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Fang B, Momigliano P, Kahilainen KK, Merilä J. Allopatric origin of sympatric whitefish morphs with insights on the genetic basis of their reproductive isolation. Evolution 2022; 76:1905-1913. [PMID: 35797649 DOI: 10.1111/evo.14559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 06/13/2022] [Accepted: 06/22/2022] [Indexed: 01/22/2023]
Abstract
The European whitefish (Coregonus lavaretus) species complex is a classic example of recent adaptive radiation. Here, we examine a whitefish population introduced to northern Finnish Lake Tsahkal in the late 1960s, where three divergent morphs (viz. littoral, pelagic, and profundal feeders) were found 10 generations after. Using demographic modeling based on genomic data, we show that whitefish morphs evolved during a phase of strict isolation, refuting a rapid sympatric divergence scenario. The lake is now an artificial hybrid zone between morphs originated in allopatry. Despite their current syntopy, clear genetic differentiation remains between two of the three morphs. Using admixture mapping, we identify five SNPs associated with gonad weight variation, a proxy for sexual maturity and spawning time. We suggest that ecological adaptations in spawning time evolved in allopatry are currently maintaining partial reproductive isolation in the absence of other barriers to gene flow.
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Affiliation(s)
- Bohao Fang
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, 00014, Finland.,Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, 02138, USA
| | - Paolo Momigliano
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, 00014, Finland.,Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, Vigo, 36310, Spain
| | - Kimmo K Kahilainen
- Lammi Biological Station, University of Helsinki, Lammi, 16900, Finland.,Kilpisjärvi Biological Station, University of Helsinki, Kilpisjärvi, 99490, Finland
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, 00014, Finland.,Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
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2
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Pappas F, Palaiokostas C. Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr ( Salvelinus alpinus). Animals (Basel) 2021; 11:899. [PMID: 33801139 PMCID: PMC8004150 DOI: 10.3390/ani11030899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/13/2021] [Accepted: 03/16/2021] [Indexed: 12/17/2022] Open
Abstract
Incorporation of genomic technologies into fish breeding programs is a modern reality, promising substantial advances regarding the accuracy of selection, monitoring the genetic diversity and pedigree record verification. Single nucleotide polymorphism (SNP) arrays are the most commonly used genomic tool, but the investments required make them unsustainable for emerging species, such as Arctic charr (Salvelinus alpinus), where production volume is low. The requirement to genotype a large number of animals for breeding practices necessitates cost effective genotyping approaches. In the current study, we used double digest restriction site-associated DNA (ddRAD) sequencing of either high or low coverage to genotype Arctic charr from the Swedish national breeding program and performed analytical procedures to assess their utility in a range of tasks. SNPs were identified and used for deciphering the genetic structure of the studied population, estimating genomic relationships and implementing an association study for growth-related traits. Missing information and underestimation of heterozygosity in the low coverage set were limiting factors in genetic diversity and genomic relationship analyses, where high coverage performed notably better. On the other hand, the high coverage dataset proved to be valuable when it comes to identifying loci that are associated with phenotypic traits of interest. In general, both genotyping strategies offer sustainable alternatives to hybridization-based genotyping platforms and show potential for applications in aquaculture selective breeding.
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Affiliation(s)
| | - Christos Palaiokostas
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7090, 750 07 Uppsala, Sweden;
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3
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Use of gene knockout to examine serotonergic control of ion uptake in zebrafish reveals the importance of controlling for genetic background: A cautionary tale. Comp Biochem Physiol A Mol Integr Physiol 2019; 238:110558. [PMID: 31446068 DOI: 10.1016/j.cbpa.2019.110558] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/25/2019] [Accepted: 08/20/2019] [Indexed: 12/13/2022]
Abstract
Freshwater (FW) fishes inhabit dilute environments and must actively absorb ions in order to counteract diffusive salt loss. Neuroendocrine control of ion uptake in FW fishes is an important feature of ion homeostasis and several important neuroendocrine factors have been identified. The role of serotonin (5-HT), however, has received less attention despite several studies pointing to a role for 5-HT in the control of ion balance. Here, we used a gene knockout approach to elucidate the role of 5-HT in regulating Na+ and Ca2+ uptake rates in larval zebrafish. Tryptophan hydroxylase (TPH) is the rate-limiting step in 5-HT synthesis and we therefore hypothesized that ion uptake rates would be altered in zebrafish larvae carrying knockout mutations in tph genes. We first examined the effect of tph1b knockout (KO) and found that tph1bKO larvae, obtained from Harvard University, had reduced rates of Na+ and Ca2+ uptake compared to wild-type (WT) larvae from our institution (uOttawa WT), lending support to our hypothesis. However, further experiments controlling for differences in genetic background demonstrated that WT larvae from Harvard University (Harvard WT) had lower ion uptake rates than those of uOttawa WT, and that ion uptake rate between Harvard WT and tph1bKO larvae were not significantly different. Therefore, our initial observation that tph1bKO larvae (Harvard source) had reduced ion uptake rates relative to uOttawa WT was a function of genetic background and not of knockout itself. These data provide a cautionary tale of the importance of controlling for genetic background in gene knockout experiments.
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4
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Jiang DL, Gu XH, Li BJ, Zhu ZX, Qin H, Meng ZN, Lin HR, Xia JH. Identifying a Long QTL Cluster Across chrLG18 Associated with Salt Tolerance in Tilapia Using GWAS and QTL-seq. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:250-261. [PMID: 30737627 DOI: 10.1007/s10126-019-09877-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 01/14/2019] [Indexed: 06/09/2023]
Abstract
Understanding the genetic mechanism of osmoregulation is important for the improvement of salt tolerance in tilapia. In our previous study, we have identified a major quantitative trait locus (QTL) region located at 23.0 Mb of chrLG18 in a Nile tilapia line by QTL-seq. However, the conservation of these QTLs in other tilapia populations or species is not clear. In this study, we successfully investigated the QTLs associated with salt tolerance in a mass cross population from the GIFT line of Nile tilapia (Oreochromis niloticus) using a ddRAD-seq-based genome-wide association study (GWAS) and in a full-sib family from the Malaysia red tilapia strain (Oreochromis spp) using QTL-seq. Our study confirmed the major QTL interval that is located at nearly 23.0 Mb of chrLG18 in Nile tilapia and revealed a long QTL cluster across chrLG18 controlling for the salt-tolerant trait in both red tilapia and Nile tilapia. This is the first GWAS analysis on salt tolerance in tilapia. Our finding provides important insights into the genetic architecture of salinity tolerance in tilapia and supplies a basis for fine mapping QTLs, marker-assisted selection, and further detailed functional analysis of the underlying genes for salt tolerance in tilapia.
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Affiliation(s)
- Dan Li Jiang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Xiao Hui Gu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Bi Jun Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zong Xian Zhu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Hui Qin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zi Ning Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Hao Ran Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jun Hong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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Myosho T, Takahashi H, Yoshida K, Sato T, Hamaguchi S, Sakamoto T, Sakaizumi M. Hyperosmotic tolerance of adult fish and early embryos are determined by discrete, single loci in the genus Oryzias. Sci Rep 2018; 8:6897. [PMID: 29720646 PMCID: PMC5932013 DOI: 10.1038/s41598-018-24621-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 03/29/2018] [Indexed: 11/09/2022] Open
Abstract
The acquisition of environmental osmolality tolerance traits in individuals and gametes is an important event in the evolution and diversification of organisms. Although teleost fish exhibit considerable intra- and interspecific variation in salinity tolerance, the genetic mechanisms underlying this trait remain unclear. Oryzias celebensis survives in sea and fresh water during both the embryonic and adult stages, whereas its close relative Oryzias woworae cannot survive in sea water at either stage. A linkage analysis using backcross progeny identified a single locus responsible for adult hyperosmotic tolerance on a fused chromosome that corresponds to O. latipes linkage groups (LGs) 6 and 23. Conversely, O. woworae eggs fertilised with O. celebensis sperm died in sea water at the cleavage stages, whereas O. celebensis eggs fertilised with O. woworae sperm developed normally, demonstrating that maternal factor(s) from O. celebensis are responsible for hyperosmotic tolerance during early development. A further linkage analysis using backcrossed females revealed a discrete single locus relating to the maternal hyperosmotic tolerance factor in a fused chromosomal region homologous to O. latipes LGs 17 and 19. These results indicate that a maternal factor governs embryonic hyperosmotic tolerance and maps to a locus distinct from that associated with adult hyperosmotic tolerance.
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Affiliation(s)
- Taijun Myosho
- Laboratory of Molecular Reproductive Biology, Institute for Environmental Science, University of Shizuoka, Shizuoka, 422-8526, Japan. .,Department of Environmental Science, Institute of Science and Technology, Niigata University, Ikarashi, Niigata, 950-2181, Japan.
| | - Hideya Takahashi
- Department of Environmental Science, Institute of Science and Technology, Niigata University, Ikarashi, Niigata, 950-2181, Japan.,Ushimado Marine Institute, Faculty of Science, Okayama University, Setouchi, Okayama, 701-4303, Japan
| | - Kento Yoshida
- Department of Environmental Science, Institute of Science and Technology, Niigata University, Ikarashi, Niigata, 950-2181, Japan
| | - Tadashi Sato
- Department of Environmental Science, Institute of Science and Technology, Niigata University, Ikarashi, Niigata, 950-2181, Japan
| | - Satoshi Hamaguchi
- Department of Environmental Science, Institute of Science and Technology, Niigata University, Ikarashi, Niigata, 950-2181, Japan
| | - Tatsuya Sakamoto
- Ushimado Marine Institute, Faculty of Science, Okayama University, Setouchi, Okayama, 701-4303, Japan
| | - Mitsuru Sakaizumi
- Department of Environmental Science, Institute of Science and Technology, Niigata University, Ikarashi, Niigata, 950-2181, Japan
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Gu XH, Jiang DL, Huang Y, Li BJ, Chen CH, Lin HR, Xia JH. Identifying a Major QTL Associated with Salinity Tolerance in Nile Tilapia Using QTL-Seq. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:98-107. [PMID: 29318417 DOI: 10.1007/s10126-017-9790-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 12/08/2017] [Indexed: 06/07/2023]
Abstract
Selection of new lines with high salinity tolerance allows for economically feasible production of tilapias in brackish water areas. Mapping QTLs and identifying the markers linked to salinity-tolerant traits are the first steps in the improvement of the tolerance in tilapia through marker-assisted selection techniques. By using QTL-seq strategy and linkage-based analysis, two significant QTL intervals (chrLG4 and chrLG18) on salinity-tolerant traits were firstly identified in the Nile tilapia. Fine mapping with microsatellite and SNP markers suggested a major QTL region that located at 23.0 Mb of chrLG18 and explained 79% of phenotypic variation with a LOD value of 95. Expression analysis indicated that at least 10 genes (e.g., LACTB2, KINH, NCOA2, DIP2C, LARP4B, PEX5R, and KCNJ9) near or within the QTL interval were significantly differentially expressed in intestines, brains, or gills under 10, 15, or 20 ppt challenges. Our findings suggest that QTL-seq can be effectively utilized in QTL mapping of salinity-tolerant traits in fish. The identified major QTL is a promising locus to improve our knowledge on the genetic mechanism of salinity tolerance in tilapia.
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Affiliation(s)
- Xiao Hui Gu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Dan Li Jiang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yan Huang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Bi Jun Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Chao Hao Chen
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Hao Ran Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jun Hong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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7
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Divergence of insulin superfamily ligands, receptors and Igf binding proteins in marine versus freshwater stickleback: Evidence of selection in known and novel genes. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2017; 25:53-61. [PMID: 29149730 DOI: 10.1016/j.cbd.2017.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/04/2017] [Accepted: 10/23/2017] [Indexed: 11/20/2022]
Abstract
Three-spine stickleback (Gasterosteus aculeatus) is a teleost model for understanding genetic, physiological and morphological changes accompanying freshwater (FW) adaptation. There is growing evidence that the insulin superfamily plays important roles in traits involved in marine and FW adaptation. We performed a candidate gene analysis to look for evidence of selection on 33 insulin superfamily ligand-receptor genes and insulin-like growth factor binding proteins (Igfbp's) in stickleback. Using genotype data from 11 marine and 10 FW populations, we calculated the number of SNPs per site in regulatory and intronic regions, the number of synonymous and nonsynonymous mutations in coding regions, Wright's fixation index (Fst), and performed t-tests to identify SNPs with divergent genotype frequencies between marine/FW versus Atlantic/Pacific populations. Next, we analysed genome-wide transcriptome data from eight tissues to assess differential gene expression. Two Igfbp's (Igfbp2a and Igfbp5a) show evidence of divergent adaptation between life-history types, and a cluster of nonsynonymous mutations in Igfbp5a exhibit high Fst in exons apparently alternatively spliced in gill. We find evidence of selection on the relaxin family ligand-receptor gene pair, Insl3-Rxfp2, known to be involved in male spermatogenesis and bone metabolism, and in the 5' regulatory region of Igf2. We also confirmed the gene and coding sequence of two unannotated relaxin family ligands. These analyses underscore the utility of candidate gene studies and indicate directions for further exploration of the function of insulin superfamily genes in FW adaptation.
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8
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Veale AJ, Russello MA. Genomic Changes Associated with Reproductive and Migratory Ecotypes in Sockeye Salmon (Oncorhynchus nerka). Genome Biol Evol 2017; 9:2921-2939. [PMID: 29045601 PMCID: PMC5737441 DOI: 10.1093/gbe/evx215] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2017] [Indexed: 12/12/2022] Open
Abstract
Mechanisms underlying adaptive evolution can best be explored using paired populations displaying similar phenotypic divergence, illuminating the genomic changes associated with specific life history traits. Here, we used paired migratory [anadromous vs. resident (kokanee)] and reproductive [shore- vs. stream-spawning] ecotypes of sockeye salmon (Oncorhynchus nerka) sampled from seven lakes and two rivers spanning three catchments (Columbia, Fraser, and Skeena) in British Columbia, Canada to investigate the patterns and processes underlying their divergence. Restriction-site associated DNA sequencing was used to genotype this sampling at 7,347 single nucleotide polymorphisms, 334 of which were identified as outlier loci and candidates for divergent selection within at least one ecotype comparison. Sixty-eight of these outliers were present in two or more comparisons, with 33 detected across multiple catchments. Of particular note, one locus was detected as the most significant outlier between shore and stream-spawning ecotypes in multiple comparisons and across catchments (Columbia, Fraser, and Snake). We also detected several genomic islands of divergence, some shared among comparisons, potentially showing linked signals of differential selection. The single nucleotide polymorphisms and genomic regions identified in our study offer a range of mechanistic hypotheses associated with the genetic basis of O. nerka life history variation and provide novel tools for informing fisheries management.
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Affiliation(s)
- Andrew J. Veale
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
- Present address: Department of Environmental and Animal Sciences, Unitec, 139 Carrington Rd, Auckland, New Zealand
| | - Michael A. Russello
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
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9
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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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10
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Abdelrahman H, ElHady M, Alcivar-Warren A, Allen S, Al-Tobasei R, Bao L, Beck B, Blackburn H, Bosworth B, Buchanan J, Chappell J, Daniels W, Dong S, Dunham R, Durland E, Elaswad A, Gomez-Chiarri M, Gosh K, Guo X, Hackett P, Hanson T, Hedgecock D, Howard T, Holland L, Jackson M, Jin Y, Khalil K, Kocher T, Leeds T, Li N, Lindsey L, Liu S, Liu Z, Martin K, Novriadi R, Odin R, Palti Y, Peatman E, Proestou D, Qin G, Reading B, Rexroad C, Roberts S, Salem M, Severin A, Shi H, Shoemaker C, Stiles S, Tan S, Tang KFJ, Thongda W, Tiersch T, Tomasso J, Prabowo WT, Vallejo R, van der Steen H, Vo K, Waldbieser G, Wang H, Wang X, Xiang J, Yang Y, Yant R, Yuan Z, Zeng Q, Zhou T. Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research. BMC Genomics 2017; 18:191. [PMID: 28219347 PMCID: PMC5319170 DOI: 10.1186/s12864-017-3557-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/06/2017] [Indexed: 12/31/2022] Open
Abstract
Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker/causal mutation-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, and transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, behaviour, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Causal gene(s) need to be identified. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, causal gene/mutation-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries.Major progress has been made in aquaculture genomics for dozens of fish and shellfish species including the development of genetic linkage maps, physical maps, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases and various stages of genome reference sequences. This paper provides a general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding, with a focus on major aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp. While the overall research priorities and the practical goals are similar across various aquaculture species, the current status in each species should dictate the next priority areas within the species. This paper is an output of the USDA Workshop for Aquaculture Genomics, Genetics, and Breeding held in late March 2016 in Auburn, Alabama, with participants from all parts of the United States.
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Affiliation(s)
- Hisham Abdelrahman
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Mohamed ElHady
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | | | - Standish Allen
- Aquaculture Genetics & Breeding Technology Center, Virginia Institute of Marine Science, Gloucester Point, VA, 23062, USA
| | - Rafet Al-Tobasei
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Lisui Bao
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ben Beck
- Aquatic Animal Health Research Unit, USDA-ARS, 990 Wire Road, Auburn, AL, 36832, USA
| | - Harvey Blackburn
- USDA-ARS-NL Wheat & Corn Collections at a Glance GRP, National Animal Germplasm Program, 1111 S. Mason St., Fort Collins, CO, 80521-4500, USA
| | - Brian Bosworth
- USDA-ARS/CGRU, 141 Experimental Station Road, Stoneville, MS, 38701, USA
| | - John Buchanan
- Center for Aquaculture Technologies, 8395 Camino Santa Fe, Suite E, San Diego, CA, 92121, USA
| | - Jesse Chappell
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - William Daniels
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Sheng Dong
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Rex Dunham
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Evan Durland
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, 97331, USA
| | - Ahmed Elaswad
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Marta Gomez-Chiarri
- Department of Fisheries, Animal & Veterinary Science, 134 Woodward Hall, 9 East Alumni Avenue, Kingston, RI, 02881, USA
| | - Kamal Gosh
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA
| | - Perry Hackett
- Department of Genetics, Cell Biology and Development, 5-108 MCB, 420 Washington Avenue SE, Minneapolis, MN, 55455, USA
| | - Terry Hanson
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Dennis Hedgecock
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-0371, USA
| | - Tiffany Howard
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Leigh Holland
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Molly Jackson
- Taylor Shellfish Farms, 130 SE Lynch RD, Shelton, WA, 98584, USA
| | - Yulin Jin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Karim Khalil
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Thomas Kocher
- Department of Biology, University of Maryland, 2132 Biosciences Research Building, College Park, MD, 20742, USA
| | - Tim Leeds
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA
| | - Ning Li
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Lauren Lindsey
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Shikai Liu
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Zhanjiang Liu
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA.
| | - Kyle Martin
- Troutlodge, 27090 Us Highway 12, Naches, WA, 98937, USA
| | - Romi Novriadi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ramjie Odin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yniv Palti
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA
| | - Eric Peatman
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Dina Proestou
- USDA ARS NEA NCWMAC Shellfish Genetics at the University Rhode Island, 469 CBLS, 120 Flagg Road, Kingston, RI, 02881, USA
| | - Guyu Qin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Benjamin Reading
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, 27695-7617, USA
| | - Caird Rexroad
- USDA ARS Office of National Programs, George Washington Carver Center Room 4-2106, 5601 Sunnyside Avenue, Beltsville, MD, 20705, USA
| | - Steven Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98105, USA
| | - Mohamed Salem
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Andrew Severin
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA, 50011, USA
| | - Huitong Shi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Craig Shoemaker
- Aquatic Animal Health Research Unit, USDA-ARS, 990 Wire Road, Auburn, AL, 36832, USA
| | - Sheila Stiles
- USDOC/NOAA, National Marine Fisheries Service, NEFSC, Milford Laboratory, Milford, Connectcut, 06460, USA
| | - Suxu Tan
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Kathy F J Tang
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Wilawan Thongda
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Terrence Tiersch
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA, 70820, USA
| | - Joseph Tomasso
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Wendy Tri Prabowo
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Roger Vallejo
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA
| | | | - Khoi Vo
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Geoff Waldbieser
- USDA-ARS/CGRU, 141 Experimental Station Road, Stoneville, MS, 38701, USA
| | - Hanping Wang
- Aquaculture Genetics and Breeding Laboratory, The Ohio State University South Centers, Piketon, OH, 45661, USA
| | - Xiaozhu Wang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yujia Yang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Roger Yant
- Hybrid Catfish Company, 1233 Montgomery Drive, Inverness, MS, 38753, USA
| | - Zihao Yuan
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Qifan Zeng
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Tao Zhou
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
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A SNP Based Linkage Map of the Arctic Charr ( Salvelinus alpinus) Genome Provides Insights into the Diploidization Process After Whole Genome Duplication. G3-GENES GENOMES GENETICS 2017; 7:543-556. [PMID: 27986793 PMCID: PMC5295600 DOI: 10.1534/g3.116.038026] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Diploidization, which follows whole genome duplication events, does not occur evenly across the genome. In salmonid fishes, certain pairs of homeologous chromosomes preserve tetraploid loci in higher frequencies toward the telomeres due to residual tetrasomic inheritance. Research suggests this occurs only in homeologous pairs where one chromosome arm has undergone a fusion event. We present a linkage map for Arctic charr (Salvelinus alpinus), a salmonid species with relatively fewer chromosome fusions. Genotype by sequencing identified 19,418 SNPs, and a linkage map consisting of 4508 markers was constructed from a subset of high quality SNPs and microsatellite markers that were used to anchor the new map to previous versions. Both male- and female-specific linkage maps contained the expected number of 39 linkage groups. The chromosome type associated with each linkage group was determined, and 10 stable metacentric chromosomes were identified, along with a chromosome polymorphism involving the sex chromosome AC04. Two instances of a weak form of pseudolinkage were detected in the telomeric regions of homeologous chromosome arms in both female and male linkage maps. Chromosome arm homologies within the Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) genomes were determined. Paralogous sequence variants (PSVs) were identified, and their comparative BLASTn hit locations showed that duplicate markers exist in higher numbers on seven pairs of homeologous arms, previously identified as preserving tetrasomy in salmonid species. Homeologous arm pairs where neither arm has been part of a fusion event in Arctic charr had fewer PSVs, suggesting faster diploidization rates in these regions.
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Kusakabe M, Ishikawa A, Ravinet M, Yoshida K, Makino T, Toyoda A, Fujiyama A, Kitano J. Genetic basis for variation in salinity tolerance between stickleback ecotypes. Mol Ecol 2016; 26:304-319. [DOI: 10.1111/mec.13875] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/30/2016] [Accepted: 09/07/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Makoto Kusakabe
- Atmosphere and Ocean Research Institute; The University of Tokyo; Kashiwanoha 5-1-5 Kashiwa Chiba 277-8564 Japan
- Department of Biological Science; Faculty of Science; Shizuoka University; 836 Ohya, Suruga-ku Shizuoka 422-8529 Japan
| | - Asano Ishikawa
- Division of Ecological Genetics; National Institute of Genetics; Yata 1111 Mishima Shizuoka 411-8540 Japan
| | - Mark Ravinet
- Division of Ecological Genetics; National Institute of Genetics; Yata 1111 Mishima Shizuoka 411-8540 Japan
- Centre for Ecological and Evolutionary Synthesis; University of Oslo; P.O. Box 1066 Blindern Oslo NO-0316 Oslo Norway
| | - Kohta Yoshida
- Division of Ecological Genetics; National Institute of Genetics; Yata 1111 Mishima Shizuoka 411-8540 Japan
| | - Takashi Makino
- Department of Ecology and Evolutionary Biology; Graduate School of Life Sciences; Tohoku University; Sendai Miyagi 980-8578 Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory; National Institute of Genetics; Yata 1111 Mishima Shizuoka 411-8540 Japan
| | - Asao Fujiyama
- Comparative Genomics Laboratory; National Institute of Genetics; Yata 1111 Mishima Shizuoka 411-8540 Japan
| | - Jun Kitano
- Division of Ecological Genetics; National Institute of Genetics; Yata 1111 Mishima Shizuoka 411-8540 Japan
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13
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Dalziel AC, Bittman J, Mandic M, Ou M, Schulte PM. Origins and functional diversification of salinity-responsive Na(+) , K(+) ATPase α1 paralogs in salmonids. Mol Ecol 2014; 23:3483-503. [PMID: 24917532 DOI: 10.1111/mec.12828] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 06/03/2014] [Accepted: 06/04/2014] [Indexed: 01/17/2023]
Abstract
The Salmoniform whole-genome duplication is hypothesized to have facilitated the evolution of anadromy, but little is known about the contribution of paralogs from this event to the physiological performance traits required for anadromy, such as salinity tolerance. Here, we determined when two candidate, salinity-responsive paralogs of the Na(+) , K(+) ATPase α subunit (α1a and α1b) evolved and studied their evolutionary trajectories and tissue-specific expression patterns. We found that these paralogs arose during a small-scale duplication event prior to the Salmoniform, but after the teleost, whole-genome duplication. The 'freshwater paralog' (α1a) is primarily expressed in the gills of Salmoniformes and an unduplicated freshwater sister species (Esox lucius) and experienced positive selection in the freshwater ancestor of Salmoniformes and Esociformes. Contrary to our predictions, the 'saltwater paralog' (α1b), which is more widely expressed than α1a, did not experience positive selection during the evolution of anadromy in the Coregoninae and Salmonine. To determine whether parallel mutations in Na(+) , K(+) ATPase α1 may contribute to salinity tolerance in other fishes, we studied independently evolved salinity-responsive Na(+) , K(+) ATPase α1 paralogs in Anabas testudineus and Oreochromis mossambicus. We found that a quarter of the mutations occurring between salmonid α1a and α1b in functionally important sites also evolved in parallel in at least one of these species. Together, these data argue that paralogs contributing to salinity tolerance evolved prior to the Salmoniform whole-genome duplication and that strong selection and/or functional constraints have led to parallel evolution in salinity-responsive Na(+) , K(+) ATPase α1 paralogs in fishes.
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Affiliation(s)
- Anne C Dalziel
- Department of Zoology, Biodiversity Research Center, University of British Columbia, 6270 University Blvd, Vancouver, British Columbia, Canada, V6T 1Z4; Department of Biology, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 Avenue de la Médecine, Québec City, Québec, Canada, G1V 0A6
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14
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Wang G, Yang E, Smith KJ, Zeng Y, Ji G, Connon R, Fangue NA, Cai JJ. Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension. Front Genet 2014; 5:312. [PMID: 25309574 PMCID: PMC4160998 DOI: 10.3389/fgene.2014.00312] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 08/20/2014] [Indexed: 01/11/2023] Open
Abstract
Despite recent success with genome-wide association studies (GWAS), identifying hypertension (HTN)-susceptibility loci in the general population remains difficult. Here, we present a novel strategy to address this challenge by studying salinity adaptation in the threespine stickleback, a fish species with diverse salt-handling ecotypes. We acclimated native freshwater (FW) and anadromous saltwater (SW) threespine sticklebacks to fresh, brackish, and sea water for 30 days, and applied RNA sequencing to determine the gene expression in fish kidneys. We identified 1844 salt-responsive genes that were differentially expressed between FW sticklebacks acclimated to different salinities and/or between SW and FW sticklebacks acclimated to full-strength sea water. Significant overlap between stickleback salt-responsive genes and human genes implicated in HTN was detected (P < 10−7, hypergeometric test), suggesting a possible similarity in genetic mechanisms of salt handling between threespine sticklebacks and humans. The overlapping genes included a newly discovered HTN gene—MAP3K15, whose expression in FW stickleback kidneys decreases with salinity. These also included genes located in the GWAS loci such as AGTRAP-PLOD1 and CYP1A1-ULK3, which contain multiple potentially causative genes contributing to HTN susceptibility that need to be prioritized for study. Taken together, we show that stickleback salt-responsive genes provide valuable information facilitating the identification of human HTN genes. Thus, threespine sticklebacks may be used as a model, complementary to existing animal models, in human HTN research.
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Affiliation(s)
- Gang Wang
- Department of Veterinary Integrative Biosciences, Texas A&M University College Station, TX, USA
| | - Ence Yang
- Department of Veterinary Integrative Biosciences, Texas A&M University College Station, TX, USA
| | - Kerri J Smith
- Interdisciplinary Program in Genetics, Texas A&M University College Station, TX, USA
| | - Yong Zeng
- Department of Veterinary Integrative Biosciences, Texas A&M University College Station, TX, USA ; Department of Automation, Xiamen University Xiamen, China
| | - Guoli Ji
- Department of Automation, Xiamen University Xiamen, China
| | - Richard Connon
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, CA, USA
| | - Nann A Fangue
- Department of Wildlife, Fish, and Conservation Biology, University of California Davis, CA, USA
| | - James J Cai
- Department of Veterinary Integrative Biosciences, Texas A&M University College Station, TX, USA ; Interdisciplinary Program in Genetics, Texas A&M University College Station, TX, USA
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Zueva KJ, Lumme J, Veselov AE, Kent MP, Lien S, Primmer CR. Footprints of directional selection in wild Atlantic salmon populations: evidence for parasite-driven evolution? PLoS One 2014; 9:e91672. [PMID: 24670947 PMCID: PMC3966780 DOI: 10.1371/journal.pone.0091672] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 02/14/2014] [Indexed: 12/15/2022] Open
Abstract
Mechanisms of host-parasite co-adaptation have long been of interest in evolutionary biology; however, determining the genetic basis of parasite resistance has been challenging. Current advances in genome technologies provide new opportunities for obtaining a genome-scale view of the action of parasite-driven natural selection in wild populations and thus facilitate the search for specific genomic regions underlying inter-population differences in pathogen response. European populations of Atlantic salmon (Salmo salar L.) exhibit natural variance in susceptibility levels to the ectoparasite Gyrodactylus salaris Malmberg 1957, ranging from resistance to extreme susceptibility, and are therefore a good model for studying the evolution of virulence and resistance. However, distinguishing the molecular signatures of genetic drift and environment-associated selection in small populations such as land-locked Atlantic salmon populations presents a challenge, specifically in the search for pathogen-driven selection. We used a novel genome-scan analysis approach that enabled us to i) identify signals of selection in salmon populations affected by varying levels of genetic drift and ii) separate potentially selected loci into the categories of pathogen (G. salaris)-driven selection and selection acting upon other environmental characteristics. A total of 4631 single nucleotide polymorphisms (SNPs) were screened in Atlantic salmon from 12 different northern European populations. We identified three genomic regions potentially affected by parasite-driven selection, as well as three regions presumably affected by salinity-driven directional selection. Functional annotation of candidate SNPs is consistent with the role of the detected genomic regions in immune defence and, implicitly, in osmoregulation. These results provide new insights into the genetic basis of pathogen susceptibility in Atlantic salmon and will enable future searches for the specific genes involved.
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Affiliation(s)
- Ksenia J. Zueva
- Department of Biology, University of Turku, Turku, Finland
- * E-mail:
| | - Jaakko Lumme
- Department of Biology, University of Oulu, Oulu, Finland
| | - Alexey E. Veselov
- Institute of Biology, Karelian Research Centre of RAS, Petrozavodsk, Russia
| | - Matthew P. Kent
- Centre for Integrative Genetics (CIGENE) and Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE) and Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
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Norman JD, Ferguson MM, Danzmann RG. An integrated transcriptomic and comparative genomic analysis of differential gene expression in Arctic charr (Salvelinus alpinus) following seawater exposure. J Exp Biol 2014; 217:4029-42. [DOI: 10.1242/jeb.107441] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Abstract
High-throughput RNA sequencing was employed to compare expression profiles in two Arctic charr (Salvelinus alpinus) families post seawater exposure to identify genes and biological processes involved in hypo-osmoregulation and regulation of salinity tolerance. To further understand the genetic architecture of hypo-osmoregulation, the genomic organization of differentially expressed (DE) genes was also analysed. Using a de novo gill transcriptome assembly we found over 2300 contigs to be DE. Major transporters from the seawater mitochondrion-rich cell (MRC) complex were up-regulated in seawater. Expression ratios for 257 differentially expressed contigs were highly correlated between families, suggesting they are strictly regulated. Based on expression profiles and known molecular pathways we inferred that seawater exposure induced changes in methylation states and elevated peroxynitrite formation in gill. We hypothesized that concomitance between DE immune genes and the transition to a hypo-osmoregulatory state could be related to Cl- sequestration by antimicrobial defence mechanisms. Gene Ontology analysis revealed that cell division genes were up-regulated, which could reflect the proliferation of ATP1α1b-type seawater MRCs. Comparative genomics analyses suggest that hypo-osmoregulation is influenced by the relative proximities among a contingent of genes on Arctic charr linkage groups AC-4 and AC-12 that exhibit homologous affinities with a region on stickleback chromosome Ga-I. This supports the hypothesis that relative gene location along a chromosome is a property of the genetic architecture of hypo-osmoregulation. Evidence of non-random structure between hypo-osmoregulation candidate genes was found on AC-1/11 and AC-28, suggesting that interchromosomal rearrangements played a role in the evolution of hypo-osmoregulation in Arctic charr.
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17
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Norman JD, Ferguson MM, Danzmann RG. Transcriptomics of salinity tolerance capacity in Arctic charr (Salvelinus alpinus): a comparison of gene expression profiles between divergent QTL genotypes. Physiol Genomics 2013; 46:123-37. [PMID: 24368751 DOI: 10.1152/physiolgenomics.00105.2013] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Osmoregulatory capabilities have played an important role in the evolution, dispersal, and diversification of vertebrates. To better understand the genetic architecture of hypo-osmoregulation in fishes and to determine which genes and biological processes affect intraspecific variation in salinity tolerance, we used mRNA sequence libraries from Arctic charr gill tissue to compare gene expression profiles in fish exhibiting divergent salinity tolerance quantitative trait locus (QTL) genotypes. We compared differentially expressed genes with QTL positions to gain insight about the nature of the underlying polymorphisms and examined gene expression within the context of genome organization to gain insight about the evolution of hypo-osmoregulation in fishes. mRNA sequencing of 18 gill tissue libraries produced 417 million reads, and the final reduced de novo transcriptome assembly consisted of 92,543 contigs. Families contained a similar number of differentially expressed contigs between high and low salinity tolerance capacity groups, and log2 expression ratios ranged from 10.4 to -8.6. We found that intraspecific variation in salinity tolerance capacity correlated with differential expression of immune response genes. Some differentially expressed genes formed clusters along linkage groups. Most clusters comprised gene pairs, though clusters of three, four, and eight genes were also observed. We postulated that conserved synteny of gene clusters on multiple ancestral and teleost chromosomes may have been preserved via purifying selection. Colocalization of QTL with differentially expressed genes suggests that polymorphisms in cis-regulatory elements are part of a majority of QTL.
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Affiliation(s)
- Joseph D Norman
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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18
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Evaluating adaptive divergence between migratory and nonmigratory ecotypes of a salmonid fish, Oncorhynchus mykiss. G3-GENES GENOMES GENETICS 2013; 3:1273-85. [PMID: 23797103 PMCID: PMC3737167 DOI: 10.1534/g3.113.006817] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Next-generation sequencing and the application of population genomic and association approaches have made it possible to detect selection and unravel the genetic basis to variable phenotypic traits. The use of these two approaches in parallel is especially attractive in nonmodel organisms that lack a sequenced and annotated genome, but only works well when population structure is not confounded with the phenotype of interest. Herein, we use population genomics in a nonmodel fish species, rainbow trout (Oncorhynchus mykiss), to better understand adaptive divergence between migratory and nonmigratory ecotypes and to further our understanding about the genetic basis of migration. Restriction site-associated DNA (RAD) tag sequencing was used to identify single-nucleotide polymorphisms (SNPs) in migrant and resident O. mykiss from two systems, one in Alaska and the other in Oregon. A total of 7920 and 6755 SNPs met filtering criteria in the Alaska and Oregon data sets, respectively. Population genetic tests determined that 1423 SNPs were candidates for selection when loci were compared between resident and migrant samples. Previous linkage mapping studies that used RAD DNA tag SNPs were available to determine the position of 1990 markers. Several significant SNPs are located in genome regions that contain quantitative trait loci for migratory-related traits, reinforcing the importance of these regions in the genetic basis of migration/residency. Annotation of genome regions linked to significant SNPs revealed genes involved in processes known to be important in migration (such as osmoregulatory function). This study adds to our growing knowledge on adaptive divergence between migratory and nonmigratory ecotypes of this species; across studies, this complex trait appears to be controlled by many loci of small effect, with some in common, but many loci not shared between populations studied.
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Alexandrou MA, Swartz BA, Matzke NJ, Oakley TH. Genome duplication and multiple evolutionary origins of complex migratory behavior in Salmonidae. Mol Phylogenet Evol 2013; 69:514-23. [PMID: 23933489 DOI: 10.1016/j.ympev.2013.07.026] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 07/21/2013] [Accepted: 07/26/2013] [Indexed: 12/26/2022]
Abstract
Multiple rounds of whole genome duplication have repeatedly marked the evolution of vertebrates, and correlate strongly with morphological innovation. However, less is known about the behavioral, physiological and ecological consequences of genome duplication, and whether these events coincide with major transitions in vertebrate complexity. The complex behavior of anadromy - where adult fishes migrate up rivers from the sea to their natal site to spawn - is well known in salmonid fishes. Some hypotheses suggest that migratory behavior evolved as a consequence of an ancestral genome duplication event, which permitted salinity tolerance and osmoregulatory plasticity. Here we test whether anadromy evolved multiple times within salmonids, and whether genome duplication coincided with the evolution of anadromy. We present a method that uses ancestral character simulation data to plot the frequency of character transitions over a time calibrated phylogenetic tree to provide estimates of the absolute timing of character state transitions. Furthermore, we incorporate extinct and extant taxa to improve on previous estimates of divergence times. We present the first phylogenetic evidence indicating that anadromy evolved at least twice from freshwater salmonid ancestors. Results suggest that genome duplication did not coincide in time with changes in migratory behavior, but preceded a transition to anadromy by 55-50 million years. Our study represents the first attempt to estimate the absolute timing of a complex behavioral trait in relation to a genome duplication event.
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Affiliation(s)
- Markos A Alexandrou
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA
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20
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Xia JH, Lin G, He X, Liu P, Liu F, Sun F, Tu R, Yue GH. Whole genome scanning and association mapping identified a significant association between growth and a SNP in the IFABP-a gene of the Asian seabass. BMC Genomics 2013; 14:295. [PMID: 23634810 PMCID: PMC3653795 DOI: 10.1186/1471-2164-14-295] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 04/25/2013] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Aquaculture is the quickest growing sector in agriculture. However, QTL for important traits have been only identified in a few aquaculture species. We conducted QTL mapping for growth traits in an Asian seabass F(2) family with 359 individuals using 123 microsatellites and 22 SNPs, and performed association mapping in four populations with 881 individuals. RESULTS Twelve and nine significant QTL, as well as 14 and 10 suggestive QTL were detected for growth traits at six and nine months post hatch, respectively. These QTL explained 0.9-12.0% of the phenotypic variance. For body weight, two QTL intervals at two stages were overlapped while the others were mapped onto different positions. The IFABP-a gene located in a significant QTL interval for growth on LG5 was cloned and characterized. A SNP in exon 3 of the gene was significantly associated with growth traits in different populations. CONCLUSIONS The results of QTL mapping for growth traits suggest that growth at different stages was controlled by some common QTL and some different QTL. Positional candidate genes and association mapping suggest that the IFABP-a is a strong candidate gene for growth. Our data supply a basis for fine mapping QTL, marker-assisted selection and further detailed analysis of the functions of the IFABP-a gene in fish growth.
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Affiliation(s)
- Jun Hong Xia
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore
| | - Grace Lin
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore
| | - Xiaoping He
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore
| | - Peng Liu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore
| | - Feng Liu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore
| | - Fei Sun
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore
| | - Rongjian Tu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore
| | - Gen Hua Yue
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore
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Chiasson MA, Quinton CD, Danzmann RG, Ferguson MM. Comparative analysis of genetic parameters and quantitative trait loci for growth traits in Fraser strain Arctic charr (Salvelinus alpinus) reared in freshwater and brackish water environments. J Anim Sci 2013; 91:2047-56. [PMID: 23478828 DOI: 10.2527/jas.2012-5656] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
To determine the potential for genetic improvement in Fraser strain Arctic charr (AC, Salvelinus alpinus), we calculated genetic parameters for BW and condition factor (K) and tested if previously identified QTL for these traits were detectable across a commercial broodstock reared in both freshwater (FRW) and brackish water (BRW). Individuals from 30 full-sib families were reared up to 29 mo of age in FRW and BRW tanks at a commercial facility. Heritability for BW and K was moderate in FRW (0.29 to 0.38) but lower in BRW (0.14 to 0.17). Genetic correlations for BW across environments were positive and moderate (0.33 to 0.67); however, equivalent K correlations were very weak (0.24 to 0.37). We identified a single BW QTL with experimentwide effects on linkage group AC-8, 4 BW QTL (AC-4, -13, -14, and -19), and 3 K QTL (AC-4, -5, and -20) with chromosomewide effects across families. Notably, the QTL on AC-8 had significant effects with BW at 3 out of 4 sampling dates in FRW and had significant allelic phase disequilibrium with BW across families, suggesting a tight coupling of the marker region to the QTL in this population. Body weight QTL were identified on AC-4 in both FRW and BRW environments and AC-4 was the only linkage group with a detectable QTL for both K and BW. Modest consistency of some QTL effects as well as moderate heritability in both environments suggests that there is some potential for genetic improvement of growth in this species even though gene × environment interactions are high.
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Affiliation(s)
- M A Chiasson
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
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Corander J, Majander KK, Cheng L, Merilä J. High degree of cryptic population differentiation in the Baltic Sea herring Clupea harengus. Mol Ecol 2013; 22:2931-40. [PMID: 23294045 DOI: 10.1111/mec.12174] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 11/01/2012] [Accepted: 11/06/2012] [Indexed: 12/27/2022]
Abstract
Marine fish species are characterized by a low degree of population differentiation at putatively neutral marker genes. This has been traditionally attributed to ecological homogeneity and a lack of obvious dispersal barriers in marine habitats, as well as to the large (effective) population sizes of most marine fish species. The herring (Clupea harengus) is a case in point - the levels of population differentiation at neutral markers, even across vast geographic areas, are typically very low (FST ≈ 0.005). We used a RAD-sequencing approach to identify 5985 novel single-nucleotide polymorphism markers (SNPs) in herring and estimated genome-wide levels of divergence using pooled DNA samples between two Baltic Sea populations separated by 387 km. We found a total of 4756 divergent SNPs (79% of all SNPs) between the populations, of which 117 showed evidence of substantial divergence, corresponding to F(ST) = 0.128 (0.125, 0.131) after accounting for possible biases due to minor alleles and uneven DNA amplification over the pooled samples. This estimate - based on screening many genomic polymorphisms - suggests the existence of hitherto unrecognized levels of genetic differentiation in this commercially important species, challenging the view of genetic homogeneity in marine fish species, and in that of the Baltic Sea herring in particular.
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Affiliation(s)
- Jukka Corander
- Department of Mathematics and Statistics, University Helsinki, FI-00014, Helsinki, Finland
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Norman JD, Robinson M, Glebe B, Ferguson MM, Danzmann RG. Genomic arrangement of salinity tolerance QTLs in salmonids: a comparative analysis of Atlantic salmon (Salmo salar) with Arctic charr (Salvelinus alpinus) and rainbow trout (Oncorhynchus mykiss). BMC Genomics 2012; 13:420. [PMID: 22916800 PMCID: PMC3480877 DOI: 10.1186/1471-2164-13-420] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 08/16/2012] [Indexed: 11/10/2022] Open
Abstract
Background Quantitative trait locus (QTL) studies show that variation in salinity tolerance in Arctic charr and rainbow trout has a genetic basis, even though both these species have low to moderate salinity tolerance capacities. QTL were observed to localize to homologous linkage group segments within putative chromosomal regions possessing multiple candidate genes. We compared salinity tolerance QTL in rainbow trout and Arctic charr to those detected in a higher salinity tolerant species, Atlantic salmon. The highly derived karyotype of Atlantic salmon allows for the assessment of whether disparity in salinity tolerance in salmonids is associated with differences in genetic architecture. To facilitate these comparisons, we examined the genomic synteny patterns of key candidate genes in the other model teleost fishes that have experienced three whole-genome duplication (3R) events which preceded a fourth (4R) whole genome duplication event common to all salmonid species. Results Nine linkage groups contained chromosome-wide significant QTL (AS-2, -4p, -4q, -5, -9, -12p, -12q, -14q -17q, -22, and −23), while a single genome-wide significant QTL was located on AS-4q. Salmonid genomes shared the greatest marker homology with the genome of three-spined stickleback. All linkage group arms in Atlantic salmon were syntenic with at least one stickleback chromosome, while 18 arms had multiple affinities. Arm fusions in Atlantic salmon were often between multiple regions bearing salinity tolerance QTL. Nine linkage groups in Arctic charr and six linkage group arms in rainbow trout currently have no synteny alignments with stickleback chromosomes, while eight rainbow trout linkage group arms were syntenic with multiple stickleback chromosomes. Rearrangements in the stickleback lineage involving fusions of ancestral arm segments could account for the 21 chromosome pairs observed in the stickleback karyotype. Conclusions Salinity tolerance in salmonids from three genera is to some extent controlled by the same loci. Synteny between QTL in salmonids and candidate genes in stickleback suggests genetic variation at candidate gene loci could affect salinity tolerance in all three salmonids investigated. Candidate genes often occur in pairs on chromosomes, and synteny patterns indicate these pairs are generally conserved in 2R, 3R, and 4R genomes. Synteny maps also suggest that the Atlantic salmon genome contains three larger syntenic combinations of candidate genes that are not evident in any of the other 2R, 3R, or 4R genomes examined. These larger synteny tracts appear to have resulted from ancestral arm fusions that occurred in the Atlantic salmon ancestor. We hypothesize that the superior hypo-osmoregulatory efficiency that is characteristic of Atlantic salmon may be related to these clusters.
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Affiliation(s)
- Joseph D Norman
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
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