Lakes region, and has been introduced outside its native range. Thirty-eight Walleye populations within six watersheds across the Eastern Highlands and other portions of the native range [...] Read more.
Walleye is an important sportfish across eastern North America, is commercially fished in the Laurentian Great Lakes region, and has been introduced outside its native range. Thirty-eight Walleye populations within six watersheds across the Eastern Highlands and other portions of the native range were screened at eight microsatellite DNA loci to better understand evolutionary history and to inform fishery management and conservation efforts. Population genetic variation showed divergent assemblages of populations, respectively, living in the Mobile Bay, Mississippi River, Eastern Highlands (Tennessee, New, and Ohio Rivers), and Great Lakes drainages today. All estimates of effective numbers of breeding individuals were under 25, and all populations within all watersheds had ~15–20% inter-individual relatedness, likely attributable to the effects of both natural demographic processes and stocking. The extent of Eastern Highlands Walleye includes both the Ohio and Tennessee River basins. Full article
(This article belongs to the Special Issue Molecular Ecology and Genetic Diversity of Fish)
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14 pages, 8477 KiB  
Article
Phylogenetic Analyses of Pristipomoides (Perciformes: Lutjanidae) Based on New Mitochondrial Genomes
by Chunhui Liu, Dezhao Li, Yue Zhang, Maxime Péré, Zhibo Zhuang, Jingyu Liu, Haolang Zhou and Xiao Chen
Fishes 2023, 8(7), 343; https://doi.org/10.3390/fishes8070343 - 28 Jun 2023
Viewed by 1136
Abstract
The species in the genus Pristipomoides are commercial fishes with high economic value. There are few studies on the phylogenetic relationship within the genus Pristipomoides at present. mtDNA has the characteristics of maternal inheritance, close gene arrangement, and a high evolutionary rate, which [...] Read more.
The species in the genus Pristipomoides are commercial fishes with high economic value. There are few studies on the phylogenetic relationship within the genus Pristipomoides at present. mtDNA has the characteristics of maternal inheritance, close gene arrangement, and a high evolutionary rate, which is an excellent tool to study the phylogeny of the species. In this study, the mitochondrial genomes of five species in the genus Pristipomoides were sequenced using the Sanger sequencing method and analyzed for their features. The mitochondrial genome length of the five species ranged from 16,499 to 16,530 bp. The start codon was ATG\GTG, and the stop codon was TAA\TAG\T--\AGG. The ratio of Ka and Ks for protein-coding genes ranged from 0 to 0.117, suggesting a strong purifying selection acting on the 13 protein-coding genes (PCGs). The gene with the highest diversity was nd2 (NADH dehydrogenase subunit 2), suggesting the highest evolutionary rate. Phylogenetic analysis of five Pristipomoides species with other species of Lutjanidae was conducted using maximum likelihood (ML) and Bayesian Inference (BI). The results showed that P. zonatus and P. auricilla were closely related to P. argyrogrammicus and P. sieboldii, respectively, and P. filamentosus and P. multidens clustered together. Furthermore, A. rutilans is deeply nested within the Pristipomoides genus, indicating a close phylogenetic relationship with the species in the Pristipomoides genus. Based on this evidence, we suggest that A. rutilans should be classified under the Pristipomoides genus and recommend a revision in its taxonomy. The molecular data and phylogenetic analysis provided in this study would be helpful for the species identification and phylogenetic studies of the family Lutjanidae. Full article
(This article belongs to the Special Issue Molecular Ecology and Genetic Diversity of Fish)
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13 pages, 3793 KiB  
Article
Screening and Identification of Interacting Proteins of Mitfa in Red Tilapia
by Bingjie Jiang, Lanmei Wang, Jianjun Fu, Wenbin Zhu, Mingkun Luo and Zaijie Dong
Fishes 2023, 8(5), 241; https://doi.org/10.3390/fishes8050241 - 5 May 2023
Viewed by 1127
Abstract
Skin color variation and differentiation are bottlenecks in the aquaculture industry of red tilapia. The mitfa gene primarily regulates melanocyte survival and proliferation in fish skin pigmentation. In this study, a recombinant expression vector for Mitfa expression was successfully constructed. After induction and [...] Read more.
Skin color variation and differentiation are bottlenecks in the aquaculture industry of red tilapia. The mitfa gene primarily regulates melanocyte survival and proliferation in fish skin pigmentation. In this study, a recombinant expression vector for Mitfa expression was successfully constructed. After induction and purification, nearly 600 μg of Mitfa protein was purified from the fermentation supernatant. His pull-down assay, followed by LC-MS/MS analysis, revealed 10 proteins that interact with the Mitfa protein. Five of these proteins were annotated in the melanogenesis and tyrosine metabolism pathways, including Krt, Tpm, Myh, Tyr and Dct. The purified Mitfa recombinant protein was injected into red tilapia, and its activity and function were examined. The expression levels of the mitfa, tyr, tyrp1, and dct genes increased greatly in the dorsal skin after injection (p < 0.05); meanwhile, the melanin content and tyrosinase activity increased significantly (p < 0.05). These findings provide a theoretical basis for comprehending the function and regulatory mechanism of the red tilapia mitfa gene. Full article
(This article belongs to the Special Issue Molecular Ecology and Genetic Diversity of Fish)
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