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Clare CI, Nichols KM, Thrower FP, Berntson EA, Hale MC. Comparative genomics of rainbow trout ( Oncorhynchus mykiss): Is the genetic architecture of migratory behavior conserved among populations? Ecol Evol 2023; 13:e10241. [PMID: 37384247 PMCID: PMC10293719 DOI: 10.1002/ece3.10241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/01/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023] Open
Abstract
Rainbow trout (Oncorhynchus mykiss) are a partially migratory species wherein some individuals undergo long-distance anadromous migrations, and others stay as residents in their native freshwater streams. The decision to migrate is known to be highly heritable, and yet, the underlying genes and alleles associated with migration are not fully characterized. Here we used a pooled approach of whole-genome sequence data from migratory and resident trout of two native populations-Sashin Creek, Alaska and Little Sheep Creek, Oregon-to obtain a genome-wide perspective of the genetic architecture of resident and migratory life history. We calculated estimates of genetic differentiation, genetic diversity, and selection between the two phenotypes to locate regions of interest and then compared these associations between populations. We identified numerous genes and alleles associated with life history development in the Sashin Creek population with a notable area on chromosome 8 that may play a critical role in the development of the migratory phenotype. However, very few alleles appeared to be associated with life history development in the Little Sheep Creek system, suggesting population-specific genetic effects are likely important in the development of anadromy. Our results indicate that a migratory life history is not controlled by a singular gene or region but supports the idea that there are many independent ways for a migratory phenotype to emerge in a population. Therefore, conserving and promoting genetic diversity in migratory individuals is paramount to conserving these populations. Ultimately, our data add to a growing body of literature that suggests that population-specific genetic effects, likely mediated through environmental variation, contribute to life history development in rainbow trout.
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Affiliation(s)
| | - Krista M. Nichols
- Conservation Biology Division, Northwest Fisheries Science CenterNational Marine Fisheries Service, National Oceanic and Atmospheric AdministrationSeattleWashingtonUSA
| | - Frank P. Thrower
- Ted Stevens Marine Research Institute, Alaska Fisheries Science Center, NOAAJuneauAlaskaUSA
| | - Ewann A. Berntson
- Conservation Biology Division, Northwest Fisheries Science CenterNational Marine Fisheries Service, National Oceanic and Atmospheric AdministrationSeattleWashingtonUSA
| | - Matthew C. Hale
- Department of BiologyTexas Christian UniversityFort WorthTexasUSA
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Detoxification Gene Families at the Genome-Wide Level of Rhus Gall Aphid Schlechtendalia chinensis. Genes (Basel) 2022; 13:genes13091627. [PMID: 36140795 PMCID: PMC9498883 DOI: 10.3390/genes13091627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 12/02/2022] Open
Abstract
The Rhus gall aphid Schlechtendalia chinensis uses the species Rhus chinensis as its primary host plant, on which galls are produced. The galls have medicinal properties and can be used in various situations due to their high tannin content. Detoxification enzymes play significant roles in the insect lifecycle. In this study, we focused on five detoxification gene families, i.e., glutathione-S-transferase (GST), ABC transporter (ABC), Carboxylesterase (CCE), cyto-chrome P450 (CYP), and UDP-glycosyltransferase (UDP), and manually annotated 144 detoxification genes of S. chinensis using genome-wide techniques. The detoxification genes appeared mostly on chromosome 1, where a total of two pair genes were identified to show tandem duplications. There were 38 gene pairs between genomes of S. chinensis and Acyrthosiphon pisum in the detoxification gene families by collinear comparison. Ka/Ks ratios showed that detoxification genes of S. chinensis were mainly affected by purification selection during evolution. The gene expression numbers of P450s and ABCs by transcriptome sequencing data were greater, while gene expression of CCEs was the highest, suggesting they might be important in the detoxification process. Our study has firstly identified the genes of the different detoxification gene families in the S. chinensis genome, and then analyzed their general features and expression, demonstrating the importance of the detoxification genes in the aphid and providing new information for further research.
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Collins EE, Romero N, Zendt JS, Narum SR. Whole-Genome Resequencing to Evaluate Life History Variation in Anadromous Migration of Oncorhynchus mykiss. Front Genet 2022; 13:795850. [PMID: 35368705 PMCID: PMC8964970 DOI: 10.3389/fgene.2022.795850] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/24/2022] [Indexed: 12/04/2022] Open
Abstract
Anadromous fish experience physiological modifications necessary to migrate between vastly different freshwater and marine environments, but some species such as Oncorhynchus mykiss demonstrate variation in life history strategies with some individuals remaining exclusively resident in freshwater, whereas others undergo anadromous migration. Because there is limited understanding of genes involved in this life history variation across populations of this species, we evaluated the genomic difference between known anadromous (n = 39) and resident (n = 78) Oncorhynchus mykiss collected from the Klickitat River, WA, USA, with whole-genome resequencing methods. Sequencing of these collections yielded 5.64 million single-nucleotide polymorphisms that were tested for significant differences between resident and anadromous groups along with previously identified candidate gene regions. Although a few regions of the genome were marginally significant, there was one region on chromosome Omy12 that provided the most consistent signal of association with anadromy near two annotated genes in the reference assembly: COP9 signalosome complex subunit 6 (CSN6) and NACHT, LRR, and PYD domain–containing protein 3 (NLRP3). Previously identified candidate genes for anadromy within the inversion region of chromosome Omy05 in coastal steelhead and rainbow trout were not informative for this population as shown in previous studies. Results indicate that the significant region on chromosome Omy12 may represent a minor effect gene for male anadromy and suggests that this life history variation in Oncorhynchus mykiss is more strongly driven by other mechanisms related to environmental rearing such as epigenetic modification, gene expression, and phenotypic plasticity. Further studies into regulatory mechanisms of this trait are needed to understand drivers of anadromy in populations of this protected species.
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Affiliation(s)
- Erin E. Collins
- Hagerman Genetics Laboratory, Columbia River Inter-Tribal Fish Commission, Hagerman, ID, United States
- *Correspondence: Erin E. Collins,
| | - Nicolas Romero
- Yakama Nation Fisheries, Yakima/Klickitat Fisheries Project, Klickitat, WA, United States
| | - Joseph S. Zendt
- Yakama Nation Fisheries, Yakima/Klickitat Fisheries Project, Klickitat, WA, United States
| | - Shawn R. Narum
- Hagerman Genetics Laboratory, Columbia River Inter-Tribal Fish Commission, Hagerman, ID, United States
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4
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Hale MC, McLaughlin R, Wilson C, Mackereth R, Nichols KM. Differential gene expression associated with behavioral variation in ecotypes of Lake Superior brook trout (Salvelinus fontinalis). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 40:100884. [PMID: 34303261 DOI: 10.1016/j.cbd.2021.100884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/06/2021] [Accepted: 07/10/2021] [Indexed: 11/17/2022]
Abstract
Associations between behaviors and the development of different life history tactics have been documented in several species of salmon, trout, and charr. While it is well known that such behaviors are heritable the genes and molecular pathways connected to these behaviors remain unknown. We used an RNA-seq approach to identify genes and molecular pathways differentially regulated in brain tissue between "shy" and "bold" brook trout (Salvelinus fontinalis). A small number of genes were differentially expressed between the behavioral types at several months after hatching and two years of age. Pathway analysis revealed that EIF2 signaling differed consistently between shy and bold individuals suggesting large-scale differences in protein synthesis between behavioral types in the brain. Additionally, the RNA-seq data were used to find polymorphisms within the brook trout genome and a GWAS approach was used to test for statistical associations between genetic variants and behavior type. One allele located in a transcription factor (TSHZ3) contained a protein-coding non-synonymous SNP suggesting that functional variation within TSHZ3 is connected to the development of different behaviors. These results suggest that the molecular basis of behavioral development is complex and due to the differential expression of many genes involved in a wide-range of different molecular pathways.
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Affiliation(s)
- Matthew C Hale
- Department of Biology, Texas Christian University, Fort Worth, TX 76129, United States of America.
| | - Robert McLaughlin
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Chris Wilson
- Aquatic Biodiversity and Conservation Unit, Ontario Ministry of Natural Resources, Trent University, Peterborough, ON K9J 7B8, Canada
| | - Robert Mackereth
- Department of Biology, Lakehead University, Thunder Bay, ON P7B 5E1, Canada
| | - Krista M Nichols
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA 98112, United States of America
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5
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Jonsson B, Jonsson N. Differences in growth between offspring of anadromous and freshwater brown trout Salmo trutta. JOURNAL OF FISH BIOLOGY 2021; 99:18-24. [PMID: 33534141 DOI: 10.1111/jfb.14693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/19/2021] [Accepted: 01/02/2021] [Indexed: 06/12/2023]
Abstract
In this study, individual growth of juvenile offspring of anadromous and freshwater resident brown trout Salmo trutta and crosses between the two from the River Imsa, Norway, was estimated. The juveniles were incubated until hatching at two temperatures (±S.D.), either 4.4 ± 1.5°C or 7.1 ± 0.6°C. Growth rate was estimated for 22 days in August-September when the fish on average were c. 8 g in wet mass, and the estimates were standardized to 1 g fish dry mass. Offspring of anadromous S. trutta grew better at both 15 and 18°C than offspring of freshwater resident S. trutta or offspring of crosses between the two S. trutta types. This difference appears not to result from a maternal effect because anadromous S. trutta grew better than the hybrids with anadromous mothers. Instead, this appears to be an inherited difference between the anadromous and the freshwater resident fish lending support to the hypothesis that anadromous and freshwater resident S. trutta in this river differ in genetic expression. Egg incubation temperature of S. trutta appeared not to influence the later growth as reported earlier from the studies of Atlantic salmon Salmo salar.
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Affiliation(s)
- Bror Jonsson
- Norwegian Institute for Nature Research, Oslo, Norway
| | - Nina Jonsson
- Norwegian Institute for Nature Research, Oslo, Norway
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Wynne R, Archer LC, Hutton SA, Harman L, Gargan P, Moran PA, Dillane E, Coughlan J, Cross TF, McGinnity P, Colgan TJ, Reed TE. Alternative migratory tactics in brown trout ( Salmo trutta) are underpinned by divergent regulation of metabolic but not neurological genes. Ecol Evol 2021; 11:8347-8362. [PMID: 34188891 PMCID: PMC8216917 DOI: 10.1002/ece3.7664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/15/2021] [Accepted: 04/18/2021] [Indexed: 12/03/2022] Open
Abstract
The occurrence of alternative morphs within populations is common, but the underlying molecular mechanisms remain poorly understood. Many animals, for example, exhibit facultative migration, where two or more alternative migratory tactics (AMTs) coexist within populations. In certain salmonid species, some individuals remain in natal rivers all their lives, while others (in particular, females) migrate to sea for a period of marine growth. Here, we performed transcriptional profiling ("RNA-seq") of the brain and liver of male and female brown trout to understand the genes and processes that differentiate between migratory and residency morphs (AMT-associated genes) and how they may differ in expression between the sexes. We found tissue-specific differences with a greater number of genes expressed differentially in the liver (n = 867 genes) compared with the brain (n = 10) between the morphs. Genes with increased expression in resident livers were enriched for Gene Ontology terms associated with metabolic processes, highlighting key molecular-genetic pathways underlying the energetic requirements associated with divergent migratory tactics. In contrast, smolt-biased genes were enriched for biological processes such as response to cytokines, suggestive of possible immune function differences between smolts and residents. Finally, we identified evidence of sex-biased gene expression for AMT-associated genes in the liver (n = 12) but not the brain. Collectively, our results provide insights into tissue-specific gene expression underlying the production of alternative life histories within and between the sexes, and point toward a key role for metabolic processes in the liver in mediating divergent physiological trajectories of migrants versus residents.
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Affiliation(s)
- Robert Wynne
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | - Louise C. Archer
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | - Stephen A. Hutton
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | - Luke Harman
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | | | - Peter A. Moran
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
- Present address:
Department of Ecological Science – Animal EcologyVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Eileen Dillane
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | - Jamie Coughlan
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | - Thomas F. Cross
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | - Philip McGinnity
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
- Marine InstituteNewportIreland
| | - Thomas J. Colgan
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
- Present address:
Institute of Organismic and Molecular EvolutionJohannes Gutenberg University MainzMainzGermany
| | - Thomas E. Reed
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
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Bootsma ML, Miller L, Sass GG, Euclide PT, Larson WA. The ghosts of propagation past: haplotype information clarifies the relative influence of stocking history and phylogeographic processes on contemporary population structure of walleye ( Sander vitreus). Evol Appl 2021; 14:1124-1144. [PMID: 33897825 PMCID: PMC8061267 DOI: 10.1111/eva.13186] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 12/05/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022] Open
Abstract
Stocking of fish is an important tool for maintaining fisheries but can also significantly alter population genetic structure and erode the portfolio of within-species diversity that is important for promoting resilience and adaptability. Walleye (Sander vitreus) are a highly valued sportfish in the midwestern United States, a region characterized by postglacial recolonization from multiple lineages and an extensive history of stocking. We leveraged genomic data and recently developed analytical approaches to explore the population structure of walleye from two midwestern states, Minnesota and Wisconsin. We genotyped 954 walleye from 23 populations at ~20,000 loci using genotyping by sequencing and tested for patterns of population structure with single-SNP and microhaplotype data. Populations from Minnesota and Wisconsin were highly differentiated from each other, with additional substructure found in each state. Population structure did not consistently adhere to drainage boundaries, as cases of high intra-drainage and low inter-drainage differentiation were observed. Low genetic structure was observed between populations from the upper Wisconsin and upper Chippewa river watersheds, which are found as few as 50 km apart and were likely homogenized through historical stocking. Nevertheless, we were able to differentiate these populations using microhaplotype-based co-ancestry analysis, providing increased resolution over previous microsatellite studies and our other single SNP-based analyses. Although our results illustrate that walleye population structure has been influenced by past stocking practices, native ancestry still exists in most populations and walleye populations may be able to purge non-native alleles and haplotypes in the absence of stocking. Our study is one of the first to use genomic tools to investigate the influence of stocking on population structure in a nonsalmonid fish and outlines a workflow leveraging recently developed analytical methods to improve resolution of complex population structure that will be highly applicable in many species and systems.
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Affiliation(s)
- Matthew L. Bootsma
- Wisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
| | - Loren Miller
- Minnesota Department of Natural ResourcesUniversity of MinnesotaSt. PaulMNUSA
| | - Greg G. Sass
- Office of Applied ScienceWisconsin Department of Natural ResourcesEscanaba Lake Research StationBoulder JunctionWIUSA
| | - Peter T. Euclide
- Wisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
| | - Wesley A. Larson
- U.S. Geological SurveyWisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
- Present address:
Ted Stevens Marine Research InstituteAlaska Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationJuneauAKUSA
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8
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The Impacts of Dam Construction and Removal on the Genetics of Recovering Steelhead ( Oncorhynchus mykiss) Populations across the Elwha River Watershed. Genes (Basel) 2021; 12:genes12010089. [PMID: 33450806 PMCID: PMC7828262 DOI: 10.3390/genes12010089] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/04/2021] [Accepted: 01/07/2021] [Indexed: 11/25/2022] Open
Abstract
Dam construction and longitudinal river habitat fragmentation disrupt important life histories and movement of aquatic species. This is especially true for Oncorhynchus mykiss that exhibits both migratory (steelhead) and non-migratory (resident rainbow) forms. While the negative effects of dams on salmonids have been extensively documented, few studies have had the opportunity to compare population genetic diversity and structure prior to and following dam removal. Here we examine the impacts of the removal of two dams on the Elwha River on the population genetics of O. mykiss. Genetic data were produced from >1200 samples collected prior to dam removal from both life history forms, and post-dam removal from steelhead. We identified three genetic clusters prior to dam removal primarily explained by isolation due to dams and natural barriers. Following dam removal, genetic structure decreased and admixture increased. Despite large O. mykiss population declines after dam construction, we did not detect shifts in population genetic diversity or allele frequencies of loci putatively involved in migratory phenotypic variation. Steelhead descendants from formerly below and above dammed populations recolonized the river rapidly after dam removal, suggesting that dam construction did not significantly reduce genetic diversity underlying O. mykiss life history strategies. These results have significant evolutionary implications for the conservation of migratory adaptive potential in O. mykiss populations above current anthropogenic barriers.
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9
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The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome. PLoS One 2020; 15:e0240935. [PMID: 33119641 PMCID: PMC7595290 DOI: 10.1371/journal.pone.0240935] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022] Open
Abstract
Sockeye salmon (Oncorhynchus nerka) is a commercially and culturally important species to the people that live along the northern Pacific Ocean coast. There are two main sockeye salmon ecotypes—the ocean-going (anadromous) ecotype and the fresh-water ecotype known as kokanee. The goal of this study was to better understand the population structure of sockeye salmon and identify possible genomic differences among populations and between the two ecotypes. In pursuit of this goal, we generated the first reference sockeye salmon genome assembly and an RNA-seq transcriptome data set to better annotate features of the assembly. Resequenced whole-genomes of 140 sockeye salmon and kokanee were analyzed to understand population structure and identify genomic differences between ecotypes. Three distinct geographic and genetic groups were identified from analyses of the resequencing data. Nucleotide variants in an immunoglobulin heavy chain variable gene cluster on chromosome 26 were found to differentiate the northwestern group from the southern and upper Columbia River groups. Several candidate genes were found to be associated with the kokanee ecotype. Many of these genes were related to ammonia tolerance or vision. Finally, the sex chromosomes of this species were better characterized, and an alternative sex-determination mechanism was identified in a subset of upper Columbia River kokanee.
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10
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Yang L, Jiang H, Chen J, Lei Y, Sun N, Lv W, Near TJ, He S. Comparative Genomics Reveals Accelerated Evolution of Fright Reaction Genes in Ostariophysan Fishes. Front Genet 2019; 10:1283. [PMID: 31921316 PMCID: PMC6936194 DOI: 10.3389/fgene.2019.01283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/21/2019] [Indexed: 11/13/2022] Open
Abstract
The ostariophysian fishes are the most species-rich clade in freshwaters. This diversification has been suggested to be associated with the fright reaction presented in most ostariophysians. However, the genetic forces that underlie fright reaction remains poorly understood. In the present study, through integrating behavioral, physiological, transcriptomic, and evolutionary genomic analyses, we found that the fright reaction has a broad impact on zebrafish at multiple levels, including changes in swimming behaviors, cortisol levels, and gene expression patterns. In total, 1,555 and 1,599 differentially expressed genes were identified in olfactory mucosae and brain of zebrafish, respectively, with a greater number upregulated after the fright reaction. Functional annotation showed that response to stress and signal transduction were strongly represented, which is directly associated with the fright reaction. These differentially expressed genes were shown to be evolved accelerated under the influence of positive selection, indicating that protein-coding evolution has played a major role in fright reaction. We found the basal vomeronasal type 2 receptors (v2r) gene, v2rl1, displayed significantly decrease expression after fright reaction, which suggests that v2rs may be important to detect the alarm substance and induce the fright reaction. Collectively, based on our transcriptome and evolutionary genomics analyses, we suggest that transcriptional plasticity of gene may play an important role in fright reaction in ostariophysian fishes.
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Affiliation(s)
- Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Haifeng Jiang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Juan Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yi Lei
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ning Sun
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenqi Lv
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT, United States
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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11
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Arostegui MC, Quinn TP. Ontogenetic and ecotypic variation in the coloration and morphology of rainbow trout (Oncorhynchus mykiss) in a stream–lake system. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Alternative ecotypes of diverse animal taxa exhibit distinct, habitat-specific phenotypes. Rainbow trout (Oncorhynchus mykiss), a salmonid fish, exhibits stream-resident (fluvial), lake-migrant (adfluvial) and ocean-migrant (anadromous) ecotypes throughout its range. We investigated the coloration, and morphology associated with swimming performance of wild, native non-anadromous rainbow trout in connected stream and lake habitats of a south-west Alaskan watershed to assess if they exhibited phenotypic diversity consistent with the presence of alternative fluvial and adfluvial ecotypes. Colour differences among rainbow trout of different size classes and habitats (stream or lake) indicated ecotype-specific pathways, diverging at the same point in ontogeny and resulting in different terminal coloration patterns. Specifically, lake-caught fish exhibited distinct silvering of the body, whereas stream-caught fish displayed banded coloration when small and bronze colour when larger. The morphology of lake-caught rainbow trout also differed from that of stream-caught fish in features associated with swimming performance, and they exhibited both shared and unique morphological patterns compared to sympatric Salvelinus species in those habitats [Dolly Varden (S. malma) in streams, and Arctic char (S. alpinus) in the lake]. Greater morphological variation within stream- than lake-caught rainbow trout, and their limited overlap in morphology, suggested population-specific partial migration. This study highlights the intraspecific diversity of migratory behaviour and how conservation of particular phenotypes depends on managing both for genotypes and for habitats.
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Affiliation(s)
- M C Arostegui
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - T P Quinn
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
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12
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Weinstein SY, Thrower FP, Nichols KM, Hale MC. A large-scale chromosomal inversion is not associated with life history development in rainbow trout from Southeast Alaska. PLoS One 2019; 14:e0223018. [PMID: 31539414 PMCID: PMC6754156 DOI: 10.1371/journal.pone.0223018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/11/2019] [Indexed: 01/12/2023] Open
Abstract
In studying the causative mechanisms behind migration and life history, the salmonids-salmon, trout, and charr-are an exemplary taxonomic group, as life history development is known to have a strong genetic component. A double inversion located on chromosome 5 in rainbow trout (Oncorhynchus mykiss) is associated with life history development in multiple populations, but the importance of this inversion has not been thoroughly tested in conjunction with other polymorphisms in the genome. To that end, we used a high-density SNP chip to genotype 192 F1 migratory and resident rainbow trout and focused our analyses to determine whether this inversion is important in life history development in a well-studied population of rainbow trout from Southeast Alaska. We identified 4,994 and 436 SNPs-predominantly outside of the inversion region-associated with life history development in the migrant and resident familial lines, respectively. Although F1 samples showed genomic patterns consistent with the double inversion on chromosome 5 (reduced observed and expected heterozygosity and an increase in linkage disequilibrium), we found no statistical association between the inversion and life history development. Progeny produced by crossing resident trout and progeny produced by crossing migrant trout both consisted of a mix of migrant and resident individuals, irrespective of the individuals' inversion haplotype on chromosome 5. This suggests that although the inversion is present at a low frequency, it is not strongly associated with migration as it is in populations of Oncorhynchus mykiss from lower latitudes.
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Affiliation(s)
- Spencer Y. Weinstein
- Department of Biology, Texas Christian University, Fort Worth, United States of America
| | - Frank P. Thrower
- Ted Stevens Marine Research Institute, Alaska Fisheries Center, NOAA, Juneau, AK, United States of America
| | - Krista M. Nichols
- Conservation Biology Division, Northwest Fisheries Science Center, Seattle, WA, United States of America
| | - Matthew C. Hale
- Department of Biology, Texas Christian University, Fort Worth, United States of America
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13
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Association Mapping Based on a Common-Garden Migration Experiment Reveals Candidate Genes for Migration Tendency in Brown Trout. G3-GENES GENOMES GENETICS 2019; 9:2887-2896. [PMID: 31289024 PMCID: PMC6723140 DOI: 10.1534/g3.119.400369] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A better understanding of the environmental and genetic contribution to migratory behavior and the evolution of traits linked to migration is crucial for fish conservation and fisheries management. Up to date, a few genes with unequivocal influence on the adoption of alternative migration strategies have been identified in salmonids. Here, we used a common garden set-up to measure individual migration distances of generally highly polymorphic brown trout Salmo trutta from two populations. Fish from the assumedly resident population showed clearly shorter migration distances than the fish from the assumed migratory population at the ages of 2 and 3 years. By using two alternative analytical pipelines with 22186 and 18264 SNPs obtained through RAD-sequencing, we searched for associations between individual migration distance, and both called genotypes and genotype probabilities. None of the SNPs showed statistically significant individual effects on migration after correction for multiple testing. By choosing a less stringent threshold, defined as an overlap of the top 0.1% SNPs identified by the analytical pipelines, GAPIT and Angsd, we identified eight candidate genes that are potentially linked to individual migration distance. While our results demonstrate large individual and population level differences in migration distances, the detected genetic associations were weak suggesting that migration traits likely have multigenic control.
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14
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Ferguson A, Reed TE, Cross TF, McGinnity P, Prodöhl PA. Anadromy, potamodromy and residency in brown trout Salmo trutta: the role of genes and the environment. JOURNAL OF FISH BIOLOGY 2019; 95:692-718. [PMID: 31197849 PMCID: PMC6771713 DOI: 10.1111/jfb.14005] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/09/2019] [Indexed: 05/10/2023]
Abstract
Brown trout Salmo trutta is endemic to Europe, western Asia and north-western Africa; it is a prominent member of freshwater and coastal marine fish faunas. The species shows two resident (river-resident, lake-resident) and three main facultative migratory life histories (downstream-upstream within a river system, fluvial-adfluvial potamodromous; to and from a lake, lacustrine-adfluvial (inlet) or allacustrine (outlet) potamodromous; to and from the sea, anadromous). River-residency v. migration is a balance between enhanced feeding and thus growth advantages of migration to a particular habitat v. the costs of potentially greater mortality and energy expenditure. Fluvial-adfluvial migration usually has less feeding improvement, but less mortality risk, than lacustrine-adfluvial or allacustrine and anadromous, but the latter vary among catchments as to which is favoured. Indirect evidence suggests that around 50% of the variability in S. trutta migration v. residency, among individuals within a population, is due to genetic variance. This dichotomous decision can best be explained by the threshold-trait model of quantitative genetics. Thus, an individual's physiological condition (e.g., energy status) as regulated by environmental factors, genes and non-genetic parental effects, acts as the cue. The magnitude of this cue relative to a genetically predetermined individual threshold, governs whether it will migrate or sexually mature as a river-resident. This decision threshold occurs early in life and, if the choice is to migrate, a second threshold probably follows determining the age and timing of migration. Migration destination (mainstem river, lake, or sea) also appears to be genetically programmed. Decisions to migrate and ultimate destination result in a number of subsequent consequential changes such as parr-smolt transformation, sexual maturity and return migration. Strong associations with one or a few genes have been found for most aspects of the migratory syndrome and indirect evidence supports genetic involvement in all parts. Thus, migratory and resident life histories potentially evolve as a result of natural and anthropogenic environmental changes, which alter relative survival and reproduction. Knowledge of genetic determinants of the various components of migration in S. trutta lags substantially behind that of Oncorhynchus mykiss and other salmonines. Identification of genetic markers linked to migration components and especially to the migration-residency decision, is a prerequisite for facilitating detailed empirical studies. In order to predict effectively, through modelling, the effects of environmental changes, quantification of the relative fitness of different migratory traits and of their heritabilities, across a range of environmental conditions, is also urgently required in the face of the increasing pace of such changes.
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Affiliation(s)
- Andrew Ferguson
- School of Biological SciencesQueen's University BelfastBelfastUK
| | - Thomas E. Reed
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Tom F. Cross
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Philip McGinnity
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Paulo A. Prodöhl
- School of Biological SciencesQueen's University BelfastBelfastUK
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15
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Campbell MA, Hale MC, McKinney GJ, Nichols KM, Pearse DE. Long-Term Conservation of Ohnologs Through Partial Tetrasomy Following Whole-Genome Duplication in Salmonidae. G3 (BETHESDA, MD.) 2019; 9:2017-2028. [PMID: 31010824 PMCID: PMC6553544 DOI: 10.1534/g3.119.400070] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/18/2019] [Indexed: 01/01/2023]
Abstract
Whole-genome duplications (WGDs) have occurred repeatedly and broadly throughout the evolutionary history of eukaryotes. However, the effects of WGD on genome function and evolution remain unclear. The salmonid WGD that occurred approximately 88 million years ago presents an excellent opportunity for studying the effects of WGD as ∼10-15% of each salmonid genome still exhibits tetrasomic inheritance. Herein, we utilized the rainbow trout (Oncorhynchus mykiss) genome assembly and brain transcriptome data to examine the fate of gene pairs (ohnologs) following the salmonid whole-genome duplication. We find higher sequence identity between ohnologs located within known tetrasomic regions than between ohnologs found in disomic regions, and that tetrasomically inherited ohnologs showed greater similarity in patterns of gene expression and per ohnolog were lower expressed, than disomically inherited ohnologs. Enrichment testing for Gene Ontology terms identified 49 over-represented terms in tetrasomically inherited ohnologs compared to disomic ohnologs. However, why these ohnologs are retained as tetrasomic is difficult to answer. It could be that we have identified salmonid specific "dangerous duplicates", that is, genes that cannot take on new roles following WGD. Alternatively, there may be adaptive advantages for retaining genes as functional duplicates in tetrasomic regions, as presumably, movement of these genes into disomic regions would affect both their sequence identity and their gene expression patterns.
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Affiliation(s)
- Matthew A Campbell
- Fisheries Ecology Division, Southwest Fisheries Science Center, Santa Cruz, CA 95060
| | - Matthew C Hale
- Department of Biology, Texas Christian University, Fort Worth, TX 76129
| | - Garrett J McKinney
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98195, and
| | - Krista M Nichols
- Conservation Biology Division, Northwest Fisheries Science Center, Seattle, WA 98112
| | - Devon E Pearse
- Fisheries Ecology Division, Southwest Fisheries Science Center, Santa Cruz, CA 95060
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16
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Arostegui MC, Quinn TP, Seeb LW, Seeb JE, McKinney GJ. Retention of a chromosomal inversion from an anadromous ancestor provides the genetic basis for alternative freshwater ecotypes in rainbow trout. Mol Ecol 2019; 28:1412-1427. [DOI: 10.1111/mec.15037] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 01/18/2019] [Accepted: 01/28/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Martin C. Arostegui
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - Thomas P. Quinn
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - Lisa W. Seeb
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - James E. Seeb
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - Garrett J. McKinney
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
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17
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Lemopoulos A, Uusi-Heikkilä S, Huusko A, Vasemägi A, Vainikka A. Comparison of Migratory and Resident Populations of Brown Trout Reveals Candidate Genes for Migration Tendency. Genome Biol Evol 2018; 10:1493-1503. [PMID: 29850813 PMCID: PMC6007540 DOI: 10.1093/gbe/evy102] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2018] [Indexed: 12/23/2022] Open
Abstract
Candidate genes associated with migration have been identified in multiple taxa: including salmonids, many of whom perform migrations requiring a series of physiological changes associated with the freshwater–saltwater transition. We screened over 5,500 SNPs for signatures of selection related to migratory behavior of brown trout Salmo trutta by focusing on ten differentially migrating freshwater populations from two watersheds (the Koutajoki and the Oulujoki). We found eight outlier SNPs potentially associated with migratory versus resident life history using multiple (≥3) outlier detection approaches. Comparison of three migratory versus resident population pairs in the Koutajoki watershed revealed seven outlier SNPs, of which three mapped close to genes ZNF665-like, GRM4-like, and PCDH8-like that have been previously associated with migration and smoltification in salmonids. Two outlier SNPs mapped to genes involved in mucus secretion (ST3GAL1-like) and osmoregulation (C14orf37-like). The last two strongly supported outlier SNPs mapped to thermally induced genes (FNTA1-like, FAM134C-like). Within the Oulujoki, the only consistent outlier SNP mapped close to a gene (EZH2) that is associated with compensatory growth in fasted trout. Our results suggest that a relatively small yet common set of genes responsible for physiological functions associated with resident and migratory life histories is evolutionarily conserved.
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Affiliation(s)
- Alexandre Lemopoulos
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.,Department of Biology, University of Turku, Finland
| | - Silva Uusi-Heikkilä
- Department of Biology, University of Turku, Finland.,Department of Biological and Environmental Science, University of Jyväskylä, Finland
| | - Ari Huusko
- Aquatic population dynamics, Natural Resources Institute Finland (Luke), Paltamo, Finland
| | - Anti Vasemägi
- Department of Biology, University of Turku, Finland.,Department of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia.,Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, Drottningholm, Sweden.,These authors shared senior authorship
| | - Anssi Vainikka
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.,These authors shared senior authorship
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18
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Houde ALS, Schulze AD, Kaukinen KH, Strohm J, Patterson DA, Beacham TD, Farrell AP, Hinch SG, Miller KM. Transcriptional shifts during juvenile Coho salmon (Oncorhynchus kisutch) life stage changes in freshwater and early marine environments. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 29:32-42. [PMID: 30419481 DOI: 10.1016/j.cbd.2018.10.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 10/13/2018] [Indexed: 11/30/2022]
Abstract
There is a paucity of information on the physiological changes that occur over the course of salmon early marine migration. Here we aim to provide insight on juvenile Coho salmon (Oncorhynchus kisutch) physiology using the changes in gene expression (cGRASP 44K microarray) of four tissues (brain, gill, muscle, and liver) across the parr to smolt transition in freshwater and through the first eight months of ocean residence. We also examined transcriptome changes with body size as a covariate. The strongest shift in the transcriptome for brain, gill, and muscle occurred between summer and fall in the ocean, representing physiological changes that we speculate may be associated with migration preparation to feeding areas. Metabolic processes in the liver were positively associated with body length, generally consistent with enhanced feeding opportunities. However, a notable exception to this metabolic pattern was for spring post-smolts sampled soon after entry into the ocean, which showed a pattern of gene expression more likely associated with depressed feeding or recent fasting. Overall, this study has revealed life stages that may be the most critical developmentally (fall post-smolt) and for survival (spring post-smolt) in the early marine environment. These life stages may warrant further investigation.
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Affiliation(s)
- Aimee Lee S Houde
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada; Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia V9T 6N7, Canada
| | - Angela D Schulze
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia V9T 6N7, Canada
| | - Karia H Kaukinen
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia V9T 6N7, Canada
| | - Jeffrey Strohm
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia V9T 6N7, Canada
| | - David A Patterson
- Fisheries and Oceans Canada, School of Resource and Environmental Management, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Terry D Beacham
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia V9T 6N7, Canada
| | - Anthony P Farrell
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Scott G Hinch
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia V9T 6N7, Canada.
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19
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Evidence of sex-bias in gene expression in the brain transcriptome of two populations of rainbow trout (Oncorhynchus mykiss) with divergent life histories. PLoS One 2018; 13:e0193009. [PMID: 29447294 PMCID: PMC5814004 DOI: 10.1371/journal.pone.0193009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 02/03/2018] [Indexed: 11/19/2022] Open
Abstract
Sex-bias in gene expression is a mechanism that can generate phenotypic variance between the sexes, however, relatively little is known about how patterns of sex-bias vary during development, and how variable sex-bias is between different populations. To that end, we measured sex-bias in gene expression in the brain transcriptome of rainbow trout (Oncorhynchus mykiss) during the first two years of development. Our sampling included from the fry stage through to when O. mykiss either migrate to the ocean or remain resident and undergo sexual maturation. Samples came from two F1 lines: One from migratory steelhead trout and one from resident rainbow trout. All samples were reared in a common garden environment and RNA sequencing (RNA-seq) was used to estimate patterns of gene expression. A total of 1,716 (4.6% of total) genes showed evidence of sex-bias in gene expression in at least one time point. The majority (96.7%) of sex-biased genes were differentially expressed during the second year of development, indicating that patterns of sex-bias in expression are tied to key developmental events, such as migration and sexual maturation. Mapping of differentially expressed genes to the O. mykiss genome revealed that the X chromosome is enriched for female upregulated genes, and this may indicate a lack of dosage compensation in rainbow trout. There were many more sex-biased genes in the migratory line than the resident line suggesting differences in patterns of gene expression in the brain between populations subjected to different forces of selection. Overall, our results suggest that there is considerable variation in the extent and identity of genes exhibiting sex-bias during the first two years of life. These differentially expressed genes may be connected to developmental differences between the sexes, and/or between adopting a resident or migratory life history.
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20
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Elias A, Thrower F, Nichols KM. Rainbow trout personality: individual behavioural variation in juvenile Oncorhynchus mykiss. BEHAVIOUR 2018. [DOI: 10.1163/1568539x-00003483] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
We evaluated the variation in dispersal, exploration, and aggression across time in juvenile progeny produced from wild caught rainbow trout (Oncorhynchus mykiss) at a critical developmental shift associated with the highest mortality in fish. By testing multiple ecologically relevant behaviours repeatedly in the same individuals, we simultaneously tested multiple hypotheses regarding personality, plasticity, and behavioural syndromes to better understand the innate behavioural variation in a population containing both migratory and resident life histories. There were consistent behavioural differences, or personality, between individuals across time, for dispersal, aggression, and exploration, unrelated to size or sex. The significant repeatabilities (0.10–0.46) indicate that these traits are potentially heritable. Also, we found both habituation in all behaviours and significant differences between individuals in the rate of that habituation, despite no evidence of a behavioural syndrome. The identification of this individual level variation is a step towards understanding which heritable traits selection could influence.
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Affiliation(s)
- Ashley Elias
- aDepartment of Biological Sciences, Purdue University, 915 W State Street, West Lafayette, IN 47907, USA
- bDepartment of Biological Sciences, North Carolina State University, 112 Derieux Place, Raleigh, NC 27695, USA
| | - Frank Thrower
- cTed Stevens Marine Research Institute, Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, AK 99801, USA
| | - Krista M. Nichols
- aDepartment of Biological Sciences, Purdue University, 915 W State Street, West Lafayette, IN 47907, USA
- dConservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA 98112, USA
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21
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Uusi-Heikkilä S, Sävilammi T, Leder E, Arlinghaus R, Primmer CR. Rapid, broad-scale gene expression evolution in experimentally harvested fish populations. Mol Ecol 2017; 26:3954-3967. [PMID: 28500794 DOI: 10.1111/mec.14179] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 04/26/2017] [Accepted: 04/28/2017] [Indexed: 01/19/2023]
Abstract
Gene expression changes potentially play an important role in adaptive evolution under human-induced selection pressures, but this has been challenging to demonstrate in natural populations. Fishing exhibits strong selection pressure against large body size, thus potentially inducing evolutionary changes in life history and other traits that may be slowly reversible once fishing ceases. However, there is a lack of convincing examples regarding the speed and magnitude of fisheries-induced evolution, and thus, the relevant underlying molecular-level effects remain elusive. We use wild-origin zebrafish (Danio rerio) as a model for harvest-induced evolution. We experimentally demonstrate broad-scale gene expression changes induced by just five generations of size-selective harvesting, and limited genetic convergence following the cessation of harvesting. We also demonstrate significant allele frequency changes in genes that were differentially expressed after five generations of size-selective harvesting. We further show that nine generations of captive breeding induced substantial gene expression changes in control stocks likely due to inadvertent selection in the captive environment. The large extent and rapid pace of the gene expression changes caused by both harvest-induced selection and captive breeding emphasizes the need for evolutionary enlightened management towards sustainable fisheries.
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Affiliation(s)
| | | | - Erica Leder
- Department of Biology, University of Turku, Turku, Finland.,Natural History Museum, University of Oslo, Oslo, Norway.,Department of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Robert Arlinghaus
- Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Division of Integrative Fisheries Management, Department of Crop and Animal Sciences, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
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22
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Larson WA, Limborg MT, McKinney GJ, Schindler DE, Seeb JE, Seeb LW. Genomic islands of divergence linked to ecotypic variation in sockeye salmon. Mol Ecol 2016; 26:554-570. [PMID: 27864910 DOI: 10.1111/mec.13933] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 10/14/2016] [Accepted: 10/25/2016] [Indexed: 12/14/2022]
Abstract
Regions of the genome displaying elevated differentiation (genomic islands of divergence) are thought to play an important role in local adaptation, especially in populations experiencing high gene flow. However, the characteristics of these islands as well as the functional significance of genes located within them remain largely unknown. Here, we used data from thousands of SNPs aligned to a linkage map to investigate genomic islands of divergence in three ecotypes of sockeye salmon (Oncorhynchus nerka) from a single drainage in southwestern Alaska. We found ten islands displaying high differentiation among ecotypes. Conversely, neutral structure observed throughout the rest of the genome was low and not partitioned by ecotype. One island on linkage group So13 was particularly large and contained six SNPs with FST > 0.14 (average FST of neutral SNPs = 0.01). Functional annotation revealed that the peak of this island contained a nonsynonymous mutation in a gene involved in growth in other species (TULP4). The islands that we discovered were relatively small (80-402 Kb), loci found in islands did not show reduced levels of diversity, and loci in islands displayed slightly elevated linkage disequilibrium. These attributes suggest that the islands discovered here were likely generated by divergence hitchhiking; however, we cannot rule out the possibility that other mechanisms may have produced them. Our results suggest that islands of divergence serve an important role in local adaptation with gene flow and represent a significant advance towards understanding the genetic basis of ecotypic differentiation.
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Affiliation(s)
- Wesley A Larson
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195-5020, USA
| | - Morten T Limborg
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195-5020, USA
| | - Garrett J McKinney
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195-5020, USA
| | - Daniel E Schindler
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195-5020, USA
| | - James E Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195-5020, USA
| | - Lisa W Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195-5020, USA
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23
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RNA-seq reveals differential gene expression in the brains of juvenile resident and migratory smolt rainbow trout (Oncorhynchus mykiss). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2016; 20:136-150. [DOI: 10.1016/j.cbd.2016.07.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 07/21/2016] [Accepted: 07/28/2016] [Indexed: 11/20/2022]
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24
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Leitwein M, Garza JC, Pearse DE. Ancestry and adaptive evolution of anadromous, resident, and adfluvial rainbow trout ( Oncorhynchus mykiss) in the San Francisco bay area: application of adaptive genomic variation to conservation in a highly impacted landscape. Evol Appl 2016; 10:56-67. [PMID: 28035235 PMCID: PMC5192794 DOI: 10.1111/eva.12416] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 08/10/2016] [Indexed: 01/01/2023] Open
Abstract
The streams draining of into San Francisco Bay, California, have been impacted by habitat alteration for over 150 years, and roads, dams, water diversions, and other impediments now block the paths of many aquatic migratory species. These changes can affect the genetic structure of fish populations, as well as driving adaptive evolution to novel environmental conditions. Here, we determine the evolutionary relationships of San Francisco Bay Area steelhead/rainbow trout (Oncorhynchus mykiss) populations and show that (i) they are more closely related to native coastal steelhead than to the California Central Valley lineage, with no evidence of introgression by domesticated hatchery rainbow trout, (ii) populations above and below barriers within watersheds are each other's closest relatives, and (iii) adaptive genomic variation associated with migratory life-history traits in O. mykiss shows substantial evolutionary differences between fish above and below dams. These findings support continued habitat restoration and protection of San Francisco Bay Area O. mykiss populations and demonstrate that ecological conditions in novel habitats above barriers to anadromy influence life-history evolution. We highlight the importance of considering the adaptive landscape in conservation and restoration programs for species living in highly modified habitats, particularly with respect to key life-history traits.
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Affiliation(s)
- Maeva Leitwein
- Technopôle Brest-Iroiserue Dumont d'Urville Institut Universitaire Européen de la Mer (IUEM) University of Brest Plouzané France; Institute of Marine Sciences University of California Santa Cruz CA USA; Present address: Institut des Sciences de l'Evolution de Montpellier (ISEM) UMR 5554 Université de ´Montpellier Montpellier Cedex 5 France
| | - John Carlos Garza
- Institute of Marine Sciences University of California Santa Cruz CA USA; Fisheries Ecology Division Southwest Fisheries Science Center National Marine Fisheries Service Santa Cruz CA USA
| | - Devon E Pearse
- Institute of Marine Sciences University of California Santa Cruz CA USA; Fisheries Ecology Division Southwest Fisheries Science Center National Marine Fisheries Service Santa Cruz CA USA
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25
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Larson WA, McKinney GJ, Seeb JE, Seeb LW. Identification and Characterization of Sex-Associated Loci in Sockeye Salmon Using Genotyping-by-Sequencing and Comparison with a Sex-Determining Assay Based on thesdYGene. J Hered 2016; 107:559-66. [DOI: 10.1093/jhered/esw043] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 07/07/2016] [Indexed: 11/12/2022] Open
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26
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Delmore KE, Liedvogel M. Investigating Factors that Generate and Maintain Variation in Migratory Orientation: A Primer for Recent and Future Work. Front Behav Neurosci 2016; 10:3. [PMID: 26834592 PMCID: PMC4720750 DOI: 10.3389/fnbeh.2016.00003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 01/04/2016] [Indexed: 01/24/2023] Open
Abstract
The amazing accuracy of migratory orientation performance across the animal kingdom is facilitated by the use of magnetic and celestial compass systems that provide individuals with both directional and positional information. Quantitative genetics analyses in several animal systems suggests that migratory orientation has a strong genetic component. Nevertheless, the exact identity of genes controlling orientation remains largely unknown, making it difficult to obtain an accurate understanding of this fascinating behavior on the molecular level. Here, we provide an overview of molecular genetic techniques employed thus far, highlight the pros and cons of various approaches, generalize results from species-specific studies whenever possible, and evaluate how far the field has come since early quantitative genetics studies. We emphasize the importance of examining different levels of molecular control, and outline how future studies can take advantage of high-resolution tracking and sequencing techniques to characterize the genomic architecture of migratory orientation.
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Affiliation(s)
- Kira E Delmore
- Behavioural Genomics Department, Max Planck Institute for Evolutionary Biology Plön, Germany
| | - Miriam Liedvogel
- Behavioural Genomics Department, Max Planck Institute for Evolutionary Biology Plön, Germany
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27
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Jones CM, Papanicolaou A, Mironidis GK, Vontas J, Yang Y, Lim KS, Oakeshott JG, Bass C, Chapman JW. Genomewide transcriptional signatures of migratory flight activity in a globally invasive insect pest. Mol Ecol 2016; 24:4901-11. [PMID: 26331997 PMCID: PMC5102652 DOI: 10.1111/mec.13362] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 07/30/2015] [Accepted: 08/24/2015] [Indexed: 01/19/2023]
Abstract
Migration is a key life history strategy for many animals and requires a suite of behavioural, morphological and physiological adaptations which together form the ‘migratory syndrome’. Genetic variation has been demonstrated for many traits that make up this syndrome, but the underlying genes involved remain elusive. Recent studies investigating migration‐associated genes have focussed on sampling migratory and nonmigratory populations from different geographic locations but have seldom explored phenotypic variation in a migratory trait. Here, we use a novel combination of tethered flight and next‐generation sequencing to determine transcriptomic differences associated with flight activity in a globally invasive moth pest, the cotton bollworm Helicoverpa armigera. By developing a state‐of‐the‐art phenotyping platform, we show that field‐collected H. armigera display continuous variation in flight performance with individuals capable of flying up to 40 km during a single night. Comparative transcriptomics of flight phenotypes drove a gene expression analysis to reveal a suite of expressed candidate genes which are clearly related to physiological adaptations required for long‐distance flight. These include genes important to the mobilization of lipids as flight fuel, the development of flight muscle structure and the regulation of hormones that influence migratory physiology. We conclude that the ability to express this complex set of pathways underlines the remarkable flexibility of facultative insect migrants to respond to deteriorating conditions in the form of migratory flight and, more broadly, the results provide novel insights into the fundamental transcriptional changes required for migration in insects and other taxa.
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Affiliation(s)
| | - Alexie Papanicolaou
- Hawkesbury Institute for the Environment, University of Western Sydney, Richmond, NSW, 2753, Australia
| | - George K Mironidis
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, GR-700 13, Heraklion Crete, Greece
| | - John Vontas
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, GR-700 13, Heraklion Crete, Greece.,Laboratory of Pesticide Science, Department of Crop Science, Agricultural University of Athens, 75 Iera Odos Street, GR-11855, Athens, Greece
| | - Yihua Yang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ka S Lim
- AgroEcology, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - John G Oakeshott
- CSIRO Ecosystems Sciences, Black Mountain, Clunies Ross Street, Canberra, ACT, 0200, Australia
| | - Chris Bass
- Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Jason W Chapman
- AgroEcology, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.,Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9EZ, UK
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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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