1
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Harris M, Kim BY, Garud N. Enrichment of hard sweeps on the X chromosome compared to autosomes in six Drosophila species. Genetics 2024; 226:iyae019. [PMID: 38366786 PMCID: PMC10990427 DOI: 10.1093/genetics/iyae019] [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: 12/06/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/18/2024] Open
Abstract
The X chromosome, being hemizygous in males, is exposed one-third of the time increasing the visibility of new mutations to natural selection, potentially leading to different evolutionary dynamics than autosomes. Recently, we found an enrichment of hard selective sweeps over soft selective sweeps on the X chromosome relative to the autosomes in a North American population of Drosophila melanogaster. To understand whether this enrichment is a universal feature of evolution on the X chromosome, we analyze diversity patterns across 6 commonly studied Drosophila species. We find an increased proportion of regions with steep reductions in diversity and elevated homozygosity on the X chromosome compared to autosomes. To assess if these signatures are consistent with positive selection, we simulate a wide variety of evolutionary scenarios spanning variations in demography, mutation rate, recombination rate, background selection, hard sweeps, and soft sweeps and find that the diversity patterns observed on the X are most consistent with hard sweeps. Our findings highlight the importance of sex chromosomes in driving evolutionary processes and suggest that hard sweeps have played a significant role in shaping diversity patterns on the X chromosome across multiple Drosophila species.
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Affiliation(s)
- Mariana Harris
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Bernard Y Kim
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Nandita Garud
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
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2
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Zurita AMI, Kyriazis CC, Lohmueller KE. The impact of non-neutral synonymous mutations when inferring selection on non-synonymous mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.07.579314. [PMID: 38370782 PMCID: PMC10871344 DOI: 10.1101/2024.02.07.579314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The distribution of fitness effects (DFE) describes the proportions of new mutations that have different effects on reproductive fitness. Accurate measurements of the DFE are important because the DFE is a fundamental parameter in evolutionary genetics and has implications for our understanding of other phenomena like complex disease or inbreeding depression. Current computational methods to infer the DFE for nonsynonymous mutations from natural variation first estimate demographic parameters from synonymous variants to control for the effects of demography and background selection. Then, conditional on these parameters, the DFE is then inferred for nonsynonymous mutations. This approach relies on the assumption that synonymous variants are neutrally evolving. However, some evidence points toward synonymous mutations having measurable effects on fitness. To test whether selection on synonymous mutations affects inference of the DFE of nonsynonymous mutations, we simulated several possible models of selection on synonymous mutations using SLiM and attempted to recover the DFE of nonsynonymous mutations using Fit∂a∂i, a common method for DFE inference. Our results show that the presence of selection on synonymous variants leads to incorrect inferences of recent population growth. Furthermore, under certain parameter combinations, inferences of the DFE can have an inflated proportion of highly deleterious nonsynonymous mutations. However, this bias can be eliminated if the correct demographic parameters are used for DFE inference instead of the biased ones inferred from synonymous variants. Our work demonstrates how unmodeled selection on synonymous mutations may affect downstream inferences of the DFE.
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Affiliation(s)
- Aina Martinez I Zurita
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
| | - Kirk E Lohmueller
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, USA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
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3
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Harris M, Kim B, Garud N. Enrichment of hard sweeps on the X chromosome compared to autosomes in six Drosophila species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.21.545888. [PMID: 38106201 PMCID: PMC10723260 DOI: 10.1101/2023.06.21.545888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The X chromosome, being hemizygous in males, is exposed one third of the time increasing the visibility of new mutations to natural selection, potentially leading to different evolutionary dynamics than autosomes. Recently, we found an enrichment of hard selective sweeps over soft selective sweeps on the X chromosome relative to the autosomes in a North American population of Drosophila melanogaster. To understand whether this enrichment is a universal feature of evolution on the X chromosome, we analyze diversity patterns across six commonly studied Drosophila species. We find an increased proportion of regions with steep reductions in diversity and elevated homozygosity on the X chromosome compared to autosomes. To assess if these signatures are consistent with positive selection, we simulate a wide variety of evolutionary scenarios spanning variations in demography, mutation rate, recombination rate, background selection, hard sweeps, and soft sweeps, and find that the diversity patterns observed on the X are most consistent with hard sweeps. Our findings highlight the importance of sex chromosomes in driving evolutionary processes and suggest that hard sweeps have played a significant role in shaping diversity patterns on the X chromosome across multiple Drosophila species.
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Affiliation(s)
- Mariana Harris
- Department of Computational Medicine, University of California Los Angeles, Los Angeles California, United States of America
| | - Bernard Kim
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Nandita Garud
- Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles California, United States of America
- Department of Human Genetics, University of California, Los Angeles, California, United States of America
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4
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Jackson B, Charlesworth B. Evidence for a force favoring GC over AT at short intronic sites in Drosophila simulans and Drosophila melanogaster. G3 GENES|GENOMES|GENETICS 2021; 11:6321237. [PMID: 34544137 PMCID: PMC8496279 DOI: 10.1093/g3journal/jkab240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022]
Abstract
Population genetics studies often make use of a class of nucleotide site free from selective pressures, in order to make inferences about population size changes or natural selection at other sites. If such neutral sites can be identified, they offer the opportunity to avoid any confounding effects of selection. Here, we investigate evolution at putatively neutrally evolving short intronic sites in natural populations of Drosophila melanogaster and Drosophila simulans, in order to understand the properties of spontaneous mutations and the extent of GC-biased gene conversion in these species. Use of data on the genetics of natural populations is advantageous because it integrates information from large numbers of individuals over long timescales. In agreement with direct evidence from observations of spontaneous mutations in Drosophila, we find a bias in the spectrum of mutations toward AT basepairs. In addition, we find that this bias is stronger in the D. melanogaster lineage than in the D. simulans lineage. The evidence for GC-biased gene conversion in Drosophila has been equivocal. Here, we provide evidence for a weak force favoring GC in both species, which is correlated with the GC content of introns and is stronger in D. simulans than in D. melanogaster.
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Affiliation(s)
- Ben Jackson
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Brian Charlesworth
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
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5
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Betancourt NJ, Rajpurohit S, Durmaz E, Fabian DK, Kapun M, Flatt T, Schmidt P. Allelic polymorphism at foxo contributes to local adaptation in Drosophila melanogaster. Mol Ecol 2021; 30:2817-2830. [PMID: 33914989 PMCID: PMC8693798 DOI: 10.1111/mec.15939] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 04/13/2021] [Indexed: 01/09/2023]
Abstract
The insulin/insulin-like growth factor signalling pathway has been hypothesized as a major determinant of life-history profiles that vary adaptively in natural populations. In Drosophila melanogaster, multiple components of this pathway vary predictably with latitude; this includes foxo, a conserved gene that regulates insulin signalling and has pleiotropic effects on a variety of fitness-associated traits. We hypothesized that allelic variation at foxo contributes to genetic variance for size-related traits that vary adaptively with latitude. We first examined patterns of variation among natural populations along a latitudinal transect in the eastern United States and show that thorax length, wing area, wing loading, and starvation tolerance exhibit significant latitudinal clines for both males and females but that development time does not vary predictably with latitude. We then generated recombinant outbred populations and show that naturally occurring allelic variation at foxo, which exhibits stronger clinality than expected, is associated with the same traits that vary with latitude in the natural populations. Our results suggest that allelic variation at foxo contributes to adaptive patterns of life-history variation in natural populations of this genetic model.
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Affiliation(s)
| | - Subhash Rajpurohit
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
- Division of Biological and Life Sciences, Ahmedabad University, Ahmedabad, India
| | - Esra Durmaz
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Daniel K. Fabian
- Department of Genetics, University of Cambridge, Cambridge, UK
- European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Martin Kapun
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Thomas Flatt
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Paul Schmidt
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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6
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Vogl C, Mikula LC. A nearly-neutral biallelic Moran model with biased mutation and linear and quadratic selection. Theor Popul Biol 2021; 139:1-17. [PMID: 33964284 DOI: 10.1016/j.tpb.2021.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 03/28/2021] [Accepted: 03/29/2021] [Indexed: 01/27/2023]
Abstract
In this article, a biallelic reversible mutation model with linear and quadratic selection is analysed. The approach reconnects to one proposed by Kimura (1979), who starts from a diffusion model and derives its equilibrium distribution up to a constant. We use a boundary-mutation Moran model, which approximates a general mutation model for small effective mutation rates, and derive its equilibrium distribution for polymorphic and monomorphic variants in small to moderately sized populations. Using this model, we show that biased mutation rates and linear selection alone can cause patterns of polymorphism within and substitution rates between populations that are usually ascribed to balancing or overdominant selection. We illustrate this using a data set of short introns and fourfold degenerate sites from Drosophila simulans and Drosophila melanogaster.
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Affiliation(s)
- Claus Vogl
- Department of Biomedical Sciences, Vetmeduni Vienna, Veterinärplatz 1, A-1210 Wien, Austria; Vienna Graduate School of Population Genetics, A-1210 Wien, Austria.
| | - Lynette Caitlin Mikula
- Centre for Biological Diversity, School of Biology, University of St. Andrews, St Andrews KY16 9TH, UK.
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7
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Kawecki TJ, Erkosar B, Dupuis C, Hollis B, Stillwell RC, Kapun M. The Genomic Architecture of Adaptation to Larval Malnutrition Points to a Trade-off with Adult Starvation Resistance in Drosophila. Mol Biol Evol 2021; 38:2732-2749. [PMID: 33677563 PMCID: PMC8233504 DOI: 10.1093/molbev/msab061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Periods of nutrient shortage impose strong selection on animal populations. Experimental studies of genetic adaptation to nutrient shortage largely focus on resistance to acute starvation at adult stage; it is not clear how conclusions drawn from these studies extrapolate to other forms of nutritional stress. We studied the genomic signature of adaptation to chronic juvenile malnutrition in six populations of Drosophila melanogaster evolved for 150 generations on an extremely nutrient-poor larval diet. Comparison with control populations evolved on standard food revealed repeatable genomic differentiation between the two set of population, involving >3,000 candidate SNPs forming >100 independently evolving clusters. The candidate genomic regions were enriched in genes implicated in hormone, carbohydrate, and lipid metabolism, including some with known effects on fitness-related life-history traits. Rather than being close to fixation, a substantial fraction of candidate SNPs segregated at intermediate allele frequencies in all malnutrition-adapted populations. This, together with patterns of among-population variation in allele frequencies and estimates of Tajima’s D, suggests that the poor diet results in balancing selection on some genomic regions. Our candidate genes for tolerance to larval malnutrition showed a high overlap with genes previously implicated in acute starvation resistance. However, adaptation to larval malnutrition in our study was associated with reduced tolerance to acute adult starvation. Thus, rather than reflecting synergy, the shared genomic architecture appears to mediate an evolutionary trade-off between tolerances to these two forms of nutritional stress.
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Affiliation(s)
- Tadeusz J Kawecki
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Berra Erkosar
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Cindy Dupuis
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Brian Hollis
- EPFL, Department of Systems Biology, Lausanne, Switzerland.,Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - R Craig Stillwell
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Martin Kapun
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland.,Department of Cell and Developmental Biology, Medical University of Vienna, Vienna, Austria
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8
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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: 58] [Impact Index Per Article: 14.5] [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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9
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Vogl C, Mikula LC, Burden CJ. Maximum likelihood estimators for scaled mutation rates in an equilibrium mutation-drift model. Theor Popul Biol 2020; 134:106-118. [PMID: 32562610 DOI: 10.1016/j.tpb.2020.06.001] [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: 11/27/2019] [Revised: 05/05/2020] [Accepted: 06/10/2020] [Indexed: 11/29/2022]
Abstract
The stationary sampling distribution of a neutral decoupled Moran or Wright-Fisher diffusion with neutral mutations is known to first order for a general rate matrix with small but otherwise unconstrained mutation rates. Using this distribution as a starting point we derive results for maximum likelihood estimates of scaled mutation rates from site frequency data under three model assumptions: a twelve-parameter general rate matrix, a nine-parameter reversible rate matrix, and a six-parameter strand-symmetric rate matrix. The site frequency spectrum is assumed to be sampled from a fixed size population in equilibrium, and to consist of allele frequency data at a large number of unlinked sites evolving with a common mutation rate matrix without selective bias. We correct an error in a previous treatment of the same problem (Burden and Tang, 2017) affecting the estimators for the general and strand-symmetric rate matrices. The method is applied to a biological dataset consisting of a site frequency spectrum extracted from short autosomal introns in a sample of Drosophila melanogaster individuals.
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Affiliation(s)
- Claus Vogl
- Department of Biomedical Sciences, Vetmeduni Vienna, Veterinärplatz 1, A-1210 Wien, Austria.
| | - Lynette C Mikula
- Centre for Biological Diversity, School of Biology, University of St. Andrews, St Andrews KY16 9TH, UK.
| | - Conrad J Burden
- Mathematical Sciences Institute, Australian National University, Canberra, Australia.
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10
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Machado HE, Lawrie DS, Petrov DA. Pervasive Strong Selection at the Level of Codon Usage Bias in Drosophila melanogaster. Genetics 2020; 214:511-528. [PMID: 31871131 PMCID: PMC7017021 DOI: 10.1534/genetics.119.302542] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/12/2019] [Indexed: 11/18/2022] Open
Abstract
Codon usage bias (CUB), where certain codons are used more frequently than expected by chance, is a ubiquitous phenomenon and occurs across the tree of life. The dominant paradigm is that the proportion of preferred codons is set by weak selection. While experimental changes in codon usage have at times shown large phenotypic effects in contrast to this paradigm, genome-wide population genetic estimates have supported the weak selection model. Here we use deep genomic population sequencing of two Drosophila melanogaster populations to measure selection on synonymous sites in a way that allowed us to estimate the prevalence of both weak and strong purifying selection. We find that selection in favor of preferred codons ranges from weak (|Nes| ∼ 1) to strong (|Nes| > 10), with strong selection acting on 10-20% of synonymous sites in preferred codons. While previous studies indicated that selection at synonymous sites could be strong, this is the first study to detect and quantify strong selection specifically at the level of CUB. Further, we find that CUB-associated polymorphism accounts for the majority of strong selection on synonymous sites, with secondary contributions of splicing (selection on alternatively spliced genes, splice junctions, and spliceosome-bound sites) and transcription factor binding. Our findings support a new model of CUB and indicate that the functional importance of CUB, as well as synonymous sites in general, have been underestimated.
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Affiliation(s)
- Heather E Machado
- Cancer, Ageing, and Somatic Mutation, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - David S Lawrie
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697-3958
| | - Dmitri A Petrov
- Department of Biology, Stanford University, California 94305-5020
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11
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Ramaekers A, Claeys A, Kapun M, Mouchel-Vielh E, Potier D, Weinberger S, Grillenzoni N, Dardalhon-Cuménal D, Yan J, Wolf R, Flatt T, Buchner E, Hassan BA. Altering the Temporal Regulation of One Transcription Factor Drives Evolutionary Trade-Offs between Head Sensory Organs. Dev Cell 2019; 50:780-792.e7. [PMID: 31447264 DOI: 10.1016/j.devcel.2019.07.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 04/24/2019] [Accepted: 07/25/2019] [Indexed: 12/30/2022]
Abstract
Size trade-offs of visual versus olfactory organs is a pervasive feature of animal evolution. This could result from genetic or functional constraints. We demonstrate that head sensory organ size trade-offs in Drosophila are genetically encoded and arise through differential subdivision of the head primordium into visual versus non-visual fields. We discover that changes in the temporal regulation of the highly conserved eyeless/Pax6 gene expression during development is a conserved mechanism for sensory trade-offs within and between Drosophila species. We identify a natural single nucleotide polymorphism in the cis-regulatory region of eyeless in a binding site of its repressor Cut that is sufficient to alter its temporal regulation and eye size. Because eyeless/Pax6 is a conserved regulator of head sensory placode subdivision, we propose that its temporal regulation is key to define the relative size of head sensory organs.
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Affiliation(s)
- Ariane Ramaekers
- Institut du Cerveau et de la Moelle Epinière (ICM) - Hôpital Pitié-Salpêtrière, Sorbonne Université, Inserm, CNRS, Paris, France.
| | - Annelies Claeys
- VIB Center for Brain and Disease, VIB, Leuven, Belgium; Center for Human Genetics, University of Leuven School of Medicine, Leuven, Belgium
| | - Martin Kapun
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Emmanuèle Mouchel-Vielh
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement, Institut de Biologie Paris Seine, LBD-IBPS), Paris, France
| | - Delphine Potier
- Aix-Marseille Université, CNRS, INSERM, CIML, Marseille, France
| | - Simon Weinberger
- VIB Center for Brain and Disease, VIB, Leuven, Belgium; Center for Human Genetics, University of Leuven School of Medicine, Leuven, Belgium
| | - Nicola Grillenzoni
- Institut du Cerveau et de la Moelle Epinière (ICM) - Hôpital Pitié-Salpêtrière, Sorbonne Université, Inserm, CNRS, Paris, France
| | - Delphine Dardalhon-Cuménal
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement, Institut de Biologie Paris Seine, LBD-IBPS), Paris, France
| | - Jiekun Yan
- VIB Center for Brain and Disease, VIB, Leuven, Belgium; Center for Human Genetics, University of Leuven School of Medicine, Leuven, Belgium
| | - Reinhard Wolf
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Erich Buchner
- Institute for Clinical Neurobiology, University Hospital Würzburg, Würzburg, Germany
| | - Bassem A Hassan
- Institut du Cerveau et de la Moelle Epinière (ICM) - Hôpital Pitié-Salpêtrière, Sorbonne Université, Inserm, CNRS, Paris, France.
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12
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Bergman J, Betancourt AJ, Vogl C. Transcription-Associated Compositional Skews in Drosophila Genes. Genome Biol Evol 2018; 10:269-275. [PMID: 29036491 PMCID: PMC5786239 DOI: 10.1093/gbe/evx200] [Citation(s) in RCA: 4] [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] [Accepted: 09/25/2017] [Indexed: 12/23/2022] Open
Abstract
In many organisms, local deviations from Chargaff's second parity rule are observed around replication and transcription start sites and within intron sequences. Here, we use expression data as well as a whole-genome data set of nearly 200 haplotypes to investigate such compositional skews in Drosophila melanogaster genes. We find a positive correlation between compositional skew and gene expression, comparable in strength to similar correlations between expression levels and genome-wide sequence features. This correlation is relatively stronger for germline, compared with somatic expression, consistent with the process of transcription-associated mutation bias. We also inferred mutation rates from alleles segregating at low frequencies in short introns, and show that, whereas the overall GC content of short introns does not conform to the equilibrium expectation, the level of the observed deviation from the second parity rule is generally consistent with the inferred rates.
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Affiliation(s)
- Juraj Bergman
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Wien, Austria
| | - Andrea J Betancourt
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
- Present address: Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Claus Vogl
- Institut für Tierzucht und Genetik, Vetmeduni Vienna, Wien, Austria
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13
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Assaf ZJ, Tilk S, Park J, Siegal ML, Petrov DA. Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations. Genome Res 2017; 27:1988-2000. [PMID: 29079675 PMCID: PMC5741049 DOI: 10.1101/gr.219956.116] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 10/20/2017] [Indexed: 11/25/2022]
Abstract
Mutations provide the raw material of evolution, and thus our ability to study evolution depends fundamentally on having precise measurements of mutational rates and patterns. We generate a data set for this purpose using (1) de novo mutations from mutation accumulation experiments and (2) extremely rare polymorphisms from natural populations. The first, mutation accumulation (MA) lines are the product of maintaining flies in tiny populations for many generations, therefore rendering natural selection ineffective and allowing new mutations to accrue in the genome. The second, rare genetic variation from natural populations allows the study of mutation because extremely rare polymorphisms are relatively unaffected by the filter of natural selection. We use both methods in Drosophila melanogaster, first generating our own novel data set of sequenced MA lines and performing a meta-analysis of all published MA mutations (∼2000 events) and then identifying a high quality set of ∼70,000 extremely rare (≤0.1%) polymorphisms that are fully validated with resequencing. We use these data sets to precisely measure mutational rates and patterns. Highlights of our results include: a high rate of multinucleotide mutation events at both short (∼5 bp) and long (∼1 kb) genomic distances, showing that mutation drives GC content lower in already GC-poor regions, and using our precise context-dependent mutation rates to predict long-term evolutionary patterns at synonymous sites. We also show that de novo mutations from independent MA experiments display similar patterns of single nucleotide mutation and well match the patterns of mutation found in natural populations.
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Affiliation(s)
- Zoe June Assaf
- Department of Genetics, Stanford University, Stanford, California 94305, USA.,Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Susanne Tilk
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Jane Park
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Mark L Siegal
- Department of Biology, New York University, New York, New York 10003, USA
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, California 94305, USA
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14
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Jackson BC, Campos JL, Haddrill PR, Charlesworth B, Zeng K. Variation in the Intensity of Selection on Codon Bias over Time Causes Contrasting Patterns of Base Composition Evolution in Drosophila. Genome Biol Evol 2017; 9:102-123. [PMID: 28082609 PMCID: PMC5381600 DOI: 10.1093/gbe/evw291] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2016] [Indexed: 12/11/2022] Open
Abstract
Four-fold degenerate coding sites form a major component of the genome, and are often used to make inferences about selection and demography, so that understanding their evolution is important. Despite previous efforts, many questions regarding the causes of base composition changes at these sites in Drosophila remain unanswered. To shed further light on this issue, we obtained a new whole-genome polymorphism data set from D. simulans. We analyzed samples from the putatively ancestral range of D. simulans, as well as an existing polymorphism data set from an African population of D. melanogaster. By using D. yakuba as an outgroup, we found clear evidence for selection on 4-fold sites along both lineages over a substantial period, with the intensity of selection increasing with GC content. Based on an explicit model of base composition evolution, we suggest that the observed AT-biased substitution pattern in both lineages is probably due to an ancestral reduction in selection intensity, and is unlikely to be the result of an increase in mutational bias towards AT alone. By using two polymorphism-based methods for estimating selection coefficients over different timescales, we show that the selection intensity on codon usage has been rather stable in D. simulans in the recent past, but the long-term estimates in D. melanogaster are much higher than the short-term ones, indicating a continuing decline in selection intensity, to such an extent that the short-term estimates suggest that selection is only active in the most GC-rich parts of the genome. Finally, we provide evidence for complex evolutionary patterns in the putatively neutral short introns, which cannot be explained by the standard GC-biased gene conversion model. These results reveal a dynamic picture of base composition evolution.
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Affiliation(s)
- Benjamin C Jackson
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - José L Campos
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Penelope R Haddrill
- Centre for Forensic Science, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Brian Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Kai Zeng
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
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15
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Gursky VV, Kozlov KN, Kulakovskiy IV, Zubair A, Marjoram P, Lawrie DS, Nuzhdin SV, Samsonova MG. Translating natural genetic variation to gene expression in a computational model of the Drosophila gap gene regulatory network. PLoS One 2017; 12:e0184657. [PMID: 28898266 PMCID: PMC5595321 DOI: 10.1371/journal.pone.0184657] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 08/28/2017] [Indexed: 11/18/2022] Open
Abstract
Annotating the genotype-phenotype relationship, and developing a proper quantitative description of the relationship, requires understanding the impact of natural genomic variation on gene expression. We apply a sequence-level model of gap gene expression in the early development of Drosophila to analyze single nucleotide polymorphisms (SNPs) in a panel of natural sequenced D. melanogaster lines. Using a thermodynamic modeling framework, we provide both analytical and computational descriptions of how single-nucleotide variants affect gene expression. The analysis reveals that the sequence variants increase (decrease) gene expression if located within binding sites of repressors (activators). We show that the sign of SNP influence (activation or repression) may change in time and space and elucidate the origin of this change in specific examples. The thermodynamic modeling approach predicts non-local and non-linear effects arising from SNPs, and combinations of SNPs, in individual fly genotypes. Simulation of individual fly genotypes using our model reveals that this non-linearity reduces to almost additive inputs from multiple SNPs. Further, we see signatures of the action of purifying selection in the gap gene regulatory regions. To infer the specific targets of purifying selection, we analyze the patterns of polymorphism in the data at two phenotypic levels: the strengths of binding and expression. We find that combinations of SNPs show evidence of being under selective pressure, while individual SNPs do not. The model predicts that SNPs appear to accumulate in the genotypes of the natural population in a way biased towards small increases in activating action on the expression pattern. Taken together, these results provide a systems-level view of how genetic variation translates to the level of gene regulatory networks via combinatorial SNP effects.
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Affiliation(s)
- Vitaly V. Gursky
- Theoretical Department, Ioffe Institute, Saint Petersburg, Russia
- Systems Biology and Bioinformatics Laboratory, Peter the Great Saint Petersburg Polytechnic University, Saint Petersburg, Russia
- * E-mail:
| | - Konstantin N. Kozlov
- Systems Biology and Bioinformatics Laboratory, Peter the Great Saint Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Ivan V. Kulakovskiy
- Engelhardt Institute of Molecular Biology, Moscow, Russia
- Vavilov Institute of General Genetics, Moscow, Russia
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Asif Zubair
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Paul Marjoram
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - David S. Lawrie
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Sergey V. Nuzhdin
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Maria G. Samsonova
- Systems Biology and Bioinformatics Laboratory, Peter the Great Saint Petersburg Polytechnic University, Saint Petersburg, Russia
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16
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Huber CD, Kim BY, Marsden CD, Lohmueller KE. Determining the factors driving selective effects of new nonsynonymous mutations. Proc Natl Acad Sci U S A 2017; 114:4465-4470. [PMID: 28400513 PMCID: PMC5410820 DOI: 10.1073/pnas.1619508114] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The distribution of fitness effects (DFE) of new mutations plays a fundamental role in evolutionary genetics. However, the extent to which the DFE differs across species has yet to be systematically investigated. Furthermore, the biological mechanisms determining the DFE in natural populations remain unclear. Here, we show that theoretical models emphasizing different biological factors at determining the DFE, such as protein stability, back-mutations, species complexity, and mutational robustness make distinct predictions about how the DFE will differ between species. Analyzing amino acid-changing variants from natural populations in a comparative population genomic framework, we find that humans have a higher proportion of strongly deleterious mutations than Drosophila melanogaster. Furthermore, when comparing the DFE across yeast, Drosophila, mice, and humans, the average selection coefficient becomes more deleterious with increasing species complexity. Last, pleiotropic genes have a DFE that is less variable than that of nonpleiotropic genes. Comparing four categories of theoretical models, only Fisher's geometrical model (FGM) is consistent with our findings. FGM assumes that multiple phenotypes are under stabilizing selection, with the number of phenotypes defining the complexity of the organism. Our results suggest that long-term population size and cost of complexity drive the evolution of the DFE, with many implications for evolutionary and medical genomics.
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Affiliation(s)
- Christian D Huber
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095;
| | - Bernard Y Kim
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095
| | - Clare D Marsden
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095;
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA 90095
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
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17
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Computation of the Likelihood of Joint Site Frequency Spectra Using Orthogonal Polynomials. COMPUTATION 2016. [DOI: 10.3390/computation4010006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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18
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Kapun M, Fabian DK, Goudet J, Flatt T. Genomic Evidence for Adaptive Inversion Clines in Drosophila melanogaster. Mol Biol Evol 2016; 33:1317-36. [PMID: 26796550 DOI: 10.1093/molbev/msw016] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Clines in chromosomal inversion polymorphisms-presumably driven by climatic gradients-are common but there is surprisingly little evidence for selection acting on them. Here we address this long-standing issue in Drosophila melanogaster by using diagnostic single nucleotide polymorphism (SNP) markers to estimate inversion frequencies from 28 whole-genome Pool-seq samples collected from 10 populations along the North American east coast. Inversions In(3L)P, In(3R)Mo, and In(3R)Payne showed clear latitudinal clines, and for In(2L)t, In(2R)NS, and In(3R)Payne the steepness of the clinal slopes changed between summer and fall. Consistent with an effect of seasonality on inversion frequencies, we detected small but stable seasonal fluctuations of In(2R)NS and In(3R)Payne in a temperate Pennsylvanian population over 4 years. In support of spatially varying selection, we observed that the cline in In(3R)Payne has remained stable for >40 years and that the frequencies of In(2L)t and In(3R)Payne are strongly correlated with climatic factors that vary latitudinally, independent of population structure. To test whether these patterns are adaptive, we compared the amount of genetic differentiation of inversions versus neutral SNPs and found that the clines in In(2L)t and In(3R)Payne are maintained nonneutrally and independent of admixture. We also identified numerous clinal inversion-associated SNPs, many of which exhibit parallel differentiation along the Australian cline and reside in genes known to affect fitness-related traits. Together, our results provide strong evidence that inversion clines are maintained by spatially-and perhaps also temporally-varying selection. We interpret our data in light of current hypotheses about how inversions are established and maintained.
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Affiliation(s)
- Martin Kapun
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Daniel K Fabian
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Thomas Flatt
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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19
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Vogl C, Bergman J. Inference of directional selection and mutation parameters assuming equilibrium. Theor Popul Biol 2015; 106:71-82. [PMID: 26597774 DOI: 10.1016/j.tpb.2015.10.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/30/2015] [Accepted: 10/07/2015] [Indexed: 01/15/2023]
Abstract
In a classical study, Wright (1931) proposed a model for the evolution of a biallelic locus under the influence of mutation, directional selection and drift. He derived the equilibrium distribution of the allelic proportion conditional on the scaled mutation rate, the mutation bias and the scaled strength of directional selection. The equilibrium distribution can be used for inference of these parameters with genome-wide datasets of "site frequency spectra" (SFS). Assuming that the scaled mutation rate is low, Wright's model can be approximated by a boundary-mutation model, where mutations are introduced into the population exclusively from sites fixed for the preferred or unpreferred allelic states. With the boundary-mutation model, inference can be partitioned: (i) the shape of the SFS distribution within the polymorphic region is determined by random drift and directional selection, but not by the mutation parameters, such that inference of the selection parameter relies exclusively on the polymorphic sites in the SFS; (ii) the mutation parameters can be inferred from the amount of polymorphic and monomorphic preferred and unpreferred alleles, conditional on the selection parameter. Herein, we derive maximum likelihood estimators for the mutation and selection parameters in equilibrium and apply the method to simulated SFS data as well as empirical data from a Madagascar population of Drosophila simulans.
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Affiliation(s)
- Claus Vogl
- Institute of Animal Breeding and Genetics, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Vienna, Austria.
| | - Juraj Bergman
- Institute of Population Genetics, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Vienna, Austria; Vienna Graduate School of Population Genetics, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Vienna, Austria.
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20
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Tandem Duplications and the Limits of Natural Selection in Drosophila yakuba and Drosophila simulans. PLoS One 2015; 10:e0132184. [PMID: 26176952 PMCID: PMC4503668 DOI: 10.1371/journal.pone.0132184] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/10/2015] [Indexed: 11/30/2022] Open
Abstract
Tandem duplications are an essential source of genetic novelty, and their variation in natural populations is expected to influence adaptive walks. Here, we describe evolutionary impacts of recently-derived, segregating tandem duplications in Drosophila yakuba and Drosophila simulans. We observe an excess of duplicated genes involved in defense against pathogens, insecticide resistance, chorion development, cuticular peptides, and lipases or endopeptidases associated with the accessory glands across both species. The observed agreement is greater than expectations on chance alone, suggesting large amounts of convergence across functional categories. We document evidence of widespread selection on the D. simulans X, suggesting adaptation through duplication is common on the X. Despite the evidence for positive selection, duplicates display an excess of low frequency variants consistent with largely detrimental impacts, limiting the variation that can effectively facilitate adaptation. Standing variation for tandem duplications spans less than 25% of the genome in D. yakuba and D. simulans, indicating that evolution will be strictly limited by mutation, even in organisms with large population sizes. Effective whole gene duplication rates are low at 1.17 × 10−9 per gene per generation in D. yakuba and 6.03 × 10−10 per gene per generation in D. simulans, suggesting long wait times for new mutations on the order of thousands of years for the establishment of sweeps. Hence, in cases where adaptation depends on individual tandem duplications, evolution will be severely limited by mutation. We observe low levels of parallel recruitment of the same duplicated gene in different species, suggesting that the span of standing variation will define evolutionary outcomes in spite of convergence across gene ontologies consistent with rapidly evolving phenotypes.
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21
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Haerty W, Ponting CP. Unexpected selection to retain high GC content and splicing enhancers within exons of multiexonic lncRNA loci. RNA (NEW YORK, N.Y.) 2015; 21:333-46. [PMID: 25589248 PMCID: PMC4338330 DOI: 10.1261/rna.047324.114] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 11/25/2014] [Indexed: 06/04/2023]
Abstract
If sequencing was possible only for genomes, and not for RNAs or proteins, then functional protein-coding exons would be recognizable by their unusual patterns of nucleotide composition, specifically a high GC content across the body of exons, and an unusual nucleotide content near their edges. RNAs and proteins can, of course, be sequenced but the extent of functionality of intergenic long noncoding RNAs (lncRNAs) remains under question owing to their low nucleotide conservation. Inspired by the nucleotide composition patterns of protein-coding exons, we sought evidence for functionality across lncRNA loci from diverse species. We found that such patterns across multiexonic lncRNA loci mirror those of proteincoding genes, although to a lesser degree: Specifically, compared with introns, lncRNA exons are GC rich. Additionally we report evidence for the action of purifying selection to preserve exonic splicing enhancers within human multiexonic lncRNAs and nucleotide composition in fruit fly lncRNAs. Our findings provide evidence for selection for more efficient rates of transcription and splicing within lncRNA loci. Despite only a minor proportion of their RNA bases being constrained, multiexonic intergenic lncRNAs appear to require accurate splicing of their exons to transact their function.
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22
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Franssen SU, Nolte V, Tobler R, Schlötterer C. Patterns of linkage disequilibrium and long range hitchhiking in evolving experimental Drosophila melanogaster populations. Mol Biol Evol 2015; 32:495-509. [PMID: 25415966 PMCID: PMC4298179 DOI: 10.1093/molbev/msu320] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Whole-genome resequencing of experimental populations evolving under a specific selection regime has become a popular approach to determine genotype-phenotype maps and understand adaptation to new environments. Despite its conceptual appeal and success in identifying some causative genes, it has become apparent that many studies suffer from an excess of candidate loci. Several explanations have been proposed for this phenomenon, but it is clear that information about the linkage structure during such experiments is needed. Until now only Pool-Seq (whole-genome sequencing of pools of individuals) data were available, which do not provide sufficient information about the correlation between linked sites. We address this problem in two complementary analyses of three replicate Drosophila melanogaster populations evolving to a new hot temperature environment for almost 70 generations. In the first analysis, we sequenced 58 haploid genomes from the founder population and evolved flies at generation 67. We show that during the experiment linkage disequilibrium (LD) increased almost uniformly over much greater distances than typically seen in Drosophila. In the second analysis, Pool-Seq time series data of the three replicates were combined with haplotype information from the founder population to follow blocks of initial haplotypes over time. We identified 17 selected haplotype-blocks that started at low frequencies in the base population and increased in frequency during the experiment. The size of these haplotype-blocks ranged from 0.082 to 4.01 Mb. Moreover, between 42% and 46% of the top candidate single nucleotide polymorphisms from the comparison of founder and evolved populations fell into the genomic region covered by the haplotype-blocks. We conclude that LD in such rising haplotype-blocks results in long range hitchhiking over multiple kilobase-sized regions. LD in such haplotype-blocks is therefore a major factor contributing to an excess of candidate loci. Although modifications of the experimental design may help to reduce the hitchhiking effect and allow for more precise mapping of causative variants, we also note that such haplotype-blocks might be well suited to study the dynamics of selected genomic regions during experimental evolution studies.
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Affiliation(s)
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - Ray Tobler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
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23
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Estimating the scaled mutation rate and mutation bias with site frequency data. Theor Popul Biol 2014; 98:19-27. [DOI: 10.1016/j.tpb.2014.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 09/11/2014] [Accepted: 10/03/2014] [Indexed: 11/16/2022]
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Computation of the Likelihood in Biallelic Diffusion Models Using Orthogonal Polynomials. COMPUTATION 2014. [DOI: 10.3390/computation2040199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group. G3-GENES GENOMES GENETICS 2014; 4:2345-51. [PMID: 25273863 PMCID: PMC4267930 DOI: 10.1534/g3.114.013532] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Here, we provide revised gene models for D. ananassae, D. yakuba, and D. simulans, which include untranslated regions and empirically verified intron-exon boundaries, as well as ortholog groups identified using a fuzzy reciprocal-best-hit blast comparison. Using these revised annotations, we perform differential expression testing using the cufflinks suite to provide a broad overview of differential expression between reproductive tissues and the carcass. We identify thousands of genes that are differentially expressed across tissues in D. yakuba and D. simulans, with roughly 60% agreement in expression patterns of orthologs in D. yakuba and D. simulans. We identify several cases of putative polycistronic transcripts, pointing to a combination of transcriptional read-through in the genome as well as putative gene fusion and fission events across taxa. We furthermore identify hundreds of lineage specific genes in each species with no blast hits among transcripts of any other Drosophila species, which are candidates for neofunctionalized proteins and a potential source of genetic novelty.
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Tobler R, Franssen SU, Kofler R, Orozco-terWengel P, Nolte V, Hermisson J, Schlötterer C. Massive habitat-specific genomic response in D. melanogaster populations during experimental evolution in hot and cold environments. Mol Biol Evol 2014; 31:364-75. [PMID: 24150039 PMCID: PMC3907058 DOI: 10.1093/molbev/mst205] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [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
Experimental evolution in combination with whole-genome sequencing (evolve and resequence [E&R]) is a promising approach to define the genotype-phenotype map and to understand adaptation in evolving populations. Many previous studies have identified a large number of putative selected sites (i.e., candidate loci), but it remains unclear to what extent these loci are genuine targets of selection or experimental noise. To address this question, we exposed the same founder population to two different selection regimes-a hot environment and a cold environment-and quantified the genomic response in each. We detected large numbers of putative selected loci in both environments, albeit with little overlap between the two sets of candidates, indicating that most resulted from habitat-specific selection. By quantifying changes across multiple independent biological replicates, we demonstrate that most of the candidate SNPs were false positives that were linked to selected sites over distances much larger than the typical linkage disequilibrium range of Drosophila melanogaster. We show that many of these mid- to long-range associations were attributable to large segregating inversions and confirm by computer simulations that such patterns could be readily replicated when strong selection acts on rare haplotypes. In light of our findings, we outline recommendations to improve the performance of future Drosophila E&R studies which include using species with negligible inversion loads, such as D. mauritiana and D. simulans, instead of D. melanogaster.
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Affiliation(s)
- Ray Tobler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | | | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | | | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - Joachim Hermisson
- Mathematics and Biosciences Group, Department of Mathematics, University of Vienna, Vienna, Austria
- Max F. Perutz Laboratories, Vienna, Austria
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Leushkin EV, Bazykin GA, Kondrashov AS. Strong mutational bias toward deletions in the Drosophila melanogaster genome is compensated by selection. Genome Biol Evol 2013; 5:514-24. [PMID: 23395983 PMCID: PMC3622295 DOI: 10.1093/gbe/evt021] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Insertions and deletions (collectively indels) obviously have a major impact on genome evolution. However, before large-scale data on indel polymorphism became available, it was difficult to estimate the strength of selection acting on indel mutations. Here, we analyze indel polymorphism and divergence in different compartments of the Drosophila melanogaster genome: exons, introns of different lengths, and intergenic regions. Data on low-frequency polymorphisms indicate that 0.036–0.039 short (1–30 nt) insertion mutations and 0.085–0.092 short deletion mutations, with mean lengths 3.23 and 4.78, respectively, occur per single-nucleotide substitution. The excess of short deletion over short insertion mutations implies that indel mutations of these lengths should lead to a loss of approximately 0.30 nt per single-nucleotide replacement. However, polymorphism and divergence data show that this deletion bias is almost completely compensated by selection: Negative selection is stronger against deletions, whereas insertions are more likely to be favored by positive selection. Among the inframe low-frequency polymorphic mutations in exons, long introns, and intergenic regions, selection prevents a larger fraction of deletions (80–87%, depending on the type of the compartment) than of insertions (70–82%) or single-nucleotide substitutions (49–73%), from reaching high frequencies. The corresponding fractions were the lowest in short introns: 66%, 47%, and 15%, respectively, consistent with the weakest selective constraint in them. The McDonald–Kreitman test shows that 32–46% of the deletions and 60–73% of the insertions that were fixed in the recent evolution of D. melanogaster are adaptive, whereas this fraction is only 0–29% for single-nucleotide substitutions.
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Affiliation(s)
- Evgeny V Leushkin
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.
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Strong purifying selection at synonymous sites in D. melanogaster. PLoS Genet 2013; 9:e1003527. [PMID: 23737754 PMCID: PMC3667748 DOI: 10.1371/journal.pgen.1003527] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 04/08/2013] [Indexed: 11/19/2022] Open
Abstract
Synonymous sites are generally assumed to be subject to weak selective constraint. For this reason, they are often neglected as a possible source of important functional variation. We use site frequency spectra from deep population sequencing data to show that, contrary to this expectation, 22% of four-fold synonymous (4D) sites in Drosophila melanogaster evolve under very strong selective constraint while few, if any, appear to be under weak constraint. Linking polymorphism with divergence data, we further find that the fraction of synonymous sites exposed to strong purifying selection is higher for those positions that show slower evolution on the Drosophila phylogeny. The function underlying the inferred strong constraint appears to be separate from splicing enhancers, nucleosome positioning, and the translational optimization generating canonical codon bias. The fraction of synonymous sites under strong constraint within a gene correlates well with gene expression, particularly in the mid-late embryo, pupae, and adult developmental stages. Genes enriched in strongly constrained synonymous sites tend to be particularly functionally important and are often involved in key developmental pathways. Given that the observed widespread constraint acting on synonymous sites is likely not limited to Drosophila, the role of synonymous sites in genetic disease and adaptation should be reevaluated.
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Leushkin EV, Bazykin GA. Short indels are subject to insertion-biased gene conversion. Evolution 2013; 67:2604-13. [PMID: 24033170 DOI: 10.1111/evo.12129] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 04/05/2013] [Indexed: 11/29/2022]
Abstract
Recombination between homologous loci is accompanied by formation of heteroduplexes. Repairing mismatches in heteroduplexes often leads to single nucleotide substitutions in a process known as gene conversion. Gene conversion was shown to be GC-biased in different organisms; that is, a W(A or T)→S(G or C) substitution is more likely in this process than a S→W substitution. Here, we show that the insertion/deletion ratio for short noncoding indels that reach fixation between species is positively correlated with the recombination rate in Drosophila melanogaster, Homo sapiens, and Saccharomyces cerevisiae. This correlation is both due to an increase of the fixation rate of insertions and decrease of the fixation rate of deletions in regions of high recombination. Whole-genome data on indel polymorphism and divergence in D. melanogaster rule out mutation biases and selection as the cause of this trend, pointing to insertion-biased gene conversion as the most likely explanation. The bias toward insertions is the strongest for single-nucleotide indels, and decreases with indel length. In regions of high recombination rate this bias leads to an up to ∼5-fold excess of fixed short insertions over deletions, and substantially affects the evolution of DNA segments.
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Affiliation(s)
- Evgeny V Leushkin
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow, 119992, Russia; Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoi Karetny pereulok, 19, Moscow, 127994, Russia.
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30
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Clemente F, Vogl C. Evidence for complex selection on four-fold degenerate sites in Drosophila melanogaster. J Evol Biol 2012; 25:2582-95. [PMID: 23020078 DOI: 10.1111/jeb.12003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 08/31/2012] [Accepted: 08/31/2012] [Indexed: 01/04/2023]
Abstract
We considered genome-wide four-fold degenerate sites from an African Drosophila melanogaster population and compared them to short introns. To include divergence and to polarize the data, we used its close relatives Drosophila simulans, Drosophila sechellia, Drosophila erecta and Drosophila yakuba as outgroups. In D. melanogaster, the GC content at four-fold degenerate sites is higher than in short introns; compared to its relatives, more AT than GC is fixed. The former has been explained by codon usage bias (CUB) favouring GC; the latter by decreased intensity of directional selection or by increased mutation bias towards AT. With a biallelic equilibrium model, evidence for directional selection comes mostly from the GC-rich ancestral base composition. Together with a slight mutation bias, it leads to an asymmetry of the unpolarized allele frequency spectrum, from which directional selection is inferred. Using a quasi-equilibrium model and polarized spectra, however, only purifying and no directional selection is detected. Furthermore, polarized spectra are proportional to those of the presumably unselected short introns. As we have no evidence for a decrease in effective population size, relaxed CUB must be due to a reduction in the selection coefficient. Going beyond the biallelic model and considering all four bases, signs of directional selection are stronger. In contrast to short introns, complementary bases show strand specificity and allele frequency spectra depend on mutation directions. Hence, the traditional biallelic model to describe the evolution of four-fold degenerate sites should be replaced by more complex models assuming only quasi-equilibrium and accounting for all four bases.
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Affiliation(s)
- F Clemente
- Institute of Population Genetics, Veterinärmedizinische Universität Wien, Vienna, Austria
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