Phylogeny of Salmonine Fishes Based on Growth Hormone Introns: Atlantic (Salmo) and Pacific (Oncorhynchus) Salmon Are Not Sister Taxa* 1 (original) (raw)
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Molecular Systematics and Evolution of the Growth Hormone Introns in the Salmoninae
Environmental Biology of Fishes, 2004
DNA sequence data was collected for the C and D introns in the duplicate growth hormone loci (GH1 and GH2) from Brachmystax lenok, two subspecies of Hucho hucho, Hucho (Parahucho) perryi, Salmo salar, Salmo trutta, Acantholingua ohridana (Salmothymus), six species of Salvelinus, eight species of Oncorhynchus including O. masou, and three outgroups including Thymallus thymallus, Coregonus artedi, and Coregonus clupeaformis. Phylogenetic analyses were performed using maximum parsimony and maximum likelihood (PAUP, version 4.08beta) with gaps as missing data and as a fifth base. B. lenok was basal in all of the trees and all of the other genera were monophyletic with the exception that A. ohridana always placed within Salmo, and H. hucho sp. often placed with B. lenok. The GH1 introns supported a sister relationship between Oncorhynchus and Salvelinus, while the combined GH2 introns were ambiguous at this node. This result contrasts with trees based on morphology and the ribosomal ITS1 sequences that support a sister relationship between Salmo and Oncorhynchus. The only estrogen response element (ERE) in the gene is found in the C intron and has mutated in GH2 in all of the species except B. lenok. The ERE element in GH1 has undergone another mutation in all of the species except for B. lenok, and members of the two genera Salvelinus and Oncorhynchus. Thus these latter two genera are the only ones with a difference in expression of GH1 and GH2 in the presence of estrogen. Differences in selective pressure on the introns in the duplicate genes in different taxa could account for the conflicting results obtained in the phylogenetic analysis.
Comparison of phylogenetic analysis in the natural salmonids by using growth hormone (GH) gene
To days, The Growth hormone (GH) gene is more important in the regulator of metabolism, osmoregulation, reproduction and skeletal growth in Livestock. GH almost in all of animals has been same function that mentioned. This hormone also is exciting skeletal cellular for more growth and replication. In Salmonids for specially, furthermore, GH gene in population of salmonids can be used as the studies of phylogenetics and finding ancient and pedigree of salmonids that some researchers used from GH gene in salmo salar and salmo trutta for studies of phylogenetics. In this study we had done sequence of fragments of GH gene in salmo trutta caspius full length of almost 2048 bp. and deposited in GeneBank (accession number, JN24163) For sequencing of GH gene in the Salmo trutta caspius, first was extracted DNA genomics from bloods and the muscles of salmons, in related to, we designed three pairs of primers from first to end of the GH gene in same sequences from salmo salar and salmo trutta that reported in GeneBank. After sequencing of fragments we analyzed fragments and compared with other sequences in salmonid fishes. In this research our aims, study of amount variation in the between salmo trutta caspius species with Atlantic salmon and also, study amount of phylogenetic variation between Salmo trutta caspius with other salmons regarding to the GH gene.
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
Genetic history of salmonid fishes of the genus Oncorhynchus
Russian Journal of Genetics, 2015
This review discusses genetic approaches to solving important problems of evolutionary biology of salmonid fishes with special reference to Pacific salmon and trout. The problems of the genetic phylogeny of salmonid fishes, including issues of the consistency/inconsistency of phylogenetic tree topologies built using genetic and phenotypic characteristics, the timing of the main phylogenetic events, the relationships among different taxa, including the mutual status of Pacific salmon and trout, and others are discussed. The problems of the tetraploidization of the salmonid fishes, as well as the dilemma of their freshwater/marine origin, and the semelparity of some of the species are reviewed.
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.
Isolation, characterization and comparison of Atlantic and Chinook salmon growth hormone 1 and 2
BMC Genomics, 2008
Background: Growth hormone (GH) is an important regulator of skeletal growth, as well as other adapted processes in salmonids. The GH gene (gh) in salmonids is represented by duplicated, non-allelic isoforms designated as gh1 and gh2. We have isolated and characterized gh-containing bacterial artificial chromosomes (BACs) of both Atlantic and Chinook salmon (Salmo salar and Oncorhynchus tshawytscha) in order to further elucidate our understanding of the conservation and regulation of these loci.
Molecular Phylogenetics and Evolution, 2018
Phylogenetic studies focusing on Salmonidae have revealed significant obstacles in trying to clarify some interspecific relationships within the Salmoninae subfamily, due to a limited number of markers typed, conflicting phylogenetic signals and ancient hybridization events. To infer reliable phylogenetic relationships, evaluate several putative scenarios of ancient hybridization, and estimate divergence times within Salmoninae, we applied restriction-site associated DNA sequencing (RAD-seq) to 43 samples, including 26 genetic lineages across 21 species, largely representing the subfamily, with an emphasis on the genus Salvelinus. We identified 28,402 loci and 28,363 putatively unlinked SNPs, which were used in downstream analyses. Using an iterative k-means partitioned dataset and a Maximum Likelihood approach; we generated a well-supported phylogeny, providing clear answers to several previous phylogenetic uncertainties. We detected several significant introgression signals, presumably ancient, in the genus Salvelinus. The most recent common ancestor of Salmonidae dates back to approximately 58.9 MY ago (50.8–64 MY) and the crown age of Salmoninae was estimated to be 37.7 MY (35.2–40.8 MY) using a Bayesian molecular dating analysis with a relaxed molecular clock. The divergence among genera of the subfamily occurred between the late Eocene and middle of the Miocene (≈38–11 MY) such as the divergence between the genus Oncorhynchus and Salvelinus, which we estimated to 21.2 MY ago (95% HPD: 19.8–23.0 MY), while species diversification took place mainly during the Neogene (≈22–1.5 MY), with more than half of these events occurring in the last 10 MY.
Variation in growth hormone (GH) of gene in exon sequence in three salmon types
We aimed to identify polymorphisms in the coding regions of the Salmo trutta caspius (s. t. caspius) growth hormone gene for comparison of the rate homology between sequences cited regards salmonids, because the variation between sequences of exons is very important at finally can change in the rate of expression of gene growth hormone, however this gene identified by marker genetics in salmonids, and in those of Salmo salar (s. salar) and salmo trutta (s. trutta). This single copy nuclear gene contains six exons, that the length of the exon fragments almost 1900 base pairs between nucleotide 35 and 1907. In s. t. caspius. Selective PCR reaction, and sequenced the products, that including fragments of from first to end of the GH gene. We also describe a novel polymorphism of the six exons fragment, these fragments indicated for studies regards evolution of fish GH genes, phylogeny of fishes, and genetic selection. The segments of GH exon were analyzed by DNAMAN program genetics. The results are shown, there were almost 90%, homology between the first three exons of S. t. caspius and S. salar accession number (AY614002.1) Regards other Salmons; S. salar (Accession number, M21573.1) and Rainbow trout there weren’t any homology, exon fragments second, third, fourth, fifth and sixth, the homology were high (almost 90-95 %), however between fragments of salmons, the rate of homology were high but the length of fragments between salmons were different. The length of fragments in s. salar more than other salmons including R. trout and S. t. caspius.