1
|
Strait JT, Grummer JA, Hoffman NF, Muhlfeld CC, Narum SR, Luikart G. Local environments, not invasive hybridization, influence cardiac performance of native trout under acute thermal stress. Evol Appl 2024; 17:e13663. [PMID: 38390377 PMCID: PMC10883762 DOI: 10.1111/eva.13663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 12/08/2023] [Accepted: 01/17/2024] [Indexed: 02/24/2024] Open
Abstract
Climate-induced expansion of invasive hybridization (breeding between invasive and native species) poses a significant threat to the persistence of many native species worldwide. In the northern U.S. Rocky Mountains, hybridization between native cutthroat trout and non-native rainbow trout has increased in recent decades due, in part, to climate-driven increases in water temperature. It has been postulated that invasive hybridization may enhance physiological tolerance to climate-induced thermal stress because laboratory studies indicate that rainbow trout have a higher thermal tolerance than cutthroat trout. Here, we assessed whether invasive hybridization improves cardiac performance response to acute water temperature stress of native wild trout populations. We collected trout from four streams with a wide range of non-native admixture among individuals and with different temperature and streamflow regimes in the upper Flathead River drainage, USA. We measured individual cardiac performance (maximum heart rate, "MaxHR", and temperature at arrhythmia, "ArrTemp") during laboratory trials with increasing water temperatures (10-28°C). Across the study populations, we observed substantial variation in cardiac performance of individual trout when exposed to thermal stress. Notably, we found significant differences in the cardiac response to thermal regimes among native cutthroat trout populations, suggesting the importance of genotype-by-environment interactions in shaping the physiological performance of native cutthroat trout. However, rainbow trout admixture had no significant effect on cardiac performance (MaxHR and ArrTemp) within any of the three populations. Our results indicate that invasive hybridization with a warmer-adapted species does not enhance the cardiac performance of native trout under warming conditions. Maintaining numerous populations across thermally and hydrologically diverse stream environments will be crucial for native trout to adapt and persist in a warming climate.
Collapse
Affiliation(s)
- Jeffrey T Strait
- Flathead Lake Biological Station, Wildlife Biology Program University of Montana Polson Montana USA
| | - Jared A Grummer
- Flathead Lake Biological Station, Wildlife Biology Program University of Montana Polson Montana USA
| | | | - Clint C Muhlfeld
- U.S. Geological Survey, Northern Rocky Mountain Science Center West Glacier Montana USA
| | - Shawn R Narum
- Columbia River Inter-Tribal Fish Commission Hagerman Idaho USA
| | - Gordon Luikart
- Flathead Lake Biological Station, Wildlife Biology Program University of Montana Polson Montana USA
| |
Collapse
|
2
|
Schwieterman GD, Hardison EA, Cox GK, Van Wert JC, Birnie-Gauvin K, Eliason EJ. Mechanisms of cardiac collapse at high temperature in a marine teleost (Girella nigrians). Comp Biochem Physiol A Mol Integr Physiol 2023; 286:111512. [PMID: 37726058 DOI: 10.1016/j.cbpa.2023.111512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 09/21/2023]
Abstract
Heat-induced mortality in ectotherms may be attributed to impaired cardiac performance, specifically a collapse in maximum heart rate (fHmax), although the physiological mechanisms driving this phenomenon are still unknown. Here, we tested two proposed factors which may restrict cardiac upper thermal limits: noxious venous blood conditions and oxygen limitation. We hypothesized elevated blood [K+] (hyperkalemia) and low oxygen (hypoxia) would reduce cardiac upper thermal limits in a marine teleost (Girella nigricans), while high oxygen (hyperoxia) would increase thermal limits. We also hypothesized higher acclimation temperatures would exacerbate the harmful effects of an oxygen limitation. Using the Arrhenius breakpoint temperature test, we measured fHmax in acutely warmed fish under control (saline injected) and hyperkalemic conditions (elevated plasma [K+]) while exposed to hyperoxia (200% air saturation), normoxia (100% air saturation), or hypoxia (20% air saturation). We also measured ventricle lactate content and venous blood oxygen partial pressure (PO2) to determine if there were universal thresholds in either metric driving cardiac collapse. Elevated [K+] was not significantly correlated with any cardiac thermal tolerance metric. Hypoxia significantly reduced cardiac upper thermal limits (Arrhenius breakpoint temperature [TAB], peak fHmax, temperature of peak heart rate [TPeak], and temperature at arrhythmia [TARR]). Hyperoxia did not alter cardiac thermal limits compared to normoxia. There was no evidence of a species-wide threshold in ventricular [lactate] or venous PO2. Here, we demonstrate that oxygen limits cardiac thermal tolerance only in instances of hypoxia, but that other physiological processes are responsible for causing temperature-induced heart failure when oxygen is not limited.
Collapse
Affiliation(s)
- Gail D Schwieterman
- Department of Ecology Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA; School of Marine Sciences, University of Maine, Orono, ME, USA; Maine Agricultural and Forest Experiment Station, Orono, ME, USA.
| | - Emily A Hardison
- Department of Ecology Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA. https://twitter.com/eahardison
| | | | - Jacey C Van Wert
- Department of Ecology Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA. https://twitter.com/jacey_van_wert
| | - Kim Birnie-Gauvin
- Department of Ecology Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA; Section for Freshwater Fisheries and Ecology, National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark. https://twitter.com/kbg_conserv
| | - Erika J Eliason
- Department of Ecology Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| |
Collapse
|
3
|
Zhao X, Zheng T, Gao T, Song N. Whole-genome resequencing reveals genetic diversity and selection signals in warm temperate and subtropical Sillago sinica populations. BMC Genomics 2023; 24:547. [PMID: 37715145 PMCID: PMC10503073 DOI: 10.1186/s12864-023-09652-3] [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: 02/26/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023] Open
Abstract
BACKGROUND Genetic diversity and heterogeneous genomic signatures in marine fish populations may result from selection pressures driven by the strong effects of environmental change. Nearshore fishes are often exposed to complex environments and human activities, especially those with small ranges. However, studies on genetic diversity and population selection signals in these species have mostly been based on a relatively small number of genetic markers. As a newly recorded species of Sillaginidae, the population genetics and genomic selection signals of Sillago sinica are fragmented or even absent. RESULTS To address this theoretical gap, we performed whole-genome resequencing of 43 S. sinica individuals from Dongying (DY), Qingdao (QD) and Wenzhou (WZ) populations and obtained 4,878,771 high-quality SNPs. Population genetic analysis showed that the genetic diversity of S. sinica populations was low, but the genetic diversity of the WZ population was higher than that of the other two populations. Interestingly, the three populations were not strictly clustered within the group defined by their sampling location but showed an obvious geographic structure signal from the warm temperate to the subtropics. With further analysis, warm-temperate populations exhibited strong selection signals in genomic regions related to nervous system development, sensory function and immune function. However, subtropical populations showed more selective signalling for environmental tolerance and stress signal transduction. CONCLUSIONS Genome-wide SNPs provide high-quality data to support genetic studies and localization of selection signals in S. sinica populations. The reduction in genetic diversity may be related to the bottleneck effect. Considering that low genetic diversity leads to reduced environmental adaptability, conservation efforts and genetic diversity monitoring of this species should be increased in the future. Differences in genomic selection signals between warm temperate and subtropical populations may be related to human activities and changes in environmental complexity. This study deepened the understanding of population genetics and genomic selection signatures in nearshore fishes and provided a theoretical basis for exploring the potential mechanisms of genomic variation in marine fishes driven by environmental selection pressures.
Collapse
Affiliation(s)
- Xiang Zhao
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, Shandong, China
| | - Tianlun Zheng
- Zhejiang Fisheries Technical Extension Center, Hangzhou, 310023, Zhejiang, China
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, China.
| | - Na Song
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, Shandong, China.
| |
Collapse
|
4
|
Seaborn T, Landguth EL, Caudill CC. Simulating plasticity as a framework for understanding habitat selection and its role in adaptive capacity and extinction risk through an expansion of CDMetaPOP. Mol Ecol Resour 2023; 23:1458-1472. [PMID: 37081173 PMCID: PMC11081408 DOI: 10.1111/1755-0998.13799] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/22/2023]
Abstract
Adaptive capacity can present challenges for modelling as it encompasses multiple ecological and evolutionary processes such as natural selection, genetic drift, gene flow and phenotypic plasticity. Spatially explicit, individual-based models provide an outlet for simulating these complex interacting eco-evolutionary processes. We expanded the existing Cost-Distance Meta-POPulation (CDMetaPOP) framework with inducible plasticity modelled as a habitat selection behaviour, using temperature or habitat quality variables, with a genetically based selection threshold conditioned on past individual experience. To demonstrate expected results in the new module, we simulated hypothetical populations and then evaluated model performance in populations of redband trout (Oncorhynchus mykiss gairdneri) across three watersheds where temperatures induce physiological stress in parts of the stream network. We ran simulations using projected warming stream temperature data under four scenarios for alleles that: (1) confer thermal tolerance, (2) bestow plastic habitat selection, (3) give both thermal tolerance and habitat selection preference and (4) do not provide either thermal tolerance or habitat selection. Inclusion of an adaptive allele decreased declines in population sizes, but this impact was greatly reduced in the relatively cool stream networks. As anticipated with the new module, high-temperature patches remained unoccupied by individuals with the allele operating plastically after exposure to warm temperatures. Using complete habitat avoidance above the stressful temperature threshold, habitat selection reduced the overall population size due to the opportunity cost of avoiding areas with increased, but not guaranteed, mortality. Inclusion of plasticity within CDMetaPOP will provide the potential for genetic or plastic traits and 'rescue' to affect eco-evolutionary dynamics for research questions and conservation applications.
Collapse
Affiliation(s)
- Travis Seaborn
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, Idaho, USA
- School of Natural Resource Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Erin L. Landguth
- Computational Ecology Laboratory & Center for Population Health Research, University of Montana, Missoula, Montana, USA
| | | |
Collapse
|
5
|
Zillig KW, FitzGerald AM, Lusardi RA, Cocherell DE, Fangue NA. Intraspecific variation among Chinook Salmon populations indicates physiological adaptation to local environmental conditions. CONSERVATION PHYSIOLOGY 2023; 11:coad044. [PMID: 37346267 PMCID: PMC10281501 DOI: 10.1093/conphys/coad044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/26/2023] [Accepted: 06/06/2023] [Indexed: 06/23/2023]
Abstract
Understanding interpopulation variation is important to predicting species responses to climate change. Recent research has revealed interpopulation variation among several species of Pacific salmonids; however, the environmental drivers of population differences remain elusive. We tested for local adaptation and countergradient variation by assessing interpopulation variation among six populations of fall-run Chinook Salmon from the western United States. Juvenile fish were reared at three temperatures (11, 16 and 20°C), and five physiological metrics were measured (routine and maximum metabolic rate, aerobic scope, growth rate and critical thermal maximum). We then tested associations between these physiological metrics and 15 environmental characteristics (e.g. rearing temperature, latitude, migration distance, etc.). Statistical associations between the five physiological metrics and 15 environmental characteristics supported our hypotheses of local adaptation. Notably, latitude was a poor predictor of population physiology. Instead, our results demonstrate that populations from warmer habitats exhibit higher thermal tolerance (i.e. critical thermal maxima), faster growth when warm acclimated and greater aerobic capacity at high temperatures. Additionally, populations with longer migrations exhibit higher metabolic capacity. However, overall metabolic capacity declined with warm acclimation, indicating that future climate change may reduce metabolic capacity, negatively affecting long-migrating populations. Linking physiological traits to environmental characteristics enables flexible, population-specific management of disparate populations in response to local conditions.
Collapse
Affiliation(s)
- Kenneth W Zillig
- Department of Wildlife, Fish and Conservation Biology, University of California, Davis, CA 95616, USA
| | - Alyssa M FitzGerald
- Institute of Marine Sciences, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, CA 95060, USA
| | - Robert A Lusardi
- Department of Wildlife, Fish and Conservation Biology, University of California, Davis, CA 95616, USA
- Center for Watershed Sciences, University of California, Davis, CA 95616, USA
| | - Dennis E Cocherell
- Department of Wildlife, Fish and Conservation Biology, University of California, Davis, CA 95616, USA
| | - Nann A Fangue
- Corresponding author: One Shields Avenue, Davis, CA 95616, USA. Tel: +1 (530) 752-4997.
| |
Collapse
|
6
|
Andrews KR, Seaborn T, Egan JP, Fagnan MW, New DD, Chen Z, Hohenlohe PA, Waits LP, Caudill CC, Narum SR. Whole genome resequencing identifies local adaptation associated with environmental variation for redband trout. Mol Ecol 2023; 32:800-818. [PMID: 36478624 PMCID: PMC9905331 DOI: 10.1111/mec.16810] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 11/20/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
Aquatic ectotherms are predicted to harbour genomic signals of local adaptation resulting from selective pressures driven by the strong influence of climate conditions on body temperature. We investigated local adaptation in redband trout (Oncorhynchus mykiss gairdneri) using genome scans for 547 samples from 11 populations across a wide range of habitats and thermal gradients in the interior Columbia River. We estimated allele frequencies for millions of single nucleotide polymorphism loci (SNPs) across populations using low-coverage whole genome resequencing, and used population structure outlier analyses to identify genomic regions under divergent selection between populations. Twelve genomic regions showed signatures of local adaptation, including two regions associated with genes known to influence migration and developmental timing in salmonids (GREB1L, ROCK1, SIX6). Genotype-environment association analyses indicated that diurnal temperature variation was a strong driver of local adaptation, with signatures of selection driven primarily by divergence of two populations in the northern extreme of the subspecies range. We also found evidence for adaptive differences between high-elevation desert vs. montane habitats at a smaller geographical scale. Finally, we estimated vulnerability of redband trout to future climate change using ecological niche modelling and genetic offset analyses under two climate change scenarios. These analyses predicted substantial habitat loss and strong genetic shifts necessary for adaptation to future habitats, with the greatest vulnerability predicted for high-elevation desert populations. Our results provide new insight into the complexity of local adaptation in salmonids, and important predictions regarding future responses of redband trout to climate change.
Collapse
Affiliation(s)
- Kimberly R Andrews
- Institute for Interdisciplinary Data Sciences (IIDS), University of Idaho, Moscow, Idaho, USA
| | - Travis Seaborn
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, Idaho, USA
| | - Joshua P Egan
- Department of Biological Sciences, College of Science, University of Idaho, Moscow, Idaho, USA.,Bell Museum of Natural History, University of Minnesota, Saint Paul, Minnesota, USA
| | - Matthew W Fagnan
- Institute for Interdisciplinary Data Sciences (IIDS), University of Idaho, Moscow, Idaho, USA
| | - Daniel D New
- Institute for Interdisciplinary Data Sciences (IIDS), University of Idaho, Moscow, Idaho, USA
| | - Zhongqi Chen
- Aquaculture Research Institute, University of Idaho, Hagerman, Idaho, USA
| | - Paul A Hohenlohe
- Department of Biological Sciences, College of Science, University of Idaho, Moscow, Idaho, USA
| | - Lisette P Waits
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, Idaho, USA
| | - Christopher C Caudill
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, Idaho, USA
| | - Shawn R Narum
- Aquaculture Research Institute, University of Idaho, Hagerman, Idaho, USA.,Columbia River Inter-Tribal Fish Commission, Hagerman, Idaho, USA
| |
Collapse
|
7
|
Van Wert JC, Hendriks B, Ekström A, Patterson DA, Cooke SJ, Hinch SG, Eliason EJ. Population variability in thermal performance of pre-spawning adult Chinook salmon. CONSERVATION PHYSIOLOGY 2023; 11:coad022. [PMID: 37152448 PMCID: PMC10157787 DOI: 10.1093/conphys/coad022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 02/22/2023] [Accepted: 04/03/2023] [Indexed: 05/09/2023]
Abstract
Climate change is causing large declines in many Pacific salmon populations. In particular, warm rivers are associated with high levels of premature mortality in migrating adults. The Fraser River watershed in British Columbia, Canada, supports some of the largest Chinook salmon (Oncorhynchus tshawytscha) runs in the world. However, the Fraser River is warming at a rate that threatens these populations at critical freshwater life stages. A growing body of literature suggests salmonids are locally adapted to their thermal migratory experience, and thus, population-specific thermal performance information can aid in management decisions. We compared the thermal performance of pre-spawning adult Chinook salmon from two populations, a coastal fall-run from the Chilliwack River (125 km cooler migration) and an interior summer-run from the Shuswap River (565 km warmer migration). We acutely exposed fish to temperatures reflecting current (12°C, 18°C) and future projected temperatures (21°C, 24°C) in the Fraser River and assessed survival, aerobic capacity (resting and maximum metabolic rates, absolute aerobic scope (AAS), muscle and ventricle citrate synthase), anaerobic capacity (muscle and ventricle lactate dehydrogenase) and recovery capacity (post-exercise metabolism, blood physiology, tissue lactate). Chilliwack Chinook salmon performed worse at high temperatures, indicated by elevated mortality, reduced breadth in AAS, enhanced plasma lactate and potassium levels and elevated tissue lactate concentrations compared with Shuswap Chinook salmon. At water temperatures exceeding the upper pejus temperatures (Tpejus, defined here as 80% of maximum AAS) of Chilliwack (18.7°C) and Shuswap (20.2°C) Chinook salmon populations, physiological performance will decline and affect migration and survival to spawn. Our results reveal population differences in pre-spawning Chinook salmon performance across scales of biological organization at ecologically relevant temperatures. Given the rapid warming of rivers, we show that it is critical to consider the intra-specific variation in thermal physiology to assist in the conservation and management of Pacific salmon.
Collapse
Affiliation(s)
- Jacey C Van Wert
- Corresponding author: Department of Ecology, Evolution & Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106-9620, USA.
| | - Brian Hendriks
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Andreas Ekström
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Department of Biological and Environmental Sciences, University of Gothenburg, 41390 Gothenburg, Sweden
| | - David A Patterson
- Fisheries and Oceans Canada, Science Branch, Cooperative Resource Management Institute, School of Resource and Environmental Management, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Steven J Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Scott G Hinch
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Erika J Eliason
- Department of Ecology, Evolution & Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106-9620, USA
| |
Collapse
|
8
|
Horowitz M, Hasin Y. Vascular compliance and left ventricular compliance cross talk: Implications for using long-term heat acclimation in cardiac care. Front Physiol 2023; 14:1074391. [PMID: 36960151 PMCID: PMC10027724 DOI: 10.3389/fphys.2023.1074391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/23/2023] [Indexed: 03/09/2023] Open
Abstract
1) The first evidence of the beneficial impact of Long-Term-Heat-Acclimation (LTHA) on cardio-vascular compliance was the positive inotropic response and improved left ventricular (LV) compliance noted when isolated hearts from LTHA rats were studied. Human echo study demonstrates that passive HA affects the right ventricle and the atria as well. 2) There is a cross-talk between vascular and cardiac compliance. Vascular compliance per se is defined by central venous pressure-Blood volume relationship-Global Vascular Compliance (GVC). It is determined by the sum of the vascular compliance of the vessels in every organ in any physiological state, varies with LTHA and thus influences cardiac performance. LTHA improves endothelial function, increases NO (nitric oxide) production, in-turn stimulating alterations in ECM (extracellular matrix) via the TGF β1-SMAD pathway. 3) LTHA is associated with transformation from fast to slow myosin, heat acclimation ischemic/hypoxic cross-tolerance and alterations in the extracellular matrix. 4) A human translational study demonstrated improved LV compliance following bypass surgery in LTHA subjects compared to controls. 5) Diastolic dysfunction and the impact of comorbidities with vascular and non- vascular origins are major contributors to the syndrome of heart failure with preserved ejection function (HFPEF). Unfortunately, there is a paucity of treatment modalities that improve diastolic dysfunction. 6) In the current mini-review we suggest that LTHA may be beneficial to HFPEF patients by remodeling cardiac compliance and vascular response.
Collapse
Affiliation(s)
- Michal Horowitz
- Laboratory of Environmental Physiology, Faculty of Dentistry, The Hebrew University of Jerusalem, Jerusalem, Israel
- *Correspondence: Michal Horowitz,
| | | |
Collapse
|
9
|
Anttila K, Mauduit F, Kanerva M, Götting M, Nikinmaa M, Claireaux G. Cardiovascular oxygen transport and peripheral oxygen extraction capacity contribute to acute heat tolerance in European seabass. Comp Biochem Physiol A Mol Integr Physiol 2023; 275:111340. [PMID: 36347467 DOI: 10.1016/j.cbpa.2022.111340] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 10/23/2022] [Accepted: 11/02/2022] [Indexed: 11/08/2022]
Abstract
This study evaluated whether different parameters describing cardiovascular function, energy metabolism, oxygen transport and oxidative stress were related to the critical thermal maximum (CTMAX) of European seabass (Dicentrarchus labrax) and if there were differential changes in these parameters during and after heat shock in animals with different CTMAX in order to characterize which physiological features make seabass vulnerable to heat waves. Seabass (n = 621) were tested for CTMAX and the physiological parameters were measured in individuals with good or poor temperature tolerance before and after a heat shock (change in temperature from 15 °C to 28 °C in 1.5 h). Fish with good thermal tolerance had larger ventricles with higher maximal heart rate during the heat shock than individuals with poor tolerance. Furthermore, they initially had a high ventricular Ca2+-ATPase activity, which was reduced to a similar level as in fish with poor tolerance following heat shock. The activity of heart lactate dehydrogenase increased in fish with high tolerance, when they were exposed to heat shock, while the aerobic enzyme activity did not differ between groups. The tolerant individuals had smaller red muscle fibers with higher myoglobin content than the poorly tolerant ones. The poorly tolerant individuals had higher hematocrit, which increased with heat shock in both groups. The poorly tolerant individuals had also higher activity of enzymes related to oxidative stress especially after heat shock. In general, CTMAX was not depending on merely one physiological factor but several organ and cellular parameters were related to the CTMAX of seabass and when working in combination they might protect the highly tolerant seabass from future heat waves.
Collapse
Affiliation(s)
- Katja Anttila
- Department of Biology, University of Turku, FI-20014 Turku, Finland.
| | - Florian Mauduit
- Université de Bretagne Occidentale, LEMAR (UMR 6539), Unité PFOM-ARN, Centre Ifremer de Bretagne, Plouzané 29280, France
| | - Mirella Kanerva
- Department of Biology, University of Turku, FI-20014 Turku, Finland
| | - Miriam Götting
- Department of Biology, University of Turku, FI-20014 Turku, Finland
| | - Mikko Nikinmaa
- Department of Biology, University of Turku, FI-20014 Turku, Finland
| | - Guy Claireaux
- Université de Bretagne Occidentale, LEMAR (UMR 6539), Unité PFOM-ARN, Centre Ifremer de Bretagne, Plouzané 29280, France
| |
Collapse
|
10
|
Chen Z, Grossfurthner L, Loxterman JL, Masingale J, Richardson BA, Seaborn T, Smith B, Waits LP, Narum SR. Applying genomics in assisted migration under climate change: Framework, empirical applications, and case studies. Evol Appl 2022; 15:3-21. [PMID: 35126645 PMCID: PMC8792483 DOI: 10.1111/eva.13335] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 11/18/2021] [Accepted: 12/01/2021] [Indexed: 12/01/2022] Open
Abstract
The rate of global climate change is projected to outpace the ability of many natural populations and species to adapt. Assisted migration (AM), which is defined as the managed movement of climate-adapted individuals within or outside the species ranges, is a conservation option to improve species' adaptive capacity and facilitate persistence. Although conservation biologists have long been using genetic tools to increase or maintain diversity of natural populations, genomic techniques could add extra benefit in AM that include selectively neutral and adaptive regions of the genome. In this review, we first propose a framework along with detailed procedures to aid collaboration among scientists, agencies, and local and regional managers during the decision-making process of genomics-guided AM. We then summarize the genomic approaches for applying AM, followed by a literature search of existing incorporation of genomics in AM across taxa. Our literature search initially identified 729 publications, but after filtering returned only 50 empirical studies that were either directly applied or considered genomics in AM related to climate change across taxa of plants, terrestrial animals, and aquatic animals; 42 studies were in plants. This demonstrated limited application of genomic methods in AM in organisms other than plants, so we provide further case studies as two examples to demonstrate the negative impact of climate change on non-model species and how genomics could be applied in AM. With the rapidly developing sequencing technology and accumulating genomic data, we expect to see more successful applications of genomics in AM, and more broadly, in the conservation of biodiversity.
Collapse
Affiliation(s)
- Zhongqi Chen
- Aquaculture Research InstituteUniversity of IdahoHagermanIdahoUSA
| | - Lukas Grossfurthner
- Bioinformatics and Computational Biology Graduate ProgramUniversity of IdahoHagermanIdahoUSA
| | - Janet L. Loxterman
- Department of Biological SciencesIdaho State UniversityPocatelloIdahoUSA
| | | | | | - Travis Seaborn
- Department of Fish and Wildlife ResourcesUniversity of IdahoMoscowIdahoUSA
| | - Brandy Smith
- Department of Biological SciencesIdaho State UniversityPocatelloIdahoUSA
| | - Lisette P. Waits
- Department of Fish and Wildlife ResourcesUniversity of IdahoMoscowIdahoUSA
| | - Shawn R. Narum
- Columbia River Inter‐Tribal Fish CommissionHagermanIdahoUSA
| |
Collapse
|
11
|
Attard CRM, Sandoval-Castillo J, Brauer CJ, Unmack PJ, Schmarr D, Bernatchez L, Beheregaray LB. Fish out of water: Genomic insights into persistence of rainbowfish populations in the desert. Evolution 2021; 76:171-183. [PMID: 34778944 DOI: 10.1111/evo.14399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/22/2021] [Accepted: 10/31/2021] [Indexed: 11/26/2022]
Abstract
How populations of aquatic fauna persist in extreme desert environments is an enigma. Individuals often breed and disperse during favorable conditions. Theory predicts that adaptive capacity should be low in small populations, such as in desert fishes. We integrated satellite-derived surface water data and population genomic diversity from 20,294 single-nucleotide polymorphisms across 344 individuals to understand metapopulation persistence of the desert rainbowfish (Melanotaenia splendida tatei) in central Australia. Desert rainbowfish showed very small effective population sizes, especially at peripheral populations, and low connectivity between river catchments. Yet, there was no evidence of population-level inbreeding and a signal of possible adaptive divergence associated with aridity was detected. Candidate genes for local adaptation included functions related to environmental cues and stressful conditions. Eco-evolutionary modeling showed that positive selection in refugial subpopulations combined with connectivity during flood periods can enable retention of adaptive diversity. Our study suggests that adaptive variation can be maintained in small populations and integrate with neutral metapopulation processes to allow persistence in the desert.
Collapse
Affiliation(s)
- Catherine R M Attard
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Chris J Brauer
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Peter J Unmack
- Centre for Applied Water Science, Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - David Schmarr
- Inland Waters and Catchment Ecology Program, SARDI Aquatic Sciences, Henley Beach, SA, 5022, Australia
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université Laval Québec, Québec, QC, G1V 0A6, Canada
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| |
Collapse
|
12
|
Intraspecific variation in thermal tolerance differs between tropical and temperate fishes. Sci Rep 2021; 11:21272. [PMID: 34711864 PMCID: PMC8553816 DOI: 10.1038/s41598-021-00695-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/12/2021] [Indexed: 11/08/2022] Open
Abstract
How ectothermic animals will cope with global warming is a critical determinant of the ecological impacts of climate change. There has been extensive study of upper thermal tolerance limits among fish species but how intraspecific variation in tolerance may be affected by habitat characteristics and evolutionary history has not been considered. Intraspecific variation is a primary determinant of species vulnerability to climate change, with implications for global patterns of impacts of ongoing warming. Using published critical thermal maximum (CTmax) data on 203 fish species, we found that intraspecific variation in upper thermal tolerance varies according to a species’ latitude and evolutionary history. Overall, tropical species show a lower intraspecific variation in thermal tolerance than temperate species. Notably, freshwater tropical species have a lower variation in tolerance than freshwater temperate species, which implies increased vulnerability to impacts of thermal stress. The extent of variation in CTmax among fish species has a strong phylogenetic signal, which may indicate a constraint on evolvability to rising temperatures in tropical fishes. That is, in addition to living closer to their upper thermal limits, tropical species may have higher sensitivity and lower adaptability to global warming compared to temperate counterparts. This is evidence that freshwater tropical fish communities, worldwide, are especially vulnerable to ongoing climate change.
Collapse
|
13
|
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
|
14
|
Clark RD, Aardema ML, Andolfatto P, Barber PH, Hattori A, Hoey JA, Montes HR, Pinsky ML. Genomic signatures of spatially divergent selection at clownfish range margins. Proc Biol Sci 2021; 288:20210407. [PMID: 34102891 PMCID: PMC8187997 DOI: 10.1098/rspb.2021.0407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/11/2021] [Indexed: 01/25/2023] Open
Abstract
Understanding how evolutionary forces interact to drive patterns of selection and distribute genetic variation across a species' range is of great interest in ecology and evolution, especially in an era of global change. While theory predicts how and when populations at range margins are likely to undergo local adaptation, empirical evidence testing these models remains sparse. Here, we address this knowledge gap by investigating the relationship between selection, gene flow and genetic drift in the yellowtail clownfish, Amphiprion clarkii, from the core to the northern periphery of the species range. Analyses reveal low genetic diversity at the range edge, gene flow from the core to the edge and genomic signatures of local adaptation at 56 single nucleotide polymorphisms in 25 candidate genes, most of which are significantly correlated with minimum annual sea surface temperature. Several of these candidate genes play a role in functions that are upregulated during cold stress, including protein turnover, metabolism and translation. Our results illustrate how spatially divergent selection spanning the range core to the periphery can occur despite the potential for strong genetic drift at the range edge and moderate gene flow from the core populations.
Collapse
Affiliation(s)
- René D. Clark
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901, USA
| | - Matthew L. Aardema
- Department of Biology, Montclair State University, 1 Normal Avenue, Montclair, NJ 07043, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, 200 Central Park West, New York, NY 10024-5102, USA
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY 10026, USA
| | - Paul H. Barber
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA 90095, USA
| | - Akihisa Hattori
- Faculty of Liberal Arts and Education, Shiga University, 2-5-1 Hiratsu, Otsu, Shiga 520-0862, Japan
| | - Jennifer A. Hoey
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901, USA
- Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | | | - Malin L. Pinsky
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901, USA
| |
Collapse
|
15
|
McKenzie DJ, Zhang Y, Eliason EJ, Schulte PM, Claireaux G, Blasco FR, Nati JJH, Farrell AP. Intraspecific variation in tolerance of warming in fishes. JOURNAL OF FISH BIOLOGY 2021; 98:1536-1555. [PMID: 33216368 DOI: 10.1111/jfb.14620] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/09/2020] [Accepted: 11/17/2020] [Indexed: 05/12/2023]
Abstract
Intraspecific variation in key traits such as tolerance of warming can have profound effects on ecological and evolutionary processes, notably responses to climate change. The empirical evidence for three primary elements of intraspecific variation in tolerance of warming in fishes is reviewed. The first is purely mechanistic that tolerance varies across life stages and as fishes become mature. The limited evidence indicates strongly that this is the case, possibly because of universal physiological principles. The second is intraspecific variation that is because of phenotypic plasticity, also a mechanistic phenomenon that buffers individuals' sensitivity to negative impacts of global warming in their lifetime, or to some extent through epigenetic effects over successive generations. Although the evidence for plasticity in tolerance to warming is extensive, more work is required to understand underlying mechanisms and to reveal whether there are general patterns. The third element is intraspecific variation based on heritable genetic differences in tolerance, which underlies local adaptation and may define long-term adaptability of a species in the face of ongoing global change. There is clear evidence of local adaptation and some evidence of heritability of tolerance to warming, but the knowledge base is limited with detailed information for only a few model or emblematic species. There is also strong evidence of structured variation in tolerance of warming within species, which may have ecological and evolutionary significance irrespective of whether it reflects plasticity or adaptation. Although the overwhelming consensus is that having broader intraspecific variation in tolerance should reduce species vulnerability to impacts of global warming, there are no sufficient data on fishes to provide insights into particular mechanisms by which this may occur.
Collapse
Affiliation(s)
- David J McKenzie
- MARBEC, University of Montpellier, CNRS, IFREMER, IRD, Montpellier, France
| | - Yangfan Zhang
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Patricia M Schulte
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Guy Claireaux
- Université de Bretagne Occidentale, LEMAR (UMR 6539), Centre Ifremer de Bretagne, Plouzané, France
| | - Felipe R Blasco
- Department of Physiological Sciences, Federal University of São Carlos, São Carlos, Brazil
- Joint Graduate Program in Physiological Sciences, Federal University of São Carlos - UFSCar/São Paulo State University, UNESP Campus Araraquara, Araraquara, Brazil
| | - Julie J H Nati
- MARBEC, University of Montpellier, CNRS, IFREMER, IRD, Montpellier, France
| | - Anthony P Farrell
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
16
|
Stahlke A, Bell D, Dhendup T, Kern B, Pannoni S, Robinson Z, Strait J, Smith S, Hand BK, Hohenlohe PA, Luikart G. Population Genomics Training for the Next Generation of Conservation Geneticists: ConGen 2018 Workshop. J Hered 2021; 111:227-236. [PMID: 32037446 PMCID: PMC7117792 DOI: 10.1093/jhered/esaa001] [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] [Received: 05/17/2019] [Accepted: 01/06/2020] [Indexed: 12/30/2022] Open
Abstract
The increasing availability and complexity of next-generation sequencing (NGS) data sets make ongoing training an essential component of conservation and population genetics research. A workshop entitled “ConGen 2018” was recently held to train researchers in conceptual and practical aspects of NGS data production and analysis for conservation and ecological applications. Sixteen instructors provided helpful lectures, discussions, and hands-on exercises regarding how to plan, produce, and analyze data for many important research questions. Lecture topics ranged from understanding probabilistic (e.g., Bayesian) genotype calling to the detection of local adaptation signatures from genomic, transcriptomic, and epigenomic data. We report on progress in addressing central questions of conservation genomics, advances in NGS data analysis, the potential for genomic tools to assess adaptive capacity, and strategies for training the next generation of conservation genomicists.
Collapse
Affiliation(s)
- Amanda Stahlke
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Donavan Bell
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT
| | - Tashi Dhendup
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT.,Department of Forest and Park Services, Ugyen Wangchuck Institute for Conservation and Environmental Research, Bumthang, Bhutan
| | - Brooke Kern
- Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT.,Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN
| | - Samuel Pannoni
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT.,Flathead Lake Biological Station, Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT
| | - Zachary Robinson
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT
| | - Jeffrey Strait
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT
| | - Seth Smith
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT.,Flathead Lake Biological Station, Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT.,Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI
| | - Brian K Hand
- Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT.,Flathead Lake Biological Station, Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT
| | - Paul A Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Gordon Luikart
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT.,Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT.,Flathead Lake Biological Station, Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT
| |
Collapse
|
17
|
Orbán L, Shen X, Phua N, Varga L. Toward Genome-Based Selection in Asian Seabass: What Can We Learn From Other Food Fishes and Farm Animals? Front Genet 2021; 12:506754. [PMID: 33968125 PMCID: PMC8097054 DOI: 10.3389/fgene.2021.506754] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/15/2021] [Indexed: 01/08/2023] Open
Abstract
Due to the steadily increasing need for seafood and the plateauing output of fisheries, more fish need to be produced by aquaculture production. In parallel with the improvement of farming methods, elite food fish lines with superior traits for production must be generated by selection programs that utilize cutting-edge tools of genomics. The purpose of this review is to provide a historical overview and status report of a selection program performed on a catadromous predator, the Asian seabass (Lates calcarifer, Bloch 1790) that can change its sex during its lifetime. We describe the practices of wet lab, farm and lab in detail by focusing onto the foundations and achievements of the program. In addition to the approaches used for selection, our review also provides an inventory of genetic/genomic platforms and technologies developed to (i) provide current and future support for the selection process; and (ii) improve our understanding of the biology of the species. Approaches used for the improvement of terrestrial farm animals are used as examples and references, as those processes are far ahead of the ones used in aquaculture and thus they might help those working on fish to select the best possible options and avoid potential pitfalls.
Collapse
Affiliation(s)
- László Orbán
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore.,Frontline Fish Genomics Research Group, Department of Applied Fish Biology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Keszthely, Hungary
| | - Xueyan Shen
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore.,Tropical Futures Institute, James Cook University, Singapore, Singapore
| | - Norman Phua
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - László Varga
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllõ, Hungary.,Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, Gödöllõ, Hungary
| |
Collapse
|
18
|
de Jong MJ, Lovatt F, Hoelzel AR. Detecting genetic signals of selection in heavily bottlenecked reindeer populations by comparing parallel founder events. Mol Ecol 2021; 30:1642-1658. [PMID: 33565631 DOI: 10.1111/mec.15837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 01/11/2021] [Accepted: 01/28/2021] [Indexed: 11/28/2022]
Abstract
Founder populations are of special interest to both evolutionary and conservation biologists, but the detection of genetic signals of selection in these populations is challenging due to their demographic history. Geographically separated founder populations likely to have been subjected to similar selection pressures provide an ideal but rare opportunity to overcome these challenges. Here we take advantage of such a situation generated when small, isolated founder populations of reindeer were established on the island of South Georgia, and using this system we look for empirical evidence of selection overcoming strong genetic drift. We generated a 70 k ddRADseq single nucleotide polymorphism database for the two parallel reindeer founder populations and screened for signatures of soft sweeps. We find evidence for a genomic region under selection shared among the two populations, and support our findings with Wright-Fisher model simulations to assess the power and specificity of interpopulation selection scans-namely Bayescan, OutFLANK, PCadapt and a newly developed scan called Genome Wide Differentiation Scan (GWDS)-in the context of pairwise source-founder comparisons. Our simulations indicate that loci under selection in small founder populations are most probably detected by GWDS, and strengthen the hypothesis that the outlier region represents a true locus under selection. We explore possible, relevant functional roles for genes in linkage with the detected outlier loci.
Collapse
Affiliation(s)
| | - Fiona Lovatt
- Department of Biosciences, Durham University, Durham, UK
| | - A Rus Hoelzel
- Department of Biosciences, Durham University, Durham, UK
| |
Collapse
|
19
|
Chen Z, Narum SR. Whole genome resequencing reveals genomic regions associated with thermal adaptation in redband trout. Mol Ecol 2020; 30:162-174. [PMID: 33135227 DOI: 10.1111/mec.15717] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 12/18/2022]
Abstract
Adaptation to local environments involves evolution of ecologically important traits and underlying physiological processes. Here, we used low coverage whole-genome resequencing (lcWGR) on individuals to identify genome regions involved in thermal adaptation in wild redband trout Oncorhynchus mykiss gairdneri, a subspecies of rainbow trout that inhabits ecosystems ranging from cold montane forests to high elevation deserts. This study includes allele frequency-based analyses for selective sweeps among populations, followed by multiple association tests for specific sets of phenotypes measured under thermal stress (acute and chronic survival/mortality; high or low cardiac performance groups). Depending on the groups in each set of analyses, sequencing reads covered 43%-75% of the genome at ≥15× and each analysis included millions of SNPs across the genome. In tests for selective sweeps among populations, a total of six chromosomal regions were significant. The further association tests for specific phenotypes revealed that the region on chromosome 4 was consistently the most significant and contains the cerk gene (ceramide kinase). This study provides insight into a potential genetic mechanism of local thermal adaptation and suggests cerk may be an important candidate gene. However, further validation of this cerk gene is necessary to determine if the association with cardiac performance results in a functional role to influence thermal performance when exposed to high water temperatures and hypoxic conditions.
Collapse
Affiliation(s)
- Zhongqi Chen
- Aquaculture Research Institute, University of Idaho, Hagerman, ID, USA
| | - Shawn R Narum
- Aquaculture Research Institute, University of Idaho, Hagerman, ID, USA.,Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
| |
Collapse
|
20
|
Collins EE, Hargrove JS, Delomas TA, Narum SR. Distribution of genetic variation underlying adult migration timing in steelhead of the Columbia River basin. Ecol Evol 2020; 10:9486-9502. [PMID: 32953077 PMCID: PMC7487220 DOI: 10.1002/ece3.6641] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/10/2020] [Accepted: 07/17/2020] [Indexed: 12/05/2022] Open
Abstract
Fish migrations are energetically costly, especially when moving between freshwater and saltwater, but are a viable strategy for Pacific salmon and trout (Oncorhynchus spp.) due to the advantageous resources available at various life stages. Anadromous steelhead (O. mykiss) migrate vast distances and exhibit variation for adult migration phenotypes that have a genetic basis at candidate genes known as greb1L and rock1. We examined the distribution of genetic variation at 13 candidate markers spanning greb1L, intergenic, and rock1 regions versus 226 neutral markers for 113 populations (n = 9,471) of steelhead from inland and coastal lineages in the Columbia River. Patterns of population structure with neutral markers reflected genetic similarity by geographic region as demonstrated in previous studies, but candidate markers clustered populations by genetic variation associated with adult migration timing. Mature alleles for late migration had the highest frequency overall in steelhead populations throughout the Columbia River, with only 9 of 113 populations that had a higher frequency of premature alleles for early migration. While a single haplotype block was evident for the coastal lineage, we identified multiple haplotype blocks for the inland lineage. The inland lineage had one haplotype block that corresponded to candidate markers within the greb1L gene and immediately upstream in the intergenic region, and the second block only contained candidate markers from the intergenic region. Haplotype frequencies had similar patterns of geographic distribution as single markers, but there were distinct differences in frequency between the two haplotype blocks for the inland lineage. This may represent multiple recombination events that differed between lineages where phenotypic differences exist between freshwater entry versus arrival timing as indicated by Micheletti et al. (2018a). Redundancy analyses were used to model environmental effects on allelic frequencies of candidate markers, and significant variables were migration distance, temperature, isothermality, and annual precipitation. This study improves our understanding of the spatial distribution of genetic variation underlying adult migration timing in steelhead as well as associated environmental factors and has direct conservation and management implications.
Collapse
Affiliation(s)
| | - John S. Hargrove
- Eagle Fish Genetics LabPacific States Marine Fisheries CommissionEagleIDUSA
| | - Thomas A. Delomas
- Eagle Fish Genetics LabPacific States Marine Fisheries CommissionEagleIDUSA
| | - Shawn R. Narum
- Columbia River Inter‐Tribal Fish CommissionHagermanIDUSA
| |
Collapse
|
21
|
Monroe AA, Zhang H, Schunter C, Ravasi T. Probing SWATH-MS as a tool for proteome level quantification in a nonmodel fish. Mol Ecol Resour 2020; 20:1647-1657. [PMID: 32687632 PMCID: PMC7689905 DOI: 10.1111/1755-0998.13229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/09/2020] [Accepted: 07/08/2020] [Indexed: 12/27/2022]
Abstract
Quantitative proteomics via mass spectrometry can provide valuable insight into molecular and phenotypic characteristics of a living system. Recent mass spectrometry developments include data‐independent acquisition (SWATH/DIA‐MS), an accurate, sensitive and reproducible method for analysing the whole proteome. The main requirement for this method is the creation of a comprehensive spectral library. New technologies have emerged producing larger and more accurate species‐specific libraries leading to a progressive collection of proteome references for multiple molecular model species. Here, for the first time, we set out to compare different spectral library constructions using multiple tissues from a coral reef fish to demonstrate its value and feasibility for nonmodel organisms. We created a large spectral library composed of 12,553 protein groups from liver and brain tissues. Via identification of differentially expressed proteins under fish exposure to elevated pCO2 and temperature, we validated the application and usefulness of these different spectral libraries. Successful identification of significant differentially expressed proteins from different environmental exposures occurred using the library with a combination of data‐independent and data‐dependent acquisition methods as well as both tissue types. Further analysis revealed expected patterns of significantly up‐regulated heat shock proteins in a dual condition of ocean warming and acidification indicating the biological accuracy and relevance of the method. This study provides the first reference spectral library for a nonmodel organism. It represents a useful guide for future building of accurate spectral library references in nonmodel organisms allowing the discovery of ecologically relevant changes in the proteome.
Collapse
Affiliation(s)
- Alison A Monroe
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Huoming Zhang
- King Abdullah University of Science and Technology, Core Labs, Thuwal, Saudi Arabia
| | - Celia Schunter
- Swire Institute of Marine Science, The School of Biological Sciences, The University of Hong Kong, Hong Kong SAR
| | - Timothy Ravasi
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Japan
| |
Collapse
|
22
|
Li YL, Xing TF, Liu JX. Genome-wide association analyses based on whole-genome sequencing of Protosalanx hyalocranius provide insights into sex determination of Salangid fishes. Mol Ecol Resour 2020; 20:1038-1049. [PMID: 32315505 DOI: 10.1111/1755-0998.13172] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 03/28/2020] [Accepted: 04/09/2020] [Indexed: 12/22/2022]
Abstract
Identification of sex determination system and sex-determining genes have important implications in conservation, ecology and evolution. However, much remains to be discovered about the evolution of different sexual determination systems in teleost fishes, of which the mechanisms of sex determination are remarkably variable. In the present study, the whole genomes of 20 males and 20 females of a Salangid fish, Protosalanx hyalocranius, were sequenced and genome wide association analyses were conducted to uncover its sex determination system and putative sex-determining genes. A total of 150 SNPs were significantly associated with sex, which showed high differentiation between sexes (FST ranged from 0.245 to 0.556). Of the 150 sex-associated SNPs, 76 SNPs displayed sex specificity with even coverage of depth and were female heterogametic, which suggested a ZZ/ZW sex determination system. Interestingly, one scaffold containing sex-specific SNPs displayed synteny to the sex chromosome of medaka. Annotations of sex-associated loci suggested that both transcriptional regulators (e.g., FOX genes) and secreted hormones and their receptors might be involved in the sex determination/differentiation of P. hyalocranius. More strikingly, we found a nonsense mutation in one copy of GALNT homology gene of all females, which suggested that "Z dosage" effect might play a vital role in the processes of sex determination/differentiation. These sex-specific loci could be a valuable resource for further research on sex determination of Salangid fishes and the results could contribute to the understanding of sex determination mechanisms and the evolution of sex chromosome in teleost fishes.
Collapse
Affiliation(s)
- Yu-Long Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Teng-Fei Xing
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jin-Xian Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| |
Collapse
|
23
|
Amish SJ, Ali O, Peacock M, Miller M, Robinson M, Smith S, Luikart G, Neville H. Assessing thermal adaptation using family‐based association and
F
ST
outlier tests in a threatened trout species. Mol Ecol 2019; 28:2573-2593. [DOI: 10.1111/mec.15100] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 03/15/2019] [Accepted: 04/01/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Stephen J. Amish
- Conservation Genomics Group, Division of Biological Sciences University of Montana Missoula Montana
- Flathead Biological Station University of Montana Polson Montana
| | - Omar Ali
- Department of Animal Science University of California Davis California
| | - Mary Peacock
- Department of Biology University of Nevada Reno Nevada
| | - Michael Miller
- Department of Animal Science University of California Davis California
| | | | - Seth Smith
- Flathead Biological Station University of Montana Polson Montana
| | - Gordon Luikart
- Conservation Genomics Group, Division of Biological Sciences University of Montana Missoula Montana
- Flathead Biological Station University of Montana Polson Montana
| | | |
Collapse
|
24
|
Luikart G, Kardos M, Hand BK, Rajora OP, Aitken SN, Hohenlohe PA. Population Genomics: Advancing Understanding of Nature. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_60] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|