1
|
Banse P, Elena SF, Beslon G. Innovation in viruses: fitness valley crossing, neutral landscapes, or just duplications? Virus Evol 2024; 10:veae078. [PMID: 39386076 PMCID: PMC11463231 DOI: 10.1093/ve/veae078] [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: 12/13/2023] [Revised: 07/19/2024] [Accepted: 09/18/2024] [Indexed: 10/12/2024] Open
Abstract
Viruses evolve by periods of relative stasis interleaved with sudden, rapid series of mutation fixations, known as evolutionary bursts. These bursts can be triggered by external factors, such as environmental changes, antiviral therapies, or spill-overs from reservoirs into novel host species. However, it has also been suggested that bursts may result from the intrinsic evolutionary dynamics of viruses. Indeed, bursts could be caused by fitness valley crossing, or a neutral exploration of a fitness plateau until an escape mutant is found. In order to investigate the importance of these intrinsic causes of evolutionary bursts, we used a simulation software package to perform massive evolution experiments of viral-like genomes. We tested two conditions: (i) after an external change and (ii) in a constant environment, with the latter condition guaranteeing the absence of an external triggering factor. As expected, an external change was almost systematically followed by an evolutionary burst. However, we also observed bursts in the constant environment as well, albeit much less frequently. We analyzed how many of these bursts are triggered by deleterious, quasi-neutral, or beneficial mutations and show that, while bursts can occasionally be triggered by valley crossing or traveling along neutral ridges, many of them were triggered by chromosomal rearrangements and, in particular, segmental duplications. Our results suggest that combinatorial differences between the different mutation types lead to punctuated evolutionary dynamics, with long periods of stasis occasionally interrupted by short periods of rapid evolution, akin to what is observed in virus evolution.
Collapse
Affiliation(s)
- Paul Banse
- INSA Lyon, INRIA, CNRS, Universite Claude Bernard Lyon 1, Ecole Centrale de Lyon, Université Lumière Lyon 2, LIRIS, UMR5205, Villeurbanne 69621, France
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Catedrático Agustín Escardino 9, Paterna, Valencia 46980, Spain
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Guillaume Beslon
- INSA Lyon, INRIA, CNRS, Universite Claude Bernard Lyon 1, Ecole Centrale de Lyon, Université Lumière Lyon 2, LIRIS, UMR5205, Villeurbanne 69621, France
| |
Collapse
|
2
|
Tawfeeq MT, Voordeckers K, van den Berg P, Govers SK, Michiels J, Verstrepen KJ. Mutational robustness and the role of buffer genes in evolvability. EMBO J 2024; 43:2294-2307. [PMID: 38719995 PMCID: PMC11183146 DOI: 10.1038/s44318-024-00109-1] [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: 11/08/2023] [Revised: 03/19/2024] [Accepted: 04/17/2024] [Indexed: 06/19/2024] Open
Abstract
Organisms rely on mutations to fuel adaptive evolution. However, many mutations impose a negative effect on fitness. Cells may have therefore evolved mechanisms that affect the phenotypic effects of mutations, thus conferring mutational robustness. Specifically, so-called buffer genes are hypothesized to interact directly or indirectly with genetic variation and reduce its effect on fitness. Environmental or genetic perturbations can change the interaction between buffer genes and genetic variation, thereby unmasking the genetic variation's phenotypic effects and thus providing a source of variation for natural selection to act on. This review provides an overview of our understanding of mutational robustness and buffer genes, with the chaperone gene HSP90 as a key example. It discusses whether buffer genes merely affect standing variation or also interact with de novo mutations, how mutational robustness could influence evolution, and whether mutational robustness might be an evolved trait or rather a mere side-effect of complex genetic interactions.
Collapse
Affiliation(s)
- Mohammed T Tawfeeq
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Karin Voordeckers
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Pieter van den Berg
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | | | - Jan Michiels
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Kevin J Verstrepen
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium.
| |
Collapse
|
3
|
Liu X, Xiao C, Xu X, Zhang J, Mo F, Chen JY, Delihas N, Zhang L, An NA, Li CY. Origin of functional de novo genes in humans from "hopeful monsters". WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1845. [PMID: 38605485 DOI: 10.1002/wrna.1845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/13/2024]
Abstract
For a long time, it was believed that new genes arise only from modifications of preexisting genes, but the discovery of de novo protein-coding genes that originated from noncoding DNA regions demonstrates the existence of a "motherless" origination process for new genes. However, the features, distributions, expression profiles, and origin modes of these genes in humans seem to support the notion that their origin is not a purely "motherless" process; rather, these genes arise preferentially from genomic regions encoding preexisting precursors with gene-like features. In such a case, the gene loci are typically not brand new. In this short review, we will summarize the definition and features of human de novo genes and clarify their process of origination from ancestral non-coding genomic regions. In addition, we define the favored precursors, or "hopeful monsters," for the origin of de novo genes and present a discussion of the functional significance of these young genes in brain development and tumorigenesis in humans. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.
Collapse
Affiliation(s)
- Xiaoge Liu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Chunfu Xiao
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Xinwei Xu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jie Zhang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Fan Mo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jia-Yu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Nicholas Delihas
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Li Zhang
- Chinese Institute for Brain Research, Beijing, China
| | - Ni A An
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Chuan-Yun Li
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Chinese Institute for Brain Research, Beijing, China
- Southwest United Graduate School, Kunming, China
| |
Collapse
|
4
|
Kovuri P, Yadav A, Sinha H. Role of genetic architecture in phenotypic plasticity. Trends Genet 2023; 39:703-714. [PMID: 37173192 DOI: 10.1016/j.tig.2023.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 04/06/2023] [Accepted: 04/11/2023] [Indexed: 05/15/2023]
Abstract
Phenotypic plasticity, the ability of an organism to display different phenotypes across environments, is widespread in nature. Plasticity aids survival in novel environments. Herein, we review studies from yeast that allow us to start uncovering the genetic architecture of phenotypic plasticity. Genetic variants and their interactions impact the phenotype in different environments, and distinct environments modulate the impact of genetic variants and their interactions on the phenotype. Because of this, certain hidden genetic variation is expressed in specific genetic and environmental backgrounds. A better understanding of the genetic mechanisms of phenotypic plasticity will help to determine short- and long-term responses to selection and how wide variation in disease manifestation occurs in human populations.
Collapse
Affiliation(s)
- Purnima Kovuri
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, IIT Madras, Chennai, India; Centre for Integrative Biology and Systems mEdicine (IBSE), IIT Madras, Chennai, India; Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai, India
| | - Anupama Yadav
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Himanshu Sinha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, IIT Madras, Chennai, India; Centre for Integrative Biology and Systems mEdicine (IBSE), IIT Madras, Chennai, India; Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai, India.
| |
Collapse
|
5
|
Rust J. Phenotype-first hypotheses, spandrels and early metazoan evolution. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2022; 44:48. [PMID: 36257998 DOI: 10.1007/s40656-022-00531-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Against the neo-Darwinian assumption that genetic factors are the principal source of variation upon which natural selection operates, a phenotype-first hypothesis strikes us as revolutionary because development would seem to constitute an independent source of variability. Richard Watson and his co-authors have argued that developmental memory constitutes one such variety of phenotypic variability. While this version of the phenotype-first hypothesis is especially well-suited for the late metazoan context, where animals have a sufficient history of selection from which to draw, appeals to developmental memory seem less plausible in the evolutionary context of the early metazoans. I provide an interpretation of Stuart Newman's account of deep metazoan phylogenesis that suggests that spandrels are, in addition to developmental memory, an important reservoir of phenotypic variability. I conclude by arguing that Gerd Müller's "side-effect hypothesis" is an illuminating generalization of the proposed non-Watsonian version of the phenotype-first hypothesis.
Collapse
Affiliation(s)
- Joshua Rust
- Stetson University, Unit 8250, 104-C Elizabeth Hall, 421 North Woodland Boulevard, DeLand, Florida, 32723, USA.
| |
Collapse
|
6
|
Parikh SB, Houghton C, Van Oss SB, Wacholder A, Carvunis A. Origins, evolution, and physiological implications of de novo genes in yeast. Yeast 2022; 39:471-481. [PMID: 35959631 PMCID: PMC9544372 DOI: 10.1002/yea.3810] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 12/03/2022] Open
Abstract
De novo gene birth is the process by which new genes emerge in sequences that were previously noncoding. Over the past decade, researchers have taken advantage of the power of yeast as a model and a tool to study the evolutionary mechanisms and physiological implications of de novo gene birth. We summarize the mechanisms that have been proposed to explicate how noncoding sequences can become protein-coding genes, highlighting the discovery of pervasive translation of the yeast transcriptome and its presumed impact on evolutionary innovation. We summarize current best practices for the identification and characterization of de novo genes. Crucially, we explain that the field is still in its nascency, with the physiological roles of most young yeast de novo genes identified thus far still utterly unknown. We hope this review inspires researchers to investigate the true contribution of de novo gene birth to cellular physiology and phenotypic diversity across yeast strains and species.
Collapse
Affiliation(s)
- Saurin B. Parikh
- Department of Computational and Systems Biology, School of Medicine, Pittsburgh Center for Evolutionary Biology and EvolutionUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Carly Houghton
- Department of Computational and Systems Biology, School of Medicine, Pittsburgh Center for Evolutionary Biology and EvolutionUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - S. Branden Van Oss
- Department of Computational and Systems Biology, School of Medicine, Pittsburgh Center for Evolutionary Biology and EvolutionUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Aaron Wacholder
- Department of Computational and Systems Biology, School of Medicine, Pittsburgh Center for Evolutionary Biology and EvolutionUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Anne‐Ruxandra Carvunis
- Department of Computational and Systems Biology, School of Medicine, Pittsburgh Center for Evolutionary Biology and EvolutionUniversity of PittsburghPittsburghPennsylvaniaUSA
| |
Collapse
|
7
|
Romero Romero ML, Landerer C, Poehls J, Toth‐Petroczy A. Phenotypic mutations contribute to protein diversity and shape protein evolution. Protein Sci 2022; 31:e4397. [PMID: 36040266 PMCID: PMC9375231 DOI: 10.1002/pro.4397] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/14/2022] [Accepted: 07/04/2022] [Indexed: 11/16/2022]
Abstract
Errors in DNA replication generate genetic mutations, while errors in transcription and translation lead to phenotypic mutations. Phenotypic mutations are orders of magnitude more frequent than genetic ones, yet they are less understood. Here, we review the types of phenotypic mutations, their quantifications, and their role in protein evolution and disease. The diversity generated by phenotypic mutation can facilitate adaptive evolution. Indeed, phenotypic mutations, such as ribosomal frameshift and stop codon readthrough, sometimes serve to regulate protein expression and function. Phenotypic mutations have often been linked to fitness decrease and diseases. Thus, understanding the protein heterogeneity and phenotypic diversity caused by phenotypic mutations will advance our understanding of protein evolution and have implications on human health and diseases.
Collapse
Affiliation(s)
- Maria Luisa Romero Romero
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
| | - Cedric Landerer
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
| | - Jonas Poehls
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
| | - Agnes Toth‐Petroczy
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
- Cluster of Excellence Physics of LifeTU DresdenDresdenGermany
| |
Collapse
|
8
|
Diaz Arenas C, Ardaševa A, Miller J, Mikheyev AS, Yokobayashi Y. Ribozyme Mutagenic Evolution: Mechanisms of Survival. ORIGINS LIFE EVOL B 2022; 51:321-339. [PMID: 34994918 DOI: 10.1007/s11084-021-09617-0] [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: 04/18/2021] [Accepted: 11/16/2021] [Indexed: 11/24/2022]
Abstract
Primeval populations replicating at high error rates required a mechanism to overcome the accumulation of mutations and information deterioration. Known strategies to overcome mutation pressures include RNA processivity, epistasis, selection, and quasispecies. We investigated the mechanism by which small molecular ribozyme populations can survive under high error rates by propagating several lineages under different mutagen concentrations. We found that every population that evolved without mutagen went extinct, while those subjected to mutagenic evolution survived. To understand how they survived, we characterized the evolved genotypic diversity, the formation of genotype-genotype interaction networks, the fitness of the most common mutants for each enzymatic step, and changes in population size along the course of evolution. We found that the elevated mutation rate was necessary for the populations to survive in the novel environment, in which all the steps of the metabolism worked to promote the survival of even less catalytically efficient ligases. Besides, an increase in population size and the mutational coupling of genotypes in close-knit networks, which helped maintain or recover lost genotypes making their disappearance transient, prevented Muller's ratchet and extinction.
Collapse
Affiliation(s)
- Carolina Diaz Arenas
- Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa Prefecture, Japan. .,Yale University, New Haven, CT, USA.
| | - Aleksandra Ardaševa
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
| | - Jonathan Miller
- Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa Prefecture, Japan
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa Prefecture, Japan.,Evolutionary Genomics Lab, Research School of Biology, Australian National University, Canberra, Australia
| | - Yohei Yokobayashi
- Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa Prefecture, Japan
| |
Collapse
|
9
|
Ogbunugafor CB. The mutation effect reaction norm (mu-rn) highlights environmentally dependent mutation effects and epistatic interactions. Evolution 2022; 76:37-48. [PMID: 34989399 DOI: 10.1111/evo.14428] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/23/2021] [Indexed: 11/27/2022]
Abstract
Since the modern synthesis, the fitness effects of mutations and epistasis have been central yet provocative concepts in evolutionary and population genetics. Studies of how the interactions between parcels of genetic information can change as a function of environmental context have added a layer of complexity to these discussions. Here I introduce the "mutation effect reaction norm" (Mu-RN), a new instrument through which one can analyze the phenotypic consequences of mutations and interactions across environmental contexts. It embodies the fusion of measurements of genetic interactions with the reaction norm, a classic depiction of the performance of genotypes across environments. I demonstrate the utility of the Mu-RN through the signature of a "compensatory ratchet" mutation that undermines reverse evolution of antimicrobial resistance. More broadly, I argue that the mutation effect reaction norm may help us resolve the dynamism and unpredictability of evolution, with implications for theoretical biology, genetic modification technology, and public health. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- C Brandon Ogbunugafor
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| |
Collapse
|
10
|
Zou X, Schaefke B, Li Y, Jia F, Sun W, Li G, Liang W, Reif T, Heyd F, Gao Q, Tian S, Li Y, Tang Y, Fang L, Hu Y, Chen W. Mammalian splicing divergence is shaped by drift, buffering in trans, and a scaling law. Life Sci Alliance 2022; 5:5/4/e202101333. [PMID: 34969779 PMCID: PMC8739531 DOI: 10.26508/lsa.202101333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 11/24/2022] Open
Abstract
This study globally investigates the allelic splicing pattern in multiple tissues of an F1 hybrid mouse and reveals the underlying driving forces shaping such tissue-dependent splicing divergence. Alternative splicing is ubiquitous, but the mechanisms underlying its pattern of evolutionary divergence across mammalian tissues are still underexplored. Here, we investigated the cis-regulatory divergences and their relationship with tissue-dependent trans-regulation in multiple tissues of an F1 hybrid between two mouse species. Large splicing changes between tissues are highly conserved and likely reflect functional tissue-dependent regulation. In particular, micro-exons frequently exhibit this pattern with high inclusion levels in the brain. Cis-divergence of splicing appears to be largely non-adaptive. Although divergence is in general associated with higher densities of sequence variants in regulatory regions, events with high usage of the dominant isoform apparently tolerate more mutations, explaining why their exon sequences are highly conserved but their intronic splicing site flanking regions are not. Moreover, we demonstrate that non-adaptive mutations are often masked in tissues where accurate splicing likely is more important, and experimentally attribute such buffering effect to trans-regulatory splicing efficiency.
Collapse
Affiliation(s)
- Xudong Zou
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Bernhard Schaefke
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
| | - Yisheng Li
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Fujian Jia
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wei Sun
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Guipeng Li
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
| | - Weizheng Liang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Tristan Reif
- Institute for Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Florian Heyd
- Institute for Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Qingsong Gao
- Laboratory for Systems Biology and Functional Genomics, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Shuye Tian
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yanping Li
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yisen Tang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Liang Fang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
| | - Yuhui Hu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wei Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China .,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
| |
Collapse
|
11
|
Differential effects of steroid hormones on levels of broad-sense heritability in a wild bird: possible mechanism of environment × genetic variance interaction? Heredity (Edinb) 2022; 128:63-76. [PMID: 34921237 PMCID: PMC8733014 DOI: 10.1038/s41437-021-00490-1] [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: 01/24/2021] [Revised: 11/27/2021] [Accepted: 11/30/2021] [Indexed: 01/03/2023] Open
Abstract
Genetic variation is one of the key concepts in evolutionary biology and an important prerequisite of evolutionary change. However, we know very little about processes that modulate its levels in wild populations. In particular, we still are to understand why genetic variances often depend on environmental conditions. One of possible environment-sensitive modulators of observed levels of genetic variance are maternal effects. In this study we attempt to experimentally test the hypothesis that maternally transmitted agents (e.g. hormones) may influence the expression of genetic variance in quantitative traits in the offspring. We manipulated the levels of steroid hormones (testosterone and corticosterone) in eggs laid by blue tits in a wild population. Our experimental setup allowed for full crossing of genetic and rearing effects with the experimental manipulation. We observed that birds treated with corticosterone exhibited a significant decrease in broad-sense genetic variance of tarsus length, and an increase in this component in body mass on the 2nd day post-hatching. Our study indicates, that maternally transmitted substances such as hormones may have measurable impact on the levels of genetic variance and hence, on the evolutionary potential of quantitative traits.
Collapse
|
12
|
Watson AK, Lopez P, Bapteste E. Hundreds of out-of-frame remodelled gene families in the E. coli pangenome. Mol Biol Evol 2021; 39:6430988. [PMID: 34792602 PMCID: PMC8788219 DOI: 10.1093/molbev/msab329] [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] [Indexed: 01/01/2023] Open
Abstract
All genomes include gene families with very limited taxonomic distributions that potentially represent new genes and innovations in protein-coding sequence, raising questions on the origins of such genes. Some of these genes are hypothesized to have formed de novo, from noncoding sequences, and recent work has begun to elucidate the processes by which de novo gene formation can occur. A special case of de novo gene formation, overprinting, describes the origin of new genes from noncoding alternative reading frames of existing open reading frames (ORFs). We argue that additionally, out-of-frame gene fission/fusion events of alternative reading frames of ORFs and out-of-frame lateral gene transfers could contribute to the origin of new gene families. To demonstrate this, we developed an original pattern-search in sequence similarity networks, enhancing the use of these graphs, commonly used to detect in-frame remodeled genes. We applied this approach to gene families in 524 complete genomes of Escherichia coli. We identified 767 gene families whose evolutionary history likely included at least one out-of-frame remodeling event. These genes with out-of-frame components represent ∼2.5% of all genes in the E. coli pangenome, suggesting that alternative reading frames of existing ORFs can contribute to a significant proportion of de novo genes in bacteria.
Collapse
Affiliation(s)
- Andrew K Watson
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, 7, quai Saint Bernard, Paris, 75005, France
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, 7, quai Saint Bernard, Paris, 75005, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, 7, quai Saint Bernard, Paris, 75005, France
| |
Collapse
|
13
|
Zheng J, Guo N, Wagner A. Mistranslation reduces mutation load in evolving proteins through negative epistasis with DNA mutations. Mol Biol Evol 2021; 38:4792-4804. [PMID: 34255074 PMCID: PMC8557407 DOI: 10.1093/molbev/msab206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Translational errors during protein synthesis cause phenotypic mutations that are several orders of magnitude more frequent than DNA mutations. Such phenotypic mutations may affect adaptive evolution through their interactions with DNA mutations. To study how mistranslation may affect the adaptive evolution of evolving proteins, we evolved populations of green fluorescent protein (GFP) in either high-mistranslation or low-mistranslation Escherichia coli hosts. In both hosts, we first evolved GFP under purifying selection for the ancestral phenotype green fluorescence, and then under directional selection toward the new phenotype yellow fluorescence. High-mistranslation populations evolved modestly higher yellow fluorescence during each generation of evolution than low-mistranslation populations. We demonstrate by high-throughput sequencing that elevated mistranslation reduced the accumulation of deleterious DNA mutations under both purifying and directional selection. It did so by amplifying the fitness effects of deleterious DNA mutations through negative epistasis with phenotypic mutations. In contrast, mistranslation did not affect the incidence of beneficial mutations. Our findings show that phenotypic mutations interact epistatically with DNA mutations. By reducing a population’s mutation load, mistranslation can affect an important determinant of evolvability.
Collapse
Affiliation(s)
- Jia Zheng
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, Switzerland
| | - Ning Guo
- Zwirnereistrasse 11, Wallisellen, Zurich, Switzerland
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, Switzerland.,The Santa Fe Institute, Santa Fe, New Mexico, USA
| |
Collapse
|
14
|
Maddamsetti R. Universal Constraints on Protein Evolution in the Long-Term Evolution Experiment with Escherichia coli. Genome Biol Evol 2021; 13:evab070. [PMID: 33856016 PMCID: PMC8233687 DOI: 10.1093/gbe/evab070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2021] [Indexed: 12/18/2022] Open
Abstract
Although it is well known that abundant proteins evolve slowly across the tree of life, there is little consensus for why this is true. Here, I report that abundant proteins evolve slowly in the hypermutator populations of Lenski's long-term evolution experiment with Escherichia coli (LTEE). Specifically, the density of all observed mutations per gene, as measured in metagenomic time series covering 60,000 generations of the LTEE, significantly anticorrelates with mRNA abundance, protein abundance, and degree of protein-protein interaction. The same pattern holds for nonsynonymous mutation density. However, synonymous mutation density, measured across the LTEE hypermutator populations, positively correlates with protein abundance. These results show that universal constraints on protein evolution are visible in data spanning three decades of experimental evolution. Therefore, it should be possible to design experiments to answer why abundant proteins evolve slowly.
Collapse
Affiliation(s)
- Rohan Maddamsetti
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| |
Collapse
|
15
|
Kosinski LJ, Masel J. Readthrough Errors Purge Deleterious Cryptic Sequences, Facilitating the Birth of Coding Sequences. Mol Biol Evol 2021; 37:1761-1774. [PMID: 32101291 DOI: 10.1093/molbev/msaa046] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
De novo protein-coding innovations sometimes emerge from ancestrally noncoding DNA, despite the expectation that translating random sequences is overwhelmingly likely to be deleterious. The "preadapting selection" hypothesis claims that emergence is facilitated by prior, low-level translation of noncoding sequences via molecular errors. It predicts that selection on polypeptides translated only in error is strong enough to matter and is strongest when erroneous expression is high. To test this hypothesis, we examined noncoding sequences located downstream of stop codons (i.e., those potentially translated by readthrough errors) in Saccharomyces cerevisiae genes. We identified a class of "fragile" proteins under strong selection to reduce readthrough, which are unlikely substrates for co-option. Among the remainder, sequences showing evidence of readthrough translation, as assessed by ribosome profiling, encoded C-terminal extensions with higher intrinsic structural disorder, supporting the preadapting selection hypothesis. The cryptic sequences beyond the stop codon, rather than spillover effects from the regular C-termini, are primarily responsible for the higher disorder. Results are robust to controlling for the fact that stronger selection also reduces the length of C-terminal extensions. These findings indicate that selection acts on 3' UTRs in Saccharomyces cerevisiae to purge potentially deleterious variants of cryptic polypeptides, acting more strongly in genes that experience more readthrough errors.
Collapse
Affiliation(s)
- Luke J Kosinski
- Molecular and Cellular Biology, University of Arizona, Tucson, AZ
| | - Joanna Masel
- Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
| |
Collapse
|
16
|
Evolution in the weak-mutation limit: Stasis periods punctuated by fast transitions between saddle points on the fitness landscape. Proc Natl Acad Sci U S A 2021; 118:2015665118. [PMID: 33472973 PMCID: PMC7848522 DOI: 10.1073/pnas.2015665118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The gradual character of evolution is a key feature of the Darwinian worldview. However, macroevolutionary events are often thought to occur in a nongradualist manner, in a regime known as punctuated equilibrium, whereby extended periods of evolutionary stasis are punctuated by rapid transitions between states. Here we analyze a simple mathematical model of population evolution on fitness landscapes and show that, for a large population in the weak-mutation limit, the process of adaptive evolution consists of extended periods of stasis, which the population spends around saddle points on the landscape, interrupted by rapid transitions to new saddle points when a beneficial mutation is fixed. Thus, phenomenologically, the default regime of biological evolution seems to closely resemble punctuated equilibrium. A mathematical analysis of the evolution of a large population under the weak-mutation limit shows that such a population would spend most of the time in stasis in the vicinity of saddle points on the fitness landscape. The periods of stasis are punctuated by fast transitions, in lnNe/s time (Ne, effective population size; s, selection coefficient of a mutation), when a new beneficial mutation is fixed in the evolving population, which accordingly moves to a different saddle, or on much rarer occasions from a saddle to a local peak. Phenomenologically, this mode of evolution of a large population resembles punctuated equilibrium (PE) whereby phenotypic changes occur in rapid bursts that are separated by much longer intervals of stasis during which mutations accumulate but the phenotype does not change substantially. Theoretically, PE has been linked to self-organized criticality (SOC), a model in which the size of “avalanches” in an evolving system is power-law-distributed, resulting in increasing rarity of major events. Here we show, however, that a PE-like evolutionary regime is the default for a very simple model of an evolving population that does not rely on SOC or any other special conditions.
Collapse
|
17
|
Jakobson CM, Jarosz DF. What Has a Century of Quantitative Genetics Taught Us About Nature's Genetic Tool Kit? Annu Rev Genet 2020; 54:439-464. [PMID: 32897739 DOI: 10.1146/annurev-genet-021920-102037] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The complexity of heredity has been appreciated for decades: Many traits are controlled not by a single genetic locus but instead by polymorphisms throughout the genome. The importance of complex traits in biology and medicine has motivated diverse approaches to understanding their detailed genetic bases. Here, we focus on recent systematic studies, many in budding yeast, which have revealed that large numbers of all kinds of molecular variation, from noncoding to synonymous variants, can make significant contributions to phenotype. Variants can affect different traits in opposing directions, and their contributions can be modified by both the environment and the epigenetic state of the cell. The integration of prospective (synthesizing and analyzing variants) and retrospective (examining standing variation) approaches promises to reveal how natural selection shapes quantitative traits. Only by comprehensively understanding nature's genetic tool kit can we predict how phenotypes arise from the complex ensembles of genetic variants in living organisms.
Collapse
Affiliation(s)
- Christopher M Jakobson
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA;
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA; .,Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| |
Collapse
|
18
|
Ruocco N, Bertocci I, Munari M, Musco L, Caramiello D, Danovaro R, Zupo V, Costantini M. Morphological and molecular responses of the sea urchin Paracentrotus lividus to highly contaminated marine sediments: The case study of Bagnoli-Coroglio brownfield (Mediterranean Sea). MARINE ENVIRONMENTAL RESEARCH 2020; 154:104865. [PMID: 32056706 DOI: 10.1016/j.marenvres.2019.104865] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/12/2019] [Accepted: 12/14/2019] [Indexed: 06/10/2023]
Abstract
Marine sediments store complex mixtures of compounds, including heavy metals, organotins and a large array of other contaminants. Sediment quality monitoring, characterization and management are priorities, due to potential impacts of the above compounds on coastal waters and their biota, especially in cases of pollutants released during dredging activities. Harbours and marinas, as well as estuaries and bays, where limited exchanges of water occurr, the accumulation of toxic compounds poses major concerns for human and environmental health. Here we report the effects of highly contaminated sediments from the site of national interest Bagnoli-Coroglio (Tyrrhenian Sea, Western Mediterranean) on the sea urchin Paracentrotus lividus, considered a good model for ecotoxicological studies. Adult sea urchins were reared one month in aquaria in the presence of contaminated sediment that was experimentally subject to different patterns of re-suspension events (mimicking the effect of natural storms occurring in the field), crossed with O2 enrichment versus natural gas exchanges in the water. The development of embryos deriving from adult urchins exposed to such experimental conditions was followed until the pluteus stage, checking the power of contaminated sediment to induce morphological malformations and its eventual buffering by high oxygenation. Real-Time qPCR analysis revealed that the expression of several genes (among the fifty analyzed, involved in different functional processes) was targeted by contaminated sediments more than those exposed in oxygen-enriched condition. Our findings have biological and ecological relevance in terms of assessing the actual impact on local organisms of chronic environmental contamination by heavy metals and polycyclic aromatic hydrocarbons affecting the Bagnoli-Coroglio area, and of exploring enhanced sediment and water oxygenation as a promising tool to mitigate the effects of contamination in future environmental restoration actions.
Collapse
Affiliation(s)
- Nadia Ruocco
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Iacopo Bertocci
- Department of Biology, University of Pisa, CoNISMa, Via Derna 1, 56126, Pisa, Italy; Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn,Villa Comunale, 80121, Naples, Italy
| | - Marco Munari
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn,Villa Comunale, 80121, Naples, Italy
| | - Luigi Musco
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn,Villa Comunale, 80121, Naples, Italy
| | - Davide Caramiello
- Unit Marine Resources for Research, Stazione Zoologica Anton Dohrn, 80121, Naples, Italy
| | - Roberto Danovaro
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy; Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, 60131, Italy
| | - Valerio Zupo
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
| | - Maria Costantini
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
| |
Collapse
|
19
|
Liu W, Kang L, Xu Q, Tao C, Yan J, Sang T. Increased expression diversity buffers the loss of adaptive potential caused by reduction of genetic diversity in new unfavourable environments. Biol Lett 2019; 15:20180583. [PMID: 30958214 DOI: 10.1098/rsbl.2018.0583] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mechanisms underlying adaptation to rapid environmental change are issues in evolutionary biology. It is widely accepted that reduction in genetic diversity when suddenly exposed to an unfavourable environment limits the adaptive potential of populations. With growing empirical evidence that expression diversity is likely to increase in the new environment, the role that expression diversity plays in adaptation needs to be theorized. Here, we first established a negative exponential relationship between expression diversity and genetic diversity using a phenomenological differential equation. We then derived a complex trade-off relationship between the changes of expression and genetic diversity, which followed a combination of exponential functions. Furthermore, we found the increase in expression diversity could buffer the loss of adaptive potential as genetic diversity decreased to a certain extent. These theoretical deductions were validated by transcriptomic data of Miscanthus lutarioriparius grown in two experimental fields and supported by good fit and random simulation. These results suggest that increased expression diversity may compensate the loss of genetic diversity and allow the populations to maintain a certain level of phenotypic variation to cope with sudden environmental change. This may buffer the quick diminishing of adaptive potential and consequently increases the change of adaptation to the new environment.
Collapse
Affiliation(s)
- Wei Liu
- 1 Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences , Beijing 100093 , People's Republic of China
| | - Lifang Kang
- 1 Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences , Beijing 100093 , People's Republic of China
| | - Qin Xu
- 1 Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences , Beijing 100093 , People's Republic of China
| | - Chengcheng Tao
- 1 Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences , Beijing 100093 , People's Republic of China.,3 University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Juan Yan
- 4 Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences , Wuhan, Hubei 430074 , People's Republic of China
| | - Tao Sang
- 1 Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences , Beijing 100093 , People's Republic of China.,2 State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences , Beijing 100093 , People's Republic of China.,3 University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| |
Collapse
|
20
|
Gibert P, Debat V, Ghalambor CK. Phenotypic plasticity, global change, and the speed of adaptive evolution. CURRENT OPINION IN INSECT SCIENCE 2019; 35:34-40. [PMID: 31325807 DOI: 10.1016/j.cois.2019.06.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/13/2019] [Accepted: 06/18/2019] [Indexed: 06/10/2023]
Abstract
The role phenotypic plasticity might play in adaptation to the ongoing climate changes is unclear. Plasticity allows for the production of a diversity of intra-generational responses, whose inter-generational evolutionary consequences are difficult to predict. In this article, we review theory and empirical studies addressing this question in insects by considering three scenarios. The first scenario corresponds to adaptive plasticity that should lead to slow or no evolution. The second scenario is the case of non-adaptive phenotypic plasticity to new environmental conditions that should lead either to extinction or, on the contrary, to rapid evolutionary change. The third scenario deals with how plasticity alters the variance selection acts upon. These scenarios are then discussed by highlighting examples of empirical studies on insects. We conclude that more studies are needed to better understand the relationship between phenotypic plasticity and evolutionary processes in insects.
Collapse
Affiliation(s)
- Patricia Gibert
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France.
| | - Vincent Debat
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP50, 75005, Paris, France
| | - Cameron K Ghalambor
- Department of Biology and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States
| |
Collapse
|
21
|
Jackson ISC. Developmental bias in the fossil record. Evol Dev 2019; 22:88-102. [PMID: 31475437 DOI: 10.1111/ede.12312] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 12/11/2022]
Abstract
The role of developmental bias and plasticity in evolution is a central research interest in evolutionary biology. Studies of these concepts and related processes are usually conducted on extant systems and have seen limited investigation in the fossil record. Here, I identify plasticity-led evolution (PLE) as a form of developmental bias accessible through scrutiny of paleontological material. I summarize the process of PLE and describe it in terms of the environmentally mediated accumulation and release of cryptic genetic variation. Given this structure, I then predict its manifestation in the fossil record, discuss its similarity to quantum evolution and punctuated equilibrium, and argue that these describe macroevolutionary patterns concordant with PLE. Finally, I suggest methods and directions towards providing evidence of PLE in the fossil record and conclude that such endeavors are likely to be highly rewarding.
Collapse
|
22
|
Zheng J, Payne JL, Wagner A. Cryptic genetic variation accelerates evolution by opening access to diverse adaptive peaks. Science 2019; 365:347-353. [DOI: 10.1126/science.aax1837] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 06/06/2019] [Indexed: 12/13/2022]
Abstract
Cryptic genetic variation can facilitate adaptation in evolving populations. To elucidate the underlying genetic mechanisms, we used directed evolution in Escherichia coli to accumulate variation in populations of yellow fluorescent proteins and then evolved these proteins toward the new phenotype of green fluorescence. Populations with cryptic variation evolved adaptive genotypes with greater diversity and higher fitness than populations without cryptic variation, which converged on similar genotypes. Populations with cryptic variation accumulated neutral or deleterious mutations that break the constraints on the order in which adaptive mutations arise. In doing so, cryptic variation opens paths to adaptive genotypes, creates historical contingency, and reduces the predictability of evolution by allowing different replicate populations to climb different adaptive peaks and explore otherwise-inaccessible regions of an adaptive landscape.
Collapse
Affiliation(s)
- Jia Zheng
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, Switzerland
| | - Joshua L. Payne
- Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, Switzerland
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, Switzerland
- The Santa Fe Institute, Santa Fe, NM, USA
| |
Collapse
|
23
|
Abstract
Evolvability is the ability of a biological system to produce phenotypic variation that is both heritable and adaptive. It has long been the subject of anecdotal observations and theoretical work. In recent years, however, the molecular causes of evolvability have been an increasing focus of experimental work. Here, we review recent experimental progress in areas as different as the evolution of drug resistance in cancer cells and the rewiring of transcriptional regulation circuits in vertebrates. This research reveals the importance of three major themes: multiple genetic and non-genetic mechanisms to generate phenotypic diversity, robustness in genetic systems, and adaptive landscape topography. We also discuss the mounting evidence that evolvability can evolve and the question of whether it evolves adaptively.
Collapse
|
24
|
Trubenová B, Krejca MS, Lehre PK, Kötzing T. Surfing on the seascape: Adaptation in a changing environment. Evolution 2019; 73:1356-1374. [PMID: 31206653 PMCID: PMC6771940 DOI: 10.1111/evo.13784] [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: 06/30/2017] [Accepted: 04/15/2019] [Indexed: 12/11/2022]
Abstract
The environment changes constantly at various time scales and, in order to survive, species need to keep adapting. Whether these species succeed in avoiding extinction is a major evolutionary question. Using a multilocus evolutionary model of a mutation-limited population adapting under strong selection, we investigate the effects of the frequency of environmental fluctuations on adaptation. Our results rely on an "adaptive-walk" approximation and use mathematical methods from evolutionary computation theory to investigate the interplay between fluctuation frequency, the similarity of environments, and the number of loci contributing to adaptation. First, we assume a linear additive fitness function, but later generalize our results to include several types of epistasis. We show that frequent environmental changes prevent populations from reaching a fitness peak, but they may also prevent the large fitness loss that occurs after a single environmental change. Thus, the population can survive, although not thrive, in a wide range of conditions. Furthermore, we show that in a frequently changing environment, the similarity of threats that a population faces affects the level of adaptation that it is able to achieve. We check and supplement our analytical results with simulations.
Collapse
Affiliation(s)
- Barbora Trubenová
- Institute of Science and Technology AustriaAm Campus 1Klosterneuburg 3400Austria
| | - Martin S. Krejca
- Hasso Plattner InstituteProf.‐Dr.‐Helmert‐Straße 2‐314482 PotsdamGermany
| | | | - Timo Kötzing
- Hasso Plattner InstituteProf.‐Dr.‐Helmert‐Straße 2‐314482 PotsdamGermany
| |
Collapse
|
25
|
Ghafari M, Weissman DB. The expected time to cross extended fitness plateaus. Theor Popul Biol 2019; 129:54-67. [PMID: 31054850 DOI: 10.1016/j.tpb.2019.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 12/28/2018] [Accepted: 03/05/2019] [Indexed: 10/25/2022]
Abstract
For a population to acquire a complex adaptation requiring multiple individually neutral mutations, it must cross a plateau in the fitness landscape. We consider plateaus involving three mutations, and show that large populations can cross them rapidly via lineages that acquire multiple mutations while remaining at low frequency, much faster than the ∝μ3 rate for simultaneous triple mutations. Plateau-crossing is fastest for very large populations. At intermediate population sizes, recombination can greatly accelerate adaptation by combining independent mutant lineages to form triple-mutants. For more frequent recombination, such that the population is kept near linkage equilibrium, we extend our analysis to find simple expressions for the expected time to cross plateaus of arbitrary width.
Collapse
Affiliation(s)
- Mahan Ghafari
- Department of Physics, Emory University, Atlanta, GA 30322, USA; Department of Genetics, University of Cambridge, UK
| | | |
Collapse
|
26
|
Sambamoorthy G, Sinha H, Raman K. Evolutionary design principles in metabolism. Proc Biol Sci 2019; 286:20190098. [PMID: 30836874 PMCID: PMC6458322 DOI: 10.1098/rspb.2019.0098] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 02/14/2019] [Indexed: 12/28/2022] Open
Abstract
Microorganisms are ubiquitous and adapt to various dynamic environments to sustain growth. These adaptations accumulate, generating new traits forming the basis of evolution. Organisms adapt at various levels, such as gene regulation, signalling, protein-protein interactions and metabolism. Of these, metabolism forms the integral core of an organism for maintaining the growth and function of a cell. Therefore, studying adaptations in metabolic networks is crucial to understand the emergence of novel metabolic capabilities. Metabolic networks, composed of enzyme-catalysed reactions, exhibit certain repeating paradigms or design principles that arise out of different selection pressures. In this review, we discuss the design principles that are known to exist in metabolic networks, such as functional redundancy, modularity, flux coupling and exaptations. We elaborate on the studies that have helped gain insights highlighting the interplay of these design principles and adaptation. Further, we discuss how evolution plays a role in exploiting such paradigms to enhance the robustness of organisms. Looking forward, we predict that with the availability of ever-increasing numbers of bacterial, archaeal and eukaryotic genomic sequences, novel design principles will be identified, expanding our understanding of these paradigms shaped by varied evolutionary processes.
Collapse
Affiliation(s)
- Gayathri Sambamoorthy
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
- Initiative for Biological Systems Engineering (IBSE), Indian Institute of Technology Madras, Chennai 600036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai 600036, India
| | - Himanshu Sinha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
- Initiative for Biological Systems Engineering (IBSE), Indian Institute of Technology Madras, Chennai 600036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai 600036, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
- Initiative for Biological Systems Engineering (IBSE), Indian Institute of Technology Madras, Chennai 600036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai 600036, India
| |
Collapse
|
27
|
Nelson P, Masel J. Evolutionary Capacitance Emerges Spontaneously during Adaptation to Environmental Changes. Cell Rep 2018; 25:249-258. [DOI: 10.1016/j.celrep.2018.09.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/26/2018] [Accepted: 09/04/2018] [Indexed: 11/28/2022] Open
|
28
|
Baalsrud HT, Tørresen OK, Solbakken MH, Salzburger W, Hanel R, Jakobsen KS, Jentoft S. De Novo Gene Evolution of Antifreeze Glycoproteins in Codfishes Revealed by Whole Genome Sequence Data. Mol Biol Evol 2018; 35:593-606. [PMID: 29216381 PMCID: PMC5850335 DOI: 10.1093/molbev/msx311] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
New genes can arise through duplication of a pre-existing gene or de novo from non-coding DNA, providing raw material for evolution of new functions in response to a changing environment. A prime example is the independent evolution of antifreeze glycoprotein genes (afgps) in the Arctic codfishes and Antarctic notothenioids to prevent freezing. However, the highly repetitive nature of these genes complicates studies of their organization. In notothenioids, afgps evolved from an extant gene, yet the evolutionary origin of afgps in codfishes is unknown. Here, we demonstrate that afgps in codfishes have evolved de novo from non-coding DNA 13-18 Ma, coinciding with the cooling of the Northern Hemisphere. Using whole-genome sequence data from several codfishes and notothenioids, we find higher copy number of afgp in species exposed to more severe freezing suggesting a gene dosage effect. Notably, antifreeze function is lost in one lineage of codfishes analogous to the afgp losses in non-Antarctic notothenioids. This indicates that selection can eliminate the antifreeze function when freezing is no longer imminent. In addition, we show that evolution of afgp-assisting antifreeze potentiating protein genes (afpps) in notothenioids coincides with origin and lineage-specific losses of afgp. The origin of afgps in codfishes is one of the first examples of an essential gene born from non-coding DNA in a non-model species. Our study underlines the power of comparative genomics to uncover past molecular signatures of genome evolution, and further highlights the impact of de novo gene origin in response to a changing selection regime.
Collapse
Affiliation(s)
- Helle Tessand Baalsrud
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Ole Kristian Tørresen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Monica Hongrø Solbakken
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Walter Salzburger
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
- Zoological Institute, University of Basel, Basel, Switzerland
| | - Reinhold Hanel
- Institute of Fisheries Ecology, Johann Heinrich von Thünen Institute, Federal Research Institute for Rural Areas, Forestry and Fisheries, Hamburg, Germany
| | - Kjetill S Jakobsen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Sissel Jentoft
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| |
Collapse
|
29
|
Ruocco N, Maria Fedele A, Costantini S, Romano G, Ianora A, Costantini M. New inter-correlated genes targeted by diatom-derived polyunsaturated aldehydes in the sea urchin Paracentrotus lividus. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 142:355-362. [PMID: 28437727 DOI: 10.1016/j.ecoenv.2017.04.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 06/07/2023]
Abstract
The marine environment is continually subjected to the action of stressors (including natural toxins), which represent a constant danger for benthic communities. In the present work using network analysis we identified ten genes on the basis of associated functions (FOXA, FoxG, GFI-1, nodal, JNK, OneCut/Hnf6, TAK1, tcf4, TCF7, VEGF) in the sea urchin Paracentrotus lividus, having key roles in different processes, such as embryonic development and asymmetry, cell fate specification, cell differentiation and morphogenesis, and skeletogenesis. These genes are correlated with three HUB genes, Foxo, Jun and HIF1A. Real Time qPCR revealed that during sea urchin embryonic development the expression levels of these genes were modulated by three diatom-derived polyunsaturated aldehydes (PUAs), decadienal, heptadienal and octadienal. Our findings show how changes in gene expression levels may be used as an early indicator of stressful conditions in the marine environment. The identification of key genes and the molecular pathways in which they are involved represents a fundamental tool in understanding how marine organisms try to afford protection against toxicants, to avoid deleterious consequences and irreversible damages. The genes identified in this work as targets for PUAs can be considered as possible biomarkers to detect exposure to different environmental pollutants.
Collapse
Affiliation(s)
- Nadia Ruocco
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; Department of Biology, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cinthia, 80126 Napoli, Italy; Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, Pozzuoli, Naples 80078, Italy
| | - Anna Maria Fedele
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Susan Costantini
- Unità di Farmacologia Sperimentale, Istituto Nazionale Tumori "Fondazione G. Pascale", IRCCS, 80131 Napoli, Italy
| | - Giovanna Romano
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Adrianna Ianora
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Maria Costantini
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy.
| |
Collapse
|
30
|
Exploring the analytical consequences of ecological subjects unwittingly neglected by the mainstream of evolutionary thought. Ecol Modell 2017. [DOI: 10.1016/j.ecolmodel.2017.03.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
31
|
Abstract
The phenomenon of de novo gene birth from junk DNA is surprising, because random polypeptides are expected to be toxic. There are two conflicting views about how de novo gene birth is nevertheless possible: the continuum hypothesis invokes a gradual gene birth process, while the preadaptation hypothesis predicts that young genes will show extreme levels of gene-like traits. We show that intrinsic structural disorder conforms to the predictions of the preadaptation hypothesis and falsifies the continuum hypothesis, with all genes having higher levels than translated junk DNA, but young genes having the highest level of all. Results are robust to homology detection bias, to the non-independence of multiple members of the same gene family, and to the false positive annotation of protein-coding genes.
Collapse
|
32
|
McLysaght A, Guerzoni D. New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation. Philos Trans R Soc Lond B Biol Sci 2016; 370:20140332. [PMID: 26323763 PMCID: PMC4571571 DOI: 10.1098/rstb.2014.0332] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The origin of novel protein-coding genes de novo was once considered so improbable as to be impossible. In less than a decade, and especially in the last five years, this view has been overturned by extensive evidence from diverse eukaryotic lineages. There is now evidence that this mechanism has contributed a significant number of genes to genomes of organisms as diverse as Saccharomyces, Drosophila, Plasmodium, Arabidopisis and human. From simple beginnings, these genes have in some instances acquired complex structure, regulated expression and important functional roles. New genes are often thought of as dispensable late additions; however, some recent de novo genes in human can play a role in disease. Rather than an extremely rare occurrence, it is now evident that there is a relatively constant trickle of proto-genes released into the testing ground of natural selection. It is currently unknown whether de novo genes arise primarily through an ‘RNA-first’ or ‘ORF-first’ pathway. Either way, evolutionary tinkering with this pool of genetic potential may have been a significant player in the origins of lineage-specific traits and adaptations.
Collapse
Affiliation(s)
- Aoife McLysaght
- Smurfit Institute of Genetics, University of Dublin, Trinity College Dublin, Dublin 2, Republic of Ireland
| | - Daniele Guerzoni
- Smurfit Institute of Genetics, University of Dublin, Trinity College Dublin, Dublin 2, Republic of Ireland
| |
Collapse
|
33
|
Xu Q, Zhu C, Fan Y, Song Z, Xing S, Liu W, Yan J, Sang T. Population transcriptomics uncovers the regulation of gene expression variation in adaptation to changing environment. Sci Rep 2016; 6:25536. [PMID: 27150248 PMCID: PMC4858677 DOI: 10.1038/srep25536] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 04/19/2016] [Indexed: 11/23/2022] Open
Abstract
Expression variation plays an important role in plant adaptation, but little is known about the factors impacting the expression variation when population adapts to changing environment. We used RNA-seq data from 80 individuals in 14 Miscanthus lutarioriparius populations, which were transplanted into a harsh environment from native habitat, to investigate the expression level, expression diversity and genetic diversity for genes expressed in both environments. The expression level of genes with lower expression level or without SNP tended to be more changeable in new environment, which suggested highly expressed genes experienced stronger purifying selection than those at lower level. Low proportion of genes with population effect confirmed the weak population structure and frequent gene flow in these populations. Meanwhile, the number of genes with environment effect was the most frequent compared with that with population effect. Our results showed that environment and genetic diversity were the main factors determining gene expression variation in population. This study could facilitate understanding the mechanisms of global gene expression variation when plant population adapts to changing environment.
Collapse
Affiliation(s)
- Qin Xu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Caiyun Zhu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangyang Fan
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihong Song
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shilai Xing
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Juan Yan
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Tao Sang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| |
Collapse
|
34
|
Effects of parental care on the accumulation and release of cryptic genetic variation: review of mechanisms and a case study of dung beetles. Evol Ecol 2016. [DOI: 10.1007/s10682-015-9813-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
35
|
Pieper B, Monniaux M, Hay A. The genetic architecture of petal number in Cardamine hirsuta. THE NEW PHYTOLOGIST 2016; 209:395-406. [PMID: 26268614 DOI: 10.1111/nph.13586] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 07/04/2015] [Indexed: 05/22/2023]
Abstract
Invariant petal number is a characteristic of most flowers and is generally robust to genetic and environmental variation. We took advantage of the natural variation found in Cardamine hirsuta petal number to investigate the genetic basis of this trait in a case where robustness was lost during evolution. We used quantitative trait locus (QTL) analysis to characterize the genetic architecture of petal number. Αverage petal number showed transgressive variation from zero to four petals in five C. hirsuta mapping populations, and this variation was highly heritable. We detected 15 QTL at which allelic variation affected petal number. The effects of these QTL were relatively small in comparison with alleles induced by mutagenesis, suggesting that natural selection may act to maintain petal number within its variable range below four. Petal number showed a temporal trend during plant ageing, as did sepal trichome number, and multi-trait QTL analysis revealed that these age-dependent traits share a common genetic basis. Our results demonstrate that petal number is determined by many genes of small effect, some of which are age-dependent, and suggests a mechanism of trait evolution via the release of cryptic variation.
Collapse
Affiliation(s)
- Bjorn Pieper
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Köln, Germany
| | - Marie Monniaux
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Köln, Germany
| | - Angela Hay
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Köln, Germany
| |
Collapse
|
36
|
Paaby AB, White AG, Riccardi DD, Gunsalus KC, Piano F, Rockman MV. Wild worm embryogenesis harbors ubiquitous polygenic modifier variation. eLife 2015; 4. [PMID: 26297805 PMCID: PMC4569889 DOI: 10.7554/elife.09178] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 08/21/2015] [Indexed: 12/28/2022] Open
Abstract
Embryogenesis is an essential and stereotypic process that nevertheless evolves
among species. Its essentiality may favor the accumulation of cryptic genetic
variation (CGV) that has no effect in the wild-type but that enhances or
suppresses the effects of rare disruptions to gene function. Here, we adapted a
classical modifier screen to interrogate the alleles segregating in natural
populations of Caenorhabditis elegans: we induced gene
knockdowns and used quantitative genetic methodology to examine how segregating
variants modify the penetrance of embryonic lethality. Each perturbation
revealed CGV, indicating that wild-type genomes harbor myriad genetic modifiers
that may have little effect individually but which in aggregate can dramatically
influence penetrance. Phenotypes were mediated by many modifiers, indicating
high polygenicity, but the alleles tend to act very specifically, indicating low
pleiotropy. Our findings demonstrate the extent of conditional functionality in
complex trait architecture. DOI:http://dx.doi.org/10.7554/eLife.09178.001 Individuals of the same species have similar, but generally not identical, DNA
sequences. This ‘genetic variation’ is due to random changes in the DNA—known as
mutations—that occur among individuals. These mutations may be passed on to
these individuals' offspring, who in turn pass them on to their descendants.
Some of these mutations may have a positive or negative effect on the ability of
the organisms to survive and reproduce, but others may have no effect at
all. The process by which an embryo forms (which is called embryogenesis) follows a
precisely controlled series of events. Within the same species, there is genetic
variation in the DNA that programs embryogenesis, but it is not clear what
effect this variation has on how the embryo develops. Here, Paaby et al. adapted
a genetics technique called a ‘modifier screen’ to study how genetic variation
affects the development of a roundworm known as Caenorhabditis
elegans. The experiments show that populations of worms harbor a lot of genetic variation
that affects how they tolerate the loss of an important gene. One by one, Paaby
et al. interrupted the activity of specific genes that embryos need in order to
develop. How this affected the embryo, and whether or not it was able to
survive, was due in large part to the naturally-occurring genetic variation in
other genes in these worms. Paaby et al.'s findings serve as a reminder that the effect of a mutation depends
on other DNA sequences in the organism. In humans, for example, a gene that
causes a genetic disease may produce severe symptoms in one patient but mild
symptoms in another. Future experiments will reveal the details of how genetic
variation affects embryogenesis, which may also provide new insights into how
complex processes in animals evolve over time. DOI:http://dx.doi.org/10.7554/eLife.09178.002
Collapse
Affiliation(s)
- Annalise B Paaby
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, United States
| | - Amelia G White
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, United States
| | - David D Riccardi
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, United States
| | - Kristin C Gunsalus
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, United States
| | - Fabio Piano
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, United States
| | - Matthew V Rockman
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, United States
| |
Collapse
|
37
|
Dlugosch KM, Anderson SR, Braasch J, Cang FA, Gillette HD. The devil is in the details: genetic variation in introduced populations and its contributions to invasion. Mol Ecol 2015; 24:2095-111. [PMID: 25846825 DOI: 10.1111/mec.13183] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/26/2015] [Accepted: 03/27/2015] [Indexed: 12/14/2022]
Abstract
The influence of genetic variation on invasion success has captivated researchers since the start of the field of invasion genetics 50 years ago. We review the history of work on this question and conclude that genetic variation-as surveyed with molecular markers-appears to shape invasion rarely. Instead, there is a significant disconnect between marker assays and ecologically relevant genetic variation in introductions. We argue that the potential for adaptation to facilitate invasion will be shaped by the details of genotypes affecting phenotypes, and we highlight three areas in which we see opportunities to make powerful new insights. (i) The genetic architecture of adaptive variation. Traits shaped by large-effect alleles may be strongly impacted by founder events yet more likely to respond to selection when genetic drift is strong. Large-effect loci may be especially relevant for traits involved in biotic interactions. (ii) Cryptic genetic variation exposed during invasion. Introductions have strong potential to uncover masked variation due to alterations in genetic and ecological environments. (iii) Genetic interactions during admixture of multiple source populations. As divergence among sources increases, positive followed by increasingly negative effects of admixture should be expected. Although generally hypothesized to be beneficial during invasion, admixture is most often reported among sources of intermediate divergence, supporting the possibility that incompatibilities among divergent source populations might be limiting their introgression. Finally, we note that these details of invasion genetics can be coupled with comparative demographic analyses to link genetic changes to the evolution of invasiveness itself.
Collapse
Affiliation(s)
- Katrina M Dlugosch
- Department of Ecology & Evolutionary Biology, University of Arizona, PO Box 210088, Tucson, AZ, 85721, USA
| | | | | | | | | |
Collapse
|
38
|
Siegal ML, Leu JY. On the Nature and Evolutionary Impact of Phenotypic Robustness Mechanisms. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2014; 45:496-517. [PMID: 26034410 PMCID: PMC4448758 DOI: 10.1146/annurev-ecolsys-120213-091705] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Biologists have long observed that physiological and developmental processes are insensitive, or robust, to many genetic and environmental perturbations. A complete understanding of the evolutionary causes and consequences of this robustness is lacking. Recent progress has been made in uncovering the regulatory mechanisms that underlie environmental robustness in particular. Less is known about robustness to the effects of mutations, and indeed the evolution of mutational robustness remains a controversial topic. The controversy has spread to related topics, in particular the evolutionary relevance of cryptic genetic variation. This review aims to synthesize current understanding of robustness mechanisms and to cut through the controversy by shedding light on what is and is not known about mutational robustness. Some studies have confused mutational robustness with non-additive interactions between mutations (epistasis). We conclude that a profitable way forward is to focus investigations (and rhetoric) less on mutational robustness and more on epistasis.
Collapse
Affiliation(s)
- Mark L Siegal
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003;
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 11529;
| |
Collapse
|
39
|
DeHaan LR, Van Tassel DL. Useful insights from evolutionary biology for developing perennial grain crops. AMERICAN JOURNAL OF BOTANY 2014; 101:1801-1819. [PMID: 25326622 DOI: 10.3732/ajb.1400084] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Annual grain crops dominate agricultural landscapes and provide the majority of calories consumed by humanity. Perennial grain crops could potentially ameliorate the land degradation and off-site impacts associated with annual grain cropping. However, herbaceous perennial plants with constitutively high allocation to harvestable seeds are rare to absent in nature. Recent trade-off theory models suggest that rugged fitness landscapes may explain the absence of this form better than sink competition models. Artificial selection for both grain production and multiyear lifespan can lead to more rapid progress in the face of fitness and genetic trade-offs than natural selection but is likely to result in plant types that differ substantially from all current domestic crops. Perennial grain domestication is also likely to require the development of selection strategies that differ from published crop breeding methods, despite their success in improving long-domesticated crops; for this purpose, we have reviewed literature in the areas of population and evolutionary genetics, domestication, and molecular biology. Rapid domestication will likely require genes with large effect that are expected to exhibit strong pleiotropy and epistasis. Cryptic genetic variation will need to be deliberately exposed both to purge mildly deleterious alleles and to generate novel agronomic phenotypes. We predict that perennial grain domestication programs will benefit from population subdivision followed by selection for simple traits in each subpopulation, the evaluation of very large populations, high selection intensity, rapid cycling through generations, and heterosis. The latter may be particularly beneficial in the development of varieties with stable yield and tolerance to crowding.
Collapse
Affiliation(s)
- Lee R DeHaan
- The Land Institute, 2440 E. Water Well Rd., Salina, Kansas 67401 USA
| | | |
Collapse
|
40
|
Trotter MV, Weissman DB, Peterson GI, Peck KM, Masel J. Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations. Evolution 2014; 68:3357-67. [PMID: 25178652 DOI: 10.1111/evo.12517] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 08/25/2014] [Indexed: 12/15/2022]
Abstract
The existence of complex (multiple-step) genetic adaptations that are "irreducible" (i.e., all partial combinations are less fit than the original genotype) is one of the longest standing problems in evolutionary biology. In standard genetics parlance, these adaptations require the crossing of a wide adaptive valley of deleterious intermediate stages. Here, we demonstrate, using a simple model, that evolution can cross wide valleys to produce "irreducibly complex" adaptations by making use of previously cryptic mutations. When revealed by an evolutionary capacitor, previously cryptic mutants have higher initial frequencies than do new mutations, bringing them closer to a valley-crossing saddle in allele frequency space. Moreover, simple combinatorics implies an enormous number of candidate combinations exist within available cryptic genetic variation. We model the dynamics of crossing of a wide adaptive valley after a capacitance event using both numerical simulations and analytical approximations. Although individual valley crossing events become less likely as valleys widen, by taking the combinatorics of genotype space into account, we see that revealing cryptic variation can cause the frequent evolution of complex adaptations.
Collapse
Affiliation(s)
- Meredith V Trotter
- Department of Biology, Stanford University, Stanford, California, 95306; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721
| | | | | | | | | |
Collapse
|
41
|
Grimbert S, Braendle C. Cryptic genetic variation uncovers evolution of environmentally sensitive parameters inCaenorhabditisvulval development. Evol Dev 2014; 16:278-91. [DOI: 10.1111/ede.12091] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Stéphanie Grimbert
- Institut de Biologie Valrose; CNRS UMR7277, Parc Valrose; 06108 Nice cedex 02 France
- INSERM U1091; 06108 Nice cedex 02 France
- Université Nice Sophia Antipolis; UFR Sciences; 06108 Nice cedex 02 France
| | - Christian Braendle
- Institut de Biologie Valrose; CNRS UMR7277, Parc Valrose; 06108 Nice cedex 02 France
- INSERM U1091; 06108 Nice cedex 02 France
- Université Nice Sophia Antipolis; UFR Sciences; 06108 Nice cedex 02 France
| |
Collapse
|
42
|
Stern A, Bianco S, Yeh MT, Wright C, Butcher K, Tang C, Nielsen R, Andino R. Costs and benefits of mutational robustness in RNA viruses. Cell Rep 2014; 8:1026-36. [PMID: 25127138 DOI: 10.1016/j.celrep.2014.07.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 05/18/2014] [Accepted: 07/11/2014] [Indexed: 12/19/2022] Open
Abstract
The accumulation of mutations in RNA viruses is thought to facilitate rapid adaptation to changes in the environment. However, most mutations have deleterious effects on fitness, especially for viruses. Thus, tolerance to mutations should determine the nature and extent of genetic diversity that can be maintained in the population. Here, we combine population genetics theory, computer simulation, and experimental evolution to examine the advantages and disadvantages of tolerance to mutations, also known as mutational robustness. We find that mutational robustness increases neutral diversity and, as expected, can facilitate adaptation to a new environment. Surprisingly, under certain conditions, robustness may also be an impediment for viral adaptation, if a highly diverse population contains a large proportion of previously neutral mutations that are deleterious in the new environment. These findings may inform therapeutic strategies that cause extinction of otherwise robust viral populations.
Collapse
Affiliation(s)
- Adi Stern
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Simone Bianco
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; IBM Research-Almaden, Industrial and Applied Genomics, 650 Harry Road, San Jose, CA 95120-6099, USA
| | - Ming Te Yeh
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Caroline Wright
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kristin Butcher
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Chao Tang
- Center for Quantitative Biology, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
43
|
Ledon-Rettig CC, Pfennig DW, Chunco AJ, Dworkin I. Cryptic Genetic Variation in Natural Populations: A Predictive Framework. Integr Comp Biol 2014; 54:783-93. [DOI: 10.1093/icb/icu077] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
|
44
|
Abstract
Cryptic genetic variation (CGV) is invisible under normal conditions, but it can fuel evolution when circumstances change. In theory, CGV can represent a massive cache of adaptive potential or a pool of deleterious alleles that are in need of constant suppression. CGV emerges from both neutral and selective processes, and it may inform about how human populations respond to change. CGV facilitates adaptation in experimental settings, but does it have an important role in the real world? Here, we review the empirical support for widespread CGV in natural populations, including its potential role in emerging human diseases and the growing evidence of its contribution to evolution.
Collapse
Affiliation(s)
- Annalise B Paaby
- Department of Biology, and Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York 10003, USA
| | - Matthew V Rockman
- Department of Biology, and Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York 10003, USA
| |
Collapse
|
45
|
Kopp M, Matuszewski S. Rapid evolution of quantitative traits: theoretical perspectives. Evol Appl 2014; 7:169-91. [PMID: 24454555 PMCID: PMC3894905 DOI: 10.1111/eva.12127] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Accepted: 09/26/2013] [Indexed: 12/14/2022] Open
Abstract
An increasing number of studies demonstrate phenotypic and genetic changes in natural populations that are subject to climate change, and there is hope that some of these changes will contribute to avoiding species extinctions ('evolutionary rescue'). Here, we review theoretical models of rapid evolution in quantitative traits that can shed light on the potential for adaptation to a changing climate. Our focus is on quantitative-genetic models with selection for a moving phenotypic optimum. We point out that there is no one-to-one relationship between the rate of adaptation and population survival, because the former depends on relative fitness and the latter on absolute fitness. Nevertheless, previous estimates that sustainable rates of genetically based change usually do not exceed 0.1 haldanes (i.e., phenotypic standard deviations per generation) are probably correct. Survival can be greatly facilitated by phenotypic plasticity, and heritable variation in plasticity can further speed up genetic evolution. Multivariate selection and genetic correlations are frequently assumed to constrain adaptation, but this is not necessarily the case and depends on the geometric relationship between the fitness landscape and the structure of genetic variation. Similar conclusions hold for adaptation to shifting spatial gradients. Recent models of adaptation in multispecies communities indicate that the potential for rapid evolution is strongly influenced by interspecific competition.
Collapse
Affiliation(s)
- Michael Kopp
- LATP UMR-CNRS 7353, Evolutionary Biology and Modeling Group, Aix Marseille UniversityMarseille, France
| | - Sebastian Matuszewski
- Mathematics and BioSciences Group, Faculty of Mathematics, University of ViennaVienna, Austria
| |
Collapse
|
46
|
Affiliation(s)
- Joanna Masel
- Ecology and Evolutionary Biology, University of Arizona, 1041 E, Lowell St, Tucson, AZ 84721, USA.
| |
Collapse
|
47
|
Gray A, Cavers S. Island biogeography, the effects of taxonomic effort and the importance of island niche diversity to single-island endemic species. Syst Biol 2013; 63:55-65. [PMID: 23985784 DOI: 10.1093/sysbio/syt060] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Island biogeography theory is fundamentally reliant on measuring the number of species per island and hence has taxonomy at its foundation. Yet as a metric used in tests of the theory, island species richness (S) has varied with time according to the level of taxonomic effort (a function of the rate of finding and describing species). Studies using a derivative of S, single-island endemic species richness (SIE S), may be prone to change in taxonomic effort. Decreases or increases in species numbers resulting from taxonomic revision or increased sampling are likely to have a large effect on values of SIE S, as they tend to be smaller than total S for the same island. Using simple biogeography models, we analysed estimates of SIE S in plants, land snails, beetles, and fungi from comprehensive data sets for eight island groups, produced species accumulation curves and applied Bayesian regression over five time periods. Explanatory power differed across taxa, but area and island age were not always the best explanatory variables, and niche diversity appeared to be important. Changing levels of SIE S over time had different effects on models with different taxa and between island archipelagos. The results indicated that the taxonomic effort that determines SIE S is important. However, as this cannot often be quantified, we suggest Bayesian approaches should be more useful than frequentist methods in evaluating SIE S in island biogeography theory. Fundamentally, the article highlights the importance of taxonomy to theoretical biogeography.
Collapse
Affiliation(s)
- Alan Gray
- Centre for Ecology and Hydrology, Bush Estate, Penicuik, Midlothian, EH26 0QB, UK
| | | |
Collapse
|
48
|
Richardson JB, Uppendahl LD, Traficante MK, Levy SF, Siegal ML. Histone variant HTZ1 shows extensive epistasis with, but does not increase robustness to, new mutations. PLoS Genet 2013; 9:e1003733. [PMID: 23990806 PMCID: PMC3749942 DOI: 10.1371/journal.pgen.1003733] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 07/05/2013] [Indexed: 12/18/2022] Open
Abstract
Biological systems produce phenotypes that appear to be robust to perturbation by mutations and environmental variation. Prior studies identified genes that, when impaired, reveal previously cryptic genetic variation. This result is typically interpreted as evidence that the disrupted gene normally increases robustness to mutations, as such robustness would allow cryptic variants to accumulate. However, revelation of cryptic genetic variation is not necessarily evidence that a mutationally robust state has been made less robust. Demonstrating a difference in robustness requires comparing the ability of each state (with the gene perturbed or intact) to suppress the effects of new mutations. Previous studies used strains in which the existing genetic variation had been filtered by selection. Here, we use mutation accumulation (MA) lines that have experienced minimal selection, to test the ability of histone H2A.Z (HTZ1) to increase robustness to mutations in the yeast Saccharomyces cerevisiae. HTZ1, a regulator of chromatin structure and gene expression, represents a class of genes implicated in mutational robustness. It had previously been shown to increase robustness of yeast cell morphology to fluctuations in the external or internal microenvironment. We measured morphological variation within and among 79 MA lines with and without HTZ1. Analysis of within-line variation confirms that HTZ1 increases microenvironmental robustness. Analysis of between-line variation shows the morphological effects of eliminating HTZ1 to be highly dependent on the line, which implies that HTZ1 interacts with mutations that have accumulated in the lines. However, lines without HTZ1 are, as a group, not more phenotypically diverse than lines with HTZ1 present. The presence of HTZ1, therefore, does not confer greater robustness to mutations than its absence. Our results provide experimental evidence that revelation of cryptic genetic variation cannot be assumed to be caused by loss of robustness, and therefore force reevaluation of prior claims based on that assumption.
Collapse
Affiliation(s)
- Joshua B. Richardson
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Locke D. Uppendahl
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Maria K. Traficante
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Sasha F. Levy
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Mark L. Siegal
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| |
Collapse
|
49
|
Tonsor SJ, Elnaccash TW, Scheiner SM. Developmental instability is genetically correlated with phenotypic plasticity, constraining heritability, and fitness. Evolution 2013; 67:2923-35. [PMID: 24094343 DOI: 10.1111/evo.12175] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 05/02/2013] [Indexed: 11/29/2022]
Abstract
Although adaptive plasticity would seem always to be favored by selection, it occurs less often than expected. This lack of ubiquity suggests that there must be trade-offs, costs, or limitations associated with plasticity. Yet, few costs have been found. We explore one type of limitation, a correlation between plasticity and developmental instability, and use quantitative genetic theory to show why one should expect a genetic correlation. We test that hypothesis using the Landsberg erecta × Cape Verde Islands recombinant inbred lines (RILs) of Arabidopsis thaliana. RILs were grown at four different nitrogen (N) supply levels that span the range of N availabilities previously documented in North American field populations. We found a significant multivariate relationship between the cross-environment trait plasticity and the within-environment, within-RIL developmental instability across 13 traits. This genetic covariation between plasticity and developmental instability has two costs. First, theory predicts diminished fitness for highly plastic lines under stabilizing selection, because their developmental instability and variance around the optimum phenotype will be greater compared to nonplastic genotypes. Second, empirically the most plastic traits exhibited heritabilities reduced by 57% on average compared to nonplastic traits. This demonstration of potential costs in inclusive fitness and heritability provoke a rethinking of the evolutionary role of plasticity.
Collapse
Affiliation(s)
- Stephen J Tonsor
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260.
| | | | | |
Collapse
|
50
|
Debat V, Peronnet F. Asymmetric flies: the control of developmental noise in Drosophila. Fly (Austin) 2013; 7:70-7. [PMID: 23519089 PMCID: PMC3732334 DOI: 10.4161/fly.23558] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 01/09/2013] [Accepted: 01/09/2013] [Indexed: 01/08/2023] Open
Abstract
What are the sources of phenotypic variation and which factors shape this variation are fundamental questions of developmental and evolutionary biology. Despite this simple formulation and intense research, controversy remains. Three points are particularly discussed: (1) whether adaptive developmental mechanisms buffering variation exist at all; (2) if yes, do they involve specific genes and processes, i.e., different from those involved in the development of the traits that are buffered?; and (3) whether different mechanisms specifically buffer the various sources of variation, i.e., genetic, environmental and stochastic, or whether a generalist process buffers them all at once. We advocate that experimental work integrating different levels of analysis will improve our understanding of the origin of phenotypic variation and thus help answering these contentious questions. In this paper, we first survey the current views on these issues, highlighting potential sources of controversy. We then focus on the stochastic part of phenotypic variation, as measured by fluctuating asymmetry, and on current knowledge about the genetic basis of developmental stability. We report our recent discovery that an individual gene, Cyclin G, plays a central role-adaptive or not-in developmental stability in Drosophila. ( 1) We discuss the implications of this discovery on the regulation of organ size and shape, and finally point out open questions.
Collapse
Affiliation(s)
- Vincent Debat
- Muséum National d'Histoire Naturelle, UMR CNRS 7205 OSEB, Département Systématique et Evolution, Paris, France.
| | | |
Collapse
|