1
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Imura K, Takeda A, Endo M, Funakoshi K. Innervation and osteoclast distribution in the inferior pharyngeal jaw of the cichlid Nile tilapia (Oreochromis niloticus). Anat Rec (Hoboken) 2024; 307:2139-2148. [PMID: 38183341 DOI: 10.1002/ar.25381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/05/2023] [Accepted: 12/21/2023] [Indexed: 01/08/2024]
Abstract
In addition to an oral jaw, cichlids have a pharyngeal jaw, which is used for crushing and processing captured prey. The teeth and morphology of the pharyngeal jaw bones adapt to changes in prey in response to changes in the growing environment. This study aimed to explore the possible involvement of the peripheral nervous system in remodeling the cichlid pharyngeal jaw by examining the innervation of the inferior pharyngeal jaw in the Nile tilapia, Oreochromis niloticus. Vagal innervation was identified in the Nile tilapia inferior pharyngeal jaw. Double staining with tartrate-resistant acid phosphatase and immunostaining with the neuronal markers, protein gene product 9.5, and acetylated tubulin, revealed that osteoclasts, which play an important role in remodeling, were distributed in the vicinity of the nerves and were in apposition with the nerve terminals. This contact between peripheral nerves and osteoclasts suggests that the peripheral nervous system may play a role in remodeling the inferior pharyngeal jaw in cichlids.
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Affiliation(s)
- Kosuke Imura
- Department of Neuroanatomy, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Akihito Takeda
- Department of Neuroanatomy, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Masato Endo
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Kengo Funakoshi
- Department of Neuroanatomy, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
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2
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Tetrault E, Aaronson B, Gilbert MC, Albertson RC. Foraging-induced craniofacial plasticity is associated with an early, robust and dynamic transcriptional response. Proc Biol Sci 2024; 291:20240215. [PMID: 38654651 PMCID: PMC11040245 DOI: 10.1098/rspb.2024.0215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/19/2024] [Indexed: 04/26/2024] Open
Abstract
Phenotypic plasticity is the ability of a single genotype to vary its phenotype in response to the environment. Plasticity of the skeletal system in response to mechanical input is widely studied, but the timing of its transcriptional regulation is not well understood. Here, we used the cichlid feeding apparatus to examine the transcriptional dynamics of skeletal plasticity over time. Using three closely related species that vary in their ability to remodel bone and a panel of 11 genes, including well-studied skeletal differentiation markers and newly characterized environmentally sensitive genes, we examined plasticity at one, two, four and eight weeks following the onset of alternate foraging challenges. We found that the plastic species exhibited environment-specific bursts in gene expression beginning at one week, followed by a sharp decline in levels, while the species with more limited plasticity exhibited consistently low levels of gene expression. This trend held across nearly all genes, suggesting that it is a hallmark of the larger plasticity regulatory network. We conclude that plasticity of the cichlid feeding apparatus is not the result of slowly accumulating gene expression difference over time, but rather is stimulated by early bursts of environment-specific gene expression followed by a return to homeostatic levels.
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Affiliation(s)
- Emily Tetrault
- Molecular and Cell Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Ben Aaronson
- Department of Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Michelle C. Gilbert
- Department of Biology, Pennsylvania State University, State College, PA 16802, USA
| | - R. Craig Albertson
- Department of Biology, University of Massachusetts, Amherst, MA 01003, USA
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3
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Lu K, Gong H, Yang D, Ye M, Fang Q, Zhang XY, Wu R. Genome-Wide Network Analysis of Above- and Below-Ground Co-growth in Populus euphratica. PLANT PHENOMICS (WASHINGTON, D.C.) 2024; 6:0131. [PMID: 38188223 PMCID: PMC10769449 DOI: 10.34133/plantphenomics.0131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 12/12/2023] [Indexed: 01/09/2024]
Abstract
Tree growth is the consequence of developmental interactions between above- and below-ground compartments. However, a comprehensive view of the genetic architecture of growth as a cohesive whole is poorly understood. We propose a systems biology approach for mapping growth trajectories in genome-wide association studies viewing growth as a complex (phenotypic) system in which above- and below-ground components (or traits) interact with each other to mediate systems behavior. We further assume that trait-trait interactions are controlled by a genetic system composed of many different interactive genes and integrate the Lotka-Volterra predator-prey model to dissect phenotypic and genetic systems into pleiotropic and epistatic interaction components by which the detailed genetic mechanism of above- and below-ground co-growth can be charted. We apply the approach to analyze linkage mapping data of Populus euphratica, which is the only tree species that can grow in the desert, and characterize several loci that govern how above- and below-ground growth is cooperated or competed over development. We reconstruct multilayer and multiplex genetic interactome networks for the developmental trajectories of each trait and their developmental covariation. Many significant loci and epistatic effects detected can be annotated to candidate genes for growth and developmental processes. The results from our model may potentially be useful for marker-assisted selection and genetic editing in applied tree breeding programs. The model provides a general tool to characterize a complete picture of pleiotropic and epistatic genetic architecture in growth traits in forest trees and any other organisms.
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Affiliation(s)
- Kaiyan Lu
- College of Science,
Beijing Forestry University, Beijing 100083, P. R. China
| | - Huiying Gong
- Center for Computational Biology, College of Biological Sciences and Technology,
Beijing Forestry University, Beijing 100083, P. R. China
| | - Dengcheng Yang
- Center for Computational Biology, College of Biological Sciences and Technology,
Beijing Forestry University, Beijing 100083, P. R. China
| | - Meixia Ye
- Center for Computational Biology, College of Biological Sciences and Technology,
Beijing Forestry University, Beijing 100083, P. R. China
| | - Qing Fang
- Faculty of Science,
Yamagata University, Yamagata 990, Japan
| | - Xiao-Yu Zhang
- College of Science,
Beijing Forestry University, Beijing 100083, P. R. China
| | - Rongling Wu
- Yanqi Lake BeijingInstitute of Mathematical Sciences and Applications, Beijing 101408, China
- Center for Computational Biology, College of Biological Sciences and Technology,
Beijing Forestry University, Beijing 100083, P. R. China
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4
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Schneider RF, Gunter HM, Salewski I, Woltering JM, Meyer A. Growth dynamics and molecular bases of evolutionary novel jaw extensions in halfbeaks and needlefishes (Beloniformes). Mol Ecol 2023; 32:5798-5811. [PMID: 37750351 DOI: 10.1111/mec.17143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 08/17/2023] [Accepted: 09/05/2023] [Indexed: 09/27/2023]
Abstract
Evolutionary novelties-derived traits without clear homology found in the ancestors of a lineage-may promote ecological specialization and facilitate adaptive radiations. Examples for such novelties include the wings of bats, pharyngeal jaws of cichlids and flowers of angiosperms. Belonoid fishes (flying fishes, halfbeaks and needlefishes) feature an astonishing diversity of extremely elongated jaw phenotypes with undetermined evolutionary origins. We investigate the development of elongated jaws in a halfbeak (Dermogenys pusilla) and a needlefish (Xenentodon cancila) using morphometrics, transcriptomics and in situ hybridization. We confirm that these fishes' elongated jaws are composed of distinct base and novel 'extension' portions. These extensions are morphologically unique to belonoids, and we describe the growth dynamics of both bases and extensions throughout early development in both studied species. From transcriptomic profiling, we deduce that jaw extension outgrowth is guided by populations of multipotent cells originating from the anterior tip of the dentary. These cells are shielded from differentiation, but proliferate and migrate anteriorly during the extension's allometric growth phase. Cells left behind at the tip leave the shielded zone and undergo differentiation into osteoblast-like cells, which deposit extracellular matrix with both bone and cartilage characteristics that mineralizes and thereby provides rigidity. Such bone has characteristics akin to histological observations on the elongated 'kype' process on lower jaws of male salmon, which may hint at common conserved regulatory underpinnings. Future studies will evaluate the molecular pathways that govern the anterior migration and proliferation of these multipotent cells underlying the belonoids' evolutionary novel jaw extensions.
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Affiliation(s)
- Ralf F Schneider
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Marine Ecology, GEOMAR, Kiel, Germany
| | - Helen M Gunter
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Inken Salewski
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Joost M Woltering
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
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5
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Levin B, Komarova A, Simonov E, Tiunov A, Levina M, Golubtsov A, Kondrashov F, Meyer A. Speciation and repeated origins of hypertrophied lips in parallel adaptive radiations of cyprinid fish from East Africa. Ecol Evol 2023; 13:e10523. [PMID: 37711500 PMCID: PMC10497736 DOI: 10.1002/ece3.10523] [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: 06/06/2023] [Revised: 08/24/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
The evolution of convergent phenotypes is one of the most interesting phenomena of repeated adaptive radiations. Here, we examined the repeated patterns of thick-lipped or "rubberlip" phenotype of cyprinid fish of the genus Labeobarbus discovered in riverine environments of the Ethiopian Highlands, East Africa. To test the adaptive value of thickened lips, identify the ecological niche of the thick-lipped ecomorphs, and test whether these ecomorphs are the products of adaptive divergence, we studied six sympatric pairs of ecomorphs with hypertrophied lips and the normal lip structure from different riverine basins. Trophic morphology, diet, stable isotope (δ15N and δ13C) signatures, as well as mtDNA markers and genome-wide SNP variation, were analyzed. Our results show that thick-lipped ecomorphs partition trophic resources with generalized ecomorphs in only one-half of the examined sympatric pairs despite the pronounced divergence in lip structure. In these thick-lipped ecomorphs that were trophically diverged, the data on their diet along with the elevated 15N values suggest an invertivorous specialization different from the basal omnivorous-detritivouros feeding mode of the generalized ecomorphs. Genetic data confirmed an independent and parallel origin of all six lipped ecomorphs. Yet, only one of those six thick-lipped ecomorphs had a notable genetic divergence with sympatric non-lipped ecomorphs based on nuclear SNPs data (F ST = 0.21). Sympatric pairs can be sorted by combinations of phenotypic, ecological, and genetic divergence from an ecologically non-functional mouth polymorphism via ecologically functional polymorphism to a matured speciation stage via divergent evolution.
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Affiliation(s)
- Boris Levin
- Papanin Institute for Biology of Inland WatersRussian Academy of SciencesYaroslavlRussia
- Zoological Institute of Russian Academy of SciencesSaint‐PetersburgRussia
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of SciencesMoscowRussia
| | - Aleksandra Komarova
- Papanin Institute for Biology of Inland WatersRussian Academy of SciencesYaroslavlRussia
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of SciencesMoscowRussia
| | - Evgeniy Simonov
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of SciencesMoscowRussia
| | - Alexei Tiunov
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of SciencesMoscowRussia
| | - Marina Levina
- Papanin Institute for Biology of Inland WatersRussian Academy of SciencesYaroslavlRussia
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of SciencesMoscowRussia
- Eco‐Analytical LaboratoryCherepovets State UniversityCherepovetsRussia
| | - Alexander Golubtsov
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of SciencesMoscowRussia
| | | | - Axel Meyer
- Department of BiologyUniversity of KonstanzKonstanzGermany
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6
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Tetrault E, Swenson J, Aaronson B, Marcho C, Albertson RC. The transcriptional state and chromatin landscape of cichlid jaw shape variation across species and environments. Mol Ecol 2023; 32:3922-3941. [PMID: 37160741 PMCID: PMC10524807 DOI: 10.1111/mec.16975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/17/2023] [Accepted: 04/24/2023] [Indexed: 05/11/2023]
Abstract
Adaptive phenotypes are shaped by a combination of genetic and environmental forces, but how they interact remains poorly understood. Here, we utilize the cichlid oral jaw apparatus to better understand these gene-by-environment effects. First, we employed RNA-seq in bony and ligamentous tissues important for jaw opening to identify differentially expressed genes between species and across foraging environments. We used two Lake Malawi species adapted to different foraging habitats along the pelagic-benthic ecomorphological axis. Our foraging treatments were designed to force animals to employ either suction or biting/scraping, which broadly mimic pelagic or benthic modes of feeding. We found a large number of differentially expressed genes between species, and while we identified relatively few differences between environments, species differences were far more pronounced when they were challenged with a pelagic versus benthic foraging mode. Expression data carried the signature of genetic assimilation, and implicated cell cycle regulation in shaping the jaw across species and environments. Next, we repeated the foraging experiment and performed ATAC-seq procedures on nuclei harvested from the same tissues. Cross-referencing results from both analyses revealed subsets of genes that were both differentially expressed and differentially accessible. This reduced dataset implicated notable candidate genes including the Hedgehog effector, KIAA0586 and the ETS transcription factor, etv4, which connects environmental stress and craniofacial morphogenesis. Taken together, these data provide novel insights into the epigenetic, genetic and cellular bases of species- and environment-specific bone shapes.
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Affiliation(s)
- Emily Tetrault
- Graduate Program in Molecular and Cell Biology, University of Massachusetts, Amherst MA, 01003, U.S.A
| | - John Swenson
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst MA, 01003, U.S.A
| | - Ben Aaronson
- Biology Department, University of Massachusetts, Amherst MA, 01003, U.S.A
| | - Chelsea Marcho
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst MA, 01003, U.S.A
| | - R. Craig Albertson
- Biology Department, University of Massachusetts, Amherst MA, 01003, U.S.A
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7
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Cai H, Des Marais DL. Revisiting regulatory coherence: accounting for temporal bias in plant gene co-expression analyses. THE NEW PHYTOLOGIST 2023; 238:16-24. [PMID: 36617750 DOI: 10.1111/nph.18720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Affiliation(s)
- Haoran Cai
- Department of Civil and Environmental Engineering, MIT, 15 Vassar St., Cambridge, MA, 02139, USA
| | - David L Des Marais
- Department of Civil and Environmental Engineering, MIT, 15 Vassar St., Cambridge, MA, 02139, USA
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8
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Island Tiger Snakes (Notechis scutatus) Gain a ‘Head Start’ in Life: How Both Phenotypic Plasticity and Evolution Underlie Skull Shape Differences. Evol Biol 2023. [DOI: 10.1007/s11692-022-09591-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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9
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Santos ME, Lopes JF, Kratochwil CF. East African cichlid fishes. EvoDevo 2023; 14:1. [PMID: 36604760 PMCID: PMC9814215 DOI: 10.1186/s13227-022-00205-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/29/2022] [Indexed: 01/06/2023] Open
Abstract
Cichlid fishes are a very diverse and species-rich family of teleost fishes that inhabit lakes and rivers of India, Africa, and South and Central America. Research has largely focused on East African cichlids of the Rift Lakes Tanganyika, Malawi, and Victoria that constitute the biodiversity hotspots of cichlid fishes. Here, we give an overview of the study system, research questions, and methodologies. Research on cichlid fishes spans many disciplines including ecology, evolution, physiology, genetics, development, and behavioral biology. In this review, we focus on a range of organismal traits, including coloration phenotypes, trophic adaptations, appendages like fins and scales, sensory systems, sex, brains, and behaviors. Moreover, we discuss studies on cichlid phylogenies, plasticity, and general evolutionary patterns, ranging from convergence to speciation rates and the proximate and ultimate mechanisms underlying these processes. From a methodological viewpoint, the last decade has brought great advances in cichlid fish research, particularly through the advent of affordable deep sequencing and advances in genetic manipulations. The ability to integrate across traits and research disciplines, ranging from developmental biology to ecology and evolution, makes cichlid fishes a fascinating research system.
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Affiliation(s)
- M. Emília Santos
- grid.5335.00000000121885934Department of Zoology, University of Cambridge, Cambridge, UK
| | - João F. Lopes
- grid.7737.40000 0004 0410 2071Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Claudius F. Kratochwil
- grid.7737.40000 0004 0410 2071Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
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10
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Ng ETH, Kinjo AR. Computational modelling of plasticity-led evolution. Biophys Rev 2022; 14:1359-1367. [PMID: 36659990 PMCID: PMC9842839 DOI: 10.1007/s12551-022-01018-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 11/10/2022] [Indexed: 12/23/2022] Open
Abstract
Plasticity-led evolution is a form of evolution where a change in the environment induces novel traits via phenotypic plasticity, after which the novel traits are genetically accommodated over generations under the novel environment. This mode of evolution is expected to resolve the problem of gradualism (i.e., evolution by the slow accumulation of mutations that induce phenotypic variation) implied by the Modern Evolutionary Synthesis, in the face of a large environmental change. While experimental works are essential for validating that plasticity-led evolution indeed happened, we need computational models to gain insight into its underlying mechanisms and make qualitative predictions. Such computational models should include the developmental process and gene-environment interactions in addition to genetics and natural selection. We point out that gene regulatory network models can incorporate all the above notions. In this review, we highlight results from computational modelling of gene regulatory networks that consolidate the criteria of plasticity-led evolution. Since gene regulatory networks are mathematically equivalent to artificial recurrent neural networks, we also discuss their analogies and discrepancies, which may help further understand the mechanisms underlying plasticity-led evolution.
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Affiliation(s)
- Eden Tian Hwa Ng
- Department of Mathematics, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE1410 Brunei Darussalam
| | - Akira R. Kinjo
- Department of Mathematics, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE1410 Brunei Darussalam
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11
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Carruthers M, Edgley DE, Saxon AD, Gabagambi NP, Shechonge A, Miska EA, Durbin R, Bridle JR, Turner GF, Genner MJ. Ecological Speciation Promoted by Divergent Regulation of Functional Genes Within African Cichlid Fishes. Mol Biol Evol 2022; 39:msac251. [PMID: 36376993 PMCID: PMC10101686 DOI: 10.1093/molbev/msac251] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Rapid ecological speciation along depth gradients has taken place repeatedly in freshwater fishes, yet molecular mechanisms facilitating such diversification are typically unclear. In Lake Masoko, an African crater lake, the cichlid Astatotilapia calliptera has diverged into shallow-littoral and deep-benthic ecomorphs with strikingly different jaw structures within the last 1,000 years. Using genome-wide transcriptome data, we explore two major regulatory transcriptional mechanisms, expression and splicing-QTL variants, and examine their contributions to differential gene expression underpinning functional phenotypes. We identified 7,550 genes with significant differential expression between ecomorphs, of which 5.4% were regulated by cis-regulatory expression QTLs, and 9.2% were regulated by cis-regulatory splicing QTLs. We also found strong signals of divergent selection on differentially expressed genes associated with craniofacial development. These results suggest that large-scale transcriptome modification plays an important role during early-stage speciation. We conclude that regulatory variants are important targets of selection driving ecologically relevant divergence in gene expression during adaptive diversification.
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Affiliation(s)
- Madeleine Carruthers
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
| | - Duncan E Edgley
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
| | - Andrew D Saxon
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
| | - Nestory P Gabagambi
- Tanzanian Fisheries Research Institute, Kyela Research
Centre, P.O. Box 98, Kyela, Mbeya, Tanzania
| | - Asilatu Shechonge
- Tanzanian Fisheries Research Institute, Dar es Salaam Research
Centre, P.O. Box 9750, Dar es Salaam, Tanzania
| | - Eric A Miska
- Wellcome/CRUK Gurdon Institute, University of Cambridge,
Cambridge CB2 1QN, United
Kingdom
- Department of Genetics, University of Cambridge,
Cambridge CB2 3EH, United
Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus,
Cambridge CB10 1SA, United Kingdom
| | - Richard Durbin
- Department of Genetics, University of Cambridge,
Cambridge CB2 3EH, United
Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus,
Cambridge CB10 1SA, United Kingdom
| | - Jon R Bridle
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
| | - George F Turner
- School of Natural Sciences, Bangor University,
Bangor, Wales LL57 2UW, United
Kingdom
| | - Martin J Genner
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
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12
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Zhao L, Yan H, Cheng L, He K, Liu Q, Luo J, Luo W, Zhang X, Yan T, Du Z, Li Z, Yang S. Metabolic response provides insights into the mechanism of adaption to hypoxia in largemouth bass (Micropterus salmoides) under intermittent hypoxic conditions. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 242:113957. [PMID: 35999769 DOI: 10.1016/j.ecoenv.2022.113957] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/02/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
In metabolism, molecular oxygen is a necessary substrate. Oxygen imbalances are linked to a variety of circumstances in the organism's homeostasis. Recently, the positive effects of hypoxia treatment in improving exercise ability and hypoxia tolerance have become a research focus. We explored the effects of intermittent hypoxia exposure (IHE, for one hour or three hours per day) on the hypoxia tolerance of largemouth bass in this study. The results showed that (1) IHE significantly reduced the LOEcrit (the critical O2 tension for loss of equilibrium) value of largemouth bass, indicating that its hypoxia tolerance was enhanced. (2) The level of oxidative stress in the liver decreased in the HH3 group (exposed to a hypoxic condition for 3 h per day) compared to HH1 group (exposed to a hypoxic condition for 1 h per day). (3) IHE reduced the content of lactic acid and enhanced the process of gluconeogenesis in the liver. (4) Importantly, lipid mobilization and fatty acid oxidation in the liver of largemouth bass were significantly enhanced during IHE. In short, the results of this study indicate that IHE can improve hypoxia tolerance by regulating the energy metabolism of largemouth bass.
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Affiliation(s)
- Liulan Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
| | - Haoxiao Yan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
| | - Liangshun Cheng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
| | - Kuo He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
| | - Qiao Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
| | - Jie Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
| | - Wei Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
| | - Xin Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
| | - Taiming Yan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
| | - Zongjun Du
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
| | - Zhiqiong Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
| | - Song Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
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13
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Tadmor E, Juravel K, Morin S, Santos-Garcia D. Evolved transcriptional responses and their trade-offs after long-term adaptation of Bemisia tabaci to a marginally-suitable host. Genome Biol Evol 2022; 14:6649882. [PMID: 35880721 PMCID: PMC9372648 DOI: 10.1093/gbe/evac118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2022] [Indexed: 11/14/2022] Open
Abstract
Although generalist insect herbivores can migrate and rapidly adapt to a broad range of host plants, they can face significant difficulties when accidentally migrating to novel and marginally-suitable hosts. What happens, both in performance and gene expression regulation, if these marginally-suitable hosts must be used for multiple generations before migration to a suitable host can take place, largely remains unknown. In this study, we established multigenerational colonies of the whitefly Bemisia tabaci, a generalist phloem-feeding species, adapted to a marginally-suitable host (habanero pepper) or an optimal host (cotton). We used reciprocal host tests to estimate the differences in performance of the populations on both hosts under optimal (30 oC) and mild-stressful (24 oC) temperature conditions, and documented the associated transcriptomic changes. The habanero pepper-adapted population greatly improved its performance on habanero pepper but did not reach its performance level on cotton, the original host. It also showed reduced performance on cotton, relative to the non-adapted population, and an antagonistic effect of the lower-temperature stressor. The transcriptomic data revealed that most of the expression changes, associated with long-term adaptation to habanero pepper, can be categorized as "evolved" with no initial plastic response. Three molecular functions dominated: enhanced formation of cuticle structural constituents, enhanced activity of oxidation-reduction processes involved in neutralization of phytotoxins and reduced production of proteins from the cathepsin B family. Taken together, these findings indicate that generalist insects can adapt to novel host plants by modifying the expression of a relatively small set of specific molecular functions.
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Affiliation(s)
- Ella Tadmor
- Department of Entomology, the Hebrew University of Jerusalem, Rehovot, Israel
| | - Ksenia Juravel
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agricultural, Food & Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shai Morin
- Department of Entomology, the Hebrew University of Jerusalem, Rehovot, Israel
| | - Diego Santos-Garcia
- Laboratory of Biometry and Evolutionary Biology University Lyon 1 - UMR CNRS 5558, Villeurbanne, France
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14
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Singh P, Irisarri I, Torres-Dowdall J, Thallinger GG, Svardal H, Lemmon EM, Lemmon AR, Koblmüller S, Meyer A, Sturmbauer C. Phylogenomics of trophically diverse cichlids disentangles processes driving adaptive radiation and repeated trophic transitions. Ecol Evol 2022; 12:e9077. [PMID: 35866021 PMCID: PMC9288888 DOI: 10.1002/ece3.9077] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 05/28/2022] [Accepted: 05/31/2022] [Indexed: 11/12/2022] Open
Abstract
Cichlid fishes of the tribe Tropheini are a striking case of adaptive radiation, exemplifying multiple trophic transitions between herbivory and carnivory occurring in sympatry with other established cichlid lineages. Tropheini evolved highly specialized eco-morphologies to exploit similar trophic niches in different ways repeatedly and rapidly. To better understand the evolutionary history and trophic adaptations of this lineage, we generated a dataset of 532 targeted loci from 21 out of the 22 described Tropheini species. We resolved the Tropheini into seven monophyletic genera and discovered one to be polyphyletic. The polyphyletic genus, Petrochromis, represents three convergent origins of the algae grazing trophic specialization. This repeated evolution of grazing may have been facilitated by adaptive introgression as we found evidence for gene flow among algae grazing genera. We also found evidence of gene flow among algae browsing genera, but gene flow was restricted between herbivorous and carnivorous genera. Furthermore, we observed no evidence supporting a hybrid origin of this radiation. Our molecular evolutionary analyses suggest that opsin genes likely evolved in response to selection pressures associated with trophic ecology in the Tropheini. We found surprisingly little evidence of positive selection in coding regions of jaw-shaping genes in this trophically diverse lineage. This suggests low degrees of freedom for further change in these genes, and possibly a larger role for regulatory variation in driving jaw adaptations. Our study emphasizes Tropheini cichlids as an important model for studying the evolution of trophic specialization and its role in speciation.
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Affiliation(s)
- Pooja Singh
- Institute of Biology University of Graz Graz Austria.,Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology University of Konstanz Constance Germany.,Institute of Ecology and Evolution University of Bern Bern Switzerland
| | - Iker Irisarri
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology University of Konstanz Constance Germany.,Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Museum Hamburg Hamburg Germany
| | - Julián Torres-Dowdall
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology University of Konstanz Constance Germany
| | - Gerhard G Thallinger
- Institute of Biomedical Informatics Graz University of Technology Graz Austria.,OMICS Center Graz, BioTechMed Graz Graz Austria
| | - Hannes Svardal
- Department of Biology University of Antwerp Antwerp Belgium.,Naturalis Biodiversity Center Leiden The Netherlands
| | - Emily Moriarty Lemmon
- Department of Biological Science Florida State University, Biomedical Research Facility Tallahassee Florida USA
| | - Alan R Lemmon
- Department of Biological Science Florida State University, Biomedical Research Facility Tallahassee Florida USA
| | | | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology University of Konstanz Constance Germany
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15
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Abouheif E. My road to the ants: A model clade for eco-evo-devo. Curr Top Dev Biol 2022; 147:231-290. [PMID: 35337451 DOI: 10.1016/bs.ctdb.2022.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
This chapter is the story of how I pioneered ants as a system for studying eco-evo-devo, a field that integrates developmental biology with ecology and evolutionary biology. One aim of eco-evo-devo is to understand how the interactions between genes and their environments during development facilitates the origin and evolution of novel phenotypes. In a series of six parts, I review some of the key discoveries from my lab on how novel worker caste systems in ants--soldiers and supersoldiers--originated and evolved. I also discuss some of the ideas that emerged from these discoveries, including the role that polyphenisms, hidden developmental potentials, and rudimentary organs play in facilitating developmental and evolutionary change. As superorganisms, I argue that ants are uniquely positioned to reveal types of variation that are often difficult to observe in nature. In doing so, they have the potential to transform our view of biology and provide new perspectives in medicine, agriculture, and biodiversity conservation. With my story I hope to inspire the next generation of biologists to continue exploring the unknown regions of phenotypic space to solve some of our most pressing societal challenges.
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Affiliation(s)
- Ehab Abouheif
- Department of Biology, McGill University, Montreal, QC, Canada.
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16
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Vandermeulen MD, Cullen PJ. Gene by Environment Interactions reveal new regulatory aspects of signaling network plasticity. PLoS Genet 2022; 18:e1009988. [PMID: 34982769 PMCID: PMC8759647 DOI: 10.1371/journal.pgen.1009988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 01/14/2022] [Accepted: 12/09/2021] [Indexed: 11/18/2022] Open
Abstract
Phenotypes can change during exposure to different environments through the regulation of signaling pathways that operate in integrated networks. How signaling networks produce different phenotypes in different settings is not fully understood. Here, Gene by Environment Interactions (GEIs) were used to explore the regulatory network that controls filamentous/invasive growth in the yeast Saccharomyces cerevisiae. GEI analysis revealed that the regulation of invasive growth is decentralized and varies extensively across environments. Different regulatory pathways were critical or dispensable depending on the environment, microenvironment, or time point tested, and the pathway that made the strongest contribution changed depending on the environment. Some regulators even showed conditional role reversals. Ranking pathways' roles across environments revealed an under-appreciated pathway (OPI1) as the single strongest regulator among the major pathways tested (RAS, RIM101, and MAPK). One mechanism that may explain the high degree of regulatory plasticity observed was conditional pathway interactions, such as conditional redundancy and conditional cross-pathway regulation. Another mechanism was that different pathways conditionally and differentially regulated gene expression, such as target genes that control separate cell adhesion mechanisms (FLO11 and SFG1). An exception to decentralized regulation of invasive growth was that morphogenetic changes (cell elongation and budding pattern) were primarily regulated by one pathway (MAPK). GEI analysis also uncovered a round-cell invasion phenotype. Our work suggests that GEI analysis is a simple and powerful approach to define the regulatory basis of complex phenotypes and may be applicable to many systems.
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Affiliation(s)
- Matthew D. Vandermeulen
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, United States of America
| | - Paul J. Cullen
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, United States of America
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17
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Inferring multilayer interactome networks shaping phenotypic plasticity and evolution. Nat Commun 2021; 12:5304. [PMID: 34489412 PMCID: PMC8421358 DOI: 10.1038/s41467-021-25086-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023] Open
Abstract
Phenotypic plasticity represents a capacity by which the organism changes its phenotypes in response to environmental stimuli. Despite its pivotal role in adaptive evolution, how phenotypic plasticity is genetically controlled remains elusive. Here, we develop a unified framework for coalescing all single nucleotide polymorphisms (SNPs) from a genome-wide association study (GWAS) into a quantitative graph. This framework integrates functional genetic mapping, evolutionary game theory, and predator-prey theory to decompose the net genetic effect of each SNP into its independent and dependent components. The independent effect arises from the intrinsic capacity of a SNP, only expressed when it is in isolation, whereas the dependent effect results from the extrinsic influence of other SNPs. The dependent effect is conceptually beyond the traditional definition of epistasis by not only characterizing the strength of epistasis but also capturing the bi-causality of epistasis and the sign of the causality. We implement functional clustering and variable selection to infer multilayer, sparse, and multiplex interactome networks from any dimension of genetic data. We design and conduct two GWAS experiments using Staphylococcus aureus, aimed to test the genetic mechanisms underlying the phenotypic plasticity of this species to vancomycin exposure and Escherichia coli coexistence. We reconstruct the two most comprehensive genetic networks for abiotic and biotic phenotypic plasticity. Pathway analysis shows that SNP-SNP epistasis for phenotypic plasticity can be annotated to protein-protein interactions through coding genes. Our model can unveil the regulatory mechanisms of significant loci and excavate missing heritability from some insignificant loci. Our multilayer genetic networks provide a systems tool for dissecting environment-induced evolution.
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18
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Casasa S, Biddle JF, Koutsovoulos GD, Ragsdale EJ. Polyphenism of a Novel Trait Integrated Rapidly Evolving Genes into Ancestrally Plastic Networks. Mol Biol Evol 2021; 38:331-343. [PMID: 32931588 PMCID: PMC7826178 DOI: 10.1093/molbev/msaa235] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Developmental polyphenism, the ability to switch between phenotypes in response to environmental variation, involves the alternating activation of environmentally sensitive genes. Consequently, to understand how a polyphenic response evolves requires a comparative analysis of the components that make up environmentally sensitive networks. Here, we inferred coexpression networks for a morphological polyphenism, the feeding-structure dimorphism of the nematode Pristionchus pacificus. In this species, individuals produce alternative forms of a novel trait—moveable teeth, which in one morph enable predatory feeding—in response to environmental cues. To identify the origins of polyphenism network components, we independently inferred coexpression modules for more conserved transcriptional responses, including in an ancestrally nonpolyphenic nematode species. Further, through genome-wide analyses of these components across the nematode family (Diplogastridae) in which the polyphenism arose, we reconstructed how network components have changed. To achieve this, we assembled and resolved the phylogenetic context for five genomes of species representing the breadth of Diplogastridae and a hypothesized outgroup. We found that gene networks instructing alternative forms arose from ancestral plastic responses to environment, specifically starvation-induced metabolism and the formation of a conserved diapause (dauer) stage. Moreover, loci from rapidly evolving gene families were integrated into these networks with higher connectivity than throughout the rest of the P. pacificus transcriptome. In summary, we show that the modular regulatory outputs of a polyphenic response evolved through the integration of conserved plastic responses into networks with genes of high evolutionary turnover.
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Affiliation(s)
- Sofia Casasa
- Department of Biology, Indiana University, Bloomington, Bloomington, IN
| | - Joseph F Biddle
- Department of Biology, Indiana University, Bloomington, Bloomington, IN
| | | | - Erik J Ragsdale
- Department of Biology, Indiana University, Bloomington, Bloomington, IN
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19
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Hulsey CD, Meyer A, Streelman JT. Convergent Evolution of Cichlid Fish Pharyngeal Jaw Dentitions in Mollusk-Crushing Predators: Comparative X-Ray Computed Tomography of Tooth Sizes, Numbers, and Replacement. Integr Comp Biol 2021; 60:656-664. [PMID: 32584994 DOI: 10.1093/icb/icaa089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Dental convergence is a hallmark of cichlid fish adaptive radiations. This type of repeated evolution characterizes both the oral jaws of these fishes as well as their pharyngeal jaws that are modified gill arches used to functionally process prey like hard-shelled mollusks. To test several hypotheses regarding the evolution of cichlid crushing pharyngeal dentitions, we used X-ray computed tomography scans to comparatively examine dental evolution in the pharyngeal jaw of a diversity of New World Heroine cichlid lineages. The substantial variation in erupted tooth sizes and numbers as well as replacement teeth found in these fishes showed several general patterns. Larger toothed species tended to have fewer teeth suggesting a potential role of spatial constraints in cichlid dental divergence. Species with larger numbers of erupted pharyngeal teeth also had larger numbers of replacement teeth. Replacement tooth size is almost exactly predicted (r = 0.99) from the size of erupted teeth across all of the species. Mollusk crushing was, therefore, highly associated with not only larger pharyngeal teeth, but also larger replacement teeth. Whether dental divergence arises as a result of environmental induced plasticity or originates via trophic polymorphism as found in the species Herichthys minckleyi, there appear to be general rules that structure interspecific divergence in cichlid pharyngeal erupted and replacement dentitions.
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Affiliation(s)
- C Darrin Hulsey
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - J Todd Streelman
- School of Biological Sciences, Institute of Technology, Atlanta, GA 30332, USA
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20
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Karagic N, Meyer A, Hulsey CD. Phenotypic Plasticity in Vertebrate Dentitions. Integr Comp Biol 2021; 60:608-618. [PMID: 32544244 DOI: 10.1093/icb/icaa077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Vertebrates interact directly with food items through their dentition, and these interactions with trophic resources could often feedback to influence tooth structure. Although dentitions are often considered to be a fixed phenotype, there is the potential for environmentally induced phenotypic plasticity in teeth to extensively influence their diversity. Here, we review the literature concerning phenotypic plasticity of vertebrate teeth. Even though only a few taxonomically disparate studies have focused on phenotypic plasticity in teeth, there are a number of ways teeth can change their size, shape, or patterns of replacement as a response to the environment. Elucidating the underlying physiological, developmental, and genetic mechanisms that generate phenotypic plasticity can clarify its potential role in the evolution of dental phenotypes.
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Affiliation(s)
- Nidal Karagic
- Department for Zoology and Evolutionary Biology, University of Konstanz, Universitätsstraße 10, Konstanz, 78467, Germany
| | - Axel Meyer
- Department for Zoology and Evolutionary Biology, University of Konstanz, Universitätsstraße 10, Konstanz, 78467, Germany
| | - C Darrin Hulsey
- Department for Zoology and Evolutionary Biology, University of Konstanz, Universitätsstraße 10, Konstanz, 78467, Germany
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21
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Gene coexpression networks reveal molecular interactions underlying cichlid jaw modularity. BMC Ecol Evol 2021; 21:62. [PMID: 33888061 PMCID: PMC8061045 DOI: 10.1186/s12862-021-01787-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 04/08/2021] [Indexed: 12/29/2022] Open
Abstract
Background The oral and pharyngeal jaw of cichlid fishes are a classic example of evolutionary modularity as their functional decoupling boosted trophic diversification and contributed to the success of cichlid adaptive radiations. Most studies until now have focused on the functional, morphological, or genetic aspects of cichlid jaw modularity. Here we extend this concept to include transcriptional modularity by sequencing whole transcriptomes of the two jaws and comparing their gene coexpression networks. Results We show that transcriptional decoupling of gene expression underlies the functional decoupling of cichlid oral and pharyngeal jaw apparatus and the two units are evolving independently in recently diverged cichlid species from Lake Tanganyika. Oral and pharyngeal jaw coexpression networks reflect the common origin of the jaw regulatory program as there is high preservation of gene coexpression modules between the two sets of jaws. However, there is substantial rewiring of genetic architecture within those modules. We define a global jaw coexpression network and highlight jaw-specific and species-specific modules within it. Furthermore, we annotate a comprehensive in silico gene regulatory network linking the Wnt and AHR signalling pathways to jaw morphogenesis and response to environmental cues, respectively. Components of these pathways are significantly differentially expressed between the oral and pharyngeal jaw apparatus. Conclusion This study describes the concerted expression of many genes in cichlid oral and pharyngeal jaw apparatus at the onset of the independent life of cichlid fishes. Our findings suggest that – on the basis of an ancestral gill arch network—transcriptional rewiring may have driven the modular evolution of the oral and pharyngeal jaws, highlighting the evolutionary significance of gene network reuse. The gene coexpression and in silico regulatory networks presented here are intended as resource for future studies on the genetics of vertebrate jaw morphogenesis and trophic adaptation. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01787-9.
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22
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Karagic N, Schneider RF, Meyer A, Hulsey CD. A Genomic Cluster Containing Novel and Conserved Genes is Associated with Cichlid Fish Dental Developmental Convergence. Mol Biol Evol 2021; 37:3165-3174. [PMID: 32579214 DOI: 10.1093/molbev/msaa153] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The two toothed jaws of cichlid fishes provide textbook examples of convergent evolution. Tooth phenotypes such as enlarged molar-like teeth used to process hard-shelled mollusks have evolved numerous times independently during cichlid diversification. Although the ecological benefit of molar-like teeth to crush prey is known, it is unclear whether the same molecular mechanisms underlie these convergent traits. To identify genes involved in the evolution and development of enlarged cichlid teeth, we performed RNA-seq on the serially homologous-toothed oral and pharyngeal jaws as well as the fourth toothless gill arch of Astatoreochromis alluaudi. We identified 27 genes that are highly upregulated on both tooth-bearing jaws compared with the toothless gill arch. Most of these genes have never been reported to play a role in tooth formation. Two of these genes (unk, rpfA) are not found in other vertebrate genomes but are present in all cichlid genomes. They also cluster genomically with two other highly expressed tooth genes (odam, scpp5) that exhibit conserved expression during vertebrate odontogenesis. Unk and rpfA were confirmed via in situ hybridization to be expressed in developing teeth of Astatotilapia burtoni. We then examined expression of the cluster's four genes in six evolutionarily independent and phylogenetically disparate cichlid species pairs each with a large- and a small-toothed species. Odam and unk commonly and scpp5 and rpfA always showed higher expression in larger toothed cichlid jaws. Convergent trophic adaptations across cichlid diversity are associated with the repeated developmental deployment of this genomic cluster containing conserved and novel cichlid-specific genes.
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Affiliation(s)
- Nidal Karagic
- Department for Zoology and Evolutionary Biology, University of Konstanz, Konstanz, Germany
| | - Ralf F Schneider
- Department for Zoology and Evolutionary Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Department for Zoology and Evolutionary Biology, University of Konstanz, Konstanz, Germany
| | - C Darrin Hulsey
- Department for Zoology and Evolutionary Biology, University of Konstanz, Konstanz, Germany
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23
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Liedtke HC, Harney E, Gomez-Mestre I. Cross-species transcriptomics uncovers genes underlying genetic accommodation of developmental plasticity in spadefoot toads. Mol Ecol 2021; 30:2220-2234. [PMID: 33730392 DOI: 10.1111/mec.15883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/29/2021] [Accepted: 02/26/2021] [Indexed: 10/21/2022]
Abstract
That hardcoded genomes can manifest as plastic phenotypes responding to environmental perturbations is a fascinating feature of living organisms. How such developmental plasticity is regulated at the molecular level is beginning to be uncovered aided by the development of -omic techniques. Here, we compare the transcriptome-wide responses of two species of spadefoot toads with differing capacity for developmental acceleration of their larvae in the face of a shared environmental risk: pond drying. By comparing gene expression profiles over time and performing cross-species network analyses, we identified orthologues and functional gene pathways whose environmental sensitivity in expression have diverged between species. Genes related to lipid, cholesterol and steroid biosynthesis and metabolism make up most of a module of genes environmentally responsive in one species, but canalized in the other. The evolutionary changes in the regulation of the genes identified through these analyses may have been key in the genetic accommodation of developmental plasticity in this system.
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Affiliation(s)
- Hans Christoph Liedtke
- Ecology, Evolution and Development Group, Department of Wetland Ecology, Estación Biológica de Doñana, CSIC, Seville, Spain
| | - Ewan Harney
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Ivan Gomez-Mestre
- Ecology, Evolution and Development Group, Department of Wetland Ecology, Estación Biológica de Doñana, CSIC, Seville, Spain
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24
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Venney CJ, Wellband KW, Heath DD. Rearing environment affects the genetic architecture and plasticity of DNA methylation in Chinook salmon. Heredity (Edinb) 2021; 126:38-49. [PMID: 32699390 PMCID: PMC7852867 DOI: 10.1038/s41437-020-0346-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 02/07/2023] Open
Abstract
Genetic architecture and phenotypic plasticity are important considerations when studying trait variation within and among populations. Since environmental change can induce shifts in the genetic architecture and plasticity of traits, it is important to consider both genetic and environmental sources of phenotypic variation. While there is overwhelming evidence for environmental effects on phenotype, the underlying mechanisms are less clear. Variation in DNA methylation is a potential mechanism mediating environmental effects on phenotype due to its sensitivity to environmental stimuli, transgenerational inheritance, and influences on transcription. To characterize the effect of environment on methylation, we created two 6 × 6 (North Carolina II) Chinook salmon breeding crosses and reared the offspring in two environments: uniform hatchery tanks and seminatural stream channels. We sampled the fish twice during development, at the alevin (larval) and fry (juvenile) stages. We measured DNA methylation at 13 genes using a PCR-based bisulfite sequencing protocol. The genetic architecture of DNA methylation differed between rearing environments, with greater additive and nonadditive genetic variance in hatchery fish and greater maternal effects in seminatural channel fish, though gene-specific variation was evident. We observed plasticity in methylation across all assayed genes, as well as gene-specific effects at two genes in alevin and six genes in fry, indicating developmental stage-specific effects of rearing environment on methylation. Characterizing genetic and environmental influences on methylation is critical for future studies on DNA methylation as a potential mechanism for acclimation and adaptation.
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Affiliation(s)
- Clare J Venney
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Ave, Windsor, ON, N9B 3P4, Canada
| | - Kyle W Wellband
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Ave, Windsor, ON, N9B 3P4, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Québec City, QC, Canada
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Ave, Windsor, ON, N9B 3P4, Canada.
- Department of Integrative Biology, University of Windsor, 401 Sunset Ave, Windsor, ON, N9B 3P4, Canada.
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25
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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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26
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Jiang L, Griffin CH, Wu R. SEGN: Inferring real-time gene networks mediating phenotypic plasticity. Comput Struct Biotechnol J 2020; 18:2510-2521. [PMID: 33005313 PMCID: PMC7516210 DOI: 10.1016/j.csbj.2020.08.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 08/27/2020] [Accepted: 08/29/2020] [Indexed: 12/13/2022] Open
Abstract
The capacity of an organism to alter its phenotype in response to environmental perturbations changes over developmental time and is a process determined by multiple genes that are co-expressed in intricate but organized networks. Characterizing the spatiotemporal change of such gene networks can offer insight into the genomic signatures underlying organismic adaptation, but it represents a major methodological challenge. Here, we integrate the holistic view of systems biology and the interactive notion of evolutionary game theory to reconstruct so-called systems evolutionary game networks (SEGN) that can autonomously detect, track, and visualize environment-induced gene networks along the time axis. The SEGN overcomes the limitations of traditional approaches by inferring context-specific networks, encapsulating bidirectional, signed, and weighted gene-gene interactions into fully informative networks, and monitoring the process of how networks topologically alter across environmental and developmental cues. Based on the design principle of SEGN, we perform a transcriptional plasticity study by culturing Euphrates poplar, a tree that can grow in the saline desert, in saline-free and saline-stress conditions. SEGN characterize previously unknown gene co-regulation that modulates the time trajectories of the trees' response to salt stress. As a marriage of multiple disciplines, SEGN shows its potential to interpret gene interdependence, predict how transcriptional co-regulation responds to various regimes, and provides a hint for exploring the mass, energetic, or signal basis that drives various types of gene interactions.
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Affiliation(s)
- Libo Jiang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Christopher H. Griffin
- Applied Research Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
| | - Rongling Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Center for Statistical Genetics, Departments of Public Health Sciences and Statistics, The Pennsylvania State University, Hershey, PA 17033, USA
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Abstract
Phenotypic plasticity describes the ability of a given genotype to produce different phenotypes in response to distinct environmental conditions. It has major implications in agronomy, animal husbandry and medicine and is also thought to facilitate evolution. Phenotypic plasticity is widely observed in the wild. It is only relatively recently that the mechanisms involved in phenotypic plasticity have been analysed. Thanks to laboratory experiments we understand better how environmental conditions are involved in phenotypic variations. This article introduces major concepts from the phenotypic plasticity field, presents briefly mechanisms involved in phenotypic plasticity and discusses the links between phenotypic plasticity and evolution.
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Affiliation(s)
- Jean-Michel Gibert
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), UMR7622, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement (IBPS-LBD), 75005 Paris, France
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28
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Hedgehog signaling is necessary and sufficient to mediate craniofacial plasticity in teleosts. Proc Natl Acad Sci U S A 2020; 117:19321-19327. [PMID: 32719137 PMCID: PMC7431006 DOI: 10.1073/pnas.1921856117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Phenotypic plasticity has emerged as an important concept in evolutionary biology. It is thought to contribute to an organism’s ability to adapt to environmental change within a single generation, which may facilitate survival and increase fitness. Furthermore, plasticity has the potential to bias the direction and/or speed of evolution by changing patterns of phenotypic variation and exposing new genetic variation to selection (i.e., flexible stem evolution). Our understanding of this important phenomenon is incomplete owing to limited knowledge of the molecular underpinnings of reaction norm evolution. Using the teleost feeding apparatus as a model, we explore this open question and show that the Hh signaling pathway underlies the ability of this structure to respond plastically to alternate feeding regimes. Phenotypic plasticity, the ability of a single genotype to produce multiple phenotypes under different environmental conditions, is critical for the origins and maintenance of biodiversity; however, the genetic mechanisms underlying plasticity as well as how variation in those mechanisms can drive evolutionary change remain poorly understood. Here, we examine the cichlid feeding apparatus, an icon of both prodigious evolutionary divergence and adaptive phenotypic plasticity. We first provide a tissue-level mechanism for plasticity in craniofacial shape by measuring rates of bone deposition within functionally salient elements of the feeding apparatus in fishes forced to employ alternate foraging modes. We show that levels and patterns of phenotypic plasticity are distinct among closely related cichlid species, underscoring the evolutionary potential of this trait. Next, we demonstrate that hedgehog (Hh) signaling, which has been implicated in the evolutionary divergence of cichlid feeding architecture, is associated with environmentally induced rates of bone deposition. Finally, to demonstrate that Hh levels are the cause of the plastic response and not simply the consequence of producing more bone, we use transgenic zebrafish in which Hh levels could be experimentally manipulated under different foraging conditions. Notably, we find that the ability to modulate bone deposition rates in different environments is dampened when Hh levels are reduced, whereas the sensitivity of bone deposition to different mechanical demands increases with elevated Hh levels. These data advance a mechanistic understanding of phenotypic plasticity in the teleost feeding apparatus and in doing so contribute key insights into the origins of adaptive morphological radiations.
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29
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Ahi EP, Duenser A, Singh P, Gessl W, Sturmbauer C. Appetite regulating genes may contribute to herbivory versus carnivory trophic divergence in haplochromine cichlids. PeerJ 2020; 8:e8375. [PMID: 31998557 PMCID: PMC6977467 DOI: 10.7717/peerj.8375] [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: 07/16/2019] [Accepted: 12/09/2019] [Indexed: 12/14/2022] Open
Abstract
Feeding is a complex behaviour comprised of satiety control, foraging, ingestion and subsequent digestion. Cichlids from the East African Great Lakes are renowned for their diverse trophic specializations, largely predicated on highly variable jaw morphologies. Thus, most research has focused on dissecting the genetic, morphological and regulatory basis of jaw and teeth development in these species. Here for the first time we explore another aspect of feeding, the regulation of appetite related genes that are expressed in the brain and control satiety in cichlid fishes. Using qPCR analysis, we first validate stably expressed reference genes in the brain of six haplochromine cichlid species at the end of larval development prior to foraging. We next evaluate the expression of 16 appetite related genes in herbivorous and carnivorous species from the parallel radiations of Lake Tanganyika, Malawi and Victoria. Interestingly, we find increased expression of two appetite-regulating genes (anorexigenic genes), cart and npy2r, in the brain of carnivorous species in all the three lakes. This supports the notion that appetite gene regulation might play a part in determining trophic niche specialization in divergent cichlid species, already prior to exposure to different diets. Our study contributes to the limited body of knowledge on the neurological circuitry that controls feeding transitions and adaptations in cichlids and other teleosts.
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Affiliation(s)
- Ehsan P. Ahi
- Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Institute of Biology, University of Graz, Graz, Austria
| | - Anna Duenser
- Institute of Biology, University of Graz, Graz, Austria
| | - Pooja Singh
- Institute of Biology, University of Graz, Graz, Austria
- Institute of Biological Sciences, University of Calgary, Calgary, Canada
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30
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Fruciano C, Meyer A, Franchini P. Divergent Allometric Trajectories in Gene Expression and Coexpression Produce Species Differences in Sympatrically Speciating Midas Cichlid Fish. Genome Biol Evol 2019; 11:1644-1657. [PMID: 31124568 PMCID: PMC6563553 DOI: 10.1093/gbe/evz108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2019] [Indexed: 12/19/2022] Open
Abstract
The mechanisms of speciation without geographic isolation (i.e., sympatric speciation) remain debated. This is due in part to the fact that the genomic landscape that could promote or hinder species divergence in the presence of gene flow is still largely unknown. However, intensive research is now centered on understanding the genetic architecture of adaptive traits associated with this process as well as how gene expression might affect these traits. Here, using RNA-Seq data, we investigated gene expression of sympatrically speciating benthic and limnetic Neotropical cichlid fishes at two developmental stages. First, we identified groups of coexpressed genes (modules) at each stage. Although there are a few large and well-preserved modules, most of the other modules are not preserved across life stages. Second, we show that later in development more and larger coexpression modules are associated with divergence between benthic and limnetic fish compared with the earlier life stage. This divergence between benthic and limnetic fish in coexpression mirrors divergence in overall expression between benthic and limnetic fish, which is more pronounced later in life. Our results reveal that already at 1-day posthatch benthic and limnetic fish diverge in (co)expression, and that this divergence becomes more substantial when fish are free-swimming but still unlikely to have divergent swimming and feeding habits. More importantly, our study describes how the coexpression of several genes through development, as opposed to individual genes, is associated with benthic–limnetic species differences, and how two morphogenetic trajectories diverge as fish grow older.
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Affiliation(s)
- Carmelo Fruciano
- Department of Biology, University of Konstanz, Germany.,Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS UMR 8197, Paris, France
| | - Axel Meyer
- Department of Biology, University of Konstanz, Germany
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31
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Xiong P, Schneider RF, Hulsey CD, Meyer A, Franchini P. Conservation and novelty in the microRNA genomic landscape of hyperdiverse cichlid fishes. Sci Rep 2019; 9:13848. [PMID: 31554838 PMCID: PMC6761260 DOI: 10.1038/s41598-019-50124-0] [Citation(s) in RCA: 15] [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: 06/13/2019] [Accepted: 09/05/2019] [Indexed: 12/23/2022] Open
Abstract
MicroRNAs (miRNAs) play crucial roles in the post-transcriptional control of messenger RNA (mRNA). These miRNA-mRNA regulatory networks are present in nearly all organisms and contribute to development, phenotypic divergence, and speciation. To examine the miRNA landscape of cichlid fishes, one of the most species-rich families of vertebrates, we profiled the expression of both miRNA and mRNA in a diverse set of cichlid lineages. Among these, we found that conserved miRNAs differ from recently arisen miRNAs (i.e. lineage specific) in average expression levels, number of target sites, sequence variability, and physical clustering patterns in the genome. Furthermore, conserved miRNA target sites tend to be enriched at the 5' end of protein-coding gene 3' UTRs. Consistent with the presumed regulatory role of miRNAs, we detected more negative correlations between the expression of miRNA-mRNA functional pairs than in random pairings. Finally, we provide evidence that novel miRNA targets sites are enriched in genes involved in protein synthesis pathways. Our results show how conserved and evolutionarily novel miRNAs differ in their contribution to the genomic landscape and highlight their particular evolutionary roles in the adaptive diversification of cichlids.
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Affiliation(s)
- Peiwen Xiong
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Ralf F Schneider
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
- Marine Ecology, Helmholtz-Zentrum für Ozeanforschung Kiel (GEOMAR), 24105 Kiel, Germany
| | - C Darrin Hulsey
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Axel Meyer
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Paolo Franchini
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany.
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32
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Ahi EP, Singh P, Duenser A, Gessl W, Sturmbauer C. Divergence in larval jaw gene expression reflects differential trophic adaptation in haplochromine cichlids prior to foraging. BMC Evol Biol 2019; 19:150. [PMID: 31340758 PMCID: PMC6657104 DOI: 10.1186/s12862-019-1483-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 07/18/2019] [Indexed: 12/11/2022] Open
Abstract
Background Understanding how variation in gene expression contributes to morphological diversity is a major goal in evolutionary biology. Cichlid fishes from the East African Great lakes exhibit striking diversity in trophic adaptations predicated on the functional modularity of their two sets of jaws (oral and pharyngeal). However, the transcriptional basis of this modularity is not so well understood, as no studies thus far have directly compared the expression of genes in the oral and pharyngeal jaws. Nor is it well understood how gene expression may have contributed to the parallel evolution of trophic morphologies across the replicate cichlid adaptive radiations in Lake Tanganyika, Malawi and Victoria. Results We set out to investigate the role of gene expression divergence in cichlid fishes from these three lakes adapted to herbivorous and carnivorous trophic niches. We focused on the development stage prior to the onset of exogenous feeding that is critical for understanding patterns of gene expression after oral and pharyngeal jaw skeletogenesis, anticipating environmental cues. This framework permitted us for the first time to test for signatures of gene expression underlying jaw modularity in convergent eco-morphologies across three independent adaptive radiations. We validated a set of reference genes, with stable expression between the two jaw types and across species, which can be important for future studies of gene expression in cichlid jaws. Next we found evidence of modular and non-modular gene expression between the two jaws, across different trophic niches and lakes. For instance, prdm1a, a skeletogenic gene with modular anterior-posterior expression, displayed higher pharyngeal jaw expression and modular expression pattern only in carnivorous species. Furthermore, we found the expression of genes in cichlids jaws from the youngest Lake Victoria to exhibit low modularity compared to the older lakes. Conclusion Overall, our results provide cross-species transcriptional comparisons of modularly-regulated skeletogenic genes in the two jaw types, implicating expression differences which might contribute to the formation of divergent trophic morphologies at the stage of larval independence prior to foraging. Electronic supplementary material The online version of this article (10.1186/s12862-019-1483-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ehsan Pashay Ahi
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria. .,Evolutionary Biology Centre, Uppsala University, Norbyvägen 18A, 75236, Uppsala, Sweden.
| | - Pooja Singh
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria
| | - Anna Duenser
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria
| | - Wolfgang Gessl
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria
| | - Christian Sturmbauer
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria
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33
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Gidmark NJ, Pos K, Matheson B, Ponce E, Westneat MW. Functional Morphology and Biomechanics of Feeding in Fishes. FEEDING IN VERTEBRATES 2019. [DOI: 10.1007/978-3-030-13739-7_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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34
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Beck SV, Räsänen K, Ahi EP, Kristjánsson BK, Skúlason S, Jónsson ZO, Leblanc CA. Gene expression in the phenotypically plastic Arctic charr (Salvelinus alpinus): A focus on growth and ossification at early stages of development. Evol Dev 2018; 21:16-30. [PMID: 30474913 PMCID: PMC9285049 DOI: 10.1111/ede.12275] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Gene expression during development shapes the phenotypes of individuals. Although embryonic gene expression can have lasting effects on developmental trajectories, few studies consider the role of maternal effects, such as egg size, on gene expression. Using qPCR, we characterize relative expression of 14 growth and/or skeletal promoting genes across embryonic development in Arctic charr (Salvelinus alpinus). We test to what extent their relative expression is correlated with egg size and size at early life‐stages within the study population. We predict smaller individuals to have higher expression of growth and skeletal promoting genes, due to less maternal resources (i.e., yolk) and prioritization of energy toward ossification. We found expression levels to vary across developmental stages and only three genes (Mmp9, Star, and Sgk1) correlated with individual size at a given developmental stage. Contrary to our hypothesis, expression of Mmp9 and Star showed a non‐linear relationship with size (at post fertilization and hatching, respectively), whilst Sgk1 was higher in larger embryos at hatching. Interestingly, these genes are also associated with craniofacial divergence of Arctic charr morphs. Our results indicate that early life‐stage variation in gene expression, concomitant to maternal effects, can influence developmental plasticity and potentially the evolution of resource polymorphism in fishes.
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Affiliation(s)
- Samantha V Beck
- Department of Aquaculture and Fish Biology, Hólar University College, Háskólinn á Hólum, Sauðárkrókur, Iceland.,Institute of Life- and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Katja Räsänen
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.,Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Ehsan P Ahi
- Institute of Life- and Environmental Sciences, University of Iceland, Reykjavík, Iceland.,Institute of Zoology, University of Graz, Universitätsplatz 2, Graz, Austria
| | - Bjarni K Kristjánsson
- Department of Aquaculture and Fish Biology, Hólar University College, Háskólinn á Hólum, Sauðárkrókur, Iceland
| | - Skúli Skúlason
- Department of Aquaculture and Fish Biology, Hólar University College, Háskólinn á Hólum, Sauðárkrókur, Iceland
| | - Zophonías O Jónsson
- Institute of Life- and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Camille A Leblanc
- Department of Aquaculture and Fish Biology, Hólar University College, Háskólinn á Hólum, Sauðárkrókur, Iceland
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35
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Irisarri I, Singh P, Koblmüller S, Torres-Dowdall J, Henning F, Franchini P, Fischer C, Lemmon AR, Lemmon EM, Thallinger GG, Sturmbauer C, Meyer A. Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes. Nat Commun 2018; 9:3159. [PMID: 30089797 PMCID: PMC6082878 DOI: 10.1038/s41467-018-05479-9] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 05/30/2018] [Indexed: 11/21/2022] Open
Abstract
Lake Tanganyika is the oldest and phenotypically most diverse of the three East African cichlid fish adaptive radiations. It is also the cradle for the younger parallel haplochromine cichlid radiations in Lakes Malawi and Victoria. Despite its evolutionary significance, the relationships among the main Lake Tanganyika lineages remained unresolved, as did the general timescale of cichlid evolution. Here, we disentangle the deep phylogenetic structure of the Lake Tanganyika radiation using anchored phylogenomics and uncover hybridization at its base, as well as early in the haplochromine radiation. This suggests that hybridization might have facilitated these speciation bursts. Time-calibrated trees support that the radiation of Tanganyika cichlids coincided with lake formation and that Gondwanan vicariance concurred with the earliest splits in the cichlid family tree. Genes linked to key innovations show signals of introgression or positive selection following colonization of lake habitats and species' dietary adaptations are revealed as major drivers of colour vision evolution. These findings shed light onto the processes shaping the evolution of adaptive radiations.
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Affiliation(s)
- Iker Irisarri
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, Madrid, 28006, Spain
| | - Pooja Singh
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany
- Institute of Biology, University of Graz, Universitätsplatz 2, Graz, 8010, Austria
| | - Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz 2, Graz, 8010, Austria
| | - Julián Torres-Dowdall
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany
| | - Frederico Henning
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Ilha do Fundão, Rio de Janeiro, 21944-970, Brazil
| | - Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany
| | - Christoph Fischer
- Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14, Graz, 8010, Austria
- OMICS Center Graz, BioTechMed Graz, Stiftingtalstraße 24, Graz, 8010, Austria
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, 32306, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Biomedical Research Facility, Tallahassee, FL, 32306, USA
| | - Gerhard G Thallinger
- Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14, Graz, 8010, Austria
- OMICS Center Graz, BioTechMed Graz, Stiftingtalstraße 24, Graz, 8010, Austria
| | - Christian Sturmbauer
- Institute of Biology, University of Graz, Universitätsplatz 2, Graz, 8010, Austria.
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany.
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, 02138, MA, USA.
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36
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De Castro S, Peronnet F, Gilles JF, Mouchel-Vielh E, Gibert JM. bric à brac (bab), a central player in the gene regulatory network that mediates thermal plasticity of pigmentation in Drosophila melanogaster. PLoS Genet 2018; 14:e1007573. [PMID: 30067846 PMCID: PMC6089454 DOI: 10.1371/journal.pgen.1007573] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 08/13/2018] [Accepted: 07/19/2018] [Indexed: 01/28/2023] Open
Abstract
Drosophila body pigmentation has emerged as a major Evo-Devo model. Using two Drosophila melanogaster lines, Dark and Pale, selected from a natural population, we analyse here the interaction between genetic variation and environmental factors to produce this complex trait. Indeed, pigmentation varies with genotype in natural populations and is sensitive to temperature during development. We demonstrate that the bric à brac (bab) genes, that are differentially expressed between the two lines and whose expression levels vary with temperature, participate in the pigmentation difference between the Dark and Pale lines. The two lines differ in a bab regulatory sequence, the dimorphic element (called here bDE). Both bDE alleles are temperature-sensitive, but the activity of the bDE allele from the Dark line is lower than that of the bDE allele from the Pale line. Our results suggest that this difference could partly be due to differential regulation by AbdB. bab has been previously reported to be a repressor of abdominal pigmentation. We show here that one of its targets in this process is the pigmentation gene tan (t), regulated via the tan abdominal enhancer (t_MSE). Furthermore, t expression is strongly modulated by temperature in the two lines. Thus, temperature sensitivity of t expression is at least partly a consequence of bab thermal transcriptional plasticity. We therefore propose that a gene regulatory network integrating both genetic variation and temperature sensitivity modulates female abdominal pigmentation. Interestingly, both bDE and t_MSE were previously shown to have been recurrently involved in abdominal pigmentation evolution in drosophilids. We propose that the environmental sensitivity of these enhancers has turned them into evolutionary hotspots. Complex traits such as size or disease susceptibility are typically modulated by both genetic variation and environmental conditions. Model organisms such as fruit flies (Drosophila) are particularly appropriate to analyse the interactions between genetic variation and environmental factors during the development of complex phenotypes. Natural populations carry high genetic variation and can be grown in controlled conditions in the laboratory. Here, we use Drosophila melanogaster female abdominal pigmentation, which is both genetically variable and modulated by the environment (temperature) to dissect this kind of interaction. We show that the pigmentation difference between two inbred fly lines is caused by genetic variation in an enhancer of the bab locus, which encodes two transcription factors controlling abdominal pigmentation. Indeed, this enhancer drives differential expression between the two lines. Interestingly, this enhancer is sensitive to temperature in both lines. We show that the effect of bab on pigmentation is mediated by the pigmentation gene tan (t) that is repressed by bab. Thus, the previously reported temperature-sensitive expression of t is a direct consequence of bab transcriptional plasticity.
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Affiliation(s)
- Sandra De Castro
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement -Institut de Biologie Paris Seine (LBD-IBPS), Team “Epigenetic control of developmental homeostasis and plasticity”, Paris, France
| | - Frédérique Peronnet
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement -Institut de Biologie Paris Seine (LBD-IBPS), Team “Epigenetic control of developmental homeostasis and plasticity”, Paris, France
| | - Jean-François Gilles
- Sorbonne Université, CNRS, Core facility, Institut de Biologie Paris Seine (IBPS), Paris, France
| | - Emmanuèle Mouchel-Vielh
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement -Institut de Biologie Paris Seine (LBD-IBPS), Team “Epigenetic control of developmental homeostasis and plasticity”, Paris, France
- * E-mail: (EM-V); (J-MG)
| | - Jean-Michel Gibert
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement -Institut de Biologie Paris Seine (LBD-IBPS), Team “Epigenetic control of developmental homeostasis and plasticity”, Paris, France
- * E-mail: (EM-V); (J-MG)
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37
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Raffini F, Fruciano C, Meyer A. Gene(s) and individual feeding behavior: Exploring eco-evolutionary dynamics underlying left-right asymmetry in the scale-eating cichlid fish Perissodus microlepis. Ecol Evol 2018; 8:5495-5507. [PMID: 29938068 PMCID: PMC6010907 DOI: 10.1002/ece3.4070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 03/22/2018] [Accepted: 03/26/2018] [Indexed: 01/09/2023] Open
Abstract
The scale‐eating cichlid fish Perissodus microlepis is a textbook example of bilateral asymmetry due to its left or right‐bending heads and of negative frequency‐dependent selection, which is proposed to maintain this stable polymorphism. The mechanisms that underlie this asymmetry remain elusive. Several studies had initially postulated a simple genetic basis for this trait, but this explanation has been questioned, particularly by reports observing a unimodal distribution of mouth shapes. We hypothesize that this unimodal distribution might be due to a combination of genetic and phenotypically plastic components. Here, we expanded on previous work by investigating a formerly identified candidate SNP associated to mouth laterality, documenting inter‐individual variation in feeding preference using stable isotope analyses, and testing their association with mouth asymmetry. Our results suggest that this polymorphism is influenced by both a polygenic basis and inter‐individual non‐genetic variation, possibly due to feeding experience, individual specialization, and intraspecific competition. We introduce a hypothesis potentially explaining the simultaneous maintenance of left, right, asymmetric and symmetric mouth phenotypes due to the interaction between diverse eco‐evolutionary dynamics including niche construction and balancing selection. Future studies will have to further tease apart the relative contribution of genetic and environmental factors and their interactions in an integrated fashion.
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Affiliation(s)
- Francesca Raffini
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany.,International Max Planck Research School (IMPRS) for Organismal Biology University of Konstanz Konstanz Germany
| | - Carmelo Fruciano
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany.,School of Earth, Environmental & Biological Sciences Queensland University of Technology Brisbane QLD Australia.,Institut de biologie de l'Ecole normale supérieure (IBENS) Ecole normale supérieure, CNRS, INSERM PSL Université, Paris France
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany.,International Max Planck Research School (IMPRS) for Organismal Biology University of Konstanz Konstanz Germany.,Radcliffe Institute for Advanced Study Harvard University Cambridge Massachusetts
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38
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Ahi EP, Sefc KM. Towards a gene regulatory network shaping the fins of the Princess cichlid. Sci Rep 2018; 8:9602. [PMID: 29942008 PMCID: PMC6018552 DOI: 10.1038/s41598-018-27977-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 06/01/2018] [Indexed: 02/08/2023] Open
Abstract
Variation in fin shape and size contributes to the outstanding morphological diversity of teleost fishes, but the regulation of fin growth has not yet been studied extensively outside the zebrafish model. A previous gene expression study addressing the ornamental elongations of unpaired fins in the African cichlid fish Neolamprologus brichardi identified three genes (cx43, mmp9 and sema3d) with strong and consistent expression differences between short and elongated fin regions. Remarkably, the expression patterns of these genes were not consistent with inferences on their regulatory interactions in zebrafish. Here, we identify a gene expression network (GRN) comprising cx43, mmp9, and possibly also sema3d by a stepwise approach of identifying co-expression modules and predicting their upstream regulators. Among the transcription factors (TFs) predicted as potential upstream regulators of 11 co-expressed genes, six TFs (foxc1, foxp1, foxd3, myc, egr2, irf8) showed expression patterns consistent with their cooperative transcriptional regulation of the gene network. Some of these TFs have already been implicated in teleost fish fin regeneration and formation. We particularly discuss the potential function of foxd3 as driver of the network and its role in the unexpected gene expression correlations observed in N. brichardi.
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Affiliation(s)
- Ehsan Pashay Ahi
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria.
| | - Kristina M Sefc
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria
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39
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Saltz JB, Bell AM, Flint J, Gomulkiewicz R, Hughes KA, Keagy J. Why does the magnitude of genotype-by-environment interaction vary? Ecol Evol 2018; 8:6342-6353. [PMID: 29988442 PMCID: PMC6024136 DOI: 10.1002/ece3.4128] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 03/27/2018] [Accepted: 03/15/2018] [Indexed: 12/15/2022] Open
Abstract
Genotype-by-environment interaction (G × E), that is, genetic variation in phenotypic plasticity, is a central concept in ecology and evolutionary biology. G×E has wide-ranging implications for trait development and for understanding how organisms will respond to environmental change. Although G × E has been extensively documented, its presence and magnitude vary dramatically across populations and traits. Despite this, we still know little about why G × E is so evident in some traits and populations, but minimal or absent in others. To encourage synthetic research in this area, we review diverse hypotheses for the underlying biological causes of variation in G × E. We extract common themes from these hypotheses to develop a more synthetic understanding of variation in G × E and suggest some important next steps.
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Affiliation(s)
| | - Alison M. Bell
- University of Illinois at Urbana‐ChampaignUrbanaIllinois
| | - Jonathan Flint
- University of California Los AngelesLos AngelesCalifornia
| | | | | | - Jason Keagy
- University of Illinois at Urbana‐ChampaignUrbanaIllinois
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40
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Affiliation(s)
- Henrik H. De Fine Licht
- Section for Organismal Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- * E-mail:
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41
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Metzger DCH, Schulte PM. Similarities in temperature-dependent gene expression plasticity across timescales in threespine stickleback (Gasterosteus aculeatus). Mol Ecol 2018; 27:2381-2396. [PMID: 29654710 DOI: 10.1111/mec.14591] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/16/2018] [Accepted: 03/26/2018] [Indexed: 12/22/2022]
Abstract
Phenotypic plasticity occurs at a variety of timescales, but little is known about the degree to which plastic responses at different timescales are associated with similar underlying molecular processes, which is critical for assessing the effects of plasticity on evolutionary trajectories. To address this issue, we identified differential gene expression in response to developmental temperature in the muscle transcriptome of adult threespine stickleback (Gasterosteus aculeatus) exposed to 12, 18 and 24°C until hatch and then held at 18°C for 9 months and compared these results to differential gene expression in response to adult thermal acclimation in stickleback developed at 18°C and then acclimated to 5 and 25°C as adults. Adult thermal acclimation affected the expression of 7,940 and 7,015 genes in response to cold and warm acclimation, respectively, and 4,851 of these genes responded in both treatments. In contrast, the expression of only 33 and 29 genes was affected by cold and warm development, respectively. The majority of the genes affected by developmental temperature were also affected by adult acclimation temperature. Many genes that were differentially expressed as a result of adult acclimation were associated with previously identified temperature-dependent effects on DNA methylation patterns, suggesting a role of epigenetic mechanisms in regulating gene expression plasticity during acclimation. Taken together, these results demonstrate similarities between the persistent effects of developmental plasticity on gene expression and the effects of adult thermal acclimation, emphasizing the potential for mechanistic links between plasticity acting at these different life stages.
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Affiliation(s)
- David C H Metzger
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Patricia M Schulte
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
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42
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Ouma WZ, Pogacar K, Grotewold E. Topological and statistical analyses of gene regulatory networks reveal unifying yet quantitatively different emergent properties. PLoS Comput Biol 2018; 14:e1006098. [PMID: 29708965 PMCID: PMC5945062 DOI: 10.1371/journal.pcbi.1006098] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 05/10/2018] [Accepted: 03/20/2018] [Indexed: 11/30/2022] Open
Abstract
Understanding complexity in physical, biological, social and information systems is predicated on describing interactions amongst different components. Advances in genomics are facilitating the high-throughput identification of molecular interactions, and graphs are emerging as indispensable tools in explaining how the connections in the network drive organismal phenotypic plasticity. Here, we describe the architectural organization and associated emergent topological properties of gene regulatory networks (GRNs) that describe protein-DNA interactions (PDIs) in several model eukaryotes. By analyzing GRN connectivity, our results show that the anticipated scale-free network architectures are characterized by organism-specific power law scaling exponents. These exponents are independent of the fraction of the GRN experimentally sampled, enabling prediction of properties of the complete GRN for an organism. We further demonstrate that the exponents describe inequalities in transcription factor (TF)-target gene recognition across GRNs. These observations have the important biological implication that they predict the existence of an intrinsic organism-specific trans and/or cis regulatory landscape that constrains GRN topologies. Consequently, architectural GRN organization drives not only phenotypic plasticity within a species, but is also likely implicated in species-specific phenotype.
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Affiliation(s)
- Wilberforce Zachary Ouma
- Molecular and Cellular Imaging Center (MCIC), Ohio Agricultural and Research Development Center (OARDC), Ohio State University, Wooster, OH, United States of America
| | - Katja Pogacar
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States of America
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States of America
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43
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Rittschof CC, Hughes KA. Advancing behavioural genomics by considering timescale. Nat Commun 2018; 9:489. [PMID: 29434301 PMCID: PMC5809431 DOI: 10.1038/s41467-018-02971-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 01/10/2018] [Indexed: 12/31/2022] Open
Abstract
Animal behavioural traits often covary with gene expression, pointing towards a genomic constraint on organismal responses to environmental cues. This pattern highlights a gap in our understanding of the time course of environmentally responsive gene expression, and moreover, how these dynamics are regulated. Advances in behavioural genomics explore how gene expression dynamics are correlated with behavioural traits that range from stable to highly labile. We consider the idea that certain genomic regulatory mechanisms may predict the timescale of an environmental effect on behaviour. This temporally minded approach could inform both organismal and evolutionary questions ranging from the remediation of early life social trauma to understanding the evolution of trait plasticity.
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Affiliation(s)
- Clare C Rittschof
- Department of Entomology, University of Kentucky, Lexington, KY, 40546, USA.
| | - Kimberly A Hughes
- Department of Biological Sciences, Florida State University, Tallahassee, FL, 32306, USA
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44
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Ahi EP, Richter F, Sefc KM. A gene expression study of ornamental fin shape in Neolamprologus brichardi, an African cichlid species. Sci Rep 2017; 7:17398. [PMID: 29234131 PMCID: PMC5727040 DOI: 10.1038/s41598-017-17778-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 11/29/2017] [Indexed: 01/14/2023] Open
Abstract
The diversity of fin morphology within and across fish taxa offers great, but still largely unexplored, opportunities to investigate the proximate mechanisms underlying fin shape variation. Relying on available genetic knowledge brought forth mainly by the comprehensive study of the zebrafish caudal fin, we explored candidate molecular mechanisms for the maintenance and formation of the conspicuously elongated filaments adorning the unpaired fins of the East African "princess cichlid" Neolamprologus brichardi. Via qPCR assays, we detected expression differences of candidate genes between elongated and short regions of intact and regenerating fins. The identified genes include skeletogenic and growth factors (igf2b, fgf3, bmp2 and bmp4), components of the WNT pathway (lef1, wnt5b and wnt10) and a regulatory network determining fin ray segment size and junction (cx43, esco2 and sema3d), as well as other genes with different roles (mmp9, msxb and pea3). Interestingly, some of these genes showed fin specific expression differences which are often neglected in studies of model fish that focus on the caudal fin. Moreover, while the observed expression patterns were generally consistent with zebrafish results, we also detected deviating expression correlations and gene functions.
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Affiliation(s)
- Ehsan Pashay Ahi
- Institute of Zoology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria.
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45
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Gunter HM, Schneider RF, Karner I, Sturmbauer C, Meyer A. Molecular investigation of genetic assimilation during the rapid adaptive radiations of East African cichlid fishes. Mol Ecol 2017; 26:6634-6653. [PMID: 29098748 DOI: 10.1111/mec.14405] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 08/06/2017] [Accepted: 08/24/2017] [Indexed: 12/19/2022]
Abstract
Adaptive radiations are characterized by adaptive diversification intertwined with rapid speciation within a lineage resulting in many ecologically specialized, phenotypically diverse species. It has been proposed that adaptive radiations can originate from ancestral lineages with pronounced phenotypic plasticity in adaptive traits, facilitating ecologically driven phenotypic diversification that is ultimately fixed through genetic assimilation of gene regulatory regions. This study aimed to investigate how phenotypic plasticity is reflected in gene expression patterns in the trophic apparatus of several lineages of East African cichlid fishes, and whether the observed patterns support genetic assimilation. This investigation used a split brood experimental design to compare adaptive plasticity in species from within and outside of adaptive radiations. The plastic response was induced in the crushing pharyngeal jaws through feeding individuals either a hard or soft diet. We find that nonradiating, basal lineages show higher levels of adaptive morphological plasticity than the derived, radiated lineages, suggesting that these differences have become partially genetically fixed during the formation of the adaptive radiations. Two candidate genes that may have undergone genetic assimilation, gif and alas1, were identified, in addition to alterations in the wiring of LPJ patterning networks. Taken together, our results suggest that genetic assimilation may have dampened the inducibility of plasticity related genes during the adaptive radiations of East African cichlids, flattening the reaction norms and canalizing their feeding phenotypes, driving adaptation to progressively more narrow ecological niches.
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Affiliation(s)
- Helen M Gunter
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany.,Zukunftskolleg, University of Konstanz, Konstanz, Germany
| | - Ralf F Schneider
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany.,International Max Planck Research School for Organismal Biology, University of Konstanz, Konstanz, Germany
| | | | | | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany.,International Max Planck Research School for Organismal Biology, University of Konstanz, Konstanz, Germany.,Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA, USA
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46
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Singh P, Börger C, More H, Sturmbauer C. The Role of Alternative Splicing and Differential Gene Expression in Cichlid Adaptive Radiation. Genome Biol Evol 2017; 9:2764-2781. [PMID: 29036566 PMCID: PMC5737861 DOI: 10.1093/gbe/evx204] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2017] [Indexed: 12/11/2022] Open
Abstract
Species diverge eco-morphologically through the continuous action of natural selection on functionally important structures, producing alternative adaptive morphologies. In cichlid fishes, the oral and pharyngeal jaws are such key structures. Adaptive variation in jaw morphology contributes to trophic specialization, which is hypothesized to fuel their rapid speciation in the East African Great Lakes. Much is known about the genes involved in cichlid jaw and craniofacial development. However, it is still unclear what salient sources of variation gave rise to trophic-niche specialization, facilitating adaptive radiation. Here, we explore two sources of transcriptional variation that may underlie species-specific disparities in jaw morphology. Using whole transcriptome RNA-sequencing, we analyze differences in gene expression and alternative splicing, at the end of postlarval development, in fully functional jaws of six species of cichlids from the Lake Tanganyika tribe Tropheini. Our data reveal a surprisingly high degree of alternative splicing events compared with gene expression differences among species and trophic types. This suggests that differential trophic adaptation of the jaw apparatus may have been shaped by transcriptional rewiring of splicing as well as gene expression variation during the rapid radiation of the Tropheini. Specifically, genes undergoing splicing across most species were found to be enriched for pharyngeal jaw gene ontology terms. Overall, jaw transcriptional patterns at postlarval developmental stage were highly dynamic and species-specific. In conclusion, this work indicates that shifts in alternative splicing could have played a more important role in cichlid adaptive radiation, and possibly adaptive radiation in general, than currently recognized.
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Affiliation(s)
- Pooja Singh
- Department of Zoology, University of Graz, Austria
- Department of Biology, University of Konstanz, Germany
| | | | - Heather More
- Department of Zoology, University of Graz, Austria
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
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47
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Lorant A, Pedersen S, Holst I, Hufford MB, Winter K, Piperno D, Ross-Ibarra J. The potential role of genetic assimilation during maize domestication. PLoS One 2017; 12:e0184202. [PMID: 28886108 PMCID: PMC5590903 DOI: 10.1371/journal.pone.0184202] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 08/18/2017] [Indexed: 11/25/2022] Open
Abstract
Domestication research has largely focused on identification of morphological and genetic differences between extant populations of crops and their wild relatives. Little attention has been paid to the potential effects of environment despite substantial known changes in climate from the time of domestication to modern day. In recent research, the exposure of teosinte (i.e., wild maize) to environments similar to the time of domestication, resulted in a plastic induction of domesticated phenotypes in teosinte. These results suggest that early agriculturalists may have selected for genetic mechanisms that cemented domestication phenotypes initially induced by a plastic response of teosinte to environment, a process known as genetic assimilation. To better understand this phenomenon and the potential role of environment in maize domestication, we examined differential gene expression in maize (Zea mays ssp. mays) and teosinte (Zea mays ssp. parviglumis) between past and present conditions. We identified a gene set of over 2000 loci showing a change in expression across environmental conditions in teosinte and invariance in maize. In fact, overall we observed both greater plasticity in gene expression and more substantial changes in co-expressionnal networks in teosinte across environments when compared to maize. While these results suggest genetic assimilation played at least some role in domestication, genes showing expression patterns consistent with assimilation are not significantly enriched for previously identified domestication candidates, indicating assimilation did not have a genome-wide effect.
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Affiliation(s)
- Anne Lorant
- Dept. of Plant Sciences, University of California Davis, Davis, CA, United States of America
| | - Sarah Pedersen
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States of America
| | - Irene Holst
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
| | - Matthew B. Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States of America
| | - Klaus Winter
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
| | - Dolores Piperno
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
- Department of Anthropology, Smithsonian National Museum of Natural History, Washington, DC, United States of America
| | - Jeffrey Ross-Ibarra
- Dept. of Plant Sciences, University of California Davis, Davis, CA, United States of America
- Genome Center and Center for Population Biology, University of California Davis, Davis, CA, United States of America
- * E-mail:
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48
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Härer A, Torres-Dowdall J, Meyer A. Rapid adaptation to a novel light environment: The importance of ontogeny and phenotypic plasticity in shaping the visual system of Nicaraguan Midas cichlid fish (Amphilophus citrinellus
spp.). Mol Ecol 2017; 26:5582-5593. [DOI: 10.1111/mec.14289] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 07/14/2017] [Accepted: 07/31/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Andreas Härer
- Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Konstanz Germany
| | - Julián Torres-Dowdall
- Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Konstanz Germany
- Zukunftskolleg; University of Konstanz; Konstanz Germany
| | - Axel Meyer
- Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Konstanz Germany
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49
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Levis NA, Serrato‐Capuchina A, Pfennig DW. Genetic accommodation in the wild: evolution of gene expression plasticity during character displacement. J Evol Biol 2017; 30:1712-1723. [DOI: 10.1111/jeb.13133] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 06/05/2017] [Accepted: 06/07/2017] [Indexed: 12/14/2022]
Affiliation(s)
- N. A. Levis
- Department of Biology University of North Carolina Chapel Hill NC USA
| | | | - D. W. Pfennig
- Department of Biology University of North Carolina Chapel Hill NC USA
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50
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Siljestam M, Östman Ö. The combined effects of temporal autocorrelation and the costs of plasticity on the evolution of plasticity. J Evol Biol 2017; 30:1361-1371. [PMID: 28485061 DOI: 10.1111/jeb.13114] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 04/27/2017] [Accepted: 05/03/2017] [Indexed: 12/14/2022]
Abstract
Adaptive phenotypic plasticity is an important source of intraspecific variation, and for many plastic traits, the costs or factors limiting plasticity seem cryptic. However, there are several different factors that may constrain the evolution of plasticity, but few models have considered costs and limiting factors simultaneously. Here we use a simulation model to investigate how the optimal level of plasticity in a population depends on a fixed maintenance fitness cost for plasticity or an incremental fitness cost for producing a plastic response in combination with environmental unpredictability (environmental fluctuation speed) limiting plasticity. Our model identifies two mechanisms that act, almost separately, to constrain the evolution of plasticity: (i) the fitness cost of plasticity scaled by the nonplastic environmental tolerance, and (ii) the environmental fluctuation speed scaled by the rate of phenotypic change. That is, the evolution of plasticity is constrained by the high cost of plasticity in combination with high tolerance for environmental variation, or fast environmental changes in combination with slow plastic response. Qualitatively similar results are found when maintenance and incremental fitness costs of plasticity are incorporated, although a larger degree of plasticity is selected for with an incremental cost. Our model highlights that it is important to consider direct fitness costs and phenotypic limitations in relation to nonplastic environmental tolerance and environmental fluctuations, respectively, to understand what constrains the evolution of phenotypic plasticity.
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Affiliation(s)
- M Siljestam
- Department of Ecology & Genetics, Uppsala University, Uppsala, Sweden
| | - Ö Östman
- Department of Ecology & Genetics, Uppsala University, Uppsala, Sweden
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