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Jernvall J, Di-Poï N, Mikkola ML, Kratochwil CF. Toward a universal measure of robustness across model organs and systems. Evol Dev 2023; 25:410-417. [PMID: 37070415 DOI: 10.1111/ede.12436] [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: 10/04/2022] [Revised: 04/03/2023] [Accepted: 04/09/2023] [Indexed: 04/19/2023]
Abstract
The development of an individual must be capable of resisting the harmful effects of internal and external perturbations. This capacity, called robustness, can make the difference between normal variation and disease. Some systems and organs are more resilient in their capacity to correct the effects of internal disturbances such as mutations. Similarly, organs and organisms differ in their capacity to be resilient against external disturbances, such as changes in temperature. Furthermore, all developmental systems must be somewhat flexible to permit evolutionary change, and understanding robustness requires a comparative framework. Over the last decades, most research on developmental robustness has been focusing on specific model systems and organs. Hence, we lack tools that would allow cross-species and cross-organ comparisons. Here, we emphasize the need for a uniform framework to experimentally test and quantify robustness across study systems and suggest that the analysis of fluctuating asymmetry might be a powerful proxy to do so. Such a comparative framework will ultimately help to resolve why and how organs of the same and different species differ in their sensitivity to internal (e.g., mutations) and external (e.g., temperature) perturbations and at what level of biological organization buffering capacities exist and therefore create robustness of the developmental system.
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Affiliation(s)
- Jukka Jernvall
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
| | - Nicolas Di-Poï
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Marja L Mikkola
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
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2
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Chen B, Bai Y, Wang J, Ke Q, Zhou Z, Zhou T, Pan Y, Wu R, Wu X, Zheng W, Xu P. Population structure and genome-wide evolutionary signatures reveal putative climate-driven habitat change and local adaptation in the large yellow croaker. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:141-154. [PMID: 37275538 PMCID: PMC10232709 DOI: 10.1007/s42995-023-00165-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 01/25/2023] [Indexed: 06/07/2023]
Abstract
The large yellow croaker (Larimichthys crocea) is one of the most economically valuable marine fish in China and is a notable species in ecological studies owing to a serious collapse of wild germplasm in the past few decades. The stock division and species distribution, which have important implications for ecological protection, germplasm recovery, and fishery resource management, have been debated since the 1960s. However, it is still uncertain even how many stocks exist in this species. To address this, we evaluated the fine-scale genetic structure of large yellow croaker populations distributed along the eastern and southern Chinese coastline based on 7.64 million SNP markers. Compared with the widely accepted stock boundaries proposed in the 1960s, our results revealed that a climate-driven habitat change probably occurred between the Naozhou (Nanhai) Stock and the Ming-Yuedong (Mindong) Stock. The boundary between these two stocks might have shifted northwards from the Pearl River Estuary to the northern area of the Taiwan Strait, accompanied by highly asymmetric introgression. In addition, we found divergent landscapes of natural selection between the stocks inhabiting northern and southern areas. The northern population exhibited highly agminated signatures of strong natural selection in genes related to developmental processes, whereas moderate and interspersed selective signatures were detected in many immune-related genes in the southern populations. These findings establish the stock status and genome-wide evolutionary landscapes of large yellow croaker, providing a basis for conservation, fisheries management and further evolutionary biology studies. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00165-2.
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Affiliation(s)
- Baohua Chen
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
- National Key Laboratory of Mariculture Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352000 China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102 China
| | - Yulin Bai
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
| | - Jiaying Wang
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
| | - Qiaozhen Ke
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
- National Key Laboratory of Mariculture Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352000 China
| | - Zhixiong Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
| | - Tao Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
| | - Ying Pan
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, 350000 China
| | - Renxie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088 China
| | - Xiongfei Wu
- Ningbo Academy of Oceanology and Fishery, Ningbo, 315012 China
| | - Weiqiang Zheng
- National Key Laboratory of Mariculture Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352000 China
| | - Peng Xu
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
- National Key Laboratory of Mariculture Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352000 China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102 China
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3
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Carrión PL, Raeymaekers JAM, De León LF, Chaves JA, Sharpe DMT, Huber SK, Herrel A, Vanhooydonck B, Gotanda KM, Koop JAH, Knutie SA, Clayton DH, Podos J, Hendry AP. The terroir of the finch: How spatial and temporal variation shapes phenotypic traits in DARWIN'S finches. Ecol Evol 2022; 12:e9399. [PMID: 36225827 PMCID: PMC9534727 DOI: 10.1002/ece3.9399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 09/19/2022] [Indexed: 11/10/2022] Open
Abstract
The term terroir is used in viticulture to emphasize how the biotic and abiotic characteristics of a local site influence grape physiology and thus the properties of wine. In ecology and evolution, such terroir (i.e., the effect of space or “site”) is expected to play an important role in shaping phenotypic traits. Just how important is the pure spatial effect of terroir (e.g., differences between sites that persist across years) in comparison to temporal variation (e.g., differences between years that persist across sites), and the interaction between space and time (e.g., differences between sites change across years)? We answer this question by analyzing beak and body traits of 4388 medium ground finches (Geospiza fortis) collected across 10 years at three locations in Galápagos. Analyses of variance indicated that phenotypic variation was mostly explained by site for beak size (η2 = 0.42) and body size (η2 = 0.43), with a smaller contribution for beak shape (η2 = 0.05) and body shape (η2 = 0.12), but still higher compared to year and site‐by‐year effects. As such, the effect of terroir seems to be very strong in Darwin's finches, notwithstanding the oft‐emphasized interannual variation. However, these results changed dramatically when we excluded data from Daphne Major, indicating that the strong effect of terroir was mostly driven by that particular population. These phenotypic results were largely paralleled in analyses of environmental variables (rainfall and vegetation indices) expected to shape terroir in this system. These findings affirm the evolutionary importance of terroir, while also revealing its dependence on other factors, such as geographical isolation.
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Affiliation(s)
- Paola L. Carrión
- Redpath Museum, Department of BiologyMcGill UniversityMontréalQuébecCanada
| | | | - Luis Fernando De León
- Department of BiologyUniversity of Massachusetts BostonBostonMassachusettsUSA,Centro de Biodiversidad y Descubrimiento de DrogasInstituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT‐AIP)PanamáRepública de Panamá,Smithsonian Tropical Research InstitutePanamáRepública de Panamá
| | - Jaime A. Chaves
- Department of BiologySan Francisco State UniversitySan FranciscoCaliforniaUSA,Colegio de Ciencias Biológicas y AmbientalesUniversidad San Francisco de QuitoQuitoEcuador
| | - Diana M. T. Sharpe
- Smithsonian Tropical Research InstitutePanamáRepública de Panamá,Worcester State UniversityWorcesterMassachusettsUSA
| | - Sarah K. Huber
- Virginia Institute of Marine ScienceCollege of William & MaryGloucester PointVirginiaUSA
| | - Anthony Herrel
- Muséum National d'Histoire NaturelleDépartement Adaptations du VivantBâtiment d'Anatomie ComparéeParisFrance
| | | | - Kiyoko M. Gotanda
- Department of Biological SciencesBrock UniversitySt. CatharinesOntarioCanada,Departement de BiologieUniversite de SherbrookeQuebecCanada
| | - Jennifer A. H. Koop
- Department of Biological SciencesNorthern Illinois UniversityDeKalbIllinoisUSA
| | - Sarah A. Knutie
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA,Institute for Systems GenomicsUniversity of ConnecticutStorrsConnecticutUSA
| | - Dale H. Clayton
- School of Biological SciencesUniversity of UtahSalt Lake CityUtahUSA
| | - Jeffrey Podos
- Department of BiologyUniversity of Massachusetts AmherstAmherstMassachusettsUSA
| | - Andrew P. Hendry
- Redpath Museum, Department of BiologyMcGill UniversityMontréalQuébecCanada
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4
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Folio DM, Gil J, Caudron A, Labonne J. Genotype-by-environment interactions drive the maintenance of genetic variation in a Salmo trutta L. hybrid zone. Evol Appl 2021; 14:2698-2711. [PMID: 34815748 PMCID: PMC8591331 DOI: 10.1111/eva.13307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 08/18/2021] [Accepted: 09/15/2021] [Indexed: 11/28/2022] Open
Abstract
Allopatric gene pools can evolve in different directions through adaptive and nonadaptive processes and are therefore a source of intraspecific diversity. The connection of these previously isolated gene pools through human intervention can lead to intraspecific diversity loss, through extirpation of native populations or hybridization. However, the mechanisms leading to these situations are not always explicitly documented and are thus rarely used to manage intraspecific diversity. In particular, genotype-by-environment (GxE) interactions can drive postzygotic reproductive isolation mechanisms that may result in a mosaic of diversity patterns, depending on the local environment. We test this hypothesis using a salmonid species (Salmo trutta) in the Mediterranean (MED) area, where intensive stocking from non-native Atlantic (ATL) origins has led to various outcomes of hybridization with the native MED lineage, going from MED resilience to total extirpation via full hybridization. We investigate patterns of offspring survival at egg stage in natural environments, based on parental genotypes in interaction with river temperature, to detect potential GxE interactions. Our results show a strong influence of maternal GxE interaction on embryonic survival, mediated by maternal effect through egg size, and a weak influence of paternal GxE interaction. In particular, when egg size is large and temperature is cold, the survival rate of offspring originating from MED females is three times higher than that of ATL females' offspring. Because river temperatures show contrast at small scale, this cold adaptation for MED females' offspring constitutes a potent postzygotic mechanism to explain small-scale spatial heterogeneity in diversity observed in MED areas where ATL fish have been stocked. It also indicates that management efforts could be specifically targeted at the environments that actively favor native intraspecific diversity through eco-evolutionary processes such as postzygotic selection.
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Affiliation(s)
- Dorinda Marie Folio
- Université de Pau et des Pays de l’AdourUMR INRAE‐UPPAEcobiopSaint‐Pée‐sur‐NivelleFrance
- SCIMABIO InterfaceThonon‐les‐BainsFrance
| | - Jordi Gil
- UMR CARRTELINRAEUSMBThonon‐les‐BainsFrance
- Conservatoire des Espaces Naturels Rhône‐AlpesVogüeFrance
| | | | - Jacques Labonne
- Université de Pau et des Pays de l’AdourUMR INRAE‐UPPAEcobiopSaint‐Pée‐sur‐NivelleFrance
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5
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Esin EV, Markevich GN, Melnik NO, Zlenko DV, Shkil FN. Ambient temperature as a factor contributing to the developmental divergence in sympatric salmonids. PLoS One 2021; 16:e0258536. [PMID: 34653206 PMCID: PMC8519426 DOI: 10.1371/journal.pone.0258536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 09/29/2021] [Indexed: 12/01/2022] Open
Abstract
Factors and mechanisms promoting resource-based radiation in animals still represent a main challenge to evolutionary biology. The modifications of phenotype tied with adaptive diversification may result from an environmentally related shift having occurred at the early stage of development. Here, we study the role of temperature dynamics on the reproductive sites in the early-life divergence and adaptive radiation of the salmonid fish Salvelinus malma dwelling in the Lake Kronotskoe basin (North-East Asia). Local sympatric charr ecomorphs demonstrate strict homing behaviour guiding the preordained distribution along tributaries and, hence, further development under different temperatures. We thoroughly assessed the annual temperature dynamics at the spawning grounds of each morph as compared to an ancestral anadromous morph. Then we carried out an experimental rearing of both under naturally diverging and uniformed temperatures. To compare the morphs' development under the dynamically changing temperatures, we have designed a method based on calculating the accumulated heat by the Arrhenius equation. The proposed equation shows a strong predictive power and, at the same time, is not bias-susceptible when the developmental temperature approximates 0°C. The temperature was found to significantly affect the charrs' early ontogeny, which underlies the divergence of developmental and growth rates between the morphs, as well as morph-specific ontogenetic adaptations to the spawning site's temperatures. As opposed to the endemic morphs from Lake Kronotskoe, the anadromous S. malma, being unexposed to selection оn highly specific reproduction conditions, showed a wide temperature tolerance, Our findings demonstrate that the hatch, onset timing of external feeding, and size dissimilarities between the sympatric morphs reveal themselves during the development under contrast temperatures. As a result of the observed developmental disparities, the morphs occupy specific definitive foraging niches in the lake.
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Affiliation(s)
- Evgeny V. Esin
- A.N. Severtsov Institute of Ecology and Evolution RAS, Moscow, Russian Federation
| | | | - Nikolai O. Melnik
- A.N. Severtsov Institute of Ecology and Evolution RAS, Moscow, Russian Federation
| | | | - Fedor N. Shkil
- A.N. Severtsov Institute of Ecology and Evolution RAS, Moscow, Russian Federation
- Koltzov Institute of Developmental Biology RAS, Moscow, Russian Federation
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6
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Dwane C, Rundle SD, Tills O, Rezende EL, Galindo J, Rolán-Alvarez E, Truebano M. Divergence in Thermal Physiology Could Contribute to Vertical Segregation in Intertidal Ecotypes of Littorina saxatilis. Physiol Biochem Zool 2021; 94:353-365. [PMID: 34431748 DOI: 10.1086/716176] [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] [Indexed: 11/03/2022]
Abstract
AbstractThermal stress is a potentially important selective agent in intertidal marine habitats, but the role that thermal tolerance might play in local adaptation across shore height has been underexplored. Northwest Spain is home to two morphologically distinct ecotypes of the periwinkle Littorina saxatilis, separated by shore height and subject to substantial differences in thermal stress exposure. However, despite other biotic and abiotic drivers of ecotype segregation being well studied, their thermal tolerance has not been previously characterized. We investigated thermal tolerance across multiple life history stages by employing the thermal death time (TDT) approach to determine (i) whether the two ecotypes differ in thermal tolerance and (ii) how any differences vary with life history stage. Adults of the two ecotypes differed in their thermal tolerance in line with their shore position: the upper-shore ecotype, which experiences more extreme temperatures, exhibited greater endurance of thermal stress compared with the lower-shore ecotype. This difference was most pronounced at the highest temperatures tested. The proximate physiological basis for these differences is unknown but likely due to a multifarious interaction of traits affecting different parts of the TDT curve. Differences in tolerance between ecotypes were less pronounced in early life history stages but increased with ontogeny, suggesting partial divergence of this trait during development. Thermal tolerance could potentially play an important role in maintaining population divergence and genetic segregation between the two ecotypes, since the increased thermal sensitivity of the lower-shore ecotype may limit its dispersal onto the upper shore and so restrict gene flow.
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7
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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.
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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
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8
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Mikles CS, Aguillon SM, Chan YL, Arcese P, Benham PM, Lovette IJ, Walsh J. Genomic differentiation and local adaptation on a microgeographic scale in a resident songbird. Mol Ecol 2020; 29:4295-4307. [PMID: 32978972 DOI: 10.1111/mec.15647] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 08/24/2020] [Accepted: 09/01/2020] [Indexed: 11/30/2022]
Abstract
Elucidating forces capable of driving species diversification in the face of gene flow remains a key goal in evolutionary biology. Song sparrows, Melospiza melodia, occur as 25 subspecies in diverse habitats across North America, are among the continent's most widespread vertebrate species, and are exemplary of many highly variable species for which the conservation of locally adapted populations may be critical to their range-wide persistence. We focus here on six morphologically distinct subspecies resident in the San Francisco Bay region, including three salt-marsh endemics and three residents in upland and riparian habitats adjacent to the Bay. We used reduced-representation sequencing to generate 2,773 SNPs to explore genetic differentiation, spatial population structure, and demographic history. Clustering separated individuals from each of the six subspecies, indicating subtle differentiation at microgeographic scales. Evidence of limited gene flow and low nucleotide diversity across all six subspecies further supports a hypothesis of isolation among locally adapted populations. We suggest that natural selection for genotypes adapted to salt marsh environments and changes in demography over the past century have acted in concert to drive the patterns of diversification reported here. Our results offer evidence of microgeographic specialization in a highly polytypic bird species long discussed as a model of sympatric speciation and rapid adaptation, and they support the hypothesis that conserving locally adapted populations may be critical to the range-wide persistence of similarly highly variable species.
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Affiliation(s)
- Chloe S Mikles
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA
| | - Stepfanie M Aguillon
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | | | - Peter Arcese
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Phred M Benham
- The Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, USA
| | - Irby J Lovette
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Jennifer Walsh
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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9
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Yebra-Pimentel ES, Reis B, Gessner J, Wuertz S, Dirks RPH. Temperature training improves transcriptional homeostasis after heat shock in juvenile Atlantic sturgeon (Acipenser oxyrinchus). FISH PHYSIOLOGY AND BIOCHEMISTRY 2020; 46:1653-1664. [PMID: 32583280 DOI: 10.1007/s10695-020-00818-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
Exposure to high temperatures can lead to thermotolerance in fish, which is hypothesized to potentially improve post-release survival in species under restocking programs, like Atlantic sturgeon. The aim of this study was to determine whether Atlantic sturgeon juveniles exposed to a 4-week temperature treatment respond differently to a subsequent heat shock than juveniles exposed to heat shock for the first time (naive fish). Response to heat shock was assessed by mapping the liver transcriptome. In total, 838 unique contigs were differentially expressed between the trained and the control group (592 downregulated, 261 upregulated, and 15 down- or upregulated, depending on the condition), corresponding to genes involved in the response to heat, tissue damage, proteolysis, and metabolism. Temperature-trained fish showed 2-4-fold fewer dysregulated contigs than naive fish, indicating their ability to maintain and recover homeostasis faster. During heat shock, hspc1 was upregulated in both experimental groups, while hspa1 and dnaja4 were exclusively upregulated in the control. Overall, compensatory mechanisms were observed in addition to the heat shock response. Only two genes, fgg and apnl, were upregulated at nearly all timepoints in both groups. Peptidases were more strongly downregulated in control fish, which also showed a reduction in lipid metabolism during recovery. Keratins, pck1, gadd45ga, and gadd45gb were differentially expressed between trained and control fish, and due to their roles in tissue protection and ER stress reduction, they might be responsible for the maintenance of the transcriptional homeostasis observed in trained fish.
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Affiliation(s)
- Elena Santidrián Yebra-Pimentel
- ZF-screens B.V., 2333 CH, Leiden, The Netherlands.
- Department of Basic Sciences and Aquatic Medicine, Norwegian University of Life Sciences, 0454, Oslo, Norway.
| | - Bruno Reis
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, 4450-208, Matosinhos, Portugal
| | - Jörn Gessner
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Sven Wuertz
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
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10
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Sävilammi T, Papakostas S, Leder EH, Vøllestad LA, Debes PV, Primmer CR. Cytosine methylation patterns suggest a role of methylation in plastic and adaptive responses to temperature in European grayling ( Thymallus thymallus) populations. Epigenetics 2020; 16:271-288. [PMID: 32660325 DOI: 10.1080/15592294.2020.1795597] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Temperature is a key environmental parameter affecting both the phenotypes and distributions of organisms, particularly ectotherms. Rapid organismal responses to thermal environmental changes have been described for several ectotherms; however, the underlying molecular mechanisms often remain unclear. Here, we studied whole genome cytosine methylation patterns of European grayling (Thymallus thymallus) embryos from five populations with contemporary adaptations of early life history traits at either 'colder' or 'warmer' spawning grounds. We reared fish embryos in a common garden experiment using two temperatures that resembled the 'colder' and 'warmer' conditions of the natal natural environments. Genome-wide methylation patterns were similar in populations originating from colder thermal origin subpopulations, whereas single nucleotide polymorphisms uncovered from the same data identified strong population structure among isolated populations, but limited structure among interconnected populations. This was surprising because the previously studied gene expression response among populations was mostly plastic, and mainly influenced by the developmental temperature. These findings support the hypothesis of the magnified role of epigenetic mechanisms in modulating plasticity. The abundance of consistently changing methylation loci between two warmer-to-colder thermal origin population pairs suggests that local adaptation has shaped the observed methylation patterns. The dynamic nature of the methylomes was further highlighted by genome-wide and site-specific plastic responses. Our findings support both the presence of a plastic response in a subset of CpG loci, and the evolutionary role of methylation divergence between populations adapting to contrasting thermal environments.
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Affiliation(s)
- Tiina Sävilammi
- Department of Biology, University of Turku , Turku, Finland.,Department of Biological and Environmental Science, University of Jyväskylä , Jyväskylä, Finland
| | | | - Erica H Leder
- Department of Biology, University of Turku , Turku, Finland.,Natural History Museum, University of Oslo , Oslo, Norway
| | - L Asbjørn Vøllestad
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo , Oslo, Norway
| | - Paul V Debes
- Organismal & Evolutionary Biology Research Program, Faculty of Biological & Environmental Sciences, University of Helsinki , Helsinki, Finland.,Institute of Biotechnology, University of Helsinki , Helsinki, Finland.,Department of Aquaculture and Fish Biology, Hólar University College , Sauðárkrókur, Iceland
| | - Craig R Primmer
- Organismal & Evolutionary Biology Research Program, Faculty of Biological & Environmental Sciences, University of Helsinki , Helsinki, Finland.,Institute of Biotechnology, University of Helsinki , Helsinki, Finland
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11
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Huml JV, Harris WE, Taylor MI, Sen R, Prudhomme C, Ellis JS. Pollution control can help mitigate future climate change impact on European grayling in the UK. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- J. Vanessa Huml
- School of Science & Environment Manchester Metropolitan University Manchester UK
- School of Biological and Marine Sciences University of Plymouth Plymouth UK
| | - W. Edwin Harris
- Crop and Environment Sciences Harper Adams University Edgmond UK
| | - Martin I. Taylor
- School of Biological Sciences University of East Anglia Norwich UK
| | - Robin Sen
- School of Science & Environment Manchester Metropolitan University Manchester UK
| | | | - Jonathan S. Ellis
- School of Biological and Marine Sciences University of Plymouth Plymouth UK
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12
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Garamszegi LZ, Temrin H, Kubinyi E, Miklósi Á, Kolm N. The role of common ancestry and gene flow in the evolution of human-directed play behaviour in dogs. J Evol Biol 2019; 33:318-328. [PMID: 31705702 DOI: 10.1111/jeb.13567] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 11/04/2019] [Indexed: 11/29/2022]
Abstract
Among-population variance of phenotypic traits is of high relevance for understanding evolutionary mechanisms that operate in relatively short timescales, but various sources of nonindependence, such as common ancestry and gene flow, can hamper the interpretations. In this comparative analysis of 138 dog breeds, we demonstrate how such confounders can independently shape the evolution of a behavioural trait (human-directed play behaviour from the Dog Mentality Assessment project). We combined information on genetic relatedness and haplotype sharing to reflect common ancestry and gene flow, respectively, and entered these into a phylogenetic mixed model to partition the among-breed variance of human-directed play behaviour while also accounting for within-breed variance. We found that 75% of the among-breed variance was explained by overall genetic relatedness among breeds, whereas 15% could be attributed to haplotype sharing that arises from gene flow. Therefore, most of the differences in human-directed play behaviour among breeds have likely been caused by constraints of common ancestry as a likely consequence of past selection regimes. On the other hand, gene flow caused by crosses among breeds has played a minor, but not negligible role. Our study serves as an example of an analytical approach that can be applied to comparative situations where the effects of shared origin and gene flow require quantification and appropriate statistical control in a within-species/among-population framework. Altogether, our results suggest that the evolutionary history of dog breeds has left remarkable signatures on the among-breed variation of a behavioural phenotype.
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Affiliation(s)
- László Zsolt Garamszegi
- Centre for Ecological Research, Institute of Ecology and Botany, Vácrátót, Hungary.,MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Loránd University, Budapest, Hungary.,Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, Seville, Spain
| | - Hans Temrin
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Enikő Kubinyi
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary
| | - Ádám Miklósi
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary.,MTA-ELTE Comparative Ethology Research Group, Budapest, Hungary
| | - Niclas Kolm
- Department of Zoology, Stockholm University, Stockholm, Sweden
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13
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Loisel A, Isla A, Daufresne M. Variation of thermal plasticity in growth and reproduction patterns: Importance of ancestral and developmental temperatures. J Therm Biol 2019; 84:460-468. [DOI: 10.1016/j.jtherbio.2019.07.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 07/09/2019] [Accepted: 07/26/2019] [Indexed: 11/25/2022]
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14
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Sunde J, Larsson P, Forsman A. Adaptations of early development to local spawning temperature in anadromous populations of pike (Esox lucius). BMC Evol Biol 2019; 19:148. [PMID: 31331267 PMCID: PMC6647320 DOI: 10.1186/s12862-019-1475-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/11/2019] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND In the wake of climate change many environments will be exposed to increased and more variable temperatures. Knowledge about how species and populations respond to altered temperature regimes is therefore important to improve projections of how ecosystems will be affected by global warming, and to aid management. We conducted a common garden, split-brood temperature gradient (4.5 °C, 9.7 °C and 12.3 °C) experiment to study the effects of temperature in two populations (10 families from each population) of anadromous pike (Esox lucius) that normally experience different temperatures during spawning. Four offspring performance measures (hatching success, day degrees until hatching, fry survival, and fry body length) were compared between populations and among families. RESULTS Temperature affected all performance measures in a population-specific manner. Low temperature had a positive effect on the Harfjärden population and a negative effect on the Lervik population. Further, the effects of temperature differed among families within populations. CONCLUSIONS The population-specific responses to temperature indicate genetic differentiation in developmental plasticity between populations, and may reflect an adaptation to low temperature during early fry development in Harfjärden, where the stream leading up to the wetland dries out relatively early in the spring, forcing individuals to spawn early. The family-specific responses to temperature treatment indicate presence of genetic variation for developmental plasticity (G x E) within both populations. Protecting between- and within-population genetic variation for developmental plasticity and high temperature-related adaptive potential of early life history traits will be key to long-term viability and persistence in the face of continued climate change.
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Affiliation(s)
- Johanna Sunde
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, SE-392 31 Kalmar, Sweden
| | - Per Larsson
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, SE-392 31 Kalmar, Sweden
| | - Anders Forsman
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, SE-392 31 Kalmar, Sweden
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15
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Klerks PL, Athrey GN, Leberg PL. Response to Selection for Increased Heat Tolerance in a Small Fish Species, With the Response Decreased by a Population Bottleneck. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00270] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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16
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Tamario C, Sunde J, Petersson E, Tibblin P, Forsman A. Ecological and Evolutionary Consequences of Environmental Change and Management Actions for Migrating Fish. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00271] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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17
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Comparative transcriptome analysis reveals potential evolutionary differences in adaptation of temperature and body shape among four Percidae species. PLoS One 2019; 14:e0215933. [PMID: 31063465 PMCID: PMC6504104 DOI: 10.1371/journal.pone.0215933] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 04/10/2019] [Indexed: 12/18/2022] Open
Abstract
Considering the divergent temperature habitats and morphological traits of four Percidae species: yellow perch (Perca flavescens), Eurasian perch (Perca fluviatilis), pike perch (Sander lucioperca), and ruffe (Gymnocephalus cernua), we stepped into the transcriptome level to discover genes and mechanisms that drive adaptation to different temperature environments and evolution in body shape. Based on 93,566 to 181,246 annotated unigenes of the four species, we identified 1,117 one-to-one orthologous genes and subsequently constructed the phylogenetic trees that are consistent with previous studies. Together with the tree, the ratios of nonsynonymous to synonymous substitutions presented decreased evolutionary rates from the D. rerio branch to the sub-branch clustered by P. flavescens and P. fluviatilis. The specific 93 fast-evolving genes and 57 positively selected genes in P. flavescens, compared with 22 shared fast-evolving genes among P. fluviatilis, G. cernua, and S. lucioperca, showed an intrinsic foundation that ensure its adaptation to the warmer Great Lakes and farther south, especially in functional terms like “Cul4-RING E3 ubiquitin ligase complex.” Meanwhile, the specific 78 fast-evolving genes and 41 positively selected genes in S. lucioperca drew a clear picture of how it evolved to a large and elongated body with camera-type eyes and muscle strength so that it could occupy the highest position in the food web. Overall, our results uncover genetic basis that support evolutionary adaptation of temperature and body shape in four Percid species, and could furthermore assist studies on environmental adaptation in fishes.
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18
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Kristensen NP, Johansson J, Jonzén N, Smith HG. Evolution of resident bird breeding phenology in a landscape with heterogeneous resource phenology and carryover effects. Evol Ecol 2018. [DOI: 10.1007/s10682-018-9951-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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19
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Kristensen NP, Johansson J, Chisholm RA, Smith HG, Kokko H. Carryover effects from natal habitat type upon competitive ability lead to trait divergence or source-sink dynamics. Ecol Lett 2018; 21:1341-1352. [PMID: 29938889 DOI: 10.1111/ele.13100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 04/27/2018] [Accepted: 05/16/2018] [Indexed: 01/26/2023]
Abstract
Local adaptation to rare habitats is difficult due to gene flow, but can occur if the habitat has higher productivity. Differences in offspring phenotypes have attracted little attention in this context. We model a scenario where the rarer habitat improves offspring's later competitive ability - a carryover effect that operates on top of local adaptation to one or the other habitat type. Assuming localised dispersal, so the offspring tend to settle in similar habitat to the natal type, the superior competitive ability of offspring remaining in the rarer habitat hampers immigration from the majority habitat. This initiates a positive feedback between local adaptation and trait divergence, which can thereafter be reinforced by coevolution with dispersal traits that match ecotype to habitat type. Rarity strengthens selection on dispersal traits and promotes linkage disequilibrium between locally adapted traits and ecotype-habitat matching dispersal. We propose that carryover effects may initiate isolation by ecology.
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Affiliation(s)
| | | | - Ryan A Chisholm
- Department of Biological Sciences, National University of Singapore, Singapore City, Singapore
| | - Henrik G Smith
- Department of Biology, Lund University, Lund, Sweden.,Centre of Environmental and Climate Research, Lund University, Lund, Sweden
| | - Hanna Kokko
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
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20
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Mäkinen H, Sävilammi T, Papakostas S, Leder E, Vøllestad LA, Primmer CR. Modularity Facilitates Flexible Tuning of Plastic and Evolutionary Gene Expression Responses during Early Divergence. Genome Biol Evol 2018; 10:77-93. [PMID: 29293993 PMCID: PMC5758911 DOI: 10.1093/gbe/evx278] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2017] [Indexed: 12/14/2022] Open
Abstract
Gene expression changes have been recognized as important drivers of adaptation to changing environmental conditions. Little is known about the relative roles of plastic and evolutionary responses in complex gene expression networks during the early stages of divergence. Large gene expression data sets coupled with in silico methods for identifying coexpressed modules now enable systems genetics approaches also in nonmodel species for better understanding of gene expression responses during early divergence. Here, we combined gene coexpression analyses with population genetics to separate plastic and population (evolutionary) effects in expression networks using small salmonid populations as a model system. We show that plastic and population effects were highly variable among the six identified modules and that the plastic effects explained larger proportion of the total eigengene expression than population effects. A more detailed analysis of the population effects using a QST - FST comparison across 16,622 annotated transcripts revealed that gene expression followed neutral expectations within modules and at the global level. Furthermore, two modules showed enrichment for genes coding for early developmental traits that have been previously identified as important phenotypic traits in thermal responses in the same model system indicating that coexpression analysis can capture expression patterns underlying ecologically important traits. We suggest that module-specific responses may facilitate the flexible tuning of expression levels to local thermal conditions. Overall, our study indicates that plasticity and neutral evolution are the main drivers of gene expression variance in the early stages of thermal adaptation in this system.
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Affiliation(s)
| | | | | | - Erica Leder
- Department of Biology, University of Turku, Finland
- Natural History Museum, University of Oslo, Norway
| | - Leif A Vøllestad
- Center for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Craig R Primmer
- Department of Biosciences, University of Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Finland
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21
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Sparks MM, Westley PAH, Falke JA, Quinn TP. Thermal adaptation and phenotypic plasticity in a warming world: Insights from common garden experiments on Alaskan sockeye salmon. GLOBAL CHANGE BIOLOGY 2017; 23:5203-5217. [PMID: 28586156 DOI: 10.1111/gcb.13782] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 05/15/2017] [Indexed: 06/07/2023]
Abstract
An important unresolved question is how populations of coldwater-dependent fishes will respond to rapidly warming water temperatures. For example, the culturally and economically important group, Pacific salmon (Oncorhynchus spp.), experience site-specific thermal regimes during early development that could be disrupted by warming. To test for thermal local adaptation and heritable phenotypic plasticity in Pacific salmon embryos, we measured the developmental rate, survival, and body size at hatching in two populations of sockeye salmon (Oncorhynchus nerka) that overlap in timing of spawning but incubate in contrasting natural thermal regimes. Using a split half-sibling design, we exposed embryos of 10 families from each of two populations to variable and constant thermal regimes. These represented both experienced temperatures by each population, and predicted temperatures under plausible future conditions based on a warming scenario from the downscaled global climate model (MIROC A1B scenario). We did not find evidence of thermal local adaptation during the embryonic stage for developmental rate or survival. Within treatments, populations hatched within 1 day of each other, on average, and among treatments, did not differ in survival in response to temperature. We did detect plasticity to temperature; embryos developed 2.5 times longer (189 days) in the coolest regime compared to the warmest regime (74 days). We also detected variation in developmental rates among families within and among temperature regimes, indicating heritable plasticity. Families exhibited a strong positive relationship between thermal variability and phenotypic variability in developmental rate but body length and mass at hatching were largely insensitive to temperature. Overall, our results indicated a lack of thermal local adaptation, but a presence of plasticity in populations experiencing contrasting conditions, as well as family-specific heritable plasticity that could facilitate adaptive change.
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Affiliation(s)
- Morgan M Sparks
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Peter A H Westley
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Jeffrey A Falke
- U.S. Geological Survey, Alaska Cooperative Fish and Wildlife Research Unit, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Thomas P Quinn
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
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22
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Perrier C, Ferchaud AL, Sirois P, Thibault I, Bernatchez L. Do genetic drift and accumulation of deleterious mutations preclude adaptation? Empirical investigation using RADseq in a northern lacustrine fish. Mol Ecol 2017; 26:6317-6335. [PMID: 29024140 DOI: 10.1111/mec.14361] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 09/05/2017] [Accepted: 09/08/2017] [Indexed: 01/01/2023]
Abstract
Understanding genomic signatures of divergent selection underlying long-term adaptation in populations located in heterogeneous environments is a key goal in evolutionary biology. In this study, we investigated neutral, adaptive and deleterious genetic variation using 7,192 SNPs in 31 Lake Trout (Salvelinus namaycush) populations (n = 673) from Québec, Canada. Average genetic diversity was low, weakly shared among lakes, and positively correlated with lake size, indicating a major role for genetic drift subsequent to lake isolation. Putatively deleterious mutations were on average at lower frequencies than the other SNPs, and their abundance relative to the entire polymorphism in each population was positively correlated with inbreeding, suggesting that the effectiveness of purifying selection was negatively correlated with inbreeding, as predicted from theory. Despite evidence for pronounced genetic drift and inbreeding, several outlier loci were associated with temperature and found in or close to genes with biologically relevant functions notably related to heat stress and immune responses. Outcomes of gene-temperature associations were influenced by the inclusion of the most inbred populations, in which allele frequencies deviated the most from model predictions. This result illustrates challenge in identifying gene-environment associations in cases of high genetic drift and restricted gene flow and suggests limited adaptation in populations experiencing higher inbreeding. We discuss the relevance of these findings for the conservation and management, notably regarding stocking and genetic rescue, of Lake Trout populations and other species inhabiting highly fragmented habitats.
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Affiliation(s)
- Charles Perrier
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.,Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 Campus CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | - Anne-Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Pascal Sirois
- Chaire de Recherche sur les Espèces Aquatiques Exploitées, Laboratoire des Sciences Aquatiques, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC, Canada
| | - Isabel Thibault
- Direction de l'expertise sur la Faune Aquatique, Ministère des Forêts de la Faune et des Parcs du Québec, Québec, QC, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
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23
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Oke KB, Rolshausen G, LeBlond C, Hendry AP. How Parallel Is Parallel Evolution? A Comparative Analysis in Fishes. Am Nat 2017; 190:1-16. [DOI: 10.1086/691989] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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24
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Rooke AC, Burness G, Fox MG. Thermal physiology of native cool-climate, and non-native warm-climate Pumpkinseed sunfish raised in a common environment. J Therm Biol 2017; 64:48-57. [DOI: 10.1016/j.jtherbio.2016.12.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 10/26/2016] [Accepted: 12/21/2016] [Indexed: 11/25/2022]
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25
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van Leeuwen CHA, Museth J, Sandlund OT, Qvenild T, Vøllestad LA. Mismatch between fishway operation and timing of fish movements: a risk for cascading effects in partial migration systems. Ecol Evol 2016; 6:2414-25. [PMID: 27110352 PMCID: PMC4834326 DOI: 10.1002/ece3.1937] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 12/10/2015] [Accepted: 12/11/2015] [Indexed: 01/20/2023] Open
Abstract
Habitat fragmentation is a growing problem worldwide. Particularly in river systems, numerous dams and weirs hamper the movement of a wide variety of species. With the aim to preserve connectivity for fish, many barriers in river systems are equipped with fishways (also called fish passages or fish ladders). However, few fishways provide full connectivity. Here we hypothesized that restricted seasonal opening times of fishways can importantly reduce their effectiveness by interfering with the timing of fish migration, for both spring- and autumn-spawning species. We empirically tested our hypothesis, and discuss the possible eco-evolutionary consequences of affected migration timing. We analyzed movements of two salmonid fishes, spring-spawning European grayling (Thymallus thymallus) and autumn-spawning brown trout (Salmo trutta), in Norway's two largest river systems. We compared their timing of upstream passage through four fishways collected over 28 years with the timing of fish movements in unfragmented river sections as monitored by radiotelemetry. Confirming our hypothesis, late opening of fishways delayed the migration of European grayling in spring, and early closure of fishways blocked migration for brown trout on their way to spawning locations during late autumn. We show in a theoretical framework how restricted opening times of fishways can induce shifts from migratory to resident behavior in potamodromous partial migration systems, and propose that this can induce density-dependent effects among fish accumulating in lower regions of rivers. Hence, fragmentation may not only directly affect the migratory individuals in the population, but may also have effects that cascade downstream and alter circumstances for resident fish. Fishway functionality is inadequate if there is a mismatch between natural fish movements and fishway opening times in the same river system, with ecological and possibly evolutionary consequences for fish populations.
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Affiliation(s)
- Casper H A van Leeuwen
- Department of Biosciences Centre for Ecological and Evolutionary Synthesis (CEES) University of Oslo Post Office Box 1066 Blindern 0316 Oslo Norway
| | - Jon Museth
- Norwegian Institute for Nature Research (NINA) Fakkelgården 2624 Lillehammer Norway
| | - Odd T Sandlund
- Norwegian Institute for Nature Research (NINA) Høgskoleringen 9 7036 Trondheim Norway
| | - Tore Qvenild
- The Environment Agency Hedmark County Statens hus Parkgata 36 2306 Hamar Norway
| | - L Asbjørn Vøllestad
- Department of Biosciences Centre for Ecological and Evolutionary Synthesis (CEES) University of Oslo Post Office Box 1066 Blindern 0316 Oslo Norway
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26
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Solberg MF, Dyrhovden L, Matre IH, Glover KA. Thermal plasticity in farmed, wild and hybrid Atlantic salmon during early development: has domestication caused divergence in low temperature tolerance? BMC Evol Biol 2016; 16:38. [PMID: 26883947 PMCID: PMC4754860 DOI: 10.1186/s12862-016-0607-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 02/01/2016] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND In the past three decades, millions of domesticated Atlantic salmon Salmo salar L. have escaped from farms into the wild. Their offspring display reduced survival in the natural environment, which demonstrates that gene-flow is likely to have a negative effect on wild populations. However, inter-population differences in introgression of farmed salmon have been observed, and the underlying ecological mechanisms remain enigmatic. We hypothesised that domestication-driven divergence in tolerance to low temperatures during early development may contribute to lower survival of farmed salmon offspring in the wild, which in turn, may influence patterns of introgression among populations exposed to different temperature regimes. We reared the offspring of 35 families of wild, farmed and hybrid origin at three temperatures (3.9, 5.6 and 12°C) from the onset of exogenous feeding and throughout their first summer. Thermal reaction norms for growth and survival were investigated along the gradient. RESULTS The main results of this study, which is based upon the analysis of juvenile salmon from five wild strains, two farmed strains and two hybrid strains, can be summarised as; (i) salmon of all origins were able to successfully initiate feeding at all temperatures and similar survival reaction norms were detected in all strains across the temperature gradient; (ii) deviating growth reaction norms were detected between strains, although this result was most likely due to an overall lack of growth in the lower temperature treatments. CONCLUSIONS This study revealed no evidence of domesticated-driven divergence in low temperature tolerance in Atlantic salmon during early development. Although the potential interaction between low temperature and other river-specific factors cannot be excluded, our results indicate that the reduced survival of farmed offspring in the wild is not explained by farmed salmon displaying impaired abilities to initiate feeding at low temperatures. We therefore suggest that the observed inter-population patterns of introgression are not low-temperature driven and that other ecological or biological factors may explain why detection of farmed salmon in wild rivers is not synonymous with introgression. In general, our results support the literature indicating that phenotypic plasticity instead of thermal adaption has been selected for in Atlantic salmon.
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Affiliation(s)
| | - Lise Dyrhovden
- Matre Research Station, Institute of Marine Research, Matredal, Norway.
| | - Ivar Helge Matre
- Matre Research Station, Institute of Marine Research, Matredal, Norway.
| | - Kevin Alan Glover
- Population Genetics Research Group, Institute of Marine Research, Bergen, Norway.
- Department of Biology, Sea Lice Research Centre, University of Bergen, Bergen, Norway.
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27
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Roulin AC, Mariadassou M, Hall MD, Walser JC, Haag C, Ebert D. High genetic variation in resting-stage production in a metapopulation: Is there evidence for local adaptation? Evolution 2015; 69:2747-56. [DOI: 10.1111/evo.12770] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 07/20/2015] [Accepted: 08/20/2015] [Indexed: 12/23/2022]
Affiliation(s)
- Anne C. Roulin
- Zoological Institute; Basel University; Vesalgasse 1 4051 Basel Switzerland
- Institute of Plant Biology; University of Zurich; Zollikerstrasse 107 8008 Zurich Switzerland
| | | | - Matthew D. Hall
- Zoological Institute; Basel University; Vesalgasse 1 4051 Basel Switzerland
- School of Biological Sciences; Monash University; Melbourne 3800 Australia
| | - Jean-Claude Walser
- Zoological Institute; Basel University; Vesalgasse 1 4051 Basel Switzerland
- Genetic Diversity Centre; Universitätstrasse 16, CHN E 55 8092 Zürich Switzerland
| | - Christoph Haag
- CNRS-UMR5175 CEFE; 1919, Route de Mende 34293 Montpellier France
| | - Dieter Ebert
- Zoological Institute; Basel University; Vesalgasse 1 4051 Basel Switzerland
- Tvärminne Zoological Station; Helsinki University; Hanko Finland
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28
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Mäkinen H, Papakostas S, Vøllestad LA, Leder EH, Primmer CR. Plastic and Evolutionary Gene Expression Responses Are Correlated in European Grayling (Thymallus thymallus) Subpopulations Adapted to Different Thermal Environments. J Hered 2015; 107:82-9. [DOI: 10.1093/jhered/esv069] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 07/17/2015] [Indexed: 02/06/2023] Open
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29
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Kubota S, Iwasaki T, Hanada K, Nagano AJ, Fujiyama A, Toyoda A, Sugano S, Suzuki Y, Hikosaka K, Ito M, Morinaga SI. A Genome Scan for Genes Underlying Microgeographic-Scale Local Adaptation in a Wild Arabidopsis Species. PLoS Genet 2015; 11:e1005361. [PMID: 26172569 PMCID: PMC4501782 DOI: 10.1371/journal.pgen.1005361] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 06/15/2015] [Indexed: 11/18/2022] Open
Abstract
Adaptive divergence at the microgeographic scale has been generally disregarded because high gene flow is expected to disrupt local adaptation. Yet, growing number of studies reporting adaptive divergence at a small spatial scale highlight the importance of this process in evolutionary biology. To investigate the genetic basis of microgeographic local adaptation, we conducted a genome-wide scan among sets of continuously distributed populations of Arabidopsis halleri subsp. gemmifera that show altitudinal phenotypic divergence despite gene flow. Genomic comparisons were independently conducted in two distinct mountains where similar highland ecotypes are observed, presumably as a result of convergent evolution. Here, we established a de novo reference genome and employed an individual-based resequencing for a total of 56 individuals. Among 527,225 reliable SNP loci, we focused on those showing a unidirectional allele frequency shift across altitudes. Statistical tests on the screened genes showed that our microgeographic population genomic approach successfully retrieve genes with functional annotations that are in line with the known phenotypic and environmental differences between altitudes. Furthermore, comparison between the two distinct mountains enabled us to screen out those genes that are neutral or adaptive only in either mountain, and identify the genes involved in the convergent evolution. Our study demonstrates that the genomic comparison among a set of genetically connected populations, instead of the commonly-performed comparison between two isolated populations, can also offer an effective screening for the genetic basis of local adaptation.
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Affiliation(s)
- Shosei Kubota
- Graduate School of Arts and Sciences, The University of Tokyo, Meguro, Tokyo, Japan; College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan.
| | - Takaya Iwasaki
- Graduate School of Arts and Sciences, The University of Tokyo, Meguro, Tokyo, Japan
| | - Kousuke Hanada
- Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa, Japan; Frontier Research Academy for Young Researchers, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan; CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Atsushi J Nagano
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Asao Fujiyama
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Atsushi Toyoda
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Sumio Sugano
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Kouki Hikosaka
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan; Graduate School of Life Sciences, Tohoku University, Sendai, Miyagai, Japan
| | - Motomi Ito
- Graduate School of Arts and Sciences, The University of Tokyo, Meguro, Tokyo, Japan
| | - Shin-Ichi Morinaga
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan; CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
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Haddeland PJ, Junge C, Serbezov D, Vøllestad LA. Genetic parentage analysis confirms a polygynandrous breeding system in the European grayling (Thymallus thymallus). PLoS One 2015; 10:e0122032. [PMID: 25793629 PMCID: PMC4368113 DOI: 10.1371/journal.pone.0122032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 02/09/2015] [Indexed: 11/26/2022] Open
Abstract
Knowing the breeding system of a species is important in order to understand individual variation in reproductive success. Large variation in reproductive success and thus reproductive skew strongly impacts on the effective number of breeders and thus the long-term effective population size (Ne). Fishes, in particular species belonging to the salmonid family, exhibit a wide diversity of breeding systems. In general, however, breeding systems are rarely studied in detail in the wild. Here we examine the breeding system of the spring-spawning European grayling Thymallus thymallus from a small Norwegian stream using parentage assignment based on the genotyping of 19 polymorphic microsatellite loci. In total 895 individual grayling fry and 154 mature grayling (57 females and 97 males) were genotyped. A total of 466 offspring were assigned a father, a mother, or a parent pair with a confidence of 90% or higher. Successfully reproducing males had on average 11.9 ± 13.3 (SD) offspring with on average 2.1 ± 1.2 partners, whereas successful females had on average 9.5 ± 12.8 offspring and 2.3 ± 1.5 partners. Parents with more partners also produced more offspring. Thus the grayling breeding system within this small stream revealed a polygynandrous breeding system, similar to what has been observed for many other salmonid fish species. The present study thus unambiguously corroborates a polygynadrous breeding system in the European grayling. This knowledge is critical for managing populations of this species, which has suffered significant local population declines throughout its range over the last several decades.
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Affiliation(s)
- Peter Jørgen Haddeland
- Center for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, P. O. Box 1066, Blindern, 0316, Oslo, Norway
- Department of Genetic Kinship and Identity, Norwegian Institute of Public Health, P. O. Box 4040, Nydalen, 0403, Oslo, Norway
| | - Claudia Junge
- Center for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, P. O. Box 1066, Blindern, 0316, Oslo, Norway
- Southern Seas Ecology Laboratories, DP418, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Dimitar Serbezov
- Center for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, P. O. Box 1066, Blindern, 0316, Oslo, Norway
- National Agency of Fisheries and Aquaculture, 17 Hristo Botev Blvd, 1606, Sofia, Bulgaria
| | - Leif Asbjørn Vøllestad
- Center for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, P. O. Box 1066, Blindern, 0316, Oslo, Norway
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Langin KM, Sillett TS, Funk WC, Morrison SA, Desrosiers MA, Ghalambor CK. Islands within an island: repeated adaptive divergence in a single population. Evolution 2015; 69:653-65. [PMID: 25645813 DOI: 10.1111/evo.12610] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 01/19/2015] [Indexed: 01/27/2023]
Abstract
Physical barriers to gene flow were once viewed as prerequisites for adaptive evolutionary divergence. However, a growing body of theoretical and empirical work suggests that divergence can proceed within a single population. Here we document genetic structure and spatially replicated patterns of phenotypic divergence within a bird species endemic to 250 km(2) Santa Cruz Island, California, USA. Island scrub-jays (Aphelocoma insularis) in three separate stands of pine habitat had longer, shallower bills than jays in oak habitat, a pattern that mirrors adaptive differences between allopatric populations of the species' mainland congener. Variation in both bill measurements was heritable, and island scrub-jays mated nonrandomly with respect to bill morphology. The population was not panmictic; instead, we found a continuous pattern of isolation by distance across the east-west axis of the island, as well as a subtle genetic discontinuity across the boundary between the largest pine stand and adjacent oak habitat. The ecological factors that appear to have facilitated adaptive differentiation at such a fine scale--environmental heterogeneity and localized dispersal--are ubiquitous in nature. These findings support recent arguments that microgeographic patterns of adaptive divergence may be more common than currently appreciated, even in mobile taxonomic groups like birds.
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Affiliation(s)
- Kathryn M Langin
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523; Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, 80523; Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, 80526.
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32
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Narum SR, Campbell NR. Transcriptomic response to heat stress among ecologically divergent populations of redband trout. BMC Genomics 2015; 16:103. [PMID: 25765850 PMCID: PMC4337095 DOI: 10.1186/s12864-015-1246-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 01/15/2015] [Indexed: 12/12/2022] Open
Abstract
Background As ectothermic organisms have evolved to differing aquatic climates, the molecular basis of thermal adaptation is a key area of research. In this study, we tested for differential transcriptional response of ecologically divergent populations of redband trout (Oncorhynchus mykiss gairdneri) that have evolved in desert and montane climates. Each pure strain and their F1 cross were reared in a common garden environment and exposed over four weeks to diel water temperatures that were similar to those experienced in desert climates within the species’ range. Gill tissues were collected from the three strains of fish (desert, montane, F1 crosses) at the peak of heat stress and tested for mRNA expression differences across the transcriptome with RNA-seq. Results Strong differences in transcriptomic response to heat stress were observed across strains confirming that fish from desert environments have evolved diverse mechanisms to cope with stressful environments. As expected, a large number of total transcripts (12,814) were differentially expressed in the study (FDR ≤ 0.05) with 2310 transcripts in common for all three strains, but the desert strain had a larger number of unique differentially expressed transcripts (2875) than the montane (1982) or the F1 (2355) strain. Strongly differentiated genes (>4 fold change and FDR ≤ 0.05) were particularly abundant in the desert strain (824 unique contigs) relative to the other two strains (montane = 58; F1 = 192). Conclusions This study demonstrated patterns of acclimation (i.e., phenotypic plasticity) within strains and evolutionary adaptation among strains in numerous genes throughout the transcriptome. Key stress response genes such as molecular chaperones (i.e., heat shock proteins) had adaptive patterns of gene expression among strains, but also a much higher number of metabolic and cellular process genes were differentially expressed in the desert strain demonstrating these biological pathways are critical for thermal adaptation to warm aquatic climates. The results of this study further elucidate the molecular basis for thermal adaptation in aquatic ecosystems and extend the potential for identifying genes that may be critical for adaptation to changing climates. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1246-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shawn R Narum
- Columbia River Inter-Tribal Fish Commission, 3059-F National Fish Hatchery Road, Hagerman, ID, 83332, USA.
| | - Nathan R Campbell
- Columbia River Inter-Tribal Fish Commission, 3059-F National Fish Hatchery Road, Hagerman, ID, 83332, USA.
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Quintela M, Johansson MP, Kristjánsson BK, Barreiro R, Laurila A. AFLPs and mitochondrial haplotypes reveal local adaptation to extreme thermal environments in a freshwater gastropod. PLoS One 2014; 9:e101821. [PMID: 25007329 PMCID: PMC4090234 DOI: 10.1371/journal.pone.0101821] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 06/11/2014] [Indexed: 01/06/2023] Open
Abstract
The way environmental variation shapes neutral and adaptive genetic variation in natural populations is a key issue in evolutionary biology. Genome scans allow the identification of the genetic basis of local adaptation without previous knowledge of genetic variation or traits under selection. Candidate loci for divergent adaptation are expected to show higher FST than neutral loci influenced solely by random genetic drift, migration and mutation. The comparison of spatial patterns of neutral markers and loci under selection may help disentangle the effects of gene flow, genetic drift and selection among populations living in contrasting environments. Using the gastropod Radix balthica as a system, we analyzed 376 AFLP markers and 25 mtDNA COI haplotypes for candidate loci and associations with local adaptation among contrasting thermal environments in Lake Mývatn, a volcanic lake in northern Iceland. We found that 2% of the analysed AFLP markers were under directional selection and 12% of the mitochondrial haplotypes correlated with differing thermal habitats. The genetic networks were concordant for AFLP markers and mitochondrial haplotypes, depicting distinct topologies at neutral and candidate loci. Neutral topologies were characterized by intense gene flow revealed by dense nets with edges connecting contrasting thermal habitats, whereas the connections at candidate loci were mostly restricted to populations within each thermal habitat and the number of edges decreased with temperature. Our results suggest microgeographic adaptation within Lake Mývatn and highlight the utility of genome scans in detecting adaptive divergence.
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Affiliation(s)
- María Quintela
- Dept of Animal Biology, Plant Biology and Ecology, Faculty of Science, University of A Coruña, A Coruña, Spain
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- * E-mail:
| | - Magnus P. Johansson
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Bjarni K. Kristjánsson
- Hólar University College, Department of Aquaculture and Fish Biology, Sauðarkrokur, Iceland
| | - Rodolfo Barreiro
- Dept of Animal Biology, Plant Biology and Ecology, Faculty of Science, University of A Coruña, A Coruña, Spain
| | - Anssi Laurila
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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Papakostas S, Vøllestad LA, Bruneaux M, Aykanat T, Vanoverbeke J, Ning M, Primmer CR, Leder EH. Gene pleiotropy constrains gene expression changes in fish adapted to different thermal conditions. Nat Commun 2014; 5:4071. [PMID: 24892934 PMCID: PMC4059932 DOI: 10.1038/ncomms5071] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/08/2014] [Indexed: 02/07/2023] Open
Abstract
Understanding the factors that shape the evolution of gene expression is a central goal in biology, but the molecular mechanisms behind this remain controversial. A related major goal is ascertaining how such factors may affect the adaptive potential of a species or population. Here we demonstrate that temperature-driven gene expression changes in fish adapted to differing thermal environments are constrained by the level of gene pleiotropy estimated by either the number of protein interactions or gene biological processes. Genes with low pleiotropy levels were the main drivers of both plastic and evolutionary global expression profile changes, while highly pleiotropic genes had limited expression response to temperature treatment. Our study provides critical insights into the molecular mechanisms by which natural populations can adapt to changing environments. In addition to having important implications for climate change adaptation, these results suggest that gene pleiotropy should be considered more carefully when interpreting expression profiling data. The factors that shape the evolution of gene expression and their role in adaptation are poorly understood. Here, Papakostas et al. show that gene pleiotropy constrains protein expression evolution in freshwater salmonids adapted to different temperatures.
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Affiliation(s)
- Spiros Papakostas
- Division of Genetics and Physiology, Department of Biology, University of Turku, Pharmacity, Itäinen Pitkäkatu 4, 20520 Turku, Finland
| | - L Asbjørn Vøllestad
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, NO-0316 Oslo, Norway
| | - Matthieu Bruneaux
- Division of Genetics and Physiology, Department of Biology, University of Turku, Pharmacity, Itäinen Pitkäkatu 4, 20520 Turku, Finland
| | - Tutku Aykanat
- Division of Genetics and Physiology, Department of Biology, University of Turku, Pharmacity, Itäinen Pitkäkatu 4, 20520 Turku, Finland
| | - Joost Vanoverbeke
- Laboratory of Aquatic Ecology, Evolution and Conservation, Department of Biology, KU Leuven, Ch. Deberiotstraat 32, 3000 Leuven, Belgium
| | - Mei Ning
- 1] Division of Genetics and Physiology, Department of Biology, University of Turku, Pharmacity, Itäinen Pitkäkatu 4, 20520 Turku, Finland [2]
| | - Craig R Primmer
- 1] Division of Genetics and Physiology, Department of Biology, University of Turku, Pharmacity, Itäinen Pitkäkatu 4, 20520 Turku, Finland [2]
| | - Erica H Leder
- 1] Division of Genetics and Physiology, Department of Biology, University of Turku, Pharmacity, Itäinen Pitkäkatu 4, 20520 Turku, Finland [2]
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35
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Díaz F, Muñoz-Valencia V, Juvinao-Quintero DL, Manzano-Martínez MR, Toro-Perea N, Cárdenas-Henao H, Hoffmann AA. Evidence for adaptive divergence of thermal responses among Bemisia tabaci populations from tropical Colombia following a recent invasion. J Evol Biol 2014; 27:1160-71. [PMID: 24800647 DOI: 10.1111/jeb.12387] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 03/11/2014] [Accepted: 03/30/2014] [Indexed: 11/29/2022]
Abstract
There is an increasing evidence that populations of ectotherms can diverge genetically in response to different climatic conditions, both within their native range and (in the case of invasive species) in their new range. Here, we test for such divergence in invasive whitefly Bemisia tabaci populations in tropical Colombia, by considering heritable variation within and between populations in survival and fecundity under temperature stress, and by comparing population differences with patterns established from putatively neutral microsatellite markers. We detected significant differences among populations linked to mean temperature (for survival) and temperature variation (for fecundity) in local environments. A QST - FST analysis indicated that phenotypic divergence was often larger than neutral expectations (QST > FST ). Particularly, for survival after a sublethal heat shock, this divergence remained linked to the local mean temperature after controlling for neutral divergence. These findings point to rapid adaptation in invasive whitefly likely to contribute to its success as a pest species. Ongoing evolutionary divergence also provides challenges in predicting the likely impact of Bemisia in invaded regions.
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Affiliation(s)
- F Díaz
- Department of Biology, Universidad del Valle, Cali, Colombia
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36
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Richardson JL, Urban MC, Bolnick DI, Skelly DK. Microgeographic adaptation and the spatial scale of evolution. Trends Ecol Evol 2014; 29:165-76. [DOI: 10.1016/j.tree.2014.01.002] [Citation(s) in RCA: 353] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 11/24/2013] [Accepted: 01/10/2014] [Indexed: 12/24/2022]
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37
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Crozier LG, Hutchings JA. Plastic and evolutionary responses to climate change in fish. Evol Appl 2014; 7:68-87. [PMID: 24454549 PMCID: PMC3894899 DOI: 10.1111/eva.12135] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 10/31/2013] [Indexed: 12/14/2022] Open
Abstract
The physical and ecological 'fingerprints' of anthropogenic climate change over the past century are now well documented in many environments and taxa. We reviewed the evidence for phenotypic responses to recent climate change in fish. Changes in the timing of migration and reproduction, age at maturity, age at juvenile migration, growth, survival and fecundity were associated primarily with changes in temperature. Although these traits can evolve rapidly, only two studies attributed phenotypic changes formally to evolutionary mechanisms. The correlation-based methods most frequently employed point largely to 'fine-grained' population responses to environmental variability (i.e. rapid phenotypic changes relative to generation time), consistent with plastic mechanisms. Ultimately, many species will likely adapt to long-term warming trends overlaid on natural climate oscillations. Considering the strong plasticity in all traits studied, we recommend development and expanded use of methods capable of detecting evolutionary change, such as the long term study of selection coefficients and temporal shifts in reaction norms, and increased attention to forecasting adaptive change in response to the synergistic interactions of the multiple selection pressures likely to be associated with climate change.
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Affiliation(s)
| | - Jeffrey A Hutchings
- Department of Biology, Dalhousie University Halifax, NS, Canada ; Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo Oslo, Norway
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38
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Richardson JL, Urban MC. STRONG SELECTION BARRIERS EXPLAIN MICROGEOGRAPHIC ADAPTATION IN WILD SALAMANDER POPULATIONS. Evolution 2013; 67:1729-40. [DOI: 10.1111/evo.12052] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 12/28/2012] [Indexed: 11/30/2022]
Affiliation(s)
- Jonathan L. Richardson
- School of Forestry & Environmental Studies, Yale University; 370 Prospect Street New Haven Connecticut 06511
- Department of Ecology & Evolutionary Biology; University of Connecticut; Storrs Connecticut 06269-3043
| | - Mark C. Urban
- Department of Ecology & Evolutionary Biology; University of Connecticut; 75 N. Eagleville Road Unit 3043 Storrs Connecticut 06269
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39
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Stelkens RB, Pompini M, Wedekind C. Testing for local adaptation in brown trout using reciprocal transplants. BMC Evol Biol 2012; 12:247. [PMID: 23249365 PMCID: PMC3567948 DOI: 10.1186/1471-2148-12-247] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 12/15/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Local adaptation can drive the divergence of populations but identification of the traits under selection remains a major challenge in evolutionary biology. Reciprocal transplant experiments are ideal tests of local adaptation, yet rarely used for higher vertebrates because of the mobility and potential invasiveness of non-native organisms. Here, we reciprocally transplanted 2500 brown trout (Salmo trutta) embryos from five populations to investigate local adaptation in early life history traits. Embryos were bred in a full-factorial design and raised in natural riverbeds until emergence. Customized egg capsules were used to simulate the natural redd environment and allowed tracking the fate of every individual until retrieval. We predicted that 1) within sites, native populations would outperform non-natives, and 2) across sites, populations would show higher performance at 'home' compared to 'away' sites. RESULTS There was no evidence for local adaptation but we found large differences in survival and hatching rates between sites, indicative of considerable variation in habitat quality. Survival was generally high across all populations (55% ± 3%), but ranged from 4% to 89% between sites. Average hatching rate was 25% ± 3% across populations ranging from 0% to 62% between sites. CONCLUSION This study provides rare empirical data on variation in early life history traits in a population network of a salmonid, and large-scale breeding and transplantation experiments like ours provide powerful tests for local adaptation. Despite the recently reported genetic and morphological differences between the populations in our study area, local adaptation at the embryo level is small, non-existent, or confined to ecological conditions that our experiment could not capture.
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Affiliation(s)
- Rike B Stelkens
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne CH-1015, Switzerland.
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40
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Walters RJ, Blanckenhorn WU, Berger D. Forecasting extinction risk of ectotherms under climate warming: an evolutionary perspective. Funct Ecol 2012. [DOI: 10.1111/j.1365-2435.2012.02045.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Richard J. Walters
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich; Winterthurerstrasse 190 CH-8057 Zürich Switzerland
- Environmental Biology; School of Biological Sciences, University of Reading; Reading RG6 6BX UK
| | - Wolf U. Blanckenhorn
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich; Winterthurerstrasse 190 CH-8057 Zürich Switzerland
| | - David Berger
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich; Winterthurerstrasse 190 CH-8057 Zürich Switzerland
- Evolutionary Biology Centre, Uppsala University; Norbyvägen 14-18 75236 Uppsala Sweden
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41
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STELKENS RIKEB, JAFFUEL GEOFFREY, ESCHER MATTHIAS, WEDEKIND CLAUS. Genetic and phenotypic population divergence on a microgeographic scale in brown trout. Mol Ecol 2012; 21:2896-915. [DOI: 10.1111/j.1365-294x.2012.05581.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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LE CORRE VALÉRIE, KREMER ANTOINE. The genetic differentiation at quantitative trait loci under local adaptation. Mol Ecol 2012; 21:1548-66. [DOI: 10.1111/j.1365-294x.2012.05479.x] [Citation(s) in RCA: 253] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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43
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Aykanat T, Bryden CA, Heath DD. Sex-biased genetic component distribution among populations: additive genetic and maternal contributions to phenotypic differences among populations of Chinook salmon. J Evol Biol 2012; 25:682-90. [PMID: 22321105 DOI: 10.1111/j.1420-9101.2012.02462.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An approach frequently used to demonstrate a genetic basis for population-level phenotypic differences is to employ common garden rearing designs, where observed differences are assumed to be attributable to primarily additive genetic effects. Here, in two common garden experiments, we employed factorial breeding designs between wild and domestic, and among wild populations of Chinook salmon (Oncorhynchus tshawytscha). We measured the contribution of additive (V(A)) and maternal (V(M)) effects to the observed population differences for 17 life history and fitness-related traits. Our results show that, in general, maternal effects contribute more to phenotypic differences among populations than additive genetic effects. These results suggest that maternal effects are important in population phenotypic differentiation and also signify that the inclusion of the maternal source of variation is critical when employing models to test population differences in salmon, such as in local adaptation studies.
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Affiliation(s)
- T Aykanat
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
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44
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Affiliation(s)
- I Keller
- Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center of Ecology, Evolution and Biochemistry, Seestrasse 79, CH-6047 Kastanienbaum, Switzerland.
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45
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Thomassen G, Barson NJ, Haugen TO, Vøllestad LA. Contemporary divergence in early life history in grayling (Thymallus thymallus). BMC Evol Biol 2011; 11:360. [PMID: 22166134 PMCID: PMC3252335 DOI: 10.1186/1471-2148-11-360] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 12/13/2011] [Indexed: 12/28/2022] Open
Abstract
Background Following colonization of new habitats and subsequent selection, adaptation to environmental conditions might be expected to be rapid. In a mountain lake in Norway, Lesjaskogsvatnet, more than 20 distinct spawning demes of grayling have been established since the lake was colonized, some 20-25 generations ago. The demes spawn in tributaries consistently exhibiting either colder or warmer temperature conditions during spawning in spring and subsequent early development during early summer. In order to explore the degree of temperature-related divergence in early development, a multi-temperature common-garden experiment was performed on embryos from four different demes experiencing different spring temperatures. Results Early developmental characters were measured to test if individuals from the four demes respond differently to the treatment temperatures. There was clear evidence of among-deme differences (genotype - environment interactions) in larval growth and yolk-to-body-size conversion efficiency. Under the cold treatment regime, larval growth rates were highest for individuals belonging to cold streams. Individuals from warm streams had the highest yolk-consumption rate under cold conditions. As a consequence, yolk-to-body-mass conversion efficiency was highest for cold-deme individuals under cold conditions. As we observed response parallelism between individuals from demes belonging to similar thermal groups for these traits, some of the differentiation seems likely to result from local adaptation Conclusion The observed differences in length at age during early larval development most likely have a genetic component, even though both directional and random processes are likely to have influenced evolutionary change in the demes under study.
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Affiliation(s)
- Gaute Thomassen
- Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, P, O, Box 1066 Blindern, NO-0316 Oslo, Norway
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FRUCIANO CARMELO, TIGANO CONCETTA, FERRITO VENERA. Geographical and morphological variation within and between colour phases inCoris julis(L. 1758), a protogynous marine fish. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01700.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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47
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48
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Junge C, Vøllestad LA, Barson NJ, Haugen TO, Otero J, Sætre GP, Leder EH, Primmer CR. Strong gene flow and lack of stable population structure in the face of rapid adaptation to local temperature in a spring-spawning salmonid, the European grayling (Thymallus thymallus). Heredity (Edinb) 2011; 106:460-71. [PMID: 21224882 PMCID: PMC3131973 DOI: 10.1038/hdy.2010.160] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 11/19/2010] [Accepted: 11/22/2010] [Indexed: 11/09/2022] Open
Abstract
Gene flow has the potential to both constrain and facilitate adaptation to local environmental conditions. The early stages of population divergence can be unstable because of fluctuating levels of gene flow. Investigating temporal variation in gene flow during the initial stages of population divergence can therefore provide insights to the role of gene flow in adaptive evolution. Since the recent colonization of Lake Lesjaskogsvatnet in Norway by European grayling (Thymallus thymallus), local populations have been established in over 20 tributaries. Multiple founder events appear to have resulted in reduced neutral variation. Nevertheless, there is evidence for local adaptation in early life-history traits to different temperature regimes. In this study, microsatellite data from almost a decade of sampling were assessed to infer population structuring and its temporal stability. Several alternative analyses indicated that spatial variation explained 2-3 times more of the divergence in the system than temporal variation. Over all samples and years, there was a significant correlation between genetic and geographic distance. However, decomposed pairwise regression analysis revealed differing patterns of genetic structure among local populations and indicated that migration outweighs genetic drift in the majority of populations. In addition, isolation by distance was observable in only three of the six years, and signals of population bottlenecks were observed in the majority of samples. Combined, the results suggest that habitat-specific adaptation in this system has preceded the development of consistent population substructuring in the face of high levels of gene flow from divergent environments.
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Affiliation(s)
- C Junge
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway.
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Fraser DJ, Weir LK, Bernatchez L, Hansen MM, Taylor EB. Extent and scale of local adaptation in salmonid fishes: review and meta-analysis. Heredity (Edinb) 2011; 106:404-20. [PMID: 21224881 DOI: 10.1038/hdy.2010.167] [Citation(s) in RCA: 239] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
What is the extent and scale of local adaptation (LA)? How quickly does LA arise? And what is its underlying molecular basis? Our review and meta-analysis on salmonid fishes estimates the frequency of LA to be ∼55-70%, with local populations having a 1.2 times average fitness advantage relative to foreign populations or to their performance in new environments. Salmonid LA is evident at a variety of spatial scales (for example, few km to>1000 km) and can manifest itself quickly (6-30 generations). As the geographic scale between populations increases, LA is generally more frequent and stronger. Yet the extent of LA in salmonids does not appear to differ from that in other assessed taxa. Moreover, the frequency with which foreign salmonid populations outperform local populations (∼23-35%) suggests that drift, gene flow and plasticity often limit or mediate LA. The relatively few studies based on candidate gene and genomewide analyses have identified footprints of selection at both small and large geographical scales, likely reflecting the specific functional properties of loci and the associated selection regimes (for example, local niche partitioning, pathogens, parasites, photoperiodicity and seasonal timing). The molecular basis of LA in salmonids is still largely unknown, but differential expression at the same few genes is implicated in the convergent evolution of certain phenotypes. Collectively, future research will benefit from an integration of classical and molecular approaches to understand: (i) species differences and how they originate, (ii) variation in adaptation across scales, life stages, population sizes and environmental gradients, and (iii) evolutionary responses to human activities.
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Affiliation(s)
- D J Fraser
- Department of Biology, Concordia University, Montreal, Québec, Canada.
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Abstract
A new study of divergence in freshwater fish provides strong evidence of rapid, temperature-mediated adaptation. This study is particularly important in the ongoing debate over the extent and significance of evolutionary response to climate change because divergence has occurred in relatively few generations in spite of ongoing gene flow and in the aftermath of a significant genetic bottleneck, factors that have previously been considered obstacles to evolution. Climate change may thus be more likely to foster contemporary evolutionary responses than has been anticipated, and I argue here for the importance of investigating their possible occurrence. See Research article: http://www.biomedcentral.com/1471-2148/10/350/abstract
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Affiliation(s)
- David Skelly
- School of Forestry and Environmental Studies, Yale University, 195 Prospect Street, New Haven, CT 06511, USA.
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