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Ősz Á, Horváth Á, Hoitsy G, Kánainé Sipos D, Keszte S, Sáfrány AJ, Marić S, Palkó C, Tóth B, Urbányi B, Kovács B. The genetic status of the Hungarian brown trout populations: exploration of a blind spot on the European map of Salmo trutta studies. PeerJ 2018; 6:e5152. [PMID: 30258703 PMCID: PMC6152457 DOI: 10.7717/peerj.5152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 06/11/2018] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Analyses of the control region sequences of European brown trout populations' mitrochondrial DNA have revealed five main evolutionary lineages (Atlantic, Danubian, Mediterranean, Adriatic, Marble) mostly relating to the main water basins; however, the hybridization between lineages were increasingly reported. Due to the hydrogeography of Hungary, wild populations should theoretically belong to the Danubian lineage, however, this has not been verified by genetic studies. METHODS In our study multiple molecular marker sets (mitochondrial sequence, microsatellites, PCR-RFLP of nuclear markers and sex marker) were used to investigate the genetic composition and population genetics of the brown trout populations in two broodstocks, six wild streams in Hungary and one Serbian population. RESULTS The admixture of Atlantic and Danubian lineages in these populations, except the Serbian population with pure Danubian origin, was observed by control region sequences of mitochondrial DNA and PCR-RFLP markers in the nuclear genome, and one unpublished Danubian haplotype was found in Hungarian populations. A sex-specific marker revealed equal gender ratio in broodstocks and Kemence stream, whereas in other wild streams the proportion of female individuals were less than 50%. Structure and principal component analyses based on the alleles of microsatellite loci also revealed overlapping populations, however the populations were still significantly different from each other and were mostly in Hardy-Weinberg equilibrium. DISCUSSION Stocking and migration can have a significant genetic impact on trout populations of wild streams, however there are no guidelines or common practices for stocking of small streams in Hungary, thus the genetic background of these populations should be considered when developing conservation actions.
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Affiliation(s)
- Ágnes Ősz
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Hungary
| | - Ákos Horváth
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Hungary
| | | | - Dóra Kánainé Sipos
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Hungary
| | - Szilvia Keszte
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Hungary
| | - Anna Júlia Sáfrány
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Hungary
| | - Saša Marić
- Institute of Zoology, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Csaba Palkó
- Department of Animal Nutrition, Institute of Animal Science, Faculty of Agricultural and Food Sciences, Széchenyi István University, Mosonmagyaróvár, Hungary
| | - Balázs Tóth
- Danube-Ipoly National Park Directorate, Budapest, Hungary
| | - Béla Urbányi
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Hungary
| | - Balázs Kovács
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Hungary
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Kawamura K, Furukawa M, Kubota M, Harada Y. Effects of stocking hatchery fish on the phenotype of indigenous populations in the amago salmon Oncorhynchus masou ishikawae in Japan. JOURNAL OF FISH BIOLOGY 2012; 81:94-109. [PMID: 22747806 DOI: 10.1111/j.1095-8649.2012.03315.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The expression of colour marks (parr marks, red and black spots) of the amago salmon Oncorhynchus masou ishikawae was compared with microsatellite information, to see the effects of stocking hatchery fish on the phenotype of indigenous populations, which face extinction through extensive stocking. A Bayesian-based assignment test suggested introgression of two exotic clusters into one indigenous cluster in the stocked area and its vicinity. The number of parr marks was significantly higher in one hatchery-origin population, which exclusively comprised one exotic cluster. An increased number of red spots in stocked hatchery fish was probably a consequence of hatchery feeding conditions. The number of black spots was correlated with body size in many populations, except for hatchery and heavily introgressed populations. Coefficients of correlation and regression of black spots with body size, which were largest in indigenous populations, decreased with an increase of introgression by hatchery fish. As indigenous populations have low genetic diversity with high relatedness, it was inferred that the height of correlation and regression coefficients in black spots is caused by high genetic homogeneity and fixation of alleles in loci related to the increase of black spots, both of which might have collapsed with introgression by hatchery fish. These results suggest the possibility that introgression by stocked fish causes a change of phenotype in indigenous populations.
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Affiliation(s)
- K Kawamura
- Bioresources, Mie University, Kurimamachiya 1577, Tsu, Mie 514-8507, Japan.
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Wilson WD, Turner TF. Phylogenetic analysis of the Pacific cutthroat trout (Oncorhynchus clarki ssp.: Salmonidae) based on partial mtDNA ND4 sequences: A closer look at the highly fragmented inland species. Mol Phylogenet Evol 2009; 52:406-15. [DOI: 10.1016/j.ympev.2009.03.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Revised: 03/17/2009] [Accepted: 03/23/2009] [Indexed: 10/20/2022]
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Chang HW, Yang JI, Huang HY, Gwo JC, Su YF, Wen CH, Chou YC. A novel growth hormone 1 gene-derived probe for Oncorhynchus masou formosanus distinguished from the Oncorhynchus subspecies. Mol Cell Probes 2009; 23:103-6. [PMID: 19162176 DOI: 10.1016/j.mcp.2008.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Revised: 12/26/2008] [Accepted: 12/29/2008] [Indexed: 10/21/2022]
Abstract
Traditional mitochondrial 16S rRNA is commonly used in many species identification studies. However, it is difficult to apply to the phylogenetic studies among the Oncorhynchus subspecies, which is a crucial need for management purposes for Oncorhynchus masou formosanus, Taiwan salmon. In this study, we have developed an improved species identification method for Taiwan salmon distinguished with other Oncorhynchus subspecies tested by exploiting PCR for growth hormone (GH) 1 gene. By comparing DNA sequences for GH1 from 11 species of Oncorhynchus subspecies we designed novel PCR primers that exploit differences between Taiwan salmon and other Oncorhynchus subspecies. Therefore, the technique is an important tool in the management of populations of the endangered land-locked Taiwan salmon preventing from their possible hybrids with other Oncorhynchus subspecies once tested.
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Affiliation(s)
- Hsueh-Wei Chang
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
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Esteve M, McLennan DA. The Phylogeny of Oncorhynchus (Euteleostei: Salmonidae) Based on Behavioral and Life History Characters. COPEIA 2007. [DOI: 10.1643/0045-8511(2007)2007[520:tpooes]2.0.co;2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Saito Y, Edpalina RR, Abe S. Isolation and characterization of salmonid telomeric and centromeric satellite DNA sequences. Genetica 2006; 131:157-66. [PMID: 17180439 DOI: 10.1007/s10709-006-9126-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Accepted: 11/17/2006] [Indexed: 10/23/2022]
Abstract
Satellite DNA clones with a 37 bp repeat unit were obtained from BglII-digested genomic DNA of Masu salmon (Oncorhynchus masou) and Chum salmon (O. keta). Fluorescence in situ hybridization (FISH) analysis with the isolated clones as a probe showed that these repetitive sequences were localized in the telomeric regions of chromosomes in both species. Southern and dot blot analyses suggested conservation of homologous sequences with similar repeat unit in other salmonids including the species of the genus Oncorhynchus and Salvelinus, but lack or scarcity of such sequences in the genus Hucho and Salmo. Similarly, polymerase chain reaction (PCR)-based cloning of satellite DNA referring to a reported Rainbow trout (O. mykiss) centromeric sequence was successful for the Oncorhynchus, Salvelinus and Hucho species. The obtained satellite DNA clones were localized with FISH in the centromeric regions of chromosomes of the species from these three genera. Although PCR cloning of the centromeric satellite DNA had failed in the Salmo species due to some base changes in the priming sites, dot blot hybridization analysis suggested conservation of homologous satellite DNA in the genus Salmo as in the other three genera. In the neighbor-joining tree of cloned centromeric satellite DNA sequences, the genus Oncorhynchus and Salvelinus formed adjacent clades, and the clade of the genus Hucho included the reported centromeric sequence of the genus Salmo. Conservation pattern and molecular phylogeny of the telomeric and centromeric satellite DNA sequences isolated herein support a close phylogenetic relationship between the genus Oncorhynchus and Salvelinus and between the Salmo and Hucho.
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Affiliation(s)
- Yasuhiro Saito
- Division of Marine Life Science, Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato, Hakodate, 041-8611, Japan
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Abstract
The Japanese medaka fish Oryzias latipes has an XX/XY sex-determination system. The Y-linked sex-determination gene DMY is a duplicate of the autosomal gene DMRT1, which encodes a DM-domain-containing transcriptional factor. DMY appears to have originated recently within Oryzias, allowing a detailed evolutionary study of the initial steps that led to the new gene and new sex-determination system. Here I analyze the publicly available DMRT1 and DMY gene sequences of Oryzias species and report the following findings. First, the synonymous substitution rate in DMY is 1.73 times that in DMRT1, consistent with the male-driven evolution hypothesis. Second, the ratio of the rate of nonsynonymous nucleotide substitution (d(N)) to that of synonymous substitution (d(S)) is significantly higher in DMY than in DMRT1. Third, in DMRT1, the d(N)/d(S) ratio for the DM domain is lower than that for non-DM regions, as expected from the functional importance of the DM domain. But in DMY, the opposite is observed and the DM domain is likely under positive Darwinian selection. Fourth, only one characteristic amino acid distinguishes all DMY sequences from all DMRT1 sequences, suggesting that a single amino acid change may be largely responsible for the establishment of DMY as the male sex-determination gene in medaka fish.
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Affiliation(s)
- Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA.
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Crespi BJ, Fulton MJ. Molecular systematics of Salmonidae: combined nuclear data yields a robust phylogeny. Mol Phylogenet Evol 2004; 31:658-79. [PMID: 15062801 DOI: 10.1016/j.ympev.2003.08.012] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2003] [Revised: 08/15/2003] [Indexed: 11/21/2022]
Abstract
The phylogeny of salmonid fishes has been the focus of intensive study for many years, but some of the most important relationships within this group remain unclear. We used 269 Genbank sequences of mitochondrial DNA (from 16 genes) and nuclear DNA (from nine genes) to infer phylogenies for 30 species of salmonids. We used maximum parsimony and maximum likelihood to analyze each gene separately, the mtDNA data combined, the nuclear data combined, and all of the data together. The phylogeny with the best overall resolution and support from bootstrapping and Bayesian analyses was inferred from the combined nuclear DNA data set, for which the different genes reinforced and complemented one another to a considerable degree. Addition of the mitochondrial DNA degraded the phylogenetic signal, apparently as a result of saturation, hybridization, selection, or some combination of these processes. By the nuclear-DNA phylogeny: (1) (Hucho hucho, Brachymystax lenok) form the sister group to (Salmo, Salvelinus, Oncorhynchus, H. perryi); (2) Salmo is the sister-group to (Oncorhynchus, Salvelinus); (3) Salvelinus is the sister-group to Oncorhynchus; and (4) Oncorhynchus masou forms a monophyletic group with O. mykiss and O. clarki, with these three taxa constituting the sister-group to the five other Oncorhynchus species. Species-level relationships within Oncorhynchus and Salvelinus were well supported by bootstrap levels and Bayesian analyses. These findings have important implications for understanding the evolution of behavior, ecology and life-history in Salmonidae.
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Affiliation(s)
- Bernard J Crespi
- Behavioural Ecology Research Group, Department of Biosciences, Simon Fraser University, 8888 University Drive, Burnaby, BC, Canada V5A 1S6.
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Abstract
Abstract
The Japanese medaka fish Oryzias latipes has an XX/XY sex-determination system. The Y-linked sex-determination gene DMY is a duplicate of the autosomal gene DMRT1, which encodes a DM-domain-containing transcriptional factor. DMY appears to have originated recently within Oryzias, allowing a detailed evolutionary study of the initial steps that led to the new gene and new sex-determination system. Here I analyze the publicly available DMRT1 and DMY gene sequences of Oryzias species and report the following findings. First, the synonymous substitution rate in DMY is 1.73 times that in DMRT1, consistent with the male-driven evolution hypothesis. Second, the ratio of the rate of nonsynonymous nucleotide substitution (dN) to that of synonymous substitution (dS) is significantly higher in DMY than in DMRT1. Third, in DMRT1, the dN/dS ratio for the DM domain is lower than that for non-DM regions, as expected from the functional importance of the DM domain. But in DMY, the opposite is observed and the DM domain is likely under positive Darwinian selection. Fourth, only one characteristic amino acid distinguishes all DMY sequences from all DMRT1 sequences, suggesting that a single amino acid change may be largely responsible for the establishment of DMY as the male sex-determination gene in medaka fish.
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Affiliation(s)
- Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
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Hurst CD, Bartlett SE, Davidson WS, Bruce IJ. The complete mitochondrial DNA sequence of the Atlantic salmon, Salmo salar. Gene 1999; 239:237-42. [PMID: 10548724 DOI: 10.1016/s0378-1119(99)00425-4] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The complete sequence of the Atlantic salmon (Salmo salar) mitochondrial genome has been determined. The entire sequence is 16665 base pairs (bp) in length, with a gene content (13 protein-coding, two ribosomal RNA [rRNA] and 22 transfer RNA [tRNA] genes) and order conforming to that observed in most other vertebrates. Base composition and codon usage have been detailed. Nucleotide and derived amino acid sequences of the 13 protein-coding genes from Atlantic salmon have been compared with their counterparts in rainbow trout. A putative structure for the origin of L-strand replication (O(L)) is proposed, and sequence features of the control region (D-loop) are described.
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Affiliation(s)
- C D Hurst
- School of Chemical and Life Sciences, University of Greenwich, London, UK.
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Oakley TH, Phillips RB. Phylogeny of salmonine fishes based on growth hormone introns: Atlantic (Salmo) and Pacific (Oncorhynchus) salmon are not sister taxa. Mol Phylogenet Evol 1999; 11:381-93. [PMID: 10196079 DOI: 10.1006/mpev.1998.0599] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Though salmonid fishes are a well-studied group, phylogenetic questions remain, especially with respect to genus-level relationships. These questions were addressed with duplicate growth hormone (GH) introns. Intron sequences from each duplicate gene yielded phylogenetic trees that were not significantly different from each other in topology. Statistical tests supported validity of the controversial monotypic genus Parahucho, monophyly of Oncorhynchus, and inclusion of Acantholingua ohridana within Salmo. Suprisingly, GH1 intron C (GH1C) did not support the widely accepted hypothesis that Oncorhynchus (Pacific salmon and trout) and Salmo (Atlantic salmon and trout) are sibling genera; GH2C was ambiguous at this node. Previously published data were also examined for support of Salmo and Oncorhynchus as sister taxa and only morphology showed significant support. If not sister taxa, the independent evolution of anadromy-the migration to sea and return to freshwater for spawning-is most parsimonious. While there was incongruence with and among published data sets, the GH1C intron phylogeny was the best hypothesis, based on currently available molecular data.
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Affiliation(s)
- T H Oakley
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, 53201, USA.
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McKay SJ, Nakayama I, Smith MJ, Devlin RH. Genetic Relationship between Masu and Amago Salmon Examined through Sequence Analysis of Nuclear and Mitochondrial DNA. Zoolog Sci 1998. [DOI: 10.2108/zsj.15.971] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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