Genetic history of salmonid fishes of the genus Oncorhynchus (original) (raw)
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Evolutionary genetic analysis of Pacific salmon and trout (Oncorhynchus)
1997
This thesis addresses the topic of molecular evolution at the genus, species, and * gene levels. DNA sequence analysis was used to resolve taxonomic and systematic problems in the salmonid genus Oncorhynchus and to examine the evolution of duplicated genes. The evolution of Pacific salmon and trout has been intensively I thank the following agencies for financial support: Fisheries and Oceans
Preliminary studies on evolutionary of genetic markers in the salmonid species
This study deals with evolutionary genetics of salmonids populations, with the special emphasis on the roles of migration, random genetic drift, mutation, and natural selection affecting the patterns of molecular variation across contemporary and historical time scales. Studies of nuclear DNA and mitochondrial genomic variation supported the hypothesis that salmonid populations differ from the geographical regions, indicating for genetic diversity between populations. This study were used some genes for nuclear DNA genomic and mitochondrial DNA genomic for evaluation of the rate diversity. We suggest that the region of geographically is important to rate of diversity between and within populations. Were used marker genetic techniques such as the microsatellites markers, SNPs, RFLP, and some genes from mitochondrial genomic that engaged on the rate of diversity in populations of salmonids. Between and within population of S. salar and S. trutta were found single mutation by SNPs technique. RFLP analysis by nuclear DNA genomic such as microsatellites and growth hormone gene and also mitochondrial DNA genomic as cytochrome b and 12S rRNA gene and markers also showed the low variation between and within salmonids populations
Genetic divergence among distinct phenotypes of sockeye salmon (Oncorhynchus nerka)
A long-standing goal of evolutionary biology is to understand the factors that drive population divergence and speciation, and phenotypic differentiation within a species is considered an intermediate step towards speciation. The overarching aim of this thesis was to compare patterns of neutral genetic differentiation against patterns of phenotypic differentiation among and within sockeye salmon (Oncorhynchus nerka) ecotypes. Chapter 1 compares genetic and phenotypic data from populations of beach and stream ecotypes of sockeye salmon in Little Togiak Lake, Alaska. Genetic data from 12 microsatellite markers were collected for three consecutive years of samples from two creeks and four beaches in Little Togiak Lake. Differentiation was high and significant between beach and creek samples in all years (FST = 0.020 - 0.066). Within ecotypes, beach spawners showed low but significant differentiation (FST =0.007), whereas stream spawners showed higher differentiation (FST=0.038). Genetic variability was also higher in beach spawners (HE=0.789) than in creek spawners (HE =0.730). Clustering analyses by the likelihood program STRUCTURE supported the hypothesis of high gene flow among beach populations and relative reproductive isolation between the creeks. In addition, beach-origin males that strayed into the creeks had shallow body depths, whereas stream-origin males that strayed onto the beaches were deeper-bodied than the creek spawners yet more shallow-bodied than other beach spawners. In Chapter 2, we examined levels of differentiation in morphological traits (age at maturity, body length at age, and body depth) and spawning timing for sockeye salmon from three geographically proximate creeks in Lake Aleknagik, Alaska. We then compared the phenotypic differentiation, measured as PST, to neutral microsatellite marker differentiation, measured as FST. No correlations were apparent between the obtained PST and FST values, and PST values were generally significantly different from zero (PST = -0.014 to 0.31) whereas FST values were not (FST = -0.0004 to 0.0016). The insignificant pairwise FST values between creek samples indicated that gene flow occurs among creeks, assuming the creek populations have reached migration-drift equilibrium. The significant phenotypic differentiation, however, suggested that strong divergent selection occurs on the phenotypic traits despite any homogenizing effects of gene flow.
Genetic Analysis of Snake River Sockeye Salmon (Oncorhynchus Nerka), 2003 Technical Report
2003
Primer sequences used to PCR amplify specific mitochondrial gene regions in Oncorhynchus nerka……………………...…... 46 Appendix B. Restriction endonucleases used to digest PCR amplified mitochondrial gene regions in this study. Number of polymorphic patterns observed indicated by (#)…………..…... 47 Appendix C. Summary of simple haplotypes by gene region and restriction endonuclease for each population……………………………... 48 Appendix D. Appendix D. Composite haplotypes and their simple haplotype digest scores sorted by occurrence (number of samples)……………………………………………………….. 50 Appendix E. Composite mtDNA haplotypes H1-H35 (Table 2) and their frequencies observed among 1720 O. nerka from 40 populations in the Pacific Northwest. Form types are resident kokanee (K), anadromous sockeye (S) and unknown (U)…………………………………………………………...… 51 Appendix F. Composite mtDNA haplotypes (H#, refer to Table 2) and their frequencies observed among 684 O. nerka from six Redfish Lake sample populations, separated by collection date. Form types are resident kokanee (K), anadromous sockeye (S) and unknown (U)…………………………………………………... 55 Appendix F. Composite mtDNA haplotypes (H#, refer to Table 2) and their frequencies observed among O. nerka from Idaho and Washington sample populations, separated by collection date. Form types are resident kokanee (K), anadromous sockeye (S) and unknown (U)……………………………………………....
Russian Journal of Marine Biology, 2017
⎯This study focuses on the strategy for the conservation of masu salmon, Oncorhynchus masou, in the northern part of the species range (via the masu populations in Sakhalin Oblast), based on data of its population structure. It is shown that masu populations that inhabit different rivers genetically differ from each other in allele frequencies at microsatellite markers. In the Naiba River basin, at least two genetically distinct masu populations exist: in the upper reaches and in a tributary, the Bolshoy Takoy River. The masu populations on Iturup Island significantly differ from those on Sakhalin Island; within Sakhalin, the masu salmon from the Chernaya River in the southwestern part of the island is genetically distinct from the southeastern Sakhalin and Aniva Bay populations. The genetic diversity of Iturup populations is substantially lower than that on Sakhalin, probably due to their small sizes. The measures for the conservation and recovery of masu salmon populations should be based primarily on their own genetic resources, or, in the case of a lack of spawners, on the base populations of their ecological/geographical region. In the latter case, masu populations of large rivers can be considered as base ones: for southeastern Sakhalin, this is masu salmon of the Naiba River; for Aniva Bay, this is masu salmon of the Lyutoga River. Transplantation of fish, fertilized eggs, or any other genetic material from a population that is different genetically and inhabits the waters with different ecological gradients should be strongly restricted. The formosan masu salmon from Taiwan Island is studied as an example of a strict genetic isolate.
Transactions of the …, 2004
Seventeen populations of Oncorhynchus mykiss were analyzed for mitochondrial haplotype diversity through either polymerase chain reaction-restriction fragment length polymorphism analysis or mitochondrial DNA sequencing. Six new mitochondrial haplotypes were observed among these populations, five in steelhead and one in Harney Basin rainbow trout. Although no distinct patterns were observed between steelhead and rainbow trout with mitochondrial DNA sequencing, Harney Basin rainbow trout populations from southeastern Oregon exhibited a high frequency of a unique new haplotype designated MYS22. Fourteen of 17 individuals within the Harney Basin rainbow trout populations possessed this haplotype. Additionally, the mitochondrial DNA haplotypes of six westslope cutthroat trout O. clarki lewisi were observed among 90 steelhead from the Tucannon River, Washington, a river in which no native or introduced cutthroat trout have been documented. Analysis of other introduced hatchery and wild stocks of steelhead and rainbow trout from throughout the interior Pacific Northwest revealed only rainbow trout and steelhead mitochondrial haplotypes. Analysis of 90 wild Tucannon River steelhead using 16 nuclear DNA markers detected only one individual with a single nuclear allele consistent with westslope cutthroat trout, although the marker may be a rare rainbow trout or steelhead nuclear allele. This suggests that a hybridization event of ancient origin probably occurred within the Tucannon River basin. This hybridization event may have occurred between Tucannon River steelhead and a now extinct native population of westslope cutthroat trout that probably arrived as a result of late Wisconsin glacial outburst floods (Missoula Floods) occurring 19,000-10,000 years before the present.
Copeia, 2007
There is no consensus between morphological and molecular data concerning the relationships within the Pacific basin salmon and trout clade Oncorhynchus. In this paper we add another source of characters to the discussion. Phylogenetic analysis of 39 behavioral and life history traits produced one tree structured (O. clarki (O. mykiss (O. masou (O. kisutch (O. tshawytscha (O. nerka (O. keta, O. gorbuscha))))))). This topology is congruent with the phylogeny based upon Bayesian analysis of all available nuclear and mitochondrial gene sequences, with the exception of two nodes: behavior supports the morphological data in breaking the sister-group relationship between O. mykiss and O. clarki, and between O. kisutch and O. tshawytscha. The behavioral traits agreed with molecular rather than morphological data in placing O. keta as the sister-group of O. gorbuscha. The behavioral traits also resolve the molecular-based ambiguity concerning the placement of O. masou, placing it as sister to the rest of the Pacific basin salmon. Behavioral plus morphological data placed Salmo, not Salvelinus, as more closely related to Oncorhynchus, but that placement was only weakly supported and awaits collection of missing data from enigmatic species such as the lake trout, Salvelinus namaycush. Overall, the phenotypic characters helped resolve ambiguities that may have been created by molecular introgression, while the molecular traits helped resolve ambiguities introduced by phenotypic homoplasy. It seems reasonable therefore, that systematists can best respond to the escalating biodiversity crisis by forming research groups to gather behavioral and ecological information while specimens are being collected for morphological and molecular analysis.
Zoological Science, 2010
The population genetic structure and phylogeography of masu salmon were investigated by using variation in the mitochondrial NADH dehydrogenase subunit 5 gene (ND5) and six polymorphic microsatellite loci among a total of 895 fish representing 18 populations collected from Japan (9), Russia (7), and Korea (2) from 2000 to 2008. An analysis of ND5 nucleotide sequences revealed 22 variable sites in about 560 bp in the 5' half of the gene, which defined 20 haplotypes, including some associated with geographical regions. Haplotype and nucleotide diversities were greater in the populations in Japan and Korea than in those in Russia, indicating greater genetic diversity in the Japanese and Korean populations than in the Russian populations. All the microsatellite loci examined showed a high level of variation, but the expected heterozygosity indicated a similar level of genetic diversity among the populations of the three regions, contrary to the results for ND5. However, AMOVA and pairwise population FST estimates for both ND5 and the microsatellite markers indicated a similar pattern of moderate genetic differentiation among populations of the three regions, and large population groups on the coasts of the Sea of Japan, Sea of Okhotsk, and Pacific Ocean in the Far East. From a mismatch distribution analysis and neutrality test, the observed genetic structure appears to have been influenced primarily by bottlenecks during glacial periods and population expansions during interglacial periods in the late Pleistocene.