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Raas MWD, Dutheil JY. The rate of adaptive molecular evolution in wild and domesticated Saccharomyces cerevisiae populations. Mol Ecol 2024; 33:e16980. [PMID: 37157166 DOI: 10.1111/mec.16980] [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: 12/16/2022] [Revised: 04/22/2023] [Accepted: 04/26/2023] [Indexed: 05/10/2023]
Abstract
Through its fermentative capacities, Saccharomyces cerevisiae was central in the development of civilisation during the Neolithic period, and the yeast remains of importance in industry and biotechnology, giving rise to bona fide domesticated populations. Here, we conduct a population genomic study of domesticated and wild populations of S. cerevisiae. Using coalescent analyses, we report that the effective population size of yeast populations decreased since the divergence with S. paradoxus. We fitted models of distributions of fitness effects to infer the rate of adaptive (ω a ) and non-adaptive (ω na ) non-synonymous substitutions in protein-coding genes. We report an overall limited contribution of positive selection to S. cerevisiae protein evolution, albeit with higher rates of adaptive evolution in wild compared to domesticated populations. Our analyses revealed the signature of background selection and possibly Hill-Robertson interference, as recombination was found to be negatively correlated withω na and positively correlated withω a . However, the effect of recombination onω a was found to be labile, as it is only apparent after removing the impact of codon usage bias on the synonymous site frequency spectrum and disappears if we control for the correlation withω na , suggesting that it could be an artefact of the decreasing population size. Furthermore, the rate of adaptive non-synonymous substitutions is significantly correlated with the residue solvent exposure, a relation that cannot be explained by the population's demography. Together, our results provide a detailed characterisation of adaptive mutations in protein-coding genes across S. cerevisiae populations.
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Affiliation(s)
- Maximilian W D Raas
- Research Group Molecular Systems Evolution, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Julien Y Dutheil
- Research Group Molecular Systems Evolution, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Unité Mixte de Recherche 5554 Institut des Sciences de l'Evolution, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
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2
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Wu Z, Wang W, Li J, Ma C, Chen L, Che Q, Zhang G, Zhu T, Li D. Evolution-Based Discovery of Polyketide Acylated Valine from a Cytochalasin-Like Gene Cluster in Simplicillium lamelliciola HDN13430. JOURNAL OF NATURAL PRODUCTS 2024; 87:1222-1229. [PMID: 38447096 DOI: 10.1021/acs.jnatprod.3c01202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Utilizing a gene evolution-oriented approach for gene cluster mining, a cryptic cytochalasin-like gene cluster (sla) in Antarctic-derived Simplicillium lamelliciola HDN13430 was identified. Compared with the canonical cytochalasin biosynthetic gene clusters (BGCs), the sla gene cluster lacks the key α,β-hydrolase gene. Heterologous expression of the sla gene cluster led to the discovery of a new compound, slamysin (1), characterized by an N-acylated amino acid structure and demonstrating weak anti-Bacillus cereus activity. These findings underscore the potential of genetic evolution in uncovering novel compounds and indicating specific adaptive evolution within specialized habitats.
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Affiliation(s)
- Zuodong Wu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Sanya Oceanographic Institute, Ocean University of China, Sanya, Hainan 572025, People's Republic of China
| | - Wenxue Wang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Sanya Oceanographic Institute, Ocean University of China, Sanya, Hainan 572025, People's Republic of China
| | - Jilong Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Sanya Oceanographic Institute, Ocean University of China, Sanya, Hainan 572025, People's Republic of China
| | - Chuanteng Ma
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Sanya Oceanographic Institute, Ocean University of China, Sanya, Hainan 572025, People's Republic of China
| | - Liangzhen Chen
- Qingdao Vland Biotech Group Co., Ltd. Qingdao, Shandong 266102, People's Republic of China
| | - Qian Che
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Sanya Oceanographic Institute, Ocean University of China, Sanya, Hainan 572025, People's Republic of China
| | - Guojian Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Sanya Oceanographic Institute, Ocean University of China, Sanya, Hainan 572025, People's Republic of China
- Laboratory for Marine Drugs and Bioproducts, Laoshan Laboratory, Qingdao, Shandong 266237, People's Republic of China
| | - Tianjiao Zhu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Sanya Oceanographic Institute, Ocean University of China, Sanya, Hainan 572025, People's Republic of China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Sanya Oceanographic Institute, Ocean University of China, Sanya, Hainan 572025, People's Republic of China
- Laboratory for Marine Drugs and Bioproducts, Laoshan Laboratory, Qingdao, Shandong 266237, People's Republic of China
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3
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Bylino OV, Ogienko AA, Batin MA, Georgiev PG, Omelina ES. Genetic, Environmental, and Stochastic Components of Lifespan Variability: The Drosophila Paradigm. Int J Mol Sci 2024; 25:4482. [PMID: 38674068 PMCID: PMC11050664 DOI: 10.3390/ijms25084482] [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: 01/04/2024] [Revised: 03/25/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Lifespan is a complex quantitative trait involving genetic and non-genetic factors as well as the peculiarities of ontogenesis. As with all quantitative traits, lifespan shows considerable variation within populations and between individuals. Drosophila, a favourite object of geneticists, has greatly advanced our understanding of how different forms of variability affect lifespan. This review considers the role of heritable genetic variability, phenotypic plasticity and stochastic variability in controlling lifespan in Drosophila melanogaster. We discuss the major historical milestones in the development of the genetic approach to study lifespan, the breeding of long-lived lines, advances in lifespan QTL mapping, the environmental factors that have the greatest influence on lifespan in laboratory maintained flies, and the mechanisms, by which individual development affects longevity. The interplay between approaches to study ageing and lifespan limitation will also be discussed. Particular attention will be paid to the interaction of different types of variability in the control of lifespan.
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Affiliation(s)
- Oleg V. Bylino
- Department of Regulation of Genetic Processes, Laboratory of Molecular Organization of the Genome, Institute of Gene Biology RAS, 119334 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Anna A. Ogienko
- Department of Regulation of Genetic Processes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Mikhail A. Batin
- Open Longevity, 15260 Ventura Blvd., Sherman Oaks, Los Angeles, CA 91403, USA
| | - Pavel G. Georgiev
- Department of Regulation of Genetic Processes, Laboratory of Molecular Organization of the Genome, Institute of Gene Biology RAS, 119334 Moscow, Russia
| | - Evgeniya S. Omelina
- Department of Regulation of Genetic Processes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
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4
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Stratakis CA. Genes and environment: An old pair in a new era. Maturitas 2023; 178:107851. [PMID: 37806009 DOI: 10.1016/j.maturitas.2023.107851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 09/16/2023] [Indexed: 10/10/2023]
Abstract
What is the relationship between our genes and the environment we live in with regard to health? Like the debate about nature or nurture in the determination of our personality and behavior, the issue of genes and environment has been discussed intensely in the last two centuries. Is it Darwin or Lamarck who is right about the basic determinants of our health, especially as we age in a rapidly changing environment? Evolutionary biology as proposed by Darwin with natural selection at its core may not be able to explain almost instant adjustments of phenotypic traits to the pressures of the environment. Epigenesis, a concept that dates from Aristotle, provides a mechanism for the environment to affect variation in genetic traits that may become heritable. Indeed, Lamarck first described the inheritance of acquired characteristics. Thus, it appears that in contemporary genetics, both Darwin and Lamarck are right: environmental pressures may affect our genes through epigenetics, in ways that allow for inheritance of the changes, a Lamarckian concept; however, evolution through natural selection is the basis for incorporation (or rejection) of new traits and their sustained inheritance, a Darwinian concept. In this review, we present the synthesis of Darwin's and Lamarck's theories, the only way to understand how our health, and that of our progeny, responds to challenging and fast-changing environmental cues. In addition, we present other examples of environment-driven changes in disease frequency or expression.
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Affiliation(s)
- Constantine A Stratakis
- NIH Clinical Center, NICHD, NIH, Bethesda, MD, USA; Research, Human Genetics & Precision Medicine, IMBB, FORTH, Heraklion, Greece; Medical Genetics, H. Dunant Hospital, Athens, Greece; Science Board, ELPEN Research Institute, Athens, Greece; European University of Cyprus, Medical School, Nicosia, Cyprus.
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5
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Marková S, Lanier HC, Escalante MA, da Cruz MOR, Horníková M, Konczal M, Weider LJ, Searle JB, Kotlík P. Local adaptation and future climate vulnerability in a wild rodent. Nat Commun 2023; 14:7840. [PMID: 38030627 PMCID: PMC10686993 DOI: 10.1038/s41467-023-43383-z] [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: 06/02/2023] [Accepted: 11/08/2023] [Indexed: 12/01/2023] Open
Abstract
As climate change continues, species pushed outside their physiological tolerance limits must adapt or face extinction. When change is rapid, adaptation will largely harness ancestral variation, making the availability and characteristics of that variation of critical importance. Here, we used whole-genome sequencing and genetic-environment association analyses to identify adaptive variation and its significance in the context of future climates in a small Palearctic mammal, the bank vole (Clethrionomys glareolus). We found that peripheral populations of bank vole in Britain are already at the extreme bounds of potential genetic adaptation and may require an influx of adaptive variation in order to respond. Analyses of adaptive loci suggest regional differences in climate variables select for variants that influence patterns of population adaptive resilience, including genes associated with antioxidant defense, and support a pattern of thermal/hypoxic cross-adaptation. Our findings indicate that understanding potential shifts in genomic composition in response to climate change may be key to predicting species' fate under future climates.
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Affiliation(s)
- Silvia Marková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic
| | - Hayley C Lanier
- School of Biological Sciences, University of Oklahoma, 730 Van Vleet Oval, Norman, OK, 73019, USA
- Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Ave, Norman, OK, 73072, USA
| | - Marco A Escalante
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic
| | - Marcos O R da Cruz
- School of Biological Sciences, University of Oklahoma, 730 Van Vleet Oval, Norman, OK, 73019, USA
- Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Ave, Norman, OK, 73072, USA
| | - Michaela Horníková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic
| | - Mateusz Konczal
- Faculty of Biology, Evolutionary Biology Group, Adam Mickiewicz University, Poznań, Poland
| | - Lawrence J Weider
- School of Biological Sciences, University of Oklahoma, 730 Van Vleet Oval, Norman, OK, 73019, USA
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Corson Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic.
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Abstract
AbstractEvolutionary biologists have thought about the role of genetic variation during adaptation for a very long time-before we understood the organization of the genetic code, the provenance of genetic variation, and how such variation influenced the phenotypes on which natural selection acts. Half a century after the discovery of the structure of DNA and the unraveling of the genetic code, we have a rich understanding of these problems and the means to both delve deeper and widen our perspective across organisms and natural populations. The 2022 Vice Presidential Symposium of the American Society of Naturalists highlighted examples of recent insights into the role of genetic variation in adaptive processes, which are compiled in this special section. The work was conducted in different parts of the world, included theoretical and empirical studies with diverse organisms, and addressed distinct aspects of how genetic variation influences adaptation. In our introductory article to the special section, we discuss some important recent insights about the generation and maintenance of genetic variation, its impacts on phenotype and fitness, its fate in natural populations, and its role in driving adaptation. By placing the special section articles in the broader context of recent developments, we hope that this overview will also serve as a useful introduction to the field.
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7
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Mansur MB, Greaves M. Convergent TP53 loss and evolvability in cancer. BMC Ecol Evol 2023; 23:54. [PMID: 37743495 PMCID: PMC10518978 DOI: 10.1186/s12862-023-02146-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/10/2023] [Indexed: 09/26/2023] Open
Abstract
Cancer cell populations evolve by a stepwise process involving natural selection of the fittest variants within a tissue ecosystem context and as modified by therapy. Genomic scrutiny of patient samples reveals an extraordinary diversity of mutational profiles both between patients with similar cancers and within the cancer cell population of individual patients. Does this signify highly divergent evolutionary trajectories or are there repetitive and predictable patterns?Major evolutionary innovations or adaptations in different species are frequently repeated, or convergent, reflecting both common selective pressures and constraints on optimal solutions. We argue this is true of evolving cancer cells, especially with respect to the TP53 gene. Functional loss variants in TP53 are the most common genetic change in cancer. We discuss the likely microenvironmental selective pressures involved and the profound impact this has on cell fitness, evolvability and probability of subsequent drug resistance.
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Affiliation(s)
- Marcela Braga Mansur
- Centre for Evolution and Cancer, The Institute of Cancer Research, ICR, London, UK
| | - Mel Greaves
- Centre for Evolution and Cancer, The Institute of Cancer Research, ICR, London, UK.
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8
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Garcia AK, Kędzior M, Taton A, Li M, Young JN, Kaçar B. Effects of RuBisCO and CO 2 concentration on cyanobacterial growth and carbon isotope fractionation. GEOBIOLOGY 2023; 21:390-403. [PMID: 36602111 DOI: 10.1111/gbi.12543] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 11/11/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Carbon isotope biosignatures preserved in the Precambrian geologic record are primarily interpreted to reflect ancient cyanobacterial carbon fixation catalyzed by Form I RuBisCO enzymes. The average range of isotopic biosignatures generally follows that produced by extant cyanobacteria. However, this observation is difficult to reconcile with several environmental (e.g., temperature, pH, and CO2 concentrations), molecular, and physiological factors that likely would have differed during the Precambrian and can produce fractionation variability in contemporary organisms that meets or exceeds that observed in the geologic record. To test a specific range of genetic and environmental factors that may impact ancient carbon isotope biosignatures, we engineered a mutant strain of the model cyanobacterium Synechococcus elongatus PCC 7942 that overexpresses RuBisCO across varying atmospheric CO2 concentrations. We hypothesized that changes in RuBisCO expression would impact the net rates of intracellular CO2 fixation versus CO2 supply, and thus whole-cell carbon isotope discrimination. In particular, we investigated the impacts of RuBisCO overexpression under changing CO2 concentrations on both carbon isotope biosignatures and cyanobacterial physiology, including cell growth and oxygen evolution rates. We found that an increased pool of active RuBisCO does not significantly affect the 13 C/12 C isotopic discrimination (εp ) at all tested CO2 concentrations, yielding εp of ≈ 23‰ for both wild-type and mutant strains at elevated CO2 . We therefore suggest that expected variation in cyanobacterial RuBisCO expression patterns should not confound carbon isotope biosignature interpretation. A deeper understanding of environmental, evolutionary, and intracellular factors that impact cyanobacterial physiology and isotope discrimination is crucial for reconciling microbially driven carbon biosignatures with those preserved in the geologic record.
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Affiliation(s)
- Amanda K Garcia
- Department of Bacteriology, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Mateusz Kędzior
- Department of Bacteriology, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Arnaud Taton
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Meng Li
- School of Oceanography, University of Washington, Seattle, Washington, USA
| | - Jodi N Young
- School of Oceanography, University of Washington, Seattle, Washington, USA
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin - Madison, Madison, Wisconsin, USA
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9
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Torres E, García-Fernández A, Iñigo D, Lara-Romero C, Morente-López J, Prieto-Benítez S, Rubio Teso ML, Iriondo JM. Facilitated Adaptation as A Conservation Tool in the Present Climate Change Context: A Methodological Guide. PLANTS (BASEL, SWITZERLAND) 2023; 12:1258. [PMID: 36986946 PMCID: PMC10053585 DOI: 10.3390/plants12061258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/04/2023] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
Climate change poses a novel threat to biodiversity that urgently requires the development of adequate conservation strategies. Living organisms respond to environmental change by migrating to locations where their ecological niche is preserved or by adapting to the new environment. While the first response has been used to develop, discuss and implement the strategy of assisted migration, facilitated adaptation is only beginning to be considered as a potential approach. Here, we present a review of the conceptual framework for facilitated adaptation, integrating advances and methodologies from different disciplines. Briefly, facilitated adaptation involves a population reinforcement that introduces beneficial alleles to enable the evolutionary adaptation of a focal population to pressing environmental conditions. To this purpose, we propose two methodological approaches. The first one (called pre-existing adaptation approach) is based on using pre-adapted genotypes existing in the focal population, in other populations, or even in closely related species. The second approach (called de novo adaptation approach) aims to generate new pre-adapted genotypes from the diversity present in the species through artificial selection. For each approach, we present a stage-by-stage procedure, with some techniques that can be used for its implementation. The associated risks and difficulties of each approach are also discussed.
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Affiliation(s)
- Elena Torres
- Departamento de Biotecnología-Biología Vegetal, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Alfredo García-Fernández
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Diana Iñigo
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Carlos Lara-Romero
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Javier Morente-López
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
- Grupo de Investigación de Ecología y Evolución en Islas, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), 38206 Tenerife, Spain
| | - Samuel Prieto-Benítez
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
- Ecotoxicology of Air Pollution, Environmental Department, CIEMAT, 28040 Madrid, Spain
| | - María Luisa Rubio Teso
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - José M. Iriondo
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
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10
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Gong J, Chen XF, Fan X, Xu J, Zhang H, Li RY, Chen SCA, Kong F, Zhang S, Sun ZY, Kang M, Liao K, Guo DW, Wan Z, Hu ZD, Chu YZ, Zhao HM, Zou GL, Shen C, Geng YY, Wu WW, Wang H, Zhao F, Lu X, He LH, Liu GM, Xu YC, Zhang JZ, Xiao M. Emergence of Antifungal Resistant Subclades in the Global Predominant Phylogenetic Population of Candida albicans. Microbiol Spectr 2023; 11:e0380722. [PMID: 36700687 PMCID: PMC9927326 DOI: 10.1128/spectrum.03807-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/19/2022] [Indexed: 01/27/2023] Open
Abstract
Candida albicans remains the most common species causing invasive candidiasis. In this study, we present the population structure of 551 global C. albicans strains. Of these, the antifungal susceptibilities of 370 strains were tested. Specifically, 66.6% of the azole-nonsusceptible (NS)/non-wild-type (NWT) strains that were tested belonged to Clade 1. A phylogenetic analysis, a principal components analysis, the population structure, and a loss of heterozygosity events revealed two nested subclades in Clade 1, namely, Clade 1-R and Clade 1-R-α, that exhibited higher azole-NS/NWT rates (75.0% and 100%, respectively). In contrast, 6.4% (21/326) of the non-Clade 1-R isolates were NS/NWT to at least 1 of 4 azoles. Notably, all of the Clade 1-R-α isolates were pan-azole-NS/NWT that carried unique A114S and Y257H double substitutions in Erg11p and had the overexpression of ABC-type efflux pumps introduced by the substitution A736V in transcript factor Tac1p. It is worth noting that the Clade 1-R and Clade 1-R-α isolates were from different cities that are distributed over a large geographic span. Our study demonstrated the presence of specific phylogenetic subclades that are associated with antifungal resistance among C. albicans Clade 1, which calls for public attention on the monitoring of the future spread of these clones. IMPORTANCE Invasive candidiasis is the most common human fungal disease among hospitalized patients, and Candida albicans is the predominant pathogen. Considering the large number of infected cases and the limited alternative therapies, the azole-resistance of C. albicans brings a huge clinical threat. Here, our study suggested that antifungal resistance in C. albicans could also be associated with phylogenetic lineages. Specifically, it was revealed that more than half of the azole-resistant C. albicans strains belonged to the same clade. Furthermore, two nested subclades of the clade exhibited extremely high azole-resistance. It is worth noting that the isolates of two subclades were from different cities that are distributed over a large geographic span in China. This indicates that the azole-resistant C. albicans subclades may develop into serious public health concerns.
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Affiliation(s)
- Jie Gong
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xin-Fei Chen
- Department of Laboratory Medicine, Sate Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Xin Fan
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Juan Xu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Han Zhang
- Department of Laboratory Medicine, Sate Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Ruo-Yu Li
- Department of Dermatology, Beijing University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
- Research Center for Medical Mycology, Beijing University, Beijing, China
| | - Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, University of Sydney, Sydney, New South Wales, Australia
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, University of Sydney, Sydney, New South Wales, Australia
| | - Shu Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zi-Yong Sun
- Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mei Kang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Kang Liao
- Department of Clinical Laboratory, First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Da-Wen Guo
- Department of Clinical Laboratory, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Zhe Wan
- Department of Dermatology, Beijing University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
| | - Zhi-Dong Hu
- Department of Clinical Laboratory, Tianjin Medical University General Hospital, Tianjin, China
| | - Yun-Zhuo Chu
- Department of Clinical Laboratory, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Hong-Mei Zhao
- Department of Clinical Laboratory, The People's Hospital of Liaoning Province, Shenyang, Liaoning, China
| | - Gui-Ling Zou
- Department of Clinical Laboratory, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Chong Shen
- Center for Statistical Science, and Department of Industrial Engineering, Tsinghua University, Beijing, China
| | - Yuan-Yuan Geng
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wei-Wei Wu
- Department of Dermatology, the Fifth People's Hospital of Hainan Province, Haikou, Hainan, China
| | - He Wang
- Dynamiker Sub-center of Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Disease, Tianjin, China
| | - Fei Zhao
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xin Lu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Li-Hua He
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Gui-Ming Liu
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ying-Chun Xu
- Department of Laboratory Medicine, Sate Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Jian-Zhong Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Meng Xiao
- Department of Laboratory Medicine, Sate Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
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11
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Multiplexed ISSR Genotyping by Sequencing (MIG-Seq). Methods Mol Biol 2023; 2638:403-414. [PMID: 36781659 DOI: 10.1007/978-1-0716-3024-2_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Multiplexed inter-simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) is a simple, rapid, and inexpensive method for detecting single-nucleotide polymorphisms (SNPs) using next-generation sequencing (NGS). The advantages of MIG-seq include easy application to various species without prior genetic information. In addition, this method opens the door to genome-wide nucleotide sequence analyses of low-quality and trace-level deoxyribonucleic acid (DNA) samples, which have previously been difficult to analyze. Another advantage is that the procedure is simple, time-saving, and inexpensive. Recently, MIG-seq has been applied to wild and cultivated plants and has produced novel results. Using invisible DNA information, questions related to gene flow through pollination and seed dispersal, the genetic structure and diversity of populations, clonality, and the hybridization of wild and cultivated plants are being rapidly answered. In this chapter, I present the results of plant research based on MIG-seq and describe the procedure for this method as a user of MIG-seq.
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12
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Martínez Sosa F, Pilot M. Molecular Mechanisms Underlying Vertebrate Adaptive Evolution: A Systematic Review. Genes (Basel) 2023; 14:416. [PMID: 36833343 PMCID: PMC9957108 DOI: 10.3390/genes14020416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/24/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Adaptive evolution is a process in which variation that confers an evolutionary advantage in a specific environmental context arises and is propagated through a population. When investigating this process, researchers have mainly focused on describing advantageous phenotypes or putative advantageous genotypes. A recent increase in molecular data accessibility and technological advances has allowed researchers to go beyond description and to make inferences about the mechanisms underlying adaptive evolution. In this systematic review, we discuss articles from 2016 to 2022 that investigated or reviewed the molecular mechanisms underlying adaptive evolution in vertebrates in response to environmental variation. Regulatory elements within the genome and regulatory proteins involved in either gene expression or cellular pathways have been shown to play key roles in adaptive evolution in response to most of the discussed environmental factors. Gene losses were suggested to be associated with an adaptive response in some contexts. Future adaptive evolution research could benefit from more investigations focused on noncoding regions of the genome, gene regulation mechanisms, and gene losses potentially yielding advantageous phenotypes. Investigating how novel advantageous genotypes are conserved could also contribute to our knowledge of adaptive evolution.
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Affiliation(s)
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, 80-680 Gdańsk, Poland
- Faculty of Biology, University of Gdańsk, 80-308 Gdańsk, Poland
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13
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Mogilicherla K, Roy A. Epigenetic regulations as drivers of insecticide resistance and resilience to climate change in arthropod pests. Front Genet 2023; 13:1044980. [PMID: 36685945 PMCID: PMC9853188 DOI: 10.3389/fgene.2022.1044980] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/19/2022] [Indexed: 01/09/2023] Open
Abstract
Arthropod pests are remarkably capable of rapidly adapting to novel forms of environmental stress, including insecticides and climate change. The dynamic interplay between epigenetics and genetics explains the largely unexplored reality underlying rapid climatic adaptation and the development of insecticide resistance in insects. Epigenetic regulation modulates gene expression by methylating DNA and acetylating histones that play an essential role in governing insecticide resistance and adaptation to climate change. This review summarises and discusses the significance of recent advances in epigenetic regulation that facilitate phenotypic plasticity in insects and their symbiotic microbes to cope with selection pressure implied by extensive insecticide applications and climate change. We also discuss how epigenetic changes are passed on to multiple generations through sexual recombination, which remains enigmatic. Finally, we explain how these epigenetic signatures can be utilized to manage insecticide resistance and pest resilience to climate change in Anthropocene.
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14
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Persson K, Stenberg S, Tamás MJ, Warringer J. Adaptation of the yeast gene knockout collection is near-perfectly predicted by fitness and diminishing return epistasis. G3 (BETHESDA, MD.) 2022; 12:6694849. [PMID: 36083011 PMCID: PMC9635671 DOI: 10.1093/g3journal/jkac240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 08/29/2022] [Indexed: 05/31/2023]
Abstract
Adaptive evolution of clonally dividing cells and microbes is the ultimate cause of cancer and infectious diseases. The possibility of constraining the adaptation of cell populations, by inhibiting proteins enhancing the evolvability, has therefore attracted interest. However, our current understanding of how genes influence adaptation kinetics is limited, partly because accurately measuring adaptation for many cell populations is challenging. We used a high-throughput adaptive laboratory evolution platform to track the adaptation of >18,000 cell populations corresponding to single-gene deletion strains in the haploid yeast deletion collection. We report that the preadaptation fitness of gene knockouts near-perfectly (R2= 0.91) predicts their adaptation to arsenic, leaving at the most a marginal role for dedicated evolvability gene functions. We tracked the adaptation of another >23,000 gene knockout populations to a diverse range of selection pressures and generalized the almost perfect (R2=0.72-0.98) capacity of preadaptation fitness to predict adaptation. We also reconstructed mutations in FPS1, ASK10, and ARR3, which together account for almost all arsenic adaptation in wild-type cells, in gene deletions covering a broad fitness range and show that the predictability of arsenic adaptation can be understood as a by global epistasis, where excluding arsenic is more beneficial to arsenic unfit cells. The paucity of genes with a meaningful evolvability effect on adaptation diminishes the prospects of developing adjuvant drugs aiming to slow antimicrobial and chemotherapy resistance.
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Affiliation(s)
- Karl Persson
- Corresponding author: Department of Biology and Biological Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden.
| | - Simon Stenberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Markus J Tamás
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Jonas Warringer
- Corresponding author: Department of Chemistry and Molecular Biology, University of Gothenburg, PO Box 462, 40530 Gothenburg, Sweden.
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15
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Winchell KM, Aviles‐Rodriguez KJ, Carlen EJ, Miles LS, Charmantier A, De León LF, Gotanda KM, Rivkin LR, Szulkin M, Verrelli BC. Moving past the challenges and misconceptions in urban adaptation research. Ecol Evol 2022; 12:e9552. [PMID: 36425909 PMCID: PMC9679025 DOI: 10.1002/ece3.9552] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 10/14/2023] Open
Abstract
Although the field of urban evolutionary ecology has recently expanded, much progress has been made in identifying adaptations that arise as a result of selective pressures within these unique environments. However, as studies within urban environments have rapidly increased, researchers have recognized that there are challenges and opportunities in characterizing urban adaptation. Some of these challenges are a consequence of increased direct and indirect human influence, which compounds long-recognized issues with research on adaptive evolution more generally. In this perspective, we discuss several common research challenges to urban adaptation related to (1) methodological approaches, (2) trait-environment relationships and the natural history of organisms, (3) agents and targets of selection, and (4) habitat heterogeneity. Ignoring these challenges may lead to misconceptions and further impede our ability to draw conclusions regarding evolutionary and ecological processes in urban environments. Our goal is to first shed light on the conceptual challenges of conducting urban adaptation research to help avoid the propagation of these misconceptions. We further summarize potential strategies to move forward productively to construct a more comprehensive picture of urban adaptation, and discuss how urban environments also offer unique opportunities and applications for adaptation research.
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Affiliation(s)
- Kristin M. Winchell
- Department of BiologyNew York UniversityNew YorkNYUSA
- Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
| | - Kevin J. Aviles‐Rodriguez
- Department of BiologyUniversity of Massachusetts BostonBostonMassachusettsUSA
- Department of BiologyFordham UniversityBronxNew YorkUSA
| | - Elizabeth J. Carlen
- Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
- Department of BiologyFordham UniversityBronxNew YorkUSA
- Living Earth CollaborativeWashington University in St. LouisSt. LouisMissouriUSA
| | - Lindsay S. Miles
- Center for Biological Data ScienceVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Anne Charmantier
- Centre d'Ecologie Fonctionnelle et EvolutiveUniversité de Montpellier, CNRS, EPHE, IRDMontpellierFrance
| | - Luis F. De León
- Department of BiologyUniversity of Massachusetts BostonBostonMassachusettsUSA
| | - Kiyoko M. Gotanda
- Department of BiologyUniversité de SherbrookeSherbrookeQuebecCanada
- Department of Biological SciencesBrock UniversitySt. Catharine'sOntarioCanada
| | - L. Ruth Rivkin
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
- Department of BiologyUniversity of Toronto MississaugaMississaugaOntarioCanada
- Centre for Urban EnvironmentsUniversity of Toronto MississaugaMississaugaOntarioCanada
| | - Marta Szulkin
- Centre of New TechnologiesUniversity of WarsawWarsawPoland
| | - Brian C. Verrelli
- Center for Biological Data ScienceVirginia Commonwealth UniversityRichmondVirginiaUSA
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16
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Chen N, Zhang H, Zang E, Liu ZX, Lan YF, Hao WL, He S, Fan X, Sun GL, Wang YL. Adaptation insights from comparative transcriptome analysis of two Opisthopappus species in the Taihang mountains. BMC Genomics 2022; 23:466. [PMID: 35751010 PMCID: PMC9233376 DOI: 10.1186/s12864-022-08703-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 06/13/2022] [Indexed: 11/29/2022] Open
Abstract
Opisthopappus is a major wild source of Asteraceae with resistance to cold and drought. Two species of this genus (Opisthopappus taihangensis and O. longilobus) have been employed as model systems to address the evolutionary history of perennial herb biomes in the Taihang Mountains of China. However, further studies on the adaptive divergence processes of these two species are currently impeded by the lack of genomic resources. To elucidate the molecular mechanisms involved, a comparative analysis of these two species was conducted. Among the identified transcription factors, the bHLH members were most prevalent, which exhibited significantly different expression levels in the terpenoid metabolic pathway. O. longilobus showed higher level of expression than did O. taihangensis in terms of terpenes biosynthesis and metabolism, particularly monoterpenoids and diterpenoids. Analyses of the positive selection genes (PSGs) identified from O. taihangensis and O. longilobus revealed that 1203 genes were related to adaptative divergence, which were under rapid evolution and/or have signs of positive selection. Differential expressions of PSG occurred primarily in the mitochondrial electron transport, starch degradation, secondary metabolism, as well as nucleotide synthesis and S-metabolism pathway processes. Several PSGs were obviously differentially expressed in terpenes biosynthesis that might result in the fragrances divergence between O. longilobus and O. taihangensis, which would provide insights into adaptation of the two species to different environments that characterized by sub-humid warm temperate and temperate continental monsoon climates. The comparative analysis for these two species in Opisthopappus not only revealed how the divergence occurred from molecular perspective, but also provided novel insights into how differential adaptations occurred in Taihang Mountains.
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Affiliation(s)
- Ning Chen
- College of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Hao Zhang
- College of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - En Zang
- College of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Zhi-Xia Liu
- College of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Ya-Fei Lan
- College of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Wei-Li Hao
- College of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Shan He
- College of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Xing Fan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Gen-Lou Sun
- Department of Biology, Saint Mary's University, Halifax, B3H3C3, Canada.
| | - Yi-Ling Wang
- College of Life Science, Shanxi Normal University, Taiyuan, 030031, China.
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17
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Evolution of Phytoplankton as Estimated from Genetic Diversity. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10040456] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Phytoplankton are photosynthetic, single-celled organisms producing almost half of all oxygen on Earth and play a central role as prey for higher organisms, making them irreplaceable in the marine food web. As Global Change proceeds, imposing rapidly intensifying selection pressures, phytoplankton are forced to undergo evolution, local extinction, or redistribution, with potentially cascading effects throughout the marine ecosystem. Recent results from the field of population genetics display high levels of standing genetic diversity in natural phytoplankton populations, providing ample ‘evolutionary options’ and implying high adaptive potential to changing conditions. This potential for adaptive evolution is realized in several studies of experimental evolution, even though most of these studies investigate the evolution of only single strains. This, however, shows that phytoplankton not only evolve from standing genetic diversity, but also rely on de novo mutations. Recent global sampling campaigns show that the immense intraspecific diversity of phytoplankton in the marine ecosystem has been significantly underestimated, meaning we are only studying a minor portion of the relevant variability in the context of Global Change and evolution. An increased understanding of genomic diversity is primarily hampered by the low number of ecologically representative reference genomes of eukaryotic phytoplankton and the functional annotation of these. However, emerging technologies relying on metagenome and transcriptome data may offer a more realistic understanding of phytoplankton diversity.
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18
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Lewis JA, Penley MJ, Sylla H, Ahumada SD, Morran LT. Antagonistic Coevolution Limits the Range of Host Defense in C. elegans Populations. Front Cell Infect Microbiol 2022. [DOI: 10.3389/fcimb.2022.758745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Host populations often evolve defenses against parasites due to the significant fitness costs imposed by infection. However, adaptation to a specific parasite may alter the effectiveness of the host’s defenses in general. Consequently, the specificity of host defense may be influenced by a host population’s evolutionary history with parasites. Further, the degree of reciprocal change within an interaction may profoundly alter the range of host defense, given that antagonistic coevolutionary interactions are predicted to favor defense against specific parasite genotypes. Here, we examined the effect of host evolutionary history on host defense range by assessing the mortality rates of Caenorhabditis elegans host populations exposed to an array of Serratia marcescens bacterial parasite strains. Importantly, each of the host populations were derived from the same genetic background but have different experimental evolution histories with parasites. Each of these histories (exposure to either heat-killed, fixed genotype, or coevolving parasites) carries a different level of evolutionary reciprocity. Overall, we observed an effect of host evolutionary history in that previously coevolved host populations were generally the most susceptible to novel parasite strains. This data demonstrates that host evolutionary history can have a significant impact on host defense, and that host-parasite coevolution can increase host susceptibility to novel parasites.
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19
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Bisschop K, Alzate A, Bonte D, Etienne RS. The demographic consequences of adaptation: evidence from experimental evolution. Am Nat 2022; 199:729-742. [DOI: 10.1086/719183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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20
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Liu S, Zhang L, Sang Y, Lai Q, Zhang X, Jia C, Long Z, Wu J, Ma T, Mao K, Street NR, Ingvarsson PK, Liu J, Wang J. Demographic history and natural selection shape patterns of deleterious mutation load and barriers to introgression across Populus genome. Mol Biol Evol 2022; 39:6505222. [PMID: 35022759 PMCID: PMC8826634 DOI: 10.1093/molbev/msac008] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Hybridization and resulting introgression are important processes shaping the tree of life and appear to be far more common than previously thought. However, how the genome evolution was shaped by various genetic and evolutionary forces after hybridization remains unresolved. Here we used whole-genome resequencing data of 227 individuals from multiple widespread Populus species to characterize their contemporary patterns of hybridization and to quantify genomic signatures of past introgression. We observe a high frequency of contemporary hybridization and confirm that multiple previously ambiguous species are in fact F1 hybrids. Seven species were identified, which experienced different demographic histories that resulted in strikingly varied efficacy of selection and burdens of deleterious mutations. Frequent past introgression has been found to be a pervasive feature throughout the speciation of these Populus species. The retained introgressed regions, more generally, tend to contain reduced genetic load and to be located in regions of high recombination. We also find that in pairs of species with substantial differences in effective population size, introgressed regions are inferred to have undergone selective sweeps at greater than expected frequencies in the species with lower effective population size, suggesting that introgression likely have higher potential to provide beneficial variation for species with small populations. Our results, therefore, illustrate that demography and recombination have interplayed with both positive and negative selection in determining the genomic evolution after hybridization.
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Affiliation(s)
- Shuyu Liu
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science & State Key Lab of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Lei Zhang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science & State Key Lab of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Yupeng Sang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science & State Key Lab of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Qiang Lai
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science & State Key Lab of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Xinxin Zhang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science & State Key Lab of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Changfu Jia
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science & State Key Lab of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Zhiqin Long
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science & State Key Lab of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Jiali Wu
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science & State Key Lab of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Tao Ma
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science & State Key Lab of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Kangshan Mao
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science & State Key Lab of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Nathaniel R Street
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Pär K Ingvarsson
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jianquan Liu
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science & State Key Lab of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Jing Wang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science & State Key Lab of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
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21
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Gay L, Dhinaut J, Jullien M, Vitalis R, Navascués M, Ranwez V, Ronfort J. Evolution of flowering time in a selfing annual plant: Roles of adaptation and genetic drift. Ecol Evol 2022; 12:e8555. [PMID: 35127051 PMCID: PMC8794724 DOI: 10.1002/ece3.8555] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 11/10/2022] Open
Abstract
Resurrection studies are a useful tool to measure how phenotypic traits have changed in populations through time. If these trait modifications correlate with the environmental changes that occurred during the time period, it suggests that the phenotypic changes could be a response to selection. Selfing, through its reduction of effective size, could challenge the ability of a population to adapt to environmental changes. Here, we used a resurrection study to test for adaptation in a selfing population of Medicago truncatula, by comparing the genetic composition and flowering times across 22 generations. We found evidence for evolution toward earlier flowering times by about two days and a peculiar genetic structure, typical of highly selfing populations, where some multilocus genotypes (MLGs) are persistent through time. We used the change in frequency of the MLGs through time as a multilocus fitness measure and built a selection gradient that suggests evolution toward earlier flowering times. Yet, a simulation model revealed that the observed change in flowering time could be explained by drift alone, provided the effective size of the population is small enough (<150). These analyses suffer from the difficulty to estimate the effective size in a highly selfing population, where effective recombination is severely reduced.
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Affiliation(s)
- Laurène Gay
- CIRADINRAEInstitut AgroUMR AGAP InstitutUniv MontpellierMontpellierFrance
| | - Julien Dhinaut
- CIRADINRAEInstitut AgroUMR AGAP InstitutUniv MontpellierMontpellierFrance
- Present address:
Evolutionary Biology and Ecology of AlgaeUPMCUniversity of Paris VI, UC, UACH, UMI 3614CNRSSorbonne UniversitésRoscoffFrance
| | - Margaux Jullien
- CIRADINRAEInstitut AgroUMR AGAP InstitutUniv MontpellierMontpellierFrance
- Present address:
INRAUniv. Paris‐SudCNRSAgroParisTechGQE – Le MoulonUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Renaud Vitalis
- CIRADINRAEInstitut AgroIRDCBGPUniv MontpellierMontpellierFrance
| | | | - Vincent Ranwez
- CIRADINRAEInstitut AgroUMR AGAP InstitutUniv MontpellierMontpellierFrance
| | - Joëlle Ronfort
- CIRADINRAEInstitut AgroUMR AGAP InstitutUniv MontpellierMontpellierFrance
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22
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Chen Y, Liu Z, Régnière J, Vasseur L, Lin J, Huang S, Ke F, Chen S, Li J, Huang J, Gurr GM, You M, You S. Large-scale genome-wide study reveals climate adaptive variability in a cosmopolitan pest. Nat Commun 2021; 12:7206. [PMID: 34893609 PMCID: PMC8664911 DOI: 10.1038/s41467-021-27510-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/22/2021] [Indexed: 12/15/2022] Open
Abstract
Understanding the genetic basis of climatic adaptation is essential for predicting species' responses to climate change. However, intraspecific variation of these responses arising from local adaptation remains ambiguous for most species. Here, we analyze genomic data from diamondback moth (Plutella xylostella) collected from 75 sites spanning six continents to reveal that climate-associated adaptive variation exhibits a roughly latitudinal pattern. By developing an eco-genetic index that combines genetic variation and physiological responses, we predict that most P. xylostella populations have high tolerance to projected future climates. Using genome editing, a key gene, PxCad, emerged from our analysis as functionally temperature responsive. Our results demonstrate that P. xylostella is largely capable of tolerating future climates in most of the world and will remain a global pest beyond 2050. This work improves our understanding of adaptive variation along environmental gradients, and advances pest forecasting by highlighting the genetic basis for local climate adaptation.
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Affiliation(s)
- Yanting Chen
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China ,grid.419897.a0000 0004 0369 313XJoint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002 China ,Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002 China ,grid.418033.d0000 0001 2229 4212Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, 350013 China
| | - Zhaoxia Liu
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China ,grid.419897.a0000 0004 0369 313XJoint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002 China ,Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002 China ,grid.449406.b0000 0004 1757 7252College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, 362000 China
| | - Jacques Régnière
- grid.146611.50000 0001 0775 5922Natural Resources Canada, Canadian Forest Service, Quebec City, QC G1V 4C7 Canada
| | - Liette Vasseur
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China ,grid.419897.a0000 0004 0369 313XJoint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002 China ,grid.411793.90000 0004 1936 9318Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1 Canada
| | - Jian Lin
- grid.256111.00000 0004 1760 2876College of Computer and Information Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Shiguo Huang
- grid.256111.00000 0004 1760 2876College of Computer and Information Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Fushi Ke
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China ,grid.419897.a0000 0004 0369 313XJoint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002 China ,Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002 China ,grid.458495.10000 0001 1014 7864Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
| | - Shaoping Chen
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China ,grid.419897.a0000 0004 0369 313XJoint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002 China ,Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002 China ,grid.418033.d0000 0001 2229 4212Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, 350013 China
| | - Jianyu Li
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China ,grid.419897.a0000 0004 0369 313XJoint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002 China ,Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002 China ,grid.418033.d0000 0001 2229 4212Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, 350013 China
| | - Jieling Huang
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China ,grid.419897.a0000 0004 0369 313XJoint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002 China ,Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002 China
| | - Geoff M. Gurr
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China ,grid.419897.a0000 0004 0369 313XJoint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002 China ,grid.1037.50000 0004 0368 0777Graham Centre, Charles Sturt University, Orange, NSW 2800 Australia
| | - Minsheng You
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China. .,Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China.
| | - Shijun You
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China. .,Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China.
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23
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Luqman H, Widmer A, Fior S, Wegmann D. Identifying loci under selection via explicit demographic models. Mol Ecol Resour 2021; 21:2719-2737. [PMID: 33964107 PMCID: PMC8596768 DOI: 10.1111/1755-0998.13415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 04/03/2021] [Accepted: 04/28/2021] [Indexed: 01/28/2023]
Abstract
Adaptive genetic variation is a function of both selective and neutral forces. To accurately identify adaptive loci, it is thus critical to account for demographic history. Theory suggests that signatures of selection can be inferred using the coalescent, following the premise that genealogies of selected loci deviate from neutral expectations. Here, we build on this theory to develop an analytical framework to identify loci under selection via explicit demographic models (LSD). Under this framework, signatures of selection are inferred through deviations in demographic parameters, rather than through summary statistics directly, and demographic history is accounted for explicitly. Leveraging the property of demographic models to incorporate directionality, we show that LSD can provide information on the environment in which selection acts on a population. This can prove useful in elucidating the selective processes underlying local adaptation, by characterizing genetic trade-offs and extending the concepts of antagonistic pleiotropy and conditional neutrality from ecological theory to practical application in genomic data. We implement LSD via approximate Bayesian computation and demonstrate, via simulations, that LSD (a) has high power to identify selected loci across a large range of demographic-selection regimes, (b) outperforms commonly applied genome-scan methods under complex demographies and (c) accurately infers the directionality of selection for identified candidates. Using the same simulations, we further characterize the behaviour of isolation-with-migration models conducive to the study of local adaptation under regimes of selection. Finally, we demonstrate an application of LSD by detecting loci and characterizing genetic trade-offs underlying flower colour in Antirrhinum majus.
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Affiliation(s)
- Hirzi Luqman
- Institute of Integrative BiologyETH ZurichZürichSwitzerland
| | - Alex Widmer
- Institute of Integrative BiologyETH ZurichZürichSwitzerland
| | - Simone Fior
- Institute of Integrative BiologyETH ZurichZürichSwitzerland
| | - Daniel Wegmann
- Department of BiologyUniversity of FribourgFribourgSwitzerland
- Swiss Institute of BioinformaticsFribourgSwitzerland
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24
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Peltier E, Vion C, Abou Saada O, Friedrich A, Schacherer J, Marullo P. Flor Yeasts Rewire the Central Carbon Metabolism During Wine Alcoholic Fermentation. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:733513. [PMID: 37744152 PMCID: PMC10512321 DOI: 10.3389/ffunb.2021.733513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/31/2021] [Indexed: 09/26/2023]
Abstract
The identification of natural allelic variations controlling quantitative traits could contribute to decipher metabolic adaptation mechanisms within different populations of the same species. Such variations could result from human-mediated selection pressures and participate to the domestication. In this study, the genetic causes of the phenotypic variability of the central carbon metabolism of Saccharomyces cerevisiae were investigated in the context of the enological fermentation. The genetic determinism of this trait was found out by a quantitative trait loci (QTL) mapping approach using the offspring of two strains belonging to the wine genetic group of the species. A total of 14 QTL were identified from which 8 were validated down to the gene level by genetic engineering. The allelic frequencies of the validated genes within 403 enological strains showed that most of the validated QTL had allelic variations involving flor yeast specific alleles. Those alleles were brought in the offspring by one parental strain that contains introgressions from the flor yeast genetic group. The causative genes identified are functionally linked to quantitative proteomic variations that would explain divergent metabolic features of wine and flor yeasts involving the tricarboxylic acid cycle (TCA), the glyoxylate shunt and the homeostasis of proton and redox cofactors. Overall, this work led to the identification of genetic factors that are hallmarks of adaptive divergence between flor yeast and wine yeast in the wine biotope. These results also reveal that introgressions originated from intraspecific hybridization events promoted phenotypic variability of carbon metabolism observed in wine strains.
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Affiliation(s)
- Emilien Peltier
- Unité de Recherche Œnologie EA 4577, USC 1366 INRA, Bordeaux INP, ISVV, Université de Bordeaux, Bordeaux, France
- Biolaffort, Bordeaux, France
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Charlotte Vion
- Unité de Recherche Œnologie EA 4577, USC 1366 INRA, Bordeaux INP, ISVV, Université de Bordeaux, Bordeaux, France
- Biolaffort, Bordeaux, France
| | - Omar Abou Saada
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | | | - Philippe Marullo
- Unité de Recherche Œnologie EA 4577, USC 1366 INRA, Bordeaux INP, ISVV, Université de Bordeaux, Bordeaux, France
- Biolaffort, Bordeaux, France
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25
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Zhao H, Sun S, Ding Y, Wang Y, Yue X, Du X, Wei Q, Fan G, Sun H, Lou Y, Yang H, Wang J, Xu X, Li L, Yang K, Xu H, Wang J, Zhu C, Wang S, Shan X, Hou Y, Wang Y, Fei B, Liu X, Jiang Z, Gao Z. Analysis of 427 genomes reveals moso bamboo population structure and genetic basis of property traits. Nat Commun 2021; 12:5466. [PMID: 34526499 PMCID: PMC8443721 DOI: 10.1038/s41467-021-25795-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 08/24/2021] [Indexed: 02/08/2023] Open
Abstract
Moso bamboo (Phyllostachys edulis) is an economically and ecologically important nontimber forestry species. Further development of this species as a sustainable bamboo resource has been hindered by a lack of population genome information. Here, we report a moso bamboo genomic variation atlas of 5.45 million single-nucleotide polymorphisms (SNPs) from whole-genome resequencing of 427 individuals covering 15 representative geographic areas. We uncover low genetic diversity, high genotype heterozygosity, and genes under balancing selection underlying moso bamboo population adaptation. We infer its demographic history with one bottleneck and its recently small population without a rebound. We define five phylogenetic groups and infer that one group probably originated by a single-origin event from East China. Finally, we conduct genome-wide association analysis of nine important property-related traits to identify candidate genes, many of which are involved in cell wall, carbohydrate metabolism, and environmental adaptation. These results provide a foundation and resources for understanding moso bamboo evolution and the genetic mechanisms of agriculturally important traits.
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Affiliation(s)
- Hansheng Zhao
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, 100102 Beijing, China ,Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, 100102 Beijing, China
| | - Shuai Sun
- grid.21155.320000 0001 2034 1839BGI-Qingdao, BGI-Shenzhen, 266555 Qingdao, China ,China National GeneBank, BGI-Shenzhen, 518120 Shenzhen, China ,grid.410726.60000 0004 1797 8419College of Life Sciences, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Yulong Ding
- grid.410625.40000 0001 2293 4910Bamboo Research Institute, Nanjing Forestry University, 210037 Nanjing, China
| | - Yue Wang
- grid.21155.320000 0001 2034 1839BGI-Qingdao, BGI-Shenzhen, 266555 Qingdao, China ,China National GeneBank, BGI-Shenzhen, 518120 Shenzhen, China
| | - Xianghua Yue
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, 100102 Beijing, China ,Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, 100102 Beijing, China
| | - Xiao Du
- grid.21155.320000 0001 2034 1839BGI-Qingdao, BGI-Shenzhen, 266555 Qingdao, China ,China National GeneBank, BGI-Shenzhen, 518120 Shenzhen, China ,grid.21155.320000 0001 2034 1839BGI-Shenzhen, 518083 Shenzhen, China
| | - Qiang Wei
- grid.410625.40000 0001 2293 4910Bamboo Research Institute, Nanjing Forestry University, 210037 Nanjing, China
| | - Guangyi Fan
- grid.21155.320000 0001 2034 1839BGI-Qingdao, BGI-Shenzhen, 266555 Qingdao, China ,China National GeneBank, BGI-Shenzhen, 518120 Shenzhen, China ,grid.21155.320000 0001 2034 1839BGI-Shenzhen, 518083 Shenzhen, China ,grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, 518083 Shenzhen, China
| | - Huayu Sun
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, 100102 Beijing, China ,Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, 100102 Beijing, China
| | - Yongfeng Lou
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, 100102 Beijing, China ,Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, 100102 Beijing, China
| | - Huanming Yang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, 518083 Shenzhen, China ,grid.21155.320000 0001 2034 1839Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, 518120 Shenzhen, China
| | - Jian Wang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, 518083 Shenzhen, China ,grid.13402.340000 0004 1759 700XJames D. Watson Institute of Genome Science, 310008 Hangzhou, China
| | - Xun Xu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, 518083 Shenzhen, China ,grid.21155.320000 0001 2034 1839Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, 518120 Shenzhen, China
| | - Lichao Li
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, 100102 Beijing, China ,Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, 100102 Beijing, China
| | - Kebin Yang
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, 100102 Beijing, China ,Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, 100102 Beijing, China
| | - Hao Xu
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, 100102 Beijing, China ,Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, 100102 Beijing, China
| | - Jiongliang Wang
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, 100102 Beijing, China ,Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, 100102 Beijing, China
| | - Chenglei Zhu
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, 100102 Beijing, China ,Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, 100102 Beijing, China
| | - Sining Wang
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, 100102 Beijing, China ,Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, 100102 Beijing, China
| | - Xuemeng Shan
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, 100102 Beijing, China ,Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, 100102 Beijing, China
| | - Yinguang Hou
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, 100102 Beijing, China ,Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, 100102 Beijing, China
| | - Yu Wang
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, 100102 Beijing, China ,Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, 100102 Beijing, China
| | - Benhua Fei
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, 100102 Beijing, China ,Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, 100102 Beijing, China
| | - Xin Liu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, 518083 Shenzhen, China ,grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, 518083 Shenzhen, China ,grid.21155.320000 0001 2034 1839BGI-Beijing, BGI-Shenzhen, 100101 Beijing, China ,grid.21155.320000 0001 2034 1839BGI-Fuyang, BGI-Shenzhen, 236009 Fuyang, China
| | - Zehui Jiang
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, 100102 Beijing, China ,Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, 100102 Beijing, China
| | - Zhimin Gao
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, 100102 Beijing, China ,Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, 100102 Beijing, China
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26
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Peltier E, Bibi-Triki S, Dutreux F, Caradec C, Friedrich A, Llorente B, Schacherer J. Dissection of quantitative trait loci in the Lachancea waltii yeast species highlights major hotspots. G3 (BETHESDA, MD.) 2021; 11:jkab242. [PMID: 34544138 PMCID: PMC8496267 DOI: 10.1093/g3journal/jkab242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/06/2021] [Indexed: 11/30/2022]
Abstract
Dissecting the genetic basis of complex trait remains a real challenge. The budding yeast Saccharomyces cerevisiae has become a model organism for studying quantitative traits, successfully increasing our knowledge in many aspects. However, the exploration of the genotype-phenotype relationship in non-model yeast species could provide a deeper insight into the genetic basis of complex traits. Here, we have studied this relationship in the Lachancea waltii species which diverged from the S. cerevisiae lineage prior to the whole-genome duplication. By performing linkage mapping analyses in this species, we identified 86 quantitative trait loci (QTL) impacting the growth in a large number of conditions. The distribution of these loci across the genome has revealed two major QTL hotspots. A first hotspot corresponds to a general growth QTL, impacting a wide range of conditions. By contrast, the second hotspot highlighted a trade-off with a disadvantageous allele for drug-free conditions which proved to be advantageous in the presence of several drugs. Finally, a comparison of the detected QTL in L. waltii with those which had been previously identified for the same trait in a closely related species, Lachancea kluyveri was performed. This analysis clearly showed the absence of shared QTL across these species. Altogether, our results represent a first step toward the exploration of the genetic architecture of quantitative trait across different yeast species.
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Affiliation(s)
- Emilien Peltier
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | | | - Fabien Dutreux
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Claudia Caradec
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Bertrand Llorente
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
- Institut Universitaire de France (IUF), Paris, France
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27
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Gai Z, Zhai J, Chen X, Jiao P, Zhang S, Sun J, Qin R, Liu H, Wu Z, Li Z. Phylogeography Reveals Geographic and Environmental Factors Driving Genetic Differentiation of Populus sect. Turanga in Northwest China. FRONTIERS IN PLANT SCIENCE 2021; 12:705083. [PMID: 34456946 PMCID: PMC8385373 DOI: 10.3389/fpls.2021.705083] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/14/2021] [Indexed: 05/28/2023]
Abstract
Populus sect. Turanga (hereafter referred to as "Populus"), including Populus euphratica and Populus pruinosa, are the predominant tree species in desert riparian forests in northwestern China. These trees play key roles in maintaining ecosystem balance, curbing desertification, and protecting biodiversity. However, the distribution area of Populus forests has been severely diminished and degraded in recent years due to increased habitat destruction and human activity. Understanding the genetic diversity among Populus individuals and populations is essential for designing conservation strategies, but comprehensive studies of their genetic diversity in northwest China are lacking. Here, we assessed the population structures and genetic diversity of 1,620 samples from 85 natural populations of Populus (59 P. euphratica and 26 P. pruinosa populations) covering all of northwestern China using 120 single nucleotide polymorphism (SNP) markers. Analysis of population structure revealed significant differentiation between these two sister species and indicated that strong geographical distribution patterns, a geographical barrier, and environmental heterogeneity shaped the extant genetic patterns of Populus. Both P. euphratica and P. pruinosa populations in southern Xinjiang had higher genetic diversity than populations in other clades, perhaps contributing to local geographic structure and strong gene flow. Analysis of molecular variance (AMOVA) identified 15% variance among and 85% variance within subpopulations. Mantel tests suggested that the genetic variation among P. euphratica and P. pruinosa populations could be explained by both geographical and environmental distance. The genetic diversity of P. euphratica showed a significant negative correlation with latitude and longitude and a positive correlation with various environmental factors, such as precipitation of warmest quarter and driest month, temperature seasonality, and annual mean temperature. These findings provide insights into how the genetic differentiation of endangered Populus species was driven by geographical and environmental factors, which should be helpful for designing strategies to protect these genetic resources in the future.
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Affiliation(s)
- Zhongshuai Gai
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, Alar, China
- College of Life Sciences, Tarim University, Alar, China
- Desert Poplar Research Center of Tarim University, Alar, China
| | - Juntuan Zhai
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, Alar, China
- College of Life Sciences, Tarim University, Alar, China
- Desert Poplar Research Center of Tarim University, Alar, China
| | - Xiangxiang Chen
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, Alar, China
- College of Life Sciences, Tarim University, Alar, China
- Desert Poplar Research Center of Tarim University, Alar, China
| | - Peipei Jiao
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, Alar, China
- College of Life Sciences, Tarim University, Alar, China
- Desert Poplar Research Center of Tarim University, Alar, China
| | - Shanhe Zhang
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, Alar, China
- College of Life Sciences, Tarim University, Alar, China
- Desert Poplar Research Center of Tarim University, Alar, China
| | - Jianhao Sun
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, Alar, China
- College of Life Sciences, Tarim University, Alar, China
- Desert Poplar Research Center of Tarim University, Alar, China
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Zhihua Wu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Zhijun Li
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, Alar, China
- College of Life Sciences, Tarim University, Alar, China
- Desert Poplar Research Center of Tarim University, Alar, China
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28
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Bohutínská M, Handrick V, Yant L, Schmickl R, Kolář F, Bomblies K, Paajanen P. De Novo Mutation and Rapid Protein (Co-)evolution during Meiotic Adaptation in Arabidopsis arenosa. Mol Biol Evol 2021; 38:1980-1994. [PMID: 33502506 PMCID: PMC8097281 DOI: 10.1093/molbev/msab001] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A sudden shift in environment or cellular context necessitates rapid adaptation. A dramatic example is genome duplication, which leads to polyploidy. In such situations, the waiting time for new mutations might be prohibitive; theoretical and empirical studies suggest that rapid adaptation will largely rely on standing variation already present in source populations. Here, we investigate the evolution of meiosis proteins in Arabidopsis arenosa, some of which were previously implicated in adaptation to polyploidy, and in a diploid, habitat. A striking and unexplained feature of prior results was the large number of amino acid changes in multiple interacting proteins, especially in the relatively young tetraploid. Here, we investigate whether selection on meiosis genes is found in other lineages, how the polyploid may have accumulated so many differences, and whether derived variants were selected from standing variation. We use a range-wide sample of 145 resequenced genomes of diploid and tetraploid A. arenosa, with new genome assemblies. We confirmed signals of positive selection in the polyploid and diploid lineages they were previously reported in and find additional meiosis genes with evidence of selection. We show that the polyploid lineage stands out both qualitatively and quantitatively. Compared with diploids, meiosis proteins in the polyploid have more amino acid changes and a higher proportion affecting more strongly conserved sites. We find evidence that in tetraploids, positive selection may have commonly acted on de novo mutations. Several tests provide hints that coevolution, and in some cases, multinucleotide mutations, might contribute to rapid accumulation of changes in meiotic proteins.
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Affiliation(s)
- Magdalena Bohutínská
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic
| | - Vinzenz Handrick
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Levi Yant
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Roswitha Schmickl
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic.,Department of Botany, University of Innsbruck, Innsbruck, Austria
| | - Kirsten Bomblies
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom.,Plant Evolutionary Genetics, Department of Biology, Institute of Molecular Plant Biology, ETH Zürich, Zurich, Switzerland
| | - Pirita Paajanen
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
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29
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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.
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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
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30
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Furness EN, Garwood RJ, Mannion PD, Sutton MD. Productivity, niche availability, species richness, and extinction risk: Untangling relationships using individual-based simulations. Ecol Evol 2021; 11:8923-8940. [PMID: 34257936 PMCID: PMC8258231 DOI: 10.1002/ece3.7730] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/11/2021] [Indexed: 11/18/2022] Open
Abstract
It has often been suggested that the productivity of an ecosystem affects the number of species that it can support. Despite decades of study, the nature, extent, and underlying mechanisms of this relationship are unclear. One suggested mechanism is the "more individuals" hypothesis (MIH). This proposes that productivity controls the number of individuals in the ecosystem, and that more individuals can be divided into a greater number of species before their population size is sufficiently small for each to be at substantial risk of extinction. Here, we test this hypothesis using REvoSim: an individual-based eco-evolutionary system that simulates the evolution and speciation of populations over geological time, allowing phenomena occurring over timescales that cannot be easily observed in the real world to be evaluated. The individual-based nature of this system allows us to remove assumptions about the nature of speciation and extinction that previous models have had to make. Many of the predictions of the MIH are supported in our simulations: Rare species are more likely to undergo extinction than common species, and species richness scales with productivity. However, we also find support for relationships that contradict the predictions of the strict MIH: species population size scales with productivity, and species extinction risk is better predicted by relative than absolute species population size, apparently due to increased competition when total community abundance is higher. Furthermore, we show that the scaling of species richness with productivity depends upon the ability of species to partition niche space. Consequently, we suggest that the MIH is applicable only to ecosystems in which niche partitioning has not been halted by species saturation. Some hypotheses regarding patterns of biodiversity implicitly or explicitly overlook niche theory in favor of neutral explanations, as has historically been the case with the MIH. Our simulations demonstrate that niche theory exerts a control on the applicability of the MIH and thus needs to be accounted for in macroecology.
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Affiliation(s)
- Euan N. Furness
- Department of Earth Sciences and EngineeringImperial College LondonLondonUK
- Grantham InstituteImperial College LondonLondonUK
| | - Russell J. Garwood
- Department of Earth and Environmental SciencesUniversity of ManchesterManchesterUK
- Earth Sciences DepartmentNatural History MuseumLondonUK
| | | | - Mark D. Sutton
- Department of Earth Sciences and EngineeringImperial College LondonLondonUK
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31
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Moreira A, Croze M, Delehelle F, Cussat-Blanc S, Luga H, Mollereau C, Balaresque P. Hearing Sensitivity of Primates: Recurrent and Episodic Positive Selection in Hair Cells and Stereocilia Protein-Coding Genes. Genome Biol Evol 2021; 13:6302699. [PMID: 34137817 PMCID: PMC8358225 DOI: 10.1093/gbe/evab133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2021] [Indexed: 12/29/2022] Open
Abstract
The large spectrum of hearing sensitivity observed in primates results from the impact of environmental and behavioral pressures to optimize sound perception and localization. Although evidence of positive selection in auditory genes has been detected in mammals including in Hominoids, selection has never been investigated in other primates. We analyzed 123 genes highly expressed in the inner ear of 27 primate species and tested to what extent positive selection may have shaped these genes in the order Primates tree. We combined both site and branch-site tests to obtain a comprehensive picture of the positively selected genes (PSGs) involved in hearing sensitivity, and drew a detailed description of the most affected branches in the tree. We chose a conservative approach, and thus focused on confounding factors potentially affecting PSG signals (alignment, GC-biased gene conversion, duplications, heterogeneous sequencing qualities). Using site tests, we showed that around 12% of these genes are PSGs, an α selection value consistent with average human genome estimates (10-15%). Using branch-site tests, we showed that the primate tree is heterogeneously affected by positive selection, with the black snub-nosed monkey, the bushbaby, and the orangutan, being the most impacted branches. A large proportion of these genes is inclined to shape hair cells and stereocilia, which are involved in the mechanotransduction process, known to influence frequency perception. Adaptive selection, and more specifically recurrent adaptive evolution, could have acted in parallel on a set of genes (ADGRV1, USH2A, PCDH15, PTPRQ, and ATP8A2) involved in stereocilia growth and the whole complex of bundle links connecting them, in species across different habitats, including high altitude and nocturnal environments.
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Affiliation(s)
- Andreia Moreira
- Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Faculté de Médecine Purpan, CNRS UMR5288, Université de Toulouse, Université Toulouse III Paul Sabatier, France.,Institut de Recherche en Informatique de Toulouse (IRIT), CNRS UMR5505, Université Toulouse III Paul Sabatier, France
| | - Myriam Croze
- Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Faculté de Médecine Purpan, CNRS UMR5288, Université de Toulouse, Université Toulouse III Paul Sabatier, France
| | - Franklin Delehelle
- Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Faculté de Médecine Purpan, CNRS UMR5288, Université de Toulouse, Université Toulouse III Paul Sabatier, France.,Institut de Recherche en Informatique de Toulouse (IRIT), CNRS UMR5505, Université Toulouse III Paul Sabatier, France
| | - Sylvain Cussat-Blanc
- Institut de Recherche en Informatique de Toulouse (IRIT), CNRS UMR5505, Université Toulouse III Paul Sabatier, France
| | - Hervé Luga
- Institut de Recherche en Informatique de Toulouse (IRIT), CNRS UMR5505, Université Toulouse III Paul Sabatier, France
| | - Catherine Mollereau
- Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Faculté de Médecine Purpan, CNRS UMR5288, Université de Toulouse, Université Toulouse III Paul Sabatier, France
| | - Patricia Balaresque
- Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Faculté de Médecine Purpan, CNRS UMR5288, Université de Toulouse, Université Toulouse III Paul Sabatier, France
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32
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Summer Is Coming! Tackling Ocean Warming in Atlantic Salmon Cage Farming. Animals (Basel) 2021; 11:ani11061800. [PMID: 34208637 PMCID: PMC8234874 DOI: 10.3390/ani11061800] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 12/22/2022] Open
Abstract
Atlantic salmon (Salmo salar) cage farming has traditionally been located at higher latitudes where cold seawater temperatures favor this practice. However, these regions can be impacted by ocean warming and heat waves that push seawater temperature beyond the thermo-tolerance limits of this species. As more mass mortality events are reported every year due to abnormal sea temperatures, the Atlantic salmon cage aquaculture industry acknowledges the need to adapt to a changing ocean. This paper reviews adult Atlantic salmon thermal tolerance limits, as well as the deleterious eco-physiological consequences of heat stress, with emphasis on how it negatively affects sea cage aquaculture production cycles. Biotechnological solutions targeting the phenotypic plasticity of Atlantic salmon and its genetic diversity, particularly that of its southernmost populations at the limit of its natural zoogeographic distribution, are discussed. Some of these solutions include selective breeding programs, which may play a key role in this quest for a more thermo-tolerant strain of Atlantic salmon that may help the cage aquaculture industry to adapt to climate uncertainties more rapidly, without compromising profitability. Omics technologies and precision breeding, along with cryopreservation breakthroughs, are also part of the available toolbox that includes other solutions that can allow cage farmers to continue to produce Atlantic salmon in the warmer waters of the oceans of tomorrow.
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33
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Twining CW, Bernhardt JR, Derry AM, Hudson CM, Ishikawa A, Kabeya N, Kainz MJ, Kitano J, Kowarik C, Ladd SN, Leal MC, Scharnweber K, Shipley JR, Matthews B. The evolutionary ecology of fatty-acid variation: Implications for consumer adaptation and diversification. Ecol Lett 2021; 24:1709-1731. [PMID: 34114320 DOI: 10.1111/ele.13771] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/20/2021] [Accepted: 04/09/2021] [Indexed: 12/20/2022]
Abstract
The nutritional diversity of resources can affect the adaptive evolution of consumer metabolism and consumer diversification. The omega-3 long-chain polyunsaturated fatty acids eicosapentaenoic acid (EPA; 20:5n-3) and docosahexaenoic acid (DHA; 22:6n-3) have a high potential to affect consumer fitness, through their widespread effects on reproduction, growth and survival. However, few studies consider the evolution of fatty acid metabolism within an ecological context. In this review, we first document the extensive diversity in both primary producer and consumer fatty acid distributions amongst major ecosystems, between habitats and amongst species within habitats. We highlight some of the key nutritional contrasts that can shape behavioural and/or metabolic adaptation in consumers, discussing how consumers can evolve in response to the spatial, seasonal and community-level variation of resource quality. We propose a hierarchical trait-based approach for studying the evolution of consumers' metabolic networks and review the evolutionary genetic mechanisms underpinning consumer adaptation to EPA and DHA distributions. In doing so, we consider how the metabolic traits of consumers are hierarchically structured, from cell membrane function to maternal investment, and have strongly environment-dependent expression. Finally, we conclude with an outlook on how studying the metabolic adaptation of consumers within the context of nutritional landscapes can open up new opportunities for understanding evolutionary diversification.
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Affiliation(s)
- Cornelia W Twining
- Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Limnological Institute, University of Konstanz, Konstanz-Egg, Germany
| | - Joey R Bernhardt
- Department of Biology, McGill University, Montréal, QC, Canada.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Alison M Derry
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada
| | - Cameron M Hudson
- Department of Fish Ecology and Evolution, Eawag, Center of Ecology, Evolution and Biochemistry, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Asano Ishikawa
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Naoki Kabeya
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology (TUMSAT, Tokyo, Japan
| | - Martin J Kainz
- WasserCluster Lunz-Inter-university Center for Aquatic Ecosystems Research, Lunz am See, Austria
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Carmen Kowarik
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Sarah Nemiah Ladd
- Ecosystem Physiology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Miguel C Leal
- ECOMARE and CESAM - Centre for Environmental and Marine Studies and Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Kristin Scharnweber
- Department of Ecology and Genetics; Limnology, Uppsala University, Uppsala, Sweden.,University of Potsdam, Plant Ecology and Nature Conservation, Potsdam-Golm, Germany
| | - Jeremy R Shipley
- Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Department of Fish Ecology and Evolution, Eawag, Center of Ecology, Evolution and Biochemistry, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Blake Matthews
- Department of Fish Ecology and Evolution, Eawag, Center of Ecology, Evolution and Biochemistry, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
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34
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Lurwanu Y, Wang Y, Wu E, He D, Waheed A, Nkurikiyimfura O, Wang Z, Shang L, Yang L, Zhan J. Increasing temperature elevates the variation and spatial differentiation of pesticide tolerance in a plant pathogen. Evol Appl 2021; 14:1274-1285. [PMID: 34025767 PMCID: PMC8127700 DOI: 10.1111/eva.13197] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/18/2022] Open
Abstract
Climate change and pesticide resistance are two of the most imminent challenges human society is facing today. Knowledge of how the evolution of pesticide resistance may be affected by climate change such as increasing air temperature on the planet is important for agricultural production and ecological sustainability in the future but is lack in scientific literatures reported from empirical research. Here, we used the azoxystrobin-Phytophthora infestans interaction in agricultural systems to investigate the contributions of environmental temperature to the evolution of pesticide resistance and infer the impacts of global warming on pesticide efficacy and future agricultural production and ecological sustainability. We achieved this by comparing azoxystrobin sensitivity of 180 P. infestans isolates sampled from nine geographic locations in China under five temperature schemes ranging from 13 to 25°C. We found that local air temperature contributed greatly to the difference of azoxystrobin tolerance among geographic populations of the pathogen. Both among-population and within-population variations in azoxystrobin tolerance increased as experimental temperatures increased. We also found that isolates with higher azoxystrobin tolerance adapted to a broader thermal niche. These results suggest that global warming may enhance the risk of developing pesticide resistance in plant pathogens and highlight the increased challenges of administering pesticides for effective management of plant diseases to support agricultural production and ecological sustainability under future thermal conditions.
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Affiliation(s)
- Yahuza Lurwanu
- Key Lab for Biopesticide and Chemical BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
- Department of Crop ProtectionFaculty of AgricultureBayero UniversityKanoNigeria
| | - Yan‐Ping Wang
- Key Lab for Biopesticide and Chemical BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - E‐Jiao Wu
- Jiangsu Key Laboratory for Horticultural Crop Genetic ImprovementInstitute of PomologyJiangsu Academy of Agricultural SciencesNanjingChina
| | - Dun‐Chun He
- School of Economics and TradeFujian Jiangxia UniversityFuzhouChina
| | - Abdul Waheed
- Key Lab for Biopesticide and Chemical BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - Oswald Nkurikiyimfura
- Key Lab for Biopesticide and Chemical BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - Zhen Wang
- Southern Potato Center of ChinaEnshi Academy of Agricultural SciencesEnshiChina
| | - Li‐Ping Shang
- Key Lab for Biopesticide and Chemical BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - Li‐Na Yang
- Institute of OceanographyMinjiang UniversityFuzhouChina
| | - Jiasui Zhan
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
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35
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Ritchie AM, Stark TL, Liberles DA. Inferring the number and position of changes in selective regime in a non-equilibrium mutation-selection framework. BMC Ecol Evol 2021; 21:39. [PMID: 33691618 PMCID: PMC7944921 DOI: 10.1186/s12862-021-01770-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 02/25/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Recovering the historical patterns of selection acting on a protein coding sequence is a major goal of evolutionary biology. Mutation-selection models address this problem by explicitly modelling fixation rates as a function of site-specific amino acid fitness values.However, they are restricted in their utility for investigating directional evolution because they require prior knowledge of the locations of fitness changes in the lineages of a phylogeny. RESULTS We apply a modified mutation-selection methodology that relaxes assumptions of equlibrium and time-reversibility. Our implementation allows us to identify branches where adaptive or compensatory shifts in the fitness landscape have taken place, signalled by a change in amino acid fitness profiles. Through simulation and analysis of an empirical data set of [Formula: see text]-lactamase genes, we test our ability to recover the position of adaptive events within the tree and successfully reconstruct initial codon frequencies and fitness profile parameters generated under the non-stationary model. CONCLUSION We demonstrate successful detection of selective shifts and identification of the affected branch on partitions of 300 codons or more. We successfully reconstruct fitness parameters and initial codon frequencies in simulated data and demonstrate that failing to account for non-equilibrium evolution can increase the error in fitness profile estimation. We also demonstrate reconstruction of plausible shifts in amino acid fitnesses in the bacterial [Formula: see text]-lactamase family and discuss some caveats for interpretation.
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Affiliation(s)
- Andrew M Ritchie
- Department of Biology, Temple University, 1900 North 12th Street, Philadelphia, PA, USA
| | - Tristan L Stark
- Department of Biology, Temple University, 1900 North 12th Street, Philadelphia, PA, USA
| | - David A Liberles
- Department of Biology, Temple University, 1900 North 12th Street, Philadelphia, PA, USA.
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36
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Zhang X, Rayner JG, Blaxter M, Bailey NW. Rapid parallel adaptation despite gene flow in silent crickets. Nat Commun 2021; 12:50. [PMID: 33397914 PMCID: PMC7782688 DOI: 10.1038/s41467-020-20263-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
Gene flow is predicted to impede parallel adaptation via de novo mutation, because it can introduce pre-existing adaptive alleles from population to population. We test this using Hawaiian crickets (Teleogryllus oceanicus) in which 'flatwing' males that lack sound-producing wing structures recently arose and spread under selection from an acoustically-orienting parasitoid. Morphometric and genetic comparisons identify distinct flatwing phenotypes in populations on three islands, localized to different loci. Nevertheless, we detect strong, recent and ongoing gene flow among the populations. Using genome scans and gene expression analysis we find that parallel evolution of flatwing on different islands is associated with shared genomic hotspots of adaptation that contain the gene doublesex, but the form of selection differs among islands and corresponds to known flatwing demographics in the wild. We thus show how parallel adaptation can occur on contemporary timescales despite gene flow, indicating that it could be less constrained than previously appreciated.
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Affiliation(s)
- Xiao Zhang
- School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK.
| | - Jack G Rayner
- School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Nathan W Bailey
- School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK.
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37
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Skinner MK, Nilsson EE. Role of environmentally induced epigenetic transgenerational inheritance in evolutionary biology: Unified Evolution Theory. ENVIRONMENTAL EPIGENETICS 2021; 7:dvab012. [PMID: 34729214 PMCID: PMC8557805 DOI: 10.1093/eep/dvab012] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/07/2021] [Accepted: 10/12/2021] [Indexed: 05/15/2023]
Abstract
The current evolutionary biology theory primarily involves genetic alterations and random DNA sequence mutations to generate the phenotypic variation required for Darwinian natural selection to act. This neo-Darwinian evolution is termed the Modern Evolution Synthesis and has been the primary paradigm for nearly 100 years. Although environmental factors have a role in neo-Darwinian natural selection, Modern Evolution Synthesis does not consider environment to impact the basic molecular processes involved in evolution. An Extended Evolutionary Synthesis has recently developed that extends the modern synthesis to consider non-genetic processes. Over the past few decades, environmental epigenetics research has been demonstrated to regulate genetic processes and directly generate phenotypic variation independent of genetic sequence alterations. Therefore, the environment can on a molecular level through non-genetic (i.e. epigenetic) mechanisms directly influence phenotypic variation, genetic variation, inheritance and adaptation. This direct action of the environment to alter phenotype that is heritable is a neo-Lamarckian concept that can facilitate neo-Darwinian (i.e. Modern Synthesis) evolution. The integration of genetics, epigenetics, Darwinian theory, Lamarckian concepts, environment, and epigenetic inheritance provides a paradigm shift in evolution theory. The role of environmental-induced epigenetic transgenerational inheritance in evolution is presented to describe a more unified theory of evolutionary biology.
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Affiliation(s)
- Michael K Skinner
- **Correspondence address. Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA. Tel: +1 509-335-1524; E-mail:
| | - Eric E Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
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38
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Li L, Shen Y, Xu X, Yang W, Li J. Fish complement C4 gene evolution and gene/protein regulatory network analyses and simulated stereo conformation of C4-MASP-2 protein complex. FISH & SHELLFISH IMMUNOLOGY 2020; 107:54-63. [PMID: 32980531 DOI: 10.1016/j.fsi.2020.09.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 09/08/2020] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
Complement C4 is a central protein by acting as pivotal molecule in the activation of the complement system. More than a decade ago, C4 gene duplication had been found in several species including fish, revealing the evolutionary origin of C4 gene. However, the evolutionary pattern and systematic function of C4 are still limited. In this study, C4 D and H types in different species groups were completely diverged. The codon usage of C4 H type in higher vertebrates were much closer to their own genome environment, in contrast to lower vertebrates, suggesting that the evolution may provide the dynamic for homogeneous codon usage between specific gene and genome. Multiple C4 sequence alignment showed that the sequences were conserved among different species. However, sequence similarity was obviously different between species C4 D and H type. Negative selection pressure was found on C4 gene evolution and it may be one of the possible reasons for the sequence broad similarity and conservation among interspecies. Proteins from C4 protein-protein interaction (PPI) network were enriched in more hematopoiesis, infections, diseases and immune-related pathways in human than zebrafish. The result suggested that the functional complexities of C4 isotypes are distinct in species from different evolutionary positions. The simulated C4 protein structures between human and grass carp shared structural similarity and the stereo structures of grass carp C4-MASP-2 protein complexes were further simulated according to a study of human. These results suggested that the interaction between C4 and MASP-2 proteins may also exist in grass carp. Our results can provide an insight for the evolutionary process of C4 and better understanding to the potential mechanism of interaction between C4 and MASP-2 in fish species.
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Affiliation(s)
- Lisen Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
| | - Yubang Shen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China.
| | - Xiaoyan Xu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
| | - Weining Yang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China.
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39
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Cohen ZP, Brevik K, Chen YH, Hawthorne DJ, Weibel BD, Schoville SD. Elevated rates of positive selection drive the evolution of pestiferousness in the Colorado potato beetle (Leptinotarsa decemlineata, Say). Mol Ecol 2020; 30:237-254. [PMID: 33095936 DOI: 10.1111/mec.15703] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 09/28/2020] [Accepted: 10/15/2020] [Indexed: 12/16/2022]
Abstract
Contextualizing evolutionary history and identifying genomic features of an insect that might contribute to its pest status is important in developing early detection and control tactics. In order to understand the evolution of pestiferousness, which we define as the accumulation of traits that contribute to an insect population's success in an agroecosystem, we tested the importance of known genomic properties associated with rapid adaptation in the Colorado potato beetle (CPB), Leptinotarsa decemlineata Say. Within the leaf beetle genus Leptinotarsa, only CPB, and a few populations therein, has risen to pest status on cultivated nightshades, Solanum. Using whole genomes from ten closely related Leptinotarsa species native to the United States, we reconstructed a high-quality species tree and used this phylogenetic framework to assess evolutionary patterns in four genomic features of rapid adaptation: standing genetic variation, gene family expansion and contraction, transposable element abundance and location, and positive selection at protein-coding genes. Throughout approximately 20 million years of history, Leptinotarsa species show little evidence of gene family turnover and transposable element variation. However, there is a clear pattern of CPB experiencing higher rates of positive selection on protein-coding genes. We determine that these rates are associated with greater standing genetic variation due to larger effective population size, which supports the theory that the demographic history contributes to rates of protein evolution. Furthermore, we identify a suite of coding genes under positive selection that are putatively associated with pestiferousness in the Colorado potato beetle lineage. They are involved in the biological processes of xenobiotic detoxification, chemosensation and hormone function.
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Affiliation(s)
- Zachary P Cohen
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - Kristian Brevik
- Department of Plant and Soil Sciences, University of Vermont, Burlington, VT, USA
| | - Yolanda H Chen
- Department of Plant and Soil Sciences, University of Vermont, Burlington, VT, USA
| | - David J Hawthorne
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Benjamin D Weibel
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
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40
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Li L, Yang W, Shen Y, Xu X, Li J. Fish complement C8 evolution, functional network analyses, and the theoretical interaction between C8 alpha chain and CD59. Mol Immunol 2020; 128:235-248. [PMID: 33160183 DOI: 10.1016/j.molimm.2020.10.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/16/2020] [Accepted: 10/18/2020] [Indexed: 12/19/2022]
Abstract
Complement C8, as a main component of the membrane attack complex, has only been identified in vertebrates. C8 comprises three subunits encoded by individual genes: C8a (alpha chain), C8b (beta chain), and C8g (gamma chain). However, in fish, there have been limited studies on the evolutionary history and systematic function of C8. In the present study, phylogenetic analysis indicated the complete divergence of C8 genes in different fish species. Codon usage bias analysis revealed the evolutionary complexity of C8 genes. Selective pressure analysis found that C8 genes have been affected by negative selection during evolution. Sequence alignment identified the sites that are under selective pressure. The systematic functions of C8 were revealed by gene co-expression and protein-protein interaction (PPI) network analyses. Notably, gene ontology enrichment analysis suggested that C8 proteins in zebrafish function mainly in the neuroendocrine system. Protein structural comparisons showed that putative functional residues and domains were conserved between the C8 subunits of human and grass carp. A preliminary study on the theoretical interaction between C8a and CD59 was performed according to the simulated protein stereo structure. The first functionally-related site was absent in the simulated conformation of the grass carp (Ctenopharyngodon idella) C8a-CD59 protein complex. We speculated that Tyr63 is involved in the functional loss of CD59 binding. The docking of CD59 to four potential sites (Met390, Ser391, Leu392, and Val405) in grass carp C8a was analyzed. The results of the present study provide a deeper understanding of the evolution and function of fish complement C8.
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Affiliation(s)
- Lisen Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
| | - Weining Yang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
| | - Yubang Shen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China.
| | - Xiaoyan Xu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China.
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41
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Lee HJ, Longnecker M, Calkins TL, Renfro AD, Fredregill CL, Debboun M, Pietrantonio PV. Detection of the Nav channel kdr-like mutation and modeling of factors affecting survivorship of Culex quinquefasciatus mosquitoes from six areas of Harris County (Houston), Texas, after permethrin field-cage tests. PLoS Negl Trop Dis 2020; 14:e0008860. [PMID: 33211688 PMCID: PMC7714350 DOI: 10.1371/journal.pntd.0008860] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 12/03/2020] [Accepted: 10/08/2020] [Indexed: 11/18/2022] Open
Abstract
Culex quinquefasciatus is one of the most important mosquito vectors of arboviruses. Currently, the fastest approach to control disease transmission is the application of synthetic adulticide insecticides. However, in highly populated urban centers the development of insecticide resistance in mosquito populations could impair insecticide efficacy and therefore, disease control. To assess the effect of resistance on vector control, females of Cx. quinquefasciatus collected from six mosquito control operational areas in Harris County, Texas, were treated in field cage tests at three different distances with the pyrethroid Permanone® 31-66 applied at the operational rate. Females were analyzed by sequencing and/or diagnostic PCR using de novo designed primers for detecting the kdr-like mutation in the voltage-gated sodium channel (L982F; TTA to TTT) (house fly kdr canonical mutation L1014F). Females from the Cx. quinquefasciatus susceptible Sebring strain and those from the six operational areas placed at 30.4 m from the treatment source were killed in the tests, while 14% of field-collected mosquitoes survived at 60.8 m, and 35% at 91.2 m from the source. The diagnostic PCR had a with 97.5% accuracy to detect the kdr-like mutation. Pyrethroid resistant mosquitoes carrying the L982F mutation were broadly distributed in Harris County at high frequency. Among mosquitoes analyzed (n = 1,028), the kdr-kdr genotype was prevalent (81.2%), the kdr-s genotype was 18%, and s-s mosquitoes were less than 1% (n = 8). A logistic regression model estimated an equal probability of survival for the genotypes kdr-kdr and kdr-s in all areas analyzed. Altogether, our results point to a high-risk situation for the pyrethroid-based arboviral disease control in Harris County.
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Affiliation(s)
- Han-Jung Lee
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
| | - Michael Longnecker
- Department of Statistics, Texas A&M University, College Station, Texas, United States of America
| | - Travis L. Calkins
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
| | - Andrew D. Renfro
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
| | - Chris L. Fredregill
- Harris County Public Health, Mosquito and Vector Control Division (HCPH-MVCD), Texas, United States of America
| | - Mustapha Debboun
- Harris County Public Health, Mosquito and Vector Control Division (HCPH-MVCD), Texas, United States of America
| | - Patricia V. Pietrantonio
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
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42
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Epigenetic Mechanisms Contribute to Evolutionary Adaptation of Gene Network Activity under Environmental Selection. Cell Rep 2020; 33:108306. [PMID: 33113358 PMCID: PMC7656290 DOI: 10.1016/j.celrep.2020.108306] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/17/2019] [Accepted: 10/02/2020] [Indexed: 11/30/2022] Open
Abstract
How evolution can be facilitated by epigenetic mechanisms has received refreshed attention recently. To explore the role epigenetic inheritance plays in evolution, we subject isogenic wild-type yeast cells expressing PGAL1-YFP (yellow fluorescent protein) to selection by daily sorting based on reporter expression. We observe expression-level reductions in multiple replicates sorted for the lowest expression that persist for several days, even after lifting the selection pressure. Reduced expression is due to factors in the galactose (GAL) network rather than global factors. Results using a constitutively active GAL network are in overall agreement with findings with the wild-type network. We find that the local chromatin environment of the reporter has a significant effect on the observed phenotype. Genome sequencing, chromatin immunoprecipitation (ChIP)-qPCR, and sporulation analysis provide further insights into the epigenetic and genetic contributors to the expression changes observed. Our work provides a comprehensive example of the role played by epigenetic mechanisms on gene network evolution. Luo et al. demonstrate how epigenetic mechanisms contribute to the evolution of gene network activity. Subjecting yeast cells to repeated environmental selection based on the activity of the galactose network, they observe sustained changes in reporter expression level. They characterize the epigenetic and genetic factors contributing to the observed phenotypes.
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43
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Cheng Y, Miller MJ, Zhang D, Song G, Jia C, Qu Y, Lei F. Comparative Genomics Reveals Evolution of a Beak Morphology Locus in a High-Altitude Songbird. Mol Biol Evol 2020; 37:2983-2988. [PMID: 32592485 DOI: 10.1093/molbev/msaa157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The Ground Tit (Pseudopodoces humilis) has lived on the Qinghai-Tibet Plateau for ∼5.7 My and has the highest altitudinal distribution among all parids. This species has evolved an elongated beak in response to long-term selection imposed by ground-foraging and cavity-nesting habits, yet the genetic basis for beak elongation remains unknown. Here, we perform genome-wide analyses across 14 parid species and identify 25 highly divergent genomic regions that are significantly associated with beak length, finding seven candidate genes involved in bone morphogenesis and remolding. Neutrality tests indicate that a model allowing for a selective sweep in the highly conserved COL27A1 gene best explains variation in beak length. We also identify two nonsynonymous fixed mutations in the collagen domain that are predicted to be functionally deleterious yet may have facilitated beak elongation. Our study provides evidence of adaptive alleles in COL27A1 with major effects on beak elongation of Ps. humilis.
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Affiliation(s)
- Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Matthew J Miller
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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44
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Zheng C, Tan L, Sang M, Ye M, Wu R. Genetic adaptation of Tibetan poplar ( Populus szechuanica var. tibetica) to high altitudes on the Qinghai-Tibetan Plateau. Ecol Evol 2020; 10:10974-10985. [PMID: 33144942 PMCID: PMC7593140 DOI: 10.1002/ece3.6508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 05/14/2020] [Accepted: 05/28/2020] [Indexed: 12/26/2022] Open
Abstract
Plant adaptation to high altitudes has long been a substantial focus of ecological and evolutionary research. However, the genetic mechanisms underlying such adaptation remain poorly understood. Here, we address this issue by sampling, genotyping, and comparing populations of Tibetan poplar, Populus szechuanica var. tibetica, distributed from low (~2,000 m) to high altitudes (~3,000 m) of Sejila Mountain on the Qinghai-Tibet Plateau. Population structure analyses allow clear classification of two groups according to their altitudinal distributions. However, in contrast to the genetic variation within each population, differences between the two populations only explain a small portion of the total genetic variation (3.64%). We identified asymmetrical gene flow from high- to low-altitude populations. Integrating population genomic and landscape genomic analyses, we detected two hotspot regions, one containing four genes associated with altitudinal variation, and the other containing ten genes associated with response to solar radiation. These genes participate in abiotic stress resistance and regulation of reproductive processes. Our results provide insight into the genetic mechanisms underlying high-altitude adaptation in Tibetan poplar.
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Affiliation(s)
- Chenfei Zheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignCenter for Computational BiologyCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Lizhi Tan
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignCenter for Computational BiologyCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Mengmeng Sang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignCenter for Computational BiologyCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Meixia Ye
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignCenter for Computational BiologyCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Rongling Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignCenter for Computational BiologyCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Center for Statistical GeneticsPennsylvania State UniversityHersheyPAUSA
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45
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DeSilva R, Dodd RS. Association of genetic and climatic variability in giant sequoia, Sequoiadendron giganteum, reveals signatures of local adaptation along moisture-related gradients. Ecol Evol 2020; 10:10619-10632. [PMID: 33072284 PMCID: PMC7548164 DOI: 10.1002/ece3.6716] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 07/28/2020] [Accepted: 08/05/2020] [Indexed: 11/12/2022] Open
Abstract
Uncovering the genetic basis of local adaptation is a major goal of evolutionary biology and conservation science alike. In an era of climate change, an understanding of how environmental factors shape adaptive diversity is crucial to predicting species response and directing management. Here, we investigate patterns of genomic variation in giant sequoia, an iconic and ecologically important tree species, using 1,364 bi-allelic single nucleotide polymorphisms (SNPs). We use an F ST outlier test and two genotype-environment association methods, latent factor mixed models (LFMMs) and redundancy analysis (RDA), to detect complex signatures of local adaptation. Results indicate 79 genomic regions of potential adaptive importance, with limited overlap between the detection methods. Of the 58 loci detected by LFMM, 51 showed strong correlations to a precipitation-driven composite variable and seven to a temperature-related variable. RDA revealed 24 outlier loci with association to climate variables, all of which showed strongest relationship to summer precipitation. Nine candidate loci were indicated by two methods. After correcting for geographic distance, RDA models using climate predictors accounted for 49% of the explained variance and showed significant correlations between SNPs and climatic factors. Here, we present evidence of local adaptation in giant sequoia along gradients of precipitation and provide a first step toward identifying genomic regions of adaptive significance. The results of this study will provide information to guide management strategies that seek to maximize adaptive potential in the face of climate change.
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Affiliation(s)
- Rainbow DeSilva
- Department of Environmental Science, Policy, and Management University of California at Berkeley Berkeley California USA
| | - Richard S Dodd
- Department of Environmental Science, Policy, and Management University of California at Berkeley Berkeley California USA
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46
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Crouch NMA. Extinction rates of non-avian dinosaur species are uncorrelated with the rate of evolution of phylogenetically informative characters. Biol Lett 2020; 16:20200231. [PMID: 32574533 PMCID: PMC7336841 DOI: 10.1098/rsbl.2020.0231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/21/2020] [Indexed: 01/13/2023] Open
Abstract
Determining the factors that shape temporal variation in species diversity is an ongoing challenge. One theory is that species exhibiting lower rates of phenotypic evolution should be more likely to go extinct as they are more susceptible to changing environmental conditions. However, little work has been done to assess whether this process shapes comparatively few lineages, or is a common mechanism shaping changes in species diversity. Here, I analyse the correlation between rates of morphological evolution and extinction at the species level using six published morphological matrices of non-avian dinosaurs. I find no correlation between the two rates at different taxonomic scales, suggesting that extinction in these groups is better described by other factors. As there is a strong prior expectation of correlated rates, I suggest that traditional morphological matrices are inappropriate for addressing this question and that the characters governing lineage persistence are independent of those with high phylogenetic signal. This may be comprehensively determined with continued development of phenomic matrices.
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Affiliation(s)
- Nicholas M. A. Crouch
- Department of the Geophysical Sciences, The University of Chicago, 5734 South Ellis Avenue, Chicago, IL 60637, USA
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47
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Popitsch N, Huber CD, Buchumenski I, Eisenberg E, Jantsch M, von Haeseler A, Gallach M. A-to-I RNA Editing Uncovers Hidden Signals of Adaptive Genome Evolution in Animals. Genome Biol Evol 2020; 12:345-357. [PMID: 32145015 PMCID: PMC7186786 DOI: 10.1093/gbe/evaa046] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2020] [Indexed: 02/06/2023] Open
Abstract
In animals, the most common type of RNA editing is the deamination of adenosines (A) into inosines (I). Because inosines basepair with cytosines (C), they are interpreted as guanosines (G) by the cellular machinery and genomically encoded G alleles at edited sites mimic the function of edited RNAs. The contribution of this hardwiring effect on genome evolution remains obscure. We looked for population genomics signatures of adaptive evolution associated with A-to-I RNA edited sites in humans and Drosophila melanogaster. We found that single nucleotide polymorphisms at edited sites occur 3 (humans) to 15 times (Drosophila) more often than at unedited sites, the nucleotide G is virtually the unique alternative allele at edited sites and G alleles segregate at higher frequency at edited sites than at unedited sites. Our study reveals that a significant fraction of coding synonymous and nonsynonymous as well as silent and intergenic A-to-I RNA editing sites are likely adaptive in the distantly related human and Drosophila lineages.
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Affiliation(s)
- Niko Popitsch
- Oxford NIHR Biomedical Research Center, Wellcome Trust Center for Human Genetics, University of Oxford, Oxford, United Kingdom
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Christian D Huber
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - Ilana Buchumenski
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Michael Jantsch
- Department for Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
- Department for Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna, Austria
| | - Arndt von Haeseler
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Miguel Gallach
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna, Austria
- iLabSystems, C/Alicante, Castellón, Spain
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48
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Montiglio PO, Gotanda KM, Kratochwil CF, Laskowski KL, Farine DR. Hierarchically embedded interaction networks represent a missing link in the study of behavioral and community ecology. Behav Ecol 2020; 31:279-286. [PMID: 32210523 PMCID: PMC7083094 DOI: 10.1093/beheco/arz168] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/05/2019] [Accepted: 08/29/2019] [Indexed: 12/19/2022] Open
Abstract
Because genes and phenotypes are embedded within individuals, and individuals within populations, interactions within one level of biological organization are inherently linked to interactors at others. Here, we expand the network paradigm to consider that nodes can be embedded within other nodes, and connections (edges) between nodes at one level of organization form "bridges" for connections between nodes embedded within them. Such hierarchically embedded networks highlight two central properties of biological systems: 1) processes occurring across multiple levels of organization shape connections among biological units at any given level of organization and 2) ecological effects occurring at a given level of organization can propagate up or down to additional levels. Explicitly considering the embedded structure of evolutionary and ecological networks can capture otherwise hidden feedbacks and generate new insights into key biological phenomena, ultimately promoting a broader understanding of interactions in evolutionary theory.
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Affiliation(s)
- P O Montiglio
- Département des Sciences Biologiques, Université du Québec à Montréal, Succursale Centre-ville, Montréal, Québec, Canada
| | - K M Gotanda
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - C F Kratochwil
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
- Zukunftskolleg, University of Konstanz, Konstanz, Konstanz, Germany
| | - K L Laskowski
- Department of Biology, & Ecology of Fishes, Leibniz-Institute of Freshwater Ecology & Inland Fisheries, Berlin, Germany
- Department of Evolution and Ecology, University of California, Davis, Davis, CA, USA
| | - D R Farine
- Department of Collective Behavior, Max Planck Institute of Animal Behavior, Universitätsstraße 10, Konstanz, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
- Edward Grey Institute of Ornithology, Department of Zoology, University of Oxford, Oxford, UK
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49
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Collins S, Boyd PW, Doblin MA. Evolution, Microbes, and Changing Ocean Conditions. ANNUAL REVIEW OF MARINE SCIENCE 2020; 12:181-208. [PMID: 31451085 DOI: 10.1146/annurev-marine-010318-095311] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Experimental evolution and the associated theory are underutilized in marine microbial studies; the two fields have developed largely in isolation. Here, we review evolutionary tools for addressing four key areas of ocean global change biology: linking plastic and evolutionary trait changes, the contribution of environmental variability to determining trait values, the role of multiple environmental drivers in trait change, and the fate of populations near their tolerance limits. Wherever possible, we highlight which data from marine studies could use evolutionary approaches and where marine model systems can advance our understanding of evolution. Finally, we discuss the emerging field of marine microbial experimental evolution. We propose a framework linking changes in environmental quality (defined as the cumulative effect on population growth rate) with population traits affecting evolutionary potential, in order to understand which evolutionary processes are likely to be most important across a range of locations for different types of marine microbes.
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Affiliation(s)
- Sinéad Collins
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom;
| | - Philip W Boyd
- Institute for Marine and Antarctic Studies, University of Tasmania, Battery Point, Tasmania 7004, Australia;
| | - Martina A Doblin
- Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales 2007, Australia;
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50
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Baltar F, Bayer B, Bednarsek N, Deppeler S, Escribano R, Gonzalez CE, Hansman RL, Mishra RK, Moran MA, Repeta DJ, Robinson C, Sintes E, Tamburini C, Valentin LE, Herndl GJ. Towards Integrating Evolution, Metabolism, and Climate Change Studies of Marine Ecosystems. Trends Ecol Evol 2019; 34:1022-1033. [DOI: 10.1016/j.tree.2019.07.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/28/2019] [Accepted: 07/02/2019] [Indexed: 11/30/2022]
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