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San L, He Z, Liu Y, Zhang Y, Cao W, Ren J, Han T, Li B, Wang G, Wang Y, Hou J. Genetic Diversity and Signatures of Selection in the Roughskin Sculpin ( Trachidermus fasciatus) Revealed by Whole Genome Sequencing. BIOLOGY 2023; 12:1427. [PMID: 37998026 PMCID: PMC10669622 DOI: 10.3390/biology12111427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 10/27/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023]
Abstract
The roughskin sculpin (Trachidermus fasciatus) is an endangered fish species in China. In recent years, artificial breeding technology has made significant progress, and the population of roughskin sculpin has recovered in the natural environment through enhancement programs and the release of juveniles. However, the effects of released roughskin sculpin on the genetic structure and diversity of wild populations remain unclear. Studies on genetic diversity analysis based on different types and numbers of molecular markers have yielded inconsistent results. In this study, we obtained 2,610,157 high-quality SNPs and 494,698 InDels through whole-genome resequencing of two farmed populations and one wild population. Both farmed populations showed consistent levels of genomic polymorphism and a slight increase in linkage compared with wild populations. The population structure of the two farmed populations was distinct from that of the wild population, but the degree of genetic differentiation was low (overall average Fst = 0.015). Selective sweep analysis showed that 523,529 genes were selected in the two farmed populations, and KEGG enrichment analysis showed that the selected genes were related to amino acid metabolism, which might be caused by artificial feeding. The findings of this study provide valuable additions to the existing genomic resources to help conserve roughskin sculpin populations.
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Affiliation(s)
- Lize San
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
- Bohai Sea Fishery Research Center, Chinese Academy of Fishery Science, Qinhuangdao 066100, China
| | - Zhongwei He
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
- Bohai Sea Fishery Research Center, Chinese Academy of Fishery Science, Qinhuangdao 066100, China
| | - Yufeng Liu
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
- Bohai Sea Fishery Research Center, Chinese Academy of Fishery Science, Qinhuangdao 066100, China
| | - Yitong Zhang
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
- Bohai Sea Fishery Research Center, Chinese Academy of Fishery Science, Qinhuangdao 066100, China
| | - Wei Cao
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
- Bohai Sea Fishery Research Center, Chinese Academy of Fishery Science, Qinhuangdao 066100, China
| | - Jiangong Ren
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
- Bohai Sea Fishery Research Center, Chinese Academy of Fishery Science, Qinhuangdao 066100, China
| | - Tian Han
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
- Bohai Sea Fishery Research Center, Chinese Academy of Fishery Science, Qinhuangdao 066100, China
- Ocean College, Hebei Agricultural University, Qinhuangdao 066009, China
| | - Bingbu Li
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
- Bohai Sea Fishery Research Center, Chinese Academy of Fishery Science, Qinhuangdao 066100, China
| | - Guixing Wang
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
- Bohai Sea Fishery Research Center, Chinese Academy of Fishery Science, Qinhuangdao 066100, China
| | - Yufen Wang
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
- Bohai Sea Fishery Research Center, Chinese Academy of Fishery Science, Qinhuangdao 066100, China
| | - Jilun Hou
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
- Bohai Sea Fishery Research Center, Chinese Academy of Fishery Science, Qinhuangdao 066100, China
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Guo Q, Gao Y, Song C, Zhang X, Wang G. Morphological and transcriptomic responses/acclimations of erect-type submerged macrophyte Hydrilla verticillata both at low-light exposure and light recovery phases. Ecol Evol 2023; 13:e10583. [PMID: 37809356 PMCID: PMC10556543 DOI: 10.1002/ece3.10583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/31/2023] [Accepted: 09/20/2023] [Indexed: 10/10/2023] Open
Abstract
Light intensity is a determinant for submerged macrophytes. Little is known about their molecular responses to low-light exposure, despite more informative and responsive than morphological traits. For erect-type submerged macrophytes, the stem is more crucial relative to the leaf in acclimation to low-light stress, but receives less attention. We determined morphological and stem transcriptomic responses/acclimations of Hydrilla verticillata to extremely and mildly low light (7.2 and 36 μmol photons m-2 s-1, respectively), that is, EL and ML, with the radiation intensity of 180 μmol photons m-2 s-1 as the control. Low-light exposure continued for 9 days, followed by a 7-day recovery phase (180 μmol photons m-2 s-1). At the exposure phase, the low-light treatments, in particular the EL, decreased the relative growth ratio, but induced greater height and longer stem internode distance and epidermal cell. Such responses/acclimations continued into the recovery phase, despite more or less changes in the magnitude. Transcriptome showed that the photosynthetic system was inhibited at the exposure phase, but the macrophyte adjusted hormone synthesis relating to cell division and elongation. Moreover, the EL activated cell stress responses such as DNA repair. Following light recovery, the macrophyte exhibited a strong-light response, although energy metabolism enhanced. Especially, the EL enriched the pathways relating to anthocyanin synthesis at such phase, indicating an activation of photoprotective mechanism. Our findings suggest that negative influences of low light occur at both low-light exposure and recovery phases, but submerged macrophytes would acclimate to light environments. Transcriptome can show molecular basis of plant responses/acclimations, including but not limited to morphology. This study establishes a bridge connecting morphological and molecular responses/acclimations.
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Affiliation(s)
- Qingchun Guo
- School of EnvironmentNanjing Normal UniversityNanjingChina
| | - Yuxuan Gao
- School of EnvironmentNanjing Normal UniversityNanjingChina
- State Key Laboratory of Vegetation and Environmental ChangeInstitute of Botany, Chinese Academy of SciencesBeijingChina
| | - Chao Song
- School of EnvironmentNanjing Normal UniversityNanjingChina
| | - Xinhou Zhang
- School of EnvironmentNanjing Normal UniversityNanjingChina
| | - Guoxiang Wang
- School of EnvironmentNanjing Normal UniversityNanjingChina
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3
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Burns MP, Schaeffer PJ, Berg DJ. Metabolic rate and osmoregulation in desert spring amphipods. CAN J ZOOL 2022. [DOI: 10.1139/cjz-2021-0195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Desert springs contain many endemic taxa and are of conservation concern due to anthropogenic activities that are expected to increase environmental salinity. Understanding the nature of osmoregulation is necessary to predict how non-vagile aquatic organisms will respond to changes. In the Chihuahuan Desert, the amphipod genus Gammarus Fabricius, 1775 is composed of two lineages. These lineages have species that currently inhabit springs ranging from 0.4 to 7.8 parts per thousand (ppt). All Gammarus in this region are of conservation concern because each is endemic to a single spring system. We exposed individuals of Gammarus colei Walters, Cannizzaro, and Berg in Walters, Cannizzaro, Trujillo and Berg, 2020 and Gammarus seideli Cannizzaro, Walters and Berg, 2018 species occupying low-salinity springs, to the range of salinities found in the Chihuahuan Desert. We measured metabolic rates as [Formula: see text] to examine the energetic cost of osmoregulation. We also measured the hemolymph osmolality of G. colei and compared that with the isosmotic line to determine the degree of osmoregulation. Neither species increased its metabolic rate across increasing salinities. However, G. colei showed an increase in hemolymph osmolality. Despite the divergence (∼66 million years ago) between the two lineages, it appears their physiological tolerances have converged, suggesting that both lineages may be able to persist when exposed to moderate salinity changes.
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Affiliation(s)
| | | | - David J. Berg
- Department of Biology, Miami University, Hamilton, OH 45011, USA
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Velotta JP, McCormick SD, Whitehead A, Durso CS, Schultz ET. Repeated Genetic Targets of Natural Selection Underlying Adaptation of Fishes to Changing Salinity. Integr Comp Biol 2022; 62:357-375. [PMID: 35661215 DOI: 10.1093/icb/icac072] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/16/2022] [Accepted: 05/05/2022] [Indexed: 11/12/2022] Open
Abstract
Ecological transitions across salinity boundaries have led to some of the most important diversification events in the animal kingdom, especially among fishes. Adaptations accompanying such transitions include changes in morphology, diet, whole-organism performance, and osmoregulatory function, which may be particularly prominent since divergent salinity regimes make opposing demands on systems that maintain ion and water balance. Research in the last decade has focused on the genetic targets underlying such adaptations, most notably by comparing populations of species that are distributed across salinity boundaries. Here, we synthesize research on the targets of natural selection using whole-genome approaches, with a particular emphasis on the osmoregulatory system. Given the complex, integrated and polygenic nature of this system, we expected that signatures of natural selection would span numerous genes across functional levels of osmoregulation, especially salinity sensing, hormonal control, and cellular ion exchange mechanisms. We find support for this prediction: genes coding for V-type, Ca2+, and Na+/K+-ATPases, which are key cellular ion exchange enzymes, are especially common targets of selection in species from six orders of fishes. This indicates that while polygenic selection contributes to adaptation across salinity boundaries, changes in ATPase enzymes may be of particular importance in supporting such transitions.
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Affiliation(s)
- Jonathan P Velotta
- Department of Biological Sciences, University of Denver, Denver, CO 80210, USA
| | - Stephen D McCormick
- USGS, Eastern Ecological Science Center, Conte Anadromous Fish Research Center, Turners Falls, MA 01376, USA.,Department of Biology, University of Massachusetts, Amherst, MA, 01003USA
| | - Andrew Whitehead
- Department of Environmental Toxicology, University of California, Davis, Davis, CA 95616, USA
| | - Catherine S Durso
- Department of Computer Science, University of Denver, Denver, CO 80210, USA
| | - Eric T Schultz
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
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5
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Blaxter M, Archibald JM, Childers AK, Coddington JA, Crandall KA, Di Palma F, Durbin R, Edwards SV, Graves JAM, Hackett KJ, Hall N, Jarvis ED, Johnson RN, Karlsson EK, Kress WJ, Kuraku S, Lawniczak MKN, Lindblad-Toh K, Lopez JV, Moran NA, Robinson GE, Ryder OA, Shapiro B, Soltis PS, Warnow T, Zhang G, Lewin HA. Why sequence all eukaryotes? Proc Natl Acad Sci U S A 2022; 119:e2115636118. [PMID: 35042801 PMCID: PMC8795522 DOI: 10.1073/pnas.2115636118] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of biodiversity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes-about 2 million species-should be sequenced to high quality to produce a digital library of life on Earth, beginning with strategic phylogenetic, ecological, and high-impact priorities. Here we discuss why we should sequence all eukaryotic species, not just a representative few scattered across the many branches of the tree of life. We suggest that many questions of evolutionary and ecological significance will only be addressable when whole-genome data representing divergences at all of the branchings in the tree of life or all species in natural ecosystems are available. We envisage that a genomic tree of life will foster understanding of the ongoing processes of speciation, adaptation, and organismal dependencies within entire ecosystems. These explorations will resolve long-standing problems in phylogenetics, evolution, ecology, conservation, agriculture, bioindustry, and medicine.
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Affiliation(s)
- Mark Blaxter
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4H7, Canada
| | - Anna K Childers
- Bee Research Laboratory, Agricultural Research Service, US Department of Agriculture (USDA), Beltsville, MD 20705
| | - Jonathan A Coddington
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Keith A Crandall
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, George Washington University, Washington, DC 20052
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC 20013
| | - Federica Di Palma
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Richard Durbin
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Jennifer A M Graves
- School of Life Sciences, La Trobe University, Bundoora, VIC 751 23, Australia
- University of Canberra, Bruce, ACT 2617, Australia
| | - Kevin J Hackett
- Crop Production and Protection, Office of National Programs, Agricultural Research Service, USDA, Beltsville, MD 20705
| | - Neil Hall
- Earlham Institute, Norwich, Norfolk NR4 7UZ, United Kingdom
| | - Erich D Jarvis
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Rebecca N Johnson
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Elinor K Karlsson
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - W John Kress
- Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012
| | - Shigehiro Kuraku
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | | | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 751 23, Sweden
| | - Jose V Lopez
- Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University, Dania Beach, FL 33004
- Guy Harvey Oceanographic Center, Dania Beach, FL 33004
| | - Nancy A Moran
- Integrative Biology, University of Texas at Austin, Austin, TX 78712
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Oliver A Ryder
- Conservation Genetics, Division of Biology, San Diego Zoo Wildlife Alliance, Escondido, CA 92027
- Department of Evolution, Behavior and Ecology, University of California, San Diego, La Jolla, CA 92039
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
- Biodiversity Institute, University of Florida, Gainesville, FL 32611
| | - Tandy Warnow
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61301
| | - Guojie Zhang
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
- China National Genebank, Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China
| | - Harris A Lewin
- Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, CA 95616
- Department of Population Health and Reproduction, University of California, Davis, CA 95616
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Paula DP. Next-Generation Sequencing and Its Impacts on Entomological Research in Ecology and Evolution. NEOTROPICAL ENTOMOLOGY 2021; 50:679-696. [PMID: 34374956 DOI: 10.1007/s13744-021-00895-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
The advent of NGS-based methods has been profoundly transforming entomological research. Through continual development and improvement of different methods and sequencing platforms, NGS has promoted mass elucidation of partial or whole genetic materials associated with beneficial insects, pests (of agriculture, forestry and animal, and human health), and species of conservation concern, helping to unravel ecological and evolutionary mechanisms and characterizing survival, trophic interactions, and dispersal. It is shifting the scale of biodiversity and environmental analyses from individuals and biodiversity indicator species to the large-scale study of communities and ecosystems using bulk samples of species or a mixed "soup" of environmental DNA. As the NGS-based methods have become more affordable, complexity demystified, and specificity and sensitivity proven, their use in entomological research has spread widely. This article presents several examples on how NGS-based methods have been used in entomology to provide incentives to apply them when appropriate and to open our minds to the expected advances in entomology that are yet to come.
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Albecker MA, Stuckert AMM, Balakrishnan CN, McCoy MW. Molecular mechanisms of local adaptation for salt-tolerance in a treefrog. Mol Ecol 2021; 30:2065-2086. [PMID: 33655636 DOI: 10.1111/mec.15867] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/12/2021] [Accepted: 02/19/2021] [Indexed: 12/18/2022]
Abstract
Salinization is a global phenomenon affecting ecosystems and forcing freshwater organisms to deal with increasing levels of ionic stress. However, our understanding of mechanisms that permit salt tolerance in amphibians is limited. This study investigates mechanisms of salt tolerance in locally adapted, coastal populations of a treefrog, Hyla cinerea. Using a common garden experiment, we (i) determine the extent that environment (i.e., embryonic and larval saltwater exposure) or genotype (i.e., coastal vs. inland) affects developmental benchmarks and transcriptome expression, and (ii) identify genes that may underpin differences in saltwater tolerance. Differences in gene expression, survival, and plasma osmolality were most strongly associated with genotype. Population genetic analyses on expressed genes also delineated coastal and inland groups based on genetic similarity. Coastal populations differentially expressed osmoregulatory genes including ion transporters (atp1b1, atp6V1g2, slc26a), cellular adhesion components (cdh26, cldn1, gjb3, ocln), and cytoskeletal components (odc1-a, tgm3). Several of these genes are the same genes expressed by euryhaline fish after exposure to freshwater, which is a novel finding for North American amphibians and suggests that these genes may be associated with local salinity adaptation. Coastal populations also highly expressed glycerol-3-phosphate dehydrogenase 1 (gpd1), which indicates they use glycerol as a compatible osmolyte to reduce water loss - another mechanism of saltwater tolerance previously unknown in frogs. These data signify that Hyla cinerea inhabiting coastal, brackish wetlands have evolved a salt-tolerant ecotype, and highlights novel candidate pathways that can lead to salt tolerance in freshwater organisms facing habitat salinization.
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Affiliation(s)
- Molly A Albecker
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
| | - Adam M M Stuckert
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
| | | | - Michael W McCoy
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
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8
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Xiong P, Hulsey CD, Fruciano C, Wong WY, Nater A, Kautt AF, Simakov O, Pippel M, Kuraku S, Meyer A, Franchini P. The comparative genomic landscape of adaptive radiation in crater lake cichlid fishes. Mol Ecol 2021; 30:955-972. [PMID: 33305470 PMCID: PMC8607476 DOI: 10.1111/mec.15774] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 11/21/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022]
Abstract
Factors ranging from ecological opportunity to genome composition might explain why only some lineages form adaptive radiations. While being rare, particular systems can provide natural experiments within an identical ecological setting where species numbers and phenotypic divergence in two closely related lineages are notably different. We investigated one such natural experiment using two de novo assembled and 40 resequenced genomes and asked why two closely related Neotropical cichlid fish lineages, the Amphilophus citrinellus species complex (Midas cichlids; radiating) and Archocentrus centrarchus (Flyer cichlid; nonradiating), have resulted in such disparate evolutionary outcomes. Although both lineages inhabit many of the same Nicaraguan lakes, whole-genome inferred demography suggests that priority effects are not likely to be the cause of the dissimilarities. Also, genome-wide levels of selection, transposable element dynamics, gene family expansion, major chromosomal rearrangements and the number of genes under positive selection were not markedly different between the two lineages. To more finely investigate particular subsets of the genome that have undergone adaptive divergence in Midas cichlids, we also examined if there was evidence for 'molecular pre-adaptation' in regions identified by QTL mapping of repeatedly diverging adaptive traits. Although most of our analyses failed to pinpoint substantial genomic differences, we did identify functional categories containing many genes under positive selection that provide candidates for future studies on the propensity of Midas cichlids to radiate. Our results point to a disproportionate role of local, rather than genome-wide factors underlying the propensity for these cichlid fishes to adaptively radiate.
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Affiliation(s)
- Peiwen Xiong
- Department of BiologyUniversity of KonstanzKonstanzGermany
| | - C. Darrin Hulsey
- Department of BiologyUniversity of KonstanzKonstanzGermany
- School of Biology and Environmental ScienceUniversity College DublinDublinIreland
| | - Carmelo Fruciano
- Department of BiologyUniversity of KonstanzKonstanzGermany
- National Research Council (CNR) – IRBIMMessinaItaly
| | - Wai Y. Wong
- Department of Molecular Evolution and DevelopmentUniversity of ViennaViennaAustria
| | | | - Andreas F. Kautt
- Department of BiologyUniversity of KonstanzKonstanzGermany
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMAUSA
| | - Oleg Simakov
- Department of Molecular Evolution and DevelopmentUniversity of ViennaViennaAustria
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Shigehiro Kuraku
- Laboratory for PhyloinformaticsRIKEN Center for Biosystems Dynamics Research (BDR)KobeJapan
| | - Axel Meyer
- Department of BiologyUniversity of KonstanzKonstanzGermany
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9
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Komoroske LM, Jeffries KM, Whitehead A, Roach JL, Britton M, Connon RE, Verhille C, Brander SM, Fangue NA. Transcriptional flexibility during thermal challenge corresponds with expanded thermal tolerance in an invasive compared to native fish. Evol Appl 2020. [DOI: 10.1111/eva.13172] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Lisa M. Komoroske
- Department of Environmental Conservation University of Massachusetts Amherst Amherst MA USA
- Department of Wildlife, Fish & Conservation Biology University of California, Davis Davis CA USA
| | - Ken M. Jeffries
- Department of Biological Sciences University of Manitoba Winnipeg MB Canada
| | - Andrew Whitehead
- Department of Environmental Toxicology University of California, Davis Davis CA USA
| | - Jennifer L. Roach
- Department of Environmental Toxicology University of California, Davis Davis CA USA
| | - Monica Britton
- Bioinformatics Core Facility, Genome Center University of California, Davis Davis CA USA
| | - Richard E. Connon
- Department of Anatomy, Physiology & Cell Biology, School of Veterinary Medicine University of California, Davis Davis CA USA
| | | | - Susanne M. Brander
- Department of Fisheries and Wildlife, Coastal Oregon Marine Experiment Station Oregon State University Corvallis OR USA
| | - Nann A. Fangue
- Department of Wildlife, Fish & Conservation Biology University of California, Davis Davis CA USA
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10
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Akman M, Carlson JE, Latimer AM. Climate explains population divergence in drought-induced plasticity of functional traits and gene expression in a South African Protea. Mol Ecol 2020; 30:255-273. [PMID: 33098695 DOI: 10.1111/mec.15705] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 10/04/2020] [Accepted: 10/06/2020] [Indexed: 12/18/2022]
Abstract
Long-term environmental variation often drives local adaptation and leads to trait differentiation across populations. Additionally, when traits change in an environment-dependent way through phenotypic plasticity, the genetic variation underlying plasticity will also be under selection. These processes could create a landscape of differentiation across populations in traits and their plasticity. Here, we performed a dry-down experiment under controlled conditions to measure responses in seedlings of a shrub species from the Cape Floristic Region, the common sugarbush (Protea repens). We measured morphological and physiological traits, and sequenced whole transcriptomes of leaf tissues from eight populations that represent both the climatic and the geographical distribution of this species. We found that there is substantial variation in how populations respond to drought, but we also observed common patterns such as reduced leaf size and leaf thickness, and up-regulation of stress-related and down-regulation of growth-related gene groups. Both high environmental heterogeneity and milder source site climates were associated with higher plasticity in various traits and co-expression gene networks. Associations between traits, trait plasticity, gene networks and the source site climate suggest that temperature may play a greater role in shaping these patterns when compared to precipitation, in line with recent changes in the region due to climate change. We also found that traits respond to climatic variation in an environment-dependent manner: some associations between traits and climate were apparent only under certain growing conditions. Together, our results uncover common responses of P. repens populations to drought, and climatic drivers of population differentiation in functional traits, gene expression and their plasticity.
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Affiliation(s)
- Melis Akman
- Department of Plant Sciences, UC Davis, Davis, CA, USA.,Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA
| | - Jane E Carlson
- Department of Biology, Nicholls State University, Thibodaux, LA, USA.,Gulf Coast Network Inventory and Monitoring Program, National Park Services, Washington, DC, USA
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11
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Laso‐Jadart R, Sugier K, Petit E, Labadie K, Peterlongo P, Ambroise C, Wincker P, Jamet J, Madoui M. Investigating population-scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866). Ecol Evol 2020; 10:8894-8905. [PMID: 32884665 PMCID: PMC7452778 DOI: 10.1002/ece3.6588] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/04/2020] [Accepted: 06/10/2020] [Indexed: 12/11/2022] Open
Abstract
Acclimation allowed by variation in gene or allele expression in natural populations is increasingly understood as a decisive mechanism, as much as adaptation, for species evolution. However, for small eukaryotic organisms, as species from zooplankton, classical methods face numerous challenges. Here, we propose the concept of allelic differential expression at the population-scale (psADE) to investigate the variation in allele expression in natural populations. We developed a novel approach to detect psADE based on metagenomic and metatranscriptomic data from environmental samples. This approach was applied on the widespread marine copepod, Oithona similis, by combining samples collected during the Tara Oceans expedition (2009-2013) and de novo transcriptome assemblies. Among a total of 25,768 single nucleotide variants (SNVs) of O. similis, 572 (2.2%) were affected by psADE in at least one population (FDR < 0.05). The distribution of SNVs under psADE in different populations is significantly shaped by population genomic differentiation (Pearson r = 0.87, p = 5.6 × 10-30), supporting a partial genetic control of psADE. Moreover, a significant amount of SNVs (0.6%) were under both selection and psADE (p < .05), supporting the hypothesis that natural selection and psADE tends to impact common loci. Population-scale allelic differential expression offers new insights into the gene regulation control in populations and its link with natural selection.
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Affiliation(s)
- Romuald Laso‐Jadart
- Génomique Métabolique, GenoscopeInstitut François Jacob, CEA, CNRS, Univ EvryUniversité Paris‐SaclayEvryFrance
- Research Federation for the study of Global Ocean Systems Ecology and EvolutionFR2022/Tara Oceans GO‐SEEParisFrance
| | - Kevin Sugier
- Génomique Métabolique, GenoscopeInstitut François Jacob, CEA, CNRS, Univ EvryUniversité Paris‐SaclayEvryFrance
| | - Emmanuelle Petit
- CEA, GenoscopeInstitut de Biologie François JacobUniversité Paris‐SaclayEvryFrance
| | - Karine Labadie
- CEA, GenoscopeInstitut de Biologie François JacobUniversité Paris‐SaclayEvryFrance
| | | | | | - Patrick Wincker
- Génomique Métabolique, GenoscopeInstitut François Jacob, CEA, CNRS, Univ EvryUniversité Paris‐SaclayEvryFrance
- Research Federation for the study of Global Ocean Systems Ecology and EvolutionFR2022/Tara Oceans GO‐SEEParisFrance
| | - Jean‐Louis Jamet
- Mediterranean Institute of Oceanology (MIO)AMU‐UTLN UM110CNRS UMR7294, IRDUMR235Equipe Ecologie Marine et Biodiversité (EMBIO)Université de ToulonToulon Cedex 9France
| | - Mohammed‐Amin Madoui
- Génomique Métabolique, GenoscopeInstitut François Jacob, CEA, CNRS, Univ EvryUniversité Paris‐SaclayEvryFrance
- Research Federation for the study of Global Ocean Systems Ecology and EvolutionFR2022/Tara Oceans GO‐SEEParisFrance
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12
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Sandoval-Castillo J, Gates K, Brauer CJ, Smith S, Bernatchez L, Beheregaray LB. Adaptation of plasticity to projected maximum temperatures and across climatically defined bioregions. Proc Natl Acad Sci U S A 2020; 117:17112-17121. [PMID: 32647058 PMCID: PMC7382230 DOI: 10.1073/pnas.1921124117] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Resilience to environmental stressors due to climate warming is influenced by local adaptations, including plastic responses. The recent literature has focused on genomic signatures of climatic adaptation, but little is known about how plastic capacity may be influenced by biogeographic and evolutionary processes. We investigate phenotypic plasticity as a target of climatic selection, hypothesizing that lineages that evolved in warmer climates will exhibit greater plastic adaptive resilience to upper thermal stress. This was experimentally tested by comparing transcriptomic responses within and among temperate, subtropical, and desert ecotypes of Australian rainbowfish subjected to contemporary and projected summer temperatures. Critical thermal maxima were estimated, and ecological niches delineated using bioclimatic modeling. A comparative phylogenetic expression variance and evolution model was used to assess plastic and evolved changes in gene expression. Although 82% of all expressed genes were found in the three ecotypes, they shared expression patterns in only 5 out of 236 genes that responded to the climate change experiment. A total of 532 genes showed signals of adaptive (i.e., genetic-based) plasticity due to ecotype-specific directional selection, and 23 of those responded to projected summer temperatures. Network analyses demonstrated centrality of these genes in thermal response pathways. The greatest adaptive resilience to upper thermal stress was shown by the subtropical ecotype, followed by the desert and temperate ecotypes. Our findings indicate that vulnerability to climate change will be highly influenced by biogeographic factors, emphasizing the value of integrative assessments of climatic adaptive traits for accurate estimation of population and ecosystem responses.
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Affiliation(s)
| | - Katie Gates
- Molecular Ecology Lab, Flinders University, Bedford Park, SA 5042, Australia
| | - Chris J Brauer
- Molecular Ecology Lab, Flinders University, Bedford Park, SA 5042, Australia
| | - Steve Smith
- Molecular Ecology Lab, Flinders University, Bedford Park, SA 5042, Australia
- Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, 1160 Vienna, Austria
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
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13
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Heras J, Aguilar A. Comparative Transcriptomics Reveals Patterns of Adaptive Evolution Associated with Depth and Age Within Marine Rockfishes (Sebastes). J Hered 2020; 110:340-350. [PMID: 30602025 DOI: 10.1093/jhered/esy070] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 12/31/2018] [Indexed: 01/21/2023] Open
Abstract
The genetic underpinnings that contribute to ecological adaptation and speciation are not completely understood, especially within marine ecosystems. These evolutionary processes can be elucidated by studying adaptive radiations, because they provide replicates of divergence within a given environment or time-frame. Marine rockfishes (genus Sebastes) are an adaptive radiation and unique model system for studying adaptive evolution in the marine realm. We investigated molecular evolution associated with ecological (depth) and life history (lifespan) divergence in 2 closely related clades of Sebastes. Brain transcriptomes were sequenced via RNA-Seq from 3 species within the subgenus Pteropodus and a pair of related congeners from the subgenus Sebastosomus in order to identify patterns of adaptive evolution. De novo assemblies from these transcriptomes were used to identify 3867 orthologous clusters, and genes subject to positive selection were identified based on all 5 species, depth, and lifespan. Within all our analyses, we identified hemoglobin subunit α to be under strong positive selection and is associated with the depth of occurrence. In our lifespan analysis we identified immune function genes under positive selection in association with maximum lifespan. This study provides insight on the molecular evolution of rockfishes and these candidate genes may provide a better understanding of how these subgenera radiated within the Northeast Pacific.
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Affiliation(s)
- Joseph Heras
- School of Natural Sciences and Graduate Group in Quantitative and Systems Biology, University of California, Merced, CA
| | - Andres Aguilar
- School of Natural Sciences and Graduate Group in Quantitative and Systems Biology, University of California, Merced, CA
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14
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Chen TH, Ma GC, Lin WH, Lee DJ, Wu SH, Liao BY, Chen M, Lin LK. Genome-Wide Microarray Analysis Suggests Transcriptomic Response May Not Play a Major Role in High- to Low-Altitude Acclimation in Harvest Mouse ( Micromys minutus). Animals (Basel) 2019; 9:ani9030092. [PMID: 30871279 PMCID: PMC6466072 DOI: 10.3390/ani9030092] [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: 02/25/2019] [Revised: 03/09/2019] [Accepted: 03/10/2019] [Indexed: 11/29/2022] Open
Abstract
Simple Summary Micromys minutus is a small rodent species that has a wide range of vertical distribution in Taiwan. By comparing the gene expression profile of the skeletal muscle tissues taken from individuals native to the high-altitude environment and those transferred to the low-altitude captive site, the Tnfrsf12a gene was demonstrated to have a differential expression pattern. Although this finding may be correlated with the altitude acclimation, the observation of only one gene transcript with significant alteration leads us to suggest that genetic response may not play a major role in altitude acclimation in M. minutus. Future comparative functional genomics studies involving other organ systems (in addition to skeletal muscles) and alarger sample size are warranted for better insight into the altitude acclimation of this small rodent species. Abstract The harvest mouse (Micromys minutus) is a small rodent species with a wide range of vertical distribution in Taiwan, extending from the sea level to 3100 m altitude. This species has recently suffered from habitat loss in high-altitude areas due to orchard cultivation, which may have resulted in mouse migration from high to low altitude. To investigate whether there is any physiological mechanism involved in altitude acclimation, rat cDNA microarray was used to compare transcriptomic patterns of the skeletal muscle tissues taken from individuals native to the high-altitude environment and those transferred to the low-altitude captive site. Of the 23,188 genes being analyzed, 47 (33 up-regulated and 14 down-regulated) were found to have differential expression (fold change > 4 or < −4, ANOVA p < 0.05). However, after multiple testing correction with a false discovery rate (FDR), only the result for Tnfrsf12a was found to be statistically significant (fold change = 13, FDR p < 0.05). The result was confirmed by quantitative polymerase chain reaction (q-PCR). The expression of Tnfrsf12a possibly relates to the skeletal muscle biology and thus can be correlated with altitude acclimation. However, finding only one gene transcript with significant alteration suggests that transcriptomic response may not play a major role in high- to low-altitude acclimation in harvest mouse.
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Affiliation(s)
- Tze-Ho Chen
- Department of Life Science, Tunghai University, Taichung 40704, Taiwan.
- Department of Obstetrics and Gynecology, Changhua Christian Hospital, Changhua 50006, Taiwan.
| | - Gwo-Chin Ma
- Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, Changhua 50046, Taiwan.
- Department of Genomic Science and Technology, Changhua Christian Hospital Healthcare System,Changhua Christian Hospital, Changhua 50046, Taiwan.
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung 40601, Taiwan.
| | - Wen-Hsiang Lin
- Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, Changhua 50046, Taiwan.
- Department of Genomic Science and Technology, Changhua Christian Hospital Healthcare System,Changhua Christian Hospital, Changhua 50046, Taiwan.
| | - Dong-Jay Lee
- Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, Changhua 50046, Taiwan.
- Department of Genomic Science and Technology, Changhua Christian Hospital Healthcare System,Changhua Christian Hospital, Changhua 50046, Taiwan.
| | - Sheng-Hai Wu
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan.
| | - Ben-Yang Liao
- Division of Biostatistics & Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County 35053, Taiwan.
| | - Ming Chen
- Department of Life Science, Tunghai University, Taichung 40704, Taiwan.
- Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, Changhua 50046, Taiwan.
- Department of Genomic Science and Technology, Changhua Christian Hospital Healthcare System,Changhua Christian Hospital, Changhua 50046, Taiwan.
- Department of Obstetrics and Gynecology, College of Medicine, National Taiwan University, Taipei 10041, Taiwan.
- Department of Medical Genetics, National Taiwan University Hospital, Taipei 10041, Taiwan.
- Department of Molecular Biotechnology, Da-Yeh University, Changhua 51591, Taiwan.
| | - Liang-Kong Lin
- Department of Life Science, Tunghai University, Taichung 40704, Taiwan.
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15
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Rojas-Hernandez N, Véliz D, Vega-Retter C. Selection of suitable reference genes for gene expression analysis in gills and liver of fish under field pollution conditions. Sci Rep 2019; 9:3459. [PMID: 30837616 PMCID: PMC6401100 DOI: 10.1038/s41598-019-40196-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/07/2019] [Indexed: 12/14/2022] Open
Abstract
To understand the role of gene expression in adaptive variation, it is necessary to examine expression variation in an ecological context. Quantitative real-time PCR (qPCR) is considered the most accurate and reliable technique to measure gene expression and to validate the data obtained by RNA-seq; however, accurate normalization is crucial. In Chile, the freshwater silverside fish Basilichthys microlepidotus inhabits both polluted and nonpolluted areas, showing differential gene expression related to pollution. In this study, we infer the stability of six potential reference genes (tubulin alpha, hypoxanthine-guanine phosphoribosyltransferase, glyceraldehyde-3-phosphate dehydrogenase, beta-actin, 60S ribosomal protein L13, and 60S ribosomal protein L8) in the gills and liver of silverside individuals inhabiting polluted and nonpolluted areas. To validate the reference genes selected, the most and least stable reference genes were used to normalize two target transcripts, one for each organ. The RefFinder tool was used to analyze and identify the most stably expressed genes. The 60S ribosomal protein L8 gene was ranked as the most stable gene for both organs. Our results show that reference gene selection influences the detection of differences in the expression levels of target genes in different organs and, also highlighting candidate reference genes that could be used in field studies.
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Affiliation(s)
- Noemí Rojas-Hernandez
- Departamento de Ciencias Ecológicas, Instituto de Ecología y Biodiversidad (IEB), Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - David Véliz
- Departamento de Ciencias Ecológicas, Instituto de Ecología y Biodiversidad (IEB), Facultad de Ciencias, Universidad de Chile, Santiago, Chile.,Núcleo Milenio de Ecología y Manejo Sustentable de Islas Oceánicas (ESMOI), Departamento de Biología Marina, Universidad Católica del Norte, Coquimbo, Chile
| | - Caren Vega-Retter
- Departamento de Ciencias Ecológicas, Instituto de Ecología y Biodiversidad (IEB), Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
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16
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Mandic M, Ramon ML, Gerstein AC, Gracey AY, Richards JG. Variable gene transcription underlies phenotypic convergence of hypoxia tolerance in sculpins. BMC Evol Biol 2018; 18:163. [PMID: 30390629 PMCID: PMC6215679 DOI: 10.1186/s12862-018-1275-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 10/18/2018] [Indexed: 01/03/2023] Open
Abstract
Background The degree by which mechanisms underlying phenotypic convergence are similar among taxa depends on the number of evolutionary paths available for selection to act upon. Likelihood of convergence will be influenced by an interplay of factors such as genetic architecture, phylogenetic history and population demography. To determine if there is convergence or divergence in mechanisms underlying phenotypic similarity, we assessed whether gene transcription patterns differed among species with similar levels of hypoxia tolerance. Results Three species of marine fish from the superfamily Cottoidea (smoothhead sculpin [Artedius lateralis], sailfin sculpin [Nautichthys oculofasciatus] and Pacific staghorn sculpin [Leptocottus armatus]), all of which have previously been shown to share the same level of hypoxia tolerance, were exposed to short-(8 h) and longer-term (72 h) hypoxia and mRNA transcripts were assessed using a custom microarray. We examined hypoxia-induced transcription patterns in metabolic and protein production pathways and found that a high proportion of genes associated with these biological processes showed significant differences among the species. Specifically, the data suggest that the smoothhead sculpin, unlike the sailfin sculpin and the Pacific staghorn sculpin, relied on amino acid degradation rather than glycolysis or fatty acid oxidation to generate ATP during hypoxia exposure. There was also variation across the species in the transcription of genes involved in protein production (e.g. mRNA processing and protein translation), such that it increased in the smoothhead sculpin, decreased in the sailfin sculpin and was variable in the Pacific staghorn sculpin. Conclusions Changes in metabolic and protein production pathways are part of the key responses of fishes to exposures to environmental hypoxia. Yet, species with similar overall hypoxia tolerance exhibited different transcriptional responses in these pathways, indicating flexibility and complexity of interactions in the evolution of the mechanisms underlying the hypoxia tolerance phenotype. The variation in the hypoxia-induced transcription of genes across species with similar hypoxia tolerance suggests that similar whole-animal phenotypes can emerge from divergent evolutionary paths that may affect metabolically important functions. Electronic supplementary material The online version of this article (10.1186/s12862-018-1275-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Milica Mandic
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada. .,Bamfield Marine Sciences Centre, 100 Pachena Dr, Bamfield, BC, V0R 1B0, Canada.
| | - Marina L Ramon
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA
| | - Aleeza C Gerstein
- Department of Genetics, Cell Biology and Development, University of Minnesota, 321 Church Street, Minneapolis, MN, 55455, USA
| | - Andrew Y Gracey
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA
| | - Jeffrey G Richards
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada.,Bamfield Marine Sciences Centre, 100 Pachena Dr, Bamfield, BC, V0R 1B0, Canada
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17
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Maynard A, Bible JM, Pespeni MH, Sanford E, Evans TG. Transcriptomic responses to extreme low salinity among locally adapted populations of Olympia oyster (Ostrea lurida). Mol Ecol 2018; 27:4225-4240. [PMID: 30193406 DOI: 10.1111/mec.14863] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 08/23/2018] [Accepted: 08/27/2018] [Indexed: 12/26/2022]
Abstract
The Olympia oyster (Ostrea lurida) is a foundation species inhabiting estuaries along the North American west coast. In California estuaries, O. lurida is adapted to local salinity regimes and populations differ in low salinity tolerance. In this study, oysters from three California populations were reared for two generations in a laboratory common garden and subsequently exposed to low salinity seawater. Comparative transcriptomics was then used to understand species-level responses to hyposmotic stress and population-level mechanisms underlying divergent salinity tolerances. Gene expression patterns indicate Olympia oysters are sensitive to hyposmotic stress: All populations respond to low salinity by up-regulating transcripts indicative of protein unfolding, DNA damage and cell cycle arrest after sub-lethal exposure. Among O. lurida populations, transcriptomic profiles differed constitutively and in response to low salinity. Despite two generations in common-garden conditions, transcripts encoding apoptosis modulators were constitutively expressed at significantly different levels in the most tolerant population. Expression of cell death regulators may facilitate cell fate decisions when salinity declines. Following low salinity exposure, oysters from the more tolerant population expressed a small number of mRNAs at significantly higher levels than less tolerant populations. Proteins encoded by these transcripts regulate ciliary activity within the mantle cavity and may function to prolong valve closure and reduce mortality in low salinity seawater. Collectively, gene expression patterns suggest sub-lethal impacts of hyposmotic stress in Olympia oysters are considerable and that even oysters with greater low salinity tolerance may be vulnerable to future freshwater flooding events.
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Affiliation(s)
- Ashley Maynard
- Department of Biological Sciences, California State University East Bay, Hayward, California
| | - Jillian M Bible
- Department of Evolution and Ecology and Bodega Marine Laboratory, University of California Davis, Bodega Bay, California.,Department of Environmental Science and Studies, Washington College, Chestertown, Maryland
| | | | - Eric Sanford
- Department of Evolution and Ecology and Bodega Marine Laboratory, University of California Davis, Bodega Bay, California
| | - Tyler G Evans
- Department of Biological Sciences, California State University East Bay, Hayward, California
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18
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Nigenda‐Morales SF, Hu Y, Beasley JC, Ruiz‐Piña HA, Valenzuela‐Galván D, Wayne RK. Transcriptomic analysis of skin pigmentation variation in the Virginia opossum (
Didelphis virginiana
). Mol Ecol 2018; 27:2680-2697. [DOI: 10.1111/mec.14712] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 04/05/2018] [Accepted: 04/17/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Sergio F. Nigenda‐Morales
- Department of Ecology and Evolutionary Biology University of California, Los Angeles Los Angeles California
| | - Yibo Hu
- Key Lab of Animal Ecology and Conservation Biology Institute of Zoology Chinese Academy of Sciences Chaoyang, Beijing China
| | - James C. Beasley
- Savannah River Ecology Lab Warnell School of Forestry and Natural Resources University of Georgia Aiken South Carolina
| | - Hugo A. Ruiz‐Piña
- Centro de Investigaciones Regionales “Dr. Hideyo Noguchi” Universidad Autónoma de Yucatán Mérida Yucatán Mexico
| | - David Valenzuela‐Galván
- Departamento de Ecología Evolutiva Centro de Investigación en Biodiversidad y Conservación Universidad Autónoma del Estado de Morelos Cuernavaca Morelos Mexico
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology University of California, Los Angeles Los Angeles California
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19
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Renn SCP, O'Rourke CF, Aubin-Horth N, Fraser EJ, Hofmann HA. Dissecting the Transcriptional Patterns of Social Dominance across Teleosts. Integr Comp Biol 2018; 56:1250-1265. [PMID: 27940616 DOI: 10.1093/icb/icw118] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In many species, under varying ecological conditions, social interactions among individuals result in the formation of dominance hierarchies. Despite general similarities, there are robust differences among dominance hierarchies across species, populations, environments, life stages, sexes, and individuals. Understanding the proximate mechanisms underlying the variation is an important step toward understanding the evolution of social behavior. However, physiological changes associated with dominance, such as gonadal maturation and somatic growth, often complicate efforts to identify the specific underlying mechanisms. Traditional gene expression analyses are useful for generating candidate gene lists, but are biased by choice of significance cut-offs and difficult to use for between-study comparisons. In contrast, complementary analysis tools allow one to both test a priori hypotheses and generate new hypotheses. Here we employ a meta-analysis of high-throughput expression profiling experiments to investigate the gene expression patterns that underlie mechanisms and evolution of behavioral social phenotypes. Specifically, we use a collection of datasets on social dominance in fish across social contexts, sex, and species. Using experimental manipulation to produce female dominance hierarchies in the cichlid Astatotilapia burtoni, heralded as a genomic model of social dominance, we generate gene lists, and assess molecular gene modules. In the dominant female gene expression profile, we demonstrate a strong pattern of up-regulation of genes previously identified as having male-biased expression and furthermore, compare expression biases between male and female dominance phenotypes. Using a threshold-free approach to identify correlation throughout ranked gene lists, we query previously published datasets associated with maternal behavior, alternative reproductive tactics, cooperative breeding, and sex-role reversal to describe correlations among these various neural gene expression profiles associated with different instances of social dominance. These complementary approaches capitalize on the high-throughput gene expression profiling from similar behavioral phenotypes in order to address the mechanisms associated with social dominance behavioral phenotypes.
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Affiliation(s)
- Suzy C P Renn
- *Department of Biology, Reed College, 3203 SE Woodstock blvd, Portland, OR 97202, USA
| | - Cynthia F O'Rourke
- *Department of Biology, Reed College, 3203 SE Woodstock blvd, Portland, OR 97202, USA
| | - Nadia Aubin-Horth
- Département de Biologie & Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Avenue de la Médecine - Local 1242 Québec G1V 0A6, QC Canada
| | - Eleanor J Fraser
- UCSF School of Medicine, 513 Parnassus Ave, Med Sci, San Francisco, CA 94122, USA
| | - Hans A Hofmann
- Department of Integrative Biology, Center for Computational Biology and Bioinformatics, The University of Texas at Austin, 2415 Speedway - C0990, Austin, TX 78705, USA
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20
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Tobler M, Kelley JL, Plath M, Riesch R. Extreme environments and the origins of biodiversity: Adaptation and speciation in sulphide spring fishes. Mol Ecol 2018; 27:843-859. [DOI: 10.1111/mec.14497] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Michael Tobler
- Division of Biology Kansas State University Manhattan KS USA
| | - Joanna L. Kelley
- School of Biological Sciences Washington State University Pullman WA USA
| | - Martin Plath
- Shaanxi Key Laboratory of Molecular Biology for Agriculture College of Animal Science and Technology Northwest A&F University Yangling Shaanxi China
| | - Rüdiger Riesch
- School of Biological Sciences Centre for Ecology, Evolution and Behaviour Royal Holloway University of London Egham Surrey UK
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21
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Current Knowledge and Recent Advances in Marine Dinoflagellate Transcriptomic Research. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2018. [DOI: 10.3390/jmse6010013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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23
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Brauer CJ, Unmack PJ, Beheregaray LB. Comparative ecological transcriptomics and the contribution of gene expression to the evolutionary potential of a threatened fish. Mol Ecol 2017; 26:6841-6856. [DOI: 10.1111/mec.14432] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/23/2017] [Accepted: 10/25/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Chris J. Brauer
- Molecular Ecology Laboratory College of Science and Engineering Flinders University Adelaide SA Australia
| | - Peter J. Unmack
- Institute for Applied Ecology University of Canberra Canberra ACT Australia
| | - Luciano B. Beheregaray
- Molecular Ecology Laboratory College of Science and Engineering Flinders University Adelaide SA Australia
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24
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Tine M. Evidence of the Complexity of Gene Expression Analysis in Fish Wild Populations. Int J Genomics 2017; 2017:1258396. [PMID: 29201893 PMCID: PMC5672613 DOI: 10.1155/2017/1258396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 08/24/2017] [Accepted: 09/18/2017] [Indexed: 11/17/2022] Open
Abstract
The present work examines the induction of the band 3 anion transport protein, mitogen-activated protein kinase, and lactate dehydrogenase, respectively related to osmolyte transport, cell volume regulation, and energy production in the gills of two tilapia strains exposed to either freshwater or hypersaline water. Overall, genes showed similar expression patterns between strains. However, a wild population survey across a range of natural habitats and salinities did not reveal the expected patterns. Although significant, the correlations between gene expression and salinity were slightly ambiguous and did not show any link with phenotypic differences in life history traits previously reported between the same populations. The differential expression was also not associated with the population genetic structure inferred from neutral markers. The results suggest that the differential expression observed is not the result of evolutionary forces such as genetic drift or adaptation by natural selection. Instead, it can be speculated that genes responded to various abiotic and biotic stressors, including factors intrinsic to animals. This study provides clear evidence of the complexity of gene expression analysis in wild populations and shows that more attention needs to be paid when selecting candidates as potential biomarkers for monitoring adaptive responses to a specific environmental perturbation.
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Affiliation(s)
- Mbaye Tine
- UFR des Sciences Agronomiques, de l'Aquaculture et des Technologies Alimentaires (UFR S2ATA), Universite Gaston Berger (UGB), Route de Ngallele BP 234, Saint-Louis, Senegal
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25
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Passow CN, Henpita C, Shaw JH, Quackenbush CR, Warren WC, Schartl M, Arias-Rodriguez L, Kelley JL, Tobler M. The roles of plasticity and evolutionary change in shaping gene expression variation in natural populations of extremophile fish. Mol Ecol 2017; 26:6384-6399. [PMID: 28926156 DOI: 10.1111/mec.14360] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 09/06/2017] [Accepted: 09/07/2017] [Indexed: 12/22/2022]
Abstract
The notorious plasticity of gene expression responses and the complexity of environmental gradients complicate the identification of adaptive differences in gene regulation among populations. We combined transcriptome analyses in nature with common-garden and exposure experiments to establish cause-effect relationships between the presence of a physiochemical stressor and expression differences, as well as to test how evolutionary change and plasticity interact to shape gene expression variation in natural systems. We studied two evolutionarily independent population pairs of an extremophile fish (Poecilia mexicana) living in toxic, hydrogen sulphide (H2 S)-rich springs and adjacent nontoxic habitats and assessed genomewide expression patterns of wild-caught and common-garden-raised individuals exposed to different concentrations of H2 S. We found that 7.7% of genes that were differentially expressed between sulphidic and nonsulphidic ecotypes remained differentially expressed in the laboratory, indicating that sources of selection other than H2 S-or plastic responses to other environmental factors-contribute substantially to gene expression patterns observed in the wild. Concordantly differentially expressed genes in the wild and the laboratory were primarily associated with H2 S detoxification, sulphur processing and metabolic physiology. While shared, ancestral plasticity played a minor role in shaping gene expression variation observed in nature, we documented evidence for evolved population differences in the constitutive expression as well as the H2 S inducibility of candidate genes. Mechanisms underlying gene expression variation also varied substantially across the two ecotype pairs. These results provide a springboard for studying evolutionary modifications of gene regulatory mechanisms that underlie expression variation in locally adapted populations.
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Affiliation(s)
| | - Chathurika Henpita
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA
| | - Jennifer H Shaw
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA
| | - Corey R Quackenbush
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA
| | - Manfred Schartl
- Physiological Chemistry, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany.,Hagler Institute for Advanced Studies and Department of Biology, Texas A&M University, College Station, TX, USA
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Villahermosa, México
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, KS, USA
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26
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Passow CN, Brown AP, Arias-Rodriguez L, Yee MC, Sockell A, Schartl M, Warren WC, Bustamante C, Kelley JL, Tobler M. Complexities of gene expression patterns in natural populations of an extremophile fish (Poecilia mexicana, Poeciliidae). Mol Ecol 2017; 26:4211-4225. [PMID: 28598519 PMCID: PMC5731456 DOI: 10.1111/mec.14198] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 05/18/2017] [Accepted: 05/24/2017] [Indexed: 12/31/2022]
Abstract
Variation in gene expression can provide insights into organismal responses to environmental stress and physiological mechanisms mediating adaptation to habitats with contrasting environmental conditions. We performed an RNA-sequencing experiment to quantify gene expression patterns in fish adapted to habitats with different combinations of environmental stressors, including the presence of toxic hydrogen sulphide (H2 S) and the absence of light in caves. We specifically asked how gene expression varies among populations living in different habitats, whether population differences were consistent among organs, and whether there is evidence for shared expression responses in populations exposed to the same stressors. We analysed organ-specific transcriptome-wide data from four ecotypes of Poecilia mexicana (nonsulphidic surface, sulphidic surface, nonsulphidic cave and sulphidic cave). The majority of variation in gene expression was correlated with organ type, and the presence of specific environmental stressors elicited unique expression differences among organs. Shared patterns of gene expression between populations exposed to the same environmental stressors increased with levels of organismal organization (from transcript to gene to physiological pathway). In addition, shared patterns of gene expression were more common between populations from sulphidic than populations from cave habitats, potentially indicating that physiochemical stressors with clear biochemical consequences can constrain the diversity of adaptive solutions that mitigate their adverse effects. Overall, our analyses provided insights into transcriptional variation in a unique system, in which adaptation to H2 S and darkness coincide. Functional annotations of differentially expressed genes provide a springboard for investigating physiological mechanisms putatively underlying adaptation to extreme environments.
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Affiliation(s)
| | - Anthony P. Brown
- Department of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Villahermosa, Tabasco, México
| | - Muh-Ching Yee
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Manfred Schartl
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany
- Texas A&M Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, TX, USA
| | - Wesley C. Warren
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Joanna L. Kelley
- Department of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, KS, USA
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27
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Runcie DE, Dorey N, Garfield DA, Stumpp M, Dupont S, Wray GA. Genomic Characterization of the Evolutionary Potential of the Sea Urchin Strongylocentrotus droebachiensis Facing Ocean Acidification. Genome Biol Evol 2017; 8:3672-3684. [PMID: 28082601 PMCID: PMC5521728 DOI: 10.1093/gbe/evw272] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2016] [Indexed: 12/19/2022] Open
Abstract
Ocean acidification (OA) is increasing due to anthropogenic CO2 emissions and poses a threat to marine species and communities worldwide. To better project the effects of acidification on organisms’ health and persistence, an understanding is needed of the 1) mechanisms underlying developmental and physiological tolerance and 2) potential populations have for rapid evolutionary adaptation. This is especially challenging in nonmodel species where targeted assays of metabolism and stress physiology may not be available or economical for large-scale assessments of genetic constraints. We used mRNA sequencing and a quantitative genetics breeding design to study mechanisms underlying genetic variability and tolerance to decreased seawater pH (-0.4 pH units) in larvae of the sea urchin Strongylocentrotus droebachiensis. We used a gene ontology-based approach to integrate expression profiles into indirect measures of cellular and biochemical traits underlying variation in larval performance (i.e., growth rates). Molecular responses to OA were complex, involving changes to several functions such as growth rates, cell division, metabolism, and immune activities. Surprisingly, the magnitude of pH effects on molecular traits tended to be small relative to variation attributable to segregating functional genetic variation in this species. We discuss how the application of transcriptomics and quantitative genetics approaches across diverse species can enrich our understanding of the biological impacts of climate change.
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Affiliation(s)
- Daniel E Runcie
- Department of Biology, Duke University, Durham, NC, USA.,Department of Plant Sciences, University of California, Davis, USA
| | - Narimane Dorey
- Department of Biological and Environmental Sciences, University of Gothenburg, Fiskebäckskil, Sweden
| | - David A Garfield
- Department of Biology, Duke University, Durham, NC, USA.,Integrative Research Institute for the Life Sciences, Humboldt University, Berlin, Germany
| | - Meike Stumpp
- Department of Biological and Environmental Sciences, University of Gothenburg, Fiskebäckskil, Sweden.,Helmholtz Centre for Ocean Sciences (GEOMAR), Kiel, Germany
| | - Sam Dupont
- Department of Biological and Environmental Sciences, University of Gothenburg, Fiskebäckskil, Sweden
| | - Gregory A Wray
- Department of Biology, Duke University, Durham, NC, USA.,Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
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28
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Wellband KW, Heath DD. Plasticity in gene transcription explains the differential performance of two invasive fish species. Evol Appl 2017; 10:563-576. [PMID: 28616064 PMCID: PMC5469171 DOI: 10.1111/eva.12463] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 01/28/2017] [Indexed: 01/06/2023] Open
Abstract
Phenotypic plasticity buffers organisms from environmental change and is hypothesized to aid the initial establishment of nonindigenous species in novel environments and postestablishment range expansion. The genetic mechanisms that underpin phenotypically plastic traits are generally poorly characterized; however, there is strong evidence that modulation of gene transcription is an important component of these responses. Here, we use RNA sequencing to examine the transcriptional basis of temperature tolerance for round and tubenose goby, two nonindigenous fish species that differ dramatically in the extent of their Great Lakes invasions despite similar invasion dates. We used generalized linear models of read count data to compare gene transcription responses of organisms exposed to increased and decreased water temperature from those at ambient conditions. We identify greater response in the magnitude of transcriptional changes for the more successful round goby compared with the less successful tubenose goby. Round goby transcriptional responses reflect alteration of biological function consistent with adaptive responses to maintain or regain homeostatic function in other species. In contrast, tubenose goby transcription patterns indicate a response to stressful conditions, but the pattern of change in biological functions does not match those expected for a return to homeostatic status. Transcriptional plasticity plays an important role in the acute thermal tolerance for these species; however, the impaired response to stress we demonstrate in the tubenose goby may contribute to their limited invasion success relative to the round goby. Transcriptional profiling allows the simultaneous assessment of the magnitude of transcriptional response as well as the biological functions involved in the response to environmental stress and is thus a valuable approach for evaluating invasion potential.
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Affiliation(s)
- Kyle W Wellband
- Great Lakes Institute for Environmental Research University of Windsor Windsor ON Canada
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research University of Windsor Windsor ON Canada.,Department of Biological Sciences University of Windsor Windsor ON Canada
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29
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Velotta JP, Wegrzyn JL, Ginzburg S, Kang L, Czesny S, O'Neill RJ, McCormick SD, Michalak P, Schultz ET. Transcriptomic imprints of adaptation to fresh water: parallel evolution of osmoregulatory gene expression in the Alewife. Mol Ecol 2017; 26:831-848. [DOI: 10.1111/mec.13983] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 11/15/2016] [Accepted: 11/18/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Jonathan P. Velotta
- Department of Ecology and Evolutionary Biology; University of Connecticut; Storrs CT 06269-3043 USA
| | - Jill L. Wegrzyn
- Department of Ecology and Evolutionary Biology; University of Connecticut; Storrs CT 06269-3043 USA
| | - Samuel Ginzburg
- Department of Ecology and Evolutionary Biology; University of Connecticut; Storrs CT 06269-3043 USA
| | - Lin Kang
- Department of Biological Sciences; Virginia Bioinformatics Institute; Virginia Tech; Blacksburg VA 24061 USA
| | - Sergiusz Czesny
- Lake Michigan Biological Station; Illinois Natural History Survey; University of Illinois; Zion IL 60099 USA
| | - Rachel J. O'Neill
- Department of Molecular and Cell Biology; University of Connecticut; Storrs CT 06269-3125 USA
| | - Stephen D. McCormick
- Conte Anadromous Fish Research Center; U.S. Geological Survey; Turners Falls MA 01376 USA
| | - Pawel Michalak
- Department of Biological Sciences; Virginia Bioinformatics Institute; Virginia Tech; Blacksburg VA 24061 USA
| | - Eric T. Schultz
- Department of Ecology and Evolutionary Biology; University of Connecticut; Storrs CT 06269-3043 USA
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30
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Discovery of Nigri/nox and Panto/pox site-specific recombinase systems facilitates advanced genome engineering. Sci Rep 2016; 6:30130. [PMID: 27444945 PMCID: PMC4957104 DOI: 10.1038/srep30130] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/27/2016] [Indexed: 12/21/2022] Open
Abstract
Precise genome engineering is instrumental for biomedical research and holds great promise for future therapeutic applications. Site-specific recombinases (SSRs) are valuable tools for genome engineering due to their exceptional ability to mediate precise excision, integration and inversion of genomic DNA in living systems. The ever-increasing complexity of genome manipulations and the desire to understand the DNA-binding specificity of these enzymes are driving efforts to identify novel SSR systems with unique properties. Here, we describe two novel tyrosine site-specific recombination systems designated Nigri/nox and Panto/pox. Nigri originates from Vibrio nigripulchritudo (plasmid VIBNI_pA) and recombines its target site nox with high efficiency and high target-site selectivity, without recombining target sites of the well established SSRs Cre, Dre, Vika and VCre. Panto, derived from Pantoea sp. aB, is less specific and in addition to its native target site, pox also recombines the target site for Dre recombinase, called rox. This relaxed specificity allowed the identification of residues that are involved in target site selectivity, thereby advancing our understanding of how SSRs recognize their respective DNA targets.
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31
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Evaluating ‘Plasticity-First’ Evolution in Nature: Key Criteria and Empirical Approaches. Trends Ecol Evol 2016; 31:563-574. [DOI: 10.1016/j.tree.2016.03.012] [Citation(s) in RCA: 300] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 03/10/2016] [Accepted: 03/14/2016] [Indexed: 01/19/2023]
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32
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Papetti C, Lucassen M, Pörtner HO. Integrated studies of organismal plasticity through physiological and transcriptomic approaches: examples from marine polar regions. Brief Funct Genomics 2016; 15:365-72. [PMID: 27345433 DOI: 10.1093/bfgp/elw024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Transcriptomic methods are now widely used in functional genomic research. The vast amount of information received from these studies comes along with the challenge of developing a precise picture of the functional consequences and the characteristic regulatory mechanisms. Here we assess recent studies in marine species and their adaptation to polar (and seasonal) cold and explore how they have been able to draw reliable conclusions from transcriptomic patterns on functional consequences in the organisms. Our analysis indicates that the interpretation of transcriptomic data suffers from insufficient understanding of the consequences for whole organism performance and fitness and comes with the risk of supporting only preliminary and superficial statements.We propose that the functional understanding of transcriptomic data may be improved by their tighter integration into overarching physiological concepts that support the more specific interpretation of the 'omics' data and, at the same time, can be developed further through embedding the transcriptomic phenomena observed. Such possibilities have not been fully exploited.In the context of thermal adaptation and limitation, we explore preliminary evidence that the concept of oxygen and capacity limited thermal tolerance (OCLTT) may provide sufficient complexity to guide the integration of such data and the development of associated functional hypotheses. At the same time, we identify a lack of methodological approaches linking genes and function to higher levels of integration, in terms of organism and ecosystem functioning, at temporal and geographical scales, to support more reliable conclusions and be predictive with respect to the effects of global changes.
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33
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Velotta JP, Jones J, Wolf CJ, Cheviron ZA. Transcriptomic plasticity in brown adipose tissue contributes to an enhanced capacity for nonshivering thermogenesis in deer mice. Mol Ecol 2016; 25:2870-86. [PMID: 27126783 DOI: 10.1111/mec.13661] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 03/04/2016] [Accepted: 04/01/2016] [Indexed: 01/08/2023]
Abstract
For small mammals living at high altitude, aerobic heat generation (thermogenesis) is essential for survival during prolonged periods of cold, but is severely impaired under conditions of hypobaric hypoxia. Recent studies in deer mice (Peromyscus maniculatus) reveal adaptive enhancement of thermogenesis in high- compared to low-altitude populations under hypoxic cold stress, an enhancement that is attributable to modifications in the aerobic metabolism of muscles used in shivering. However, because small mammals rely heavily on nonshivering mechanisms for cold acclimatization, we tested for evidence of adaptive divergence in nonshivering thermogenesis (NST) under hypoxia. To do so, we measured NST and characterized transcriptional profiles of brown adipose tissue (BAT) in high- and low-altitude deer mice that were (i) wild-caught and acclimatized to their native altitude, and (ii) born and reared under common garden conditions at low elevation. We found that NST performance under hypoxia is enhanced in wild-caught, high-altitude deer mice, a difference that is associated with increased expression of coregulated genes that influence several physiological traits. These traits include vascularization and O2 supply to BAT, brown adipocyte proliferation and the uncoupling of oxidative phosphorylation from ATP synthesis in the generation of heat. Our results suggest that acclimatization to hypoxic cold stress is facilitated by enhancement of nonshivering heat production, which is driven by regulatory plasticity in a suite of genes that influence intersecting physiological pathways.
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Affiliation(s)
- Jonathan P Velotta
- Department of Animal Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61081, USA
| | - Jennifer Jones
- Department of Animal Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61081, USA
| | - Cole J Wolf
- Department of Animal Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61081, USA
| | - Zachary A Cheviron
- Department of Animal Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61081, USA
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34
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Conserved effects of salinity acclimation on thermal tolerance and hsp70 expression in divergent populations of threespine stickleback (Gasterosteus aculeatus). J Comp Physiol B 2016; 186:879-89. [DOI: 10.1007/s00360-016-0998-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/28/2016] [Accepted: 05/10/2016] [Indexed: 10/21/2022]
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35
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Smith MD, Hoffman AM, Avolio ML. Gene expression patterns of two dominant tallgrass prairie species differ in response to warming and altered precipitation. Sci Rep 2016; 6:25522. [PMID: 27174156 PMCID: PMC4865957 DOI: 10.1038/srep25522] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 04/15/2016] [Indexed: 11/09/2022] Open
Abstract
To better understand the mechanisms underlying plant species responses to climate change, we compared transcriptional profiles of the co-dominant C4 grasses, Andropogon gerardii Vitman and Sorghastrum nutans (L.) Nash, in response to increased temperatures and more variable precipitation regimes in a long-term field experiment in native tallgrass prairie. We used microarray probing of a closely related model species (Zea mays) to assess correlations in leaf temperature (Tleaf) and leaf water potential (LWP) and abundance changes of ~10,000 transcripts in leaf tissue collected from individuals of both species. A greater number of transcripts were found to significantly change in abundance levels with Tleaf and LWP in S. nutans than in A. gerardii. S. nutans also was more responsive to short-term drought recovery than A. gerardii. Water flow regulating transcripts associated with stress avoidance (e.g., aquaporins), as well as those involved in the prevention and repair of damage (e.g., antioxidant enzymes, HSPs), were uniquely more abundant in response to increasing Tleaf in S. nutans. The differential transcriptomic responses of the co-dominant C4 grasses suggest that these species may cope with and respond to temperature and water stress at the molecular level in distinct ways, with implications for tallgrass prairie ecosystem function.
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Affiliation(s)
- Melinda D. Smith
- Department of Biology and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
| | - Ava M. Hoffman
- Department of Biology and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
| | - Meghan L. Avolio
- National Socio-Environmental Synthesis Center, Annapolis, MD, 21401, USA
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36
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Bougas B, Normandeau E, Grasset J, Defo MA, Campbell PGC, Couture P, Bernatchez L. Transcriptional response of yellow perch to changes in ambient metal concentrations-A reciprocal field transplantation experiment. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2016; 173:132-142. [PMID: 26867186 DOI: 10.1016/j.aquatox.2015.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 12/18/2015] [Accepted: 12/20/2015] [Indexed: 06/05/2023]
Abstract
Recent local adaptation to pollution has been evidenced in several organisms inhabiting environments heavily contaminated by metals. Nevertheless, the molecular mechanisms underlying adaptation to high metal concentrations are poorly understood, especially in fishes. Yellow perch (Perca flavescens) populations from lakes in the mining area of Rouyn-Noranda (QC, Canada) have been faced with metal contamination for about 90 years. Here, we examine gene transcription patterns of fish reciprocally transplanted between a reference and a metal-contaminated lake and also fish caged in their native lake. After four weeks, 111 genes were differentially transcribed in metal-naïve fish transferred to the metal-contaminated lake, revealing a plastic response to metal exposure. Genes involved in the citric cycle and beta-oxidation pathways were under-transcribed, suggesting a potential strategy to mitigate the effects of metal stress by reducing energy turnover. However, metal-contaminated fish transplanted to the reference lake did not show any transcriptomic response, indicating a reduced plastic response capability to sudden reduction in metal concentrations. Moreover, the transcription of other genes, especially ones involved in energy metabolism, was affected by caging. Overall, our results highlight environmental stress response mechanisms in yellow perch at the transcriptomic level and support a rapid adaptive response to metal exposure through genetic assimilation.
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Affiliation(s)
- Bérénice Bougas
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec (Québec) G1V 0A6, Canada.
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec (Québec) G1V 0A6, Canada
| | - Julie Grasset
- Institut National de la Recherche Scientifique, Centre Eau Terre Environnement 490, rue de la Couronne, Québec (Québec) G1K 9A9, Canada
| | - Michel A Defo
- Institut National de la Recherche Scientifique, Centre Eau Terre Environnement 490, rue de la Couronne, Québec (Québec) G1K 9A9, Canada
| | - Peter G C Campbell
- Institut National de la Recherche Scientifique, Centre Eau Terre Environnement 490, rue de la Couronne, Québec (Québec) G1K 9A9, Canada
| | - Patrice Couture
- Institut National de la Recherche Scientifique, Centre Eau Terre Environnement 490, rue de la Couronne, Québec (Québec) G1K 9A9, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec (Québec) G1V 0A6, Canada
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37
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Blanco-Bercial L, Bucklin A. New view of population genetics of zooplankton: RAD-seq analysis reveals population structure of the North Atlantic planktonic copepod Centropages typicus. Mol Ecol 2016; 25:1566-80. [PMID: 26857348 DOI: 10.1111/mec.13581] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 01/24/2016] [Accepted: 02/01/2016] [Indexed: 01/08/2023]
Abstract
Detection of population genetic structure of zooplankton at medium-to-small spatial scales in the absence of physical barriers has remained challenging and controversial. The large population sizes and high rates of gene flow characteristic of zooplankton have made resolution of geographical differentiation very difficult, especially when using few genetic markers and assuming equilibrium conditions. Next-generation sequencing now allows simultaneous sampling of hundreds to thousands of genetic markers; new analytical approaches allow studies under nonequilibrium conditions and directional migration. Samples of the North Atlantic Ocean planktonic copepod, Centropages typicus, were analysed using restriction site-associated DNA (RAD) sequencing on a PROTON platform. Although prior studies revealed no genetic differentiation of populations across the geographical range of the species, analysis of RAD tags showed significant structure across the North Atlantic Ocean. We also compared the likelihood for models of connectivity among NW Atlantic populations under various directional flow scenarios that replicate oceanographic conditions of the sampled domain. High-density marker sampling with RAD sequencing markedly outperformed other technical and analytical approaches in detection of population genetic structure and characterization of connectivity of this high geneflow zooplankton species.
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Affiliation(s)
- L Blanco-Bercial
- Department of Marine Sciences, University of Connecticut, 1080 Shennecossett Rd, Groton, CT, 06340, USA.,Bermuda Institute of Ocean Sciences, 17 Biological Station, St. George's, GE 01, Bermuda
| | - A Bucklin
- Department of Marine Sciences, University of Connecticut, 1080 Shennecossett Rd, Groton, CT, 06340, USA
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38
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Davidson RL, Weber RJM, Liu H, Sharma-Oates A, Viant MR. Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data. Gigascience 2016; 5:10. [PMID: 26913198 PMCID: PMC4765054 DOI: 10.1186/s13742-016-0115-8] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 02/06/2016] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Metabolomics is increasingly recognized as an invaluable tool in the biological, medical and environmental sciences yet lags behind the methodological maturity of other omics fields. To achieve its full potential, including the integration of multiple omics modalities, the accessibility, standardization and reproducibility of computational metabolomics tools must be improved significantly. RESULTS Here we present our end-to-end mass spectrometry metabolomics workflow in the widely used platform, Galaxy. Named Galaxy-M, our workflow has been developed for both direct infusion mass spectrometry (DIMS) and liquid chromatography mass spectrometry (LC-MS) metabolomics. The range of tools presented spans from processing of raw data, e.g. peak picking and alignment, through data cleansing, e.g. missing value imputation, to preparation for statistical analysis, e.g. normalization and scaling, and principal components analysis (PCA) with associated statistical evaluation. We demonstrate the ease of using these Galaxy workflows via the analysis of DIMS and LC-MS datasets, and provide PCA scores and associated statistics to help other users to ensure that they can accurately repeat the processing and analysis of these two datasets. Galaxy and data are all provided pre-installed in a virtual machine (VM) that can be downloaded from the GigaDB repository. Additionally, source code, executables and installation instructions are available from GitHub. CONCLUSIONS The Galaxy platform has enabled us to produce an easily accessible and reproducible computational metabolomics workflow. More tools could be added by the community to expand its functionality. We recommend that Galaxy-M workflow files are included within the supplementary information of publications, enabling metabolomics studies to achieve greater reproducibility.
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Affiliation(s)
- Robert L. Davidson
- />GigaScience, BGI-Hong Kong Co. Ltd, Tai Po Industrial Estate, 16 Dai Fu Street, Tai Po, NT Hong Kong
- />School of Biosciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Ralf J. M. Weber
- />School of Biosciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Haoyu Liu
- />School of Biosciences, University of Birmingham, Birmingham, B15 2TT UK
| | | | - Mark R. Viant
- />School of Biosciences, University of Birmingham, Birmingham, B15 2TT UK
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39
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Kelley JL, Arias-Rodriguez L, Patacsil Martin D, Yee MC, Bustamante CD, Tobler M. Mechanisms Underlying Adaptation to Life in Hydrogen Sulfide-Rich Environments. Mol Biol Evol 2016; 33:1419-34. [PMID: 26861137 PMCID: PMC4868117 DOI: 10.1093/molbev/msw020] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Hydrogen sulfide (H2S) is a potent toxicant interfering with oxidative phosphorylation in mitochondria and creating extreme environmental conditions in aquatic ecosystems. The mechanistic basis of adaptation to perpetual exposure to H2S remains poorly understood. We investigated evolutionarily independent lineages of livebearing fishes that have colonized and adapted to springs rich in H2S and compared their genome-wide gene expression patterns with closely related lineages from adjacent, nonsulfidic streams. Significant differences in gene expression were uncovered between all sulfidic and nonsulfidic population pairs. Variation in the number of differentially expressed genes among population pairs corresponded to differences in divergence times and rates of gene flow, which is consistent with neutral drift driving a substantial portion of gene expression variation among populations. Accordingly, there was little evidence for convergent evolution shaping large-scale gene expression patterns among independent sulfide spring populations. Nonetheless, we identified a small number of genes that was consistently differentially expressed in the same direction in all sulfidic and nonsulfidic population pairs. Functional annotation of shared differentially expressed genes indicated upregulation of genes associated with enzymatic H2S detoxification and transport of oxidized sulfur species, oxidative phosphorylation, energy metabolism, and pathways involved in responses to oxidative stress. Overall, our results suggest that modification of processes associated with H2S detoxification and toxicity likely complement each other to mediate elevated H2S tolerance in sulfide spring fishes. Our analyses allow for the development of novel hypotheses about biochemical and physiological mechanisms of adaptation to extreme environments.
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Affiliation(s)
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Villahermosa, Tabasco, México
| | | | - Muh-Ching Yee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA
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40
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Huang Y, Chain FJJ, Panchal M, Eizaguirre C, Kalbe M, Lenz TL, Samonte IE, Stoll M, Bornberg-Bauer E, Reusch TBH, Milinski M, Feulner PGD. Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks. Mol Ecol 2016; 25:943-58. [PMID: 26749022 PMCID: PMC4790908 DOI: 10.1111/mec.13520] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 11/18/2015] [Accepted: 12/10/2015] [Indexed: 12/16/2022]
Abstract
The observation of habitat-specific phenotypes suggests the action of natural selection. The three-spined stickleback (Gasterosteus aculeatus) has repeatedly colonized and adapted to diverse freshwater habitats across the northern hemisphere since the last glaciation, while giving rise to recurring phenotypes associated with specific habitats. Parapatric lake and river populations of sticklebacks harbour distinct parasite communities, a factor proposed to contribute to adaptive differentiation between these ecotypes. However, little is known about the transcriptional response to the distinct parasite pressure of those fish in a natural setting. Here, we sampled wild-caught sticklebacks across four geographical locations from lake and river habitats differing in their parasite load. We compared gene expression profiles between lake and river populations using 77 whole-transcriptome libraries from two immune-relevant tissues, the head kidney and the spleen. Differential expression analyses revealed 139 genes with habitat-specific expression patterns across the sampled population pairs. Among the 139 differentially expressed genes, eight are annotated with an immune function and 42 have been identified as differentially expressed in previous experimental studies in which fish have been immune challenged. Together, these findings reinforce the hypothesis that parasites contribute to adaptation of sticklebacks in lake and river habitats.
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Affiliation(s)
- Yun Huang
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Frédéric J J Chain
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.,Department of Biology, McGill University, Montreal, QC, Canada, H3A 1B1
| | - Mahesh Panchal
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.,Bioinformatics Infrastructures for Life Sciences (BILS), Uppsala Biomedicinska Centrum (BMC), Husargatan 3, 751 23, Uppsala, Sweden.,Institute of Medical Biochemistry and Microbiology, Uppsala Biomedicinska Centrum (BMC), Husargatan 3, 751 23, Uppsala, Sweden
| | - Christophe Eizaguirre
- School of Biological and Chemical Sciences, Queen Mary University of London, E1 4NS, London, UK
| | - Martin Kalbe
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Tobias L Lenz
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Irene E Samonte
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Monika Stoll
- Institute of Human Genetics, Genetic Epidemiology, Westfälische Wilhelms University, 48149, Münster, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, Evolutionary Bioinformatics, Westfälische Wilhelms University, 48149, Münster, Germany
| | - Thorsten B H Reusch
- Evolutionary Ecology of Marine Fishes, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24105, Kiel, Germany
| | - Manfred Milinski
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Philine G D Feulner
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.,Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047, Kastanienbaum, Switzerland
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41
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Storz JF, Cheviron ZA. Functional Genomic Insights into Regulatory Mechanisms of High-Altitude Adaptation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 903:113-28. [PMID: 27343092 DOI: 10.1007/978-1-4899-7678-9_8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent studies of indigenous human populations at high altitude have provided proof-of-principle that genome scans of DNA polymorphism can be used to identify candidate loci for hypoxia adaptation. When integrated with experimental analyses of physiological phenotypes, genome-wide surveys of DNA polymorphism and tissue-specific transcriptional profiles can provide insights into actual mechanisms of adaptation. It has been suggested that adaptive phenotypic evolution is largely mediated by cis-regulatory changes in genes that are located at integrative control points in regulatory networks. This hypothesis can be tested by conducting transcriptomic analyses of hypoxic signaling pathways in conjunction with experimental measures of vascular oxygen supply and metabolic pathway flux. Such studies may reveal whether the architecture of gene regulatory networks can be used to predict which loci (and which types of loci) are likely to be "hot spots" for adaptive physiological evolution. Functional genomic studies of deer mice (Peromyscus maniculatus) demonstrate how the integrated analysis of variation in tissue-specific transcriptomes, whole-animal physiological performance, and various subordinate traits can yield insights into the mechanistic underpinnings of high-altitude adaptation.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA.
| | - Zachary A Cheviron
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
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42
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Jones BM, Wcislo WT, Robinson GE. Developmental Transcriptome for a Facultatively Eusocial Bee, Megalopta genalis. G3 (BETHESDA, MD.) 2015; 5:2127-35. [PMID: 26276382 PMCID: PMC4592995 DOI: 10.1534/g3.115.021261] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/12/2015] [Indexed: 11/18/2022]
Abstract
Transcriptomes provide excellent foundational resources for mechanistic and evolutionary analyses of complex traits. We present a developmental transcriptome for the facultatively eusocial bee Megalopta genalis, which represents a potential transition point in the evolution of eusociality. A de novo transcriptome assembly of Megalopta genalis was generated using paired-end Illumina sequencing and the Trinity assembler. Males and females of all life stages were aligned to this transcriptome for analysis of gene expression profiles throughout development. Gene Ontology analysis indicates that stage-specific genes are involved in ion transport, cell-cell signaling, and metabolism. A number of distinct biological processes are upregulated in each life stage, and transitions between life stages involve shifts in dominant functional processes, including shifts from transcriptional regulation in embryos to metabolism in larvae, and increased lipid metabolism in adults. We expect that this transcriptome will provide a useful resource for future analyses to better understand the molecular basis of the evolution of eusociality and, more generally, phenotypic plasticity.
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Affiliation(s)
- Beryl M Jones
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois, Urbana, Illinois 61801 Smithsonian Tropical Research Institute, Panama City, Panama 20521-9100 Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
| | - William T Wcislo
- Smithsonian Tropical Research Institute, Panama City, Panama 20521-9100
| | - Gene E Robinson
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois, Urbana, Illinois 61801 Department of Entomology, University of Illinois, Urbana, Illinois 61801 Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801 Neuroscience Program, University of Illinois, Urbana, Illinois 61801
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43
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Dalziel AC, Martin N, Laporte M, Guderley H, Bernatchez L. Adaptation and acclimation of aerobic exercise physiology in Lake Whitefish ecotypes (Coregonus clupeaformis). Evolution 2015; 69:2167-86. [PMID: 26177840 DOI: 10.1111/evo.12727] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 06/30/2015] [Indexed: 12/17/2022]
Abstract
The physiological mechanisms underlying local adaptation in natural populations of animals, and whether the same mechanisms contribute to adaptation and acclimation, are largely unknown. Therefore, we tested for evolutionary divergence in aerobic exercise physiology in laboratory bred, size-matched crosses of ancestral, benthic, normal Lake Whitefish (Coregonus clupeaformis) and derived, limnetic, more actively swimming "dwarf" ecotypes. We acclimated fish to constant swimming (emulating limnetic foraging) and control conditions (emulating normal activity levels) to simultaneously study phenotypic plasticity. We found extensive divergence between ecotypes: dwarf fish generally had constitutively higher values of traits related to oxygen transport (ventricle size) and use by skeletal muscle (percent oxidative muscle, mitochondrial content), and also evolved differential plasticity of mitochondrial function (Complex I activity and flux through Complexes I-IV and IV). The effects of swim training were less pronounced than differences among ecotypes and the traits which had a significant training effect (ventricle protein content, ventricle malate dehydrogenase activity, and muscle Complex V activity) did not differ among ecotypes. Only one trait, ventricle mass, varied in a similar manner with acclimation and adaptation and followed a pattern consistent with genetic accommodation. Overall, the physiological and biochemical mechanisms underlying acclimation and adaptation to swimming activity in Lake Whitefish differ.
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Affiliation(s)
- Anne C Dalziel
- Departement de Biologie, Pavillon Charles-Eugène-Marchand, 1030 Avenue de la Médecine Université Laval, Québec City, Québec, Canada, G1V 0A6.
| | - Nicolas Martin
- Departement de Biologie, Pavillon Charles-Eugène-Marchand, 1030 Avenue de la Médecine Université Laval, Québec City, Québec, Canada, G1V 0A6.,School of Medicine, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Martin Laporte
- Departement de Biologie, Pavillon Charles-Eugène-Marchand, 1030 Avenue de la Médecine Université Laval, Québec City, Québec, Canada, G1V 0A6
| | - Helga Guderley
- Departement de Biologie, Pavillon Charles-Eugène-Marchand, 1030 Avenue de la Médecine Université Laval, Québec City, Québec, Canada, G1V 0A6.,Department of Biology, Life Science Centre, Dalhousie University, 1355 Oxford Street PO BOX 15000, Halifax, NS, Canada, B3H 4R2
| | - Louis Bernatchez
- Departement de Biologie, Pavillon Charles-Eugène-Marchand, 1030 Avenue de la Médecine Université Laval, Québec City, Québec, Canada, G1V 0A6
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44
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Storz JF, Bridgham JT, Kelly SA, Garland T. Genetic approaches in comparative and evolutionary physiology. Am J Physiol Regul Integr Comp Physiol 2015; 309:R197-214. [PMID: 26041111 PMCID: PMC4525326 DOI: 10.1152/ajpregu.00100.2015] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/23/2015] [Indexed: 01/04/2023]
Abstract
Whole animal physiological performance is highly polygenic and highly plastic, and the same is generally true for the many subordinate traits that underlie performance capacities. Quantitative genetics, therefore, provides an appropriate framework for the analysis of physiological phenotypes and can be used to infer the microevolutionary processes that have shaped patterns of trait variation within and among species. In cases where specific genes are known to contribute to variation in physiological traits, analyses of intraspecific polymorphism and interspecific divergence can reveal molecular mechanisms of functional evolution and can provide insights into the possible adaptive significance of observed sequence changes. In this review, we explain how the tools and theory of quantitative genetics, population genetics, and molecular evolution can inform our understanding of mechanism and process in physiological evolution. For example, lab-based studies of polygenic inheritance can be integrated with field-based studies of trait variation and survivorship to measure selection in the wild, thereby providing direct insights into the adaptive significance of physiological variation. Analyses of quantitative genetic variation in selection experiments can be used to probe interrelationships among traits and the genetic basis of physiological trade-offs and constraints. We review approaches for characterizing the genetic architecture of physiological traits, including linkage mapping and association mapping, and systems approaches for dissecting intermediary steps in the chain of causation between genotype and phenotype. We also discuss the promise and limitations of population genomic approaches for inferring adaptation at specific loci. We end by highlighting the role of organismal physiology in the functional synthesis of evolutionary biology.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska;
| | - Jamie T Bridgham
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon
| | - Scott A Kelly
- Department of Zoology, Ohio Wesleyan University, Delaware, Ohio; and
| | - Theodore Garland
- Department of Biology, University of California, Riverside, Riverside, California
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45
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Evans TG. Considerations for the use of transcriptomics in identifying the ‘genes that matter’ for environmental adaptation. J Exp Biol 2015; 218:1925-35. [DOI: 10.1242/jeb.114306] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
ABSTRACT
Transcriptomics has emerged as a powerful approach for exploring physiological responses to the environment. However, like any other experimental approach, transcriptomics has its limitations. Transcriptomics has been criticized as an inappropriate method to identify genes with large impacts on adaptive responses to the environment because: (1) genes with large impacts on fitness are rare; (2) a large change in gene expression does not necessarily equate to a large effect on fitness; and (3) protein activity is most relevant to fitness, and mRNA abundance is an unreliable indicator of protein activity. In this review, these criticisms are re-evaluated in the context of recent systems-level experiments that provide new insight into the relationship between gene expression and fitness during environmental stress. In general, these criticisms remain valid today, and indicate that exclusively using transcriptomics to screen for genes that underlie environmental adaptation will overlook constitutively expressed regulatory genes that play major roles in setting tolerance limits. Standard practices in transcriptomic data analysis pipelines may also be limiting insight by prioritizing highly differentially expressed and conserved genes over those genes that undergo moderate fold-changes and cannot be annotated. While these data certainly do not undermine the continued and widespread use of transcriptomics within environmental physiology, they do highlight the types of research questions for which transcriptomics is best suited and the need for more gene functional analyses. Such information is pertinent at a time when transcriptomics has become increasingly tractable and many researchers may be contemplating integrating transcriptomics into their research programs.
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46
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Evans TG, Padilla-Gamiño JL, Kelly MW, Pespeni MH, Chan F, Menge BA, Gaylord B, Hill TM, Russell AD, Palumbi SR, Sanford E, Hofmann GE. Ocean acidification research in the 'post-genomic' era: Roadmaps from the purple sea urchin Strongylocentrotus purpuratus. Comp Biochem Physiol A Mol Integr Physiol 2015; 185:33-42. [PMID: 25773301 DOI: 10.1016/j.cbpa.2015.03.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/07/2015] [Accepted: 03/08/2015] [Indexed: 01/26/2023]
Abstract
Advances in nucleic acid sequencing technology are removing obstacles that historically prevented use of genomics within ocean change biology. As one of the first marine calcifiers to have its genome sequenced, purple sea urchins (Strongylocentrotus purpuratus) have been the subject of early research exploring genomic responses to ocean acidification, work that points to future experiments and illustrates the value of expanding genomic resources to other marine organisms in this new 'post-genomic' era. This review presents case studies of S. purpuratus demonstrating the ability of genomic experiments to address major knowledge gaps within ocean acidification. Ocean acidification research has focused largely on species vulnerability, and studies exploring mechanistic bases of tolerance toward low pH seawater are comparatively few. Transcriptomic responses to high pCO₂ seawater in a population of urchins already encountering low pH conditions have cast light on traits required for success in future oceans. Secondly, there is relatively little information on whether marine organisms possess the capacity to adapt to oceans progressively decreasing in pH. Genomics offers powerful methods to investigate evolutionary responses to ocean acidification and recent work in S. purpuratus has identified genes under selection in acidified seawater. Finally, relatively few ocean acidification experiments investigate how shifts in seawater pH combine with other environmental factors to influence organism performance. In S. purpuratus, transcriptomics has provided insight into physiological responses of urchins exposed simultaneously to warmer and more acidic seawater. Collectively, these data support that similar breakthroughs will occur as genomic resources are developed for other marine species.
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Affiliation(s)
- Tyler G Evans
- Department of Biological Sciences, California State University East Bay, Hayward, CA 94542, USA.
| | | | - Morgan W Kelly
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Melissa H Pespeni
- Department of Biology, University of Vermont, Burlington, VT 05405, USA
| | - Francis Chan
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331-2914, USA
| | - Bruce A Menge
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331-2914, USA
| | - Brian Gaylord
- Department of Evolution and Ecology and Bodega Marine Laboratory, University of California Davis, Bodega Bay, CA 94923, USA
| | - Tessa M Hill
- Department of Geology and Bodega Marine Laboratory, University of California Davis, Bodega Bay, CA 94923, USA
| | - Ann D Russell
- Department of Geology, University of California Davis, Davis, CA 95616, USA
| | - Stephen R Palumbi
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950, USA
| | - Eric Sanford
- Department of Evolution and Ecology and Bodega Marine Laboratory, University of California Davis, Bodega Bay, CA 94923, USA
| | - Gretchen E Hofmann
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106-9620, USA
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47
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Porcelli D, Butlin RK, Gaston KJ, Joly D, Snook RR. The environmental genomics of metazoan thermal adaptation. Heredity (Edinb) 2015; 114:502-14. [PMID: 25735594 PMCID: PMC4815515 DOI: 10.1038/hdy.2014.119] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 11/06/2014] [Accepted: 11/11/2014] [Indexed: 01/07/2023] Open
Abstract
Continued and accelerating change in the thermal environment places an ever-greater priority on understanding how organisms are going to respond. The paradigm of ‘move, adapt or die', regarding ways in which organisms can respond to environmental stressors, stimulates intense efforts to predict the future of biodiversity. Assuming that extinction is an unpalatable outcome, researchers have focussed attention on how organisms can shift in their distribution to stay in the same thermal conditions or can stay in the same place by adapting to a changing thermal environment. How likely these respective outcomes might be depends on the answer to a fundamental evolutionary question, namely what genetic changes underpin adaptation to the thermal environment. The increasing access to and decreasing costs of next-generation sequencing (NGS) technologies, which can be applied to both model and non-model systems, provide a much-needed tool for understanding thermal adaptation. Here we consider broadly what is already known from non-NGS studies about thermal adaptation, then discuss the benefits and challenges of different NGS methodologies to add to this knowledge base. We then review published NGS genomics and transcriptomics studies of thermal adaptation to heat stress in metazoans and compare these results with previous non-NGS patterns. We conclude by summarising emerging patterns of genetic response and discussing future directions using these increasingly common techniques.
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Affiliation(s)
- D Porcelli
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - R K Butlin
- 1] Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK [2] Sven Lovén Centre-Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - K J Gaston
- Environment and Sustainability Institute, University of Exeter, Penryn, UK
| | - D Joly
- 1] Laboratoire Evolution, Génomes et Spéciation, CNRS-UPR 9034, Gif sur Yvette, France [2] Université Paris-Sud, Orsay, France
| | - R R Snook
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
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48
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Alvarez M, Schrey AW, Richards CL. Ten years of transcriptomics in wild populations: what have we learned about their ecology and evolution? Mol Ecol 2015; 24:710-25. [PMID: 25604587 DOI: 10.1111/mec.13055] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 12/16/2014] [Accepted: 12/18/2014] [Indexed: 12/13/2022]
Abstract
Molecular ecology has moved beyond the use of a relatively small number of markers, often noncoding, and it is now possible to use whole-genome measures of gene expression with microarrays and RNAseq (i.e. transcriptomics) to capture molecular response to environmental challenges. While transcriptome studies are shedding light on the mechanistic basis of traits as complex as personality or physiological response to catastrophic events, these approaches are still challenging because of the required technical expertise, difficulties with analysis and cost. Still, we found that in the last 10 years, 575 studies used microarrays or RNAseq in ecology. These studies broadly address three questions that reflect the progression of the field: (i) How much variation in gene expression is there and how is it structured? (ii) How do environmental stimuli affect gene expression? (iii) How does gene expression affect phenotype? We discuss technical aspects of RNAseq and microarray technology, and a framework that leverages the advantages of both. Further, we highlight future directions of research, particularly related to moving beyond correlation and the development of additional annotation resources. Measuring gene expression across an array of taxa in ecological settings promises to enrich our understanding of ecology and genome function.
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Affiliation(s)
- Mariano Alvarez
- Department of Integrative Biology, University of South Florida, 4202 E. Fowler Avenue, Tampa, FL, 33620, USA
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49
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Stillman JH, Armstrong E. Genomics Are Transforming Our Understanding of Responses to Climate Change. Bioscience 2015. [DOI: 10.1093/biosci/biu219] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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50
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Brennan RS, Galvez F, Whitehead A. Reciprocal osmotic challenges reveal mechanisms of divergence in phenotypic plasticity in the killifish Fundulus heteroclitus. J Exp Biol 2015; 218:1212-22. [DOI: 10.1242/jeb.110445] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 02/16/2015] [Indexed: 12/12/2022]
Abstract
The killifish Fundulus heteroclitus is an estuarine species with broad physiological plasticity enabling acclimation to diverse stressors. Previous work suggests freshwater populations expanded their physiology to accommodate low salinity environments, however, it is unknown if this compromises their tolerance to high salinity. We employed a comparative approach to investigate the mechanisms of a derived freshwater phenotype and the fate of an ancestral euryhaline phenotype after invasion of a freshwater environment. We compared physiological and transcriptomic responses to high and low salinity stress in fresh and brackish water populations and found an enhanced plasticity to low salinity in the freshwater population coupled with a reduced ability to acclimate to high salinity. Transcriptomic data identified genes with a conserved common response, a conserved salinity dependent response, and responses associated with population divergence. Conserved common acclimation responses revealed stress responses and alterations in cell-cycle regulation as important mechanisms in the general osmotic response. Salinity-specific responses included the regulation of genes involved in ion transport, intracellular calcium, energetic processes, and cellular remodeling. Genes diverged between populations were primarily those showing salinity-specific expression and included those regulating polyamine homeostasis and cell cycle. Additionally, when populations were matched with their native salinity, expression patterns were consistent with the concept of “transcriptomic resilience,” suggesting local adaptation. These findings provide insight into the fate of a plastic phenotype after a shift in environmental salinity and help to reveal mechanisms allowing for euryhalinity.
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Affiliation(s)
- Reid S. Brennan
- Department of Environmental Toxicology, University of California-Davis, California, 95616, USA
| | - Fernando Galvez
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Andrew Whitehead
- Department of Environmental Toxicology, University of California-Davis, California, 95616, USA
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