1
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Nosil P, de Carvalho CF, Villoutreix R, Zamorano LS, Sinclair-Waters M, Planidin NP, Parchman TL, Feder J, Gompert Z. Evolution repeats itself in replicate long-term studies in the wild. SCIENCE ADVANCES 2024; 10:eadl3149. [PMID: 38787954 PMCID: PMC11122682 DOI: 10.1126/sciadv.adl3149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 04/22/2024] [Indexed: 05/26/2024]
Abstract
The extent to which evolution is repeatable remains debated. Here, we study changes over time in the frequency of cryptic color-pattern morphs in 10 replicate long-term field studies of a stick insect, each spanning at least a decade (across 30 years of total data). We find predictable "up-and-down" fluctuations in stripe frequency in all populations, representing repeatable evolutionary dynamics based on standing genetic variation. A field experiment demonstrates that these fluctuations involve negative frequency-dependent natural selection (NFDS). These fluctuations rely on demographic and selective variability that pushes populations away from equilibrium, such that they can reliably move back toward it via NFDS. Last, we show that the origin of new cryptic forms is associated with multiple structural genomic variants such that which mutations arise affects evolution at larger temporal scales. Thus, evolution from existing variation is predictable and repeatable, but mutation adds complexity even for traits evolving deterministically under natural selection.
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Affiliation(s)
- Patrik Nosil
- Theoretical and Experimental Ecology (SETE), CNRS, 2 route du CNRS, 09200 Moulis, France
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | | | - Laura S. Zamorano
- Theoretical and Experimental Ecology (SETE), CNRS, 2 route du CNRS, 09200 Moulis, France
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | | | | | - Jeffrey Feder
- Department of Biology, Notre Dame University, South Bend, IN 11111, USA
| | - Zach Gompert
- Department of Biology, Utah State University, Logan, UT 84322, USA
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2
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Foster BJ, McCulloch GA, Foster Y, Kroos GC, King TM, Waters JM. ebony underpins Batesian mimicry in melanic stoneflies. Mol Ecol 2023; 32:4986-4998. [PMID: 37503654 DOI: 10.1111/mec.17085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/06/2023] [Accepted: 07/13/2023] [Indexed: 07/29/2023]
Abstract
The evolution of Batesian mimicry - whereby harmless species avoid predation through their resemblance to harmful species - has long intrigued biologists. In rare cases, Batesian mimicry is linked to intraspecific colour variation, in which only some individuals within a population resemble a noxious 'model'. Here, we assess intraspecific colour variation within a widespread New Zealand stonefly, wherein highly melanized individuals of Zelandoperla closely resemble a chemically defended aposematic stonefly, Austroperla cyrene. We assess convergence in the colour pattern of these two species, compare their relative palatability to predators, and use genome-wide association mapping to assess the genetic basis of this resemblance. Our analysis reveals that melanized Zelandoperla overlap significantly with Austroperla in colour space but are significantly more palatable to predators, implying that they are indeed Batesian mimics. Analysis of 194,773 genome-wide SNPs reveals an outlier locus (ebony) strongly differentiating melanic versus non-melanic Zelandoperla. Genotyping of 338 specimens from a single Zelandoperla population indicates that ebony explains nearly 70% of the observed variance in melanism. As ebony has a well-documented role in insect melanin biosynthesis, our findings indicate this locus has a conserved function across deeply divergent hexapod lineages. Distributional records suggest a link between the occurrence of melanic Zelandoperla and the forested ecosystems where the model Austroperla is abundant, suggesting the potential for adaptive shifts in this system underpinned by environmental change.
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Affiliation(s)
- Brodie J Foster
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | | | - Yasmin Foster
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Gracie C Kroos
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Tania M King
- Department of Zoology, University of Otago, Dunedin, New Zealand
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3
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Villoutreix R, de Carvalho CF, Feder JL, Gompert Z, Nosil P. Disruptive selection and the evolution of discrete color morphs in Timema stick insects. SCIENCE ADVANCES 2023; 9:eabm8157. [PMID: 37000882 PMCID: PMC10065444 DOI: 10.1126/sciadv.abm8157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
A major unresolved issue in biology is why phenotypic and genetic variation is sometimes continuous, yet other times packaged into discrete units of diversity, such as morphs, ecotypes, and species. In theory, ecological discontinuities can impose strong disruptive selection that promotes the evolution of discrete forms, but direct tests of this hypothesis are lacking. Here, we show that Timema stick insects exhibit genetically determined color morphs that range from weakly to strongly discontinuous. Color data from nature and a manipulative field experiment demonstrate that greater morph differentiation is associated with shifts from host plants exhibiting more continuous color variation to those exhibiting greater coloration distance between green leaves and brown stems, the latter of which generates strong disruptive selection. Our results show how ecological factors can promote discrete variation, and we further present results on how this can have variable effects on the genetic differentiation that promotes speciation.
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Affiliation(s)
| | - Clarissa F. de Carvalho
- CEFE, Université Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Departamento de Ecologia e Biologia Evolutiva, UNIFESP, Diadema 09972-270, Brazil
| | - Jeffrey L. Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | | | - Patrik Nosil
- CEFE, Université Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Department of Biology, Utah State University, Logan, UT 84322, USA
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4
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Gompert Z, Flaxman SM, Feder JL, Chevin LM, Nosil P. Laplace's demon in biology: Models of evolutionary prediction. Evolution 2022; 76:2794-2810. [PMID: 36193839 DOI: 10.1111/evo.14628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 08/23/2022] [Accepted: 08/30/2022] [Indexed: 01/22/2023]
Abstract
Our ability to predict natural phenomena can be limited by incomplete information. This issue is exemplified by "Laplace's demon," an imaginary creature proposed in the 18th century, who knew everything about everything, and thus could predict the full nature of the universe forward or backward in time. Quantum mechanics, among other things, has cast doubt on the possibility of Laplace's demon in the full sense, but the idea still serves as a useful metaphor for thinking about the extent to which prediction is limited by incomplete information on deterministic processes versus random factors. Here, we use simple analytical models and computer simulations to illustrate how data limits can be captured in a Bayesian framework, and how they influence our ability to predict evolution. We show how uncertainty in measurements of natural selection, or low predictability of external environmental factors affecting selection, can greatly reduce predictive power, often swamping the influence of intrinsic randomness caused by genetic drift. Thus, more accurate knowledge concerning the causes and action of natural selection is key to improving prediction. Fortunately, our analyses and simulations show quantitatively that reasonable improvements in data quantity and quality can meaningfully increase predictability.
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Affiliation(s)
| | | | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Luis-Miguel Chevin
- CEFE, Univ Montpellier, Montpellier, France.,CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Patrik Nosil
- CEFE, Univ Montpellier, Montpellier, France.,CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
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5
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Chaturvedi S, Gompert Z, Feder JL, Osborne OG, Muschick M, Riesch R, Soria-Carrasco V, Nosil P. Climatic similarity and genomic background shape the extent of parallel adaptation in Timema stick insects. Nat Ecol Evol 2022; 6:1952-1964. [PMID: 36280782 PMCID: PMC7613875 DOI: 10.1038/s41559-022-01909-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 09/13/2022] [Indexed: 12/15/2022]
Abstract
Evolution can repeat itself, resulting in parallel adaptations in independent lineages occupying similar environments. Moreover, parallel evolution sometimes, but not always, uses the same genes. Two main hypotheses have been put forth to explain the probability and extent of parallel evolution. First, parallel evolution is more likely when shared ecologies result in similar patterns of natural selection in different taxa. Second, parallelism is more likely when genomes are similar because of shared standing variation and similar mutational effects in closely related genomes. Here we combine ecological, genomic, experimental and phenotypic data with Bayesian modelling and randomization tests to quantify the degree of parallelism and its relationship with ecology and genetics. Our results show that the extent to which genomic regions associated with climate are parallel among species of Timema stick insects is shaped collectively by shared ecology and genomic background. Specifically, the extent of genomic parallelism decays with divergence in climatic conditions (that is, habitat or ecological similarity) and genomic similarity. Moreover, we find that climate-associated loci are likely subject to selection in a field experiment, overlap with genetic regions associated with cuticular hydrocarbon traits and are not strongly shaped by introgression between species. Our findings shed light on when evolution is most expected to repeat itself.
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Affiliation(s)
- Samridhi Chaturvedi
- Department of Integrative Biology, University of California, Berkeley, CA, USA.
- Department of Biology and Ecology Center, Utah State University, Logan, UT, USA.
| | - Zachariah Gompert
- Department of Biology and Ecology Center, Utah State University, Logan, UT, USA.
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Owen G Osborne
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, UK
| | - Moritz Muschick
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Rüdiger Riesch
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | | | - Patrik Nosil
- Department of Biology and Ecology Center, Utah State University, Logan, UT, USA
- CEFE, Univ. Montpellier, CNRS, EPHE, IRD, Univ. Paul Valéry Montpellier 3, Montpellier, France
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6
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Heinze P, Dieker P, Rowland HM, Schielzeth H. Evidence for morph-specific substrate choice in a green-brown polymorphic grasshopper. Behav Ecol 2021; 33:17-26. [PMID: 35197804 PMCID: PMC8857936 DOI: 10.1093/beheco/arab133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 08/11/2021] [Accepted: 11/02/2021] [Indexed: 11/14/2022] Open
Abstract
Abstract
Orthopteran insects are characterized by high variability in body coloration, in particular featuring a widespread green-brown color polymorphism. The mechanisms that contribute to the maintenance of this apparently balanced polymorphism are not yet understood. To investigate whether morph-dependent microhabitat choice might contribute to the continued coexistence of multiple morphs, we studied substrate choice in the meadow grasshopper Pseudochorthippus parallelus. The meadow grasshopper occurs in multiple discrete, genetically determined color morphs that range from uniform brown to uniform green. We tested whether three common morphs preferentially choose differently colored backgrounds in an experimental arena. We found that a preference for green backgrounds was most pronounced in uniform green morphs. If differential choices improve morph-specific performance in natural habitats via crypsis and/or thermoregulatory benefits, they could help to equalize fitness differences among color morphs and potentially produce frequency-dependent microhabitat competition, though difference appear too small to serve as the only explanation. We also measured the reflectance of the grasshoppers and backgrounds and used visual modeling to quantify the detectability of the different morphs to a range of potential predators. Multiple potential predators, including birds and spiders, are predicted to distinguish between morphs chromatically, while other species, possibly including grasshoppers themselves, will perceive only differences in brightness. Our study provides the first evidence that morph-specific microhabitat choice might be relevant to the maintenance of the green-brown polymorphisms in grasshoppers and shows that visual distinctness of color morphs varies between perceivers.
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Affiliation(s)
- Pauline Heinze
- Population Ecology Group, Institute of Ecology and Evolution, Friedrich Schiller University Jena, Dornburger Straße, Jena, Germany
| | - Petra Dieker
- Population Ecology Group, Institute of Ecology and Evolution, Friedrich Schiller University Jena, Dornburger Straße, Jena, Germany
| | - Hannah M Rowland
- Research Group Predators and Toxic Prey, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße, Jena, Germany
| | - Holger Schielzeth
- Population Ecology Group, Institute of Ecology and Evolution, Friedrich Schiller University Jena, Dornburger Straße, Jena, Germany
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7
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Garcia-Elfring A, Paccard A, Thurman TJ, Wasserman BA, Palkovacs EP, Hendry AP, Barrett RDH. Using seasonal genomic changes to understand historical adaptation to new environments: Parallel selection on stickleback in highly-variable estuaries. Mol Ecol 2021; 30:2054-2064. [PMID: 33713378 DOI: 10.1111/mec.15879] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/21/2022]
Abstract
Parallel evolution is considered strong evidence for natural selection. However, few studies have investigated the process of parallel selection as it plays out in real time. The common approach is to study historical signatures of selection in populations already well adapted to different environments. Here, to document selection under natural conditions, we study six populations of threespine stickleback (Gasterosteus aculeatus) inhabiting bar-built estuaries that undergo seasonal cycles of environmental changes. Estuaries are periodically isolated from the ocean due to sandbar formation during dry summer months, with concurrent environmental shifts that resemble the long-term changes associated with postglacial colonization of freshwater habitats by marine populations. We used pooled whole-genome sequencing to track seasonal allele frequency changes in six of these populations and search for signatures of natural selection. We found consistent changes in allele frequency across estuaries, suggesting a potential role for parallel selection. Functional enrichment among candidate genes included transmembrane ion transport and calcium binding, which are important for osmoregulation and ion balance. The genomic changes that occur in threespine stickleback from bar-built estuaries could provide a glimpse into the early stages of adaptation that have occurred in many historical marine to freshwater transitions.
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Affiliation(s)
- Alan Garcia-Elfring
- Department of Biology, Redpath Museum, McGill University, Montreal, QC, Canada
| | - Antoine Paccard
- Department of Biology, Redpath Museum, McGill University, Montreal, QC, Canada.,McGill University Genome Center, McGill University, Montreal, QC, Canada
| | - Timothy J Thurman
- Department of Biology, Redpath Museum, McGill University, Montreal, QC, Canada
| | - Ben A Wasserman
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Eric P Palkovacs
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Andrew P Hendry
- Department of Biology, Redpath Museum, McGill University, Montreal, QC, Canada
| | - Rowan D H Barrett
- Department of Biology, Redpath Museum, McGill University, Montreal, QC, Canada
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8
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Ecology shapes epistasis in a genotype-phenotype-fitness map for stick insect colour. Nat Ecol Evol 2020; 4:1673-1684. [PMID: 32929238 DOI: 10.1038/s41559-020-01305-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 08/19/2020] [Indexed: 01/06/2023]
Abstract
Genetic interactions such as epistasis are widespread in nature and can shape evolutionary dynamics. Epistasis occurs due to nonlinearity in biological systems, which can arise via cellular processes that convert genotype to phenotype and via selective processes that connect phenotype to fitness. Few studies in nature have connected genotype to phenotype to fitness for multiple potentially interacting genetic variants. Thus, the causes of epistasis in the wild remain poorly understood. Here, we show that epistasis for fitness is an emergent and predictable property of nonlinear selective processes. We do so by measuring the genetic basis of cryptic colouration and survival in a field experiment with stick insects. We find that colouration shows a largely additive genetic basis but with some effects of epistasis that enhance differentiation between colour morphs. In terms of fitness, different combinations of loci affecting colouration confer high survival in one host-plant treatment. Specifically, nonlinear correlational selection for specific combinations of colour traits in this treatment drives the emergence of pairwise and higher-order epistasis for fitness at loci underlying colour. In turn, this results in a rugged fitness landscape for genotypes. In contrast, fitness epistasis was dampened in another treatment, where selection was weaker. Patterns of epistasis that are shaped by ecologically based selection could be common and central to understanding fitness landscapes, the dynamics of evolution and potentially other complex systems.
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9
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Mas A, Lagadeuc Y, Vandenkoornhuyse P. Reflections on the Predictability of Evolution: Toward a Conceptual Framework. iScience 2020; 23:101736. [PMID: 33225244 PMCID: PMC7666346 DOI: 10.1016/j.isci.2020.101736] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Evolution is generally considered to be unpredictable because genetic variations are known to occur randomly. However, remarkable patterns of repeated convergent evolution are observed, for instance, loss of pigments by organisms living in caves. Analogous phenotypes appear in similar environments, sometimes in response to similar constraints. Alongside randomness, a certain evolutionary determinism also exists, for instance, the selection of particular phenotypes subjected to particular environmental constraints in the “evolutionary funnel.” We pursue the idea that eco-evolutionary specialization is in some way determinist. The conceptual framework of phenotypic changes entailing specialization presented in this essay explains how evolution can be predicted. We also discuss how the predictability of evolution could be tested using the case of metabolic specialization through gene losses. We also put forward that microorganisms could be key models to test and possibly make headway evolutionary predictions and knowledge about evolution.
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Affiliation(s)
- Alix Mas
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, Avenue Leclerc, Rennes Cedex 35042, France
| | - Yvan Lagadeuc
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, Avenue Leclerc, Rennes Cedex 35042, France
| | - Philippe Vandenkoornhuyse
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, Avenue Leclerc, Rennes Cedex 35042, France
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10
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Jamie GA, Meier JI. The Persistence of Polymorphisms across Species Radiations. Trends Ecol Evol 2020; 35:795-808. [DOI: 10.1016/j.tree.2020.04.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/08/2020] [Accepted: 04/16/2020] [Indexed: 12/12/2022]
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11
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Villoutreix R, de Carvalho CF, Soria-Carrasco V, Lindtke D, De-la-Mora M, Muschick M, Feder JL, Parchman TL, Gompert Z, Nosil P. Large-scale mutation in the evolution of a gene complex for cryptic coloration. Science 2020; 369:460-466. [PMID: 32703880 DOI: 10.1126/science.aaz4351] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 02/29/2020] [Accepted: 05/19/2020] [Indexed: 11/02/2022]
Abstract
The types of mutations affecting adaptation in the wild are only beginning to be understood. In particular, whether structural changes shape adaptation by suppressing recombination or by creating new mutations is unresolved. Here, we show that multiple linked but recombining loci underlie cryptic color morphs of Timema chumash stick insects. In a related species, these loci are found in a region of suppressed recombination, forming a supergene. However, in seven species of Timema, we found that a megabase-size "supermutation" has deleted color loci in green morphs. Moreover, we found that balancing selection likely contributes more to maintaining this mutation than does introgression. Our results show how suppressed recombination and large-scale mutation can help to package gene complexes into discrete units of diversity such as morphs, ecotypes, or species.
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Affiliation(s)
- Romain Villoutreix
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.,Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 CNRS-Université de Montpellier, École Pratique des Hautes Études, Université Paul Valéry, 34293 Montpellier 5, France
| | | | - Víctor Soria-Carrasco
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Dorothea Lindtke
- Department of Biological Sciences, University of Bern, Bern CH-3012, Switzerland
| | - Marisol De-la-Mora
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.,Escuela Nacional de Estudios Superiores, Unidad Juriquilla, Querétaro 76230, México
| | - Moritz Muschick
- Institute of Ecology and Evolution, University of Bern, Bern 3012, Switzerland.,Department of Fish Ecology & Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum CH-6047, Switzerland
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Thomas L Parchman
- Department of Biology, University of Nevada-Reno, Reno, NV 89557, USA
| | - Zach Gompert
- Department of Biology, Utah State University, Logan, UT 84322, USA
| | - Patrik Nosil
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK. .,Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 CNRS-Université de Montpellier, École Pratique des Hautes Études, Université Paul Valéry, 34293 Montpellier 5, France.,Department of Biology, Utah State University, Logan, UT 84322, USA
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12
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Ding BY, Niu J, Shang F, Yang L, Zhang W, Smagghe G, Wang JJ. Parental silencing of a horizontally transferred carotenoid desaturase gene causes a reduction of red pigment and fitness in the pea aphid. PEST MANAGEMENT SCIENCE 2020; 76:2423-2433. [PMID: 32056367 DOI: 10.1002/ps.5783] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/18/2020] [Accepted: 02/13/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Aphids obtained carotenoid biosynthesis genes via horizontal gene transfers from fungi. However, the roles of these genes in the contributions of in aphids'adaptation and whether these genes could be used as RNAi-based pest control targets are not yet clear. Thus, in this study we used parental RNAi to analyze the potential function of a carotenoid desaturase gene (CdeB) by combined molecular and chemical approaches in the pea aphid (Acyrthosiphon pisum). RESULTS Transcriptional analyses showed that CdeB was significantly more highly expressed in the red morphs compared to the green ones and was associated with the production of red carotenoid. Co-transferring of pET28a-CdeB (the CdeB gene was cloned into pET28a) and pACCRT-EIB (produced lycopene) showed a deep red color in the bacterial precipitate and produced more of a red pigment, lycopene, in vitro. Parental gene-silencing of CdeB resulted in a lower body color intensity in the treated aphids and following generations in vivo. Interestingly, the dsCdeB treatment also reduced aphid performance as reflected by a delay in nymphal developmental duration, lower weight, smaller number, and altered age structure of the population. CONCLUSION Our results demonstrate that CdeB is involved in red color formation and the silencing of this gene by parental RNAi reduced fitness in the pea aphid. The results enhance our understanding of the biosynthesis of carotenoid in aphids and provide insights into the potential ecological significance of carotenoids in the adaptation of the aphid's biology to the environment and developing environmentally friendly control strategies for this pest.
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Affiliation(s)
- Bi-Yue Ding
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jinzhi Niu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Feng Shang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Li Yang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Wei Zhang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Guy Smagghe
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
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13
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Schielzeth H, Dieker P. The green-brown polymorphism of the club-legged grasshopper Gomphocerus sibiricus is heritable and appears genetically simple. BMC Evol Biol 2020; 20:63. [PMID: 32487064 PMCID: PMC7268444 DOI: 10.1186/s12862-020-01630-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 05/18/2020] [Indexed: 11/24/2022] Open
Abstract
Background Local coexistence of distinct, genetically determined color morphs can be unstable and transitional. Stable, long-term coexistence requires some form of balancing selection to protect morphs from getting lost by directional selection or genetic drift. However, not all phenotypic polymorphism need to have a genetic basis. We here report on the genetic basis of two color polymorphisms in the club-legged grasshopper Gomphocerus sibiricus: a green-brown polymorphism that is phylogenetically and geographically widespread among orthopteran insects and a pied-brown pattern polymorphism that is shared among many gomphocerine grasshoppers. Results We found a remarkably clear outcome of matings within and between morph that suggest not only that the green-brown polymorphism is heritable in this species, but that results can be most parsimoniously explained by a single autosomal locus with two alleles in which the green allele is dominant over the brown allele. A few individuals did not match this pattern and suggest the existence of genetic modifiers and/or developmental phenocopies. We also show that the pied-brown polymorphism is highly heritable, although the evidence for the involvement of one or more loci is less clear-cut. Conclusions Overall, our data demonstrate that the two polymorphisms are heritable in the club-legged grasshopper and appear genetically simple, at least with respect to green morphs. The results are consistent with the idea that the synthesis or transport of a pigment involved in the production of green coloration (likely biliverdin) is lost by homozygosity for loss-of-function alleles in brown individuals. The apparently simple genetic architecture of the green-brown polymorphism offer potential for studying balancing selection in the field and for genetic mapping in this species.
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Affiliation(s)
- Holger Schielzeth
- Population Ecology Group, Institute of Ecology and Evolution, Friedrich Schiller University Jena, Dornburger Straße 159, 07743, Jena, Germany.
| | - Petra Dieker
- Population Ecology Group, Institute of Ecology and Evolution, Friedrich Schiller University Jena, Dornburger Straße 159, 07743, Jena, Germany.,Present Address: Thünen Institute of Biodiversity, Bundesallee 65, 38116, Braunschweig, Germany
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14
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Bakovic V, Schuler H, Schebeck M, Feder JL, Stauffer C, Ragland GJ. Host plant-related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi. Mol Ecol 2019; 28:4648-4666. [PMID: 31495015 PMCID: PMC6899720 DOI: 10.1111/mec.15239] [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] [Received: 08/16/2018] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022]
Abstract
Elucidating the mechanisms and conditions facilitating the formation of biodiversity are central topics in evolutionary biology. A growing number of studies imply that divergent ecological selection may often play a critical role in speciation by counteracting the homogenising effects of gene flow. Several examples involve phytophagous insects, where divergent selection pressures associated with host plant shifts may generate reproductive isolation, promoting speciation. Here, we use ddRADseq to assess the population structure and to test for host‐related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi (L., 1758) (Diptera: Tephritidae). This tephritid is distributed throughout Europe and western Asia, and has adapted to two different genera of host plants, Prunus spp. (cherries) and Lonicera spp. (honeysuckle). Our data imply that geographic distance and geomorphic barriers serve as the primary factors shaping genetic population structure across the species range. Locally, however, flies genetically cluster according to host plant, with consistent allele frequency differences displayed by a subset of loci between Prunus and Lonicera flies across four sites surveyed in Germany and Norway. These 17 loci display significantly higher FST values between host plants than others. They also showed high levels of linkage disequilibrium within and between Prunus and Lonicera flies, supporting host‐related selection and reduced gene flow. Our findings support the existence of sympatric host races in R. cerasi embedded within broader patterns of geographic variation in the fly, similar to the related apple maggot, Rhagoletis pomonella, in North America.
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Affiliation(s)
- Vid Bakovic
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria.,Department of Biology, IFM, University of Linköping, Linköping, Sweden
| | - Hannes Schuler
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy
| | - Martin Schebeck
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Christian Stauffer
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Gregory J Ragland
- Department of Integrative Biology, University of Colorado-Denver, Denver, CO, USA
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15
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Brien MN, Enciso-Romero J, Parnell AJ, Salazar PA, Morochz C, Chalá D, Bainbridge HE, Zinn T, Curran EV, Nadeau NJ. Phenotypic variation in Heliconius erato crosses shows that iridescent structural colour is sex-linked and controlled by multiple genes. Interface Focus 2018; 9:20180047. [PMID: 30603067 DOI: 10.1098/rsfs.2018.0047] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2018] [Indexed: 11/12/2022] Open
Abstract
Bright, highly reflective iridescent colours can be seen across nature and are produced by the scattering of light from nanostructures. Heliconius butterflies have been widely studied for their diversity and mimicry of wing colour patterns. Despite iridescence evolving multiple times in this genus, little is known about the genetic basis of the colour and the development of the structures which produce it. Heliconius erato can be found across Central and South America, but only races found in western Ecuador and Colombia have developed blue iridescent colour. Here, we use crosses between iridescent and non-iridescent races of H. erato to study phenotypic variation in the resulting F2 generation. Using measurements of blue colour from photographs, we find that iridescent structural colour is a quantitative trait controlled by multiple genes, with strong evidence for loci on the Z sex chromosome. Iridescence is not linked to the Mendelian colour pattern locus that also segregates in these crosses (controlled by the gene cortex). Small-angle X-ray scattering data show that spacing between longitudinal ridges on the scales, which affects the intensity of the blue reflectance, also varies quantitatively in F2 crosses.
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Affiliation(s)
- Melanie N Brien
- Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
| | - Juan Enciso-Romero
- Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK.,Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Bogotá, Colombia
| | - Andrew J Parnell
- Department of Physics and Astronomy, University of Sheffield, Hicks Building, Hounsfield Road, Sheffield S3 7RH, UK
| | - Patricio A Salazar
- Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK.,Centro de Investigación en Biodiversidad y Cambio Climático (BioCamb), Universidad Tecnológica Indoamérica, Quito, Ecuador
| | | | | | - Hannah E Bainbridge
- Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
| | - Thomas Zinn
- ESRF - The European Synchrotron, 38043 Grenoble Cedex 9, France
| | - Emma V Curran
- Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
| | - Nicola J Nadeau
- Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
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16
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Dieker P, Beckmann L, Teckentrup J, Schielzeth H. Spatial analyses of two color polymorphisms in an alpine grasshopper reveal a role of small-scale heterogeneity. Ecol Evol 2018; 8:7273-7284. [PMID: 30151148 PMCID: PMC6106198 DOI: 10.1002/ece3.4156] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 02/15/2018] [Accepted: 03/29/2018] [Indexed: 11/05/2022] Open
Abstract
Discrete color polymorphisms represent a fascinating aspect of intraspecific diversity. Color morph ratios often vary clinally, but in some cases, there are no marked clines and mixes of different morphs occur at appreciable frequencies in most populations. This poses the questions of how polymorphisms are maintained. We here study the spatial and temporal distribution of a very conspicuous color polymorphism in the club-legged grasshopper Gomphocerus sibiricus. The species occurs in a green and a nongreen (predominately brown) morph, a green-brown polymorphism that is common among Orthopteran insects. We sampled color morph ratios at 42 sites across the alpine range of the species and related color morph ratios to local habitat parameters and climatic conditions. Green morphs occurred in both sexes, and their morph ratios were highly correlated among sites, suggesting shared control of the polymorphism in females and males. We found that in at least 40 of 42 sites green and brown morphs co-occurred with proportions of green ranging from 0% to 70% with significant spatial heterogeneity. The proportion of green individuals tended to increase with decreasing summer and winter precipitations. Nongreen individuals can be further distinguished into brown and pied individuals, and again, this polymorphism is shared with other grasshopper species. We found pied individuals at all sites with proportions ranging from 3% to 75%, with slight, but significant variation between years. Pied morphs show a clinal increase in frequency from east to west and decreased with altitude and lower temperatures and were more common on grazed sites. The results suggest that both small-scale and large-scale spatial heterogeneity affects color morph ratios. The almost universal co-occurrence of all three color morphs argues against strong effects of genetic drift. Instead, the data suggest that small-scale migration-selection balance and/or local balancing selection maintain populations polymorphic.
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Affiliation(s)
- Petra Dieker
- Department of Evolutionary BiologyBielefeld UniversityBielefeldGermany
- Department of Population EcologyInstitute of Ecology and EvolutionFriedrich Schiller University JenaJenaGermany
| | - Luisa Beckmann
- Department of Evolutionary BiologyBielefeld UniversityBielefeldGermany
| | - Julia Teckentrup
- Department of Evolutionary BiologyBielefeld UniversityBielefeldGermany
| | - Holger Schielzeth
- Department of Evolutionary BiologyBielefeld UniversityBielefeldGermany
- Department of Population EcologyInstitute of Ecology and EvolutionFriedrich Schiller University JenaJenaGermany
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17
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Schielzeth H, Rios Villamil A, Burri R. Success and failure in replication of genotype-phenotype associations: How does replication help in understanding the genetic basis of phenotypic variation in outbred populations? Mol Ecol Resour 2018; 18:739-754. [PMID: 29575806 DOI: 10.1111/1755-0998.12780] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 03/09/2018] [Accepted: 03/09/2018] [Indexed: 12/29/2022]
Abstract
Recent developments in sequencing technologies have facilitated genomewide mapping of phenotypic variation in natural populations. Such mapping efforts face a number of challenges potentially leading to low reproducibility. However, reproducible research forms the basis of scientific progress. We here discuss the options for replication and the reasons for potential nonreproducibility. We then review the evidence for reproducible quantitative trait loci (QTL) with a focus on natural animal populations. Existing case studies of replication fall into three categories: (i) traits that have been mapped to major effect loci (including chromosomal inversion and supergenes) by independent research teams; (ii) QTL fine-mapped in discovery populations; and (iii) attempts to replicate QTL across multiple populations. Major effect loci, in particular those associated with inversions, have been successfully replicated in several cases within and across populations. Beyond such major effect variants, replication has been more successful within than across populations, suggesting that QTL discovered in natural populations may often be population-specific. This suggests that biological causes (differences in linkage patterns, allele frequencies or context-dependencies of QTL) contribute to nonreproducibility. Evidence from other fields, notably animal breeding and QTL mapping in humans, suggests that a significant fraction of QTL is indeed reproducible in direction and magnitude at least within populations. However, there is also a large number of QTL that cannot be easily reproduced. We put forward that more studies should explicitly address the causes and context-dependencies of QTL signals, in particular to disentangle linkage differences, allele frequency differences and gene-by-environment interactions as biological causes of nonreproducibility of QTL, especially between populations.
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Affiliation(s)
- Holger Schielzeth
- Population Ecology Group, Institute of Ecology and Evolution, Friedrich Schiller University, Jena, Germany
| | - Alejandro Rios Villamil
- Population Ecology Group, Institute of Ecology and Evolution, Friedrich Schiller University, Jena, Germany
| | - Reto Burri
- Population Ecology Group, Institute of Ecology and Evolution, Friedrich Schiller University, Jena, Germany
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18
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San-Jose LM, Roulin A. Genomics of coloration in natural animal populations. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0337. [PMID: 28533454 DOI: 10.1098/rstb.2016.0337] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2017] [Indexed: 12/28/2022] Open
Abstract
Animal coloration has traditionally been the target of genetic and evolutionary studies. However, until very recently, the study of the genetic basis of animal coloration has been mainly restricted to model species, whereas research on non-model species has been either neglected or mainly based on candidate approaches, and thereby limited by the knowledge obtained in model species. Recent high-throughput sequencing technologies allow us to overcome previous limitations, and open new avenues to study the genetic basis of animal coloration in a broader number of species and colour traits, and to address the general relevance of different genetic structures and their implications for the evolution of colour. In this review, we highlight aspects where genome-wide studies could be of major utility to fill in the gaps in our understanding of the biology and evolution of animal coloration. The new genomic approaches have been promptly adopted to study animal coloration although substantial work is still needed to consider a larger range of species and colour traits, such as those exhibiting continuous variation or based on reflective structures. We argue that a robust advancement in the study of animal coloration will also require large efforts to validate the functional role of the genes and variants discovered using genome-wide tools.This article is part of the themed issue 'Animal coloration: production, perception, function and application'.
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Affiliation(s)
- Luis M San-Jose
- Department of Ecology and Evolution, University of Lausanne, Building Le Biophore, 1015 Lausanne, Switzerland
| | - Alexandre Roulin
- Department of Ecology and Evolution, University of Lausanne, Building Le Biophore, 1015 Lausanne, Switzerland
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19
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Armstrong C, Richardson DS, Hipperson H, Horsburgh GJ, Küpper C, Percival‐Alwyn L, Clark M, Burke T, Spurgin LG. Genomic associations with bill length and disease reveal drift and selection across island bird populations. Evol Lett 2018; 2:22-36. [PMID: 30283662 PMCID: PMC6121843 DOI: 10.1002/evl3.38] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 12/15/2022] Open
Abstract
Island species provide excellent models for investigating how selection and drift operate in wild populations, and for determining how these processes act to influence local adaptation and speciation. Here, we examine the role of selection and drift in shaping genomic and phenotypic variation across recently separated populations of Berthelot's pipit (Anthus berthelotii), a passerine bird endemic to three archipelagos in the Atlantic. We first characterized genetic diversity and population structuring that supported previous inferences of a history of recent colonizations and bottlenecks. We then tested for regions of the genome associated with the ecologically important traits of bill length and malaria infection, both of which vary substantially across populations in this species. We identified a SNP associated with variation in bill length among individuals, islands, and archipelagos; patterns of variation at this SNP suggest that both phenotypic and genotypic variation in bill length is largely shaped by founder effects. Malaria was associated with SNPs near/within genes involved in the immune response, but this relationship was not consistent among archipelagos, supporting the view that disease resistance is complex and rapidly evolving. Although we found little evidence for divergent selection at candidate loci for bill length and malaria resistance, genome scan analyses pointed to several genes related to immunity and metabolism as having important roles in divergence and adaptation. Our findings highlight the utility and challenges involved with combining association mapping and population genetic analysis in nonequilibrium populations, to disentangle the effects of drift and selection on shaping genotypes and phenotypes.
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Affiliation(s)
- Claire Armstrong
- School of Biological Sciences, University of East AngliaNorwich Research ParkNorwich NR4 7TJUnited Kingdom
| | - David S. Richardson
- School of Biological Sciences, University of East AngliaNorwich Research ParkNorwich NR4 7TJUnited Kingdom
| | - Helen Hipperson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant SciencesUniversity of SheffieldSheffield S10 2TNUnited Kingdom
| | - Gavin J. Horsburgh
- NERC Biomolecular Analysis Facility, Department of Animal and Plant SciencesUniversity of SheffieldSheffield S10 2TNUnited Kingdom
| | - Clemens Küpper
- Max Planck Institute for Ornithology82319 SeewiesenGermany
| | | | - Matt Clark
- Earlham InstituteNorwich Research ParkNorwich NR4 7UZUnited Kingdom
| | - Terry Burke
- NERC Biomolecular Analysis Facility, Department of Animal and Plant SciencesUniversity of SheffieldSheffield S10 2TNUnited Kingdom
| | - Lewis G. Spurgin
- School of Biological Sciences, University of East AngliaNorwich Research ParkNorwich NR4 7TJUnited Kingdom
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20
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Lindtke D, Lucek K, Soria-Carrasco V, Villoutreix R, Farkas TE, Riesch R, Dennis SR, Gompert Z, Nosil P. Long-term balancing selection on chromosomal variants associated with crypsis in a stick insect. Mol Ecol 2017; 26:6189-6205. [DOI: 10.1111/mec.14280] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 07/12/2017] [Accepted: 07/24/2017] [Indexed: 01/02/2023]
Affiliation(s)
- Dorothea Lindtke
- Department of Biological Sciences; University of Calgary; Calgary AB Canada
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
| | - Kay Lucek
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
- Department of Environmental Sciences; University of Basel; Basel Switzerland
| | | | - Romain Villoutreix
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
| | - Timothy E. Farkas
- Department of Ecology and Evolutionary Biology; University of Connecticut; Storrs CT USA
| | - Rüdiger Riesch
- School of Biological Sciences; Royal Holloway; University of London; Egham UK
| | - Stuart R. Dennis
- Department of Aquatic Ecology; Eawag: Swiss Federal Institute of Aquatic Science and Technology; Dübendorf Switzerland
| | - Zach Gompert
- Department of Biology; Utah State University; Logan UT USA
| | - Patrik Nosil
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
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21
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McGirr JA, Martin CH. Novel Candidate Genes Underlying Extreme Trophic Specialization in Caribbean Pupfishes. Mol Biol Evol 2017; 34:873-888. [PMID: 28028132 PMCID: PMC5850223 DOI: 10.1093/molbev/msw286] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The genetic changes responsible for evolutionary transitions from generalist to specialist phenotypes are poorly understood. Here we examine the genetic basis of craniofacial traits enabling novel trophic specialization in a sympatric radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas. This recent radiation consists of a generalist species and two novel specialists: a small-jawed "snail-eater" and a large-jawed "scale-eater." We genotyped 12 million single nucleotide polymorphisms (SNPs) by whole-genome resequencing of 37 individuals of all three species from nine populations and integrated genome-wide divergence scans with association mapping to identify divergent regions containing putatively causal SNPs affecting jaw size-the most rapidly diversifying trait in this radiation. A mere 22 fixed variants accompanied extreme ecological divergence between generalist and scale-eater species. We identified 31 regions (20 kb) containing variants fixed between specialists that were significantly associated with variation in jaw size which contained 11 genes annotated for skeletal system effects and 18 novel candidate genes never previously associated with craniofacial phenotypes. Six of these 31 regions showed robust signs of hard selective sweeps after accounting for demographic history. Our data are consistent with predictions based on quantitative genetic models of adaptation, suggesting that the effect sizes of regions influencing jaw phenotypes are positively correlated with distance between fitness peaks on a complex adaptive landscape.
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Affiliation(s)
- Joseph A. McGirr
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC
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22
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Rodríguez-Verdugo A, Buckley J, Stapley J. The genomic basis of eco-evolutionary dynamics. Mol Ecol 2017; 26:1456-1464. [PMID: 28160333 DOI: 10.1111/mec.14045] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 01/22/2017] [Accepted: 01/25/2017] [Indexed: 12/30/2022]
Abstract
Recent recognition that ecological and evolutionary processes can operate on similar timescales has led to a rapid increase in theoretical and empirical studies on eco-evolutionary dynamics. Progress in the fields of evolutionary biology, genomics and ecology is greatly enhancing our understanding of rapid adaptive processes, the predictability of adaptation and the genetics of ecologically important traits. However, progress in these fields has proceeded largely independently of one another. In an attempt to better integrate these fields, the centre for 'Adaptation to a Changing Environment' organized a conference entitled 'The genomic basis of eco-evolutionary change' and brought together experts in ecological genomics and eco-evolutionary dynamics. In this review, we use the work of the invited speakers to summarize eco-evolutionary dynamics and discuss how they are relevant for understanding and predicting responses to contemporary environmental change. Then, we show how recent advances in genomics are contributing to our understanding of eco-evolutionary dynamics. Finally, we highlight the gaps in our understanding of eco-evolutionary dynamics and recommend future avenues of research in eco-evolutionary dynamics.
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Affiliation(s)
- Alejandra Rodríguez-Verdugo
- Adaptation to a Changing Environment, ETH Zürich, 8092, Zürich, Switzerland.,Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland
| | - James Buckley
- Adaptation to a Changing Environment, ETH Zürich, 8092, Zürich, Switzerland
| | - Jessica Stapley
- Adaptation to a Changing Environment, ETH Zürich, 8092, Zürich, Switzerland
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23
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Vertacnik KL, Linnen CR. Evolutionary genetics of host shifts in herbivorous insects: insights from the age of genomics. Ann N Y Acad Sci 2017; 1389:186-212. [DOI: 10.1111/nyas.13311] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/16/2016] [Accepted: 12/22/2016] [Indexed: 12/25/2022]
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24
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Byers KJRP, Xu S, Schlüter PM. Molecular mechanisms of adaptation and speciation: why do we need an integrative approach? Mol Ecol 2016; 26:277-290. [DOI: 10.1111/mec.13678] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/18/2016] [Accepted: 04/21/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Kelsey J. R. P. Byers
- Department of Systematic and Evolutionary Botany; University of Zurich; Zollikerstrasse 107 CH-8008 Zurich Switzerland
| | - Shuqing Xu
- Max Planck Institute for Chemical Ecology; Hans-Knöll-Straße 8 D-07745 Jena Germany
| | - Philipp M. Schlüter
- Department of Systematic and Evolutionary Botany; University of Zurich; Zollikerstrasse 107 CH-8008 Zurich Switzerland
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