1
|
Assessing Genetic Variation in Wild and Domesticated Pikeperch Populations: Implications for Conservation and Fish Farming. Animals (Basel) 2022; 12:ani12091178. [PMID: 35565604 PMCID: PMC9102197 DOI: 10.3390/ani12091178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 12/30/2022] Open
Abstract
Simple Summary The pikeperch Sander lucioperca (Linnaeus, 1758) is an important fish species in the development of European aquaculture. The aquaculture of a fish species can be facilitated by knowing the genetic variability within and among populations. Here, we assessed the genetic background of 8 wild populations along with 13 broodstocks (i.e., from fish farms) of pikeperch through a combination of genetic markers. We underlined that current broodstocks have a genetic diversity similar to wild populations. When focusing on genetic differentiation, we highlight that European pikeperch populations are divided into two groups: one predominantly present in Northern Europe and around the Baltic Sea and another mainly in Central Europe. Broodstocks appear to contain fish of a single origin with only a few exceptions. Ultimately, we have proposed baseline information about genetic diversity of pikeperch along with a genetic tool that can help pikeperch producers manage and improve their fish stock. Abstract The pikeperch is a freshwater/brackish water fish species with growing interest for European aquaculture. Wild populations show signs of decline in many areas of the species natural range due to human activities. The comparative evaluation of genetic status in wild and domesticated populations is extremely useful for the future establishment of genetic breeding programs. The main objective of the present study was to assess and compare the genetic variability of 13 domesticated populations from commercial farms and 8 wild populations, developing an efficient microsatellite multiplex tool for genotyping. Partial cytochrome b gene sequences were also used to infer phylogeographic relationships. Results show that on average, the domesticated populations do not exhibit significantly lower levels of genetic diversity compared to the wild ones and do not suffer from inbreeding. Nuclear data provide evidence that pikeperch populations in Europe belong to at least two genetically differentiated groups: the first one is predominantly present in Northern Europe and around the Baltic Sea, while the second one comprises populations from Central Europe. In this second group, Hungarian origin populations constitute a differentiated stock that needs special consideration. Aquaculture broodstocks analyzed appear to contain fish of a single origin with only a few exceptions.
Collapse
|
2
|
Marić S, Stanković D, Sušnik Bajec S, Vukić J, Šanda R, Stefanov T, Nikolić D, Snoj A. Perils of brown trout (Salmo spp.) mitigation-driven translocations: a case study from the Vlasina Plateau, Southeast Serbia. Biol Invasions 2022. [DOI: 10.1007/s10530-021-02688-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
3
|
Quilodrán CS, Tsoupas A, Currat M. The Spatial Signature of Introgression After a Biological Invasion With Hybridization. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.569620] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The accumulation of genome-wide molecular data has emphasized the important role of hybridization in the evolution of many organisms, which may carry introgressed genomic segments resulting from past admixture events with other taxa. Despite a number of examples of hybridization occurring during biological invasions, the resulting spatial patterns of genomic introgression remain poorly understood. Preliminary simulation studies have suggested a heterogeneous spatial level of introgression for invasive taxa after range expansion. We investigated in detail the robustness of this pattern and its persistence over time for both invasive and local organisms. Using spatially explicit simulations, we explored the spatial distribution of introgression across the area of colonization of an invasive taxon hybridizing with a local taxon. The general pattern for neutral loci supported by our results is an increasing introgression of local genes into the invasive taxon with the increase in the distance from the source of the invasion and a decreasing introgression of invasive genes into the local taxon. However, we also show there is some variation in this general trend depending on the scenario investigated. Spatial heterogeneity of introgression within a given taxon is thus an expected neutral pattern in structured populations after a biological invasion with a low to moderate amount of hybridization. We further show that this pattern is consistent with published empirical observations. Using additional simulations, we argue that the spatial pattern of Neanderthal introgression in modern humans, which has been documented to be higher in Asia than in Europe, can be explained by a model of hybridization with Neanderthals in Eurasia during the range expansion of modern humans from Africa. Our results support the view that weak hybridization during range expansion may explain spatially heterogeneous introgression patterns without the need to invoke selection.
Collapse
|
4
|
Molnár T, Benedek I, Kovács B, Zsolnai A, Lehoczky I. Genetic consequences of pond production of a pikeperch ( Sander lucioperca L.) stock with natural origin: the effects of changed selection pressure and reduced population size. PeerJ 2020; 8:e8745. [PMID: 32211234 PMCID: PMC7083162 DOI: 10.7717/peerj.8745] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 02/13/2020] [Indexed: 11/20/2022] Open
Abstract
The pikeperch (Sander lucioperca L.) possesses great potential for diversifying European aquaculture. However, studies on the genetic risk of stocking natural waters with farmed individuals of this species have been limited. Even the effect of pond culture on the genetic composition of stocks with natural-origin has not yet been determined. Our study aimed to compare the genetic variability of a wild living pikeperch population, a pond cultured broodstock (originating from the wild population) and its offspring generation. We also aimed to detect the potential signs of selection using three different methods. By analyzing the molecular data with 14 microsatellite markers, we illustrated that the impact of pond culture on the genetic diversity of fish stocks is similar to hatchery rearing due to its diversity reducing effect caused by using lower effective population sizes. Although the heterozygosity was similar in all populations (Ho = 0.68–0.71), the average number of alleles and allelic richness were significantly lower in the pond cultured stocks (NA = 7.5 and 6; AR = 7.5 and 5.9) compared to the wild population (NA = 11.00, AR = 10.47). Despite the semi-natural conditions of the present study, we detected changing selection pressure in one of the 14 microsatellite markers.
Collapse
Affiliation(s)
- Tamás Molnár
- Institute of Environmental Sciences and Nature Conservation, Kaposvár University, Kaposvár, Hungary.,Department of Aquaculture, Szent István University, Gödöllő, Hungary.,Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, Gödöllő, Hungary
| | - Ildikó Benedek
- Institute of Environmental Sciences and Nature Conservation, Kaposvár University, Kaposvár, Hungary
| | - Balázs Kovács
- Department of Aquaculture, Szent István University, Gödöllő, Hungary
| | - Attila Zsolnai
- Research Institute for Animal Breeding, Nutrition and Meat Science (ATHK), National Agricultural Research and Innovation Centre, Herceghalom, Hungary
| | - István Lehoczky
- Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, Gödöllő, Hungary
| |
Collapse
|
5
|
Wang D, Gao L, Tian H, Dong W, Duan X, Liu S, Chen D. Population genetics and sympatric divergence of the freshwater gudgeon, Gobiobotia filifer, in the Yangtze River inferred from mitochondrial DNA. Ecol Evol 2020; 10:50-58. [PMID: 31993113 PMCID: PMC6972953 DOI: 10.1002/ece3.5746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 09/09/2019] [Accepted: 09/16/2019] [Indexed: 12/02/2022] Open
Abstract
The ecosystem and Pleistocene glaciations play important roles in population demography. The freshwater gudgeon, Gobiobotia filifer, is an endemic benthic fish in the Yangtze River and is a good model for ecological and evolutionary studies. This study aimed to decode the population structure of G. filifer in the Yangtze River and reveal whether divergence occurred before or after population radiation. A total of 292 specimens from eight locations in the upper and middle reaches of the Yangtze River were collected from 2014 to 2016 and analyzed via mitochondrial DNA Cyt b gene sequencing. A moderately high level of genetic diversity was found without structures among the population. However, phylogenetic and network topology showed two distinct haplotype groups, and each group contained a similar proportion of individuals from all sampled sites. This suggested the existence of two genetically divergent source populations in G. filifer. We deduced that a secondary contact of distinct glacial refugia was the main factor creating sympatric populations of G. filifer, and climate improvement promoted population expansion and colonization.
Collapse
Affiliation(s)
- Dengqiang Wang
- Yangtze River Fisheries Research InstituteChinese Academy of Fishery ScienceWuhanChina
| | - Lei Gao
- Yangtze River Fisheries Research InstituteChinese Academy of Fishery ScienceWuhanChina
| | - Huiwu Tian
- Yangtze River Fisheries Research InstituteChinese Academy of Fishery ScienceWuhanChina
| | - Weiwei Dong
- Yangtze River Fisheries Research InstituteChinese Academy of Fishery ScienceWuhanChina
- School of Life ScienceSouthwest UniversityChongqingChina
| | - Xinbin Duan
- Yangtze River Fisheries Research InstituteChinese Academy of Fishery ScienceWuhanChina
| | - Shaoping Liu
- Yangtze River Fisheries Research InstituteChinese Academy of Fishery ScienceWuhanChina
| | - Daqing Chen
- Yangtze River Fisheries Research InstituteChinese Academy of Fishery ScienceWuhanChina
| |
Collapse
|
6
|
Nguinkal JA, Brunner RM, Verleih M, Rebl A, de Los Ríos-Pérez L, Schäfer N, Hadlich F, Stüeken M, Wittenburg D, Goldammer T. The First Highly Contiguous Genome Assembly of Pikeperch ( Sander lucioperca), an Emerging Aquaculture Species in Europe. Genes (Basel) 2019; 10:E708. [PMID: 31540274 PMCID: PMC6770990 DOI: 10.3390/genes10090708] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/27/2019] [Accepted: 09/08/2019] [Indexed: 01/14/2023] Open
Abstract
The pikeperch (Sander lucioperca) is a fresh and brackish water Percid fish natively inhabiting the northern hemisphere. This species is emerging as a promising candidate for intensive aquaculture production in Europe. Specific traits like cannibalism, growth rate and meat quality require genomics based understanding, for an optimal husbandry and domestication process. Still, the aquaculture community is lacking an annotated genome sequence to facilitate genome-wide studies on pikeperch. Here, we report the first highly contiguous draft genome assembly of Sander lucioperca. In total, 413 and 66 giga base pairs of DNA sequencing raw data were generated with the Illumina platform and PacBio Sequel System, respectively. The PacBio data were assembled into a final assembly size of ~900 Mb covering 89% of the 1,014 Mb estimated genome size. The draft genome consisted of 1966 contigs ordered into 1,313 scaffolds. The contig and scaffold N50 lengths are 3.0 Mb and 4.9 Mb, respectively. The identified repetitive structures accounted for 39% of the genome. We utilized homologies to other ray-finned fishes, and ab initio gene prediction methods to predict 21,249 protein-coding genes in the Sander lucioperca genome, of which 88% were functionally annotated by either sequence homology or protein domains and signatures search. The assembled genome spans 97.6% and 96.3% of Vertebrate and Actinopterygii single-copy orthologs, respectively. The outstanding mapping rate (99.9%) of genomic PE-reads on the assembly suggests an accurate and nearly complete genome reconstruction. This draft genome sequence is the first genomic resource for this promising aquaculture species. It will provide an impetus for genomic-based breeding studies targeting phenotypic and performance traits of captive pikeperch.
Collapse
Affiliation(s)
- Julien Alban Nguinkal
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Ronald Marco Brunner
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Marieke Verleih
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Alexander Rebl
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Lidia de Los Ríos-Pérez
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Nadine Schäfer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Frieder Hadlich
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Marcus Stüeken
- State Research Center of Agriculture and Fisheries M-V, 17194 Hohen Wangelin, Germany.
| | - Dörte Wittenburg
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Tom Goldammer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| |
Collapse
|
7
|
Dulski T, Zakęś Z, Ciesielski S. Characterization of the gut microbiota in early life stages of pikeperch Sander lucioperca. JOURNAL OF FISH BIOLOGY 2018; 92:94-104. [PMID: 29124770 DOI: 10.1111/jfb.13496] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 09/27/2017] [Indexed: 06/07/2023]
Abstract
This study characterized the gastrointestinal microbiome of nine juvenile farmed pikeperch Sander lucioperca using a metagenomics approach based on bacterial 16S rRNA gene sequencing. Potential changes in the gut microbiota during 2 months of S. lucioperca juvenile life were investigated. Results revealed that gut microbiota was dominated by Proteobacteria (95-92%), while other phyla Firmicutes (1-1·5%) and Actinobacteria (0·9-1·5%) were less abundant. At the family level, fish-gut microbiota were dominated by Enterobacteriaceae, which constituted c. 83% of all DNA sequence reads. Such a situation was present in all of the examined fish except one, which showed a different proportion of particular microbial taxa than the other fish. In this fish, a higher relative abundance (%) of Fusobacteria (21·0%), Bacteroidetes (9·5%) and Firmicutes (7·5%) was observed. There were no significant differences in the gut microbiome structure at different stages of development in the examined fish. This may indicate that Proteobacteria inhabiting the gut microbiota at an early stage of life are a necessary component of the pikeperch microbiome that may support proper nutrition of the fish. The information obtained on the gut microbiome could be useful in determining juvenile S. lucioperca health and improving rearing conditions by welfare monitoring in aquaculture.
Collapse
Affiliation(s)
- T Dulski
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Słoneczna 45G street, 10-709, Olsztyn, Poland
| | - Z Zakęś
- Department of Aquaculture, The Stanislaw Sakowicz Inland Fisheries Institute, ul. Oczapowskiego 10, 10-719, Olsztyn, Poland
| | - S Ciesielski
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Słoneczna 45G street, 10-709, Olsztyn, Poland
| |
Collapse
|
8
|
Arlinghaus R, Beardmore B, Riepe C, Meyerhoff J, Pagel T. Species-specific preferences of German recreational anglers for freshwater fishing experiences, with emphasis on the intrinsic utilities of fish stocking and wild fishes. JOURNAL OF FISH BIOLOGY 2014; 85:1843-1867. [PMID: 25469949 DOI: 10.1111/jfb.12546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 09/18/2014] [Indexed: 06/04/2023]
Abstract
To answer the question, whether anglers have an intrinsic preference for stocking or a preference for catch outcomes (e.g. catch rates) believed to be maintained by stocking, a discrete choice experiment was conducted among a sample of anglers (n = 1335) in Lower Saxony, Germany. After controlling for catch aspects of the fishing experience, no significant influence of two stocking attributes (stocking frequency and composition of the catch in terms of wild v. hatchery fishes) on the utility gained from fishing was found for any of the freshwater species that were studied. It was concluded that the previously documented large appreciation of fish stocking by anglers may be indicative of an underlying preference for sufficiently high catches rather than reflect an intrinsic preference for stocking or the catching of wild fishes per se.
Collapse
Affiliation(s)
- R Arlinghaus
- Recreational Fisheries Laboratory, Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; Division of Integrative Fisheries Management, Albrecht-Daniel-Thaer Institute of Crop and Agricultural Sciences, Faculty of Life Sciences & Integrative Institute for the Transformation of Human-Environment Systems (IRI THESys), Humboldt-Universität zu Berlin, Germany
| | | | | | | | | |
Collapse
|