Genetic Diversity of Domesticated and Natural Fish Populations: Patterns and Processes

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Animal Diversity".

Deadline for manuscript submissions: closed (31 March 2023) | Viewed by 9182

Special Issue Editors


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Guest Editor
Station d’Ecologie Théorique et Expérimentale, UPR 2021, Centre National pour la Recherche Scientifique et Université Paul Sabatier, 09200 Moulis, France
Interests: freshwater ecology; population (epi-)genetics; ecosystem functioning; host-parasite interactions; evolutionary ecology; habitat fragmentation; conservation biology
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Guest Editor
Station d’Ecologie Théorique et Expérimentale, UPR 2021, Centre National pour la Recherche Scientifique et Université Paul Sabatier, 09200 Moulis, France
Interests: spatial genetics and genomics; landscape ecology; wildlife conservation; biostatistics

Special Issue Information

Dear Colleagues,

Marine and freshwater fishes display an exceptional diversity and are a major source of protein for many humans worldwide. They also occupy a central place in marine and freshwater trophic chains and are therefore the keystone of many ecosystems. For all these reasons, it is our common duty towards future generations to preserve the long-term integrity of fish populations. Documenting and preserving the genetic diversity of marine and freshwater fish populations is critical for their long-term sustainability. Indeed, genetic diversity ensures the potential for adaptation to environmental changes, including warming, habitat destruction or the spread of pathogens. Preserving fish diversity is important not only for conservation but also for fisheries and aquaculture since natural (or artificial) selection of genetic variants is one of the processes allowing the persistence of exploited populations and the optimization of yields. This Special Issue provides a unique opportunity to synthetize the most recent findings on the genetic diversity of natural, harvested and domesticated fish populations, both in marine and freshwater ecosystems. The goal of this Special Issue is to reveal spatial and temporal patterns of genetic diversity in fish populations, but also to identify the processes that generate these patterns. We are open to a wide range of contributions from the fields of landscape genetics, phylogeography, phylogenetics or macrogenetics, covering landscape- to continental-scale studies, as well as contemporary to geological time scales. Studies focusing on patterns of both neutral and functional genetic diversity through the use of genomic, transcriptomic and/or epigenetic markers are particularity welcome since “-omic” tools now permit routinely and jointly inspecting both aspects of fish genetic diversity. Similarly, studies investigating processes underlying spatiotemporal patterns of fish genetic diversity through advanced statistics or simulations would be relevant contributions to this Special Issue. Beyond these objectives, our aim is to attract studies with strong applied perspectives since genetic diversity is at the heart of many empirical applications such as wildlife conservation, habitat restoration or management of aquaculture and fisheries.

Dr. Simon Blanchet
Dr. Jérôme G Prunier
Guest Editors

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Keywords

  • genetic, genomic and epigenetic diversity
  • freshwater and marine fish species
  • spatiotemporal patterns and processes
  • conservation and restoration
  • aquaculture and fishery management

Published Papers (5 papers)

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Research

16 pages, 3403 KiB  
Article
Spatial Patterns of Neutral and Functional Genetic Variations along Dendritic Networks of Riverscape in Brown Trout Populations
by Laurine Gouthier, Eloïse Duval, Simon Blanchet, Géraldine Loot, Charlotte Veyssière, Maxime Galan, Erwan Quéméré and Lisa Jacquin
Diversity 2023, 15(6), 784; https://doi.org/10.3390/d15060784 - 17 Jun 2023
Viewed by 1098
Abstract
Understanding how environmental gradients shape the spatial patterns of intraspecific genetic diversity is a central issue in ecological and evolutionary sciences. In riverine ecosystems, there is generally an increase in neutral genetic diversity downstream, as well as an increase in genetic differentiation among [...] Read more.
Understanding how environmental gradients shape the spatial patterns of intraspecific genetic diversity is a central issue in ecological and evolutionary sciences. In riverine ecosystems, there is generally an increase in neutral genetic diversity downstream, as well as an increase in genetic differentiation among upstream populations. However, selective pressures may vary markedly along the upstream–downstream gradient, which could modify these patterns, but this has rarely been tested empirically. Here, we investigated how environmental gradients in a river network could shape the spatial patterns of intraspecific genetic diversity and differentiation in both neutral SNP markers and functional genetic markers putatively under natural selection (candidate SNPs associated with physiological functions and immune Major Histocompatibility Complex (MHC) loci) in wild brown trout populations. First, we showed that both the distance from the confluence and the centrality on the river network could explain the variation in genetic diversity and differentiation. Second, we found that both neutral and functional markers followed a similar pattern, with a higher genetic diversity and a lower genetic differentiation among populations that were more central and/or near to the confluence. This study highlights the importance of considering both the spatial and hydrological factors of a river network to understand and predict the role of dendritic connectivity in the spatial patterns of genetic diversity and differentiation in wild fish populations. Full article
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21 pages, 7656 KiB  
Article
Comparing the Utility of Microsatellites and Single Nucleotide Polymorphisms in Conservation Genetics: Insights from a Study on Two Freshwater Fish Species in France
by Jérôme G. Prunier, Charlotte Veyssière, Géraldine Loot and Simon Blanchet
Diversity 2023, 15(5), 681; https://doi.org/10.3390/d15050681 - 18 May 2023
Viewed by 1122
Abstract
Biodiversity is facing an unprecedented crisis and substantial efforts are needed to conserve natural populations, especially in river ecosystems. The use of molecular tools to guide conservation practices in rivers has grown in popularity over the last decades, but the amount of precision [...] Read more.
Biodiversity is facing an unprecedented crisis and substantial efforts are needed to conserve natural populations, especially in river ecosystems. The use of molecular tools to guide conservation practices in rivers has grown in popularity over the last decades, but the amount of precision and/or biological information that would be gained by switching from the traditional short tandem repeats (STRs) to the increasingly used single nucleotide polymorphisms (SNPs) is still debated. Here, we compared the usefulness of STRs and SNPs to study spatial patterns of genetic variability in two freshwater fish species (Phoxinus dragarum and Gobio occitaniae) in southern France. SNPs were obtained from a pool-seq procedure and mapped to new genome assemblies. They provided much more precise estimates of genetic diversity and genetic differentiation than STRs, but both markers allowed the detection of very similar genetic structures in each species, which could be useful for delineating conservation units. While both markers provided similar outcomes, there were two discrepancies in genetic structures that could, nonetheless, be explained by unrecorded stocking events. Overall, we demonstrated that SNPs are not unconditionally superior to STRs in the context of large-scale riverscape genetic conservation, and that the choice of marker should primarily be based on research questions and resources available. Full article
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10 pages, 1328 KiB  
Article
Genetic Diversity of Chinese Longsnout Catfish (Leiocassis longirostris) in Four Farmed Populations Based on 20 New Microsatellite DNA Markers
by Lu Zhang, Chenyan Mou, Jian Zhou, Hua Ye, Zhen Wei, Hongyu Ke, Zhipeng Huang, Yuanliang Duan, Zhongmeng Zhao, Han Zhao, Huadong Li, Jun Du and Qiang Li
Diversity 2022, 14(8), 654; https://doi.org/10.3390/d14080654 - 13 Aug 2022
Cited by 2 | Viewed by 1400
Abstract
Freshwater aquaculture has a long and vibrant tradition in China. The Chinese longsnout catfish (Leiocassis longirostris) is a popular economic freshwater fish native to China. Understanding the genetic structure of L. longirostris populations is important for ensuring the efficacy of management [...] Read more.
Freshwater aquaculture has a long and vibrant tradition in China. The Chinese longsnout catfish (Leiocassis longirostris) is a popular economic freshwater fish native to China. Understanding the genetic structure of L. longirostris populations is important for ensuring the efficacy of management practices and the sustainability of future increases in production. In this study, we used Illumina sequencing technology to isolate 20 novel polymorphic microsatellites from the genome of L. longirostris. These microsatellites were used to analyze the genetic diversity of 240 L. longrostris individuals from four populations. Genetic diversity parameters (NA, HO, HE, I, PIC, and FST) of the four farmed L. longirostris populations were analyzed. The level of genetic differentiation among the four farmed L. longirostris populations (inferred by pairwise comparisons of FST values) was low, but the genetic diversity of these populations was high, indicating that they still provide useful sources of genetic variation that could aid in breeding efforts. The STRUCTURE and ADMIXTURE analyses indicated that admixture might be occurring in the four L. longirostris populations, especially between the MS and YB populations. Understanding the genetic diversity of farmed L. longirostris populations and inbreeding prevention could greatly aid in breeding and production. These newly isolated microsatellite markers and the high genetic diversity of L. longirostris populations in the main breeding areas have important implications for the breeding and stock management of L. longirostris. Full article
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16 pages, 2013 KiB  
Article
Genetic Structure and Diversity of Native Tench (Tinca tinca L. 1758) Populations in Hungary—Establishment of Basic Knowledge Base for a Breeding Program
by Fatema Ali Al Fatle, Erika Edviné Meleg, Zoltán Sallai, Gergely Szabó, Eszter Várkonyi, Béla Urbányi, Balázs Kovács, Tamás Molnár and István Lehoczky
Diversity 2022, 14(5), 336; https://doi.org/10.3390/d14050336 - 25 Apr 2022
Cited by 3 | Viewed by 1860
Abstract
Tench is a cyprinid fish that has undergone human-induced translocations. The natural populations of the species are on the decline due to habitat loss and spawning grounds degradation. The genetic diversity of seven natural populations was investigated to establish the genetic knowledge base [...] Read more.
Tench is a cyprinid fish that has undergone human-induced translocations. The natural populations of the species are on the decline due to habitat loss and spawning grounds degradation. The genetic diversity of seven natural populations was investigated to establish the genetic knowledge base for successful conservation efforts and for selective breeding. Twelve microsatellite markers, the sequencing of a 615 bp section of mtDNA (Cytb) and PCR-RFLP analysis of two nuclear markers (Act) and (RpS7) were used to analyze the genetic variation and structure among 175 individuals. All microsatellite loci were found to have moderate levels of polymorphism. The pairwise Fst values between population pairings were moderate; the populations were aligned to four clusters. The Cytb gene showed 20 haplotypes; 67.1% of individuals were categorized as Eastern, while 32.9% to the Western haplogroup. Analysis of the Act and RpS7 genes showed that the level of hybridization among the two haplogroups is high within the sampled populations. Hungarian Tench populations are genetically less diverse compared to natural populations in Western-Europe, but they still represent valuable genetic resources and Lake Fertő, Lake Kolon and Csörnöc-Herpenyő populations can be optimal candidates for future selective breeding programs. Full article
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18 pages, 3431 KiB  
Article
Investigating Genetic Diversity and Genomic Signatures of Hatchery-Induced Evolution in Gilthead Seabream (Sparus aurata) Populations
by Konstantinos Gkagkavouzis, Spiros Papakostas, Francesco Maroso, Nikoleta Karaiskou, Adrian Carr, Einar Eg Nielsen, Luca Bargelloni and Alexandros Triantafyllidis
Diversity 2021, 13(11), 563; https://doi.org/10.3390/d13110563 - 05 Nov 2021
Cited by 6 | Viewed by 2411
Abstract
The identification of the genetic basis of domestication in fish species is of timely importance for the aquaculture industry in order to increase productivity, quality, and the welfare of farmed fish. The goal of this study is to investigate the largely unknown aquaculture-induced [...] Read more.
The identification of the genetic basis of domestication in fish species is of timely importance for the aquaculture industry in order to increase productivity, quality, and the welfare of farmed fish. The goal of this study is to investigate the largely unknown aquaculture-induced evolution in gilthead seabream, which is one of the most important farmed fish in the Mediterranean region. We used a panel of 1159 genome-wide SNPs, and genotyped 956 fish from 23 wild populations of Mediterranean-wide distribution and 362 farmed fish from five Greek hatcheries. We assessed the genetic diversity of the sampled populations and contrasted the results of four different approaches of outlier detection methods. We recognized one very strong candidate and two good candidate SNPs with evidence for aquaculture-induced evolution in gilthead seabream. The annotation of these SNPs revealed neighboring genes with biological roles from stress tolerance and disease resistance to sexual maturation that may explain our observations. In conclusion, we demonstrate that the genome of gilthead seabream, despite the fact that the species is often suggested to be in the early stages of the domestication process, shows evidence of aquaculture-induced evolution. We report on a list of genes that may explain our observations and that may be investigated further. We anticipate that our findings will stimulate additional research with the use of SNP panels of higher density that can elucidate the genomic architecture of domestication in this species of high aquacultural interest. Full article
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