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Moreira JDR, Rosa BL, Lira BS, Lima JE, Correia LNF, Otoni WC, Figueira A, Freschi L, Sakamoto T, Peres LEP, Rossi M, Zsögön A. Auxin-driven ecophysiological diversification of leaves in domesticated tomato. PLANT PHYSIOLOGY 2022; 190:113-126. [PMID: 35639975 PMCID: PMC9434155 DOI: 10.1093/plphys/kiac251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/22/2022] [Indexed: 05/29/2023]
Abstract
Heterobaric leaves have bundle sheath extensions (BSEs) that compartmentalize the parenchyma, whereas homobaric leaves do not. The presence of BSEs affects leaf hydraulics and photosynthetic rate. The tomato (Solanum lycopersicum) obscuravenosa (obv) mutant lacks BSEs. Here, we identify the obv gene and the causative mutation, a nonsynonymous amino acid change that disrupts a C2H2 zinc finger motif in a putative transcription factor. This mutation exists as a polymorphism in the natural range of wild tomatoes but has increased in frequency in domesticated tomatoes, suggesting that the latter diversified into heterobaric and homobaric leaf types. The obv mutant displays reduced vein density, leaf hydraulic conductance and photosynthetic assimilation rate. We show that these and other pleiotropic effects on plant development, including changes in leaf insertion angle, leaf margin serration, minor vein density, and fruit shape, are controlled by OBV via changes in auxin signaling. Loss of function of the transcriptional regulator AUXIN RESPONSE FACTOR 4 (ARF4) also results in defective BSE development, revealing an additional component of a genetic module controlling aspects of leaf development important for ecological adaptation and subject to breeding selection.
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Affiliation(s)
- Juliene d R Moreira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Bruno L Rosa
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Bruno S Lira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, Brazil
| | - Joni E Lima
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Minas Gerais, Brazil
| | - Ludmila N F Correia
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Wagner C Otoni
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Antonio Figueira
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, 13400-970 Piracicaba, São Paulo, Brazil
| | - Luciano Freschi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, Brazil
| | - Tetsu Sakamoto
- Bioinformatics Multidisciplinary Environment, Instituto Metrópole Digital, Universidade Federal Do Rio Grande Do Norte, 59078-400 Natal, Rio Grande do Norte, Brazil
| | - Lázaro E P Peres
- Laboratory of Hormonal Control of Plant Development, Departamento de Ciências Biológicas (LCB), Escola Superior de Agricultura “Luiz de Queiroz,” Universidade de São Paulo, CP 09, 13418-900 Piracicaba, São Paulo, Brazil
| | - Magdalena Rossi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, Brazil
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van Dorp L, Acman M, Richard D, Shaw LP, Ford CE, Ormond L, Owen CJ, Pang J, Tan CCS, Boshier FAT, Ortiz AT, Balloux F. Emergence of genomic diversity and recurrent mutations in SARS-CoV-2. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 83:104351. [PMID: 32387564 PMCID: PMC7199730 DOI: 10.1016/j.meegid.2020.104351] [Citation(s) in RCA: 508] [Impact Index Per Article: 127.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 04/30/2020] [Accepted: 05/02/2020] [Indexed: 02/06/2023]
Abstract
SARS-CoV-2 is a SARS-like coronavirus of likely zoonotic origin first identified in December 2019 in Wuhan, the capital of China's Hubei province. The virus has since spread globally, resulting in the currently ongoing COVID-19 pandemic. The first whole genome sequence was published on January 5 2020, and thousands of genomes have been sequenced since this date. This resource allows unprecedented insights into the past demography of SARS-CoV-2 but also monitoring of how the virus is adapting to its novel human host, providing information to direct drug and vaccine design. We curated a dataset of 7666 public genome assemblies and analysed the emergence of genomic diversity over time. Our results are in line with previous estimates and point to all sequences sharing a common ancestor towards the end of 2019, supporting this as the period when SARS-CoV-2 jumped into its human host. Due to extensive transmission, the genetic diversity of the virus in several countries recapitulates a large fraction of its worldwide genetic diversity. We identify regions of the SARS-CoV-2 genome that have remained largely invariant to date, and others that have already accumulated diversity. By focusing on mutations which have emerged independently multiple times (homoplasies), we identify 198 filtered recurrent mutations in the SARS-CoV-2 genome. Nearly 80% of the recurrent mutations produced non-synonymous changes at the protein level, suggesting possible ongoing adaptation of SARS-CoV-2. Three sites in Orf1ab in the regions encoding Nsp6, Nsp11, Nsp13, and one in the Spike protein are characterised by a particularly large number of recurrent mutations (>15 events) which may signpost convergent evolution and are of particular interest in the context of adaptation of SARS-CoV-2 to the human host. We additionally provide an interactive user-friendly web-application to query the alignment of the 7666 SARS-CoV-2 genomes.
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Affiliation(s)
- Lucy van Dorp
- UCL Genetics Institute, University College London, London WC1E 6BT, UK.
| | - Mislav Acman
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Damien Richard
- Cirad, UMR PVBMT, F-97410, St Pierre, Réunion, France; Université de la Réunion, UMR PVBMT, F-97490, St Denis, Réunion, France
| | - Liam P Shaw
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Charlotte E Ford
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Louise Ormond
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | | | - Juanita Pang
- UCL Genetics Institute, University College London, London WC1E 6BT, UK; Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Cedric C S Tan
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | | | - Arturo Torres Ortiz
- UCL Genetics Institute, University College London, London WC1E 6BT, UK; Department of Infectious Disease, Imperial College, London W2 1NY, UK
| | - François Balloux
- UCL Genetics Institute, University College London, London WC1E 6BT, UK.
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Abstract
In evolutionary biology, it is generally assumed that evolution occurs in the weak mutation limit, that is, the frequency of multiple mutations simultaneously occurring in the same genome and the same generation is negligible. We employ mathematical modeling to show that, although under the typical parameter values of the evolutionary process the probability of multimutational leaps is indeed low, they might become substantially more likely under stress, when the mutation rate is dramatically elevated. We hypothesize that stress-induced mutagenesis in microbes is an evolvable adaptive strategy. Multimutational leaps might matter also in other cases of substantially increased mutation rate, such as growing tumors or evolution of primordial replicators. Is evolution always gradual or can it make leaps? We examine a mathematical model of an evolutionary process on a fitness landscape and obtain analytic solutions for the probability of multimutation leaps, that is, several mutations occurring simultaneously, within a single generation in 1 genome, and being fixed all together in the evolving population. The results indicate that, for typical, empirically observed combinations of the parameters of the evolutionary process, namely, effective population size, mutation rate, and distribution of selection coefficients of mutations, the probability of a multimutation leap is low, and accordingly the contribution of such leaps is minor at best. However, we show that, taking sign epistasis into account, leaps could become an important factor of evolution in cases of substantially elevated mutation rates, such as stress-induced mutagenesis in microbes. We hypothesize that stress-induced mutagenesis is an evolvable adaptive strategy.
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Khera AV, Chaffin M, Wade KH, Zahid S, Brancale J, Xia R, Distefano M, Senol-Cosar O, Haas ME, Bick A, Aragam KG, Lander ES, Smith GD, Mason-Suares H, Fornage M, Lebo M, Timpson NJ, Kaplan LM, Kathiresan S. Polygenic Prediction of Weight and Obesity Trajectories from Birth to Adulthood. Cell 2019; 177:587-596.e9. [PMID: 31002795 PMCID: PMC6661115 DOI: 10.1016/j.cell.2019.03.028] [Citation(s) in RCA: 389] [Impact Index Per Article: 77.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/07/2018] [Accepted: 03/12/2019] [Indexed: 12/30/2022]
Abstract
Severe obesity is a rapidly growing global health threat. Although often attributed to unhealthy lifestyle choices or environmental factors, obesity is known to be heritable and highly polygenic; the majority of inherited susceptibility is related to the cumulative effect of many common DNA variants. Here we derive and validate a new polygenic predictor comprised of 2.1 million common variants to quantify this susceptibility and test this predictor in more than 300,000 individuals ranging from middle age to birth. Among middle-aged adults, we observe a 13-kg gradient in weight and a 25-fold gradient in risk of severe obesity across polygenic score deciles. In a longitudinal birth cohort, we note minimal differences in birthweight across score deciles, but a significant gradient emerged in early childhood and reached 12 kg by 18 years of age. This new approach to quantify inherited susceptibility to obesity affords new opportunities for clinical prevention and mechanistic assessment.
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Affiliation(s)
- Amit V Khera
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Division of Cardiology, Massachusetts General Hospital, Boston, MA 02114, USA; Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Mark Chaffin
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kaitlin H Wade
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 1TH, UK; Population Health Science, Bristol Medical School, Bristol, Bristol BS8 1TH, UK; Avon Longitudinal Study of Parents and Children, Bristol BS8 1TH, UK
| | - Sohail Zahid
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Joseph Brancale
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Obesity, Metabolism, and Nutrition Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rui Xia
- The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Marina Distefano
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA 02139, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Pathology, Harvard Medical School, Cambridge, MA 02115, USA
| | - Ozlem Senol-Cosar
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA 02139, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Pathology, Harvard Medical School, Cambridge, MA 02115, USA
| | - Mary E Haas
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexander Bick
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Krishna G Aragam
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Division of Cardiology, Massachusetts General Hospital, Boston, MA 02114, USA; Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Eric S Lander
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Program in Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 1TH, UK; Population Health Science, Bristol Medical School, Bristol, Bristol BS8 1TH, UK
| | - Heather Mason-Suares
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA 02139, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Pathology, Harvard Medical School, Cambridge, MA 02115, USA
| | - Myriam Fornage
- The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Matthew Lebo
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA 02139, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Pathology, Harvard Medical School, Cambridge, MA 02115, USA
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 1TH, UK; Population Health Science, Bristol Medical School, Bristol, Bristol BS8 1TH, UK; Avon Longitudinal Study of Parents and Children, Bristol BS8 1TH, UK
| | - Lee M Kaplan
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Obesity, Metabolism, and Nutrition Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sekar Kathiresan
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Division of Cardiology, Massachusetts General Hospital, Boston, MA 02114, USA; Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
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Deleterious Mutation Burden and Its Association with Complex Traits in Sorghum ( Sorghum bicolor). Genetics 2019; 211:1075-1087. [PMID: 30622134 PMCID: PMC6404259 DOI: 10.1534/genetics.118.301742] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 12/22/2018] [Indexed: 11/18/2022] Open
Abstract
Sorghum (Sorghum bicolor (L.) Moench) is a major staple food cereal for millions of people worldwide. Valluru et al. identify putative deleterious mutations among ∼5.5M segregating variants of 229 diverse sorghum... Sorghum (Sorghum bicolor L.) is a major food cereal for millions of people worldwide. The sorghum genome, like other species, accumulates deleterious mutations, likely impacting its fitness. The lack of recombination, drift, and the coupling with favorable loci impede the removal of deleterious mutations from the genome by selection. To study how deleterious variants impact phenotypes, we identified putative deleterious mutations among ∼5.5 M segregating variants of 229 diverse biomass sorghum lines. We provide the whole-genome estimate of the deleterious burden in sorghum, showing that ∼33% of nonsynonymous substitutions are putatively deleterious. The pattern of mutation burden varies appreciably among racial groups. Across racial groups, the mutation burden correlated negatively with biomass, plant height, specific leaf area (SLA), and tissue starch content (TSC), suggesting that deleterious burden decreases trait fitness. Putatively deleterious variants explain roughly one-half of the genetic variance. However, there is only moderate improvement in total heritable variance explained for biomass (7.6%) and plant height (average of 3.1% across all stages). There is no advantage in total heritable variance for SLA and TSC. The contribution of putatively deleterious variants to phenotypic diversity therefore appears to be dependent on the genetic architecture of traits. Overall, these results suggest that incorporating putatively deleterious variants into genomic models slightly improves prediction accuracy because of extensive linkage. Knowledge of deleterious variants could be leveraged for sorghum breeding through either genome editing and/or conventional breeding that focuses on the selection of progeny with fewer deleterious alleles.
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6
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Savisaar R, Hurst LD. Exonic splice regulation imposes strong selection at synonymous sites. Genome Res 2018; 28:1442-1454. [PMID: 30143596 PMCID: PMC6169883 DOI: 10.1101/gr.233999.117] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 07/31/2018] [Indexed: 01/17/2023]
Abstract
What proportion of coding sequence nucleotides have roles in splicing, and how strong is the selection that maintains them? Despite a large body of research into exonic splice regulatory signals, these questions have not been answered. This is because, to our knowledge, previous investigations have not explicitly disentangled the frequency of splice regulatory elements from the strength of the evolutionary constraint under which they evolve. Current data are consistent both with a scenario of weak and diffuse constraint, enveloping large swaths of sequence, as well as with well-defined pockets of strong purifying selection. In the former case, natural selection on exonic splice enhancers (ESEs) might primarily act as a slight modifier of codon usage bias. In the latter, mutations that disrupt ESEs are likely to have large fitness and, potentially, clinical effects. To distinguish between these scenarios, we used several different methods to determine the distribution of selection coefficients for new mutations within ESEs. The analyses converged to suggest that ∼15%-20% of fourfold degenerate sites are part of functional ESEs. Most of these sites are under strong evolutionary constraint. Therefore, exonic splice regulation does not simply impose a weak bias that gently nudges coding sequence evolution in a particular direction. Rather, the selection to preserve these motifs is a strong force that severely constrains the evolution of a substantial proportion of coding nucleotides. Thus synonymous mutations that disrupt ESEs should be considered as a potentially common cause of single-locus genetic disorders.
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Affiliation(s)
- Rosina Savisaar
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
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Lind PA, Arvidsson L, Berg OG, Andersson DI. Variation in Mutational Robustness between Different Proteins and the Predictability of Fitness Effects. Mol Biol Evol 2017; 34:408-418. [PMID: 28025272 DOI: 10.1093/molbev/msw239] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Random mutations in genes from disparate protein classes may have different distributions of fitness effects (DFEs) depending on different structural, functional, and evolutionary constraints. We measured the fitness effects of 156 single mutations in the genes encoding AraC (transcription factor), AraD (enzyme), and AraE (transporter) used for bacterial growth on l-arabinose. Despite their different molecular functions these genes all had bimodal DFEs with most mutations either being neutral or strongly deleterious, providing a general expectation for the DFE. This contrasts with the unimodal DFEs previously obtained for ribosomal protein genes where most mutations were slightly deleterious. Based on theoretical considerations, we suggest that the 33-fold higher average mutational robustness of ribosomal proteins is due to stronger selection for reduced costs of translational and transcriptional errors. Whereas the large majority of synonymous mutations were deleterious for ribosomal proteins genes, no fitness effects could be detected for the AraCDE genes. Four mutations in AraC and AraE increased fitness, suggesting that slightly advantageous mutations make up a significant fraction of the DFE, but that they often escape detection due to the limited sensitivity of commonly used fitness assays. We show that the fitness effects of amino acid substitutions can be predicted based on evolutionary conservation, but those weakly deleterious mutations are less reliably detected. This suggests that large-effect mutations and the fraction of highly deleterious mutations can be computationally predicted, but that experiments are required to characterize the DFE close to neutrality, where many mutations ultimately fixed in a population will occur.
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Affiliation(s)
- Peter A Lind
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Lars Arvidsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Otto G Berg
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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8
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Stitziel NO, Khera AV, Wang X, Bierhals AJ, Vourakis AC, Sperry AE, Natarajan P, Klarin D, Emdin CA, Zekavat SM, Nomura A, Erdmann J, Schunkert H, Samani NJ, Kraus WE, Shah SH, Yu B, Boerwinkle E, Rader DJ, Gupta N, Frossard PM, Rasheed A, Danesh J, Lander ES, Gabriel S, Saleheen D, Musunuru K, Kathiresan S. ANGPTL3 Deficiency and Protection Against Coronary Artery Disease. J Am Coll Cardiol 2017; 69:2054-2063. [PMID: 28385496 DOI: 10.1016/j.jacc.2017.02.030] [Citation(s) in RCA: 312] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 02/03/2017] [Accepted: 02/07/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND Familial combined hypolipidemia, a Mendelian condition characterized by substantial reductions in all 3 major lipid fractions, is caused by mutations that inactivate the gene angiopoietin-like 3 (ANGPTL3). Whether ANGPTL3 deficiency reduces risk of coronary artery disease (CAD) is unknown. OBJECTIVES The study goal was to leverage 3 distinct lines of evidence-a family that included individuals with complete (compound heterozygote) ANGPTL3 deficiency, a population based-study of humans with partial (heterozygote) ANGPTL3 deficiency, and biomarker levels in patients with myocardial infarction (MI)-to test whether ANGPTL3 deficiency is associated with lower risk for CAD. METHODS We assessed coronary atherosclerotic burden in 3 individuals with complete ANGPTL3 deficiency and 3 wild-type first-degree relatives using computed tomography angiography. In the population, ANGPTL3 loss-of-function (LOF) mutations were ascertained in up to 21,980 people with CAD and 158,200 control subjects. LOF mutations were defined as nonsense, frameshift, and splice-site variants, along with missense variants resulting in <25% of wild-type ANGPTL3 activity in a mouse model. In a biomarker study, circulating ANGPTL3 concentration was measured in 1,493 people who presented with MI and 3,232 control subjects. RESULTS The 3 individuals with complete ANGPTL3 deficiency showed no evidence of coronary atherosclerotic plaque. ANGPTL3 gene sequencing demonstrated that approximately 1 in 309 people was a heterozygous carrier for an LOF mutation. Compared with those without mutation, heterozygous carriers of ANGPTL3 LOF mutations demonstrated a 17% reduction in circulating triglycerides and a 12% reduction in low-density lipoprotein cholesterol. Carrier status was associated with a 34% reduction in odds of CAD (odds ratio: 0.66; 95% confidence interval: 0.44 to 0.98; p = 0.04). Individuals in the lowest tertile of circulating ANGPTL3 concentrations, compared with the highest, had reduced odds of MI (adjusted odds ratio: 0.65; 95% confidence interval: 0.55 to 0.77; p < 0.001). CONCLUSIONS ANGPTL3 deficiency is associated with protection from CAD.
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Affiliation(s)
- Nathan O Stitziel
- Cardiovascular Division, Department of Medicine, Department of Genetics, and McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri.
| | - Amit V Khera
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Xiao Wang
- Cardiovascular Institute, Division of Cardiovascular Medicine, Department of Medicine, and Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Andrew J Bierhals
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, Missouri
| | | | | | - Pradeep Natarajan
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Derek Klarin
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Connor A Emdin
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Seyedeh M Zekavat
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Akihiro Nomura
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Jeanette Erdmann
- Institute for Integrative and Experimental Genomics, University of Lübeck, Lübeck, Germany; DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, Lübeck, Germany
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Technische Universität München, Munich, Germany; DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom; NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| | - William E Kraus
- Duke Molecular Physiology Institute and the Division of Cardiology, Department of Medicine, Duke University, Durham, North Carolina
| | - Svati H Shah
- Duke Molecular Physiology Institute and the Division of Cardiology, Department of Medicine, Duke University, Durham, North Carolina
| | - Bing Yu
- Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, Texas; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Eric Boerwinkle
- Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, Texas; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Daniel J Rader
- Cardiovascular Institute, Division of Cardiovascular Medicine, Department of Medicine, and Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Namrata Gupta
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | | | - Asif Rasheed
- Center for Non-Communicable Diseases, Karachi, Pakistan
| | - John Danesh
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom; Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom; National Institute of Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, United Kingdom
| | - Eric S Lander
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Stacey Gabriel
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Danish Saleheen
- Center for Non-Communicable Diseases, Karachi, Pakistan; Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kiran Musunuru
- Cardiovascular Institute, Division of Cardiovascular Medicine, Department of Medicine, and Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Sekar Kathiresan
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts.
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Abstract
Although the human germline mutation rate is higher than that in any other well-studied species, the rate is not exceptional once the effective genome size and effective population size are taken into consideration. Human somatic mutation rates are substantially elevated above those in the germline, but this is also seen in other species. What is exceptional about humans is the recent detachment from the challenges of the natural environment and the ability to modify phenotypic traits in ways that mitigate the fitness effects of mutations, e.g., precision and personalized medicine. This results in a relaxation of selection against mildly deleterious mutations, including those magnifying the mutation rate itself. The long-term consequence of such effects is an expected genetic deterioration in the baseline human condition, potentially measurable on the timescale of a few generations in westernized societies, and because the brain is a particularly large mutational target, this is of particular concern. Ultimately, the price will have to be covered by further investment in various forms of medical intervention. Resolving the uncertainties of the magnitude and timescale of these effects will require the establishment of stable, standardized, multigenerational measurement procedures for various human traits.
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10
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Kono TJY, Fu F, Mohammadi M, Hoffman PJ, Liu C, Stupar RM, Smith KP, Tiffin P, Fay JC, Morrell PL. The Role of Deleterious Substitutions in Crop Genomes. Mol Biol Evol 2016; 33:2307-17. [PMID: 27301592 PMCID: PMC4989107 DOI: 10.1093/molbev/msw102] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Populations continually incur new mutations with fitness effects ranging from lethal to adaptive. While the distribution of fitness effects of new mutations is not directly observable, many mutations likely either have no effect on organismal fitness or are deleterious. Historically, it has been hypothesized that a population may carry many mildly deleterious variants as segregating variation, which reduces the mean absolute fitness of the population. Recent advances in sequencing technology and sequence conservation-based metrics for inferring the functional effect of a variant permit examination of the persistence of deleterious variants in populations. The issue of segregating deleterious variation is particularly important for crop improvement, because the demographic history of domestication and breeding allows deleterious variants to persist and reach moderate frequency, potentially reducing crop productivity. In this study, we use exome resequencing of 15 barley accessions and genome resequencing of 8 soybean accessions to investigate the prevalence of deleterious single nucleotide polymorphisms (SNPs) in the protein-coding regions of the genomes of two crops. We conclude that individual cultivars carry hundreds of deleterious SNPs on average, and that nonsense variants make up a minority of deleterious SNPs. Our approach identifies known phenotype-altering variants as deleterious more frequently than the genome-wide average, suggesting that putatively deleterious variants are likely to affect phenotypic variation. We also report the implementation of a SNP annotation tool BAD_Mutations that makes use of a likelihood ratio test based on alignment of all currently publicly available Angiosperm genomes.
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Affiliation(s)
- Thomas J Y Kono
- Department of Agronomy and Plant Genetics, University of Minnesota
| | - Fengli Fu
- Department of Agronomy and Plant Genetics, University of Minnesota
| | - Mohsen Mohammadi
- Department of Agronomy and Plant Genetics, University of Minnesota Department of Agronomy, Purdue University
| | - Paul J Hoffman
- Department of Agronomy and Plant Genetics, University of Minnesota
| | - Chaochih Liu
- Department of Agronomy and Plant Genetics, University of Minnesota
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota
| | - Kevin P Smith
- Department of Agronomy and Plant Genetics, University of Minnesota
| | - Peter Tiffin
- Department of Plant Biology, University of Minnesota
| | | | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota
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11
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Ragsdale AP, Coffman AJ, Hsieh P, Struck TJ, Gutenkunst RN. Triallelic Population Genomics for Inferring Correlated Fitness Effects of Same Site Nonsynonymous Mutations. Genetics 2016; 203:513-23. [PMID: 27029732 PMCID: PMC4858796 DOI: 10.1534/genetics.115.184812] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/19/2016] [Indexed: 12/27/2022] Open
Abstract
The distribution of mutational effects on fitness is central to evolutionary genetics. Typical univariate distributions, however, cannot model the effects of multiple mutations at the same site, so we introduce a model in which mutations at the same site have correlated fitness effects. To infer the strength of that correlation, we developed a diffusion approximation to the triallelic frequency spectrum, which we applied to data from Drosophila melanogaster We found a moderate positive correlation between the fitness effects of nonsynonymous mutations at the same codon, suggesting that both mutation identity and location are important for determining fitness effects in proteins. We validated our approach by comparing it to biochemical mutational scanning experiments, finding strong quantitative agreement, even between different organisms. We also found that the correlation of mutational fitness effects was not affected by protein solvent exposure or structural disorder. Together, our results suggest that the correlation of fitness effects at the same site is a previously overlooked yet fundamental property of protein evolution.
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Affiliation(s)
- Aaron P Ragsdale
- Program in Applied Mathematics, University of Arizona, Tucson, Arizona 85721
| | - Alec J Coffman
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - PingHsun Hsieh
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721
| | - Travis J Struck
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Ryan N Gutenkunst
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
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12
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Weber CC, Nabholz B, Romiguier J, Ellegren H. Kr/Kc but not dN/dS correlates positively with body mass in birds, raising implications for inferring lineage-specific selection. Genome Biol 2015; 15:542. [PMID: 25607475 PMCID: PMC4264323 DOI: 10.1186/s13059-014-0542-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 11/13/2014] [Indexed: 02/02/2023] Open
Abstract
Background The ratio of the rates of non-synonymous and synonymous substitution (dN/dS) is commonly used to estimate selection in coding sequences. It is often suggested that, all else being equal, dN/dS should be lower in populations with large effective size (Ne) due to increased efficacy of purifying selection. As Ne is difficult to measure directly, life history traits such as body mass, which is typically negatively associated with population size, have commonly been used as proxies in empirical tests of this hypothesis. However, evidence of whether the expected positive correlation between body mass and dN/dS is consistently observed is conflicting. Results Employing whole genome sequence data from 48 avian species, we assess the relationship between rates of molecular evolution and life history in birds. We find a negative correlation between dN/dS and body mass, contrary to nearly neutral expectation. This raises the question whether the correlation might be a method artefact. We therefore in turn consider non-stationary base composition, divergence time and saturation as possible explanations, but find no clear patterns. However, in striking contrast to dN/dS, the ratio of radical to conservative amino acid substitutions (Kr/Kc) correlates positively with body mass. Conclusions Our results in principle accord with the notion that non-synonymous substitutions causing radical amino acid changes are more efficiently removed by selection in large populations, consistent with nearly neutral theory. These findings have implications for the use of dN/dS and suggest that caution is warranted when drawing conclusions about lineage-specific modes of protein evolution using this metric. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0542-8) contains supplementary material, which is available to authorized users.
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13
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Khatri BS, Goldstein RA. A coarse-grained biophysical model of sequence evolution and the population size dependence of the speciation rate. J Theor Biol 2015; 378:56-64. [PMID: 25936759 PMCID: PMC4457359 DOI: 10.1016/j.jtbi.2015.04.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 02/20/2015] [Accepted: 04/20/2015] [Indexed: 11/29/2022]
Abstract
Speciation is fundamental to understanding the huge diversity of life on Earth. Although still controversial, empirical evidence suggests that the rate of speciation is larger for smaller populations. Here, we explore a biophysical model of speciation by developing a simple coarse-grained theory of transcription factor-DNA binding and how their co-evolution in two geographically isolated lineages leads to incompatibilities. To develop a tractable analytical theory, we derive a Smoluchowski equation for the dynamics of binding energy evolution that accounts for the fact that natural selection acts on phenotypes, but variation arises from mutations in sequences; the Smoluchowski equation includes selection due to both gradients in fitness and gradients in sequence entropy, which is the logarithm of the number of sequences that correspond to a particular binding energy. This simple consideration predicts that smaller populations develop incompatibilities more quickly in the weak mutation regime; this trend arises as sequence entropy poises smaller populations closer to incompatible regions of phenotype space. These results suggest a generic coarse-grained approach to evolutionary stochastic dynamics, allowing realistic modelling at the phenotypic level.
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Affiliation(s)
- Bhavin S Khatri
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK; Division of Infection & Immunity, University College London, London WC1E 6BT, UK.
| | - Richard A Goldstein
- Division of Infection & Immunity, University College London, London WC1E 6BT, UK.
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14
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An estimate of the average number of recessive lethal mutations carried by humans. Genetics 2015; 199:1243-54. [PMID: 25697177 PMCID: PMC4391560 DOI: 10.1534/genetics.114.173351] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/11/2015] [Indexed: 12/27/2022] Open
Abstract
The effects of inbreeding on human health depend critically on the number and severity of recessive, deleterious mutations carried by individuals. In humans, existing estimates of these quantities are based on comparisons between consanguineous and nonconsanguineous couples, an approach that confounds socioeconomic and genetic effects of inbreeding. To overcome this limitation, we focused on a founder population that practices a communal lifestyle, for which there is almost complete Mendelian disease ascertainment and a known pedigree. Focusing on recessive lethal diseases and simulating allele transmissions, we estimated that each haploid set of human autosomes carries on average 0.29 (95% credible interval [0.10, 0.84]) recessive alleles that lead to complete sterility or death by reproductive age when homozygous. Comparison to existing estimates in humans suggests that a substantial fraction of the total burden imposed by recessive deleterious variants is due to single mutations that lead to sterility or death between birth and reproductive age. In turn, comparison to estimates from other eukaryotes points to a surprising constancy of the average number of recessive lethal mutations across organisms with markedly different genome sizes.
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15
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Causes of natural variation in fitness: evidence from studies of Drosophila populations. Proc Natl Acad Sci U S A 2015; 112:1662-9. [PMID: 25572964 DOI: 10.1073/pnas.1423275112] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA sequencing has revealed high levels of variability within most species. Statistical methods based on population genetics theory have been applied to the resulting data and suggest that most mutations affecting functionally important sequences are deleterious but subject to very weak selection. Quantitative genetic studies have provided information on the extent of genetic variation within populations in traits related to fitness and the rate at which variability in these traits arises by mutation. This paper attempts to combine the available information from applications of the two approaches to populations of the fruitfly Drosophila in order to estimate some important parameters of genetic variation, using a simple population genetics model of mutational effects on fitness components. Analyses based on this model suggest the existence of a class of mutations with much larger fitness effects than those inferred from sequence variability and that contribute most of the standing variation in fitness within a population caused by the input of mildly deleterious mutations. However, deleterious mutations explain only part of this standing variation, and other processes such as balancing selection appear to make a large contribution to genetic variation in fitness components in Drosophila.
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16
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Peng B. Reproducible simulations of realistic samples for next-generation sequencing studies using Variant Simulation Tools. Genet Epidemiol 2014; 39:45-52. [PMID: 25395236 DOI: 10.1002/gepi.21867] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 09/14/2014] [Accepted: 09/26/2014] [Indexed: 12/31/2022]
Abstract
Computer simulations have been widely used to validate and evaluate the power of statistical methods for genetic epidemiological studies. Although a large number of simulation methods and software packages have been developed for genome-wide association studies, methodological and bioinformatics challenges have limited their applications in simulating datasets for whole-genome and whole-exome sequencing studies. With the development of more sophisticated statistical methods that make fuller use of available data and our knowledge of the human genome, there is a pressing need for genetic simulators that capture more features of empirical data (e.g., multiallele variants, indels, use of the Variant Call Format) and the human genome (e.g., functional annotations of genetic variants). This article introduces Variant Simulation Tools (VST), a module of Variant Tools for the simulation of genetic variants for sequencing-based genetic epidemiological studies. Although multiple simulation engines are provided, the core of VST is a novel forward-time simulation engine that simulates real nucleotide sequences of the human genome using DNA mutation models, fine-scale recombination maps, and a selection model based on amino acid changes of translated protein sequences. The design of VST allows users to easily create and distribute simulation methods and simulated datasets for a variety of applications and encourages fair comparison between statistical methods through the use of existing or reproduced simulated datasets.
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Affiliation(s)
- Bo Peng
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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17
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Denisov SV, Bazykin GA, Sutormin R, Favorov AV, Mironov AA, Gelfand MS, Kondrashov AS. Weak negative and positive selection and the drift load at splice sites. Genome Biol Evol 2014; 6:1437-47. [PMID: 24966225 PMCID: PMC4079205 DOI: 10.1093/gbe/evu100] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2014] [Indexed: 11/30/2022] Open
Abstract
Splice sites (SSs) are short sequences that are crucial for proper mRNA splicing in eukaryotic cells, and therefore can be expected to be shaped by strong selection. Nevertheless, in mammals and in other intron-rich organisms, many of the SSs often involve nonconsensus (Nc), rather than consensus (Cn), nucleotides, and beyond the two critical nucleotides, the SSs are not perfectly conserved between species. Here, we compare the SS sequences between primates, and between Drosophila fruit flies, to reveal the pattern of selection acting at SSs. Cn-to-Nc substitutions are less frequent, and Nc-to-Cn substitutions are more frequent, than neutrally expected, indicating, respectively, negative and positive selection. This selection is relatively weak (1 < |4Nes| < 4), and has a similar efficiency in primates and in Drosophila. Within some nucleotide positions, the positive selection in favor of Nc-to-Cn substitutions is weaker than the negative selection maintaining already established Cn nucleotides; this difference is due to site-specific negative selection favoring current Nc nucleotides. In general, however, the strength of negative selection protecting the Cn alleles is similar in magnitude to the strength of positive selection favoring replacement of Nc alleles, as expected under the simple nearly neutral turnover. In summary, although a fraction of the Nc nucleotides within SSs is maintained by selection, the abundance of deleterious nucleotides in this class suggests a substantial genome-wide drift load.
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Affiliation(s)
- Stepan V Denisov
- A.A. Kharkevich Insitute for Information Transmission Problems RAS, Moscow, Russia
| | - Georgii A Bazykin
- A.A. Kharkevich Insitute for Information Transmission Problems RAS, Moscow, RussiaFaculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Roman Sutormin
- Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexander V Favorov
- Division of Oncology Biostatistics, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MDLaboratory of System Biology and Computational Genetics, Department of Computational System Biology, N.I. Vavilov Institute of General Genetics, Moscow, RussiaLaboratory of Bioinformatics, State Research Institute of Genetics and Selection of Industrial Microorganism (GosNIIGenetika), Moscow, Russia
| | - Andrey A Mironov
- A.A. Kharkevich Insitute for Information Transmission Problems RAS, Moscow, RussiaFaculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail S Gelfand
- A.A. Kharkevich Insitute for Information Transmission Problems RAS, Moscow, RussiaFaculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexey S Kondrashov
- Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, RussiaLife Sciences Institute and Department of Ecology and Evolutionary Biology, University of Michigan
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18
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Searching for missing heritability: designing rare variant association studies. Proc Natl Acad Sci U S A 2014; 111:E455-64. [PMID: 24443550 DOI: 10.1073/pnas.1322563111] [Citation(s) in RCA: 416] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genetic studies have revealed thousands of loci predisposing to hundreds of human diseases and traits, revealing important biological pathways and defining novel therapeutic hypotheses. However, the genes discovered to date typically explain less than half of the apparent heritability. Because efforts have largely focused on common genetic variants, one hypothesis is that much of the missing heritability is due to rare genetic variants. Studies of common variants are typically referred to as genomewide association studies, whereas studies of rare variants are often simply called sequencing studies. Because they are actually closely related, we use the terms common variant association study (CVAS) and rare variant association study (RVAS). In this paper, we outline the similarities and differences between RVAS and CVAS and describe a conceptual framework for the design of RVAS. We apply the framework to address key questions about the sample sizes needed to detect association, the relative merits of testing disruptive alleles vs. missense alleles, frequency thresholds for filtering alleles, the value of predictors of the functional impact of missense alleles, the potential utility of isolated populations, the value of gene-set analysis, and the utility of de novo mutations. The optimal design depends critically on the selection coefficient against deleterious alleles and thus varies across genes. The analysis shows that common variant and rare variant studies require similarly large sample collections. In particular, a well-powered RVAS should involve discovery sets with at least 25,000 cases, together with a substantial replication set.
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19
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Takakura J, Nishimura T, Watanuki S. Visual information without thermal energy may induce thermoregulatory-like cardiovascular responses. J Physiol Anthropol 2013; 32:26. [PMID: 24373765 PMCID: PMC3904752 DOI: 10.1186/1880-6805-32-26] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Accepted: 11/27/2013] [Indexed: 11/23/2022] Open
Abstract
Background Human core body temperature is kept quasi-constant regardless of varying thermal environments. It is well known that physiological thermoregulatory systems are under the control of central and peripheral sensory organs that are sensitive to thermal energy. If these systems wrongly respond to non-thermal stimuli, it may disturb human homeostasis. Methods Fifteen participants viewed video images evoking hot or cold impressions in a thermally constant environment. Cardiovascular indices were recorded during the experiments. Correlations between the ‘hot-cold’ impression scores and cardiovascular indices were calculated. Results The changes of heart rate, cardiac output, and total peripheral resistance were significantly correlated with the ‘hot-cold’ impression scores, and the tendencies were similar to those in actual thermal environments corresponding to the impressions. Conclusions The present results suggest that visual information without any thermal energy can affect physiological thermoregulatory systems at least superficially. To avoid such ‘virtual’ environments disturbing human homeostasis, further study and more attention are needed.
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Affiliation(s)
- Jun'ya Takakura
- Graduate School of Integrated Frontier Science, Kyushu University, 4-9-1, Shiobaru, Minami-Ku, Fukuoka, Japan.
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20
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Blaser O, Grossen C, Neuenschwander S, Perrin N. SEX-CHROMOSOME TURNOVERS INDUCED BY DELETERIOUS MUTATION LOAD. Evolution 2012; 67:635-45. [DOI: 10.1111/j.1558-5646.2012.01810.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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21
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Popadin KY, Nikolaev SI, Junier T, Baranova M, Antonarakis SE. Purifying selection in mammalian mitochondrial protein-coding genes is highly effective and congruent with evolution of nuclear genes. Mol Biol Evol 2012; 30:347-55. [PMID: 22983951 DOI: 10.1093/molbev/mss219] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The mammalian mitochondrial genomes differ from the nuclear genomes by maternal inheritance, absence of recombination, and higher mutation rate. All these differences decrease the effective population size of mitochondrial genome and make it more susceptible to accumulation of slightly deleterious mutations. It was hypothesized that mitochondrial genes, especially in species with low effective population size, irreversibly degrade leading to decrease of organismal fitness and even to extinction of species through the mutational meltdown. To interrogate this hypothesis, we compared the purifying selections acting on the representative set of mitochondrial (potentially degrading) and nuclear (potentially not degrading) protein-coding genes in species with different effective population size. For 21 mammalian species, we calculated the ratios of accumulation of slightly deleterious mutations approximated by Kn/Ks separately for mitochondrial and nuclear genomes. The 75% of variation in Kn/Ks is explained by two independent variables: type of a genome (mitochondrial or nuclear) and effective population size of species approximated by generation time. First, we observed that purifying selection is more effective in mitochondria than in the nucleus that implies strong evolutionary constraints of mitochondrial genome. Mitochondrial de novo nonsynonymous mutations have at least 5-fold more harmful effect when compared with nuclear. Second, Kn/Ks of mitochondrial and nuclear genomes is positively correlated with generation time of species, indicating relaxation of purifying selection with decrease of species-specific effective population size. Most importantly, the linear regression lines of mitochondrial and nuclear Kn/Ks's from generation times of species are parallel, indicating congruent relaxation of purifying selection in both genomes. Thus, our results reveal that the distribution of selection coefficients of de novo nonsynonymous mitochondrial mutations has a similar shape with the distribution of de novo nonsynonymous nuclear mutations, but its mean is five times smaller. The harmful effect of mitochondrial de novo nonsynonymous mutations triggers highly effective purifying selection, which maintains the fitness of the mammalian mitochondrial genome.
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Affiliation(s)
- Konstantin Yu Popadin
- Department of Genetic Medicine and Development, University of Geneva Medical School and iGE3 Institute of Genetics and Genomics of Geneva, Switzerland.
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22
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Abstract
The central preoccupation of human genetics is an effort to understand the genotypic basis of human phenotypic diversity. Although recent progress in identifying the genes that, when mutated, underlie major genetic diseases has been rapid, knowledge of the genetic influences on the vast range of variable, and at least partially heritable, traits that constitute the "normal" range of human phenotypic variation lags. Spectacular advances in our knowledge of human genetic variation have laid the groundwork for a synthesis of insights from medical genetics, population genetics, molecular evolution, and the study of human origins that places basic constraints on models of human genetic individuality. Balancing selection, local adaptation, mutation-selection balance, and founder effects have all extensively shaped contemporary genetic variation. Long-term-balancing selection appears largely to reflect the consequences of host-pathogen arms races. Local adaptation has been widespread-and involved responses to a plethora of selective pressures, some identifiable but most unknown. However, it appears to be a combination of mutation-selection balance and founder effects that largely accounts for genetic individuality. If true, this inference has major implications for future research programs in human genetics.
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Affiliation(s)
- Maynard V Olson
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA.
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23
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24
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Keightley PD. Rates and fitness consequences of new mutations in humans. Genetics 2012; 190:295-304. [PMID: 22345605 PMCID: PMC3276617 DOI: 10.1534/genetics.111.134668] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 11/13/2011] [Indexed: 12/13/2022] Open
Abstract
The human mutation rate per nucleotide site per generation (μ) can be estimated from data on mutation rates at loci causing Mendelian genetic disease, by comparing putatively neutrally evolving nucleotide sequences between humans and chimpanzees and by comparing the genome sequences of relatives. Direct estimates from genome sequencing of relatives suggest that μ is about 1.1 × 10(-8), which is about twofold lower than estimates based on the human-chimp divergence. This implies that an average of ~70 new mutations arise in the human diploid genome per generation. Most of these mutations are paternal in origin, but the male:female mutation rate ratio is currently uncertain and might vary even among individuals within a population. On the basis of a method proposed by Kondrashov and Crow, the genome-wide deleterious mutation rate (U) can be estimated from the product of the number of nucleotide sites in the genome, μ, and the mean selective constraint per site. Although the presence of many weakly selected mutations in human noncoding DNA makes this approach somewhat problematic, estimates are U ≈ 2.2 for the whole diploid genome per generation and 0.35 for mutations that change an amino acid of a protein-coding gene. A genome-wide deleterious mutation rate of 2.2 seems higher than humans could tolerate if natural selection is "hard," but could be tolerated if selection acts on relative fitness differences between individuals or if there is synergistic epistasis. I argue that in the foreseeable future, an accumulation of new deleterious mutations is unlikely to lead to a detectable decline in fitness of human populations.
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Affiliation(s)
- Peter D Keightley
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom.
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25
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Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models. Genetics 2011; 190:1101-15. [PMID: 22209901 PMCID: PMC3296245 DOI: 10.1534/genetics.111.136432] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Estimation of the distribution of selection coefficients of mutations is a long-standing issue in molecular evolution. In addition to population-based methods, the distribution can be estimated from DNA sequence data by phylogenetic-based models. Previous models have generally found unimodal distributions where the probability mass is concentrated between mildly deleterious and nearly neutral mutations. Here we use a sitewise mutation–selection phylogenetic model to estimate the distribution of selection coefficients among novel and fixed mutations (substitutions) in a data set of 244 mammalian mitochondrial genomes and a set of 401 PB2 proteins from influenza. We find a bimodal distribution of selection coefficients for novel mutations in both the mitochondrial data set and for the influenza protein evolving in its natural reservoir, birds. Most of the mutations are strongly deleterious with the rest of the probability mass concentrated around mildly deleterious to neutral mutations. The distribution of the coefficients among substitutions is unimodal and symmetrical around nearly neutral substitutions for both data sets at adaptive equilibrium. About 0.5% of the nonsynonymous mutations and 14% of the nonsynonymous substitutions in the mitochondrial proteins are advantageous, with 0.5% and 24% observed for the influenza protein. Following a host shift of influenza from birds to humans, however, we find among novel mutations in PB2 a trimodal distribution with a small mode of advantageous mutations.
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26
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Wilson DJ, Hernandez RD, Andolfatto P, Przeworski M. A population genetics-phylogenetics approach to inferring natural selection in coding sequences. PLoS Genet 2011; 7:e1002395. [PMID: 22144911 PMCID: PMC3228810 DOI: 10.1371/journal.pgen.1002395] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 10/08/2011] [Indexed: 01/23/2023] Open
Abstract
Through an analysis of polymorphism within and divergence between species, we can hope to learn about the distribution of selective effects of mutations in the genome, changes in the fitness landscape that occur over time, and the location of sites involved in key adaptations that distinguish modern-day species. We introduce a novel method for the analysis of variation in selection pressures within and between species, spatially along the genome and temporally between lineages. We model codon evolution explicitly using a joint population genetics-phylogenetics approach that we developed for the construction of multiallelic models with mutation, selection, and drift. Our approach has the advantage of performing direct inference on coding sequences, inferring ancestral states probabilistically, utilizing allele frequency information, and generalizing to multiple species. We use a Bayesian sliding window model for intragenic variation in selection coefficients that efficiently combines information across sites and captures spatial clustering within the genome. To demonstrate the utility of the method, we infer selective pressures acting in Drosophila melanogaster and D. simulans from polymorphism and divergence data for 100 X-linked coding regions.
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Affiliation(s)
- Daniel J Wilson
- Department of Human Genetics and Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA.
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27
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Samuels ME. Saturation of the human phenome. Curr Genomics 2011; 11:482-99. [PMID: 21532833 PMCID: PMC3048311 DOI: 10.2174/138920210793175886] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2010] [Revised: 06/22/2010] [Accepted: 06/22/2010] [Indexed: 12/26/2022] Open
Abstract
The phenome is the complete set of phenotypes resulting from genetic variation in populations of an organism. Saturation of a phenome implies the identification and phenotypic description of mutations in all genes in an organism, potentially constrained to those encoding proteins. The human genome is believed to contain 20-25,000 protein coding genes, but only a small fraction of these have documented mutant phenotypes, thus the human phenome is far from complete. In model organisms, genetic saturation entails the identification of multiple mutant alleles of a gene or locus, allowing a consistent description of mutational phenotypes for that gene. Saturation of several model organisms has been attempted, usually by targeting annotated coding genes with insertional transposons (Drosophila melanogaster, Mus musculus) or by sequence directed deletion (Saccharomyces cerevisiae) or using libraries of antisense oligonucleotide probes injected directly into animals (Caenorhabditis elegans, Danio rerio). This paper reviews the general state of the human phenome, and discusses theoretical and practical considerations toward a saturation analysis in humans. Throughout, emphasis is placed on high penetrance genetic variation, of the kind typically asociated with monogenic versus complex traits.
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Affiliation(s)
- Mark E Samuels
- Centre de Recherche de Ste-Justine, 3175, Côte Ste-Catherine, Montréal QC H3T 1C5, Canada
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28
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Breen MS, Kondrashov FA. Mitochondrial pathogenic mutations are population-specific. Biol Direct 2010; 5:68. [PMID: 21194457 PMCID: PMC3022564 DOI: 10.1186/1745-6150-5-68] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 12/31/2010] [Indexed: 01/09/2023] Open
Abstract
Background Surveying deleterious variation in human populations is crucial for our understanding, diagnosis and potential treatment of human genetic pathologies. A number of recent genome-wide analyses focused on the prevalence of segregating deleterious alleles in the nuclear genome. However, such studies have not been conducted for the mitochondrial genome. Results We present a systematic survey of polymorphisms in the human mitochondrial genome, including those predicted to be deleterious and those that correspond to known pathogenic mutations. Analyzing 4458 completely sequenced mitochondrial genomes we characterize the genetic diversity of different types of single nucleotide polymorphisms (SNPs) in African (L haplotypes) and non-African (M and N haplotypes) populations. We find that the overall level of polymorphism is higher in the mitochondrial compared to the nuclear genome, although the mitochondrial genome appears to be under stronger selection as indicated by proportionally fewer nonsynonymous than synonymous substitutions. The African mitochondrial genomes show higher heterozygosity, a greater number of polymorphic sites and higher frequencies of polymorphisms for synonymous, benign and damaging polymorphism than non-African genomes. However, African genomes carry significantly fewer SNPs that have been previously characterized as pathogenic compared to non-African genomes. Conclusions Finding SNPs classified as pathogenic to be the only category of polymorphisms that are more abundant in non-African genomes is best explained by a systematic ascertainment bias that favours the discovery of pathogenic polymorphisms segregating in non-African populations. This further suggests that, contrary to the common disease-common variant hypothesis, pathogenic mutations are largely population-specific and different SNPs may be associated with the same disease in different populations. Therefore, to obtain a comprehensive picture of the deleterious variability in the human population, as well as to improve the diagnostics of individuals carrying African mitochondrial haplotypes, it is necessary to survey different populations independently. Reviewers This article was reviewed by Dr Mikhail Gelfand, Dr Vasily Ramensky (nominated by Dr Eugene Koonin) and Dr David Rand (nominated by Dr Laurence Hurst).
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Yampolsky LY, Bouzinier MA. Evolutionary patterns of amino acid substitutions in 12 Drosophila genomes. BMC Genomics 2010; 11 Suppl 4:S10. [PMID: 21143793 PMCID: PMC3005911 DOI: 10.1186/1471-2164-11-s4-s10] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Harnessing vast amounts of genomic data in phylogenetic context stemming from massive sequencing of multiple closely related genomes requires new tools and approaches. We present a tool for the genome-wide analysis of frequencies and patterns of amino acid substitutions in multiple alignments of genes' coding regions, and a database of amino acid substitutions in the phylogeny of 12 Drosophila genomes. We illustrate the use of these resources to address three types of evolutionary genomics questions: about fluxes in amino acid composition in proteins, about asymmetries in amino acid substitutions and about patterns of molecular evolution in duplicated genes. RESULTS We demonstrate that amino acid composition of Drosophila proteins underwent a significant shift over the last 70 million years encompassed by the studied phylogeny, with less common amino acids (Cys, Met, His) increasing in frequency and more common ones (Ala, Leu, Glu) becoming less frequent. These fluxes are strongly correlated with polarity of source and destination amino acids, resulting in overall systematic decrease of mean polarity of amino acids found in Drosophila proteins. Frequency and radicality of amino acid substitutions are higher in paralogs than in orthologous single-copy genes and are higher in gene families with paralogs than in gene families without surviving duplications. Rate and radicality of substitutions, as expected, are negatively correlated with overall level and uniformity of gene expression. However, these correlations are not observed for substitutions occurring in duplicated genes, indicating a different selective constraint on the evolution of paralogous sequences. Clades resulting from duplications show a marked asymmetry in rate and radicality of amino acid substitutions, possibly a signal of widespread neofunctionalization. These patterns differ among protein families of different functionality, with genes coding for RNA-binding proteins differing from most other functional groups in terms of amino acid substitution patterns in duplicated and single-copy genes. CONCLUSIONS We demonstrate that deep phylogenetic analysis of amino acid substitutions can reveal interesting genome-wide patterns. Amino acid composition of drosophilid proteins is shaped by fluxes similar to those previously observed in prokaryotic, yeast and mammalian genomes, indicating globally present patterns. Increased frequency and radicality of amino acid substitutions in duplicated genes and the presence of asymmetry of these parameters between paralogous clades indicate widespread neofunctionalization among paralogs as the mechanism of duplication retention.
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Affiliation(s)
- Lev Y Yampolsky
- Department of Biological sciences, East Tennessee State University, Johnson City, TN 37614, USA.
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30
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King CR, Rathouz PJ, Nicolae DL. An evolutionary framework for association testing in resequencing studies. PLoS Genet 2010; 6:e1001202. [PMID: 21085648 PMCID: PMC2978703 DOI: 10.1371/journal.pgen.1001202] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Accepted: 10/07/2010] [Indexed: 11/17/2022] Open
Abstract
Sequencing technologies are becoming cheap enough to apply to large numbers of study participants and promise to provide new insights into human phenotypes by bringing to light rare and previously unknown genetic variants. We develop a new framework for the analysis of sequence data that incorporates all of the major features of previously proposed approaches, including those focused on allele counts and allele burden, but is both more general and more powerful. We harness population genetic theory to provide prior information on effect sizes and to create a pooling strategy for information from rare variants. Our method, EMMPAT (Evolutionary Mixed Model for Pooled Association Testing), generates a single test per gene (substantially reducing multiple testing concerns), facilitates graphical summaries, and improves the interpretation of results by allowing calculation of attributable variance. Simulations show that, relative to previously used approaches, our method increases the power to detect genes that affect phenotype when natural selection has kept alleles with large effect sizes rare. We demonstrate our approach on a population-based re-sequencing study of association between serum triglycerides and variation in ANGPTL4.
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Affiliation(s)
- C Ryan King
- Department of Health Studies, University of Chicago, Chicago, Illinois, United States of America.
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31
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Naugler CT. Population genetics of cancer cell clones: possible implications of cancer stem cells. Theor Biol Med Model 2010; 7:42. [PMID: 21062473 PMCID: PMC2994797 DOI: 10.1186/1742-4682-7-42] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Accepted: 11/09/2010] [Indexed: 11/13/2022] Open
Abstract
Background The population dynamics of the various clones of cancer cells existing within a tumour is complex and still poorly understood. Cancer cell clones can be conceptualized as sympatric asexual species, and as such, the application of theoretical population genetics as it pertains to asexual species may provide additional insights. Results The number of generations of tumour cells within a cancer has been estimated at a minimum of 40, but high cancer cell mortality rates suggest that the number of cell generations may actually be in the hundreds. Such a large number of generations would easily allow natural selection to drive clonal evolution assuming that selective advantages of individual clones are within the range reported for free-living animal species. Tumour cell clonal evolution could also be driven by variation in the intrinsic rates of increase of different clones or by genetic drift. In every scenario examined, the presence of cancer stem cells would require lower selection pressure or less variation in intrinsic rates of increase. Conclusions The presence of cancer stem cells may result in more rapid clonal evolution. Specific predictions from theoretical population genetics may lead to a greater understanding of this process.
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Affiliation(s)
- Christopher T Naugler
- Department of Pathology and Laboratory Medicine, University of Calgary and Calgary Laboratory Services, C414, Diagnostic and Scientific Centre, 9, 3535 Research Road NW, Calgary AB, T2L 2K8 Canada.
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32
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Gorlov IP, Gorlova OY, Frazier ML, Spitz MR, Amos CI. Evolutionary evidence of the effect of rare variants on disease etiology. Clin Genet 2010; 79:199-206. [PMID: 20831747 DOI: 10.1111/j.1399-0004.2010.01535.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The common disease/common variant hypothesis has been popular for describing the genetic architecture of common human diseases for several years. According to the originally stated hypothesis, one or a few common genetic variants with a large effect size control the risk of common diseases. A growing body of evidence, however, suggests that rare single-nucleotide polymorphisms (SNPs), i.e. those with a minor allele frequency of less than 5%, are also an important component of the genetic architecture of common human diseases. In this study, we analyzed the relevance of rare SNPs to the risk of common diseases from an evolutionary perspective and found that rare SNPs are more likely than common SNPs to be functional and tend to have a stronger effect size than do common SNPs. This observation, and the fact that most of the SNPs in the human genome are rare, suggests that rare SNPs are a crucial element of the genetic architecture of common human diseases. We propose that the next generation of genomic studies should focus on analyzing rare SNPs. Further, targeting patients with a family history of the disease, an extreme phenotype, or early disease onset may facilitate the detection of risk-associated rare SNPs.
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Affiliation(s)
- I P Gorlov
- Department of Genitourinary Medical Oncology Department of Epidemiology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
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Toll-Riera M, Laurie S, Albà MM. Lineage-specific variation in intensity of natural selection in mammals. Mol Biol Evol 2010; 28:383-98. [PMID: 20688808 DOI: 10.1093/molbev/msq206] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The molecular clock hypothesis states that protein-coding genes evolve at an approximately constant rate. However, this is only expected to be true as long as the function and the tertiary structure of the molecule remain unaltered. An important implication of this statement is that significant deviations in the rate of evolution of a gene with respect to the species clock are likely to reflect functional and/or structural alterations. Here, we present a method to identify such deviations and apply it to a data set of 2,929 high-quality coding sequence alignments corresponding to one-to-one orthologous genes from six mammalian species--human, macaque, mouse, rat, cow, and dog. Deviated branches are defined as those that present significant alterations in both the rate of nonsynonymous substitutions (dN) and the selective pressure (dN/dS). Strikingly, we find that as many as 24.5% of the genes show branch-specific deviations in dN and dN/dS, though this is a relatively well-conserved set of genes. Around half of these genes show branch-specific acceleration of evolutionary rates. Positive selection (PS) tests based on divergence data only identify 17.7% of the accelerated branches. Failure to identify PS in accelerated branches with an excess of radical amino acid replacements suggests that these tests are conservative. Interestingly, genes with accelerated branches are significantly enriched in neural proteins, indicating that this type of protein might play a more important role than previously thought in species diversification, although they are generally not detected by PS tests. We discuss in detail several examples of genes that show lineage-specific evolutionary rate acceleration and are involved in synaptic transmission, chemosensory perception, and ubiquitination.
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Affiliation(s)
- Macarena Toll-Riera
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics, Fundació Institut Municipal d'Investigació Mèdica, Barcelona Biomedical Research Park, Barcelona, Spain
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34
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Jordan DM, Ramensky VE, Sunyaev SR. Human allelic variation: perspective from protein function, structure, and evolution. Curr Opin Struct Biol 2010; 20:342-50. [PMID: 20399638 PMCID: PMC2921592 DOI: 10.1016/j.sbi.2010.03.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Accepted: 03/22/2010] [Indexed: 01/20/2023]
Abstract
It is widely anticipated that the coming year will be marked by the complete characterization of DNA sequence of protein-coding regions of thousands of human individuals. A number of existing computational methods use comparative protein sequence analysis and analysis of protein structure to predict the functional effect of coding human alleles. Functional and structural analysis of coding allelic variants can inform various aspects of research on human genetic variation. In population and evolutionary genetics it helps estimate the strength of purifying selection against deleterious missense mutations and study the imprint of demographic history on deleterious genetic variation. In medical genetics it may assist in the interpretation of uncharacterized mutations in genes involved in monogenic and oligogenic diseases. It has a potential to facilitate medical sequencing studies searching for genes underlying Mendelian diseases or harboring rare alleles involved in complex traits.
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Affiliation(s)
- Daniel M. Jordan
- Division of Genetics, Brigham & Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Program in Biophysics, Harvard University, Cambridge, Massachusetts, USA
| | - Vasily E. Ramensky
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Shamil R. Sunyaev
- Division of Genetics, Brigham & Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
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35
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Abstract
Although mutation provides the fuel for phenotypic evolution, it also imposes a substantial burden on fitness through the production of predominantly deleterious alleles, a matter of concern from a human-health perspective. Here, recently established databases on de novo mutations for monogenic disorders are used to estimate the rate and molecular spectrum of spontaneously arising mutations and to derive a number of inferences with respect to eukaryotic genome evolution. Although the human per-generation mutation rate is exceptionally high, on a per-cell division basis, the human germline mutation rate is lower than that recorded for any other species. Comparison with data from other species demonstrates a universal mutational bias toward A/T composition, and leads to the hypothesis that genome-wide nucleotide composition generally evolves to the point at which the power of selection in favor of G/C is approximately balanced by the power of random genetic drift, such that variation in equilibrium genome-wide nucleotide composition is largely defined by variation in mutation biases. Quantification of the hazards associated with introns reveals that mutations at key splice-site residues are a major source of human mortality. Finally, a consideration of the long-term consequences of current human behavior for deleterious-mutation accumulation leads to the conclusion that a substantial reduction in human fitness can be expected over the next few centuries in industrialized societies unless novel means of genetic intervention are developed.
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Affiliation(s)
- Michael Lynch
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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36
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Evolution in health and medicine Sackler colloquium: Genetic architecture of a complex trait and its implications for fitness and genome-wide association studies. Proc Natl Acad Sci U S A 2010; 107 Suppl 1:1752-6. [PMID: 20133822 DOI: 10.1073/pnas.0906182107] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A model is investigated in which mutations that affect a complex trait (e.g., heart disease) also affect fitness because the trait is a component of fitness or because the mutations have pleiotropic effects on fitness. The model predicts that the genetic variance, and hence the heritability, in the trait is contributed by mutations at low frequency in the population, unless the mean strength of selection of mutations that affect the trait is very small or weakly selected mutations tend to contribute disproportionately to the trait compared with strongly selected mutations. Furthermore, it is shown that each rare mutation tends to contribute more to the variance than each common mutation. These results may explain why most genome-wide association studies have failed to find associations that explain much of the variance. It is also shown that most of the variance in fitness contributed by new nonsynonymous mutations is caused by mutations at very low frequency in the population. This implies that most low-frequency SNPs, which are observed in current resequencing studies of, for example, 100 chromosomes, probably have little impact on the variance in fitness or traits. Finally, it is shown that the variance contributed by a category of mutations (e.g., coding or regulatory) depends largely upon the mean strength of selection; this has implications for understanding which types of mutations are likely to be responsible for the variance in fitness and inherited disease.
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37
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Nackley AG, Diatchenko L. Assessing potential functionality of catechol-O-methyltransferase (COMT) polymorphisms associated with pain sensitivity and temporomandibular joint disorders. Methods Mol Biol 2010; 617:375-393. [PMID: 20336436 DOI: 10.1007/978-1-60327-323-7_28] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Catechol-O-methyltransferase (COMT) is an enzyme that plays a key role in the modulation of catechol-dependent functions such as cognition, cardiovascular function, and pain processing. Recently, our group demonstrated that three common haplotypes of the human COMT gene, divergent in two synonymous and one nonsynonymous position, are associated with experimental pain sensitivity and onset of temporomandibular joint disorder. In order to determine the functional mechanisms whereby these haplotypes contribute to pain processing, a series of in vitro experiments were performed. Haplotypes divergent in synonymous changes exhibited the largest difference in COMT enzymatic activity because of reduced amount of translated protein. The major COMT haplotypes varied significantly with respect to mRNA local stem-loop structures such that the most stable structure was associated with the lowest protein levels and enzymatic activity. Site-directed mutagenesis that eliminated the stable structure restored the amount of translated protein. These data provide the first demonstration that combinations of commonly observed alleles in the coding region of the human COMT gene can significantly affect the secondary structure of corresponding mRNA transcripts, which in turn leads to dramatic alterations in the translation efficiency of enzyme crucial for a variety of essential functions. The protocols applied to the study of these molecular genetic mechanisms are detailed herein.
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Affiliation(s)
- Andrea G Nackley
- Center for Neurosensory Disorders, University of North Carolina, Chapel Hill, NC, USA.
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38
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Stoltzfus A, Yampolsky LY. Climbing mount probable: mutation as a cause of nonrandomness in evolution. J Hered 2009; 100:637-47. [PMID: 19625453 DOI: 10.1093/jhered/esp048] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The classic view of evolution as "shifting gene frequencies" in the Modern Synthesis literally means that evolution is the modulation of existing variation ("standing variation"), as opposed to a "new mutations" view of evolution as a 2-step process of mutational origin followed by acceptance-or-rejection (via selection and drift). The latter view has received renewed attention, yet its implications for evolutionary causation still are not widely understood. We review theoretical results showing that this conception of evolution allows for a role of mutation as a cause of nonrandomness, a role that could be important but has been misconceived and associated misleadingly with neutral evolution. Specifically, biases in the introduction of variation, including mutational biases, may impose predictable biases on evolution, with no necessary dependence on neutrality. As an example of how important such effects may be, we present a new analysis partitioning the variance in mean rates of amino acid replacement during human-chimpanzee divergence to components of codon mutation and amino acid exchangeability. The results indicate that mutational effects are not merely important but account for most of the variance explained. The challenge that such results pose for comparative genomics is to address mutational effects as a necessary part of any analysis of causal factors. To meet this challenge requires developing knowledge of mutation as a biological process, understanding how mutation imposes propensities on evolution, and applying methods of analysis that incorporate mutational effects.
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Affiliation(s)
- Arlin Stoltzfus
- Center for Advanced Research in Biotechnology, Rockville, MD 20850, USA.
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39
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Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations. Genome Res 2009; 19:1562-9. [PMID: 19546171 DOI: 10.1101/gr.091991.109] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
As the cost of DNA sequencing drops, we are moving beyond one genome per species to one genome per individual to improve prevention, diagnosis, and treatment of disease by using personal genotypes. Computational methods are frequently applied to predict impairment of gene function by nonsynonymous mutations in individual genomes and single nucleotide polymorphisms (nSNPs) in populations. These computational tools are, however, known to fail 15%-40% of the time. We find that accurate discrimination between benign and deleterious mutations is strongly influenced by the long-term (among species) history of positions that harbor those mutations. Successful prediction of known disease-associated mutations (DAMs) is much higher for evolutionarily conserved positions and for original-mutant amino acid pairs that are rarely seen among species. Prediction accuracies for nSNPs show opposite patterns, forecasting impediments to building diagnostic tools aiming to simultaneously reduce both false-positive and false-negative errors. The relative allele frequencies of mutations diagnosed as benign and damaging are predicted by positional evolutionary rates. These allele frequencies are modulated by the relative preponderance of the mutant allele in the set of amino acids found at homologous sites in other species (evolutionarily permissible alleles [EPAs]). The nSNPs found in EPAs are biochemically less severe than those missing from EPAs across all allele frequency categories. Therefore, it is important to consider position evolutionary rates and EPAs when interpreting the consequences and population frequencies of human mutations. The impending sequencing of thousands of human and many more vertebrate genomes will lead to more accurate classifiers needed in real-world applications.
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40
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Measuring the rates of spontaneous mutation from deep and large-scale polymorphism data. Genetics 2009; 182:1219-32. [PMID: 19528323 DOI: 10.1534/genetics.109.105692] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The rates and patterns of spontaneous mutation are fundamental parameters of molecular evolution. Current methodology either tries to measure such rates and patterns directly in mutation-accumulation experiments or tries to infer them indirectly from levels of divergence or polymorphism. While experimental approaches are constrained by the low rate at which new mutations occur, indirect approaches suffer from their underlying assumption that mutations are effectively neutral. Here I present a maximum-likelihood approach to estimate mutation rates from large-scale polymorphism data. It is demonstrated that the method is not sensitive to demography and the distribution of selection coefficients among mutations when applied to mutations at sufficiently low population frequencies. With the many large-scale sequencing projects currently underway, for instance, the 1000 genomes project in humans, plenty of the required low-frequency polymorphism data will shortly become available. My method will allow for an accurate and unbiased inference of mutation rates and patterns from such data sets at high spatial resolution. I discuss how the assessment of several long-standing problems of evolutionary biology would benefit from the availability of accurate mutation rate estimates.
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41
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Detection of genetic association and a functional polymorphism of dynamin 1 gene with nicotine dependence in European and African Americans. Neuropsychopharmacology 2009; 34:1351-9. [PMID: 18987626 PMCID: PMC2656577 DOI: 10.1038/npp.2008.197] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Although it has been documented that dynamin 1 gene (DNM1) is significantly modulated by nicotine in animal models, its association with nicotine dependence (ND) in human population remained to be unexplored. To determine whether DNM1 is associated with ND, in this study, we genotyped seven single-nucleotide polymorphisms (SNPs) within this gene in 602 nuclear families of either African-American (AA) or European-American (EA) origin. Individual SNP-based association analysis revealed a significant association of SNP rs3003609 with smoking quantity (SQ; P=0.0031) and Heaviness of Smoking Index (HSI; P=0.0042) in the EA sample. Furthermore, our haplotype-based association analyses indicated that haplotypes T-G-T, formed by rs2502731-rs2229917-rs3003609 (at a frequency of 54%), G-T-A, formed by rs2229917-rs3003609-rs16930313 (at a frequency of 52%), and T-A-G, formed by rs3003609-rs16930313-rs7022174 (at a frequency of 52%) are significantly associated with SQ (Z=-2.44 to -2.92; P=0.015-0.0055) and HSI (Z=-2.52 to -2.67; P=0.012-0.0076) in the EA sample. In the AA sample, another haplotype, G-T-A, formed by rs7875406-rs2502731-rs2229917, at a frequency of 12% was significantly associated with SQ (Z=-2.58; P=0.0098). Finally, by using in vitro gene expression assays, we demonstrated that the T allele of rs3003609 in the exon 9 of DNM1 significantly decreases the expression of DNM1, by 27.1% at the mRNA and 22.0% at the protein level, suggesting that rs3003609 represents a functional polymorphism affecting DNM1 expression and may partly contributed to the observed association of the gene with ND in our samples. Taken together, our findings indicate that DNM1 is likely involved in the etiology of ND and represents a plausible candidate for further investigation in independent samples.
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42
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Abstract
Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or ‘forest’ of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
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43
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Power of deep, all-exon resequencing for discovery of human trait genes. Proc Natl Acad Sci U S A 2009; 106:3871-6. [PMID: 19202052 DOI: 10.1073/pnas.0812824106] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability to sequence cost-effectively all of the coding regions of a given individual genome is rapidly approaching, with the potential for whole-genome resequencing not far behind. Initiatives are currently underway to phenotype hundreds of thousands of individuals for major human traits. Here, we determine the power for de novo discovery of genes related to human traits by resequencing all human exons in a clinical population. We analyze the potential of the gene discovery strategy that combines multiple rare variants from the same gene and treats genes, rather than individual alleles, as the units for the association test. By using computer simulations based on deep resequencing data for the European population, we show that genes meaningfully affecting a human trait can be identified in an unbiased fashion, although large sample sizes would be required to achieve substantial power.
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Abstract
Human genes responsible for inherited diseases are important for the understanding of human disease. We investigated the degree of polymorphism and divergence in the human disease genes to elucidate the effect of natural selection on human disease genes. In particular, the effect of disease dominance was incorporated into the analysis. Both dominant disease genes (DDG) and recessive disease genes (RDG) had a higher mutation rate per site and encoded longer proteins than the nondisease genes, which exposed the disease genes to a faster flux of new mutations. Using an unbiased polymorphism dataset, we found that, proportionally, RDG harbor more nonsynonymous polymorphisms compared with DDG. We estimated the selection intensity on the disease genes using polymorphism and divergence data and determined whether the different patterns of polymorphism and divergence between DDG and RDG could be explained by the difference in only dominance. Even after the dominance effect was considered, the selection intensity on RDG was significantly different from DDG, suggesting that the deleterious effect of the dominant and recessive disease mutations are fundamentally different.
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45
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Borštnik B, Oblak B, Pumpernik D. The Evolutionary Constraints in Mutational Replacements. Evol Biol 2009. [DOI: 10.1007/978-3-642-00952-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Zhang L, Watson LT. Analysis of the fitness effect of compensatory mutations. HFSP JOURNAL 2008; 3:47-54. [PMID: 19649156 PMCID: PMC2689613 DOI: 10.2976/1.2990075] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Indexed: 11/19/2022]
Abstract
This paper extends previous work on the Darwinian evolutionary fitness effect of the fixation of deleterious mutations by incorporating compensatory mutations, which are mutations (deleterious by themselves) that ameliorate other deleterious mutations, thus reducing the genetic load of populations. Since having compensatory mutations essentially changes the distributional shapes of deleterious mutations, the effect of compensatory mutations is studied by comparing distributions of deleterious mutations without compensatory mutations to those with compensatory mutations. The effect of effective population size (N(e)), fitness distributional shape, and mutation rate on population fitness reduction is studied. Results indicate that, first, the smaller a population's N(e), the larger the effect of compensatory mutations on fitness recovery, and the compensatory effect increases sharply with decreasing N(e). Second, the larger the squared coefficient of variation in the fitness effect of deleterious mutations, the larger the effect of compensatory mutations. Third, for fixed N(e), the higher the rate of deleterious mutations, the more effective compensatory mutation is in fitness recovery, and this effect is more pronounced for smaller N(e).
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Affiliation(s)
- Liqing Zhang
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061
| | - Layne T. Watson
- Departments of Computer Science and Mathematics, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061
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Wright SI, Andolfatto P. The Impact of Natural Selection on the Genome: Emerging Patterns inDrosophilaandArabidopsis. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2008. [DOI: 10.1146/annurev.ecolsys.39.110707.173342] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Stephen I. Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St., Toronto, Ontario, M5S 3B2 Canada,
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544,
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Schmidt S, Gerasimova A, Kondrashov FA, Adzuhbei IA, Kondrashov AS, Sunyaev S. Hypermutable non-synonymous sites are under stronger negative selection. PLoS Genet 2008; 4:e1000281. [PMID: 19043566 PMCID: PMC2583910 DOI: 10.1371/journal.pgen.1000281] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2007] [Accepted: 10/27/2008] [Indexed: 12/04/2022] Open
Abstract
Mutation rate varies greatly between nucleotide sites of the human genome and depends both on the global genomic location and the local sequence context of a site. In particular, CpG context elevates the mutation rate by an order of magnitude. Mutations also vary widely in their effect on the molecular function, phenotype, and fitness. Independence of the probability of occurrence of a new mutation's effect has been a fundamental premise in genetics. However, highly mutable contexts may be preserved by negative selection at important sites but destroyed by mutation at sites under no selection. Thus, there may be a positive correlation between the rate of mutations at a nucleotide site and the magnitude of their effect on fitness. We studied the impact of CpG context on the rate of human–chimpanzee divergence and on intrahuman nucleotide diversity at non-synonymous coding sites. We compared nucleotides that occupy identical positions within codons of identical amino acids and only differ by being within versus outside CpG context. Nucleotides within CpG context are under a stronger negative selection, as revealed by their lower, proportionally to the mutation rate, rate of evolution and nucleotide diversity. In particular, the probability of fixation of a non-synonymous transition at a CpG site is two times lower than at a CpG site. Thus, sites with different mutation rates are not necessarily selectively equivalent. This suggests that the mutation rate may complement sequence conservation as a characteristic predictive of functional importance of nucleotide sites. Mutations occur in some sites in the genome more frequently than in others. Similarly, mutations in some sites have greater consequences than in others. The effect of mutations might not be independent of the frequency with which mutations occur. Indeed, sites where mutations happen frequently will be preserved if the effects of these mutations are severe or will otherwise be allowed to mutate if there are no consequences for the organism. We compared both human–chimpanzee differences and sequence variation among humans in protein coding genes. We found that highly mutable nucleotide sites, such as the dinucleotide CpG, are on average more important and more frequently preserved by natural selection. Using this information, together with other features such as sequence conservation, opens a new perspective to predict the effect of human mutations, including their potential involvement in diseases.
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Affiliation(s)
- Steffen Schmidt
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Anna Gerasimova
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Fyodor A. Kondrashov
- Section on Ecology, Behavior, and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Ivan A. Adzuhbei
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alexey S. Kondrashov
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail: (ASK); (SS)
| | - Shamil Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (ASK); (SS)
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49
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Divergence and Polymorphism Under the Nearly Neutral Theory of Molecular Evolution. J Mol Evol 2008; 67:418-26. [DOI: 10.1007/s00239-008-9146-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2008] [Revised: 05/26/2008] [Accepted: 07/14/2008] [Indexed: 11/26/2022]
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50
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Hughes AL. Near neutrality: leading edge of the neutral theory of molecular evolution. Ann N Y Acad Sci 2008; 1133:162-79. [PMID: 18559820 DOI: 10.1196/annals.1438.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The nearly neutral theory represents a development of Kimura's neutral theory of molecular evolution that makes testable predictions that go beyond a mere null model. Recent evidence has strongly supported several of these predictions, including the prediction that slightly deleterious variants will accumulate in a species that has undergone a severe bottleneck or in cases where recombination is reduced or absent. Because bottlenecks often occur in speciation and slightly deleterious mutations in coding regions will usually be nonsynonymous, we should expect that the ratio of nonsynonymous to synonymous fixed differences between species should often exceed the ratio of nonsynonymous to synonymous polymorphisms within species. Many data support this prediction, although they have often been wrongly interpreted as evidence for positive Darwinian selection. The use of conceptually flawed tests for positive selection has become widespread in recent years, seriously harming the quest for an understanding of genome evolution. When properly analyzed, many (probably most) claimed cases of positive selection will turn out to involve the fixation of slightly deleterious mutations by genetic drift in bottlenecked populations. Slightly deleterious variants are a transient feature of evolution in the long term, but they have substantially affected contemporary species, including our own.
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Affiliation(s)
- Austin L Hughes
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg., 700 Sumter St., Columbia, South Carolina 29208, USA.
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