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Vera M, Aparicio E, Heras S, Abras A, Casanova A, Roldán MI, García-Marin JL. Regional environmental and climatic concerns on preserving native gene pools of a least concern species: Brown trout lineages in Mediterranean streams. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 862:160739. [PMID: 36502686 DOI: 10.1016/j.scitotenv.2022.160739] [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: 08/31/2022] [Revised: 11/10/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
The European brown trout, Salmo trutta, is a cold-adapted fish reported as a Least Concern species in the IUCN Red List. This species colonized new territories from southern refuges during the last glacial melting, but during the 20th century suffered from anthropic impacts on its habitats. The long-time survival of the species relies on the genetic diversity within and among populations. Brown trout is among the genetically most diverse vertebrate species; however, native populations in Mediterranean rivers have dramatically suffered of introgressive hybridization from extensive releases of evolutionary distant non-native Atlantic stocks. In addition, in Mediterranean rivers climate change will result in unsuitable conditions for the species during the 21st century. Using brown trout populations at the headstreams of a Pyrenean river as a model, this paper revised how hatchery releases have affected the native gene pools and how environmental and climatic variables controlled the amount of local introgression at intra-basin level. Introgressive hybridization was detected in all studied sites. Ten times larger divergence was observed among populations at tributaries than among populations along the main stem. A highly impacted population distributed in a long transect in the main stem suggested that hatchery fish move towards the main stem wherever released. From already highly impacted populations and despite the cessation of hatchery releases, warmer temperatures and lower precipitation expected from climate change will extend the introgressive hybridization along the basin, contributing to the extinction of the native gene pools. Based on available morphological distinction of native, hatchery and hybrid brown trout, we advocate the involvement of regional social groups (e.g. riverside dwellers, anglers, conservationists, hikers) in citizen science programs to detect the spread of non-native phenotypes along the rivers. These are cheap and fast methods to collaborate with fishery managers in the preservation and recovery of the regional native populations.
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Affiliation(s)
- Manuel Vera
- Departamento de Zoología, Xenética e Antropología Física, Campus Lugo, Universidad de Santiago de Compostela, 27002 Lugo, Spain.
| | - Enric Aparicio
- GRECO, Institute of Aquatic Ecology, University of Girona, 17071 Girona, Spain
| | - Sandra Heras
- Laboratori d'Ictiologia Genètica, Campus Montilivi, Universitat de Girona, 17003 Girona, Spain.
| | - Alba Abras
- Laboratori d'Ictiologia Genètica, Campus Montilivi, Universitat de Girona, 17003 Girona, Spain.
| | - Adrián Casanova
- Laboratori d'Ictiologia Genètica, Campus Montilivi, Universitat de Girona, 17003 Girona, Spain
| | - Maria-Inés Roldán
- Laboratori d'Ictiologia Genètica, Campus Montilivi, Universitat de Girona, 17003 Girona, Spain.
| | - Jose-Luis García-Marin
- Laboratori d'Ictiologia Genètica, Campus Montilivi, Universitat de Girona, 17003 Girona, Spain.
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Dysin AP, Shcherbakov YS, Nikolaeva OA, Terletskii VP, Tyshchenko VI, Dementieva NV. Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics. Genes (Basel) 2022; 13:genes13122221. [PMID: 36553488 PMCID: PMC9778375 DOI: 10.3390/genes13122221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/19/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
The salmon family is one of the most iconic and economically important fish families, primarily possessing meat of excellent taste as well as irreplaceable nutritional and biological value. One of the most common and, therefore, highly significant members of this family, the Atlantic salmon (Salmo salar L.), was not without reason one of the first fish species for which a high-quality reference genome assembly was produced and published. Genomic advancements are becoming increasingly essential in both the genetic enhancement of farmed salmon and the conservation of wild salmon stocks. The salmon genome has also played a significant role in influencing our comprehension of the evolutionary and functional ramifications of the ancestral whole-genome duplication event shared by all Salmonidae species. Here we provide an overview of the current state of research on the genomics and phylogeny of the various most studied subfamilies, genera, and individual salmonid species, focusing on those studies that aim to advance our understanding of salmonid ecology, physiology, and evolution, particularly for the purpose of improving aquaculture production. This review should make potential researchers pay attention to the current state of research on the salmonid genome, which should potentially attract interest in this important problem, and hence the application of new technologies (such as genome editing) in uncovering the genetic and evolutionary features of salmoniforms that underlie functional variation in traits of commercial and scientific importance.
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Affiliation(s)
- Artem P. Dysin
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
- Correspondence:
| | - Yuri S. Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Olga A. Nikolaeva
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Valerii P. Terletskii
- All-Russian Research Veterinary Institute of Poultry Science-Branch of the Federal Scientific Center, All-Russian Research and Technological Poultry Institute (ARRVIPS), Lomonosov, 198412 St. Petersburg, Russia
| | - Valentina I. Tyshchenko
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Natalia V. Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
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3
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Shedko SV. Molecular Dating of Phylogeny of Sturgeons (Acipenseridae) Based on Total Evidence Analysis. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422060084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Wang Y, Xiong F, Song Z. Molecular Phylogeny and Adaptive Mitochondrial DNA Evolution of Salmonids (Pisces: Salmonidae). Front Genet 2022; 13:903240. [PMID: 35783273 PMCID: PMC9249015 DOI: 10.3389/fgene.2022.903240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/10/2022] [Indexed: 11/18/2022] Open
Abstract
Salmonids are composed of anadromous and freshwater fishes, which is an important model for studying adaptive evolution. Herein, 49 salmonid complete mitochondrial genomes and those of two outgroups were used to infer a robust phylogeny for the family Salmonidae. The BI and RAxML phylogenetic trees based on 13 concatenated mitochondrial protein-coding genes showed well-supported nodes, and topologies were highly congruent. The concatenated 13 mitochondrial protein-coding genes, ND2, ND3, and ND5 genes were shown to have significantly larger dN/dS ratios in anadromous species than in freshwater species of Salmonidae, but the CYTB gene had significantly smaller dN/dS in anadromous species. The FEL analysis identified positively selected sites and negatively selected sites in each mitochondrial protein-coding gene separately. The RELAX program revealed that the ATP8 and CYTB genes supported intensified selection of the anadromous lineages. Our results demonstrated the phylogeny of Salmonidae and explored the mitochondrial DNA evolution pattern between anadromous and freshwater salmonids.
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Affiliation(s)
- Ying Wang
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Fei Xiong
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, China
- *Correspondence: Fei Xiong, ; Zhaobin Song,
| | - Zhaobin Song
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- *Correspondence: Fei Xiong, ; Zhaobin Song,
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5
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Brunner SR, Varga JFA, Dixon B. Antimicrobial Peptides of Salmonid Fish: From Form to Function. BIOLOGY 2020; 9:E233. [PMID: 32824728 PMCID: PMC7464209 DOI: 10.3390/biology9080233] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023]
Abstract
Antimicrobial peptides (AMPs) are small, usually cationic, and amphiphilic molecules that play a crucial role in molecular and cellular host defense against pathogens, tissue damage, and infection. AMPs are present in all metazoans and several have been discovered in teleosts. Some teleosts, such as salmonids, have undergone whole genome duplication events and retained a diverse AMP repertoire. Salmonid AMPs have also been shown to possess diverse and potent antibacterial, antiviral, and antiparasitic activity and are induced by a variety of factors, including dietary components and specific molecules also known as pathogen-associated molecular patterns (PAMPs), which may activate downstream signals to initiate transcription of AMP genes. Moreover, a multitude of cell lines have been established from various salmonid species, making it possible to study host-pathogen interactions in vitro, and several of these cell lines have been shown to express various AMPs. In this review, the structure, function, transcriptional regulation, and immunomodulatory role of salmonid AMPs are highlighted in health and disease. It is important to characterize and understand how salmonid AMPs function as this may lead to a better understanding of host-pathogen interactions with implications for aquaculture and medicine.
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Affiliation(s)
- Sascha R. Brunner
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (S.R.B.); (J.F.A.V.)
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Joseph F. A. Varga
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (S.R.B.); (J.F.A.V.)
| | - Brian Dixon
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (S.R.B.); (J.F.A.V.)
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6
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Bohling J. Evaluating the effect of reference genome divergence on the analysis of empirical RADseq datasets. Ecol Evol 2020; 10:7585-7601. [PMID: 32760550 PMCID: PMC7391306 DOI: 10.1002/ece3.6483] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/18/2020] [Accepted: 05/20/2020] [Indexed: 12/29/2022] Open
Abstract
The advent of high-throughput sequencing (HTS) has made genomic-level analyses feasible for nonmodel organisms. A critical step of many HTS pipelines involves aligning reads to a reference genome to identify variants. Despite recent initiatives, only a fraction of species has publically available reference genomes. Therefore, a common practice is to align reads to the genome of an organism related to the target species; however, this could affect read alignment and bias genotyping. In this study, I conducted an experiment using empirical RADseq datasets generated for two species of salmonids (Actinopterygii; Teleostei; Salmonidae) to address these questions. There are currently reference genomes for six salmonids of varying phylogenetic distance. I aligned the RADseq data to all six genomes and identified variants with several different genotypers, which were then fed into population genetic analyses. Increasing phylogenetic distance between target species and reference genome reduced the proportion of reads that successfully aligned and mapping quality. Reference genome also influenced the number of SNPs that were generated and depth at those SNPs, although the affect varied by genotyper. Inferences of population structure were mixed: increasing reference genome divergence reduced estimates of differentiation but similar patterns of population relationships were found across scenarios. These findings reveal how the choice of reference genome can influence the output of bioinformatic pipelines. It also emphasizes the need to identify best practices and guidelines for the burgeoning field of biodiversity genomics.
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Affiliation(s)
- Justin Bohling
- Abernathy Fish Technology Center US Fish and Wildlife Service Longview WA USA
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7
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Shedko SV. The Rate of Mitochondrial Cytochrome b Gene Evolution according to the Analysis of Recent (about 12 000 Years) Isolation of Charrs Salvelinus of Lake Kronotskoe. RUSS J GENET+ 2020. [DOI: 10.1134/s102279541909014x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Oleinik AG, Skurikhina LA, Kukhlevsky AD, Bondar EI. Genetic Differentiation of the Arctic Phylogenetic Group of Charr from Northeast Asia and North America. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419030116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Sävilammi T, Primmer CR, Varadharajan S, Guyomard R, Guiguen Y, Sandve SR, Vøllestad LA, Papakostas S, Lien S. The Chromosome-Level Genome Assembly of European Grayling Reveals Aspects of a Unique Genome Evolution Process Within Salmonids. G3 (BETHESDA, MD.) 2019; 9:1283-1294. [PMID: 30833292 PMCID: PMC6505133 DOI: 10.1534/g3.118.200919] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/04/2019] [Indexed: 12/13/2022]
Abstract
Salmonids represent an intriguing taxonomical group for investigating genome evolution in vertebrates due to their relatively recent last common whole genome duplication event, which occurred between 80 and 100 million years ago. Here, we report on the chromosome-level genome assembly of European grayling (Thymallus thymallus), which represents one of the earliest diverged salmonid subfamilies. To achieve this, we first generated relatively long genomic scaffolds by using a previously published draft genome assembly along with long-read sequencing data and a linkage map. We then merged those scaffolds by applying synteny evidence from the Atlantic salmon (Salmo salar) genome. Comparisons of the European grayling genome assembly to the genomes of Atlantic salmon and Northern pike (Esox lucius), the latter used as a nonduplicated outgroup, detailed aspects of the characteristic chromosome evolution process that has taken place in European grayling. While Atlantic salmon and other salmonid genomes are portrayed by the typical occurrence of numerous chromosomal fusions, European grayling chromosomes were confirmed to be fusion-free and were characterized by a relatively large proportion of paracentric and pericentric inversions. We further reported on transposable elements specific to either the European grayling or Atlantic salmon genome, on the male-specific sdY gene in the European grayling chromosome 11A, and on regions under residual tetrasomy in the homeologous European grayling chromosome pairs 9A-9B and 25A-25B. The same chromosome pairs have been observed under residual tetrasomy in Atlantic salmon and in other salmonids, suggesting that this feature has been conserved since the subfamily split.
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Affiliation(s)
- Tiina Sävilammi
- Department of Biology, University of Turku, 20014 Turku, Finland
| | - Craig R Primmer
- Organismal & Evolutionary Biology Research Program, Faculty of Biological & Environmental Sciences
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | | | - René Guyomard
- INRA, UMR1313 GABI Génétique Animale et Biologie Intégrative, Domaine de Vilvert, 78352, Jouy-en-Josas Cedex, France
| | - Yann Guiguen
- INRA, UR1037 Fish Physiology and Genomics, F-35000, Rennes, France
| | - Simen R Sandve
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1430 Ås, Norway
| | | | | | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1430 Ås, Norway
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10
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Inferring phylogenetic structure, hybridization and divergence times within Salmoninae (Teleostei: Salmonidae) using RAD-sequencing. Mol Phylogenet Evol 2018; 124:82-99. [DOI: 10.1016/j.ympev.2018.02.022] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 01/11/2018] [Accepted: 02/20/2018] [Indexed: 11/24/2022]
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11
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Artamonova VS, Kolmakova OV, Kirillova EA, Makhrov AA. Phylogeny of Salmonoid Fishes (Salmonoidei) Based on mtDNA COI Gene Sequences (Barcoding). CONTEMP PROBL ECOL+ 2018. [DOI: 10.1134/s1995425518030022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Tong GX, Xu W, Zhang YQ, Zhang QY, Yin JS, Kuang YY. De novo assembly and characterization of the Hucho taimen transcriptome. Ecol Evol 2017; 8:1271-1285. [PMID: 29375797 PMCID: PMC5773338 DOI: 10.1002/ece3.3735] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/22/2017] [Accepted: 11/27/2017] [Indexed: 11/10/2022] Open
Abstract
Taimen (Hucho taimen) is an important ecological and economic species that is classified as vulnerable by the IUCN Red List of Threatened Species; however, limited genomic information is available on this species. RNA‐Seq is a useful tool for obtaining genetic information and developing genetic markers for nonmodel species in addition to its application in gene expression profiling. In this study, we performed a comprehensive RNA‐Seq analysis of taimen. We obtained 157 M clean reads (14.7 Gb) and used them to de novo assemble a high‐quality transcriptome with a N50 size of 1,060 bp. In the assembly, 82% of the transcripts were annotated using several databases, and 14,666 of the transcripts contained a full open reading frame. The assembly covered 75% of the transcripts of Atlantic salmon and 57.3% of the protein‐coding genes of rainbow trout. To learn about the genome evolution, we performed a systematic comparative analysis across 11 teleosts including eight salmonids and found 313 unique gene families in taimen. Using Atlantic salmon and rainbow trout transcriptomes as the background, we identified 250 positive selection transcripts. The pathway enrichment analysis revealed a unique characteristic of taimen: It possesses more immune‐related genes than Atlantic salmon and rainbow trout; moreover, some genes have undergone strong positive selection. We also developed a pipeline for identifying microsatellite marker genotypes in samples and successfully identified 24 polymorphic microsatellite markers for taimen. These data and tools are useful for studying conservation genetics, phylogenetics, evolution among salmonids, and selective breeding for threatened taimen.
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Affiliation(s)
- Guang-Xiang Tong
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences Daoli District, Harbin Heilongjiang Province China
| | - Wei Xu
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences Daoli District, Harbin Heilongjiang Province China
| | - Yong-Quan Zhang
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences Daoli District, Harbin Heilongjiang Province China
| | - Qing-Yu Zhang
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences Daoli District, Harbin Heilongjiang Province China
| | - Jia-Sheng Yin
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences Daoli District, Harbin Heilongjiang Province China
| | - You-Yi Kuang
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences Daoli District, Harbin Heilongjiang Province China
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Horreo JL. Revisiting the mitogenomic phylogeny of Salmoninae: new insights thanks to recent sequencing advances. PeerJ 2017; 5:e3828. [PMID: 28948107 PMCID: PMC5609519 DOI: 10.7717/peerj.3828] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 08/29/2017] [Indexed: 12/24/2022] Open
Abstract
The phylogeny of the Salmonidae family, the only living one of the Order Salmoniformes, remains still unclear because of several reasons. Such reasons include insufficient taxon sampling and/or DNA information. The use of complete mitochondrial genomes (mitogenomics) could provide some light on it, but despite the high number of mitogenomes of species belonging to this family published during last years, an integrative work containing all this information has not been done. In this work, the phylogeny of 46 Salmonidae species was inferred from their mitogenomic sequences. Results include a Bayesian molecular-dated phylogenetic tree with very high statistical support showing Coregoninae and Salmoninae as sister subfamilies, as well as several new phylogenetic relationships among species and genus of the family. All these findings contribute to improve our understanding of the Salmonidae systematics and could have consequences on related evolutionary studies, as well as highlight the importance of revisiting phylogenies with integrative studies.
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Affiliation(s)
- Jose L. Horreo
- Department of Biodiversity and Evolutionary Biology, National Museum of Natural Sciences (CSIC), Madrid, Spain
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14
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Veale AJ, Russello MA. An ancient selective sweep linked to reproductive life history evolution in sockeye salmon. Sci Rep 2017; 7:1747. [PMID: 28496186 PMCID: PMC5431894 DOI: 10.1038/s41598-017-01890-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 04/05/2017] [Indexed: 11/09/2022] Open
Abstract
Study of parallel (or convergent) phenotypic evolution can provide important insights into processes driving sympatric, ecologically-mediated divergence and speciation, as ecotype pairs may provide a biological replicate of the underlying signals and mechanisms. Here, we provide evidence for a selective sweep creating an island of divergence associated with reproductive behavior in sockeye salmon (Oncorhynchus nerka), identifying a series of linked single nucleotide polymorphisms across a ~22,733 basepair region spanning the leucine-rich repeat-containing protein 9 gene exhibiting signatures of divergent selection associated with stream- and shore-spawning in both anadromous and resident forms across their pan-Pacific distribution. This divergence likely occurred ~3.8 Mya (95% HPD = 2.1–6.03 Mya), after sockeye separated from pink (O. gorbuscha) and chum (O. keta) salmon, but prior to the Pleistocene glaciations. Our results suggest recurrent evolution of reproductive ecotypes across the native range of O. nerka is at least partially associated with divergent selection of pre-existing genetic variation within or linked to this region. As sockeye salmon are unique among Pacific salmonids in their flexibility to spawn in lake-shore benthic environments, this region provides great promise for continued investigation of the genomic basis of O. nerka life history evolution, and, more broadly, for increasing our understanding of the heritable basis of adaptation of complex traits in novel environments.
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Affiliation(s)
- Andrew J Veale
- Department of Biology, The University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, British Columbia, V1V 1V7, Canada.,Department of Zoology, University of Otago, 340 Great King Street, Dunedin, 9016, New Zealand
| | - Michael A Russello
- Department of Biology, The University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, British Columbia, V1V 1V7, Canada.
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15
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Balakirev ES, Romanov NS, Ayala FJ. Complete mitochondrial genome of the yellow-spotted grayling Thymallus flavomaculatus (Salmoniformes, Salmonidae). Mitochondrial DNA B Resour 2016; 1:289-290. [PMID: 33644361 PMCID: PMC7871843 DOI: 10.1080/23802359.2016.1166081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
The complete mitochondrial genome was sequenced in two individuals of yellow-spotted grayling Thymallus flavomaculatus. The genome sequences are 16,659 bp in size, and the gene arrangement, composition and size are very similar to the salmonid fish genomes published previously. The low level of sequence divergence detected between the genome of Th. flavomaculatus and the GenBank complete mitochondrial genomes of the Th. yaluensis (KJ866484) and Th. grubii (KF649073) may likely be due to recent divergence of the species and/or historical hybridization and interspecific replacement of mtDNA.
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Affiliation(s)
- Evgeniy S. Balakirev
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA
- A. V. Zhirmunsky Institute of Marine Biology, Far Eastern Branch, Russian Academy of Science, Vladivostok, Russia
- Far Eastern Federal University, Vladivostok, Russia
| | - N. S. Romanov
- A. V. Zhirmunsky Institute of Marine Biology, Far Eastern Branch, Russian Academy of Science, Vladivostok, Russia
| | - Francisco J. Ayala
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA
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Abstract
Until now, fossil remains of Hucho Gunther, 1866 are known only from the Oligocene - middle Miocene strata of Baikal Russia, and from the late Pleistocene of Germany. New specimens, now identified as Hucho sp., come from the late Miocene of southern Ukraine. Numerous fragments of opercular bones and jaw teeth, morphologically similar to those in the extant genus Hucho, were found in Kubanka 2, Cherevychnoe 3, Tretya Krucha localities and dated by the late Sarmatian - early Maeotian (10-8 Ma). Th ese remains document the first appearance of huchen in geological past of Europe, filling in gap in distribution of this genus during the late Neogene, and throw light upon its biogeographical history.
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17
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Doadrio I, Perea S, Yahyaoui A. Two new species of atlantic trout (Actinopterygii, Salmonidae) from Morocco. GRAELLSIA 2015. [DOI: 10.3989/graellsia.2015.v71.142] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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18
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Gonen S, Bishop SC, Houston RD. Exploring the utility of cross-laboratory RAD-sequencing datasets for phylogenetic analysis. BMC Res Notes 2015; 8:299. [PMID: 26152111 PMCID: PMC4495686 DOI: 10.1186/s13104-015-1261-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 06/25/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Restriction site-Associated DNA sequencing (RAD-Seq) is widely applied to generate genome-wide sequence and genetic marker datasets. RAD-Seq has been extensively utilised, both at the population level and across species, for example in the construction of phylogenetic trees. However, the consistency of RAD-Seq data generated in different laboratories, and the potential use of cross-species orthologous RAD loci in the estimation of genetic relationships, have not been widely investigated. This study describes the use of SbfI RAD-Seq data for the estimation of evolutionary relationships amongst ten teleost fish species, using previously established phylogeny as a benchmark. RESULTS The number of orthologous SbfI RAD loci identified decreased with increasing evolutionary distance between the species, with several thousand loci conserved across five salmonid species (divergence ~50 MY), and several hundred conserved across the more distantly related teleost species (divergence ~100-360 MY). The majority (>70%) of loci identified between the more distantly related species were genic in origin, suggesting that the bias of SbfI towards genic regions is useful for identifying distant orthologs. Interspecific single nucleotide variants at each orthologous RAD locus were identified. Evolutionary relationships estimated using concatenated sequences of interspecific variants were congruent with previously published phylogenies, even for distantly (divergence up to ~360 MY) related species. CONCLUSION Overall, this study has demonstrated that orthologous SbfI RAD loci can be identified across closely and distantly related species. This has positive implications for the repeatability of SbfI RAD-Seq and its potential to address research questions beyond the scope of the original studies. Furthermore, the concordance in tree topologies and relationships estimated in this study with published teleost phylogenies suggests that similar meta-datasets could be utilised in the prediction of evolutionary relationships across populations and species with readily available RAD-Seq datasets, but for which relationships remain uncharacterised.
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Affiliation(s)
- Serap Gonen
- The Roslin Institute, University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK.
| | - Stephen C Bishop
- The Roslin Institute, University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK.
| | - Ross D Houston
- The Roslin Institute, University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK.
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Slynko YV, Stolbunova VV, Mendsaykhan B. Genetic variation of the mtDNA cyt b locus in graylings (Thymalus sp.: Thymalidae, Pisces) introduced into the Baydrag Gol River of the Valley of Lakes basin (Mongolia). RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415060149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Osinov AG, Senchukova AL, Mugue NS, Pavlov SD, Chereshnev IA. Speciation and genetic divergence of three species of charr from ancient Lake El'gygytgyn (Chukotka) and their phylogenetic relationships with other representatives of the genusSalvelinus. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12559] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
| | - Anna L. Senchukova
- Biological Faculty; Lomonosov Moscow State University; Moscow 119991 Russia
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences; Moscow Russia
| | - Nikolai S. Mugue
- Russian Federal Research Institute of Fisheries and Oceanography (VNIRO); Moscow 107140 Russia
| | - Sergei D. Pavlov
- Biological Faculty; Lomonosov Moscow State University; Moscow 119991 Russia
| | - Igor A. Chereshnev
- Institute of Biological Problems of the Far North; Far East Branch; Russian Academy of Sciences; Magadan 685000 Russia
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21
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Shedko SV, Miroshnichenko IL, Nemkova GA. Complete mitochondrial genome of the endangered Sakhalin taimen Parahucho perryi (Salmoniformes, Salmonidae). ACTA ACUST UNITED AC 2013; 25:265-6. [PMID: 23795829 DOI: 10.3109/19401736.2013.800498] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome sequence of Parahucho perryi has been obtained by the next generation sequencing, which contained 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes and non-coding control region with the total length of 16,651 bp. The gene content, arrangement, codon usage and base composition of P. perryi mitogenome are identical to those observed in salmonids and most other teleost fishes. The sequence data could provide useful information for the studies on molecular systematics and conservation genetics.
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Affiliation(s)
- Sergei V Shedko
- Institute of Biology and Soil Science, Far East Branch, Russian Academy of Sciences , Vladivostok , Russia
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