1
|
Ros A, Brinker A. Thermotactic behaviour in lacustrine and riverine forms of Salmo trutta and its relevance to an emerging parasitic disease (PKD) in the wake of climate change. Sci Rep 2024; 14:13539. [PMID: 38866937 PMCID: PMC11169546 DOI: 10.1038/s41598-024-64137-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 06/05/2024] [Indexed: 06/14/2024] Open
Abstract
The thermotactic response of brown trout (Salmo trutta) was examined with the goal to investigate potential effects of the emerging temperature-dependent fatal trout disease PKD (proliferative kidney disease). First the differences in cold-water preferences of two forms of brown trout, lacustrine (migratory) and riverine, were determined. Second, it was studied whether this preference was changed in fish infected with PKD. The experiment involved a one-week habituation period at 14 °C in a two-chamber runway followed by a week of 3 °C temperature difference between the two runways. The fish could freely move between lanes via an opening at the end where food was provided. The temperature manipulation was repeated twice, and there were 3 trials per experimental group. All fish developed a clear spatial preference in the test. Lacustrine trout demonstrated a preference for warmer water, while riverine trout preferred cooler water. This may increase the risk to PKD in the lacustrine form. Most strikingly, riverine trout experimentally exposed to Tetracapsuloides bryosalmonae, the parasite that causes PKD, demonstrated stronger cold-seeking behaviour than control fish. Cold seeking behaviour suggests the occurrence of a disease-induced behavioural chill response, which may play an important role in disease recovery. This demonstrates the significance of protecting river connectivity and cold-water sanctuaries as management strategies for preserving salmonid populations in a warming climate.
Collapse
Affiliation(s)
- Albert Ros
- Fisheries Research Station Baden-Württemberg, LAZBW, Argenweg 50/1, 88085, Langenargen, Germany.
| | - Alexander Brinker
- Fisheries Research Station Baden-Württemberg, LAZBW, Argenweg 50/1, 88085, Langenargen, Germany
- University of Konstanz, Mainaustraße 252, 78464, Konstanz, Germany
| |
Collapse
|
2
|
Ara MG, McCulloch GA, Dutoit L, Wallis GP, Ingram T. Genomics reveals repeated landlocking of diadromous fish on an isolated island. Ecol Evol 2024; 14:e10987. [PMID: 38371863 PMCID: PMC10870334 DOI: 10.1002/ece3.10987] [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: 10/21/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 02/20/2024] Open
Abstract
Landlocking of diadromous fish in freshwater systems can have significant genomic consequences. For instance, the loss of the migratory life stage can dramatically reduce gene flow across populations, leading to increased genetic structuring and stronger effects of local adaptation. These genomic consequences have been well-studied in some mainland systems, but the evolutionary impacts of landlocking in island ecosystems are largely unknown. In this study, we used a genotyping-by-sequencing (GBS) approach to examine the evolutionary history of landlocking in common smelt (Retropinna retropinna) on Chatham Island, a small isolated oceanic island 800 kilometres east of mainland New Zealand. We examined the relationship between Chatham Island and mainland smelt and used coalescent analyses to test the number and timing of landlocking events on Chatham Island. Our genomic analysis, based on 21,135 SNPs across 169 individuals, revealed that the Chatham Island smelt was genomically distinct from the mainland New Zealand fish, consistent with a single ancestral colonisation event of Chatham Island in the Pleistocene. Significant genetic structure was also evident within the Chatham Island smelt, with a diadromous Chatham Island smelt group, along with three geographically structured landlocked groups. Coalescent demographic analysis supported three independent landlocking events, with this loss of diadromy significantly pre-dating human colonisation. Our results illustrate how landlocking of diadromous fish can occur repeatedly across a narrow spatial scale, and highlight a unique system to study the genomic basis of repeated adaptation.
Collapse
Affiliation(s)
- Motia G. Ara
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
- Department of Marine Fisheries and OceanographyPatuakhali Science and Technology UniversityPatuakhaliBangladesh
| | | | - Ludovic Dutoit
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | | | - Travis Ingram
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
| |
Collapse
|
3
|
Barr K, Bossu CM, Bay RA, Anderson EC, Belthoff J, Trulio LA, Chromczak D, Wisinski CL, Smith TB, Ruegg KC. Genetic and environmental drivers of migratory behavior in western burrowing owls and implications for conservation and management. Evol Appl 2023; 16:1889-1900. [PMID: 38143900 PMCID: PMC10739168 DOI: 10.1111/eva.13600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 12/26/2023] Open
Abstract
Migration is driven by a combination of environmental and genetic factors, but many questions remain about those drivers. Potential interactions between genetic and environmental variants associated with different migratory phenotypes are rarely the focus of study. We pair low coverage whole genome resequencing with a de novo genome assembly to examine population structure, inbreeding, and the environmental factors associated with genetic differentiation between migratory and resident breeding phenotypes in a species of conservation concern, the western burrowing owl (Athene cunicularia hypugaea). Our analyses reveal a dichotomy in gene flow depending on whether the population is resident or migratory, with the former being genetically structured and the latter exhibiting no signs of structure. Among resident populations, we observed significantly higher genetic differentiation, significant isolation-by-distance, and significantly elevated inbreeding. Among migratory breeding groups, on the other hand, we observed lower genetic differentiation, no isolation-by-distance, and substantially lower inbreeding. Using genotype-environment association analysis, we find significant evidence for relationships between migratory phenotypes (i.e., migrant versus resident) and environmental variation associated with cold temperatures during the winter and barren, open habitats. In the regions of the genome most differentiated between migrants and residents, we find significant enrichment for genes associated with the metabolism of fats. This may be linked to the increased pressure on migrants to process and store fats more efficiently in preparation for and during migration. Our results provide a significant contribution toward understanding the evolution of migratory behavior and vital insight into ongoing conservation and management efforts for the western burrowing owl.
Collapse
Affiliation(s)
- Kelly Barr
- Center for Tropical ResearchInstitute of the Environment and Sustainability, University of California, Los AngelesLos AngelesCaliforniaUSA
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Christen M. Bossu
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Rachael A. Bay
- Department of Evolution and EcologyUniversity of California, DavisDavisCaliforniaUSA
| | - Eric C. Anderson
- Fisheries Ecology Division, Southwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCaliforniaUSA
- Department of Fish, Wildlife, and Conservation BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Jim Belthoff
- Raptor Research Center and Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Lynne A. Trulio
- Department of Environmental StudiesSan José State UniversitySan JoseCaliforniaUSA
| | - Debra Chromczak
- Burrowing Owl Researcher & ConsultantRiegelsvillePennsylvaniaUSA
| | | | - Thomas B. Smith
- Center for Tropical ResearchInstitute of the Environment and Sustainability, University of California, Los AngelesLos AngelesCaliforniaUSA
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Kristen C. Ruegg
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
| |
Collapse
|
4
|
Sauliutė G, Makaras T, Pažusienė J, Valskienė R, Bučaitė A, Markuckas A, Markovskaja S, Stankevičiūtė M. A comparative analysis of multi-biomarker responses to environmental stress: Evaluating differences in landfill leachate and pathogenic oomycete effects between wild and captive Salmo trutta. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 897:165420. [PMID: 37433333 DOI: 10.1016/j.scitotenv.2023.165420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/07/2023] [Accepted: 07/07/2023] [Indexed: 07/13/2023]
Abstract
Phenotypic plasticity is one of the major means by which organisms can manage with environmental factor changes. Captivity-related stress and artificial rearing settings have been shown to dramatically alter fish response plasticity in terms of physiology, behavior, and health, potentially reducing overall fitness and fish survival. Understanding the variations in plasticity between captive-bred (kept in a homogenous environment) and wild fish populations in response to varied environmental pressures is becoming increasingly important, particularly in risk assessment research. In this study, we investigated whether captive-bred trout (Salmo trutta) are more susceptible to stress stimuli than their wild counterparts. In both wild and captive-bred trout, we investigated a battery of biomarkers that depicts the effects at various levels of biological organization in response to landfill leachate as a chemical pollutant, and after exposure to pathogenic oomycetes Saprolegnia parasitica. According to the findings, wild trout were more susceptible to chemical stimuli based on cytogenetic damage and catalase activity changes, whereas captive-bred trout were more sensitive to biological stress as evidenced by changes in overall fish activity and increasing cytogenetic damage in gills erythrocytes. Our findings emphasize the significance of exercising caution when conducting risk assessments of environmental pollutants using captive-bred animals, especially when seeking to extrapolate hazards and better understand the consequences of environmental contamination on wild fish populations. Additional comparative studies are required to investigate the impact of environmental stressors on multi-biomarker responses in both wild and captive fish populations in order to uncover changes in the plasticity of various traits that can result in adaptation or maladaptation to environmental stimuli within these fish populations, affecting data comparability and transferability to wildlife.
Collapse
Affiliation(s)
- Gintarė Sauliutė
- Laboratory of Ecotoxicology, Nature Research Centre, Akademijos St. 2, 08412 Vilnius, Lithuania.
| | - Tomas Makaras
- Laboratory of Ecotoxicology, Nature Research Centre, Akademijos St. 2, 08412 Vilnius, Lithuania
| | - Janina Pažusienė
- Laboratory of Ecotoxicology, Nature Research Centre, Akademijos St. 2, 08412 Vilnius, Lithuania
| | - Roberta Valskienė
- Laboratory of Ecotoxicology, Nature Research Centre, Akademijos St. 2, 08412 Vilnius, Lithuania
| | - Agnė Bučaitė
- Laboratory of Ecotoxicology, Nature Research Centre, Akademijos St. 2, 08412 Vilnius, Lithuania; Institute of Biosciences, Vilnius University Life Sciences Centre, Saulėtekio av. 7, 10257 Vilnius, Lithuania
| | - Arvydas Markuckas
- Department of Biochemistry and Molecular Biology, Vilnius University Life Sciences Centre, Saulėtekio av. 7, 10257 Vilnius, Lithuania
| | - Svetlana Markovskaja
- Laboratory of Mycology, Nature Research Centre, Akademijos St. 2, 08412 Vilnius, Lithuania
| | - Milda Stankevičiūtė
- Laboratory of Ecotoxicology, Nature Research Centre, Akademijos St. 2, 08412 Vilnius, Lithuania.
| |
Collapse
|
5
|
Lähteenmäki L, Orell P, Romakkaniemi A, Snickars M. Spawning migration behaviour of sea trout (Salmo trutta L.) in a boreal river system: effects of flow conditions and obstacles on migratory activity. JOURNAL OF FISH BIOLOGY 2023; 102:479-491. [PMID: 36480233 DOI: 10.1111/jfb.15286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
In this study, radio telemetry was used to examine the upstream spawning migration behaviour of anadromous brown trout (sea trout), Salmo trutta L., in a boreal river system, the River Isojoki, western Finland. The aim was to study the movement activity and migration characteristics of trout during the upstream spawning migration, as well as to locate the important spawning habitats and study the spawning characteristics. Furthermore, the authors analysed how flow conditions and a hydropower dam, with adjacent fishways, affected the upstream spawning migration. Tagged trout spawned in both the main stem and four tributaries, with spawning taking place from early October to November. The movement activity of radio-tagged trout was influenced by a hydropower dam (Perus dam), with spring migrators spending prolonged periods at the dam area, postponing the migration upstream. Flow conditions affected the total time spent at the dam area, as well as the movement activity in the free-flowing sections above the dam, with increasing flow stimulating activity. In addition, time of river ascent and location of spawning area had a significant effect on the movement activity of tagged trout. These results are further evidence that synergistic effects of flow and migratory obstacles can negatively influence migrations of anadromous fish, regardless of constructed fishways. The management of flow regimes and the efficiency of fishways are vital, as climate change will likely influence the flow and increase the water temperature of boreal river systems, further aggravating issues caused by obstacles.
Collapse
Affiliation(s)
- Linus Lähteenmäki
- Environmental and Marine Biology, Faculty of Science and Engineering, Åbo Akademi University, Åbo, Finland
| | - Panu Orell
- Natural Resources Institute Finland (Luke), Oulu, Finland
| | | | - Martin Snickars
- Environmental and Marine Biology, Faculty of Science and Engineering, Åbo Akademi University, Åbo, Finland
| |
Collapse
|
6
|
Sun CF, Zhang XH, Dong JJ, You XX, Tian YY, Gao FY, Zhang HT, Shi Q, Ye X, Shi Q, Ye X. Whole-genome resequencing reveals recent signatures of selection in five populations of largemouth bass ( Micropterus salmoides). Zool Res 2023; 44:78-89. [PMID: 36349358 PMCID: PMC9841193 DOI: 10.24272/j.issn.2095-8137.2022.274] [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] [Indexed: 11/09/2022] Open
Abstract
Largemouth bass ( Micropterus salmoides) is an economically important fish species in North America, Europe, and China. Various genetic improvement programs and domestication processes have modified its genome sequence through selective pressure, leaving nucleotide signals that can be detected at the genomic level. In this study, we sequenced 149 largemouth bass fish, including protospecies (imported from the US) and improved breeds (four domestic breeding populations from China). We detected genomic regions harboring certain genes associated with improved traits, which may be useful molecular markers for practical domestication, breeding, and selection. Subsequent analyses of genetic diversity and population structure revealed that the improved breeds have undergone more rigorous genetic changes. Through selective signal analysis, we identified hundreds of putative selective sweep regions in each largemouth bass line. Interestingly, we predicted 103 putative candidate genes potentially subjected to selection, including several associated with growth (p sst1 and grb10), early development ( klf9, sp4, and sp8), and immune traits ( pkn2, sept2, bcl6, and ripk2). These candidate genes represent potential genomic landmarks that could be used to improve important traits of biological and commercial interest. In summary, this study provides a genome-wide map of genetic variations and selection footprints in largemouth bass, which may benefit genetic studies and accelerate genetic improvement of this economically important fish.
Collapse
Affiliation(s)
- Cheng-Fei Sun
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Xin-Hui Zhang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun-Jian Dong
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Xin-Xin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan-Yuan Tian
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Feng-Ying Gao
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - He-Tong Zhang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China,E-mail:
| | - Xing Ye
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China,
| | | | | | | | | | | | | |
Collapse
|
7
|
Golizeh M, Nam J, Chatelain E, Jackson Y, Ohlund LB, Rasoolizadeh A, Camargo FV, Mahrouche L, Furtos A, Sleno L, Ndao M. New metabolic signature for Chagas disease reveals sex steroid perturbation in humans and mice. Heliyon 2022; 8:e12380. [PMID: 36590505 PMCID: PMC9800200 DOI: 10.1016/j.heliyon.2022.e12380] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/29/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
The causative agent of Chagas disease (CD), Trypanosoma cruzi, claims thousands of lives each year. Current diagnostic tools are insufficient to ensure parasitological detection in chronically infected patients has been achieved. A host-derived metabolic signature able to distinguish CD patients from uninfected individuals and assess antiparasitic treatment efficiency is introduced. Serum samples were collected from chronic CD patients, prior to and three years after treatment, and subjected to untargeted metabolomics analysis against demographically matched CD-negative controls. Five metabolites were confirmed by high-resolution tandem mass spectrometry. Several database matches for sex steroids were significantly altered in CD patients. A murine experiment corroborated sex steroid perturbation in T. cruzi-infected mice, particularly in male animals. Proteomics analysis also found increased steroidogenesis in the testes of infected mice. Metabolic alterations identified in this study shed light on the pathogenesis and provide the basis for developing novel assays for the diagnosis and screening of CD patients.
Collapse
Affiliation(s)
- Makan Golizeh
- Department of Mathematical and Physical Sciences, Concordia University of Edmonton, Edmonton, Alberta, Canada,National Reference Centre for Parasitology, Research Institute of McGill University Health Centre, Montreal, Quebec, Canada
| | - John Nam
- National Reference Centre for Parasitology, Research Institute of McGill University Health Centre, Montreal, Quebec, Canada,Infectious Diseases and Immunity in Global Health (IDIGH) Program, Research Institute of McGill University Health Centre, Montreal, Quebec, Canada
| | - Eric Chatelain
- Drugs for Neglected Diseases initiative, Geneva, Switzerland
| | - Yves Jackson
- Division of Primary Care Medicine, Geneva University Hospitals and University of Geneva, Geneva, Switzerland
| | - Leanne B. Ohlund
- Chemistry Department, Université du Québec à Montréal, Montreal, Quebec, Canada,Center for Excellence in Research on Orphan Diseases – Fondation Courtois (CERMO-FC), Montreal, Quebec, Canada
| | - Asieh Rasoolizadeh
- National Reference Centre for Parasitology, Research Institute of McGill University Health Centre, Montreal, Quebec, Canada
| | - Fabio Vasquez Camargo
- National Reference Centre for Parasitology, Research Institute of McGill University Health Centre, Montreal, Quebec, Canada
| | - Louiza Mahrouche
- Chemistry Department, Regional Centre for Mass Spectrometry, Université de Montréal, Montreal, Quebec, Canada
| | - Alexandra Furtos
- Chemistry Department, Regional Centre for Mass Spectrometry, Université de Montréal, Montreal, Quebec, Canada
| | - Lekha Sleno
- Chemistry Department, Université du Québec à Montréal, Montreal, Quebec, Canada,Center for Excellence in Research on Orphan Diseases – Fondation Courtois (CERMO-FC), Montreal, Quebec, Canada,Corresponding author.
| | - Momar Ndao
- National Reference Centre for Parasitology, Research Institute of McGill University Health Centre, Montreal, Quebec, Canada,Infectious Diseases and Immunity in Global Health (IDIGH) Program, Research Institute of McGill University Health Centre, Montreal, Quebec, Canada,Department of Experimental Medicine, McGill University, Montreal, Quebec, Canada,Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada,Corresponding author.
| |
Collapse
|
8
|
Magris G, Marroni F, D’Agaro E, Vischi M, Chiabà C, Scaglione D, Kijas J, Messina M, Tibaldi E, Morgante M. ddRAD-seq reveals the genetic structure and detects signals of selection in Italian brown trout. Genet Sel Evol 2022; 54:8. [PMID: 35100964 PMCID: PMC8805291 DOI: 10.1186/s12711-022-00698-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 01/14/2022] [Indexed: 01/29/2023] Open
Abstract
Background Brown trout is one of the most widespread fresh-water fish species in Europe. The evolutionary history of and phylogenetic relationships between brown trout populations are complex, and this is especially true for Italian populations, which are heavily influenced in different ways by stocking practices. The characterization of the genetic structure of Italian brown trout populations may give information on the risk of losing endemic Italian populations due to lack of genetic diversity or to admixture with stocking populations. The identification of signatures of selection, and the information deriving from dense genotyping data will help genotype-informed breeding programs. We used a ddRAD-seq approach to obtain more than 100,000 single nucleotide polymorphisms (SNPs), and to characterize the population structure and signatures of selection in 90 brown trout samples. Results Italian brown trout populations are genetically differentiated, although the stocking practices have introduced strong admixture in endemic Italian trout, especially with the Atlantic lineage. Most of the analysed populations showed high levels of kinship and inbreeding. We detected putative signatures of selection using different approaches, and investigated if the regions were enriched for functional categories. Several regions putatively under selection and characterized by a reduction in heterozygosity across all the studied populations are enriched for genes involved in the response to viral infections. Conclusions Our results, which show evidence of admixture with the Atlantic lineage (commonly used for stocking), confirm the need for controlling stocking practices, in order to avoid the erosion of the endemic gene pool; given the apparently high levels of kinship and inbreeding in local populations, our results also show the need to take action for increasing gene diversity. In addition, we used the genetically-distinct lineages to detect signatures of selection and we identified putative signatures of selection in several regions associated with resistance to infectious diseases. These constitute candidate regions for the study of resistance to infections in wild and farmed trout. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00698-7.
Collapse
|
9
|
Salisbury S, McCracken GR, Perry R, Keefe D, Layton KKS, Kess T, Nugent CM, Leong JS, Bradbury IR, Koop BF, Ferguson MM, Ruzzante DE. The Genomic Consistency of the Loss of Anadromy in an Arctic Fish (Salvelinus alpinus). Am Nat 2022; 199:617-635. [DOI: 10.1086/719122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
10
|
Sunde J, Yıldırım Y, Tibblin P, Bekkevold D, Skov C, Nordahl O, Larsson P, Forsman A. Drivers of neutral and adaptive differentiation in pike (Esox lucius) populations from contrasting environments. Mol Ecol 2021; 31:1093-1110. [PMID: 34874594 DOI: 10.1111/mec.16315] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 01/28/2023]
Abstract
Understanding how eco-evolutionary processes and environmental factors drive population differentiation and adaptation are key challenges in evolutionary biology of relevance for biodiversity protection. Differentiation requires at least partial reproductive separation, which may result from different modes of isolation such as geographic isolation (allopatry) or isolation by distance (IBD), resistance (IBR), and environment (IBE). Despite that multiple modes might jointly influence differentiation, studies that compare the relative contributions are scarce. Using RADseq, we analyse neutral and adaptive genetic diversity and structure in 11 pike (Esox lucius) populations from contrasting environments along a latitudinal gradient (54.9-63.6°N), to investigate the relative effects of IBD, IBE and IBR, and to assess whether the effects differ between neutral and adaptive variation, or across structural levels. Patterns of neutral and adaptive variation differed, probably reflecting that they have been differently affected by stochastic and deterministic processes. The importance of the different modes of isolation differed between neutral and adaptive diversity, yet were consistent across structural levels. Neutral variation was influenced by interactions among all three modes of isolation, with IBR (seascape features) playing a central role, wheares adaptive variation was mainly influenced by IBE (environmental conditions). Taken together, this and previous studies suggest that it is common that multiple modes of isolation interactively shape patterns of genetic variation, and that their relative contributions differ among systems. To enable identification of general patterns and understand how various factors influence the relative contributions, it is important that several modes are simultaneously investigated in additional populations, species and environmental settings.
Collapse
Affiliation(s)
- Johanna Sunde
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Yeşerin Yıldırım
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Petter Tibblin
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Dorte Bekkevold
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Christian Skov
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Oscar Nordahl
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Per Larsson
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Anders Forsman
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| |
Collapse
|
11
|
Salisbury SJ, Ruzzante DE. Genetic Causes and Consequences of Sympatric Morph Divergence in Salmonidae: A Search for Mechanisms. Annu Rev Anim Biosci 2021; 10:81-106. [PMID: 34758272 DOI: 10.1146/annurev-animal-051021-080709] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Repeatedly and recently evolved sympatric morphs exhibiting consistent phenotypic differences provide natural experimental replicates of speciation. Because such morphs are observed frequently in Salmonidae, this clade provides a rare opportunity to uncover the genomic mechanisms underpinning speciation. Such insight is also critical for conserving salmonid diversity, the loss of which could have significant ecological and economic consequences. Our review suggests that genetic differentiation among sympatric morphs is largely nonparallel apart from a few key genes that may be critical for consistently driving morph differentiation. We discuss alternative levels of parallelism likely underlying consistent morph differentiation and identify several factors that may temper this incipient speciation between sympatric morphs, including glacial history and contemporary selective pressures. Our synthesis demonstrates that salmonids are useful for studying speciation and poses additional research questions to be answered by future study of this family. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- S J Salisbury
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada; ,
| | - D E Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada; ,
| |
Collapse
|
12
|
Cádiz MI, López ME, Díaz-Domínguez D, Cáceres G, Marin-Nahuelpi R, Gomez-Uchida D, Canales-Aguirre CB, Orozco-terWengel P, Yáñez JM. Detection of selection signatures in the genome of a farmed population of anadromous rainbow trout (Oncorhynchus mykiss). Genomics 2021; 113:3395-3404. [PMID: 34339816 DOI: 10.1016/j.ygeno.2021.07.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 07/06/2021] [Accepted: 07/28/2021] [Indexed: 11/26/2022]
Abstract
Domestication processes and artificial selection are likely to leave signatures that can be detected at a molecular level in farmed rainbow trout (Oncorhynchus mykiss). These signatures of selection are genomic regions that contain functional genetic variants conferring a higher fitness to their bearers. We genotyped 749 rainbow trout from a commercial population using a rainbow trout Axiom 57 K SNP array panel and identified putative genomic regions under selection using the pcadapt, Composite Likelihood Ratio (CLR) and Integrated Haplotype Score (iHS) methods. After applying quality-control pipelines and statistical analyses, we detected 12, 96 and 16 SNPs putatively under selection, associated with 96, 781 and 115 candidate genes, respectively. Several of these candidate genes were associated with growth, early development, reproduction, behavior and immune system traits. In addition, some of the SNPs were found in interesting regions located in autosomal inversions on Omy05 and Omy20. These findings could represent a genome-wide map of selection signatures in farmed rainbow trout and could be important in explaining domestication and selection for genetic traits of commercial interest.
Collapse
Affiliation(s)
- María I Cádiz
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur, Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago 8820808, Chile; Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - María E López
- Department of Aquatic Resources, Swedish University of Agricultural Sciences, Drottningholm, Sweden
| | | | - Giovanna Cáceres
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur, Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago 8820808, Chile; Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile
| | - Rodrigo Marin-Nahuelpi
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - Daniel Gomez-Uchida
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - Cristian B Canales-Aguirre
- Centro i~Mar, Universidad de Los Lagos, Camino Chinquihue 6 km, Puerto Montt, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | | | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile.
| |
Collapse
|
13
|
Duval E, Skaala Ø, Quintela M, Dahle G, Delaval A, Wennevik V, Glover KA, Hansen MM. Long-term monitoring of a brown trout (Salmo trutta) population reveals kin-associated migration patterns and contributions by resident trout to the anadromous run. BMC Ecol Evol 2021; 21:143. [PMID: 34256705 PMCID: PMC8276402 DOI: 10.1186/s12862-021-01876-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/02/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND In species showing partial migration, as is the case for many salmonid fishes, it is important to assess how anthropogenic pressure experienced by migrating individuals affects the total population. We focused on brown trout (Salmo trutta) from the Guddal River in the Norwegian Hardanger Fjord system, which encompasses both resident and anadromous individuals. Aquaculture has led to increased anthropogenic pressure on brown trout during the marine phase in this region. Fish traps in the Guddal River allow for sampling all ascending anadromous spawners and descending smolts. We analyzed microsatellite DNA markers from all individuals ascending in 2006-2016, along with all emigrating smolts in 2017. We investigated (1) if there was evidence for declines in census numbers and effective population size during that period, (2) if there was association between kinship and migration timing in smolts and anadromous adults, and (3) to what extent resident trout were parents of outmigrating smolts. RESULTS Census counts of anadromous spawners showed no evidence for a decline from 2006 to 2016, but were lower than in 2000-2005. Estimates of effective population size also showed no trends of declines during the study period. Sibship reconstruction of the 2017 smolt run showed significant association between kinship and migration timing, and a similar association was indicated in anadromous spawners. Parentage assignment of 2017 smolts with ascending anadromous trout as candidate parents, and assuming that unknown parents represented resident trout, showed that 70% of smolts had at least one resident parent and 24% had two resident parents. CONCLUSIONS The results bear evidence of a population that after an initial decline has stabilized at a lower number of anadromous spawners. The significant association between kinship and migration timing in smolts suggests that specific episodes of elevated mortality in the sea could disproportionally affect some families and reduce overall effective population size. Finally, the results based on parentage assignment demonstrate a strong buffering effect of resident trout in case of elevated marine mortality affecting anadromous trout, but also highlight that increased mortality of anadromous trout, most of which are females, may lower overall production in the system.
Collapse
Affiliation(s)
- Eloïse Duval
- Department of Biology, Aarhus University, Ny Munkegade 114, 8000, Aarhus C, Denmark.
- Theoretical and Experimental Ecology Station, UMR-5321, CNRS, University of Toulouse III Paul Sabatier, 2 route du CNRS, 09200, Moulis, France.
| | - Øystein Skaala
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway.
| | - María Quintela
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway
| | - Geir Dahle
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway
| | - Aurélien Delaval
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway
- Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Vidar Wennevik
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway
| | - Kevin A Glover
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway
- Institute of Biology, University of Bergen, Bergen, Norway
| | - Michael M Hansen
- Department of Biology, Aarhus University, Ny Munkegade 114, 8000, Aarhus C, Denmark.
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway.
| |
Collapse
|
14
|
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.
Collapse
Affiliation(s)
- Bror Jonsson
- Norwegian Institute for Nature Research, Oslo, Norway
| | - Nina Jonsson
- Norwegian Institute for Nature Research, Oslo, Norway
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Villoutreix R, Ayala D, Joron M, Gompert Z, Feder JL, Nosil P. Inversion breakpoints and the evolution of supergenes. Mol Ecol 2021; 30:2738-2755. [PMID: 33786937 PMCID: PMC7614923 DOI: 10.1111/mec.15907] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 02/04/2021] [Accepted: 03/23/2021] [Indexed: 12/17/2022]
Abstract
The coexistence of discrete morphs that differ in multiple traits is common within natural populations of many taxa. Such morphs are often associated with chromosomal inversions, presumably because the recombination suppressing effects of inversions help maintain alternate adaptive combinations of alleles across the multiple loci affecting these traits. However, inversions can also harbour selected mutations at their breakpoints, leading to their rise in frequency in addition to (or independent from) their role in recombination suppression. In this review, we first describe the different ways that breakpoints can create mutations. We then critically examine the evidence for the breakpoint-mutation and recombination suppression hypotheses for explaining the existence of discrete morphs associated with chromosomal inversions. We find that the evidence that inversions are favoured due to recombination suppression is often indirect. The evidence that breakpoints harbour mutations that are adaptive is also largely indirect, with the characterization of inversion breakpoints at the sequence level being incomplete in most systems. Direct tests of the role of suppressed recombination and breakpoint mutations in inversion evolution are thus needed. Finally, we emphasize how the two hypotheses of recombination suppression and breakpoint mutation can act in conjunction, with implications for understanding the emergence of supergenes and their evolutionary dynamics. We conclude by discussing how breakpoint characterization could improve our understanding of complex, discrete phenotypic forms in nature.
Collapse
Affiliation(s)
- Romain Villoutreix
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier
3, Montpellier 34293, France
| | - Diego Ayala
- UMR MIVEGEC, Univ. Montpellier, CNRS, IRD, 34934 Montpellier, France
| | - Mathieu Joron
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier
3, Montpellier 34293, France
| | | | - Jeffrey L. Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame,
Indiana 46556, USA
| | - Patrik Nosil
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier
3, Montpellier 34293, France
| |
Collapse
|
17
|
Know your enemy - transcriptome of myxozoan Tetracapsuloides bryosalmonae reveals potential drug targets against proliferative kidney disease in salmonids. Parasitology 2021; 148:726-739. [PMID: 33478602 PMCID: PMC8056827 DOI: 10.1017/s003118202100010x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The myxozoan Tetracapsuloides bryosalmonae is a widely spread endoparasite that causes proliferative kidney disease (PKD) in salmonid fish. We developed an in silico pipeline to separate transcripts of T. bryosalmonae from the kidney tissue of its natural vertebrate host, brown trout (Salmo trutta). After stringent filtering, we constructed a partial transcriptome assembly T. bryosalmonae, comprising 3427 transcripts. Based on homology-restricted searches of the assembled parasite transcriptome and Atlantic salmon (Salmo salar) proteome, we identified four protein targets (Endoglycoceramidase, Legumain-like protease, Carbonic anhydrase 2, Pancreatic lipase-related protein 2) for the development of anti-parasitic drugs against T. bryosalmonae. Earlier work of these proteins on parasitic protists and helminths suggests that the identified anti-parasitic drug targets represent promising chemotherapeutic candidates also against T. bryosalmonae, and strengthen the view that the known inhibitors can be effective in evolutionarily distant organisms. In addition, we identified differentially expressed T. bryosalmonae genes between moderately and severely infected fish, indicating an increased abundance of T. bryosalmonae sporogonic stages in fish with low parasite load. In conclusion, this study paves the way for future genomic research in T. bryosalmonae and represents an important step towards the development of effective drugs against PKD.
Collapse
|
18
|
Abstract
Diadromy, the predictable movements of individuals between marine and freshwater environments, is biogeographically and phylogenetically widespread across fishes. Thus, despite the high energetic and potential fitness costs involved in moving between distinct environments, diadromy appears to be an effective life history strategy. Yet, the origin and molecular mechanisms that underpin this migratory behavior are not fully understood. In this review, we aim first to summarize what is known about diadromy in fishes; this includes the phylogenetic relationship among diadromous species, a description of the main hypotheses regarding its origin, and a discussion of the presence of non-migratory populations within diadromous species. Second, we discuss how recent research based on -omics approaches (chiefly genomics, transcriptomics, and epigenomics) is beginning to provide answers to questions on the genetic bases and origin(s) of diadromy. Finally, we suggest future directions for -omics research that can help tackle questions on the evolution of diadromy.
Collapse
Affiliation(s)
- M. Lisette Delgado
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Daniel E. Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| |
Collapse
|
19
|
Delgado ML, Manosalva A, Urbina MA, Habit E, Link O, Ruzzante DE. Genomic basis of the loss of diadromy in Galaxias maculatus: Insights from reciprocal transplant experiments. Mol Ecol 2020; 29:4857-4870. [PMID: 33048403 DOI: 10.1111/mec.15686] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/18/2022]
Abstract
Diadromy is known for having major effects on the distribution and richness of aquatic species, and so does its loss. The loss of diadromy has led to the diversification of many species, yet research focusing on understanding its molecular basis and consequences are limited. This is particularly true for amphidromous species despite being the most abundant group of diadromous species. Galaxias maculatus, an amphidromous species and one of the most widely distributed fishes in the Southern Hemisphere, exhibits many instances of nonmigratory or resident populations. The existence of naturally replicated resident populations in Patagonia can serve as an ideal system for the study of the mechanisms that lead to the loss of the diadromy and its ecological and evolutionary consequences. Here, we studied two adjacent river systems in which resident populations are genetically differentiated yet derived from the same diadromous population. By combining a reciprocal transplant experiment with genomic data, we showed that the two resident populations followed different evolutionary pathways by exhibiting a differential response in their capacity to survive in salt water. While one resident population was able to survive salt water, the other was not. Genomic analyses provided insights into the genes that distinguished (a) migratory from nonmigratory populations; (b) populations that can vs those that cannot survive a saltwater environment; and (c) between these resident populations. This study demonstrates that the loss of diadromy can be achieved by different pathways and that environmental (selection) and random (genetic drift) forces shape this dynamic evolutionary process.
Collapse
Affiliation(s)
| | - Aliro Manosalva
- Departamento de Sistemas Acuáticos, Facultad de Ciencias Ambientales y Centro EULA, Universidad de Concepción, Concepción, Chile
| | - Mauricio A Urbina
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile.,Instituto Milenio de Oceanografía (IMO), Universidad de Concepción, Concepción, Chile
| | - Evelyn Habit
- Departamento de Sistemas Acuáticos, Facultad de Ciencias Ambientales y Centro EULA, Universidad de Concepción, Concepción, Chile
| | - Oscar Link
- Departamento de Ingeniería Civil, Facultad de Ingeniería, Universidad de Concepción, Concepción, Chile
| | | |
Collapse
|
20
|
Salisbury SJ, McCracken GR, Perry R, Keefe D, Layton KK, Kess T, Nugent CM, Leong JS, Bradbury IR, Koop BF, Ferguson MM, Ruzzante DE. Limited genetic parallelism underlies recent, repeated incipient speciation in geographically proximate populations of an Arctic fish (
Salvelinus alpinus
). Mol Ecol 2020; 29:4280-4294. [DOI: 10.1111/mec.15634] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/20/2020] [Accepted: 08/24/2020] [Indexed: 12/16/2022]
Affiliation(s)
| | | | - Robert Perry
- Department of Environment Fish and Wildlife Division Government of Yukon Whitehorse YT Canada
| | - Donald Keefe
- Department of Environment and Conservation Wildlife Division Government of Newfoundland and Labrador Corner Brook NL Canada
| | - Kara K.S. Layton
- Department of Fisheries and Oceans Northwest Atlantic Fisheries Centre St. John's NL Canada
- Department of Ocean Sciences Memorial University of Newfoundland St. John's NL Canada
| | - Tony Kess
- Department of Fisheries and Oceans Northwest Atlantic Fisheries Centre St. John's NL Canada
| | - Cameron M. Nugent
- Department of Integrative Biology University of Guelph Guelph ON Canada
| | - Jong S. Leong
- Department of Biology University of Victoria Victoria BC Canada
| | - Ian R. Bradbury
- Department of Biology Dalhousie University Halifax NS Canada
- Department of Fisheries and Oceans Northwest Atlantic Fisheries Centre St. John's NL Canada
- Department of Ocean Sciences Memorial University of Newfoundland St. John's NL Canada
| | - Ben F. Koop
- Department of Biology University of Victoria Victoria BC Canada
- Centre for Biomedical Research University of Victoria Victoria BC Canada
| | - Moira M. Ferguson
- Department of Integrative Biology University of Guelph Guelph ON Canada
| | | |
Collapse
|
21
|
Jamie GA, Meier JI. The Persistence of Polymorphisms across Species Radiations. Trends Ecol Evol 2020; 35:795-808. [DOI: 10.1016/j.tree.2020.04.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/08/2020] [Accepted: 04/16/2020] [Indexed: 12/12/2022]
|
22
|
Abstract
Migration is a complex trait that often has genetic underpinnings. However, it is unclear if migratory behaviour itself is inherited (direct genetic control), or if the decision to migrate is instead the outcome of a set of physiological traits (indirect genetic control). For steelhead/rainbow trout (Oncorhynchus mykiss), migration is strongly linked to a large genomic region across their range. Here, we demonstrate a shared allelic basis between early life growth rate and migratory behaviour. Next, we demonstrate that early life growth differs among resident/migratory genotypes in wild juveniles several months prior to migration, with resident genotypes achieving a larger size in their first few months of life than migratory genotypes. We suggest that the genetic basis of migration is likely indirect and mediated by physiological traits such as growth rate. Evolutionary benefits of this indirect genetic mechanism likely include flexibility among individuals and persistence of life-history diversity within and among populations.
Collapse
Affiliation(s)
- Suzanne J Kelson
- Global Water Center, Biology Department, University of Nevada, Reno, NV, USA
| | - Stephanie M Carlson
- Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Michael R Miller
- Department of Animal Science, University of California, Davis, CA, USA
| |
Collapse
|
23
|
Burridge CP, Waters JM. Does migration promote or inhibit diversification? A case study involving the dominant radiation of temperate Southern Hemisphere freshwater fishes. Evolution 2020; 74:1954-1965. [DOI: 10.1111/evo.14066] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/08/2020] [Accepted: 07/20/2020] [Indexed: 12/11/2022]
|
24
|
Cádiz MI, López ME, Díaz-Domínguez D, Cáceres G, Yoshida GM, Gomez-Uchida D, Yáñez JM. Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus). Sci Rep 2020; 10:11514. [PMID: 32661317 PMCID: PMC7359307 DOI: 10.1038/s41598-020-68064-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 06/16/2020] [Indexed: 01/24/2023] Open
Abstract
Nile tilapia belongs to the second most cultivated group of fish in the world, mainly because of its favorable characteristics for production. Genetic improvement programs and domestication process of Nile tilapia may have modified the genome through selective pressure, leaving signals that can be detected at the molecular level. In this work, signatures of selection were identified using genome-wide SNP data, by two haplotype-based (iHS and Rsb) and one FST based method. Whole-genome re-sequencing of 326 individuals from three strains (A, B and C) of farmed tilapia maintained in Brazil and Costa Rica was carried out using Illumina HiSeq 2500 technology. After applying conventional SNP-calling and quality-control filters, ~ 1.3 M high-quality SNPs were inferred and used as input for the iHS, Rsb and FST based methods. We detected several candidate genes putatively subjected to selection in each strain. A considerable number of these genes are associated with growth (e.g. NCAPG, KLF3, TBC1D1, TTN), early development (e.g. FGFR3, PFKFB3), and immunity traits (e.g. NLRC3, PIGR, MAP1S). These candidate genes represent putative genomic landmarks that could be associated to traits of biological and commercial interest in farmed Nile tilapia.
Collapse
Affiliation(s)
- María I Cádiz
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, 8820808, La Pintana, Santiago, Chile.,Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur, Universidad de Chile, Santa Rosa 11315, 8820808, La Pintana, Santiago, Chile
| | - María E López
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, 8820808, La Pintana, Santiago, Chile.,Department of Animal Breeding and Genetics, Swedish University of Agriculturall Sciences, Uppsala, Sweden
| | - Diego Díaz-Domínguez
- Departamento de Ciencias de la Computación, Universidad de Chile, Santiago, Chile
| | - Giovanna Cáceres
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, 8820808, La Pintana, Santiago, Chile.,Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur, Universidad de Chile, Santa Rosa 11315, 8820808, La Pintana, Santiago, Chile
| | - Grazyella M Yoshida
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, 8820808, La Pintana, Santiago, Chile
| | - Daniel Gomez-Uchida
- Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile.,Núcleo Milenio INVASAL, Concepción, Chile
| | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, 8820808, La Pintana, Santiago, Chile. .,Núcleo Milenio INVASAL, Concepción, Chile.
| |
Collapse
|
25
|
Waters J, Emerson B, Arribas P, McCulloch G. Dispersal Reduction: Causes, Genomic Mechanisms, and Evolutionary Consequences. Trends Ecol Evol 2020; 35:512-522. [DOI: 10.1016/j.tree.2020.01.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/23/2020] [Accepted: 01/29/2020] [Indexed: 12/23/2022]
|
26
|
Bekkevold D, Höjesjö J, Nielsen EE, Aldvén D, Als TD, Sodeland M, Kent MP, Lien S, Hansen MM. Northern European Salmo trutta (L.) populations are genetically divergent across geographical regions and environmental gradients. Evol Appl 2020; 13:400-416. [PMID: 31993085 PMCID: PMC6976966 DOI: 10.1111/eva.12877] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 09/06/2019] [Accepted: 09/22/2019] [Indexed: 12/19/2022] Open
Abstract
The salmonid fish Brown trout is iconic as a model for the application of conservation genetics to understand and manage local interspecific variation. However, there is still scant information about relationships between local and large-scale population structure, and to what extent geographical and environmental variables are associated with barriers to gene flow. We used information from 3,782 mapped SNPs developed for the present study and conducted outlier tests and gene-environment association (GEA) analyses in order to examine drivers of population structure. Analyses comprised >2,600 fish from 72 riverine populations spanning a central part of the species' distribution in northern Europe. We report hitherto unidentified genetic breaks in population structure, indicating strong barriers to gene flow. GEA loci were widely spread across genomic regions and showed correlations with climatic, abiotic and geographical parameters. In some cases, individual loci showed consistent GEA across the geographical regions Britain, Europe and Scandinavia. In other cases, correlations were observed only within a sub-set of regions, suggesting that locus-specific variation was associated with local processes. A paired-population sampling design allowed us to evaluate sampling effects on detection of outlier loci and GEA. Two widely applied methods for outlier detection (pcadapt and bayescan) showed low overlap in loci identified as statistical outliers across sub-sets of data. Two GEA analytical approaches (LFMM and RDA) showed good correspondence concerning loci associated with specific variables, but LFMM identified five times more statistically significant associations than RDA. Our results emphasize the importance of carefully considering the statistical methods applied for the hypotheses being tested in outlier analysis. Sampling design may have lower impact on results if the objective is to identify GEA loci and their population distribution. Our study provides new insights into trout populations, and results have direct management implications in serving as a tool for identification of conservation units.
Collapse
Affiliation(s)
- Dorte Bekkevold
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | - Johan Höjesjö
- Department of Biological & Environmental SciencesUniversity of GothenburgGothenburgSweden
| | - Einar Eg Nielsen
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | | | | | - Marte Sodeland
- Department of Natural SciencesUniversity of AgderKristiansandNorway
| | | | - Sigbjørn Lien
- Faculty of BiosciencesNorwegian University of Life SciencesÅsNorway
| | - Michael Møller Hansen
- Department of Bioscience – Genetics, Ecology and EvolutionAarhus UniversityAarhusDenmark
| |
Collapse
|
27
|
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.
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
Corush JB. Evolutionary patterns of diadromy in fishes: more than a transitional state between marine and freshwater. BMC Evol Biol 2019; 19:168. [PMID: 31412761 PMCID: PMC6694556 DOI: 10.1186/s12862-019-1492-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 07/31/2019] [Indexed: 12/20/2022] Open
Abstract
Background Across the tree of life there are numerous evolutionary transitions between different habitats (i.e., aquatic and terrestrial or marine and freshwater). Many of these dramatic evolutionary shifts parallel developmental shifts that require physiological, anatomical and behavioral changes for survival and reproduction. Diadromy (scheduled movement between marine and freshwater) has been characterized as a behavior that acts as an evolutionary intermediate state between marine and freshwater environments, implying that diadromous lineages are evolutionarily transient. This hypothesis comes with assumptions regarding the rates of evolutionary transitions in and out of diadromy as well as rates of speciation and extinction in diadromous fishes. Results Based on a published phylogeny of 7822 species of ray-finned fishes, state speciation and extinction models of evolutionary transition between marine, freshwater, and diadromous species suggest transition rates out of diadromy are 5–100 times higher that transition between marine and freshwater or into diadromy. Additionally, high speciation and low extinction rates separate diadromous fishes from marine and freshwater species. As a result, net diversification (net diversification = speciation – extinction) is about 7–40 times higher in diadromous fishes compared to freshwater and marine respectively. Together the transition, speciation, and extinction rates suggest diadromy is the least stable of the three states. Conclusion Evolutionary transitions to diadromy are rare in fishes. However, once established, diversification rates in diadromous lineages are high compared to both marine and freshwater species. Diadromous lineages tend to be more transient than marine or freshwater lineages and are found to give rise to marine and freshwater specialists in addition to diadromous descendants. Although diadromy is not a necessary evolutionary intermediate between marine and freshwater, these results support the interpretation of diadromy as an important, occasionally intermediate state, that contributes to biodiversity in fishes in all environments. This evolutionary instability of diadromous lineages is counteracted by their relatively high diversification rates. These findings highlight the importance of integrating the dynamics of diversification and major evolutionary transitions for understanding macroevolutionary patterns. Electronic supplementary material The online version of this article (10.1186/s12862-019-1492-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Joel B Corush
- Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, TN, 37996, USA.
| |
Collapse
|
30
|
Ralston J, Lorenc L, Montes M, DeLuca WV, Kirchman JJ, Woodworth BK, Mackenzie SA, Newman A, Cooke HA, Freeman NE, Sutton AO, Tauzer L, Norris DR. Length polymorphisms at two candidate genes explain variation of migratory behaviors in blackpoll warblers ( Setophaga striata). Ecol Evol 2019; 9:8840-8855. [PMID: 31410284 PMCID: PMC6686290 DOI: 10.1002/ece3.5436] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/30/2019] [Accepted: 06/15/2019] [Indexed: 12/12/2022] Open
Abstract
Migratory behaviors such as the timing and duration of migration are genetically inherited and can be under strong natural selection, yet we still know very little about the specific genes or molecular pathways that control these behaviors. Studies in candidate genes Clock and Adcyap1 have revealed that both of these loci can be significantly correlated with migratory behaviors in birds, though observed relationships appear to vary across species. We investigated geographic genetic structure of Clock and Adcyap1 in four populations of blackpoll warblers (Setophaga striata), a Neotropical-Nearctic migrant that exhibits geographic variation in migratory timing and duration across its boreal breeding distribution. Further, we used data on migratory timing and duration, obtained from light-level geolocator trackers to investigate candidate genotype-phenotype relationships at the individual level. While we found no geographic structure in either candidate gene, we did find evidence that candidate gene lengths are correlated with five of the six migratory traits. Maximum Clock allele length was significantly and negatively associated with spring arrival date. Minimum Adcyap1 allele length was significantly and negatively associated with spring departure date and positively associated with fall arrival date at the wintering grounds. Additionally, we found a significant interaction between Clock and Adcyap1 allele lengths on both spring and fall migratory duration. Adcyap1 heterozygotes also had significantly shorter migration duration in both spring and fall compared to homozygotes. Our results support the growing body of evidence that Clock and Adcyap1 allele lengths are correlated with migratory behaviors in birds.
Collapse
Affiliation(s)
- Joel Ralston
- Department of BiologySaint Mary's CollegeNotre DameINUSA
| | - Lydia Lorenc
- Department of BiologySaint Mary's CollegeNotre DameINUSA
| | - Melissa Montes
- Department of BiologySaint Mary's CollegeNotre DameINUSA
| | - William V. DeLuca
- Department of Environmental ConservationUniversity of MassachusettsAmherstMAUSA
| | | | - Bradley K. Woodworth
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
- School of Biological SciencesThe University of QueenslandBrisbaneQueenslandAustralia
| | | | - Amy Newman
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | | | | | - Alex O. Sutton
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | - Lila Tauzer
- Wildlife Conservation Society CanadaWhitehorseYTCanada
| | - D. Ryan Norris
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| |
Collapse
|
31
|
Lehnert SJ, Kess T, Bentzen P, Kent MP, Lien S, Gilbey J, Clément M, Jeffery NW, Waples RS, Bradbury IR. Genomic signatures and correlates of widespread population declines in salmon. Nat Commun 2019; 10:2996. [PMID: 31278264 PMCID: PMC6611788 DOI: 10.1038/s41467-019-10972-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 06/11/2019] [Indexed: 12/27/2022] Open
Abstract
Global losses of biodiversity are occurring at an unprecedented rate, but causes are often unidentified. Genomic data provide an opportunity to isolate drivers of change and even predict future vulnerabilities. Atlantic salmon (Salmo salar) populations have declined range-wide, but factors responsible are poorly understood. Here, we reconstruct changes in effective population size (Ne) in recent decades for 172 range-wide populations using a linkage-based method. Across the North Atlantic, Ne has significantly declined in >60% of populations and declines are consistently temperature-associated. We identify significant polygenic associations with decline, involving genomic regions related to metabolic, developmental, and physiological processes. These regions exhibit changes in presumably adaptive diversity in declining populations consistent with contemporary shifts in body size and phenology. Genomic signatures of widespread population decline and associated risk scores allow direct and potentially predictive links between population fitness and genotype, highlighting the power of genomic resources to assess population vulnerability.
Collapse
Affiliation(s)
- S J Lehnert
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 E White Hills Rd, St. John's, Newfoundland, A1C 5X1, Canada.
| | - T Kess
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 E White Hills Rd, St. John's, Newfoundland, A1C 5X1, Canada
| | - P Bentzen
- Biology Department, Dalhousie University, 6050 University Avenue, Halifax, NS, B3H 4R2, Canada
| | - M P Kent
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, 1430, Norway
| | - S Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, 1430, Norway
| | - J Gilbey
- Marine Scotland Science, Freshwater Fisheries Laboratory, Faskally, Pitlochry, PH16 5LB, UK
| | - M Clément
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute of Memorial University of Newfoundland, 155 Ridge Rd, St. John's, NL, A1C 5R3, Canada
- Labrador Institute, Memorial University of Newfoundland, 219 Hamilton River Rd, Happy Valley-Goose Bay, NL, A0P 1E0, Canada
| | - N W Jeffery
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Dr, Dartmouth, NS, B2Y 4A2, Canada
| | - R S Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, 98112, USA
| | - I R Bradbury
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 E White Hills Rd, St. John's, Newfoundland, A1C 5X1, Canada
- Biology Department, Dalhousie University, 6050 University Avenue, Halifax, NS, B3H 4R2, Canada
| |
Collapse
|
32
|
Ågren A, Vainikka A, Janhunen M, Hyvärinen P, Piironen J, Kortet R. Experimental crossbreeding reveals strain-specific variation in mortality, growth and personality in the brown trout (Salmo trutta). Sci Rep 2019; 9:2771. [PMID: 30808889 PMCID: PMC6391471 DOI: 10.1038/s41598-018-35794-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 11/12/2018] [Indexed: 01/13/2023] Open
Abstract
Although hybridization between populations with low genetic diversity may induce heterosis, it can also lead to reduced fitness of hybrid offspring through outbreeding depression and loss of local adaptations. Using a half-sib mating design, we studied on brown trout (Salmo trutta) how hybridization of migratory hatchery-strain females with males from various strains would affect early mortality, growth and personality in F1 offspring. No differences in mortality or alevin body length were found between the crossing groups by the end of the yolk-sac stage. At later developmental stages, higher mortality and slower growth in one of the geographically distant hybrid groups indicated potential outbreeding depression. The personality component indicating boldness and exploration tendency showed fairly low genetic variation and no phenotypic differences among the crossing groups while the personality component related to freezing behavior indicated stronger freezing responses in the purebred and local cross strain when compared to the two other strains. However, the purebred hatchery strain possessed stronger additive genetic tendency for boldness and explorative behavior, and weaker genetic tendency for freezing behavior, when compared to the wild × hatchery hybrid group. Our results add to the cumulating evidence of risks related to the stocking of fish strains from non-native origins.
Collapse
Affiliation(s)
- Anni Ågren
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101, Joensuu, Finland
| | - Anssi Vainikka
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101, Joensuu, Finland
| | - Matti Janhunen
- Natural Resources Institute Finland (Luke), Aquatic production systems, Myllytie 1, FI-31600, Jokioinen, Finland
| | - Pekka Hyvärinen
- Natural Resources Institute Finland (Luke), Aquatic population dynamics, Manamansalontie 90, FI-88300, Paltamo, Finland
| | - Jorma Piironen
- Natural Resources Institute Finland (Luke), Aquatic population dynamics, Yliopistonkatu 6, FI-80100, Joensuu, Finland
| | - Raine Kortet
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101, Joensuu, Finland.
| |
Collapse
|
33
|
Lemopoulos A, Prokkola JM, Uusi‐Heikkilä S, Vasemägi A, Huusko A, Hyvärinen P, Koljonen M, Koskiniemi J, Vainikka A. Comparing RADseq and microsatellites for estimating genetic diversity and relatedness - Implications for brown trout conservation. Ecol Evol 2019; 9:2106-2120. [PMID: 30847096 PMCID: PMC6392366 DOI: 10.1002/ece3.4905] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/30/2018] [Accepted: 12/21/2018] [Indexed: 12/24/2022] Open
Abstract
The conservation and management of endangered species requires information on their genetic diversity, relatedness and population structure. The main genetic markers applied for these questions are microsatellites and single nucleotide polymorphisms (SNPs), the latter of which remain the more resource demanding approach in most cases. Here, we compare the performance of two approaches, SNPs obtained by restriction-site-associated DNA sequencing (RADseq) and 16 DNA microsatellite loci, for estimating genetic diversity, relatedness and genetic differentiation of three, small, geographically close wild brown trout (Salmo trutta) populations and a regionally used hatchery strain. The genetic differentiation, quantified as F ST, was similar when measured using 16 microsatellites and 4,876 SNPs. Based on both marker types, each brown trout population represented a distinct gene pool with a low level of interbreeding. Analysis of SNPs identified half- and full-siblings with a higher probability than the analysis based on microsatellites, and SNPs outperformed microsatellites in estimating individual-level multilocus heterozygosity. Overall, the results indicated that moderately polymorphic microsatellites and SNPs from RADseq agreed on estimates of population genetic structure in moderately diverged, small populations, but RADseq outperformed microsatellites for applications that required individual-level genotype information, such as quantifying relatedness and individual-level heterozygosity. The results can be applied to other small populations with low or moderate levels of genetic diversity.
Collapse
Affiliation(s)
- Alexandre Lemopoulos
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandJoensuuFinland
- Department of BiologyUniversity of TurkuTurkuFinland
| | - Jenni M. Prokkola
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandJoensuuFinland
- Institute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Silva Uusi‐Heikkilä
- Department of BiologyUniversity of TurkuTurkuFinland
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Anti Vasemägi
- Department of BiologyUniversity of TurkuTurkuFinland
- Department of Aquatic Resources, Institute of Freshwater ResearchSwedish University of Agricultural SciencesDrottningholmSweden
- Estonian University of Life SciencesInstitute of Veterinary Medicine and Animal SciencesTartuEstonia
| | - Ari Huusko
- Natural Resources Institute Finland (Luke), Kainuu Fisheries Research StationPaltamoFinland
| | - Pekka Hyvärinen
- Natural Resources Institute Finland (Luke), Kainuu Fisheries Research StationPaltamoFinland
| | | | - Jarmo Koskiniemi
- Department of Agricultural SciencesUniversity of HelsinkiHelsinkiFinland
| | - Anssi Vainikka
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandJoensuuFinland
| |
Collapse
|