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Jeffries DL, Lawson-Handley L, Lamatsch DK, Olsén KH, Sayer CD, Hänfling B. Towards the conservation of the crucian carp in Europe: Prolific hybridization but no evidence for introgression between native and non-native taxa. Mol Ecol 2024:e17515. [PMID: 39212263 DOI: 10.1111/mec.17515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 07/02/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024]
Abstract
Hybridization plays a pivotal role in evolution, influencing local adaptation and speciation. However, it can also reduce biodiversity, which is especially damaging when native and non-native species meet. Hybridization can threaten native species via competition (with vigorous hybrids), reproductive resource wastage and gene introgression. The latter, in particular, could result in increased fitness in invasive species, decreased fitness of natives and compromise reintroduction or recovery conservation practices. In this study, we use a combination of RAD sequencing and microsatellites for a range-wide sample set of 1366 fish to evaluate the potential for hybridization and introgression between native crucian carp (Carassius carassius) and three non-native taxa (Carassius auratus auratus, Carassius auratus gibelio and Cyprinus carpio) in European water bodies. We found hybridization between native and non-native taxa in 82% of populations with non-natives present, highlighting the potential for substantial ecological impacts from hybrids on crucian carp populations. However, despite such high rates of hybridization, we could find no evidence of introgression between these taxa. The presence of triploid backcrosses in at least two populations suggests that the lack of introgression among these taxa is likely due to meiotic dysfunction in hybrids, leading to the production of polyploid offspring which are unable to reproduce sexually. This result is promising for crucian reintroduction programs, as it implies limited risk to the genetic integrity of source populations. Future research should investigate the reproductive potential of triploid hybrids and the ecological pressures hybrids impose on C. carassius.
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Affiliation(s)
- Daniel L Jeffries
- Evolutionary Biology Group, School of Biological, Biomedical and Environmental Sciences, University of Hull, Hull, UK
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Lori Lawson-Handley
- Evolutionary Biology Group, School of Biological, Biomedical and Environmental Sciences, University of Hull, Hull, UK
| | - Dunja K Lamatsch
- Universität Innsbruck, Research Department for Limnology, Mondsee, Austria
| | - K Håkan Olsén
- School of Natural Sciences, Technology and Environmental Studies, Södetörn University, Huddinge, Stockholm, Sweden
| | - Carl D Sayer
- Pond Restoration Research Group, Department of Geography, University College London, London, UK
| | - Bernd Hänfling
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Institute for Biodiversity and Freshwater Conservation, University of the Highlands and Islands, Inverness, UK
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2
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Lu M, Zhou L, Gui JF. Evolutionary mechanisms and practical significance of reproductive success and clonal diversity in unisexual vertebrate polyploids. SCIENCE CHINA. LIFE SCIENCES 2024; 67:449-459. [PMID: 38198030 DOI: 10.1007/s11427-023-2486-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/01/2023] [Indexed: 01/11/2024]
Abstract
Unisexual reproduction is generally relevant to polyploidy, and unisexual vertebrates are often considered an evolutionary "dead end" due to the accumulation of deleterious mutations and absence of genetic diversity. However, some unisexual polyploids have developed strategies to avoid genomic decay, and thus provide ideal models to unveil unexplored evolutionary mechanisms, from the reproductive success to clonal diversity creation. This article reviews the evolutionary mechanisms for overcoming meiotic barrier and generating genetic diversity in unisexual vertebrates, and summarizes recent research advancements in the polyploid Carassius complex. Gynogenetic gibel carp (Carassius gibelio) is a unique amphitriploid that has undergone a recurrent autotriploidy and has overcome the bottleneck of triploid sterility via gynogenesis. Recently, an efficient strategy in which ploidy changes, including from amphitriploid to amphitetraploid, then from amphitetraploid to novel amphitriploid, drive unisexual-sexual-unisexual reproduction transition and clonal diversity has been revealed. Based on this new discovery, multigenomic reconstruction biotechnology has been used to breed a novel strain with superior growth and stronger disease resistance. Moreover, a unique reproduction mode that combines both abilities of ameiotic oogenesis and sperm-egg fusion, termed as ameio-fusiongensis, has been discovered, and it provides an efficient approach to synthesize sterile allopolyploids. In order to avoid ecological risks upon escape and protect the sustainable property rights of the aquaculture seed industry, a controllable fertility biotechnology approach for precise breeding is being developed by integrating sterile allopolyploid synthesis and gene-editing techniques. This review provides novel insights into the origin and evolution of unisexual vertebrates and into the attempts being made to exploit new breeding biotechnologies in aquaculture.
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Affiliation(s)
- Meng Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, the Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, the Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, the Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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3
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Feng X, Zhu R, Jia Y, Tong J, Yu X, Pang M, Liu C, Sui X, Chen Y. Genetic diversity and population structure of the invasive populations of goldfish Carassius auratus complex in Tibet. Biol Invasions 2023. [DOI: 10.1007/s10530-023-03027-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
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4
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Lu M, Li Z, Zhu ZY, Peng F, Wang Y, Li XY, Wang ZW, Zhang XJ, Zhou L, Gui JF. Changes in Ploidy Drive Reproduction Transition and Genomic Diversity in a Polyploid Fish Complex. Mol Biol Evol 2022; 39:msac188. [PMID: 36056821 PMCID: PMC9486886 DOI: 10.1093/molbev/msac188] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Unisexual animals are commonly found in some polyploid species complexes, and most of these species have had a long evolutionary history. However, their method for avoiding genomic decay remains unclear. The polyploid Carassius complex naturally comprises the sexual amphidiploid C. auratus (crucian carp or goldfish) (AABB) and the gynogenetic amphitriploid C. gibelio (gibel carp) (AAABBB). Recently, we developed a fertile synthetic amphitetraploid (AAAABBBB) male from C. gibelio by incorporating a C. auratus genome. In this study, we generated novel amphitriploids (AAABBB) by backcrossing the amphitetraploid male with the amphidiploid C. auratus. Whole-genome resequencing revealed the genomic changes, including recombination and independent assortment between homologs of C. gibelio and C. auratus. The fertility, sex determination system, oocyte development, and fertilization behaviors of the novel amphitriploids were investigated. Approximately 80% of the novel amphitriploid females recovered the unisexual gynogenesis ability. Intriguingly, two types of primary oocyte (with and without homolog synapsis) were discovered, and their distinct development fates were observed. Type I oocytes entered apoptosis due to improper synaptonemal complex assembly and incomplete double-strand break repair, whereas subsequent type II oocytes bypassed meiosis through an alternative ameiotic pathway to develop into mature eggs. Moreover, gynogenesis was stabilized in their offspring, and a new array of diverse gynogenetic amphitriploid clones was produced. These revealed genomic changes and detailed cytological data provide comprehensive evidence that changes in ploidy drive unisexual and sexual reproduction transition, thereby resulting in genomic diversity and allowing C. gibelio avoid genomic decay.
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Affiliation(s)
- Meng Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, the Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, the Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zi-Yu Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, the Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Peng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, the Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, the Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, the Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhong-Wei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, the Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, the Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, the Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, the Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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5
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Knytl M, Forsythe A, Kalous L. A Fish of Multiple Faces, Which Show Us Enigmatic and Incredible Phenomena in Nature: Biology and Cytogenetics of the Genus Carassius. Int J Mol Sci 2022; 23:8095. [PMID: 35897665 PMCID: PMC9330404 DOI: 10.3390/ijms23158095] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/16/2022] Open
Abstract
Sexual vs. asexual reproduction-unisexual vs. bisexual populations-diploid vs. polyploid biotypes-genetic vs. environmental sex determination: all these natural phenomena are associated with the genus of teleost fish, Carassius. This review places emphasis on two Carassius entities with completely different biological characteristics: one globally widespread and invasive Carassius gibelio, and the other C. carassius with a decreasing trend of natural occurrence. Comprehensive biological and cytogenetic knowledge of both entities, including the physical interactions between them, can help to balance the advantages of highly invasive and disadvantages of threatened species. For example, the benefits of a wide-ranged colonization can lead to the extinction of native species or be compensated by parasitic enemies and lead to equilibrium. This review emphasizes the comprehensive biology and cytogenetic knowledge and the importance of the Carassius genus as one of the most useful experimental vertebrate models for evolutionary biology and genetics. Secondly, the review points out that effective molecular cytogenetics should be used for the identification of various species, ploidy levels, and hybrids. The proposed investigation of these hallmark characteristics in Carassius may be applied in conservation efforts to sustain threatened populations in their native ranges. Furthermore, the review focuses on the consequences of the co-occurrence of native and non-native species and outlines future perspectives of Carassius research.
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Affiliation(s)
- Martin Knytl
- Department of Cell Biology, Faculty of Science, Charles University, 12843 Prague, Czech Republic
| | - Adrian Forsythe
- Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, 75236 Uppsala, Sweden;
| | - Lukáš Kalous
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 16521 Prague, Czech Republic;
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Gu Q, Wang S, Zhong H, Yuan H, Yang J, Yang C, Huang X, Xu X, Wang Y, Wei Z, Wang J, Liu S. Phylogeographic relationships and the evolutionary history of the Carassius auratus complex with a newly born homodiploid raw fish (2nNCRC). BMC Genomics 2022; 23:242. [PMID: 35350975 PMCID: PMC8962218 DOI: 10.1186/s12864-022-08468-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 03/14/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
An important aspect of studying evolution is to understand how new species are formed and their uniqueness is maintained. Hybridization can lead to the formation of new species through reorganization of the adaptive system and significant changes in phenotype. Interestingly, eight stable strains of 2nNCRC derived from interspecies hybridization have been established in our laboratory. To examine the phylogeographical pattern of the widely distributed genus Carassius across Eurasia and investigate the possible homoploid hybrid origin of the Carassius auratus complex lineage in light of past climatic events, the mitochondrial genome (mtDNA) and one nuclear DNA were used to reconstruct the phylogenetic relationship between the C. auratus complex and 2nNCRC and to assess how demographic history, dispersal and barriers to gene flow have led to the current distribution of the C. auratus complex.
Results
As expected, 2nNCRC had a very close relationship with the C. auratus complex and similar morphological characteristics to those of the C. auratus complex, which is genetically distinct from the other three species of Carassius. The estimation of divergence time and ancestral state demonstrated that the C. auratus complex possibly originated from the Yangtze River basin in China. There were seven sublineages of the C. auratus complex across Eurasia and at least four mtDNA lineages endemic to particular geographical regions in China. The primary colonization route from China to Mongolia and the Far East (Russia) occurred during the Late Pliocene, and the diversification of other sublineages of the C. auratus complex specifically coincided with the interglacial stage during the Early and Mid-Pleistocene in China.
Conclusion
Our results support the origin of the C. auratus complex in China, and its wide distribution across Eurasia was mainly due to natural Pleistocene dispersal and recent anthropogenic translocation. The sympatric distribution of the ancestral area for both parents of 2nNCRC and the C. auratus complex, as well as the significant changes in the structure of pharyngeal teeth and morphological characteristics between 2nNCRC and its parents, imply that homoploid hybrid speciation (HHS) for C. auratus could likely have occurred in nature. The diversification pattern indicated an independent evolutionary history of the C. auratus complex, which was not separated from the most recent common ancestor of C. carassius or C. cuvieri. Considering that the paleoclimate oscillation and the development of an eastward-flowing drainage system during the Pliocene and Pleistocene in China provided an opportunity for hybridization between divergent lineages, the formation of 2nNCRC in our laboratory could be a good candidate for explaining the HHS of C. auratus in nature.
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7
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Tong JF, Zhou L, Li S, Lu LF, Li ZC, Li Z, Gan RH, Mou CY, Zhang QY, Wang ZW, Zhang XJ, Wang Y, Gui JF. Two Duplicated Ptpn6 Homeologs Cooperatively and Negatively Regulate RLR-Mediated IFN Response in Hexaploid Gibel Carp. Front Immunol 2021; 12:780667. [PMID: 34899743 PMCID: PMC8662705 DOI: 10.3389/fimmu.2021.780667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/11/2021] [Indexed: 01/28/2023] Open
Abstract
Src homology region 2 domain-containing phosphatase 1 (SHP1), encoded by the protein tyrosine phosphatase nonreceptor type 6 (ptpn6) gene, belongs to the family of protein tyrosine phosphatases (PTPs) and participates in multiple signaling pathways of immune cells. However, the mechanism of SHP1 in regulating fish immunity is largely unknown. In this study, we first identified two gibel carp (Carassius gibelio) ptpn6 homeologs (Cgptpn6-A and Cgptpn6-B), each of which had three alleles with high identities. Then, relative to Cgptpn6-B, dominant expression in adult tissues and higher upregulated expression of Cgptpn6-A induced by polyinosinic-polycytidylic acid (poly I:C), poly deoxyadenylic-deoxythymidylic (dA:dT) acid and spring viremia of carp virus (SVCV) were uncovered. Finally, we demonstrated that CgSHP1-A (encoded by the Cgptpn6-A gene) and CgSHP1-B (encoded by the Cgptpn6-B gene) act as negative regulators of the RIG-I-like receptor (RLR)-mediated interferon (IFN) response via two mechanisms: the inhibition of CaTBK1-induced phosphorylation of CaMITA shared by CgSHP1-A and CgSHP1-B, and the autophagic degradation of CaMITA exclusively by CgSHP1-A. Meanwhile, the data support that CgSHP1-A and CgSHP1-B have sub-functionalized and that CgSHP1-A overwhelmingly dominates CgSHP1-B in the process of RLR-mediated IFN response. The current study not only sheds light on the regulative mechanism of SHP1 in fish immunity, but also provides a typical case of duplicated gene evolutionary fates.
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Affiliation(s)
- Jin-Feng Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
| | - Shun Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Long-Feng Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhuo-Cong Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
| | - Rui-Hai Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
| | - Cheng-Yan Mou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Qi-Ya Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhong-Wei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
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Keszte S, Ferincz A, Tóth-Ihász K, Balogh RE, Staszny Á, Hegyi Á, Takács P, Urbanyi B, Kovács B. Mitochondrial sequence diversity reveals the hybrid origin of invasive gibel carp ( Carassius gibelio) populations in Hungary. PeerJ 2021; 9:e12441. [PMID: 34966576 PMCID: PMC8663655 DOI: 10.7717/peerj.12441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/15/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Invasive gibel carp, Carassius gibelio (Bloch, 1782) has become well-established in the Hungarian waters and now are spreading in the European waters. On major concern now is the potential hybridization between gibel carp and the other invasive species in the Carassius auratus complex (CAC), which may further accelerate the spread of the whole invasive species complex. The identification of gibel carp and their hybrids is difficult because of its morphological similarity to the other species in CAC. Here we carry out a genomic assessment to understand the history of gibel carp invasion and its phylogenetic relationship with the other species in CAC. Three loci of the mitochondrial genome (D-loop, CoI, Cytb) were used to determine the phylogenetic origin of individuals and relarionship among six gibel carp populations and the other species in the CAC. METHODOLGY A total of 132 gibel carp samples from six locations in Southern Transdanubia (Hungary) were collected after phenotypic identification to measure the genetic diversity within and among gibel carp populations of Southern Transdanubia (Hungary). The genetic background was examined by the sequences of the mitochondrial genome: D-loop, Cytochrome c oxidase I (CoI) and Cytochrome b (Cytb). Mitochondrial genetic markers are excellent tools for phylogenetic studies because they are maternally inherited. Successfully identified haplotypes were aligned and with reference sequences in nucleotide databases (i.e., NCBI-BLAST: National Centre for Biotechnology Information and BOLD: Barcode of Life Data System). The phylogenetic relationships among gibel carp populations were then analyzed together with the reference sequences to understand the relationship and the level of hybridization with the species in CAC. RESULTS Among the 132 aligned D-loop sequences 22 haplotypes were identified. Further examination of representative individuals of the 22 haplotypes, six Cytb and four CoI sequences were detected. The largest number of haplotypes of all three loci were found in Lake Balaton, the largest shallow lake in Central Europe. Based on the NCBI-BLAST alignment of the D-loop, haplotypes of Carassius auratus auratus and Carassius a. buergeri in CAC were identified in the C. gibelio samples. Further analysis of haplotypes with the other two mitochondrial markers confirmed the occurrence of intragenus hybridization of C. gibelio in the Hungarian waters. CONCLUSION By using three mitochondrial markers (D-loop, Cytb, CoI), we genomically characterized a gibel carp-complex in Hungarian waters and assessed the C. gibelio phylogenetic status between them. Hybrid origin of locally invasive Carassius taxon was detected in Hungary. It points out that invasive species are not only present in Hungary but reproduce with each other in the waters, further accelerating their spread.
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Affiliation(s)
- Szilvia Keszte
- Department of Freshwater Fish Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agricultural and Life Sciences, Gödöllő, Magyarország
| | - Arpad Ferincz
- Department of Freshwater Fish Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agricultural and Life Sciences, Gödöllő, Magyarország
| | - Katalin Tóth-Ihász
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agricultural and Life Science, Gödöllő, Magyarország
| | - Réka Enikő Balogh
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agricultural and Life Science, Gödöllő, Magyarország
| | - Ádám Staszny
- Department of Freshwater Fish Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agricultural and Life Sciences, Gödöllő, Magyarország
| | - Árpád Hegyi
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agricultural and Life Sciences, Gödöllő, Magyarország
| | - Péter Takács
- Fish and Conservation Ecology Research Group, Balaton Limnological Research Institute, Tihany, Magyarország
| | - Bela Urbanyi
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agricultural and Life Sciences, Gödöllő, Magyarország
| | - Balázs Kovács
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agricultural and Life Science, Gödöllő, Magyarország
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9
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Mishina T, Takeshima H, Takada M, Iguchi K, Zhang C, Zhao Y, Kawahara-Miki R, Hashiguchi Y, Tabata R, Sasaki T, Nishida M, Watanabe K. Interploidy gene flow involving the sexual-asexual cycle facilitates the diversification of gynogenetic triploid Carassius fish. Sci Rep 2021; 11:22485. [PMID: 34795357 PMCID: PMC8602411 DOI: 10.1038/s41598-021-01754-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/28/2021] [Indexed: 11/23/2022] Open
Abstract
Asexual vertebrates are rare and at risk of extinction due to their restricted adaptability through the loss of genetic recombination. We explore the mechanisms behind the generation and maintenance of genetic diversity in triploid asexual (gynogenetic) Carassius auratus fish, which is widespread in East Asian fresh waters and exhibits one of the most extensive distribution among asexual vertebrates despite its dependence on host sperm. Our analyses of genetic composition using dozens of genetic markers and genome-wide transcriptome sequencing uncover admixed genetic composition of Japanese asexual triploid Carassius consisting of both the diverged Japanese and Eurasian alleles, suggesting the involvement of Eurasian lineages in its origin. However, coexisting sexual diploid relatives and asexual triploids in Japan show regional genetic similarity in both mitochondrial and nuclear markers. These results are attributed to a unique unidirectional gene flow from diploids to sympatric triploids, with the involvement of occasional sexual reproduction. Additionally, the asexual triploid shows a weaker population structure than the sexual diploid, and multiple triploid lineages coexist in most Japanese rivers. The generated diversity via repeated interploidy gene flow as well as an increased establishment of immigrants is assumed to offset the cost of asexual reproduction and might contribute to the successful broad distribution of this asexual vertebrate.
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Affiliation(s)
- Tappei Mishina
- Laboratory of Animal Ecology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.
- Laboratory for Chromosome Segregation, RIKEN Center for Biosystems Dynamics Research, Chuo-ku, Kobe, 650-0047, Japan.
| | - Hirohiko Takeshima
- Research Institute for Humanity and Nature, Kita-ku, Kyoto, 603-8047, Japan
- Department of Marine Biology, Tokai University, Shimizu, Shizuoka, 424-8610, Japan
| | - Mikumi Takada
- Atmosphere and Ocean Research Institute, University of Tokyo, Kashiwa, Chiba, 277-8564, Japan
| | - Kei'ichiro Iguchi
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, 852-8521, Japan
| | - Chunguang Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Yahui Zhao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Ryouka Kawahara-Miki
- NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-ku, Tokyo, 156-8502, Japan
| | - Yasuyuki Hashiguchi
- Department of Biology, Osaka Medical and Pharmaceutical University, Takatsuki, Osaka, 569-0801, Japan
| | - Ryoichi Tabata
- Laboratory of Animal Ecology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
- Lake Biwa Museum, 1091 Oroshimo, Kusatsu, Shiga, 525-0001, Japan
| | - Takeshi Sasaki
- Graduate School of Human and Animal-Plant Relationships, Tokyo University of Agriculture, Atsugi, Kanagawa, 243-0034, Japan
| | - Mutsumi Nishida
- University of the Ryukyus, Nakagami-gun, Okinawa, 903-0213, Japan
| | - Katsutoshi Watanabe
- Laboratory of Animal Ecology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.
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Pobedintseva MA, Reshetnikova SN, Serdyukova NA, Bishani A, Trifonov VA, Interesova EA. Genetic Diversity of the Prussian Carp Carassius gibelio (Cyprinidae) in the Middle Ob Basin. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421040116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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11
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Bishani A, Prokopov DY, Romanenko SA, Molodtseva AS, Perelman PL, Interesova EA, Beklemisheva VR, Graphodatsky AS, Trifonov VA. Evolution of Tandemly Arranged Repetitive DNAs in Three Species of Cyprinoidei with Different Ploidy Levels. Cytogenet Genome Res 2021; 161:32-42. [PMID: 33677437 DOI: 10.1159/000513274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/10/2020] [Indexed: 11/19/2022] Open
Abstract
Polyploid species represent a challenge for both cytogenetic and genomic studies due to their high chromosome numbers and the morphological similarity between their paralogous chromosomes. This paper describes the use of low-coverage high-throughput sequencing to identify the 14 most abundant tandemly arranged repetitive elements in the paleotetraploid genome of the crucian carp (Carassius carassius, 2n = 100). These repetitive elements were then used for molecular cytogenetic studies of a closely related functionally triploid form of the Prussian carp (Carassius gibelio, 3n = 150 + Bs) and a relatively distant diploid species, the tench (Tinca tinca, 2n = 48). According to their distribution on the chromosomes of the 3 aforementioned species, the repetitive elements here identified can be divided into 5 groups: (1) those specific to a single genomic locus in both Carassius species, despite the recent carp-specific genome duplication; (2) those located in a single genomic locus of T. tinca, but amplified in one or both Carassius species; (3) those massively amplified in the B chromosomes of C. gibelio; (4) those located in a single locus in C. gibelio, but amplified in many blocks in C. carassius; and (5) those located in multiple pericentromeric loci in both Carassius species. Our data indicate that some of the repetitive elements are highly conserved in cyprinoid species and may serve as good cytogenetic and genomic markers for discriminating paralogous chromosomes, while others are evolutionarily recent, and their amplification may be related to the last whole-genome duplication event.
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Affiliation(s)
- Ali Bishani
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russian Federation, .,Novosibirsk State University, Novosibirsk, Russian Federation,
| | - Dmitry Y Prokopov
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russian Federation
| | - Svetlana A Romanenko
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russian Federation
| | - Anna S Molodtseva
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russian Federation
| | - Polina L Perelman
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russian Federation
| | - Elena A Interesova
- Department of Ichthyology and Hydrobiology, Tomsk State University, Tomsk, Russian Federation
| | | | | | - Vladimir A Trifonov
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russian Federation.,Novosibirsk State University, Novosibirsk, Russian Federation
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Coexistence of Three Divergent mtDNA Lineages in Northeast Asia Provides New Insights into Phylogeography of Goldfish ( Carssius auratus). Animals (Basel) 2020; 10:ani10101785. [PMID: 33019665 PMCID: PMC7650769 DOI: 10.3390/ani10101785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/12/2020] [Accepted: 09/19/2020] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Goldfish (Carassius auratus) is a well-known fish as food and as a pet, which is also frequently used as experimental animal. A unique mtDNA sequence was detected in a sample from our experimental station, which motivated us to study genetic constitution of goldfish in Northeast Asia. Three divergent mtDNA lineages were confirmed to coexist in this region. Two of which corresponded to the known lineages (C2 and C6), which was consistent with the zoogeographical records that there were two sympatric subspecies in Amur river basin. However, the third one (lineage C7) was largely neglected in the previous studies. Our results suggested lineage C7 had a wide distribution from Central Asia to Northeast Asia. Abstract Goldfish (Carassius aurautus), which is a middle size cyprinid, widely distribute throughout Eurasia. Phylogeographic studies using mtDNA markers have revealed several divergent lineages within goldfish. In this study, mtDNA variations were determined to elucidate the phylogeographical pattern and genetic structure of goldfish in Northeast Asia. A total of 1054 individuals from Amur river basin were analyzed, which including five newly collected populations and four previously reported populations. Three distinct mtDNA lineages were identified in those samples, two of which corresponded to two known lineages C2 and C6, respectively. The third lineage referred to as C7, following six known lineages of goldfish in mainland Eurasia. AMOVA results suggested that most of the genetic variations were among lineages, rather than among populations or twice samplings. We noted that the control region (CR) and cytochrome b (cytb) sequences of lineage C7 have been reported in previous studies, respectively. However, the evolutionary position and distribution pattern of this lineage was not discussed in the context of the species. Our results showed that “odd” CR and “hidden” cytb sequences from Central Asia represent the same mtDNA lineage of goldfish. The known samples of C7 lineage were collected from Central Asia (Eastern Kazakhstan and Western Mongolia) to East Asia (Northeast China and Far East Russia), which suggested that it had a wider distribution, rather than limit in Central Asia.
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Mezherin SV, Pukhtaevych PP, Kokodiy SV. The Polyclonal Structure of Unisexual Prussian Carp (Carassius gibelio (Bloch, 1782)) Settlements in Northern Ukraine: Comparison Analysis of Allozyme Markers and Chromosome Numbers. CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720010119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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High genetic diversity in an invasive freshwater fish species, Carassius gibelio, suggests establishment success at the frontier between native and invasive ranges. ZOOL ANZ 2019. [DOI: 10.1016/j.jcz.2019.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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15
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Lu WJ, Gao FX, Wang Y, Zhang QY, Li Z, Zhang XJ, Zhou L, Gui JF. Differential expression of innate and adaptive immune genes in the survivors of three gibel carp gynogenetic clones after herpesvirus challenge. BMC Genomics 2019; 20:432. [PMID: 31138127 PMCID: PMC6540555 DOI: 10.1186/s12864-019-5777-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/07/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Accompanied with rapid growth and high density aquaculture, gibel carp has been seriously threatened by Carassius auratus herpesvirus (CaHV) since 2012. In previous study, distinct CaHV resistances and immune responses were revealed in the diseased individuals of three gibel carp gynogenetic clones (A+, F and H). However, little is known about the gene expression changes in the survivors after CaHV challenge, particularly their differences of innate and adaptive immune system between susceptible clone and resistant clone. RESULTS We firstly confirmed the CaHV carrier state in the survivors of three gibel carp clones after CaHV challenge by evaluating the abundances of five CaHV genes. The assay of viral loads indicated the resistant clone H possessed not only stronger resistance but also higher tolerance to CaHV. Then, 2818, 4047 and 3323 differentially expressed unigenes (DEUs) were screened from the head-kidney transcriptome profiles of survivors compared with controls from clone A+, F and H. GO and KEGG analysis suggested that a persistent immune response might sustain in resistant clone H and F, while susceptible clone A+ had a long-term impact on the circulatory system which was consistent with the major symptoms of bleeding caused by CaHV. Among the top 30 enriched pathways of specifically up-regulated DEUs in respective clones, 26, 7 and 15 pathways in clone H, F and A+ were associated with infections, diseases, or immune-related pathways respectively. In addition, 20 pathways in clone F belonged to "metabolism" or "biogenesis", and 7 pathways involved in "circulatory system" were enriched in clone A+. Significantly, we revealed the differential expression changes of IFN system genes and immunoglobulin (Ig) genes among the survivors of three clones. Finally, myosins and Igs were identified as co-expression modules which were positively or negatively correlated to CaHV viral loads respectively. CONCLUSIONS Our results revealed the common and distinct gene expression changes in immune and circulatory system in the survivors of three gibel carp gynogenetic clones with different CaHV resistances. The current study represents a paradigm of differential innate and adaptive immune reactions in teleost, and will be beneficial to the disease-resistance breeding of gibel carp.
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Affiliation(s)
- Wei-Jia Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072 Hubei China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Fan-Xiang Gao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072 Hubei China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Institute of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098 China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072 Hubei China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Qi-Ya Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072 Hubei China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072 Hubei China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072 Hubei China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072 Hubei China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072 Hubei China
- University of Chinese Academy of Sciences, Beijing, 100049 China
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Omori Y, Kon T. Goldfish: an old and new model system to study vertebrate development, evolution and human disease. J Biochem 2019; 165:209-218. [PMID: 30219851 DOI: 10.1093/jb/mvy076] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/13/2018] [Indexed: 02/02/2023] Open
Abstract
The goldfish (Carassius auratus) is a domesticated cyprinid teleost closely related to the crucian carp. Goldfish domestication occurred in South China around 1,000 years ago. At least 180 variants and 70 genetically established strains are currently produced. These strains possess diverse phenotypes in body shape, colouration, scales, and fin, eye and hood morphology. These include biologically interesting phenotypes that have not been observed in mutants of zebrafish or medaka. In addition, goldfish strains have been maintained in a non-wild environment for several hundreds of generations, and certain goldfish strains have phenotypes similar to some human diseases. The recent progress in the assembly of the whole-genome sequence of goldfish provides strong tools for a genetic analysis of these phenotypes. The whole-genome duplication (WGD) event occurred in the goldfish genome 8-14 million years ago; this is one of the latest WGD in vertebrates. Goldfish are a useful model for studying genome evolution after the WGD event. This review focuses on the potential for goldfish as a model system in understanding the molecular basis of vertebrate development and evolution and human diseases.
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Affiliation(s)
- Yoshihiro Omori
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, Japan
| | - Tetsuo Kon
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, Japan
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Phylogeography of freshwater planorbid snails reveals diversification patterns in Eurasian continental islands. BMC Evol Biol 2018; 18:164. [PMID: 30400816 PMCID: PMC6219199 DOI: 10.1186/s12862-018-1273-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 10/08/2018] [Indexed: 01/19/2023] Open
Abstract
Background Islands have traditionally been the centre of evolutionary biological research, but the dynamics of immigration and differentiation at continental islands have not been well studied. Therefore, we focused on the Japanese archipelago, the continental islands located at the eastern end of the Eurasian continent. While the Japanese archipelago is characterised by high biodiversity and rich freshwater habitats, the origin and formation mechanisms of its freshwater organisms are not clear. In order to clarify the history of the planorbid gastropod fauna, we conducted phylogenetic analysis, divergence time estimation, ancestral state reconstruction, and lineage diversity estimations. Results Our analyses revealed the formation process of the planorbid fauna in the Japanese archipelago. Most lineages in the Japanese archipelago have closely related lineages on the continent, and the divergence within the Japanese lineages presumably occurred after the late Pliocene. In addition, each lineage is characterised by different phylogeographical patterns, suggesting that immigration routes from the continent to the Japanese archipelago differ among lineages. Furthermore, a regional lineage diversity plot showed that the present diversity in the Japanese archipelago potentially reflects the differentiation of lineages within the islands after the development of the Japanese archipelago. Conclusions Although additional taxon sampling and genetic analysis focused on each lineage are needed, our results suggest that immigration from multiple routes just prior to the development of the Japanese archipelago and subsequent diversification within the islands are major causes of the present-day diversity of the Japanese planorbid fauna. Electronic supplementary material The online version of this article (10.1186/s12862-018-1273-3) contains supplementary material, which is available to authorized users.
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Abe G, Li IJ, Lee SH, Ota KG. A novel allele of the goldfish chdB gene: Functional evaluation and evolutionary considerations. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2018; 330:372-383. [PMID: 30387925 PMCID: PMC6587777 DOI: 10.1002/jez.b.22831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/07/2018] [Accepted: 09/24/2018] [Indexed: 12/23/2022]
Abstract
The twin tail of ornamental goldfish is known to be caused by a nonsense mutation in one chordin paralogue gene. Our previous molecular studies in goldfish revealed that the ancestral
chordin gene was duplicated, creating the
chdA and
chdB genes, and the subsequent introduction of a stop codon allele in the
chdA gene (
chdAE127X) caused the twin‐tail morphology. The
chdAE127X allele was positively selected by breeders, and the allele was genetically fixed in the ornamental twin‐tail goldfish population. However, little is known about the evolutionary history of the
chdB paralogue, begging the question: are there the functionally distinct alleles at the
chdB locus, and if so, how did they evolve? To address these questions, we conducted molecular sequencing of the
chdB gene from five different goldfish strains and discovered two alleles at the
chdB gene locus; the two alleles are designated
chdB1 and
chdB2. The
chdB1 allele is the major allele and was found in all investigated goldfish strains, whereas the
chdB2 allele is minor, having only been found in one twin‐tail strain. Genetic analyses further suggested that these two alleles are functionally different with regard to survivability (
chdB1 >
chdB2). These results led us to presume that in contrast to the
chdA locus, the
chdB locus has tended to be eliminated from the population. We also discuss how the
chdB2 allele was retained in the goldfish population, despite its disadvantageous function. This study provides empirical evidence of the long‐term retention of a disadvantageous allele under domesticated conditions.
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Affiliation(s)
- Gembu Abe
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan.,Laboratory of Organ Morphogenesis, Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Ing-Jia Li
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
| | - Shu-Hua Lee
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
| | - Kinya G Ota
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
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Rylková K, Petrtýl M, Bui AT, Kalous L. Just a Vietnamese goldfish or another Carassius? Validity of Carassius argenteaphthalmusNguyen & Ngo, 2001 (Teleostei: Cyprinidae). J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kateřina Rylková
- Department of Genetics and Breeding; Faculty of Agrobiology, Food and Natural Resources; Czech University of Life Sciences Prague; Prague Czech Republic
| | - Miloslav Petrtýl
- Department of Zoology and Fisheries; Faculty of Agrobiology, Food and Natural Resources; Czech University of Life Sciences Prague; Prague Czech Republic
| | - Anh T. Bui
- Department of Science, Technology and Environment; Ministry of Agriculture and Rural Development; Hanoi Viet Nam
| | - Lukáš Kalous
- Department of Zoology and Fisheries; Faculty of Agrobiology, Food and Natural Resources; Czech University of Life Sciences Prague; Prague Czech Republic
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Zhang D, Zou H, Wu SG, Li M, Jakovlić I, Zhang J, Chen R, Li WX, Wang GT. Three new Diplozoidae mitogenomes expose unusual compositional biases within the Monogenea class: implications for phylogenetic studies. BMC Evol Biol 2018; 18:133. [PMID: 30176801 PMCID: PMC6122551 DOI: 10.1186/s12862-018-1249-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 08/20/2018] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND As the topologies produced by previous molecular and morphological studies were contradictory and unstable (polytomy), evolutionary relationships within the Diplozoidae family and the Monogenea class (controversial relationships among the Discocotylinea, Microcotylinea and Gastrocotylinea suborders) remain unresolved. Complete mitogenomes carry a relatively large amount of information, sufficient to provide a much higher phylogenetic resolution than traditionally used morphological traits and/or single molecular markers. However, their implementation is hampered by the scarcity of available monogenean mitogenomes. Therefore, we sequenced and characterized mitogenomes belonging to three Diplozoidae family species, and conducted comparative genomic and phylogenomic analyses for the entire Monogenea class. RESULTS Taxonomic identification was inconclusive, so two of the species were identified merely to the genus level. The complete mitogenomes of Sindiplozoon sp. and Eudiplozoon sp. are 14,334 bp and 15,239 bp in size, respectively. Paradiplozoon opsariichthydis (15,385 bp) is incomplete: an approximately 2000 bp-long gap within a non-coding region could not be sequenced. Each genome contains the standard 36 genes (atp8 is missing). G + T content and the degree of GC- and AT-skews of these three mitogenome (and their individual elements) were higher than in other monogeneans. nad2, atp6 and nad6 were the most variable PCGs, whereas cox1, nad1 and cytb were the most conserved. Mitochondrial phylogenomics analysis, conducted using concatenated amino acid sequences of all PCGs, indicates that evolutionary relationships of the three genera are: (Eudiplozoon, (Paradiplozoon, Sindiplozoon)); and of the three suborders: (Discocotylinea, (Microcotylinea, Gastrocotylinea)). These intergeneric relationships were also supported by the skewness and principal component analyses. CONCLUSIONS Our results show that nad2, atp6 and nad6 (fast-evolving) would be better candidates than cox1 (slow-evolving) for species identification and population genetics studies in Diplozoidae. Nucleotide bias and codon and amino acid usage patterns of the three diplozoid mitogenomes are more similar to cestodes and trematodes than to other monogenean flatworms. This unusual mutational bias was reflected in disproportionately long branches in the phylogram. Our study offsets the scarcity of molecular data for the subclass Polyopisthocotylea to some extent, and might provide important new insights into the evolutionary history of the three genera and three suborders.
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Affiliation(s)
- Dong Zhang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Shan G. Wu
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Ming Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Biolake, Wuhan, 430075 People’s Republic of China
| | - Jin Zhang
- Bio-Transduction Lab, Biolake, Wuhan, 430075 People’s Republic of China
| | - Rong Chen
- Bio-Transduction Lab, Biolake, Wuhan, 430075 People’s Republic of China
| | - Wen X. Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Gui T. Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
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Parrino V, Cappello T, Costa G, Cannavà C, Sanfilippo M, Fazio F, Fasulo S. Comparative study of haematology of two teleost fish (Mugil cephalus and Carassius auratus) from different environments and feeding habits. EUROPEAN ZOOLOGICAL JOURNAL 2018. [DOI: 10.1080/24750263.2018.1460694] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- V. Parrino
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - T. Cappello
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - G. Costa
- Department of Human Pathology in Adult and Developmental Age, University of Messina, Messina, Italy
| | - C. Cannavà
- Department of Human Pathology in Adult and Developmental Age, University of Messina, Messina, Italy
| | - M. Sanfilippo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - F. Fazio
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - S. Fasulo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
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Trujillo-González A, Becker JA, Hutson KS. Parasite Dispersal From the Ornamental Goldfish Trade. ADVANCES IN PARASITOLOGY 2018; 100:239-281. [PMID: 29753340 DOI: 10.1016/bs.apar.2018.03.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Goldfish, Carassius auratus Linnaeus, 1758, are immensely popular ornamental cyprinid fish, traded in more than 100 countries. For more than 500 years, human translocation has facilitated the spread of goldfish globally, which has enabled numerous and repeated introductions of parasite taxa that infect them. The parasite fauna assemblage of goldfish is generally well documented, but few studies provide evidence of parasite coinvasion following the release of goldfish. This review provides a comprehensive synopsis of parasites that infect goldfish in farmed, aquarium-held, native, and invasive populations globally and summarises evidence for the cointroduction and coinvasion of goldfish parasites. More than 113 species infect goldfish in their native range, of which 26 species have probably coinvaded with the international trade of goldfish. Of these, Schyzocotyle acheilognathi (Cestoda: Bothriocephalidae), Ichthyophthirius multifiliis (Ciliophora: Ichthyophthiriidae), Argulus japonicus (Crustacea: Argulidae), Lernaea cyprinacea (Crustacea: Ergasilidae), Dactylogyrus anchoratus, Dactylogyrus vastator and Dactylogyrus formosus (Monogenea: Dactylogyridae) are common to invasive goldfish populations in more than four countries and are considered a high risk of continued spread. Coinvasive parasites include species with direct and complex life cycles, which have successfully colonised new environments through utilisation of either new native hosts or suitable invasive hosts. Specifically, I. multifiliis, A. japonicus and L. cyprinacea can cause harm to farmed freshwater fish species and are important parasites to consider for biosecurity. These species may threaten other aquatic animal industries given their low host specificity and adaptable life histories. Future attention to biosecurity, management and border detection methods could limit the continued spread of exotic parasites from the ornamental trade of goldfish.
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Affiliation(s)
- Alejandro Trujillo-González
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.
| | - Joy A Becker
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, NSW, Australia
| | - Kate S Hutson
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
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Knytl M, Kalous L, Rylková K, Choleva L, Merilä J, Ráb P. Morphologically indistinguishable hybrid Carassius female with 156 chromosomes: A threat for the threatened crucian carp, C. carassius, L. PLoS One 2018; 13:e0190924. [PMID: 29360831 PMCID: PMC5779652 DOI: 10.1371/journal.pone.0190924] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 12/25/2017] [Indexed: 01/10/2023] Open
Abstract
The crucian carp Carassius carassius (Linnaeus, 1758), is native to many European freshwaters. Despite its wide distribution, the crucian carp is declining in both the number and sizes of populations across much of its range. Here we studied 30 individuals of a putative pure population from Helsinki, Finland. Despite clear external morphological features of C. carassius, an individual was of a higher ploidy level than the others. We therefore applied a set of molecular genetic (S7 nuclear and cytochrome b mitochondrial genes) and cytogenetic tools (sequential fluorescent 4’, 6-diamidino-2-phenylindole [DAPI], Chromomycin A3 [CMA3], C-banding and in situ hybridization [FISH] with both 5S and 28S ribosomal DNA probes) to determine its origin. While all examined characteristics of a diploid representative male (CCAHe2Fi) clearly corresponded to those of C. carassius, a triploid individual (CCAHe1Fi) was more complex. Phylogenetic analysis revealed that the nuclear genome of CCAHe1Fi contained three haploid sets: two C. gibelio and one C. carassius. However the mitochondrial DNA was that of C. gibelio, demonstrating its hybrid origin. The FISH revealed three strong (more intensive) 5S rDNA loci, confirming the triploid status, and an additional 24 weak (less intensive) signals were observed in the chromosome complement of CCAHe1Fi. On the other hand, only two strong and 16 weak 5S rDNA signals were visible on the chromosomes of the CCAHe2Fi male. 28S rDNA FISH revealed four strong signals in both CCAHe1Fi and CCAHe2Fi individuals. CMA3 staining revealed four to six CMA3-positive bands of CCAHe1Fi, while that of diploids contained only two to four. The fact that a polyploid hybrid Carassius female with a strong invasive potential may share morphological characters typical for endangered C. carassius highlights a need to combine genetic investigations of Carassius cryptic diversity with conservation measures of C. carassius in Europe.
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Affiliation(s)
- Martin Knytl
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
- * E-mail:
| | - Lukáš Kalous
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Kateřina Rylková
- Department of Genetics and Breeding, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Lukáš Choleva
- The Czech Academy of Sciences, Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, Liběchov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Juha Merilä
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Finland
| | - Petr Ráb
- The Czech Academy of Sciences, Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, Liběchov, Czech Republic
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Liu XL, Li XY, Jiang FF, Wang ZW, Li Z, Zhang XJ, Zhou L, Gui JF. Numerous mitochondrial DNA haplotypes reveal multiple independent polyploidy origins of hexaploids in Carassius species complex. Ecol Evol 2017; 7:10604-10615. [PMID: 29299242 PMCID: PMC5743492 DOI: 10.1002/ece3.3462] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 08/09/2017] [Accepted: 08/11/2017] [Indexed: 01/08/2023] Open
Abstract
Evolutionary trajectory and occurrence history of polyploidy have been extensively studied in plants, but they remain quite elusive in vertebrates. Here, we sampled and gathered 4,159 specimens of polyploid Carassius species complex including 1,336 tetraploids and 2,823 hexaploids from a large geographic scale (49 localities) across East Asia, and identified a huge number of 427 diverse haplotypes of mitochondrial control region, in which 74 haplotypes with total occurrence frequency up to 75.498% were shared by hexaploids and tetraploids. Significantly, these diverse haplotypes were clustered into four major lineages, and many haplotypes of hexaploids and tetraploids were intermixed in every lineage. Moreover, the evolutionary trajectory and occurrence history of four different lineages were revealed by a simplified time-calibrated phylogenetic tree, and their geographic distribution frequencies and haplotype diversity were also analyzed. Furthermore, lineage C and D were revealed to undergo population expansion throughout mainland China. Therefore, our current data indicate that hexaploids should undergo multiple independent polyploidy origins from sympatric tetraploids in the polyploid Carassius species complex across East Asia.
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Affiliation(s)
- Xiao-Li Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences University of the Chinese Academy of Sciences Wuhan China
| | - Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences University of the Chinese Academy of Sciences Wuhan China
| | - Fang-Fang Jiang
- State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences University of the Chinese Academy of Sciences Wuhan China
| | - Zhong-Wei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences University of the Chinese Academy of Sciences Wuhan China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences University of the Chinese Academy of Sciences Wuhan China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences University of the Chinese Academy of Sciences Wuhan China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences University of the Chinese Academy of Sciences Wuhan China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences University of the Chinese Academy of Sciences Wuhan China
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BIOCHEMISTRY PANEL REFERENCE INTERVALS FOR JUVENILE GOLDFISH (CARASSIUS AURATUS). J Zoo Wildl Med 2017; 48:776-785. [DOI: 10.1638/2015-0287.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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26
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Liu XL, Jiang FF, Wang ZW, Li XY, Li Z, Zhang XJ, Chen F, Mao JF, Zhou L, Gui JF. Wider geographic distribution and higher diversity of hexaploids than tetraploids in Carassius species complex reveal recurrent polyploidy effects on adaptive evolution. Sci Rep 2017; 7:5395. [PMID: 28710383 PMCID: PMC5511294 DOI: 10.1038/s41598-017-05731-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 06/01/2017] [Indexed: 01/08/2023] Open
Abstract
Polyploidy roles on adaptive evolution and ecological novelty have been extensively studied in plants but remained unclear in vertebrates owing to the rare polyploidy incidences. Here, a huge number of 3105 specimens in Carassius species complex including 2211 hexaploids and 894 tetraploids were sampled from 34 locations through mainland China. And hexaploids had wider geographic distribution than tetraploids especially in the areas with high altitude, high latitude and low annual precipitation. Then, an approximate 1050 bp transferrin (tf) fragments were amplified from all the samples, and 526 tf alleles were identified from a total of 37260 sequences at last. Intriguingly, higher nucleotide diversity of tf alleles in hexaploids than in tetraploids was revealed. Moreover, via phylogenetic analysis of tf alleles, potential origin center of Carassius species complex was deduced to be Yangtze River basin and hexaploids should undergo multiple independent polyploidy origins from sympatric tetraploids. These findings indicate that the hexaploids might possess stronger environmental adaptation and ecological novelty than the tetraploids, which provide an association paradigm of recurrent polyploidy and ecological context in polyploid vertebrates.
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Affiliation(s)
- Xiao-Li Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Fang-Fang Jiang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Zhong-Wei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Fan Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Jian-Feng Mao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, 430072, Hubei, China.
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Cheng ST, Herricks EE, Tsai WP, Chang FJ. Assessing the natural and anthropogenic influences on basin-wide fish species richness. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 572:825-836. [PMID: 27592326 DOI: 10.1016/j.scitotenv.2016.07.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 07/15/2016] [Accepted: 07/15/2016] [Indexed: 06/06/2023]
Abstract
Theory predicts that the number of fish species increases with river size in natural free-flowing rivers, but the relationship is lost under intensive exploitation of water resources associated with dams and/or landscape developments. In this paper, we aim to identify orthomorphic issues that disrupt theoretical species patterns based on a multi-year, basin-wide assessment in the Danshuei River Watershed of Taiwan. We hypothesize that multiple human-induced modifications fragment habitat areas leading to decreases of local fish species richness. We integrally relate natural and anthropogenic influences on fish species richness by a multiple linear regression model that is driven by a combination of factors including river network structure controls, water quality alterations of habitat, and disruption of channel connectivity with major discontinuities in habitat caused by dams. We found that stream order is a major forcing factor representing natural influence on fish species richness. In addition to stream order, we identified dams, dissolved oxygen deficiency (DO), and excessive total phosphorus (TP) as major anthropogenic influences on the richness of fish species. Our results showed that anthropogenic influences were operating at various spatial scales that inherently regulate the physical, chemical, and biological condition of fish habitats. Moreover, our probability-based risk assessment revealed causes of species richness reduction and opportunities for mitigation. Risks of species richness reduction caused by dams were determined by the position of dams and the contribution of tributaries in the drainage network. Risks associated with TP and DO were higher in human-activity-intensified downstream reaches. Our methodology provides a structural framework for assessing changes in basin-wide fish species richness under the mixed natural and human-modified river network and habitat conditions. Based on our analysis results, we recommend that a focus on landscape and riverine habitats and maintaining long-term monitoring programs are crucial for effective watershed management and river conservation plans.
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Affiliation(s)
- Su-Ting Cheng
- Department of Bioenvironmental Systems Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan, ROC
| | - Edwin E Herricks
- Department of Civil and Environmental Engineering, College of Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Avenue, Urbana, IL 61801, USA
| | - Wen-Ping Tsai
- Department of Bioenvironmental Systems Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan, ROC
| | - Fi-John Chang
- Department of Bioenvironmental Systems Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan, ROC.
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28
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Mori E, Menchetti M, Cantini M, Bruni G, Santini G, Bertolino S. Twenty years’ monitoring of a population of Italian crested newts Triturus carnifex: strong site fidelity and shifting population structure in response to restoration. ETHOL ECOL EVOL 2016. [DOI: 10.1080/03949370.2016.1236040] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Emiliano Mori
- Dipartimento di Scienze della Vita, Università di Siena, Via P.A. Mattioli 4, 53100 Siena, Italy
| | - Mattia Menchetti
- Dipartimento di Biologia, Università di Firenze, Via Madonna del Piano 6, 50019 Sesto Fiorentino (Firenze), Italy
| | - Matteo Cantini
- Dipartimento di Biologia, Università di Firenze, Via Madonna del Piano 6, 50019 Sesto Fiorentino (Firenze), Italy
| | - Giacomo Bruni
- Dipartimento di Biologia, Università di Firenze, Via Madonna del Piano 6, 50019 Sesto Fiorentino (Firenze), Italy
| | - Giacomo Santini
- Dipartimento di Biologia, Università di Firenze, Via Madonna del Piano 6, 50019 Sesto Fiorentino (Firenze), Italy
| | - Sandro Bertolino
- DISAFA, Università di Torino, Largo Paolo Braccini 2, 10095 Grugliasco (Torino), Italy
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29
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Abstract
Genomic DNAs isolated from crucian carp of four rivers, belonging to the family Cyprinidae was amplified by seven oligonucleotides primers. In the present study, we employed hierarchical clustering method in order to reveal genetic distances and variations. Crucian carp was acquired from Hangang river (CAH), Geumgang river (CAG), Nakdonggang river (CAN) and Yeongsangang river (CAY). The primer BION-12 generated the most loci (a total of 50) with an average of 10 in the CAY population. The primer BION-10 generated the least loci (a total of 19), with an average of 3.8 in the CAG population, in comparison to the other primers used. Seven oligonucleotides primers made 16.7 average no. per primer of specific loci in the CAH population, 7.4 in the CAG population, 8.6 in the CAN population and 0.9 in the CAY population, respectively. The specific loci generated by oligonucleotides primers revealed inter-individual-specific characteristics, thus disclosing DNA polymorphisms. The dendrogram obtained by the seven oligonucleotides primers indicates four genetic clusters. The genetic distance that displayed significant molecular differences was between individuals no.06 and no.08 from the CAG population (genetic distance = 0.036), while the genetic distance among the five individuals that displayed significant molecular differences was between individuals no.08 and no.09 from the CAG population (genetic distance = 0.088). With regard to average bandsharing value (BS) results, individuals from CAY population (0.985±0.009) exhibited higher bandsharing values than did individuals from CAH population (0.779±0.049) (P<0.05). Relatively, individuals of CAY population were fairly closely related to that of CAN location (genetic distance between two populations<0.016).
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Affiliation(s)
- Jun-Hyub Jeon
- Dept. of Aquatic Life Medicine, College of Ocean Science and Technology, Kunsan National University, Gunsan 54150, Korea
| | - Jong-Man Yoon
- Dept. of Aquatic Life Medicine, College of Ocean Science and Technology, Kunsan National University, Gunsan 54150, Korea
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30
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Jeffries DL, Copp GH, Lawson Handley L, Olsén KH, Sayer CD, Hänfling B. Comparing RADseq and microsatellites to infer complex phylogeographic patterns, an empirical perspective in the Crucian carp, Carassius carassius, L. Mol Ecol 2016; 25:2997-3018. [PMID: 26971882 DOI: 10.1111/mec.13613] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 02/19/2016] [Accepted: 02/29/2016] [Indexed: 12/16/2022]
Abstract
The conservation of threatened species must be underpinned by phylogeographic knowledge. This need is epitomized by the freshwater fish Carassius carassius, which is in decline across much of its European range. Restriction site-associated DNA sequencing (RADseq) is increasingly used for such applications; however, RADseq is expensive, and limitations on sample number must be weighed against the benefit of large numbers of markers. This trade-off has previously been examined using simulation studies; however, empirical comparisons between these markers, especially in a phylogeographic context, are lacking. Here, we compare the results from microsatellites and RADseq for the phylogeography of C. carassius to test whether it is more advantageous to genotype fewer markers (microsatellites) in many samples, or many markers (SNPs) in fewer samples. These data sets, along with data from the mitochondrial cytochrome b gene, agree on broad phylogeographic patterns, showing the existence of two previously unidentified C. carassius lineages in Europe: one found throughout northern and central-eastern European drainages and a second almost exclusively confined to the Danubian catchment. These lineages have been isolated for approximately 2.15 m years and should be considered separate conservation units. RADseq recovered finer population structure and stronger patterns of IBD than microsatellites, despite including only 17.6% of samples (38% of populations and 52% of samples per population). RADseq was also used along with approximate Bayesian computation to show that the postglacial colonization routes of C. carassius differ from the general patterns of freshwater fish in Europe, likely as a result of their distinctive ecology.
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Affiliation(s)
- Daniel L Jeffries
- Evolutionary Biology Group, School of Biological, Biomedical and Environmental Sciences, University of Hull, Hardy Building, Hull, HU6 7RX, UK.,Salmon & Freshwater Team, Cefas, Pakefield Road, Lowestoft, Suffolk, NR33 0HT, UK
| | - Gordon H Copp
- Salmon & Freshwater Team, Cefas, Pakefield Road, Lowestoft, Suffolk, NR33 0HT, UK.,Department of Life and Environmental Sciences, Faculty of Science and Technology, Bournemouth University, Poole, UK
| | - Lori Lawson Handley
- Evolutionary Biology Group, School of Biological, Biomedical and Environmental Sciences, University of Hull, Hardy Building, Hull, HU6 7RX, UK
| | - K Håkan Olsén
- School of Natural Science, Technology and Environmental Studies, Södertörn University, Alfred Nobels allé 7, Flemingsberg, Huddinge, 141 89, Sweden
| | - Carl D Sayer
- Environmental Change Research Centre, Department of Geography, University College London, Pearson Building, Gower Street, London, WC1E 6BT, UK
| | - Bernd Hänfling
- Evolutionary Biology Group, School of Biological, Biomedical and Environmental Sciences, University of Hull, Hardy Building, Hull, HU6 7RX, UK
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Tabata R, Kakioka R, Tominaga K, Komiya T, Watanabe K. Phylogeny and historical demography of endemic fishes in Lake Biwa: the ancient lake as a promoter of evolution and diversification of freshwater fishes in western Japan. Ecol Evol 2016; 6:2601-23. [PMID: 27066244 PMCID: PMC4798153 DOI: 10.1002/ece3.2070] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/16/2016] [Accepted: 02/22/2016] [Indexed: 01/21/2023] Open
Abstract
To elucidate the origins of the endemic fish of Lake Biwa, an ancient lake in Japan, and the role of the lake in the diversification of freshwater fish in western Japan, we established a molecular phylogenetic framework with an absolute time scale and inferred the historical demography of a large set of fish species in and around the lake. We used mtDNA sequences obtained from a total of 190 specimens, including 11 endemic species of Lake Biwa and their related species, for phylogenetic analyses with divergence time estimations and from a total of 2319 specimens of 42 species (including 14 endemics) occurring in the lake for population genetic analyses. Phylogenetic analysis suggested that some of the endemic species diverged from their closest relatives earlier (1.3–13.0 Ma) than the period in which the present environmental characteristics of the lake started to develop (ca. 0.4 Ma), whereas others diverged more recently (after 0.4 Ma). In contrast, historical demographic parameters suggested that almost all species, including endemic and nonendemic ones, expanded their populations after the development of the present lake environment. In phylogeographic analyses, common or very close haplotypes of some species were obtained from Lake Biwa and other regions of western Japan. The phylogenetic and historical demographic evidence suggests that there was a time lag between phylogenetic divergence and population establishment and that phenotypic adaptation of some endemic species to the limnetic environment occurred much later than the divergences of those endemic lineages. Population structure and phylogeographic patterns suggest that Lake Biwa has functioned not only as the center of adaptive evolution but also as a reservoir for fish diversity in western Japan.
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Affiliation(s)
- Ryoichi Tabata
- Graduate School of Science Kyoto University Kitashirakawa-Oiwakecho Sakyo Kyoto 606-8502 Japan
| | - Ryo Kakioka
- Graduate School of Science Kyoto University Kitashirakawa-Oiwakecho Sakyo Kyoto 606-8502 Japan; Research Institute for Humanity and Nature 457-4 Kamigamo-Motoyama Kita-ku Kyoto 603-8047 Japan
| | - Koji Tominaga
- Graduate School of Science Kyoto University Kitashirakawa-Oiwakecho Sakyo Kyoto606-8502 Japan; Kwansei Gakuin Senior High School 1-155 Uegahara-ichibancho Nishinomiya Hyogo 662-8501 Japan
| | - Takefumi Komiya
- Graduate School of Science Kyoto University Kitashirakawa-Oiwakecho Sakyo Kyoto 606-8502 Japan
| | - Katsutoshi Watanabe
- Graduate School of Science Kyoto University Kitashirakawa-Oiwakecho Sakyo Kyoto 606-8502 Japan
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Miyazaki Y, Teramura A, Senou H. Biodiversity data mining from Argus-eyed citizens: the first illegal introduction record of Lepomis macrochirus macrochirus Rafinesque, 1819 in Japan based on Twitter information. Zookeys 2016:123-33. [PMID: 27110154 PMCID: PMC4829683 DOI: 10.3897/zookeys.569.7577] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 01/28/2016] [Indexed: 11/15/2022] Open
Abstract
An apparent illegal introduction of Lepomismacrochirusmacrochirus from Yokohama City, Kanagawa Prefecture, Japan, is reported based on a juvenile specimen and a photograph of two adults collected on 14 June 2015 and deposited in the Kangawa Prefectural Museum of Natural History. The specimens and photographs were initially reported on the internet-based social networking site, Twitter. Two specimens of Carassiusauratus, including an aquarium form, were also reported at the same locality and date, suggesting that the illegal introductions originated from an aquarium release. Our report demonstrates an example of web data mining in the discipline of Citizen Science.
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Affiliation(s)
- Yusuke Miyazaki
- Kanagawa Prefectural Museum of Natural History, 499 Iryuda, Odawara-shi, Kanagawa 250-0031, Japan
| | - Akinori Teramura
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Hiroshi Senou
- Kanagawa Prefectural Museum of Natural History, 499 Iryuda, Odawara-shi, Kanagawa 250-0031, Japan
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Šimková A, Hyršl P, Halačka K, Vetešník L. Physiological and condition-related traits in the gynogenetic-sexual Carassius auratus complex: different investments promoting the coexistence of two reproductive forms? BMC Evol Biol 2015; 15:154. [PMID: 26245328 PMCID: PMC4545816 DOI: 10.1186/s12862-015-0438-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 07/29/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Carassius auratus complex is an extraordinary species complex including the diploid and polyploid forms exhibiting asexual and sexual reproduction modes. The coexistence of both forms in the same habitats is currently reported. The stable coexistence of asexual and sexual forms assumes some disadvantages for asexuals that balance the costs of sex. In our study, we hypothesized and tested the differences in physiological (including heamatological and immunological), growth-related, condition-related, and fitness-related traits between gynogenetic females and sexuals. RESULTS Our results revealed similar growth performance in gynogenetic females and sexuals measured by body size and weight, or expressed by condition factor. The energy allocation in reproduction measured by the relative size of gonads revealed no difference between gynogenetic and sexual females; in addition, both females in spawning expressed the same estradiol levels in blood plasma. We found a gender specific trade-off between investment in reproduction and immunocompetence (measured by the spleen-somatic index). Higher aerobic performance expressed by the heart index and higher oxygen-carrying capacity were found in sexual males, with increasing values before and during spawning. Our study evidenced significantly lower aerobic performance but higher oxygen-carrying capacity per erythrocyte in gynogenetic females when compared to sexuals. IgM production differed between gynogens and sexuals of C. auratus complex. CONCLUSIONS Our study indicates that a similar amount of energy is invested by both gynogenetic and sexual females of C. auratus complex in reproductive behaviour. We suggest that lower aerobic performance in gynogens may represent their physiological disadvantage balancing the cost of sexual reproduction. A trade-off between the number of erythrocytes and the oxygen-carrying capacity per erythrocyte in sexual males and gynogenetic females may contribute to the coexistence of gynogenetic and sexual forms. In addition, the differences in specific immunity between gynogens and sexuals may also reduce the evolutionary disadvantage of sexual reproduction. In conclusion, we propose that several mechanisms contribute to the coexistence of the gynogenetic-sexual C. auratus complex.
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Affiliation(s)
- Andrea Šimková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic.
| | - Pavel Hyršl
- Institute of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic.
| | - Karel Halačka
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Květná 8, 603 65, Brno, Czech Republic.
| | - Lukáš Vetešník
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Květná 8, 603 65, Brno, Czech Republic.
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Doğaç E, Ağdamar S, Keskin E, Tarkan AS, Yapıcı S, Acar Ü. Mitochondrial genetic variations of an introduced freshwater fish, goldfish Carassius auratus at the frontier between Europe and Asia (western Anatolia, Turkey): proximity to Europe rather than East Asia? Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4008-4014. [PMID: 25648924 DOI: 10.3109/19401736.2014.1003820] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Carassius auratus is one of the most significant ornamental and food fishes of the world that is globally distributed and well known. Although it is known to have existed at least for six decades and expanding its distribution range in Turkish waters, there is a dearth of information on genetic structure and variations of goldfish in Turkey. In this study, four mitochondrial genes (Cytochrome b, cytochrome oxidase II, 12S ribosomal RNA, and 16S ribosomal RNA) were used to infer the genetic variations of goldfish populations sampled from western part of Anatolia, Turkey. Three populations were clustered under three haplotypes for each gene and all haplotypes were special. Cytochrome b was found to have more variable sites and higher genetic diversity than other genes. According to the haplotype networks, goldfish populations in Turkey showed high level of genetic structuring and originated from the common haplotype known in native East Asian populations of the species. Extensive sampling scheme covering whole Anatolia should provide better understanding on the dispersal pattern of the species.
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Affiliation(s)
- Ersin Doğaç
- a Department of Medicinal and Aromatic Plants , Köyceğiz Vocational School, Muğla Sıtkı Koçman University , Muğla , Turkey
| | - Sevan Ağdamar
- b Faculty of Fisheries , Muğla Sıtkı Koçman University , Muğla , Turkey , and
| | - Emre Keskin
- c Department of Fisheries and Aquaculture, Faculty of Agriculture , Ankara University , Ankara , Turkey
| | - Ali Serhan Tarkan
- b Faculty of Fisheries , Muğla Sıtkı Koçman University , Muğla , Turkey , and
| | - Sercan Yapıcı
- b Faculty of Fisheries , Muğla Sıtkı Koçman University , Muğla , Turkey , and
| | - Ümit Acar
- b Faculty of Fisheries , Muğla Sıtkı Koçman University , Muğla , Turkey , and
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35
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Cho MY, Won KM, Kim JW, Jee BY, Park MA, Hong S. Detection of koi herpesvirus (KHV) in healthy cyprinid seed stock. DISEASES OF AQUATIC ORGANISMS 2014; 112:29-36. [PMID: 25392040 DOI: 10.3354/dao02784] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Koi herpesvirus (KHV) disease is a lethal disease in common carp, an important food fish in Asian countries, the seed of which is used in restocking programs for freshwater fishery management. We inspected apparently healthy seed stock of common carp Cyprinus carpio L. and Siberian crucian carp Carassius auratus for the presence of KHV using PCR-based diagnostic tests as a part of a stock enhancement program from 2009 to 2010 in Korea. Consequently, KHV was detected from 24 of 232 inspections with yearly detection percentages of 5.2% in 2009 and 15.5% in 2010 using PCR primer sets for TK or SphI-5 as recommended by the OIE Manual of Diagnostic Tests for Aquatic Animals. Results indicate that the SphI-5 primer set was slightly more sensitive than the TK primer set, as shown by a higher detection rate. To determine the genotype of the KHV strains detected in this study, ORF40-specific PCR amplification was conducted, and the PCR products from 6 samples showed 100% nucleotide sequence identity with a Japanese strain (GenBank accession number AP008984) but not with US (DG657948) and Israeli strains (DG177346). This report conclusively demonstrated the presence of KHV in externally healthy seed of common carp and Siberian crucian carp, indicating a possible risk that subclinically infected seed stock can be released with a potential threat to wild populations.
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Affiliation(s)
- Mi-Young Cho
- Aquatic Life Disease Control Division, National Fisheries Research and Development Institute, Busan 619-902, Korea
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36
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Expression characterization of testicular DMRT1 in both Sertoli cells and spermatogenic cells of polyploid gibel carp. Gene 2014; 548:119-25. [DOI: 10.1016/j.gene.2014.07.031] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 07/03/2014] [Accepted: 07/11/2014] [Indexed: 11/19/2022]
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Li XY, Zhang XJ, Li Z, Hong W, Liu W, Zhang J, Gui JF. Evolutionary history of two divergent Dmrt1 genes reveals two rounds of polyploidy origins in gibel carp. Mol Phylogenet Evol 2014; 78:96-104. [PMID: 24859683 DOI: 10.1016/j.ympev.2014.05.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 04/30/2014] [Accepted: 05/03/2014] [Indexed: 11/27/2022]
Abstract
Polyploidy lineages, despite very rare in vertebrates, have been proposed to play significant role in speciation and evolutionary success, but the occurrence history and consequences are still largely unknown. In this study, we used the conserved Dmrt1 to analyze polyploidy occurrence and evolutionary process in polyploid gibel carp. We identified two divergent Dmrt1 genes and respectively localized the two genes on three homologous chromosomes. Subsequently, the corresponding full-length cDNAs and genomic sequences of Dmrt1 genes were also characterized from the closely related species including Carassius auratus auratus and Cyprinus carpio, and their two Dmrt1 genes were respectively localized on two homologous chromosomes. Significantly, the evolutionary relationship analyses among cDNA and genomic DNA sequences of these Dmrt1 genes revealed two rounds of polyploidy origins in the gibel carp: an early polyploidy might result in an common tetraploid ancestor of Carassius auratus gibelio, Carassius auratus auratus and Cyprinus carpio before 18.49 million years ago (Mya), and an late polyploidy might occur from evolutionary branch of Carassius auratus at around 0.51 Mya, which lead to the occurrence of the hexaploid gibel carp. Therefore, this study provides clear genetic evidence for understanding occurrence time and historical process of polyploidy in polyploid vertebrates.
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Affiliation(s)
- Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Wei Hong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Wei Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Jun Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate University of the Chinese Academy of Sciences, Wuhan 430072, China.
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Wang J, Liu S, Xiao J, Tao M, Zhang C, Luo K, Liu Y. Evidence for the evolutionary origin of goldfish derived from the distant crossing of red crucian carp × common carp. BMC Genet 2014; 15:33. [PMID: 24628745 PMCID: PMC3995517 DOI: 10.1186/1471-2156-15-33] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 03/12/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Distant hybridization can generate transgressive hybrid phenotypes that lead to the formation of new populations or species with increased genetic variation. In this study, we produced an experimental hybrid goldfish (EG) by distant crossing of red crucian carp (Carassius auratus) × common carp (Cyprinus carpio) followed by gynogenesis. RESULTS We evaluated the phenotype, ploidy level, gonadal structure, and 5S rDNA of the EG. Diploid EG possessed a high level of genetic variation, which was stably inherited. In particular, the EG combined transgressive phenotypes, including a forked tail and shortened caudal peduncle, traits that are present in common goldfish. The EG and common goldfish share a number of morphological and genetic similarities. CONCLUSIONS Using the EG, we provide new evidence that goldfish originated from hybridization of red crucian carp × common carp.
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Affiliation(s)
| | - Shaojun Liu
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha 410081, China.
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39
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Tempo and mode of recurrent polyploidization in the Carassius auratus species complex (Cypriniformes, Cyprinidae). Heredity (Edinb) 2014; 112:415-27. [PMID: 24398883 DOI: 10.1038/hdy.2013.121] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 09/29/2013] [Accepted: 10/01/2013] [Indexed: 11/09/2022] Open
Abstract
Polyploidization is an evolutionarily rare but important mechanism in both plants and animals because it increases genetic diversity. Goldfish of the Carassius auratus species complex can be tetraploids, hexaploids and octaploids. Polyploidization events have occurred repeatedly in goldfish, yet the extent of this phenomenon and its phyletic history are poorly understood. We explore the origin, tempo and frequency of polyploidization in Chinese and Japanese goldfish using both mitochondrial (mtDNA) and nuclear DNA sequences from up to 1202 individuals including the outgroup taxon, Cyprinus carpio. Analyses of de novo nuclear gene data resolve two clusters of alleles and the pattern supports the prior hypothesis of an ancient allotetraploidization for Carassius. Alleles shared by tetraploid and hexaploid individuals indicate recent autoploidizations within the C. auratus complex. Sympatric tetraploids and hexaploids share mtDNA haplotypes and these frequently occur independently within six well-supported lineages and sublineages on a small spatial scale. Gene flow estimates (Fst values) indicate that hexaploids differ only slightly from sympatric tetraploids, if at all. In contrast, allopatric populations of tetraploids and hexaploids differ from one another to a far greater extent. Gene flow between sampled localities appears to be limited. Coalescence-based time estimations for hexaploids reveal that the oldest lineage within any sampled locality is around one million years old, which is very young. Sympatric, recurrent autoploidization occurs in all sampled populations of the C. auratus complex. Goldfish experience polyploidization events more frequently than any other vertebrate.
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40
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Cheng L, Zhang Y, Lu CY, Li C, Sun XW. Development and characterization of four moderate multiplex microsatellite panels in crucian carp (Carassius auratus). CONSERV GENET RESOUR 2013. [DOI: 10.1007/s12686-013-9917-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Kalous L, Rylková K, Bohlen J, Sanda R, Petrtýl M. New mtDNA data reveal a wide distribution of the Japanese ginbuna Carassius langsdorfii in Europe. JOURNAL OF FISH BIOLOGY 2013; 82:703-707. [PMID: 23398078 DOI: 10.1111/j.1095-8649.2012.03492.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In this study, records on the occurrence of the Japanese ginbuna Carassius langsdorfii from northern Germany, north-western Italy and southern Bosnia and Herzegovina are presented. The new findings, in addition to former studies reported in the Czech Republic and Greece, show that C. langsdorfii is much more widespread in Europe than was previously believed.
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Affiliation(s)
- L Kalous
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Science Prague, Praha, Czech Republic.
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Collares-Pereira M, Matos I, Morgado-Santos M, Coelho M. Natural Pathways towards Polyploidy in Animals: TheSqualius alburnoidesFish Complex as a Model System to Study Genome Size and Genome Reorganization in Polyploids. Cytogenet Genome Res 2013; 140:97-116. [DOI: 10.1159/000351729] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Podlesnykh AV, Apalikova OV, Brykov VA. Phylogenetic relationships of silver crucian carp in Carassius auratus complex based on mtDNA analysis. RUSS J GENET+ 2012. [DOI: 10.1134/s1022795412120113] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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45
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Jiang FF, Wang ZW, Zhou L, Jiang L, Zhang XJ, Apalikova OV, Brykov VA, Gui JF. High male incidence and evolutionary implications of triploid form in northeast Asia Carassius auratus complex. Mol Phylogenet Evol 2012; 66:350-9. [PMID: 23099150 DOI: 10.1016/j.ympev.2012.10.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 10/01/2012] [Accepted: 10/08/2012] [Indexed: 10/27/2022]
Abstract
Carassius auratus complex is believed to originate from East Eurasia and consist of diploid and triploid forms. Diploid form reproduces sexually, whereas triploid form possesses mixture modes of unisexual gynogenesis and sexual reproduction, which makes it a unique case to study evolutionary issues among vertebrates. In this study, we identified 337 triploid individuals from 386 specimens of Carassius auratus complex sampled from 4 different sites of Xingkai Lake and Suifen River on the northeast Asia transboundary areas of Russia and China, and found that triploids were ubiquitous, whereas diploids existed only in SII site of Suifen River. Triploid males were detected in all surveyed sites, and an unusually high triploid male incidence (23%) was found in the Chinese reach of Suifen River. Then, nuclear and cytoplasmic markers were used to analyze their genetic diversity and phylogenetic relationship. A total of 61 distinct tf alleles and 35 mtDNA CR haplotypes were revealed. Higher genetic diversity and divergence were confirmed in triploids than in diploids, and identical genetic background between triploid males and females was demonstrated. Moreover, evolutionary implications and roles of triploid males were suggested in population proliferation and diversity creation of the triploid form.
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Affiliation(s)
- Fang-Fang Jiang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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46
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Cheng L, Liang LQ, Sun XW. The complete mitochondrial genome of the crucian carp, Carassius carassius (Cypriniformes, Cyprinidae). MITOCHONDRIAL DNA 2012; 23:350-351. [PMID: 22708851 DOI: 10.3109/19401736.2012.690753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The complete mitochondrial genome of Carassius carassius was determined to be 16,597 bp long circular molecule with a typical gene arrangement of vertebrate mitochondrial DNA. Its control region contains two copies of unit (TTCYCAATATAA) at 3' ends, which has never been reported before for Carassius species. Phylogenetic trees based on 12 protein-coding genes on heavy strand confirmed that the complete mtDNA sequence of crucian carp was reported in this study for the first time.
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Affiliation(s)
- Lei Cheng
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, People's Republic of China
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47
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Wouters J, Janson S, Lusková V, Olsén KH. Molecular identification of hybrids of the invasive gibel carp Carassius auratus gibelio and crucian carp Carassius carassius in Swedish waters. JOURNAL OF FISH BIOLOGY 2012; 80:2595-2604. [PMID: 22650435 DOI: 10.1111/j.1095-8649.2012.03312.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Both mitochondrial DNA sequence and two nuclear microsatellite markers were used to confirm the identity of the first record of Carassius auratus gibelio in the western (Swedish) Baltic Sea region. A total of 49 fishes were analysed, where 22 were from three Swedish sites connected to the Baltic Sea. The D-loop mitochondrial DNA sequences showed that 16 of 22 Swedish fishes were related to C. a. gibelio. The phylogenetic analysis of these sequences showed that these fish are probably not native, but represent different lineages of C. a. gibelio from China, Japan and Russia. All except three of these 16 fishes had microsatellite alleles suggesting hybridization with Carassius carassius. These findings suggest that a cryptic invasion of C. a. gibelio might be in progress.
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Affiliation(s)
- J Wouters
- School of Life Sciences, Södertörn University, SE-141 89 Huddinge, Sweden.
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48
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Jakovlić I, Gui JF. Recent invasion and low level of divergence between diploid and triploid forms of Carassius auratus complex in Croatia. Genetica 2011; 139:789-804. [PMID: 21644055 DOI: 10.1007/s10709-011-9584-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Accepted: 05/23/2011] [Indexed: 10/18/2022]
Abstract
Carassius auratus is an invasive species in European waters, comprising a complex of diploid and polyploid forms with different modes of reproduction. However, the evolutionary history and relationships between the diploids and polyploids are still unresolved. In this study, 51.5% diploids and 48.5% triploids, including four triploid males, were discovered among the 363 individuals sampled in Croatia. We used eight microsatellite loci and mitochondrial displacement loop sequences to analyze the structure and origin of populations; and to attempt to infer the evolutionary history of the two different forms in Croatia. Microsatellite analyses revealed high allelic and clonal diversity, corroborating that high propagule vectors can compensate for the negative effects of genetic bottlenecks in successful invasive species. The absence of significant population structuring confirmed recent origin and rapid spreading of populations. No evidence was found for the existence of native European populations. Distances between individuals using both nuclear and mtDNA markers revealed the absence of substantial clustering on the ploidy level, while the split between the different ploidies on population level was only partial, suggesting that the reproductive isolation between the two forms is either of a very recent origin, or that there exists uni-, or bidirectional gene flow between the diploid and triploid forms.
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Affiliation(s)
- Ivan Jakovlić
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, 430072 Wuhan, People's Republic of China
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49
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Kalous L, Knytl M. Karyotype diversity of the offspring resulting from reproduction experiment between diploid male and triploid female of silver Prussian carp,Carassius gibelio(Cyprinidae, Actinopterygii). FOLIA ZOOLOGICA 2011. [DOI: 10.25225/fozo.v60.i2.a5.2011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Lukáš Kalous
- Czech University of Life Sciences Prague, Faculty of Agrobiology, Food and Natural Resources, Department of Zoology and Fisheries, 165 21 Praha 6-Suchdol, Czech Republic
- Joint Laboratory of Genetics, Physiology and Reproduction of Fishes of Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, v.v.i., 277 21 Liběchov and University of South Bohemia in České Budějovice, Research Institute of Fish Culture and Hydrobiology, 389 25 Vodňany, Czech Republic
| | - Martin Knytl
- Czech University of Life Sciences Prague, Faculty of Agrobiology, Food and Natural Resources, Department of Zoology and Fisheries, 165 21 Praha 6-Suchdol, Czech Republic
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