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Zhang HY, Zhao ZX, Xu J, Xu P, Bai QL, Yang SY, Jiang LK, Chen BH. Population genetic analysis of aquaculture salmonid populations in China using a 57K rainbow trout SNP array. PLoS One 2018; 13:e0202582. [PMID: 30118517 PMCID: PMC6097679 DOI: 10.1371/journal.pone.0202582] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 08/05/2018] [Indexed: 12/21/2022] Open
Abstract
Various salmonid species are cultivated in cold water aquaculture. However, due to limited genomic data resources, specific high-throughput genotyping tools are not available to many of the salmonid species. In this study, a 57K single nucleotide polymorphism (SNP) array for rainbow trout (Oncorhynchus mykiss) was utilized to detect polymorphisms in seven salmonid species, including Hucho taimen, Oncorhynchus masou, Salvelinus fontinalis, Brachymystax lenok, Salvelinus leucomaenis, O. kisutch, and O. mykiss. The number of polymorphic markers per population ranged from 3,844 (O. kisutch) to 53,734 (O. mykiss), indicating that the rainbow trout SNP array was applicable as a universal genotyping tool for other salmonid species. Among the six other salmonid populations from four genera, 28,882 SNPs were shared, whereas 525 SNPs were polymorphic in all four genera. The genetic diversity and population relationships of the seven salmonid species were studied by principal component analysis (PCA). The phylogenetic relationships among populations were analyzed using the maximum likelihood method, which indicated that the shared SNP markers provide reliable genomic information for population genetic analyses in common aquaculture salmonid fishes. Furthermore, this obtained genomic information may be applicable for population genetic evaluation, marker-assisted breeding, and propagative parent selection in fry production.
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Affiliation(s)
- Han-Yuan Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Zi-Xia Zhao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
- * E-mail: (ZXZ); (PX)
| | - Jian Xu
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Peng Xu
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- * E-mail: (ZXZ); (PX)
| | - Qing-Li Bai
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Shi-Yong Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Yaan, China
| | - Li-Kun Jiang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Bao-Hua Chen
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
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Tougard C, Justy F, Guinand B, Douzery EJP, Berrebi P. Salmo macrostigma (Teleostei, Salmonidae): Nothing more than a brown trout (S. trutta) lineage? JOURNAL OF FISH BIOLOGY 2018; 93:302-310. [PMID: 29992566 DOI: 10.1111/jfb.13751] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 03/07/2018] [Indexed: 06/08/2023]
Abstract
We examined specimens of the macrostigma trout Salmo macrostigma, which refers to big black spots on the flanks, to assess whether it is an example of taxonomic inflation within the brown trout Salmo trutta complex. Using new specimens, publicly available data and a mitogenomic protocol to amplify the control and cytochrome b regions of the mitochondrial genome from degraded museum samples, including one syntype specimen, the present study shows that the macrostigma trout is not a valid species. Our results suggest the occurrence of a distinct evolutionary lineage of S. trutta in North Africa and Sicily. The name of the North African lineage is proposed for this lineage, which was found to be sister to the Atlantic lineage of brown trout, S. trutta.
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Affiliation(s)
| | - Fabienne Justy
- ISEM, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, France
| | - Bruno Guinand
- ISEM, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, France
| | | | - Patrick Berrebi
- ISEM, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, France
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Roman I, Bourgeois Y, Reyes-Velasco J, Jensen OP, Waldman J, Boissinot S. Contrasted patterns of divergence and gene flow among five fish species in a Mongolian rift lake following glaciation. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly083] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Ivana Roman
- Department of Biology, Queens College, the City University of New York, Flushing, NY, USA
| | - Yann Bourgeois
- New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Jacobo Reyes-Velasco
- New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Olaf P Jensen
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
| | - John Waldman
- Department of Biology, Queens College, the City University of New York, Flushing, NY, USA
| | - Stephane Boissinot
- New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
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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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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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56
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Schönhuth S, Vukić J, Šanda R, Yang L, Mayden RL. Phylogenetic relationships and classification of the Holarctic family Leuciscidae (Cypriniformes: Cyprinoidei). Mol Phylogenet Evol 2018; 127:781-799. [PMID: 29913311 DOI: 10.1016/j.ympev.2018.06.026] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 06/12/2018] [Accepted: 06/15/2018] [Indexed: 12/15/2022]
Abstract
The phylogenetic relationships and classification of the freshwater fish order Cypriniformes, like many other species-rich groups of vertebrates, has evolved over time with some consistency and inconsistencies of relationships across various studies. Within Cypriniformes, the Holarctic family Leuciscidae is one of the most widely distributed and highly diverse monophyletic groups of cyprinoids. Despite several studies conducted on this group, alternative hypotheses exist as to the composition and relationships within Leuciscidae. Here we assess the extent, composition, phylogenetic relationships, and taxonomy of this highly diverse group of fishes, using multiple mitochondrial and nuclear loci and a comprehensive and dense taxonomic sampling. Analyses of 418 specimens (410 species) resolve a well-supported Leuciscidae including 362 specimens (358 taxa) in six well-supported subfamilies/major clades: Pseudaspininae/Far East Asian clade (FEA); Laviniinae/North American Western clade (WC); Plagopterinae/North American Creek Chub-Plagopterin clade (CC-P); Leuciscinae/Eurasian Old World clade (OW) (minus Phoxinus) plus North American Notemigonus; Phoxininae/Eurasian Phoxinus clade (PHX); and Pogonichthyinae/North American clade (NA) including all remaining leuciscids. Within Leuciscidae, neither the traditional phoxinins (Phoxinus, FEA, Nearctic genera) nor all Nearctic genera (minus Notemigonus) are resolved as monophyletic; whereas the WC and CC-P form two independent lineages from remaining North American cyprinoids. A close relationship exists between Eurasian Phoxinus, NA, and OW clades, while FEA is the sister group to all remaining Leuciscidae. Major lineages resolved within these six subfamilies are mostly congruent with some previous studies. Our results suggests a complex evolutionary history of this diverse and widespread group of fishes.
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Affiliation(s)
- Susana Schönhuth
- Biology Department, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO 63103, USA.
| | - Jasna Vukić
- Department of Ecology, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague, Czech Republic
| | - Radek Šanda
- Department of Zoology, National Museum, Vaclavske namesti 68, 115 79 Prague, Czech Republic
| | - Lei Yang
- Florida Museum of Natural History, University of Florida, 1659 Museum Rd., Gainesville, FL 32611, USA
| | - Richard L Mayden
- Biology Department, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO 63103, USA
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Tarver JE, Taylor RS, Puttick MN, Lloyd GT, Pett W, Fromm B, Schirrmeister BE, Pisani D, Peterson KJ, Donoghue PCJ. Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss. Genome Biol Evol 2018; 10:1457-1470. [PMID: 29788279 PMCID: PMC6007596 DOI: 10.1093/gbe/evy096] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2018] [Indexed: 12/18/2022] Open
Abstract
microRNAs are conserved noncoding regulatory factors implicated in diverse physiological and developmental processes in multicellular organisms, as causal macroevolutionary agents and for phylogeny inference. However, the conservation and phylogenetic utility of microRNAs has been questioned on evidence of pervasive loss. Here, we show that apparent widespread losses are, largely, an artefact of poorly sampled and annotated microRNAomes. Using a curated data set of animal microRNAomes, we reject the view that miRNA families are never lost, but they are rarely lost (92% are never lost). A small number of families account for a majority of losses (1.7% of families account for >45% losses), and losses are associated with lineages exhibiting phenotypic simplification. Phylogenetic analyses based on the presence/absence of microRNA families among animal lineages, and based on microRNA sequences among Osteichthyes, demonstrate the power of these small data sets in phylogenetic inference. Perceptions of widespread evolutionary loss of microRNA families are due to the uncritical use of public archives corrupted by spurious microRNA annotations, and failure to discriminate false absences that occur because of incomplete microRNAome annotation.
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Affiliation(s)
- James E Tarver
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Richard S Taylor
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Mark N Puttick
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
- Department of Biology and Biochemistry, University of Bath, United Kingdom
| | - Graeme T Lloyd
- School of Earth and Environment, University of Leeds, United Kingdom
| | - Walker Pett
- Department of Ecology, Evolution and Organismal Biology, Iowa State University
| | - Bastian Fromm
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Norway
| | - Bettina E Schirrmeister
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Davide Pisani
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire
| | - Philip C J Donoghue
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
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Ninua L, Tarkhnishvili D, Gvazava E. Phylogeography and taxonomic status of trout and salmon from the Ponto-Caspian drainages, with inferences on European Brown Trout evolution and taxonomy. Ecol Evol 2018; 8:2645-2658. [PMID: 29531683 PMCID: PMC5838059 DOI: 10.1002/ece3.3884] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 12/07/2017] [Accepted: 01/02/2018] [Indexed: 01/19/2023] Open
Abstract
Current taxonomy of western Eurasian trout leaves a number of questions open; it is not clear to what extent some species are distinct genetically and morphologically. The purpose of this paper was to explore phylogeography and species boundaries in freshwater and anadromous trout from the drainages of the Black and the Caspian Seas (Ponto-Caspian). We studied morphology and mitochondrial phylogeny, combining samples from the western Caucasus within the potential range of five nominal species of trout that are thought to inhabit this region, and using the sequences available from GenBank. Our results suggest that the genetic diversity of trout in the Ponto-Caspian region is best explained with the fragmentation of catchments. (1) All trout species from Ponto-Caspian belong to the same mitochondrial clade, separated from the other trout since the Pleistocene; (2) the southeastern Black Sea area is the most likely place of diversification of this clade, which is closely related to the clades from Anatolia; (3) The species from the Black Sea and the Caspian Sea drainages are monophyletic; (4) except for the basal lineage of the Ponto-Caspian clade, Salmo rizeensis, all the lineages produce anadromous forms; (5) genetic diversification within the Ponto-Caspian clade is related to Pleistocene glacial waves; (6) the described morphological differences between the species are not fully diagnostic, and some earlier described differences depend on body size; the differences between freshwater and marine forms exceed those between the different lineages. We suggest a conservative taxonomic approach, using the names S. rizeensis and Salmo labrax for trout from the Black Sea basin and Salmo caspius and Salmo ciscaucasicus for the fish from the Caspian basin.
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Affiliation(s)
- Levan Ninua
- Institute of EcologyIlia State UniversityTbilisiGeorgia
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59
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Whole genome duplications have provided teleosts with many roads to peptide loaded MHC class I molecules. BMC Evol Biol 2018; 18:25. [PMID: 29471808 PMCID: PMC5824609 DOI: 10.1186/s12862-018-1138-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 02/15/2018] [Indexed: 12/31/2022] Open
Abstract
Background In sharks, chickens, rats, frogs, medaka and zebrafish there is haplotypic variation in MHC class I and closely linked genes involved in antigen processing, peptide translocation and peptide loading. At least in chicken, such MHCIa haplotypes of MHCIa, TAP2 and Tapasin are shown to influence the repertoire of pathogen epitopes being presented to CD8+ T-cells with subsequent effect on cell-mediated immune responses. Results Examining MHCI haplotype variation in Atlantic salmon using transcriptome and genome resources we found little evidence for polymorphism in antigen processing genes closely linked to the classical MHCIa genes. Looking at other genes involved in MHCI assembly and antigen processing we found retention of functional gene duplicates originating from the second vertebrate genome duplication event providing cyprinids, salmonids, and neoteleosts with the potential of several different peptide-loading complexes. One of these gene duplications has also been retained in the tetrapod lineage with orthologs in frogs, birds and opossum. Conclusion We postulate that the unique salmonid whole genome duplication (SGD) is responsible for eliminating haplotypic content in the paralog MHCIa regions possibly due to frequent recombination and reorganization events at early stages after the SGD. In return, multiple rounds of whole genome duplications has provided Atlantic salmon, other teleosts and even lower vertebrates with alternative peptide loading complexes. How this affects antigen presentation remains to be established. Electronic supplementary material The online version of this article (10.1186/s12862-018-1138-9) contains supplementary material, which is available to authorized users.
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Guðbrandsson J, Franzdóttir SR, Kristjánsson BK, Ahi EP, Maier VH, Kapralova KH, Snorrason SS, Jónsson ZO, Pálsson A. Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs. PeerJ 2018; 6:e4345. [PMID: 29441236 PMCID: PMC5807978 DOI: 10.7717/peerj.4345] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/19/2018] [Indexed: 02/06/2023] Open
Abstract
Phenotypic differences between closely related taxa or populations can arise through genetic variation or be environmentally induced, leading to altered transcription of genes during development. Comparative developmental studies of closely related species or variable populations within species can help to elucidate the molecular mechanisms related to evolutionary divergence and speciation. Studies of Arctic charr (Salvelinus alpinus) and related salmonids have revealed considerable phenotypic variation among populations and in Arctic charr many cases of extensive variation within lakes (resource polymorphism) have been recorded. One example is the four Arctic charr morphs in the ∼10,000 year old Lake Thingvallavatn, which differ in numerous morphological and life history traits. We set out to investigate the molecular and developmental roots of this polymorphism by studying gene expression in embryos of three of the morphs reared in a common garden set-up. We performed RNA-sequencing, de-novo transcriptome assembly and compared gene expression among morphs during an important timeframe in early development, i.e., preceding the formation of key trophic structures. Expectedly, developmental time was the predominant explanatory variable. As the data were affected by some form of RNA-degradation even though all samples passed quality control testing, an estimate of 3'-bias was the second most common explanatory variable. Importantly, morph, both as an independent variable and as interaction with developmental time, affected the expression of numerous transcripts. Transcripts with morph effect, separated the three morphs at the expression level, with the two benthic morphs being more similar. However, Gene Ontology analyses did not reveal clear functional enrichment of transcripts between groups. Verification via qPCR confirmed differential expression of several genes between the morphs, including regulatory genes such as AT-Rich Interaction Domain 4A (arid4a) and translin (tsn). The data are consistent with a scenario where genetic divergence has contributed to differential expression of multiple genes and systems during early development of these sympatric Arctic charr morphs.
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Affiliation(s)
- Jóhannes Guðbrandsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Freshwater Division, Marine and Freshwater Research Institute, Reykjavík, Iceland
| | - Sigríður Rut Franzdóttir
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Biomedical Center, University of Iceland, Reykjavík, Iceland
| | | | - Ehsan Pashay Ahi
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Karl-Franzens-Universität, Graz, Austria
| | - Valerie Helene Maier
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Biomedical Center, University of Iceland, Reykjavík, Iceland
| | | | | | - Zophonías Oddur Jónsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Biomedical Center, University of Iceland, Reykjavík, Iceland
| | - Arnar Pálsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Biomedical Center, University of Iceland, Reykjavík, Iceland
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61
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Carruthers M, Yurchenko AA, Augley JJ, Adams CE, Herzyk P, Elmer KR. De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species. BMC Genomics 2018; 19:32. [PMID: 29310597 PMCID: PMC5759245 DOI: 10.1186/s12864-017-4379-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 12/11/2017] [Indexed: 12/21/2022] Open
Abstract
Background Salmonid fishes exhibit high levels of phenotypic and ecological variation and are thus ideal model systems for studying evolutionary processes of adaptive divergence and speciation. Furthermore, salmonids are of major interest in fisheries, aquaculture, and conservation research. Improving understanding of the genetic mechanisms underlying traits in these species would significantly progress research in these fields. Here we generate high quality de novo transcriptomes for four salmonid species: Atlantic salmon (Salmo salar), brown trout (Salmo trutta), Arctic charr (Salvelinus alpinus), and European whitefish (Coregonus lavaretus). All species except Atlantic salmon have no reference genome publicly available and few if any genomic studies to date. Results We used paired-end RNA-seq on Illumina to generate high coverage sequencing of multiple individuals, yielding between 180 and 210 M reads per species. After initial assembly, strict filtering was used to remove duplicated, redundant, and low confidence transcripts. The final assemblies consisted of 36,505 protein-coding transcripts for Atlantic salmon, 35,736 for brown trout, 33,126 for Arctic charr, and 33,697 for European whitefish and are made publicly available. Assembly completeness was assessed using three approaches, all of which supported high quality of the assemblies: 1) ~78% of Actinopterygian single-copy orthologs were successfully captured in our assemblies, 2) orthogroup inference identified high overlap in the protein sequences present across all four species (40% shared across all four and 84% shared by at least two), and 3) comparison with the published Atlantic salmon genome suggests that our assemblies represent well covered (~98%) protein-coding transcriptomes. Thorough comparison of the generated assemblies found that 84-90% of transcripts in each assembly were orthologous with at least one of the other three species. We also identified 34-37% of transcripts in each assembly as paralogs. We further compare completeness and annotation statistics of our new assemblies to available related species. Conclusion New, high-confidence protein-coding transcriptomes were generated for four ecologically and economically important species of salmonids. This offers a high quality pipeline for such complex genomes, represents a valuable contribution to the existing genomic resources for these species and provides robust tools for future investigation of gene expression and sequence evolution in these and other salmonid species. Electronic supplementary material The online version of this article (10.1186/s12864-017-4379-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Madeleine Carruthers
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, G12 8QQ, Glasgow, UK
| | - Andrey A Yurchenko
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, G12 8QQ, Glasgow, UK
| | - Julian J Augley
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, G61 1QH, Glasgow, UK.,Present Address: Fios Genomics Ltd., Nine Edinburgh Bioquarter, 9 Little France Road, Edinburgh, EH16 4UX, UK
| | - Colin E Adams
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, G12 8QQ, Glasgow, UK.,Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, G63 0AW, UK
| | - Pawel Herzyk
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, G61 1QH, Glasgow, UK.,Institute of Molecular, Cell & Systems Biology, College of Medical, Veterinary & Life Sciences, University of Glasgow, G12 8QQ, Glasgow, UK
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, G12 8QQ, Glasgow, UK.
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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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63
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Makhrov AA. A Narrowing of the Phenotypic Diversity Range after Large Rearrangements of the Karyotype in Salmonidae: The Relationship between Saltational Genome Rearrangements and Gradual Adaptive Evolution. Genes (Basel) 2017; 8:E297. [PMID: 29077033 PMCID: PMC5704210 DOI: 10.3390/genes8110297] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/18/2017] [Accepted: 10/24/2017] [Indexed: 11/16/2022] Open
Abstract
The problem of how a gradual development of ecological and morphological adaptations combines with large genome rearrangements, which have been found to occur in the phylogeny of many groups of organisms, is a matter of discussion in the literature. The objective of this work was to study the problem with the example of salmonids, whose evolution included at least six events of multiple chromosome fusions. Large karyotype rearrangements are associated with a decrease in ecological and morphological diversity in salmonids. In the above example, genome rearrangements seem to distort the function of the genetic systems that are responsible for the occurrence of certain ecological forms in salmonids.
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Affiliation(s)
- A A Makhrov
- A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow 119071, Russia.
- Institute of Biophysics of Siberian Branch of Federal Research Center "Krasnoyarsk Science Center" of Russian Academy of Sciences, Akademgorodok, 50/50, Krasnoyarsk 660036, Russia.
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Rodgers TW, Olson JR, Klobucar SL, Mock KE. Quantitative PCR assays for detection of five arctic fish species: Lota lota, Cottus cognatus, Salvelinus alpinus, Salvelinus malma, and Thymallus arcticus from environmental DNA. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0883-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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65
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Jacobs A, Womack R, Chen M, Gharbi K, Elmer KR. Significant Synteny and Colocalization of Ecologically Relevant Quantitative Trait Loci Within and Across Species of Salmonid Fishes. Genetics 2017; 207:741-754. [PMID: 28760747 PMCID: PMC5629336 DOI: 10.1534/genetics.117.300093] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 07/21/2017] [Indexed: 11/18/2022] Open
Abstract
The organization of functional regions within genomes has important implications for evolutionary potential. Considerable research effort has gone toward identifying the genomic basis of phenotypic traits of interest through quantitative trait loci (QTL) analyses. Less research has assessed the arrangement of QTL in the genome within and across species. To investigate the distribution, extent of colocalization, and the synteny of QTL for ecologically relevant traits, we used a comparative genomic mapping approach within and across a range of salmonid species. We compiled 943 QTL from all available species [lake whitefish (Coregonus clupeaformis), coho salmon (Oncorhynchus kisutch), rainbow trout (O. mykiss), Chinook salmon (O. tshawytscha), Atlantic salmon (Salmo salar), and Arctic charr (Salvelinus alpinus)]. We developed a novel analytical framework for mapping and testing the distribution of these QTL. We found no correlation between QTL density and gene density at the chromosome level but did at the fine-scale. Two chromosomes were significantly enriched for QTL. We found multiple synteny blocks for morphological, life history, and physiological traits across species, but only morphology and physiology had significantly more than expected. Two or three pairs of traits were significantly colocalized in three species (lake whitefish, coho salmon, and rainbow trout). Colocalization and fine-scale synteny suggest genetic linkage between traits within species and a conserved genetic basis across species. However, this pattern was weak overall, with colocalization and synteny being relatively rare. These findings advance our understanding of the role of genomic organization in the renowned ecological and phenotypic variability of salmonid fishes.
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Affiliation(s)
- Arne Jacobs
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, UK
| | - Robyn Womack
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, UK
| | - Mel Chen
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, UK
- School of Mathematics and Statistics, College of Science and Engineering, University of Glasgow, G12 8QQ, UK
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, EH9 3FL, UK
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, UK
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66
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Oleinik AG, Skurikhina LA, Kukhlevsky AD, Bondar EI. Genetic relationships of Chukchi charr Salvelinus andriashevi and Taranetz charr Salvelinus taranetzi. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417100076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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67
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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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68
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Yao L, Li H, Martin RD, Moreau CS, Malhi RS. Tracing the phylogeographic history of Southeast Asian long-tailed macaques through mitogenomes of museum specimens. Mol Phylogenet Evol 2017; 116:227-238. [PMID: 28863929 DOI: 10.1016/j.ympev.2017.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 05/23/2017] [Accepted: 08/13/2017] [Indexed: 12/01/2022]
Abstract
The biogeographical history of Southeast Asia is complicated due to the continuous emergences and disappearances of land bridges throughout the Pleistocene. Here, we use long-tailed macaques (Macaca fascicularis), which are widely distributed throughout the mainland and islands of Southeast Asia, asa model for better understanding the biogeographical patterns of diversification in this geographically complex region. A reliable intraspecific phylogeny including individuals from localities on oceanic islands, continental islands, and the mainland is needed to trace relatedness along with the pattern and timing of colonization in this region. We used high-throughput sequencing techniques to sequence mitochondrial genomes (mitogenomes) from 95 Southeast Asian M. fascicularis specimens housed at natural history museums around the world. To achieve a comprehensive picture, we more than tripled the mitogenome sample size for M. fascicularis from previous studies, and for the first time included documented samples from the Philippines and several small Indonesian islands. Confirming the result from a previous, recent intraspecific phylogeny for M. fascicularis, the newly reconstructed phylogeny of 135 specimens divides the samples into two major clades: Clade A includes haplotypes from the mainland and some from northern Sumatra, while Clade B includes all insular haplotypes along with lineages from southern Sumatra. This study resolves a previous disparity by revealing a disjunction in the origin of Sumatran macaques, with separate lineages originating within the two major clades, suggesting that at least two major migrations to Sumatra occurred. However, our dated phylogeny reveals that the two major clades split ∼1.88Ma, which is earlier than in previously published phylogenies. Our new data reveal that most Philippine macaque lineages diverged from the Borneo stock within the last ∼0.06-0.43Ma. Finally, our study provides insight into successful sequencing of DNA across museums and shotgun sequencing of DNA specimens asa method to sequence the mitogenome.
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Affiliation(s)
- Lu Yao
- Committee on Evolutionary Biology, University of Chicago, 1025 E. 57th St., Culver Hall 402, Chicago, IL 60637, USA; Integrative Research Center, The Field Museum of Natural History, 1400 S. Lake Shore Dr., Chicago, IL 60605, USA.
| | - Hongjie Li
- Department of Anthropology, University of Illinois at Urbana-Champaign, 607 S. Mathews Ave., 109 Davenport Hall, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 W Gregory Dr., Urbana, IL 61820, USA
| | - Robert D Martin
- Committee on Evolutionary Biology, University of Chicago, 1025 E. 57th St., Culver Hall 402, Chicago, IL 60637, USA; Integrative Research Center, The Field Museum of Natural History, 1400 S. Lake Shore Dr., Chicago, IL 60605, USA; Institute of Evolutionary Medicine, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Corrie S Moreau
- Committee on Evolutionary Biology, University of Chicago, 1025 E. 57th St., Culver Hall 402, Chicago, IL 60637, USA; Integrative Research Center, The Field Museum of Natural History, 1400 S. Lake Shore Dr., Chicago, IL 60605, USA
| | - Ripan S Malhi
- Department of Anthropology, University of Illinois at Urbana-Champaign, 607 S. Mathews Ave., 109 Davenport Hall, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 W Gregory Dr., Urbana, IL 61820, USA
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69
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Sutherland BJG, Rico C, Audet C, Bernatchez L. Sex Chromosome Evolution, Heterochiasmy, and Physiological QTL in the Salmonid Brook Charr Salvelinus fontinalis. G3 (BETHESDA, MD.) 2017; 7:2749-2762. [PMID: 28626004 PMCID: PMC5555479 DOI: 10.1534/g3.117.040915] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/13/2017] [Indexed: 02/06/2023]
Abstract
Whole-genome duplication (WGD) can have large impacts on genome evolution, and much remains unknown about these impacts. This includes the mechanisms of coping with a duplicated sex determination system and whether this has an impact on increasing the diversity of sex determination mechanisms. Other impacts include sexual conflict, where alleles having different optimums in each sex can result in sequestration of genes into nonrecombining sex chromosomes. Sex chromosome development itself may involve sex-specific recombination rate (i.e., heterochiasmy), which is also poorly understood. The family Salmonidae is a model system for these phenomena, having undergone autotetraploidization and subsequent rediploidization in most of the genome at the base of the lineage. The salmonid master sex determining gene is known, and many species have nonhomologous sex chromosomes, putatively due to transposition of this gene. In this study, we identify the sex chromosome of Brook Charr Salvelinus fontinalis and compare sex chromosome identities across the lineage (eight species and four genera). Although nonhomology is frequent, homologous sex chromosomes and other consistencies are present in distantly related species, indicating probable convergence on specific sex and neo-sex chromosomes. We also characterize strong heterochiasmy with 2.7-fold more crossovers in maternal than paternal haplotypes with paternal crossovers biased to chromosome ends. When considering only rediploidized chromosomes, the overall heterochiasmy trend remains, although with only 1.9-fold more recombination in the female than the male. Y chromosome crossovers are restricted to a single end of the chromosome, and this chromosome contains a large interspecific inversion, although its status between males and females remains unknown. Finally, we identify quantitative trait loci (QTL) for 21 unique growth, reproductive, and stress-related phenotypes to improve knowledge of the genetic architecture of these traits important to aquaculture and evolution.
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Affiliation(s)
- Ben J G Sutherland
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Ciro Rico
- School of Marine Studies, Molecular Diagnostics Laboratory, University of the South Pacific, Suva, Fiji
- Department of Wetland Ecology, Estación Biológica de Doñana (EBD-CSIC), 41092 Sevilla, Spain
| | - Céline Audet
- Institut des Sciences de la Mer de Rimouski, Université du Québec à Rimouski, Quebec G5L 3A1, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
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70
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Prince DJ, O’Rourke SM, Thompson TQ, Ali OA, Lyman HS, Saglam IK, Hotaling TJ, Spidle AP, Miller MR. The evolutionary basis of premature migration in Pacific salmon highlights the utility of genomics for informing conservation. SCIENCE ADVANCES 2017; 3:e1603198. [PMID: 28835916 PMCID: PMC5559211 DOI: 10.1126/sciadv.1603198] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 07/19/2017] [Indexed: 05/15/2023]
Abstract
The delineation of conservation units (CUs) is a challenging issue that has profound implications for minimizing the loss of biodiversity and ecosystem services. CU delineation typically seeks to prioritize evolutionary significance, and genetic methods play a pivotal role in the delineation process by quantifying overall differentiation between populations. Although CUs that primarily reflect overall genetic differentiation do protect adaptive differences between distant populations, they do not necessarily protect adaptive variation within highly connected populations. Advances in genomic methodology facilitate the characterization of adaptive genetic variation, but the potential utility of this information for CU delineation is unclear. We use genomic methods to investigate the evolutionary basis of premature migration in Pacific salmon, a complex behavioral and physiological phenotype that exists within highly connected populations and has experienced severe declines. Strikingly, we find that premature migration is associated with the same single locus across multiple populations in each of two different species. Patterns of variation at this locus suggest that the premature migration alleles arose from a single evolutionary event within each species and were subsequently spread to distant populations through straying and positive selection. Our results reveal that complex adaptive variation can depend on rare mutational events at a single locus, demonstrate that CUs reflecting overall genetic differentiation can fail to protect evolutionarily significant variation that has substantial ecological and societal benefits, and suggest that a supplemental framework for protecting specific adaptive variation will sometimes be necessary to prevent the loss of significant biodiversity and ecosystem services.
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Affiliation(s)
- Daniel J. Prince
- Department of Animal Science, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
- Center for Watershed Sciences, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Sean M. O’Rourke
- Department of Animal Science, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Tasha Q. Thompson
- Department of Animal Science, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Omar A. Ali
- Department of Animal Science, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Hannah S. Lyman
- Department of Animal Science, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Ismail K. Saglam
- Department of Animal Science, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
- Ecological Sciences Research Laboratories, Department of Biology, Hacettepe University, Beytepe, Ankara 06800, Turkey
| | - Thomas J. Hotaling
- Salmon River Restoration Council, 25631 Sawyers Bar Road, Sawyers Bar, CA 96027, USA
| | - Adrian P. Spidle
- Northwest Indian Fisheries Commission, 6730 Martin Way East, Olympia, WA 98516, USA
| | - Michael R. Miller
- Department of Animal Science, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
- Center for Watershed Sciences, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
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71
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Oleinik AG, Skurikhina LA, Kukhlevsky AD, Bondar EI. First report of the mitochondrial DNA sequences of Chukchi Charr ( Salvelinus andriashevi, Salmonidae). Mitochondrial DNA B Resour 2017; 2:363-365. [PMID: 33473829 PMCID: PMC7800534 DOI: 10.1080/23802359.2017.1339211] [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] [Indexed: 11/06/2022] Open
Abstract
Three mitochondrial DNA regions were sequenced in two individuals of the Chukchi charr Salvelinus andriashevi from Lake Istihed (Chukotka): the entire gene sequences of cytochrome b and cytochrome c oxidase-1, and control region. The low level of sequence divergence detected between the sequences suggests that S. andriashevi is probably an isolated population of the Taranetz charr S. taranetzi. The genealogy of mtDNA haplotypes confirms the phylogenetic closeness of S. andriashevi, S. taranetzi, Salvelinus sp. 4 (Lake Nachikinskoe), S. krogiusae (Lake Dal'nee), S. boganidae and S. elgyticus (Lake Elgygytgyn), and S. a. erythrinus (NWT).
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Affiliation(s)
- Alla G. Oleinik
- A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology FEB RAS, Vladivostok, Russia
| | - Lubov A. Skurikhina
- A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology FEB RAS, Vladivostok, Russia
| | - Andrey D. Kukhlevsky
- A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology FEB RAS, Vladivostok, Russia
- Department of Genetics, Far Eastern Federal University, Vladivostok, Russia
| | - Evgeniia I. Bondar
- A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology FEB RAS, Vladivostok, Russia
- Department of Genetics, Far Eastern Federal University, Vladivostok, Russia
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72
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A Dense Brown Trout ( Salmo trutta) Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral Diversity. G3-GENES GENOMES GENETICS 2017; 7:1365-1376. [PMID: 28235829 PMCID: PMC5386884 DOI: 10.1534/g3.116.038497] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
High-density linkage maps are valuable tools for conservation and eco-evolutionary issues. In salmonids, a complex rediploidization process consecutive to an ancient whole genome duplication event makes linkage maps of prime importance for investigating the evolutionary history of chromosome rearrangements. Here, we developed a high-density consensus linkage map for the brown trout (Salmo trutta), a socioeconomically important species heavily impacted by human activities. A total of 3977 ddRAD markers were mapped and ordered in 40 linkage groups using sex- and lineage-averaged recombination distances obtained from two family crosses. Performing map comparison between S. trutta and its sister species, S. salar, revealed extensive chromosomal rearrangements. Strikingly, all of the fusion and fission events that occurred after the S. salar/S. trutta speciation happened in the Atlantic salmon branch, whereas the brown trout remained closer to the ancestral chromosome structure. Using the strongly conserved synteny within chromosome arms, we aligned the brown trout linkage map to the Atlantic salmon genome sequence to estimate the local recombination rate in S. trutta at 3721 loci. A significant positive correlation between recombination rate and within-population nucleotide diversity (π) was found, indicating that selection constrains variation at linked neutral sites in brown trout. This new high-density linkage map provides a useful genomic resource for future aquaculture, conservation, and eco-evolutionary studies in brown trout.
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73
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Pankova MV, Kukhlevsky AD, Brykov VA. Fish growth hormone genes: Divergence of coding sequences in salmonid fishes. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795416100082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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74
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Padula VM, Causey D, López JA. Mitochondrial DNA phylogeography of least cisco Coregonus sardinella in Alaska. JOURNAL OF FISH BIOLOGY 2017; 90:1001-1020. [PMID: 28058718 DOI: 10.1111/jfb.13220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 10/14/2016] [Indexed: 06/06/2023]
Abstract
This study presents the first detailed analysis of the mitochondrial DNA diversity of least cisco Coregonus sardinella in Alaska using a 678 bp segment of the control region (D-loop) of the mitochondrial genome. Findings suggest that the history of C. sardinella in Alaska differs from that of other species of Coregonus present in the state and surrounding regions. The examined populations of C. sardinella are genetically diverse across Alaska. Sixty-eight distinct mitochondrial haplotypes were identified among 305 individuals sampled from nine locations. The haplotype minimum spanning network and phylogeny showed a modest level of geographic segregation among haplotypes, suggesting high levels of on-going or recent connectivity among distant populations. Observed ΦST values and the results of homogeneity and AMOVAs indicate incipient genetic differentiation between aggregations in three broad regional groups. Sites north of the Brooks Range formed one group, sites in the Yukon and Selawik Rivers formed a second group and sites south of the Yukon drainage formed the third group. Overall, the sequence data showed that a large proportion of mtDNA genetic variation in C. sardinella is shared across Alaska, but this variation is not homogeneously distributed across all regions and for all haplotype groups.
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Affiliation(s)
- V M Padula
- Fisheries Division, College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 905 N. Koyukuk Drive, Fairbanks, AK, 99775, U.S.A
| | - D Causey
- Department of Biological Sciences, University of Alaska Anchorage, 3101 Science Circle, CPISB 101, Anchorage, AK, 99508, U.S.A
| | - J A López
- Fisheries Division, College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 905 N. Koyukuk Drive, Fairbanks, AK, 99775, U.S.A
- University of Alaska Fairbanks, Museum of the North, 907 Yukon Drive, Fairbanks, AK, 99775, U.S.A
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75
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Sutherland BJG, Gosselin T, Normandeau E, Lamothe M, Isabel N, Audet C, Bernatchez L. Salmonid Chromosome Evolution as Revealed by a Novel Method for Comparing RADseq Linkage Maps. Genome Biol Evol 2016; 8:3600-3617. [PMID: 28173098 PMCID: PMC5381510 DOI: 10.1093/gbe/evw262] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2016] [Indexed: 12/13/2022] Open
Abstract
Whole genome duplication (WGD) can provide material for evolutionary innovation. Family Salmonidae is ideal for studying the effects of WGD as the ancestral salmonid underwent WGD relatively recently, ∼65 Ma, then rediploidized and diversified. Extensive synteny between homologous chromosome arms occurs in extant salmonids, but each species has both conserved and unique chromosome arm fusions and fissions. Assembly of large, outbred eukaryotic genomes can be difficult, but structural rearrangements within such taxa can be investigated using linkage maps. RAD sequencing provides unprecedented ability to generate high-density linkage maps for nonmodel species, but can result in low numbers of homologous markers between species due to phylogenetic distance or differences in library preparation. Here, we generate a high-density linkage map (3,826 markers) for the Salvelinus genera (Brook Charr S. fontinalis), and then identify corresponding chromosome arms among the other available salmonid high-density linkage maps, including six species of Oncorhynchus, and one species for each of Salmo, Coregonus, and the nonduplicated sister group for the salmonids, Northern Pike Esox lucius for identifying post-duplicated homeologs. To facilitate this process, we developed MapComp to identify identical and proximate (i.e. nearby) markers between linkage maps using a reference genome of a related species as an intermediate, increasing the number of comparable markers between linkage maps by 5-fold. This enabled a characterization of the most likely history of retained chromosomal rearrangements post-WGD, and several conserved chromosomal inversions. Analyses of RADseq-based linkage maps from other taxa will also benefit from MapComp, available at: https://github.com/enormandeau/mapcomp/
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Affiliation(s)
- Ben J. G. Sutherland
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Thierry Gosselin
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Manuel Lamothe
- Centre de Foresterie des Laurentides, Ressources Naturelles Canada, Québec, QC, Canada
| | - Nathalie Isabel
- Centre de Foresterie des Laurentides, Ressources Naturelles Canada, Québec, QC, Canada
| | - Céline Audet
- Institut des Sciences de la Mer de Rimouski, Université du Québec à Rimouski, Rimouski, QC, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
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76
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Pavey SA, Laporte M, Normandeau E, Gaudin J, Letourneau L, Boisvert S, Corbeil J, Audet C, Bernatchez L. Draft genome of the American Eel (Anguilla rostrata). Mol Ecol Resour 2016; 17:806-811. [PMID: 27754597 DOI: 10.1111/1755-0998.12608] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 10/12/2016] [Accepted: 10/13/2016] [Indexed: 11/28/2022]
Abstract
Freshwater eels (Anguilla sp.) have large economic, cultural, ecological and aesthetic importance worldwide, but they suffered more than 90% decline in global stocks over the past few decades. Proper genetic resources, such as sequenced, assembled and annotated genomes, are essential to help plan sustainable recoveries by identifying physiological, biochemical and genetic mechanisms that caused the declines or that may lead to recoveries. Here, we present the first sequenced genome of the American eel. This genome contained 305 043 contigs (N50 = 7397) and 79 209 scaffolds (N50 = 86 641) for a total size of 1.41 Gb, which is in the middle of the range of previous estimations for this species. In addition, protein-coding regions, including introns and flanking regions, are very well represented in the genome, as 95.2% of the 458 core eukaryotic genes and 98.8% of the 248 ultra-conserved subset were represented in the assembly and a total of 26 564 genes were annotated for future functional genomics studies. We performed a candidate gene analysis to compare three genes among all three freshwater eel species and, congruent with the phylogenetic relationships, Japanese eel (A. japanica) exhibited the most divergence. Overall, the sequenced genome presented in this study is a crucial addition to the presently available genetic tools to help guide future conservation efforts of freshwater eels.
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Affiliation(s)
- Scott A Pavey
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand, Québec, QC, G1V 0A6, Canada.,Department of Biological Sciences and Canadian Rivers Institute, University of New Brunswick, Saint-John, NB, E2L 4L5, Canada
| | - Martin Laporte
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand, Québec, QC, G1V 0A6, Canada
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand, Québec, QC, G1V 0A6, Canada
| | - Jérémy Gaudin
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand, Québec, QC, G1V 0A6, Canada
| | - Louis Letourneau
- McGill University and Génome Québec Innovation Centre, Montréal, QC, H3A0G1, Canada
| | - Sébastien Boisvert
- Faculty of Medicine, CHUL Research Center, Université Laval, Québec, QC, G1V4G2, Canada
| | - Jacques Corbeil
- Faculty of Medicine, CHUL Research Center, Université Laval, Québec, QC, G1V4G2, Canada
| | - Céline Audet
- Institut des sciences de la mer de Rimouski, Université du Québec à Rimouski, Rimouski, Québec, G5L 3A1, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand, Québec, QC, G1V 0A6, Canada
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Young MK, Isaak DJ, McKelvey KS, Wilcox TM, Pilgrim KL, Carim KJ, Campbell MR, Corsi MP, Horan DL, Nagel DE, Schwartz MK. Climate, Demography, and Zoogeography Predict Introgression Thresholds in Salmonid Hybrid Zones in Rocky Mountain Streams. PLoS One 2016; 11:e0163563. [PMID: 27828980 PMCID: PMC5102351 DOI: 10.1371/journal.pone.0163563] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/11/2016] [Indexed: 11/19/2022] Open
Abstract
Among the many threats posed by invasions of nonnative species is introgressive hybridization, which can lead to the genomic extinction of native taxa. This phenomenon is regarded as common and perhaps inevitable among native cutthroat trout and introduced rainbow trout in western North America, despite that these taxa naturally co-occur in some locations. We conducted a synthetic analysis of 13,315 genotyped fish from 558 sites by building logistic regression models using data from geospatial stream databases and from 12 published studies of hybridization to assess whether environmental covariates could explain levels of introgression between westslope cutthroat trout and rainbow trout in the U.S. northern Rocky Mountains. A consensus model performed well (AUC, 0.78–0.86; classification success, 72–82%; 10-fold cross validation, 70–82%) and predicted that rainbow trout introgression was significantly associated with warmer water temperatures, larger streams, proximity to warmer habitats and to recent sources of rainbow trout propagules, presence within the historical range of rainbow trout, and locations further east. Assuming that water temperatures will continue to rise in response to climate change and that levels of introgression outside the historical range of rainbow trout will equilibrate with those inside that range, we applied six scenarios across a 55,234-km stream network that forecast 9.5–74.7% declines in the amount of habitat occupied by westslope cutthroat trout populations of conservation value, but not the wholesale loss of such populations. We conclude that introgression between these taxa is predictably related to environmental conditions, many of which can be manipulated to foster largely genetically intact populations of westslope cutthroat trout and help managers prioritize conservation activities.
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Affiliation(s)
- Michael K. Young
- National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, USDA Forest Service, Missoula, Montana, United States of America
- * E-mail:
| | - Daniel J. Isaak
- Rocky Mountain Research Station, USDA Forest Service, Boise, Idaho, United States of America
| | - Kevin S. McKelvey
- National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, USDA Forest Service, Missoula, Montana, United States of America
| | - Taylor M. Wilcox
- National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, USDA Forest Service, Missoula, Montana, United States of America
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Kristine L. Pilgrim
- National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, USDA Forest Service, Missoula, Montana, United States of America
| | - Kellie J. Carim
- National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, USDA Forest Service, Missoula, Montana, United States of America
| | - Matthew R. Campbell
- Eagle Fish Genetics Laboratory, Idaho Department of Fish and Game, Eagle, Idaho, United States of America
| | - Matthew P. Corsi
- Idaho Department of Fish and Game, Coeur d'Alene, Idaho, United States of America
| | - Dona L. Horan
- Rocky Mountain Research Station, USDA Forest Service, Boise, Idaho, United States of America
| | - David E. Nagel
- Rocky Mountain Research Station, USDA Forest Service, Boise, Idaho, United States of America
| | - Michael K. Schwartz
- National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, USDA Forest Service, Missoula, Montana, United States of America
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78
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Michel B, Clamens AL, Béthoux O, Kergoat GJ, Condamine FL. A first higher-level time-calibrated phylogeny of antlions (Neuroptera: Myrmeleontidae). Mol Phylogenet Evol 2016; 107:103-116. [PMID: 27780793 DOI: 10.1016/j.ympev.2016.10.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 10/20/2016] [Accepted: 10/21/2016] [Indexed: 10/20/2022]
Abstract
In this study, we reconstruct the first time-calibrated phylogeny of the iconic antlion family, the Myrmeleontidae (Neuroptera: Myrmeleontiformia). We use maximum likelihood and Bayesian inference to analyse a molecular dataset based on seven mitochondrial and nuclear gene markers. The dataset encompasses 106 species of Neuroptera, including 94 antlion species. The resulting phylogenetic framework provides support for a myrmeleontid classification distinguishing four subfamilies: Acanthaclisinae, Myrmeleontinae, Palparinae, and Stilbopteryginae. Within Myrmeleontinae, Myrmecaelurini and Nemoleontini are recovered as monophyletic clades; Gepini also appears as a valid tribe, distinct from Myrmecaelurini whereas Myrmecaelurini and Nesoleontini on one hand and Brachynemurini and Dendroleontini on the other hand, appear closely related. Some preliminary information related to generic and specific levels are also implied from our results, such as the paraphyly of several genera. Dating analyses based on thoroughly evaluated fossil calibrations indicate that the antlion family likely originated in the Cretaceous, between 135 and 138 million years ago (depending on the set of fossil calibrations), and that all higher-level lineages appeared during the Early Cretaceous. This first phylogenetic hypothesis will provide a valuable basis to further expand the taxonomic coverage and molecular sampling, and to lay the foundations of future systematic revisions.
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Affiliation(s)
- Bruno Michel
- CIRAD, UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), 755 Avenue du Campus Agropolis, 34988 Montferrier-sur-Lez, France.
| | - Anne-Laure Clamens
- INRA, UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), 755 Avenue du Campus Agropolis, 34988 Montferrier-sur-Lez, France
| | - Olivier Béthoux
- Sorbonne Universités, UPMC Univ Paris 06, MNHN, CNRS, Centre de Recherche sur la Paléobiodiversité et les Paléoenvironnements (CR2P), Paris, France
| | - Gael J Kergoat
- INRA, UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), 755 Avenue du Campus Agropolis, 34988 Montferrier-sur-Lez, France
| | - Fabien L Condamine
- CNRS, UMR 5554 Institut des Sciences de l'Evolution (Université de Montpellier), Place Eugène Bataillon, 34095 Montpellier, France.
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79
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Bolotov IN, Vikhrev IV, Bespalaya YV, Gofarov MY, Kondakov AV, Konopleva ES, Bolotov NN, Lyubas AA. Multi-locus fossil-calibrated phylogeny, biogeography and a subgeneric revision of the Margaritiferidae (Mollusca: Bivalvia: Unionoida). Mol Phylogenet Evol 2016; 103:104-121. [DOI: 10.1016/j.ympev.2016.07.020] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 07/01/2016] [Accepted: 07/18/2016] [Indexed: 11/16/2022]
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80
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Dion-Côté AM, Symonová R, Lamaze FC, Pelikánová Š, Ráb P, Bernatchez L. Standing chromosomal variation in Lake Whitefish species pairs: the role of historical contingency and relevance for speciation. Mol Ecol 2016; 26:178-192. [PMID: 27545583 DOI: 10.1111/mec.13816] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 08/08/2016] [Accepted: 08/11/2016] [Indexed: 12/19/2022]
Abstract
The role of chromosome changes in speciation remains a debated topic, although demographic conditions associated with divergence should promote their appearance. We tested a potential relationship between chromosome changes and speciation by studying two Lake Whitefish (Coregonus clupeaformis) lineages that recently colonized postglacial lakes following allopatry. A dwarf limnetic species evolved repeatedly from the normal benthic species, becoming reproductively isolated. Lake Whitefish hybrids experience mitotic and meiotic instability, which may result from structurally divergent chromosomes. Motivated by this observation, we test the hypothesis that chromosome organization differs between Lake Whitefish species pairs using cytogenetics. While chromosome and fundamental numbers are conserved between the species (2n = 80, NF = 98), we observe extensive polymorphism of subtle karyotype traits. We describe intrachromosomal differences associated with heterochromatin and repetitive DNA, and test for parallelism among three sympatric species pairs. Multivariate analyses support the hypothesis that differentiation at the level of subchromosomal markers mostly appeared during allopatry. Yet we find no evidence for parallelism between species pairs among lakes, consistent with colonization effect or postcolonization differentiation. The reported intrachromosomal polymorphisms do not appear to play a central role in driving adaptive divergence between normal and dwarf Lake Whitefish. We discuss how chromosomal differentiation in the Lake Whitefish system may contribute to the destabilization of mitotic and meiotic chromosome segregation in hybrids, as documented previously. The chromosome structures detected here are still difficult to sequence and assemble, demonstrating the value of cytogenetics as a complementary approach to understand the genomic bases of speciation.
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Affiliation(s)
- Anne-Marie Dion-Côté
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, Québec, Canada, G1V 0A6
| | - Radka Symonová
- Research Institute for Limnology, University of Innsbruck, Mondseestraße 9, A-5310, Mondsee, Austria
| | - Fabien C Lamaze
- Ontario Institut for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada, M5G 0A3
| | - Šárka Pelikánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, AS CR, vvi, Liběchov, 277 21, Czech Republic
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, AS CR, vvi, Liběchov, 277 21, Czech Republic
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, Québec, Canada, G1V 0A6
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81
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Targeted sequencing for high-resolution evolutionary analyses following genome duplication in salmonid fish: Proof of concept for key components of the insulin-like growth factor axis. Mar Genomics 2016; 30:15-26. [PMID: 27346185 DOI: 10.1016/j.margen.2016.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 06/11/2016] [Accepted: 06/11/2016] [Indexed: 12/25/2022]
Abstract
High-throughput sequencing has revolutionised comparative and evolutionary genome biology. It has now become relatively commonplace to generate multiple genomes and/or transcriptomes to characterize the evolution of large taxonomic groups of interest. Nevertheless, such efforts may be unsuited to some research questions or remain beyond the scope of some research groups. Here we show that targeted high-throughput sequencing offers a viable alternative to study genome evolution across a vertebrate family of great scientific interest. Specifically, we exploited sequence capture and Illumina sequencing to characterize the evolution of key components from the insulin-like growth (IGF) signalling axis of salmonid fish at unprecedented phylogenetic resolution. The IGF axis represents a central governor of vertebrate growth and its core components were expanded by whole genome duplication in the salmonid ancestor ~95Ma. Using RNA baits synthesised to genes encoding the complete family of IGF binding proteins (IGFBP) and an IGF hormone (IGF2), we captured, sequenced and assembled orthologous and paralogous exons from species representing all ten salmonid genera. This approach generated 299 novel sequences, most as complete or near-complete protein-coding sequences. Phylogenetic analyses confirmed congruent evolutionary histories for all nineteen recognized salmonid IGFBP family members and identified novel salmonid-specific IGF2 paralogues. Moreover, we reconstructed the evolution of duplicated IGF axis paralogues across a replete salmonid phylogeny, revealing complex historic selection regimes - both ancestral to salmonids and lineage-restricted - that frequently involved asymmetric paralogue divergence under positive and/or relaxed purifying selection. Our findings add to an emerging literature highlighting diverse applications for targeted sequencing in comparative-evolutionary genomics. We also set out a viable approach to obtain large sets of nuclear genes for any member of the salmonid family, which should enable insights into the evolutionary role of whole genome duplication before additional nuclear genome sequences become available.
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82
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Weir LK, Kindsvater HK, Young KA, Reynolds JD. Sneaker Males Affect Fighter Male Body Size and Sexual Size Dimorphism in Salmon. Am Nat 2016; 188:264-71. [PMID: 27420790 DOI: 10.1086/687253] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Large male body size is typically favored by directional sexual selection through competition for mates. However, alternative male life-history phenotypes, such as "sneakers," should decrease the strength of sexual selection acting on body size of large "fighter" males. We tested this prediction with salmon species; in southern populations, where sneakers are common, fighter males should be smaller than in northern populations, where sneakers are rare, leading to geographical clines in sexual size dimorphism (SSD). Consistent with our prediction, fighter male body size and SSD (fighter male∶female size) increase with latitude in species with sneaker males (Atlantic salmon Salmo salar and masu salmon Oncorhynchus masou) but not in species without sneakers (chum salmon Oncorhynchus keta and pink salmon Oncorhynchus gorbuscha). This is the first evidence that sneaker males affect SSD across populations and species, and it suggests that alternative male mating strategies may shape the evolution of body size.
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83
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Dulmaa A, Slynko YV, Gordon NY, Stolbunova VV, Politov DV. Coregonus peled (Gmelin) transplanted into Ulaagchny Khar lake (western mongolia) showed no evidence of hybridization with other introduced Coregonus species. CONTEMP PROBL ECOL+ 2016. [DOI: 10.1134/s1995425516020037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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84
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Kindsvater HK, Braun DC, Otto SP, Reynolds JD. Costs of reproduction can explain the correlated evolution of semelparity and egg size: theory and a test with salmon. Ecol Lett 2016; 19:687-96. [PMID: 27146705 DOI: 10.1111/ele.12607] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 03/07/2016] [Accepted: 03/18/2016] [Indexed: 11/30/2022]
Abstract
Species' life history traits, including maturation age, number of reproductive bouts, offspring size and number, reflect adaptations to diverse biotic and abiotic selection pressures. A striking example of divergent life histories is the evolution of either iteroparity (breeding multiple times) or semelparity (breed once and die). We analysed published data on salmonid fishes and found that semelparous species produce larger eggs, that egg size and number increase with salmonid body size among populations and species and that migratory behaviour and parity interact. We developed three hypotheses that might explain the patterns in our data and evaluated them in a stage-structured modelling framework accounting for different growth and survival scenarios. Our models predict the observation of small eggs in iteroparous species when egg size is costly to maternal survival or egg number is constrained. By exploring trait co-variation in salmonids, we generate new hypotheses for the evolution of trade-offs among life history traits.
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Affiliation(s)
- Holly K Kindsvater
- Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Douglas C Braun
- School of Resource and Environmental Management, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada.,InStream Fisheries Research Inc., Vancouver, British Columbia, V5M 4V8, Canada
| | - Sarah P Otto
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - John D Reynolds
- Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
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85
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Faulks L, Östman Ö. Genetic Diversity and Hybridisation between Native and Introduced Salmonidae Fishes in a Swedish Alpine Lake. PLoS One 2016; 11:e0152732. [PMID: 27032100 PMCID: PMC4816307 DOI: 10.1371/journal.pone.0152732] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 03/18/2016] [Indexed: 01/11/2023] Open
Abstract
Understanding the processes underlying diversification can aid in formulating appropriate conservation management plans that help maintain the evolutionary potential of taxa, particularly under human-induced activities and climate change. Here we assessed the microsatellite genetic diversity and structure of three salmonid species, two native (Arctic charr, Salvelinus alpinus and brown trout, Salmo trutta) and one introduced (brook charr, Salvelinus fontinalis), from an alpine lake in sub-arctic Sweden, Lake Ånn. The genetic diversity of the three species was similar and sufficiently high from a conservation genetics perspective: corrected total heterozygosity, H’T = 0.54, 0.66, 0.60 and allelic richness, AR = 4.93, 5.53 and 5.26 for Arctic charr, brown trout and brook charr, respectively. There were indications of elevated inbreeding coefficients in brown trout (GIS = 0.144) and brook charr (GIS = 0.129) although sibling relationships were likely a confounding factor, as a high proportion of siblings were observed in all species within and among sampling locations. Overall genetic structure differed between species, Fst = 0.01, 0.02 and 0.04 in Arctic charr, brown trout and brook charr respectively, and there was differentiation at only a few specific locations. There was clear evidence of hybridisation between the native Arctic charr and the introduced brook charr, with 6% of individuals being hybrids, all of which were sampled in tributary streams. The ecological and evolutionary consequences of the observed hybridisation are priorities for further research and the conservation of the evolutionary potential of native salmonid species.
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Affiliation(s)
- Leanne Faulks
- Department of Ecology and Genetics – Animal Ecology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Sugadaira Montane Research Centre, University of Tsukuba, Sugadaira-kogen 1278–294, Ueda, Nagano, 386–2204, Japan
- * E-mail:
| | - Örjan Östman
- Department of Ecology and Genetics – Animal Ecology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Department of Aquatic Resources, Institute of Coastal Research, Skolvägen 6, 742 42 Öregrund, Sweden
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86
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Ritchie AM, Lo N, Ho SYW. Examining the sensitivity of molecular species delimitations to the choice of mitochondrial marker. ORG DIVERS EVOL 2016. [DOI: 10.1007/s13127-016-0275-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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87
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Jacobsen MW, da Fonseca RR, Bernatchez L, Hansen MM. Comparative analysis of complete mitochondrial genomes suggests that relaxed purifying selection is driving high nonsynonymous evolutionary rate of the NADH2 gene in whitefish (Coregonus ssp.). Mol Phylogenet Evol 2015; 95:161-70. [PMID: 26654959 DOI: 10.1016/j.ympev.2015.11.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 11/06/2015] [Accepted: 11/13/2015] [Indexed: 11/29/2022]
Abstract
Several studies have recently reported evidence for positive selection acting on the mitochondrial genome (mitogenome), emphasizing its potential role in adaptive divergence and speciation. In this study we searched 107 full mitogenomes of recently diverged species and lineages of whitefish (Coregonus ssp.) for signals of positive selection. These salmonids show several distinct morphological and ecological differences that may be associated with energetics and therefore potentially positive selection at the mitogenome level. We found that purifying selection and genetic drift were the predominant evolutionary forces acting on the analyzed mitogenomes. However, the NADH dehydrogenase 2 gene (ND2) showed a highly elevated dN/dS ratio compared to the other mitochondrial genes, which was significantly higher in whitefish compared to other salmonids. We therefore further examined nonsynonymous evolution in ND2 by (i) mapping amino acid changes to a protein model structure which showed that they were located away from key functional residues of the protein, (ii) locating them in the sequences of other species of fish (Salmonidae, Anguillidae, Scombridae and Percidae) only to find pronounced overlap of nonsynonymous regions. We thus conclude that relaxed purifying selection is driving the evolution of ND2 by affecting mostly regions that have lower functional relevance.
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Affiliation(s)
- Magnus W Jacobsen
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark.
| | - Rute R da Fonseca
- Department of Bioinformatics and RNA Biology, University of Copenhagen, Ole Maaløesvej 5, 2200 København N, Denmark
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, 1030, Avenue de la Médecine, Université Laval, Québec, Québec, Canada G1V 0A6
| | - Michael M Hansen
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark
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88
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McKinney GJ, Seeb LW, Larson WA, Gomez‐Uchida D, Limborg MT, Brieuc MSO, Everett MV, Naish KA, Waples RK, Seeb JE. An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (
Oncorhynchus tshawytscha
). Mol Ecol Resour 2015; 16:769-83. [DOI: 10.1111/1755-0998.12479] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/08/2015] [Accepted: 10/14/2015] [Indexed: 12/31/2022]
Affiliation(s)
- G. J. McKinney
- School of Aquatic and Fishery Sciences University of Washington Seattle WA 98195‐5020 USA
| | - L. W. Seeb
- School of Aquatic and Fishery Sciences University of Washington Seattle WA 98195‐5020 USA
| | - W. A. Larson
- School of Aquatic and Fishery Sciences University of Washington Seattle WA 98195‐5020 USA
| | - D. Gomez‐Uchida
- School of Aquatic and Fishery Sciences University of Washington Seattle WA 98195‐5020 USA
| | - M. T. Limborg
- School of Aquatic and Fishery Sciences University of Washington Seattle WA 98195‐5020 USA
| | - M. S. O. Brieuc
- School of Aquatic and Fishery Sciences University of Washington Seattle WA 98195‐5020 USA
| | - M. V. Everett
- School of Aquatic and Fishery Sciences University of Washington Seattle WA 98195‐5020 USA
| | - K. A. Naish
- School of Aquatic and Fishery Sciences University of Washington Seattle WA 98195‐5020 USA
| | - R. K. Waples
- School of Aquatic and Fishery Sciences University of Washington Seattle WA 98195‐5020 USA
| | - J. E. Seeb
- School of Aquatic and Fishery Sciences University of Washington Seattle WA 98195‐5020 USA
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89
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Kimmel CB, Watson S, Couture RB, McKibben NS, Nichols JT, Richardson SE, Noakes DLG. Patterns of variation and covariation in the shapes of mandibular bones of juvenile salmonids in the genus Oncorhynchus. Evol Dev 2015; 17:302-14. [PMID: 26372063 DOI: 10.1111/ede.12135] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
What is the nature of evolutionary divergence of the jaw skeleton within the genus Oncorhynchus? How can two associated bones evolve new shapes and still maintain functional integration? Here, we introduce and test a "concordance" hypothesis, in which an extraordinary matching of the evolutionary shape changes of the dentary and angular articular serves to preserve their fitting together. To test this hypothesis, we examined morphologies of the dentary and angular articular at parr (juvenile) stage, and at three levels of biological organization—between salmon and trout, between sister species within both salmon and trout, and among three types differing in life histories within one species, Oncorhynchus mykiss. The comparisons show bone shape divergences among the groups at each level; morphological divergence between salmon and trout is marked even at this relatively early life history stage. We observed substantial matching between the two mandibular bones in both pattern and amount of shape variation, and in shape covariation across species. These findings strongly support the concordance hypothesis, and reflect functional and/or developmental constraint on morphological evolution. We present evidence for developmental modularity within both bones. The locations of module boundaries were predicted from the patterns of evolutionary divergences, and for the dentary, at least, would appear to facilitate its functional association with the angular articular. The modularity results suggest that development has biased the course of evolution.
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Affiliation(s)
- Charles B Kimmel
- Institute for Neuroscience, University of Oregon, Eugene, OR, USA
| | - Sawyer Watson
- Institute for Neuroscience, University of Oregon, Eugene, OR, USA
| | | | | | - James T Nichols
- Institute for Neuroscience, University of Oregon, Eugene, OR, USA
| | | | - David L G Noakes
- Oregon Hatchery Research Center, Alsea, OR, USA.,Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
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90
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Ma B, Jiang H, Sun P, Chen J, Li L, Zhang X, Yuan L. Phylogeny and dating of divergences within the genus Thymallus (Salmonidae: Thymallinae) using complete mitochondrial genomes. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3602-11. [DOI: 10.3109/19401736.2015.1079824] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Bo Ma
- Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China,
| | - Haiying Jiang
- Guangdong Entomological Institute/South China Institute of Endangered Animals, Guangzhou, China,
- Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangzhou, China, and
- Guangdong Key Laboratory of Integrated Pest Management in Agriculture, Guangzhou, China
| | - Peng Sun
- Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China,
| | - Jinping Chen
- Guangdong Entomological Institute/South China Institute of Endangered Animals, Guangzhou, China,
- Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangzhou, China, and
- Guangdong Key Laboratory of Integrated Pest Management in Agriculture, Guangzhou, China
| | - Linmiao Li
- Guangdong Entomological Institute/South China Institute of Endangered Animals, Guangzhou, China,
- Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangzhou, China, and
- Guangdong Key Laboratory of Integrated Pest Management in Agriculture, Guangzhou, China
| | - Xiujuan Zhang
- Guangdong Entomological Institute/South China Institute of Endangered Animals, Guangzhou, China,
- Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangzhou, China, and
- Guangdong Key Laboratory of Integrated Pest Management in Agriculture, Guangzhou, China
| | - Lihong Yuan
- Guangdong Entomological Institute/South China Institute of Endangered Animals, Guangzhou, China,
- Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangzhou, China, and
- Guangdong Key Laboratory of Integrated Pest Management in Agriculture, Guangzhou, China
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91
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Hahn C, Weiss SJ, Stojanovski S, Bachmann L. Co-Speciation of the Ectoparasite Gyrodactylus teuchis (Monogenea, Platyhelminthes) and Its Salmonid Hosts. PLoS One 2015; 10:e0127340. [PMID: 26080029 PMCID: PMC4469311 DOI: 10.1371/journal.pone.0127340] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 04/13/2015] [Indexed: 11/18/2022] Open
Abstract
Co-speciation is a fundamental concept of evolutionary biology and intuitively appealing, yet in practice hard to demonstrate as it is often blurred by other evolutionary processes. We investigate the phylogeographic history of the monogenean ectoparasites Gyrodactylus teuchis and G. truttae on European salmonids of the genus Salmo. Mitochondrial cytochrome oxidase subunit 1 and the nuclear ribosomal internal transcribed spacer 2 were sequenced for 189 Gyrodactylus individuals collected from 50 localities, distributed across most major European river systems, from the Iberian- to the Balkan Peninsula. Despite both anthropogenic and naturally caused admixture of the principal host lineages among major river basins, co-phylogenetic analyses revealed significant global congruence for host and parasite phylogenies, providing firm support for co-speciation of G. teuchis and its salmonid hosts brown trout (S. trutta) and Atlantic salmon (S. salar). The major split within G. teuchis, coinciding with the initial divergence of the hosts was dated to ~1.5 My BP, using a Bayesian framework based on an indirect calibration point obtained from the host phylogeny. The presence of G. teuchis in Europe thus predates some of the major Pleistocene glaciations. In contrast, G. truttae exhibited remarkably low intraspecific genetic diversity. Given the direct life cycle and potentially high transmission potential of gyrodactylids, this finding is interpreted as indication for a recent emergence (<60 ky BP) of G. truttae via a host-switch. Our study thus suggests that instances of two fundamentally different mechanisms of speciation (co-speciation vs. host-switching) may have occurred on the same hosts in Europe within a time span of less than 1.5 My in two gyrodactylid ectoparasite species.
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Affiliation(s)
- Christoph Hahn
- Natural History Museum, University of Oslo, 0318, Oslo, Norway
- School for Biological, Biomedical and Environmental Science, University of Hull, Hull, HU6 7RX, United Kingdom
- * E-mail:
| | - Steven J. Weiss
- Institute of Zoology, Karl-Franzens University of Graz, 8010, Graz, Austria
| | - Stojmir Stojanovski
- Department of Fish Parasitology, Hydrobiological Institute, 6000, Ohrid, R. Macedonia
| | - Lutz Bachmann
- Natural History Museum, University of Oslo, 0318, Oslo, Norway
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92
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Epithelial Cadherin Determines Resistance to Infectious Pancreatic Necrosis Virus in Atlantic Salmon. Genetics 2015; 200:1313-26. [PMID: 26041276 DOI: 10.1534/genetics.115.175406] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/15/2015] [Indexed: 01/12/2023] Open
Abstract
Infectious pancreatic necrosis virus (IPNV) is the cause of one of the most prevalent diseases in farmed Atlantic salmon (Salmo salar). A quantitative trait locus (QTL) has been found to be responsible for most of the genetic variation in resistance to the virus. Here we describe how a linkage disequilibrium-based test for deducing the QTL allele was developed, and how it was used to produce IPN-resistant salmon, leading to a 75% decrease in the number of IPN outbreaks in the salmon farming industry. Furthermore, we describe how whole-genome sequencing of individuals with deduced QTL genotypes was used to map the QTL down to a region containing an epithelial cadherin (cdh1) gene. In a coimmunoprecipitation assay, the Cdh1 protein was found to bind to IPNV virions, strongly indicating that the protein is part of the machinery used by the virus for internalization. Immunofluorescence revealed that the virus colocalizes with IPNV in the endosomes of homozygous susceptible individuals but not in the endosomes of homozygous resistant individuals. A putative causal single nucleotide polymorphism was found within the full-length cdh1 gene, in phase with the QTL in all observed haplotypes except one; the absence of a single, all-explaining DNA polymorphism indicates that an additional causative polymorphism may contribute to the observed QTL genotype patterns. Cdh1 has earlier been shown to be necessary for the internalization of certain bacteria and fungi, but this is the first time the protein is implicated in internalization of a virus.
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93
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Gudbrandsson J, Ahi EP, Franzdottir SR, Kapralova KH, Kristjansson BK, Steinhaeuser SS, Maier VH, Johannesson IM, Snorrason SS, Jonsson ZO, Palsson A. The developmental transcriptome of contrasting Arctic charr (Salvelinus alpinus) morphs. F1000Res 2015; 4:136. [PMID: 27635217 PMCID: PMC5007756 DOI: 10.12688/f1000research.6402.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/10/2024] Open
Abstract
Species and populations with parallel evolution of specific traits can help illuminate how predictable adaptations and divergence are at the molecular and developmental level. Following the last glacial period, dwarfism and specialized bottom feeding morphology evolved rapidly in several landlocked Arctic charrSalvelinus alpinuspopulations in Iceland. To study the genetic divergence between small benthic morphs and limnetic morphs, we conducted RNA-sequencing charr embryos at four stages in early development. We studied two stocks with contrasting morphologies: the small benthic (SB) charr from Lake Thingvallavatn and Holar aquaculture (AC) charr.The data reveal significant differences in expression of several biological pathways during charr development. There was also an expression difference between SB- and AC-charr in genes involved in energy metabolism and blood coagulation genes. We confirmed differing expression of five genes in whole embryos with qPCR, includinglysozymeandnatterin-likewhich was previously identified as a fish-toxin of a lectin family that may be a putative immunopeptide. We also verified differential expression of 7 genes in the developing head that associated consistently with benthic v.s.limnetic morphology (studied in 4 morphs). Comparison of single nucleotide polymorphism (SNP) frequencies reveals extensive genetic differentiation between the SB and AC-charr (~1300 with more than 50% frequency difference). Curiously, three derived alleles in the otherwise conserved 12s and 16s mitochondrial ribosomal RNA genes are found in benthic charr.The data implicate multiple genes and molecular pathways in divergence of small benthic charr and/or the response of aquaculture charr to domestication. Functional, genetic and population genetic studies on more freshwater and anadromous populations are needed to confirm the specific loci and mutations relating to specific ecological traits in Arctic charr.
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94
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Mee JA, Bernatchez L, Reist JD, Rogers SM, Taylor EB. Identifying designatable units for intraspecific conservation prioritization: a hierarchical approach applied to the lake whitefish species complex (Coregonus spp.). Evol Appl 2015; 8:423-41. [PMID: 26029257 PMCID: PMC4430767 DOI: 10.1111/eva.12247] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 01/05/2015] [Indexed: 01/19/2023] Open
Abstract
The concept of the designatable unit (DU) affords a practical approach to identifying diversity below the species level for conservation prioritization. However, its suitability for defining conservation units in ecologically diverse, geographically widespread and taxonomically challenging species complexes has not been broadly evaluated. The lake whitefish species complex (Coregonus spp.) is geographically widespread in the Northern Hemisphere, and it contains a great deal of variability in ecology and evolutionary legacy within and among populations, as well as a great deal of taxonomic ambiguity. Here, we employ a set of hierarchical criteria to identify DUs within the Canadian distribution of the lake whitefish species complex. We identified 36 DUs based on (i) reproductive isolation, (ii) phylogeographic groupings, (iii) local adaptation and (iv) biogeographic regions. The identification of DUs is required for clear discussion regarding the conservation prioritization of lake whitefish populations. We suggest conservation priorities among lake whitefish DUs based on biological consequences of extinction, risk of extinction and distinctiveness. Our results exemplify the need for extensive genetic and biogeographic analyses for any species with broad geographic distributions and the need for detailed evaluation of evolutionary history and adaptive ecological divergence when defining intraspecific conservation units.
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Affiliation(s)
- Jonathan A Mee
- Department of Biological Sciences, University of CalgaryCalgary, AB, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébec, QC, Canada
| | | | - Sean M Rogers
- Department of Biological Sciences, University of CalgaryCalgary, AB, Canada
| | - Eric B Taylor
- Department of Zoology, Biodiversity Research Centre and Beaty Biodiversity Museum, University of British ColumbiaVancouver, BC, Canada
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95
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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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96
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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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97
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98
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Recknagel H, Jacobs A, Herzyk P, Elmer KR. Double-digest RAD sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with nonmodel organisms. Mol Ecol Resour 2015; 15:1316-29. [DOI: 10.1111/1755-0998.12406] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 03/10/2015] [Accepted: 03/16/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Hans Recknagel
- Institute of Biodiversity, Animal Health & Comparative Medicine; College of Medical, Veterinary & Life Sciences; University of Glasgow; Glasgow G12 8QQ UK
| | - Arne Jacobs
- Institute of Biodiversity, Animal Health & Comparative Medicine; College of Medical, Veterinary & Life Sciences; University of Glasgow; Glasgow G12 8QQ UK
| | - Pawel Herzyk
- Glasgow Polyomics; Wolfson Wohl Cancer Research Centre; University of Glasgow; Garscube Campus Bearsden G61 1QH UK
- Institute of Molecular, Cell & Systems Biology; College of Medical, Veterinary & Life Sciences; University of Glasgow; Glasgow G12 8QQ UK
| | - Kathryn R. Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine; College of Medical, Veterinary & Life Sciences; University of Glasgow; Glasgow G12 8QQ UK
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99
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Oleinik AG, Skurikhina LA, Brykov VA. Phylogeny of charrs of the genus Salvelinus based on mitochondrial DNA data. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415010093] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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100
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Bain PA, Ogino Y, Miyagawa S, Iguchi T, Kumar A. Differential ligand selectivity of androgen receptors α and β from Murray-Darling rainbowfish (Melanotaenia fluviatilis). Gen Comp Endocrinol 2015; 212:84-91. [PMID: 25644213 DOI: 10.1016/j.ygcen.2015.01.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 01/20/2015] [Accepted: 01/24/2015] [Indexed: 11/16/2022]
Abstract
Androgen receptors (ARs) mediate the physiological effects of androgens in vertebrates. In fishes, AR-mediated pathways can be modulated by aquatic contaminants, resulting in the masculinisation of female fish or diminished secondary sex characteristics in males. The Murray-Darling rainbowfish (Melanotaenia fluviatilis) is a small-bodied freshwater teleost used in Australia as a test species for environmental toxicology research. We determined concentration-response profiles for selected agonists and antagonists of rainbowfish ARα and ARβ using transient transactivation assays. For both ARα and ARβ, the order of potency of natural agonists was 11-ketotestosterone (11-KT)>5α-dihydrotestosterone>testosterone>androstenedione. Methyltestosterone was a highly potent agonist of both receptors relative to 11-KT. The relative potency of the veterinary growth-promoting androgen, 17β-trenbolone, varied by more than a factor of 5 between ARα and ARβ. The non-steroidal anti-androgen bicalutamide exhibited high inhibitory potency relative to the structurally related model anti-androgen, flutamide. The inhibitory potency of the agricultural fungicide, vinclozolin, was approximately 1.7-fold relative to flutamide for ARα, but over 20-fold in the case of ARβ. Fluorescent protein tagging of ARs showed that the rainbowfish ARα subtype is constitutively localised to the nucleus, while ARβ is cytoplasmic in the absence of ligand, an observation which agrees with the reported subcellular localisation of AR subtypes from other teleost species. Collectively, these data suggest that M. fluviatilis ARα and ARβ respond differently to environmental AR modulators and that in vivo sensitivity to contaminants may depend on the tissue distribution of the AR subtypes at the time of exposure.
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Affiliation(s)
- Peter A Bain
- Land and Water Flagship, Commonwealth Scientific and Industrial Research Organisation, PMB 2, Glen Osmond, South Australia 5064, Australia.
| | - Yukiko Ogino
- Division of Molecular Environmental Endocrinology, National Institute for Basic Biology, Nishigonaka-38 Myodaijicho, Okazaki, Aichi Prefecture 444-0867, Japan
| | - Shinichi Miyagawa
- Division of Molecular Environmental Endocrinology, National Institute for Basic Biology, Nishigonaka-38 Myodaijicho, Okazaki, Aichi Prefecture 444-0867, Japan
| | - Taisen Iguchi
- Division of Molecular Environmental Endocrinology, National Institute for Basic Biology, Nishigonaka-38 Myodaijicho, Okazaki, Aichi Prefecture 444-0867, Japan
| | - Anupama Kumar
- Land and Water Flagship, Commonwealth Scientific and Industrial Research Organisation, PMB 2, Glen Osmond, South Australia 5064, Australia
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