1
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Yang F, Crossley MS, Schrader L, Dubovskiy IM, Wei SJ, Zhang R. Polygenic adaptation contributes to the invasive success of the Colorado potato beetle. Mol Ecol 2022; 31:5568-5580. [PMID: 35984732 DOI: 10.1111/mec.16666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 07/03/2022] [Accepted: 08/15/2022] [Indexed: 12/24/2022]
Abstract
How invasive species cope with novel selective pressures with limited genetic variation is a fundamental question in molecular ecology. Several mechanisms have been proposed, but they can lack generality. Here, we addressed an alternative solution, polygenic adaptation, wherein traits that arise from multiple combinations of loci may be less sensitive to loss of variation during invasion. We tested the polygenic signal of environmental adaptation of Colorado potato beetle (CPB) introduced in Eurasia. Population genomic analyses showed declining genetic diversity in the eastward expansion of Eurasian populations, and weak population genetic structure (except for the invasion fronts in Asia). Demographic history showed that all populations shared a strong bottleneck about 100 years ago when CPB was introduced to Europe. Genome scans revealed a suite of genes involved in activity regulation functions that are plausibly related to cold stress, including some well-founded functions (e.g., the activity of phosphodiesterase, the G-protein regulator) and discrete functions. Such polygenic architecture supports the hypothesis that polygenic adaptation and potentially genetic redundancy can fuel the adaptation of CPB despite strong genetic depletion, thus representing a promising general mechanism for resolving the genetic paradox of invasion. More broadly, most complex traits based on polygenes may be less sensitive to invasive bottlenecks, thus ensuring the evolutionary success of invasive species in novel environments.
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Affiliation(s)
- Fangyuan Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Beijing Academy of Agriculture and Forestry Sciences, Institute of Plant and Environmental Protection, Beijing, China
| | - Michael S Crossley
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, Delaware, USA
| | - Lukas Schrader
- Institute for Evolution & Biodiversity, University of Münster, Münster, Germany
| | - Ivan M Dubovskiy
- Laboratory of Biological Plant Protection and Biotechnology, Novosibirsk State Agrarian University, Novosibirsk, Russia
| | - Shu-Jun Wei
- Beijing Academy of Agriculture and Forestry Sciences, Institute of Plant and Environmental Protection, Beijing, China
| | - Runzhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
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2
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Rodríguez M, Pagola L, Norry FM, Ferrero P. Cardiac performance in heat-stressed flies of heat-susceptible and heat-resistant Drosophila melanogaster. JOURNAL OF INSECT PHYSIOLOGY 2021; 133:104268. [PMID: 34171365 DOI: 10.1016/j.jinsphys.2021.104268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/24/2021] [Accepted: 06/17/2021] [Indexed: 06/13/2023]
Abstract
Thermotolerance is a complex trait that can greatly differ between heat-susceptible (HS) and heat-adapted populations of small insects including Drosophila, with short-term effects after a sub-lethal level of heat stress on many physiological functions. Cardiac performance could accordingly be more robust in heat-resistant (HR) than in HS individuals under heat stress. Here, we tested heart performance under heat-stress effects in two recombinant inbred lines (RIL) of Drosophila melanogaster that dramatically differ in heat knockdown resistance. Heart rate did not strongly differ between heat-susceptible and heat-tolerant flies after a sub-lethal heat stress. Instead, heat-susceptible flies showed a much higher arrhythmia incidence, a longer duration of each heartbeat, and a larger amount of bradycardia than heat-tolerant flies. The highly conserved cardiac proteins SERCA, RyR and NCX that participate in the excitation/contraction coupling, did not differ in activity level between HR and HS flies. Available information for both RIL suggests that heart performance under heat stress may be linked, at least partially, to candidate genes of previously identified quantitative trait loci (QTL) for thermotolerance. This study indicates that HR flies can be genetically more robust in their heart performance than HS flies under even sub-lethal levels of heat stress.
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Affiliation(s)
- Maia Rodríguez
- Departamento de Ciencias Básicas y Experimentales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Pergamino 2700, Buenos Aires, Argentina
| | - Lucía Pagola
- Centro de Investigaciones Cardiovasculares 'Dr. Horacio E. Cingolani', Facultad de Ciencias Médicas, UNLP, La Plata 1900, Buenos Aires, Argentina
| | - Fabian M Norry
- Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Universidad de Buenos Aires, C-1428-EHA Buenos Aires, Argentina; Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA) - CONICET, Universidad de Buenos Aires, C-1428-EHA Buenos Aires, Argentina.
| | - Paola Ferrero
- Departamento de Ciencias Básicas y Experimentales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Pergamino 2700, Buenos Aires, Argentina; Centro de Investigaciones Cardiovasculares 'Dr. Horacio E. Cingolani', Facultad de Ciencias Médicas, UNLP, La Plata 1900, Buenos Aires, Argentina.
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3
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Konorov EA, Yurchenko V, Patraman I, Lukashev A, Oyun N. The effects of genetic drift and genomic selection on differentiation and local adaptation of the introduced populations of Aedes albopictus in southern Russia. PeerJ 2021; 9:e11776. [PMID: 34327056 PMCID: PMC8308624 DOI: 10.7717/peerj.11776] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 06/23/2021] [Indexed: 01/05/2023] Open
Abstract
Background Asian tiger mosquito Aedes albopictus is an arbovirus vector that has spread from its native habitation areal in Southeast Asia throughout North and South Americas, Europe, and Africa. Ae. albopictus was first detected in the Southern Federal District of the Russian Federation in the subtropical town of Sochi in 2011. In subsequent years, this species has been described in the continental areas with more severe climate and lower winter temperatures. Methods Genomic analysis of pooled Ae. albopictus samples collected in the mosquito populations in the coastal and continental regions of the Krasnodar Krai was conducted to look for the genetic changes associated with the spread and potential cold adaptation in Ae. albopictus. Results The results of the phylogenetic analysis based on mitochondrial genomes corresponded well with the hypothesis that Ae. albopictus haplotype A1a2a1 was introduced into the region from a single source. Population analysis revealed the role of dispersal and genetic drift in the local adaptation of the Asian tiger mosquito. The absence of shared haplotypes between the samples and high fixation indices suggest that gene flow between samples was heavily restricted. Mitochondrial and genomic differentiation together with different distances between dispersal routes, natural and anthropogenic barriers and local effective population size reduction could lead to difficulties in local climatic adaptations due to reduced selection effectiveness. We have found genomic regions with selective sweep patterns which can be considered as having been affected by recent selection events. The genes located in these regions participate in neural protection, lipid conservation, and cuticle formation during diapause. These processes were shown to be important for cold adaptation in the previous transcriptomic and proteomic studies. However, the population history and relatively low coverage obtained in the present article could have negatively affect sweep detection.
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Affiliation(s)
- Evgenii A Konorov
- Vavilov Institute of General Genetics of Russian Academy of Science, Moscow, Russian Federation.,V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences, Moscow, Russian Federation
| | - Vyacheslav Yurchenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russian Federation.,Life Science Research Centre, University of Ostrava, Ostrava, Czech Republic
| | - Ivan Patraman
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russian Federation.,Federal State Budgetary Institution "National Research Centre for Epidemiology and Microbiology named after the Honorary Academician N. F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russian Federation
| | - Alexander Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russian Federation
| | - Nadezhda Oyun
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russian Federation.,Federal State Budgetary Institution "National Research Centre for Epidemiology and Microbiology named after the Honorary Academician N. F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russian Federation.,Department of Entomology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russian Federation
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4
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Huang Y, Lack JB, Hoppel GT, Pool JE. Parallel and Population-specific Gene Regulatory Evolution in Cold-Adapted Fly Populations. Genetics 2021; 218:6275754. [PMID: 33989401 PMCID: PMC8864734 DOI: 10.1093/genetics/iyab077] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 05/10/2021] [Indexed: 11/15/2022] Open
Abstract
Changes in gene regulation at multiple levels may comprise an important share of the molecular changes underlying adaptive evolution in nature. However, few studies have assayed within- and between-population variation in gene regulatory traits at a transcriptomic scale, and therefore inferences about the characteristics of adaptive regulatory changes have been elusive. Here, we assess quantitative trait differentiation in gene expression levels and alternative splicing (intron usage) between three closely related pairs of natural populations of Drosophila melanogaster from contrasting thermal environments that reflect three separate instances of cold tolerance evolution. The cold-adapted populations were known to show population genetic evidence for parallel evolution at the SNP level, and here we find evidence for parallel expression evolution between them, with stronger parallelism at larval and adult stages than for pupae. We also implement a flexible method to estimate cis- vs trans-encoded contributions to expression or splicing differences at the adult stage. The apparent contributions of cis- vs trans-regulation to adaptive evolution vary substantially among population pairs. While two of three population pairs show a greater enrichment of cis-regulatory differences among adaptation candidates, trans-regulatory differences are more likely to be implicated in parallel expression changes between population pairs. Genes with significant cis-effects are enriched for signals of elevated genetic differentiation between cold- and warm-adapted populations, suggesting that they are potential targets of local adaptation. These findings expand our knowledge of adaptive gene regulatory evolution and our ability to make inferences about this important and widespread process.
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Affiliation(s)
- Yuheng Huang
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.,Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Justin B Lack
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.,Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Grant T Hoppel
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - John E Pool
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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5
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False and true positives in arthropod thermal adaptation candidate gene lists. Genetica 2021; 149:143-153. [PMID: 33963492 DOI: 10.1007/s10709-021-00122-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/27/2021] [Indexed: 10/21/2022]
Abstract
Genome-wide studies are prone to false positives due to inherently low priors and statistical power. One approach to ameliorate this problem is to seek validation of reported candidate genes across independent studies: genes with repeatedly discovered effects are less likely to be false positives. Inversely, genes reported only as many times as expected by chance alone, while possibly representing novel discoveries, are also more likely to be false positives. We show that, across over 30 genome-wide studies that reported Drosophila and Daphnia genes with possible roles in thermal adaptation, the combined lists of candidate genes and orthologous groups are rapidly approaching the total number of genes and orthologous groups in the respective genomes. This is consistent with the expectation of high frequency of false positives. The majority of these spurious candidates have been identified by one or a few studies, as expected by chance alone. In contrast, a noticeable minority of genes have been identified by numerous studies with the probabilities of such discoveries occurring by chance alone being exceedingly small. For this subset of genes, different studies are in agreement with each other despite differences in the ecological settings, genomic tools and methodology, and reporting thresholds. We provide a reference set of presumed true positives among Drosophila candidate genes and orthologous groups involved in response to changes in temperature, suitable for cross-validation purposes. Despite this approach being prone to false negatives, this list of presumed true positives includes several hundred genes, consistent with the "omnigenic" concept of genetic architecture of complex traits.
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6
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Bogaerts‐Márquez M, Guirao‐Rico S, Gautier M, González J. Temperature, rainfall and wind variables underlie environmental adaptation in natural populations of Drosophila melanogaster. Mol Ecol 2021; 30:938-954. [PMID: 33350518 PMCID: PMC7986194 DOI: 10.1111/mec.15783] [Citation(s) in RCA: 10] [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] [Received: 05/07/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 02/06/2023]
Abstract
While several studies in a diverse set of species have shed light on the genes underlying adaptation, our knowledge on the selective pressures that explain the observed patterns lags behind. Drosophila melanogaster is a valuable organism to study environmental adaptation because this species originated in Southern Africa and has recently expanded worldwide, and also because it has a functionally well-annotated genome. In this study, we aimed to decipher which environmental variables are relevant for adaptation of D. melanogaster natural populations in Europe and North America. We analysed 36 whole-genome pool-seq samples of D. melanogaster natural populations collected in 20 European and 11 North American locations. We used the BayPass software to identify single nucleotide polymorphisms (SNPs) and transposable elements (TEs) showing signature of adaptive differentiation across populations, as well as significant associations with 59 environmental variables related to temperature, rainfall, evaporation, solar radiation, wind, daylight hours, and soil type. We found that in addition to temperature and rainfall, wind related variables are also relevant for D. melanogaster environmental adaptation. Interestingly, 23%-51% of the genes that showed significant associations with environmental variables were not found overly differentiated across populations. In addition to SNPs, we also identified 10 reference transposable element insertions associated with environmental variables. Our results showed that genome-environment association analysis can identify adaptive genetic variants that are undetected by population differentiation analysis while also allowing the identification of candidate environmental drivers of adaptation.
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Affiliation(s)
- María Bogaerts‐Márquez
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
- The European Drosophila Population Genomics Consortium (DrosEU)Université de MontpellierMontpellierFrance
| | - Sara Guirao‐Rico
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
- The European Drosophila Population Genomics Consortium (DrosEU)Université de MontpellierMontpellierFrance
| | - Mathieu Gautier
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgroUniversité de MontpellierMontpellierFrance
| | - Josefa González
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
- The European Drosophila Population Genomics Consortium (DrosEU)Université de MontpellierMontpellierFrance
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7
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Kapun M, Barrón MG, Staubach F, Obbard DJ, Wiberg RAW, Vieira J, Goubert C, Rota-Stabelli O, Kankare M, Bogaerts-Márquez M, Haudry A, Waidele L, Kozeretska I, Pasyukova EG, Loeschcke V, Pascual M, Vieira CP, Serga S, Montchamp-Moreau C, Abbott J, Gibert P, Porcelli D, Posnien N, Sánchez-Gracia A, Grath S, Sucena É, Bergland AO, Guerreiro MPG, Onder BS, Argyridou E, Guio L, Schou MF, Deplancke B, Vieira C, Ritchie MG, Zwaan BJ, Tauber E, Orengo DJ, Puerma E, Aguadé M, Schmidt P, Parsch J, Betancourt AJ, Flatt T, González J. Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses. Mol Biol Evol 2020; 37:2661-2678. [PMID: 32413142 PMCID: PMC7475034 DOI: 10.1093/molbev/msaa120] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterize variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.
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Affiliation(s)
- Martin Kapun
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Evolutionary Biology and Environmental Sciences, University of Zürich, Zürich, Switzerland
- Division of Cell and Developmental Biology, Medical University of Vienna, Vienna, Austria
| | - Maite G Barrón
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Fabian Staubach
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolutionary Biology and Ecology, University of Freiburg, Freiburg, Germany
| | - Darren J Obbard
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - R Axel W Wiberg
- The European Drosophila Population Genomics Consortium (DrosEU)
- Centre for Biological Diversity, School of Biology, University of St. Andrews, St Andrews, Scotland
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
| | - Jorge Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal
| | - Clément Goubert
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
| | - Omar Rota-Stabelli
- The European Drosophila Population Genomics Consortium (DrosEU)
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’ Adige, Italy
| | - Maaria Kankare
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - María Bogaerts-Márquez
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Annabelle Haudry
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Lena Waidele
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolutionary Biology and Ecology, University of Freiburg, Freiburg, Germany
| | - Iryna Kozeretska
- The European Drosophila Population Genomics Consortium (DrosEU)
- General and Medical Genetics Department, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
- State Institution National Antarctic Scientific Center of Ministry of Education and Science of Ukraine, Kyiv, Ukraine
| | - Elena G Pasyukova
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratory of Genome Variation, Institute of Molecular Genetics of RAS, Moscow, Russia
| | - Volker Loeschcke
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Bioscience—Genetics, Ecology and Evolution, Aarhus University, Aarhus C, Denmark
| | - Marta Pascual
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Cristina P Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal
| | - Svitlana Serga
- The European Drosophila Population Genomics Consortium (DrosEU)
- General and Medical Genetics Department, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Catherine Montchamp-Moreau
- The European Drosophila Population Genomics Consortium (DrosEU)
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
| | - Jessica Abbott
- The European Drosophila Population Genomics Consortium (DrosEU)
- Section for Evolutionary Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Patricia Gibert
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Damiano Porcelli
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Animal and Plant Sciences, Sheffield, United Kingdom
| | - Nico Posnien
- The European Drosophila Population Genomics Consortium (DrosEU)
- Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Universität Göttingen, Göttingen, Germany
| | - Alejandro Sánchez-Gracia
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Sonja Grath
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Élio Sucena
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Alan O Bergland
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, University of Virginia, Charlottesville, VA
| | - Maria Pilar Garcia Guerreiro
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Banu Sebnem Onder
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, Faculty of Science, Hacettepe University, Ankara, Turkey
| | - Eliza Argyridou
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Lain Guio
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Mads Fristrup Schou
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Bioscience—Genetics, Ecology and Evolution, Aarhus University, Aarhus C, Denmark
- Section for Evolutionary Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Bart Deplancke
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Bio-engineering, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Cristina Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Michael G Ritchie
- The European Drosophila Population Genomics Consortium (DrosEU)
- Centre for Biological Diversity, School of Biology, University of St. Andrews, St Andrews, Scotland
| | - Bas J Zwaan
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratory of Genetics, Department of Plant Sciences, Wageningen University, Wageningen, Netherlands
| | - Eran Tauber
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Dorcas J Orengo
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Eva Puerma
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Montserrat Aguadé
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Paul Schmidt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, University of Pennsylvania, Philadelphia, PA
| | - John Parsch
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Andrea J Betancourt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolution, Ecology, and Behaviour, University of Liverpool, Liverpool, United Kingdom
| | - Thomas Flatt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Josefa González
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
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8
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Functional Analysis of a Putative Target of Spatially Varying Selection in the Menin1 Gene of Drosophila melanogaster. G3-GENES GENOMES GENETICS 2019; 9:73-80. [PMID: 30404774 PMCID: PMC6325912 DOI: 10.1534/g3.118.200818] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
While significant effort has been devoted to investigating the potential influence of spatially varying selection on genomic variation, relatively little effort has been devoted to experimental analysis of putative variants or genes experiencing such selection. Previous population genetic work identified an amino acid polymorphism in the Mnn1 gene as one of the most strongly latitudinally differentiated SNPs in the genome of Drosophila melanogaster in the United States and Australia. Here we report the results of our transgenic analysis of this amino acid polymorphism. Genotypes carrying alternative Mnn1 alleles differed in multiple phenotypes in a direction generally consistent with phenotypic differences previously observed along latitudinal clines. These results support inferences from earlier population genomic work that this variant influences fitness, and support the idea that the alleles exhibiting clines may be likely to have pleiotropic effects that are correlated along the axes favored by natural selection.
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9
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Kauranen H, Kinnunen J, Hiillos AL, Lankinen P, Hopkins D, Wiberg RAW, Ritchie MG, Hoikkala A. Selection for reproduction under short photoperiods changes diapause-associated traits and induces widespread genomic divergence. J Exp Biol 2019; 222:jeb.205831. [DOI: 10.1242/jeb.205831] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 09/04/2019] [Indexed: 12/30/2022]
Abstract
The incidence of reproductive diapause is a critical aspect of life history in overwintering insects from temperate regions. Much has been learned about the timing, physiology and genetics of diapause in a range of insects, but how the multiple changes involved in this and other photoperiodically regulated traits are interrelated is not well understood. We performed quasinatural selection on reproduction under short photoperiods in a northern fly species, Drosophila montana, to trace the effects of photoperiodic selection on traits regulated by the photoperiodic timer and / or by a circadian clock system. Selection changed several traits associated with reproductive diapause, including the critical day length for diapause (CDL), the frequency of diapausing females under photoperiods that deviate from daily 24 h cycles and cold tolerance, towards the phenotypes typical of lower latitudes. However, selection had no effect on the period of free-running locomotor activity rhythm regulated by the circadian clock in fly brain. At a genomic level, selection induced extensive divergence between the selection and control line replicates in 16 gene clusters involved in signal transduction, membrane properties, immunologlobulins and development. These changes resembled ones detected between latitudinally divergent D. montana populations in the wild and involved SNP divergence associated with several genes linked with diapause induction. Overall, our study shows that photoperiodic selection for reproduction under short photoperiods affects diapause-associated traits without disrupting the central clock network generating circadian rhythms in fly locomor activity.
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Affiliation(s)
- Hannele Kauranen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Johanna Kinnunen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Anna-Lotta Hiillos
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Pekka Lankinen
- Department of Biology, University of Oulu, Oulu, Finland
| | - David Hopkins
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - R. Axel W. Wiberg
- School of Biology, Dyers Brae House, University of St. Andrews, Fife, KY16 9TH, St. Andrews, UK
| | - Michael G. Ritchie
- School of Biology, Dyers Brae House, University of St. Andrews, Fife, KY16 9TH, St. Andrews, UK
| | - Anneli Hoikkala
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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10
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Henriques D, Wallberg A, Chávez-Galarza J, Johnston JS, Webster MT, Pinto MA. Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula. Sci Rep 2018; 8:11145. [PMID: 30042407 PMCID: PMC6057950 DOI: 10.1038/s41598-018-29469-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/06/2018] [Indexed: 12/25/2022] Open
Abstract
The availability of powerful high-throughput genomic tools, combined with genome scans, has helped identifying genes and genetic changes responsible for environmental adaptation in many organisms, including the honeybee. Here, we resequenced 87 whole genomes of the honeybee native to Iberia and used conceptually different selection methods (Samβada, LFMM, PCAdapt, iHs) together with in sillico protein modelling to search for selection footprints along environmental gradients. We found 670 outlier SNPs, most of which associated with precipitation, longitude and latitude. Over 88.7% SNPs laid outside exons and there was a significant enrichment in regions adjacent to exons and UTRs. Enrichment was also detected in exonic regions. Furthermore, in silico protein modelling suggests that several non-synonymous SNPs are likely direct targets of selection, as they lead to amino acid replacements in functionally important sites of proteins. We identified genomic signatures of local adaptation in 140 genes, many of which are putatively implicated in fitness-related functions such as reproduction, immunity, olfaction, lipid biosynthesis and circadian clock. Our genome scan suggests that local adaptation in the Iberian honeybee involves variations in regions that might alter patterns of gene expression and in protein-coding genes, which are promising candidates to underpin adaptive change in the honeybee.
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Affiliation(s)
- Dora Henriques
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, 5300-253, Bragança, Portugal
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE -751 23, Uppsala, Sweden
| | - Julio Chávez-Galarza
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, 5300-253, Bragança, Portugal
- Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, La Molina, Lima, Peru
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, 77843-2475, USA
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE -751 23, Uppsala, Sweden
| | - M Alice Pinto
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, 5300-253, Bragança, Portugal.
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11
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Waldvogel AM, Wieser A, Schell T, Patel S, Schmidt H, Hankeln T, Feldmeyer B, Pfenninger M. The genomic footprint of climate adaptation in Chironomus riparius. Mol Ecol 2018; 27:1439-1456. [PMID: 29473242 DOI: 10.1111/mec.14543] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 02/09/2018] [Accepted: 02/09/2018] [Indexed: 12/31/2022]
Abstract
The gradual heterogeneity of climatic factors poses varying selection pressures across geographic distances that leave signatures of clinal variation in the genome. Separating signatures of clinal adaptation from signatures of other evolutionary forces, such as demographic processes, genetic drift and adaptation, to nonclinal conditions of the immediate local environment is a major challenge. Here, we examine climate adaptation in five natural populations of the harlequin fly Chironomus riparius sampled along a climatic gradient across Europe. Our study integrates experimental data, individual genome resequencing, Pool-Seq data and population genetic modelling. Common-garden experiments revealed significantly different population growth rates at test temperatures corresponding to the population origin along the climate gradient, suggesting thermal adaptation on the phenotypic level. Based on a population genomic analysis, we derived empirical estimates of historical demography and migration. We used an FST outlier approach to infer positive selection across the climate gradient, in combination with an environmental association analysis. In total, we identified 162 candidate genes as genomic basis of climate adaptation. Enriched functions among these candidate genes involved the apoptotic process and molecular response to heat, as well as functions identified in studies of climate adaptation in other insects. Our results show that local climate conditions impose strong selection pressures and lead to genomic adaptation despite strong gene flow. Moreover, these results imply that selection to different climatic conditions seems to converge on a functional level, at least between different insect species.
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Affiliation(s)
- Ann-Marie Waldvogel
- Molecular Ecology Group, Institute for Ecology, Evolution & Diversity, Goethe-University, Frankfurt am Main, Hesse, Germany.,Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hesse, Germany
| | - Andreas Wieser
- Molecular Ecology Group, Institute for Ecology, Evolution & Diversity, Goethe-University, Frankfurt am Main, Hesse, Germany.,Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hesse, Germany
| | - Tilman Schell
- Molecular Ecology Group, Institute for Ecology, Evolution & Diversity, Goethe-University, Frankfurt am Main, Hesse, Germany.,Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hesse, Germany
| | - Simit Patel
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hesse, Germany
| | - Hanno Schmidt
- Pathology, Microbiology & Immunology, University of California - Davis, Davis, CA, USA
| | - Thomas Hankeln
- Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, Johannes Gutenberg-University, Mainz, Rhineland-Palatinate, Germany
| | - Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hesse, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hesse, Germany
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12
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Revisiting Adaptive Potential, Population Size, and Conservation. Trends Ecol Evol 2017; 32:506-517. [PMID: 28476215 DOI: 10.1016/j.tree.2017.03.012] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/28/2017] [Accepted: 03/31/2017] [Indexed: 11/24/2022]
Abstract
Additive genetic variance (VA) reflects the potential for evolutionary shifts and can be low for some traits or populations. High VA is critical for the conservation of threatened species under selection to facilitate adaptation. Theory predicts tight associations between population size and VA, but data from some experimental models, and managed and natural populations do not always support this prediction. However, VA comparisons often have low statistical power, are undertaken in highly controlled environments distinct from natural habitats, and focus on traits with limited ecological relevance. Moreover, investigations of VA typically fail to consider rare alleles, genetic load, or linkage disequilibrium, resulting in deleterious effects associated with favored alleles in small populations. Large population size remains essential for ensuring adaptation.
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13
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Pegoraro M, Zonato V, Tyler ER, Fedele G, Kyriacou CP, Tauber E. Geographical analysis of diapause inducibility in European Drosophila melanogaster populations. JOURNAL OF INSECT PHYSIOLOGY 2017; 98:238-244. [PMID: 28131702 DOI: 10.1016/j.jinsphys.2017.01.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/18/2017] [Accepted: 01/23/2017] [Indexed: 06/06/2023]
Abstract
Seasonal overwintering in insects represents an adaptation to stressful environments and in European Drosophila melanogaster females, low temperatures and short photoperiods can induce an ovarian diapause. Diapause may represent a recent (<15Ky) adaptation to the colonisation of temperate Europe by D. melanogaster from tropical sub-Saharan Africa, because African D. melanogaster and the sibling species D. simulans, have been reported to fail to undergo diapause. Over the past few centuries, D. melanogaster have also invaded North America and Australia, and eastern populations on both continents show a predictable latitudinal cline in diapause induction. In Europe however, a new diapause-enhancing timeless allele, ls-tim, is observed at high levels in southern Italy (∼80%), where it appears to have arisen and has spread throughout the continent with a frequency of ∼20% in Scandinavia. Given the phenotype of ls-tim and its geographical distribution, we might predict that it would work against any latitudinal cline in diapause induction within Europe. Indeed we reveal that any latitudinal cline for diapause in Europe is very weak, as predicted by ls-tim frequencies. In contrast, we determine ls-tim frequencies in North America and observe that they would be expected to strengthen the latitudinal pattern of diapause. Our results reveal how a newly arisen mutation, can, via the stochastic nature of where it initially arose, blur an otherwise adaptive geographical pattern.
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Affiliation(s)
- Mirko Pegoraro
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Valeria Zonato
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Elizabeth R Tyler
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Giorgio Fedele
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | | | - Eran Tauber
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK; Department of Evolutionary & Environmental Biology, University of Haifa, Haifa 3498838, Israel
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14
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Mitchell CL, Latuszek CE, Vogel KR, Greenlund IM, Hobmeier RE, Ingram OK, Dufek SR, Pecore JL, Nip FR, Johnson ZJ, Ji X, Wei H, Gailing O, Werner T. α-amanitin resistance in Drosophila melanogaster: A genome-wide association approach. PLoS One 2017; 12:e0173162. [PMID: 28241077 PMCID: PMC5328632 DOI: 10.1371/journal.pone.0173162] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/15/2017] [Indexed: 11/17/2022] Open
Abstract
We investigated the mechanisms of mushroom toxin resistance in the Drosophila Genetic Reference Panel (DGRP) fly lines, using genome-wide association studies (GWAS). While Drosophila melanogaster avoids mushrooms in nature, some lines are surprisingly resistant to α-amanitin—a toxin found solely in mushrooms. This resistance may represent a pre-adaptation, which might enable this species to invade the mushroom niche in the future. Although our previous microarray study had strongly suggested that pesticide-metabolizing detoxification genes confer α-amanitin resistance in a Taiwanese D. melanogaster line Ama-KTT, none of the traditional detoxification genes were among the top candidate genes resulting from the GWAS in the current study. Instead, we identified Megalin, Tequila, and widerborst as candidate genes underlying the α-amanitin resistance phenotype in the North American DGRP lines, all three of which are connected to the Target of Rapamycin (TOR) pathway. Both widerborst and Tequila are upstream regulators of TOR, and TOR is a key regulator of autophagy and Megalin-mediated endocytosis. We suggest that endocytosis and autophagy of α-amanitin, followed by lysosomal degradation of the toxin, is one of the mechanisms that confer α-amanitin resistance in the DGRP lines.
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Affiliation(s)
- Chelsea L Mitchell
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Dr., Houghton, MI, United States of America
| | - Catrina E Latuszek
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Dr., Houghton, MI, United States of America
| | - Kara R Vogel
- Department of Neurology, University of Wisconsin School of Medicine and Public Health, 1300 University Ave., Madison, WI, United States of America
| | - Ian M Greenlund
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Dr., Houghton, MI, United States of America
| | - Rebecca E Hobmeier
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Dr., Houghton, MI, United States of America
| | - Olivia K Ingram
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Dr., Houghton, MI, United States of America
| | - Shannon R Dufek
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Dr., Houghton, MI, United States of America
| | - Jared L Pecore
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Dr., Houghton, MI, United States of America
| | - Felicia R Nip
- College of Human Medicine, Michigan State University, Clinical Center, East Lansing, MI, United States of America
| | - Zachary J Johnson
- U.S. Forest Service, Salt Lake Ranger District 6944 S, 3000 E, Salt Lake City, UT, United States of America
| | - Xiaohui Ji
- School of Forest Resources and Environmental Sciences, Michigan Technological University, 1400 Townsend Dr., Houghton, MI, United States of America
| | - Hairong Wei
- School of Forest Resources and Environmental Sciences, Michigan Technological University, 1400 Townsend Dr., Houghton, MI, United States of America
| | - Oliver Gailing
- School of Forest Resources and Environmental Sciences, Michigan Technological University, 1400 Townsend Dr., Houghton, MI, United States of America
| | - Thomas Werner
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Dr., Houghton, MI, United States of America
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15
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Abstract
Drosophila melanogaster originated in tropical Africa before expanding into strikingly different temperate climates in Eurasia and beyond. Here, we find elevated cold tolerance in three distinct geographic regions: beyond the well-studied non-African case, we show that populations from the highlands of Ethiopia and South Africa have significantly increased cold tolerance as well. We observe greater cold tolerance in outbred versus inbred flies, but only in populations with higher inversion frequencies. Each cold-adapted population shows lower inversion frequencies than a closely-related warm-adapted population, suggesting that inversion frequencies may decrease with altitude in addition to latitude. Using the FST-based "Population Branch Excess" statistic (PBE), we found only limited evidence for parallel genetic differentiation at the scale of ∼4 kb windows, specifically between Ethiopian and South African cold-adapted populations. And yet, when we looked for single nucleotide polymorphisms (SNPs) with codirectional frequency change in two or three cold-adapted populations, strong genomic enrichments were observed from all comparisons. These findings could reflect an important role for selection on standing genetic variation leading to "soft sweeps". One SNP showed sufficient codirectional frequency change in all cold-adapted populations to achieve experiment-wide significance: an intronic variant in the synaptic gene Prosap. Another codirectional outlier SNP, at senseless-2, had a strong association with our cold trait measurements, but in the opposite direction as predicted. More generally, proteins involved in neurotransmission were enriched as potential targets of parallel adaptation. The ability to study cold tolerance evolution in a parallel framework will enhance this classic study system for climate adaptation.
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Affiliation(s)
- John E. Pool
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI
| | | | - Justin B. Lack
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI
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16
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A Variable Genetic Architecture of Melanic Evolution in Drosophila melanogaster. Genetics 2016; 204:1307-1319. [PMID: 27638419 PMCID: PMC5105859 DOI: 10.1534/genetics.116.192492] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/14/2016] [Indexed: 12/30/2022] Open
Abstract
Unraveling the genetic architecture of adaptive phenotypic divergence is a fundamental quest in evolutionary biology. In Drosophila melanogaster, high-altitude melanism has evolved in separate mountain ranges in sub-Saharan Africa, potentially as an adaptation to UV intensity. We investigated the genetic basis of this melanism in three populations using a new bulk segregant analysis mapping method. We identified 19 distinct QTL regions from nine mapping crosses, with several QTL peaks overlapping between two or all populations, and yet different crosses involving the same melanic population commonly yielded distinct QTL. The strongest QTL often overlapped well-known pigmentation genes, but we typically did not find wide signals of genetic differentiation (FST) between lightly and darkly pigmented populations at these genes. Instead, we found small numbers of highly differentiated SNPs at the probable causative genes. A simulation analysis showed that these patterns of polymorphism were consistent with selection on standing genetic variation. Overall, our results suggest that, even for potentially simpler traits like pigmentation, the complexity of adaptive trait evolution poses important challenges for QTL mapping and population genetic analysis.
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17
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Flatt T. Genomics of clinal variation in Drosophila: disentangling the interactions of selection and demography. Mol Ecol 2016; 25:1023-6. [PMID: 26919307 DOI: 10.1111/mec.13534] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 01/09/2016] [Indexed: 12/23/2022]
Abstract
Clines in phenotypes and genotype frequencies across environmental gradients are commonly taken as evidence for spatially varying selection. Classical examples include the latitudinal clines in various species of Drosophila, which often occur in parallel fashion on multiple continents. Today, genomewide analysis of such clinal systems provides a fantastic opportunity for unravelling the genetics of adaptation, yet major challenges remain. A well-known but often neglected problem is that demographic processes can also generate clinality, independent of or coincident with selection. A closely related issue is how to identify true genic targets of clinal selection. In this issue of Molecular Ecology, three studies illustrate these challenges and how they might be met. Bergland et al. report evidence suggesting that the well-known parallel latitudinal clines in North American and Australian D. melanogaster are confounded by admixture from Africa and Europe, highlighting the importance of distinguishing demographic from adaptive clines. In a companion study, Machado et al. provide the first genomic comparison of latitudinal differentiation in D. melanogaster and its sister species D. simulans. While D. simulans is less clinal than D. melanogaster, a significant fraction of clinal genes is shared between both species, suggesting the existence of convergent adaptation to clinaly varying selection pressures. Finally, by drawing on several independent sources of evidence, Božičević et al. identify a functional network of eight clinal genes that are likely involved in cold adaptation. Together, these studies remind us that clinality does not necessarily imply selection and that separating adaptive signal from demographic noise requires great effort and care.
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Affiliation(s)
- Thomas Flatt
- Department of Ecology and Evolution, University of Lausanne, Lausanne, CH-1015, Switzerland
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