51
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Cocker JM, Wright J, Li J, Swarbreck D, Dyer S, Caccamo M, Gilmartin PM. Primula vulgaris (primrose) genome assembly, annotation and gene expression, with comparative genomics on the heterostyly supergene. Sci Rep 2018; 8:17942. [PMID: 30560928 PMCID: PMC6299000 DOI: 10.1038/s41598-018-36304-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 11/14/2018] [Indexed: 11/24/2022] Open
Abstract
Primula vulgaris (primrose) exhibits heterostyly: plants produce self-incompatible pin- or thrum-form flowers, with anthers and stigma at reciprocal heights. Darwin concluded that this arrangement promotes insect-mediated cross-pollination; later studies revealed control by a cluster of genes, or supergene, known as the S (Style length) locus. The P. vulgaris S locus is absent from pin plants and hemizygous in thrum plants (thrum-specific); mutation of S locus genes produces self-fertile homostyle flowers with anthers and stigma at equal heights. Here, we present a 411 Mb P. vulgaris genome assembly of a homozygous inbred long homostyle, representing ~87% of the genome. We annotate over 24,000 P. vulgaris genes, and reveal more genes up-regulated in thrum than pin flowers. We show reduced genomic read coverage across the S locus in other Primula species, including P. veris, where we define the conserved structure and expression of the S locus genes in thrum. Further analysis reveals the S locus has elevated repeat content (64%) compared to the wider genome (37%). Our studies suggest conservation of S locus genetic architecture in Primula, and provide a platform for identification and evolutionary analysis of the S locus and downstream targets that regulate heterostyly in diverse heterostylous species.
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Affiliation(s)
- Jonathan M Cocker
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom.,Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom
| | - Jonathan Wright
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom
| | - Jinhong Li
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom.,Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom
| | - Sarah Dyer
- National Institute for Agricultural Botany, Huntingdon Road, Cambridge, CB3 0LE, United Kingdom
| | - Mario Caccamo
- National Institute for Agricultural Botany, Huntingdon Road, Cambridge, CB3 0LE, United Kingdom
| | - Philip M Gilmartin
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom. .,Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom.
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52
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Zhou L, Xiao Q, Bi J, Wang Z, Li Y. RabGTD: a comprehensive database of rabbit genome and transcriptome. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:5053987. [PMID: 30010730 PMCID: PMC6047408 DOI: 10.1093/database/bay075] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/22/2018] [Indexed: 12/28/2022]
Abstract
The rabbit is a very important species for both biomedical research and agriculture animal breeding. They are not only the most-used experimental animals for the production of antibodies, but also widely used for studying a variety of human diseases. Here we developed RabGTD, the first comprehensive rabbit database containing both genome and transcriptome data generated by next-generation sequencing. Genomic variations coming from 79 samples were identified and annotated, including 33 samples of wild rabbits and 46 samples of domestic rabbits with diverse populations. Gene expression profiles of 86 tissue samples were complied, including those from the most commonly used models for hyperlipidemia and atherosclerosis. RabGTD is a web-based and open-access resource, which also provides convenient functions and friendly interfaces of searching, browsing and downloading for users to explore the big data. Database URL: http://www.picb.ac.cn/RabGTD/
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Affiliation(s)
- Lu Zhou
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Xuhui District, Shanghai 200031, China.,University of Chinese Academy of Sciences, 52 Sanlihe Rd., Xicheng District, Beijing 100049, China
| | - Qingyu Xiao
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Xuhui District, Shanghai 200031, China.,University of Chinese Academy of Sciences, 52 Sanlihe Rd., Xicheng District, Beijing 100049, China
| | - Jie Bi
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Xuhui District, Shanghai 200031, China.,University of Chinese Academy of Sciences, 52 Sanlihe Rd., Xicheng District, Beijing 100049, China
| | - Zhen Wang
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Xuhui District, Shanghai 200031, China
| | - Yixue Li
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Xuhui District, Shanghai 200031, China.,Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, 1278 Keyuan Rd., Pudong District, Shanghai 201203, China.,Collaborative Innovation Center for Genetics and Development, Fudan University, 2005 Songhu Rd., Yangpu District, Shanghai 200433, China
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53
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Jordan KW, Wang S, He F, Chao S, Lun Y, Paux E, Sourdille P, Sherman J, Akhunova A, Blake NK, Pumphrey MO, Glover K, Dubcovsky J, Talbert L, Akhunov ED. The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:1039-1054. [PMID: 29952048 PMCID: PMC6174997 DOI: 10.1111/tpj.14009] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 05/21/2018] [Accepted: 06/06/2018] [Indexed: 05/18/2023]
Abstract
Recombination affects the fate of alleles in populations by imposing constraints on the reshuffling of genetic information. Understanding the genetic basis of these constraints is critical for manipulating the recombination process to improve the resolution of genetic mapping, and reducing the negative effects of linkage drag and deleterious genetic load in breeding. Using sequence-based genotyping of a wheat nested association mapping (NAM) population of 2,100 recombinant inbred lines created by crossing 29 diverse lines, we mapped QTL affecting the distribution and frequency of 102 000 crossovers (CO). Genome-wide recombination rate variation was mostly defined by rare alleles with small effects together explaining up to 48.6% of variation. Most QTL were additive and showed predominantly trans-acting effects. The QTL affecting the proximal COs also acted additively without increasing the frequency of distal COs. We showed that the regions with decreased recombination carry more single nucleotide polymorphisms (SNPs) with possible deleterious effects than the regions with a high recombination rate. Therefore, our study offers insights into the genetic basis of recombination rate variation in wheat and its effect on the distribution of deleterious SNPs across the genome. The identified trans-acting additive QTL can be utilized to manipulate CO frequency and distribution in the large polyploid wheat genome opening the possibility to improve the efficiency of gene pyramiding and reducing the deleterious genetic load in the low-recombining pericentromeric regions of chromosomes.
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Affiliation(s)
| | - Shichen Wang
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
- Present address:
TEES‐AgriLife Center for Bioinformatics and Genomic Systems EngineeringTexas A&M University101 Gateway, Suite ACollege StationTX77845USA
| | - Fei He
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Shiaoman Chao
- USDA‐ARS Cereal Crops Research Unit1605 Albrecht Blvd NFargoNDUSA
| | - Yanni Lun
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
- Present address:
TEES‐AgriLife Center for Bioinformatics and Genomic Systems EngineeringTexas A&M University101 Gateway, Suite ACollege StationTX77845USA
| | - Etienne Paux
- INRA GDEC Auvergne‐Rhône‐AlpesClermont‐FerrandFrance
| | | | | | - Alina Akhunova
- Integrated Genomics FacilityKansas State UniversityManhattanKSUSA
| | | | | | - Karl Glover
- Department of Agronomy, Horticulture and Plant ScienceSouth Dakota State UniversityBrookingsSDUSA
| | - Jorge Dubcovsky
- Department of Plant SciencesUniversity of CaliforniaDavis, DavisCAUSA
- Howard Hughes Medical InstituteChevy ChaseMD20815USA
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54
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Support for the Dominance Theory in Drosophila Transcriptomes. Genetics 2018; 210:703-718. [PMID: 30131345 PMCID: PMC6216581 DOI: 10.1534/genetics.118.301229] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/10/2018] [Indexed: 12/14/2022] Open
Abstract
Interactions among divergent elements of transcriptional networks from different species can lead to misexpression in hybrids through regulatory incompatibilities, some with the potential to generate sterility. While the possible contribution of faster-male evolution to this misexpression has been explored, the role of the hemizygous X chromosome (i.e., the dominance theory for transcriptomes) remains yet to be determined. Here, we study genome-wide patterns of gene expression in females and males of Drosophila yakuba, Drosophila santomea and their hybrids. We used attached-X stocks to specifically test the dominance theory, and we uncovered a significant contribution of recessive alleles on the X chromosome to hybrid misexpression. Our analyses also suggest a contribution of weakly deleterious regulatory mutations to gene expression divergence in genes with sex-biased expression, but only in the sex toward which the expression is biased (e.g., genes with female-biased expression when analyzed in females). In the opposite sex, we found stronger selective constraints on gene expression divergence. Although genes with a high degree of male-biased expression show a clear signal of faster-X evolution of gene expression, we also detected slower-X evolution in other gene classes (e.g., female-biased genes). This slower-X effect is mediated by significant decreases in cis- and trans-regulatory divergence. The distinct behavior of X-linked genes with a high degree of male-biased expression is consistent with these genes experiencing a higher incidence of positively selected regulatory mutations than their autosomal counterparts.
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55
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Ho EKH, Agrawal AF. Mutation accumulation in selfing populations under fluctuating selection. Evolution 2018; 72:1759-1772. [DOI: 10.1111/evo.13553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 06/26/2018] [Accepted: 07/01/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Eddie K. H. Ho
- Department of Ecology and Evolutionary Biology University of Toronto 25 Willcocks Street Toronto ON M5S 3B2 Canada
| | - Aneil F. Agrawal
- Department of Ecology and Evolutionary Biology University of Toronto 25 Willcocks Street Toronto ON M5S 3B2 Canada
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56
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Avia K, Lipinska AP, Mignerot L, Montecinos AE, Jamy M, Ahmed S, Valero M, Peters AF, Cock JM, Roze D, Coelho SM. Genetic Diversity in the UV Sex Chromosomes of the Brown Alga Ectocarpus. Genes (Basel) 2018; 9:E286. [PMID: 29882839 PMCID: PMC6027523 DOI: 10.3390/genes9060286] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 05/30/2018] [Accepted: 06/05/2018] [Indexed: 12/24/2022] Open
Abstract
Three types of sex chromosome system exist in nature: diploid XY and ZW systems and haploid UV systems. For many years, research has focused exclusively on XY and ZW systems, leaving UV chromosomes and haploid sex determination largely neglected. Here, we perform a detailed analysis of DNA sequence neutral diversity levels across the U and V sex chromosomes of the model brown alga Ectocarpus using a large population dataset. We show that the U and V non-recombining regions of the sex chromosomes (SDR) exhibit about half as much neutral diversity as the autosomes. This difference is consistent with the reduced effective population size of these regions compared with the rest of the genome, suggesting that the influence of additional factors such as background selection or selective sweeps is minimal. The pseudoautosomal region (PAR) of this UV system, in contrast, exhibited surprisingly high neutral diversity and there were several indications that genes in this region may be under balancing selection. The PAR of Ectocarpus is known to exhibit unusual genomic features and our results lay the foundation for further work aimed at understanding whether, and to what extent, these structural features underlie the high level of genetic diversity. Overall, this study fills a gap between available information on genetic diversity in XY/ZW systems and UV systems and significantly contributes to advancing our knowledge of the evolution of UV sex chromosomes.
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Affiliation(s)
- Komlan Avia
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, University of Paris VI, UC, UACH, UMI 3614, 29688 Roscoff, France.
| | - Agnieszka P Lipinska
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Laure Mignerot
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Alejandro E Montecinos
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, University of Paris VI, UC, UACH, UMI 3614, 29688 Roscoff, France.
- Facultad de Ciencias, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile.
| | - Mahwash Jamy
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Sophia Ahmed
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Myriam Valero
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, University of Paris VI, UC, UACH, UMI 3614, 29688 Roscoff, France.
| | | | - J Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Denis Roze
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, University of Paris VI, UC, UACH, UMI 3614, 29688 Roscoff, France.
| | - Susana M Coelho
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
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57
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Keller MC. Evolutionary Perspectives on Genetic and Environmental Risk Factors for Psychiatric Disorders. Annu Rev Clin Psychol 2018; 14:471-493. [DOI: 10.1146/annurev-clinpsy-050817-084854] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Matthew C. Keller
- Department of Psychology and Neuroscience and the Institute for Behavioral Genetics, University of Colorado at Boulder, Boulder, Colorado 80309, USA
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58
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Pardiñas AF, Holmans P, Pocklington AJ, Escott-Price V, Ripke S, Carrera N, Legge SE, Bishop S, Cameron D, Hamshere ML, Han J, Hubbard L, Lynham A, Mantripragada K, Rees E, MacCabe JH, McCarroll SA, Baune BT, Breen G, Byrne EM, Dannlowski U, Eley TC, Hayward C, Martin NG, McIntosh AM, Plomin R, Porteous DJ, Wray NR, Caballero A, Geschwind DH, Huckins LM, Ruderfer DM, Santiago E, Sklar P, Stahl EA, Won H, Agerbo E, Als TD, Andreassen OA, Bækvad-Hansen M, Mortensen PB, Pedersen CB, Børglum AD, Bybjerg-Grauholm J, Djurovic S, Durmishi N, Pedersen MG, Golimbet V, Grove J, Hougaard DM, Mattheisen M, Molden E, Mors O, Nordentoft M, Pejovic-Milovancevic M, Sigurdsson E, Silagadze T, Hansen CS, Stefansson K, Stefansson H, Steinberg S, Tosato S, Werge T, Collier DA, Rujescu D, Kirov G, Owen MJ, O'Donovan MC, Walters JTR. Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection. Nat Genet 2018; 50:381-389. [PMID: 29483656 PMCID: PMC5918692 DOI: 10.1038/s41588-018-0059-2] [Citation(s) in RCA: 983] [Impact Index Per Article: 163.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/07/2018] [Indexed: 12/13/2022]
Abstract
Schizophrenia is a debilitating psychiatric condition often associated with poor quality of life and decreased life expectancy. Lack of progress in improving treatment outcomes has been attributed to limited knowledge of the underlying biology, although large-scale genomic studies have begun to provide insights. We report a new genome-wide association study of schizophrenia (11,260 cases and 24,542 controls), and through meta-analysis with existing data we identify 50 novel associated loci and 145 loci in total. Through integrating genomic fine-mapping with brain expression and chromosome conformation data, we identify candidate causal genes within 33 loci. We also show for the first time that the common variant association signal is highly enriched among genes that are under strong selective pressures. These findings provide new insights into the biology and genetic architecture of schizophrenia, highlight the importance of mutation-intolerant genes and suggest a mechanism by which common risk variants persist in the population.
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Affiliation(s)
- Antonio F Pardiñas
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Andrew J Pocklington
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Valentina Escott-Price
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Stephan Ripke
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry and Psychotherapy, Charité, Campus Mitte, Berlin, Germany
| | - Noa Carrera
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Sophie E Legge
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Sophie Bishop
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Darren Cameron
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Marian L Hamshere
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Jun Han
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Leon Hubbard
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Amy Lynham
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Kiran Mantripragada
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Elliott Rees
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - James H MacCabe
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bernhard T Baune
- Discipline of Psychiatry, University of Adelaide, Adelaide, South Australia, Australia
| | - Gerome Breen
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR Biomedical Research Centre for Mental Health, Maudsley Hospital and Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Enda M Byrne
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Udo Dannlowski
- Department of Psychiatry and Psychotherapy, University of Münster, Münster, Germany
| | - Thalia C Eley
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Caroline Hayward
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Nicholas G Martin
- School of Psychology, University of Queensland, Brisbane, Queensland, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Robert Plomin
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - David J Porteous
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Naomi R Wray
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología. Facultad de Biología, Universidad de Vigo, Vigo, Spain
| | - Daniel H Geschwind
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Laura M Huckins
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Douglas M Ruderfer
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Enrique Santiago
- Departamento de Biología Funcional. Facultad de Biología, Universidad de Oviedo, Oviedo, Spain
| | - Pamela Sklar
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eli A Stahl
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hyejung Won
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Esben Agerbo
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Thomas D Als
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Ole A Andreassen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- NORMENT, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Marie Bækvad-Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Preben Bo Mortensen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Carsten Bøcker Pedersen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Anders D Børglum
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Jonas Bybjerg-Grauholm
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Srdjan Djurovic
- NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Naser Durmishi
- Department of Child and Adolescent Psychiatry, University Clinic of Psychiatry, Skopje, Macedonia
| | - Marianne Giørtz Pedersen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Vera Golimbet
- Department of Clinical Genetics, Mental Health Research Center, Moscow, Russia
| | - Jakob Grove
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - David M Hougaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Manuel Mattheisen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Espen Molden
- Center for Psychopharmacology, Diakonhjemmet Hospital, Oslo, Norway
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Merete Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Mental Health Services in the Capital Region of Denmark, Mental Health Center Copenhagen, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Teimuraz Silagadze
- Department of Psychiatry and Drug Addiction, Tbilisi State Medical University (TSMU), Tbilisi, Georgia
| | - Christine Søholm Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | | | | | | | - Sarah Tosato
- Section of Psychiatry, Department of Public Health and Community Medicine, University of Verona, Verona, Italy
| | - Thomas Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - David A Collier
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Discovery Neuroscience Research, Eli Lilly and Company, Lilly Research Laboratories, Windlesham, UK
| | - Dan Rujescu
- Department of Psychiatry, University of Halle, Halle, Germany
- Department of Psychiatry, University of Munich, Munich, Germany
| | - George Kirov
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.
| | - James T R Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.
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59
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Platt A, Weber CC, Liberles DA. Protein evolution depends on multiple distinct population size parameters. BMC Evol Biol 2018; 18:17. [PMID: 29422024 PMCID: PMC5806465 DOI: 10.1186/s12862-017-1085-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/20/2017] [Indexed: 01/08/2023] Open
Abstract
That population size affects the fate of new mutations arising in genomes, modulating both how frequently they arise and how efficiently natural selection is able to filter them, is well established. It is therefore clear that these distinct roles for population size that characterize different processes should affect the evolution of proteins and need to be carefully defined. Empirical evidence is consistent with a role for demography in influencing protein evolution, supporting the idea that functional constraints alone do not determine the composition of coding sequences. Given that the relationship between population size, mutant fitness and fixation probability has been well characterized, estimating fitness from observed substitutions is well within reach with well-formulated models. Molecular evolution research has, therefore, increasingly begun to leverage concepts from population genetics to quantify the selective effects associated with different classes of mutation. However, in order for this type of analysis to provide meaningful information about the intra- and inter-specific evolution of coding sequences, a clear definition of concepts of population size, what they influence, and how they are best parameterized is essential. Here, we present an overview of the many distinct concepts that “population size” and “effective population size” may refer to, what they represent for studying proteins, and how this knowledge can be harnessed to produce better specified models of protein evolution.
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Affiliation(s)
- Alexander Platt
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, 19121, USA
| | - Claudia C Weber
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, 19121, USA
| | - David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, 19121, USA.
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60
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Reddy S, Kimball RT, Pandey A, Hosner PA, Braun MJ, Hackett SJ, Han KL, Harshman J, Huddleston CJ, Kingston S, Marks BD, Miglia KJ, Moore WS, Sheldon FH, Witt CC, Yuri T, Braun EL. Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling. Syst Biol 2018; 66:857-879. [PMID: 28369655 DOI: 10.1093/sysbio/syx041] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 03/22/2017] [Indexed: 01/27/2023] Open
Abstract
Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life. However, it has become clear that analyses of these large genomic data sets can also result in conflicting estimates of phylogeny. Here, we use the early divergences in Neoaves, the largest clade of extant birds, as a "model system" to understand the basis for incongruence among phylogenomic trees. We were motivated by the observation that trees from two recent avian phylogenomic studies exhibit conflicts. Those studies used different strategies: 1) collecting many characters [$\sim$ 42 mega base pairs (Mbp) of sequence data] from 48 birds, sometimes including only one taxon for each major clade; and 2) collecting fewer characters ($\sim$ 0.4 Mbp) from 198 birds, selected to subdivide long branches. However, the studies also used different data types: the taxon-poor data matrix comprised 68% non-coding sequences whereas coding exons dominated the taxon-rich data matrix. This difference raises the question of whether the primary reason for incongruence is the number of sites, the number of taxa, or the data type. To test among these alternative hypotheses we assembled a novel, large-scale data matrix comprising 90% non-coding sequences from 235 bird species. Although increased taxon sampling appeared to have a positive impact on phylogenetic analyses the most important variable was data type. Indeed, by analyzing different subsets of the taxa in our data matrix we found that increased taxon sampling actually resulted in increased congruence with the tree from the previous taxon-poor study (which had a majority of non-coding data) instead of the taxon-rich study (which largely used coding data). We suggest that the observed differences in the estimates of topology for these studies reflect data-type effects due to violations of the models used in phylogenetic analyses, some of which may be difficult to detect. If incongruence among trees estimated using phylogenomic methods largely reflects problems with model fit developing more "biologically-realistic" models is likely to be critical for efforts to reconstruct the tree of life. [Birds; coding exons; GTR model; model fit; Neoaves; non-coding DNA; phylogenomics; taxon sampling.].
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Affiliation(s)
- Sushma Reddy
- Biology Department, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, USA
| | - Rebecca T Kimball
- Department of Biology, University of Florida, Gainesville, FL 32607, USA
| | - Akanksha Pandey
- Department of Biology, University of Florida, Gainesville, FL 32607, USA
| | - Peter A Hosner
- Department of Biology, University of Florida, Gainesville, FL 32607, USA.,Florida Museum of Natural History, University of Florida, Gainesville, FL 32607, USA
| | - Michael J Braun
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD 20742, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution-MRC 163, PO Box 37012, Washington, DC 20013-7012, USA
| | - Shannon J Hackett
- Zoology Department, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA
| | - Kin-Lan Han
- Department of Biology, University of Florida, Gainesville, FL 32607, USA
| | | | - Christopher J Huddleston
- Collections Program, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA
| | - Sarah Kingston
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD 20742, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution-MRC 163, PO Box 37012, Washington, DC 20013-7012, USA.,Bowdoin College, Department of Biology and Coastal Studies Center, 6500 College Station, Brunwick, ME 04011, USA
| | - Ben D Marks
- Zoology Department, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA
| | - Kathleen J Miglia
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA
| | - William S Moore
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA
| | - Frederick H Sheldon
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
| | - Christopher C Witt
- Department of Biology and Museum of Southwestern Biology, University 15 of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Tamaki Yuri
- Department of Biology, University of Florida, Gainesville, FL 32607, USA.,Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Avenue, Norman, OK 73072, USA
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL 32607, USA.,Genetics Institute, University of Florida, Gainesville, FL 32607, USA
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61
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Cavoto E, Neuenschwander S, Goudet J, Perrin N. Sex-antagonistic genes, XY recombination and feminized Y chromosomes. J Evol Biol 2018; 31:416-427. [DOI: 10.1111/jeb.13235] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 01/20/2023]
Affiliation(s)
- E. Cavoto
- Department of Ecology and Evolution; University of Lausanne; Lausanne Switzerland
| | - S. Neuenschwander
- Department of Ecology and Evolution; University of Lausanne; Lausanne Switzerland
- Vital-IT; Swiss Institute of Bioinformatics; Lausanne Switzerland
| | - J. Goudet
- Department of Ecology and Evolution; University of Lausanne; Lausanne Switzerland
- Swiss Institute of Bioinformatics; Lausanne Switzerland
| | - N. Perrin
- Department of Ecology and Evolution; University of Lausanne; Lausanne Switzerland
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62
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Beaudry FEG, Barrett SCH, Wright SI. Genomic Loss and Silencing on the Y Chromosomes of Rumex. Genome Biol Evol 2017; 9:3345-3355. [PMID: 29211839 PMCID: PMC5737746 DOI: 10.1093/gbe/evx254] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2017] [Indexed: 12/19/2022] Open
Abstract
Across many unrelated lineages of plants and animals, Y chromosomes show a recurrent pattern of gene degeneration and loss, but the relative importance of inefficient selection, adaptive gene silencing, and neutral genetic drift in causing degeneration remain poorly understood. Here, we use next-generation genome and transcriptome sequencing to investigate patterns of ongoing Y chromosome degeneration in two annual plant species of Rumex (Polygonaceae) differing in their degree of degeneration and sex chromosome heteromorphism. We find evidence for both gene loss as well as silencing in these young plant sex chromosomes. Our analyses revealed significantly more gene deletion relative to silencing in R. rothschildianus, which has had a larger nonrecombining region for a longer period than R. hastatulus, consistent with this system being at a more advanced stage of degeneration. Intra- and interspecific comparisons of genomic coverage and heterozygosity indicated that loss of expression precedes gene deletion, implying that the final stages of mutation accumulation and gene loss may often occur neutrally. We found no evidence for adaptive silencing of genes that have lost expression. Our results suggest that the initial spread of deleterious regulatory variants and/or epigenetic silencing may be an important driver of early degeneration of Y chromosomes.
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Affiliation(s)
- Felix E G Beaudry
- Department of Ecology & Evolutionary Biology, University of Toronto, Ontario, Canada
| | - Spencer C H Barrett
- Department of Ecology & Evolutionary Biology, University of Toronto, Ontario, Canada
| | - Stephen I Wright
- Department of Ecology & Evolutionary Biology, University of Toronto, Ontario, Canada
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63
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Jackson BC, Campos JL, Haddrill PR, Charlesworth B, Zeng K. Variation in the Intensity of Selection on Codon Bias over Time Causes Contrasting Patterns of Base Composition Evolution in Drosophila. Genome Biol Evol 2017; 9:102-123. [PMID: 28082609 PMCID: PMC5381600 DOI: 10.1093/gbe/evw291] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2016] [Indexed: 12/11/2022] Open
Abstract
Four-fold degenerate coding sites form a major component of the genome, and are often used to make inferences about selection and demography, so that understanding their evolution is important. Despite previous efforts, many questions regarding the causes of base composition changes at these sites in Drosophila remain unanswered. To shed further light on this issue, we obtained a new whole-genome polymorphism data set from D. simulans. We analyzed samples from the putatively ancestral range of D. simulans, as well as an existing polymorphism data set from an African population of D. melanogaster. By using D. yakuba as an outgroup, we found clear evidence for selection on 4-fold sites along both lineages over a substantial period, with the intensity of selection increasing with GC content. Based on an explicit model of base composition evolution, we suggest that the observed AT-biased substitution pattern in both lineages is probably due to an ancestral reduction in selection intensity, and is unlikely to be the result of an increase in mutational bias towards AT alone. By using two polymorphism-based methods for estimating selection coefficients over different timescales, we show that the selection intensity on codon usage has been rather stable in D. simulans in the recent past, but the long-term estimates in D. melanogaster are much higher than the short-term ones, indicating a continuing decline in selection intensity, to such an extent that the short-term estimates suggest that selection is only active in the most GC-rich parts of the genome. Finally, we provide evidence for complex evolutionary patterns in the putatively neutral short introns, which cannot be explained by the standard GC-biased gene conversion model. These results reveal a dynamic picture of base composition evolution.
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Affiliation(s)
- Benjamin C Jackson
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - José L Campos
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Penelope R Haddrill
- Centre for Forensic Science, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Brian Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Kai Zeng
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
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64
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Kamdem C, Fouet C, White BJ. Chromosome arm-specific patterns of polymorphism associated with chromosomal inversions in the major African malaria vector, Anopheles funestus. Mol Ecol 2017; 26:5552-5566. [PMID: 28833796 PMCID: PMC5927613 DOI: 10.1111/mec.14335] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 08/08/2017] [Accepted: 08/14/2017] [Indexed: 02/02/2023]
Abstract
Chromosomal inversions facilitate local adaptation of beneficial mutations and modulate genetic polymorphism, but the extent of their effects within the genome is still insufficiently understood. The genome of Anopheles funestus, a malaria mosquito endemic to sub-Saharan Africa, contains an impressive number of paracentric polymorphic inversions, which are unevenly distributed among chromosomes and provide an excellent framework for investigating the genomic impacts of chromosomal rearrangements. Here, we present results of a fine-scale analysis of genetic variation within the genome of two weakly differentiated populations of Anopheles funestus inhabiting contrasting moisture conditions in Cameroon. Using population genomic analyses, we found that genetic divergence between the two populations is centred on regions of the genome corresponding to three inversions, which are characterized by high values of FST , absolute sequence divergence and fixed differences. Importantly, in contrast to the 2L chromosome arm, which is collinear, nucleotide diversity is significantly reduced along the entire length of three autosome arms bearing multiple overlapping chromosomal rearrangements. These findings support the idea that interactions between reduced recombination and natural selection within inversions contribute to sculpt nucleotide polymorphism across chromosomes in An. funestus.
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Affiliation(s)
- Colince Kamdem
- Department of Entomology, University of California, Riverside, CA 92521
| | - Caroline Fouet
- Department of Entomology, University of California, Riverside, CA 92521
| | - Bradley J. White
- Department of Entomology, University of California, Riverside, CA 92521
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65
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Crowson D, Barrett SCH, Wright SI. Purifying and Positive Selection Influence Patterns of Gene Loss and Gene Expression in the Evolution of a Plant Sex Chromosome System. Mol Biol Evol 2017; 34:1140-1154. [PMID: 28158772 DOI: 10.1093/molbev/msx064] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Sex chromosomes are unique regions of the genome, with a host of properties that distinguish them from autosomes and from each other. Although there is extensive theory describing sex chromosome formation and subsequent degeneration of the Y chromosome, the relative importance of processes governing degeneration is poorly understood. In particular, it is not known whether degeneration occurs solely as a direct result of inefficient selection due to loss of recombination, or whether adaptive gene silencing on the Y chromosome results in most degeneration occurring neutrally. We used comparative transcriptome data from two related annual plants with highly heteromorphic sex chromosomes, Rumex rothschildianus and Rumex hastatulus, to investigate the patterns and processes underlying Y chromosome degeneration. The rate of degeneration varied greatly between the two species. In R. rothschildianus, we infer widespread gene loss, higher than previously reported for any plant. Gene loss was not random: genes with lower constraint and those not expressed during the haploid phase were more likely to be lost. There was indirect evidence of adaptive evolution on the Y chromosome from the over-expression of Y alleles in certain genes with sex-biased gene expression. There was no complete dosage compensation, but there was evidence for targeted dosage compensation occurring in more selectively constrained genes. Overall, our results are consistent with selective interference playing the dominant role in the degeneration of the Y chromosome, rather than adaptive gene silencing.
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Affiliation(s)
- Daisy Crowson
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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66
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Johri P, Krenek S, Marinov GK, Doak TG, Berendonk TU, Lynch M. Population Genomics of Paramecium Species. Mol Biol Evol 2017; 34:1194-1216. [PMID: 28204679 DOI: 10.1093/molbev/msx074] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Population-genomic analyses are essential to understanding factors shaping genomic variation and lineage-specific sequence constraints. The dearth of such analyses for unicellular eukaryotes prompted us to assess genomic variation in Paramecium, one of the most well-studied ciliate genera. The Paramecium aurelia complex consists of ∼15 morphologically indistinguishable species that diverged subsequent to two rounds of whole-genome duplications (WGDs, as long as 320 MYA) and possess extremely streamlined genomes. We examine patterns of both nuclear and mitochondrial polymorphism, by sequencing whole genomes of 10-13 worldwide isolates of each of three species belonging to the P. aurelia complex: P. tetraurelia, P. biaurelia, P. sexaurelia, as well as two outgroup species that do not share the WGDs: P. caudatum and P. multimicronucleatum. An apparent absence of global geographic population structure suggests continuous or recent dispersal of Paramecium over long distances. Intergenic regions are highly constrained relative to coding sequences, especially in P. caudatum and P. multimicronucleatum that have shorter intergenic distances. Sequence diversity and divergence are reduced up to ∼100-150 bp both upstream and downstream of genes, suggesting strong constraints imposed by the presence of densely packed regulatory modules. In addition, comparison of sequence variation at non-synonymous and synonymous sites suggests similar recent selective pressures on paralogs within and orthologs across the deeply diverging species. This study presents the first genome-wide population-genomic analysis in ciliates and provides a valuable resource for future studies in evolutionary and functional genetics in Paramecium.
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Affiliation(s)
- Parul Johri
- Department of Biology, Indiana University, Bloomington, IN
| | - Sascha Krenek
- Institute of Hydrobiology, Technische Universität Dresden, Dresden, Germany
| | | | - Thomas G Doak
- Department of Biology, Indiana University, Bloomington, IN.,National Center for Genome Analysis Support, Indiana University, Bloomington, IN
| | - Thomas U Berendonk
- Institute of Hydrobiology, Technische Universität Dresden, Dresden, Germany
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, IN
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67
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Pengelly RJ, Vergara-Lope A, Alyousfi D, Jabalameli MR, Collins A. Understanding the disease genome: gene essentiality and the interplay of selection, recombination and mutation. Brief Bioinform 2017; 20:267-273. [DOI: 10.1093/bib/bbx110] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Indexed: 12/24/2022] Open
Affiliation(s)
- Reuben J Pengelly
- Genetic Epidemiology and Genomic Informatics, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Alejandra Vergara-Lope
- Genetic Epidemiology and Genomic Informatics, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Dareen Alyousfi
- Genetic Epidemiology and Genomic Informatics, Faculty of Medicine, University of Southampton, Southampton, UK
| | - M Reza Jabalameli
- Genetic Epidemiology and Genomic Informatics, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Andrew Collins
- Genetic Epidemiology and Genomic Informatics, Faculty of Medicine, University of Southampton, Southampton, UK
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68
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Hill-Robertson Interference Reduces Genetic Diversity on a Young Plant Y-Chromosome. Genetics 2017; 207:685-695. [PMID: 28811388 DOI: 10.1534/genetics.117.300142] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 08/03/2017] [Indexed: 11/18/2022] Open
Abstract
X and Y chromosomes differ in effective population size (Ne ), rates of recombination, and exposure to natural selection, all of which can affect patterns of genetic diversity. On Y chromosomes with suppressed recombination, natural selection is expected to eliminate linked neutral variation, and lower the Ne of Y compared to X chromosomes or autosomes. However, female-biased sex ratios and high variance in male reproductive success can also reduce Y-linked Ne , making it difficult to infer the causes of low Y-diversity. Here, we investigate the factors affecting levels of polymorphism during sex chromosome evolution in the dioecious plant Rumexhastatulus (Polygonaceae). Strikingly, we find that neutral diversity for genes on the Y chromosome is, on average, 2.1% of the value for their X-linked homologs, corresponding to a chromosome-wide reduction of 93% compared to the standard neutral expectation. We demonstrate that the magnitude of this diversity loss is inconsistent with reduced male Ne caused by neutral processes. Instead, using forward simulations and estimates of the distribution of deleterious fitness effects, we show that Y chromosome diversity loss can be explained by purifying selection acting in aggregate over a large number of genetically linked sites. Simulations also suggest that our observed level of Y-diversity is consistent with the joint action of purifying and positive selection, but only for models in which there were fewer constrained sites than we empirically estimated. Given the relatively recent origin of R. hastatulus sex chromosomes, our results imply that Y-chromosome degeneration in the early stages may be largely driven by selective interference rather than by neutral genetic drift of silenced Y-linked genes.
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69
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Ravinet M, Faria R, Butlin RK, Galindo J, Bierne N, Rafajlović M, Noor MAF, Mehlig B, Westram AM. Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow. J Evol Biol 2017; 30:1450-1477. [DOI: 10.1111/jeb.13047] [Citation(s) in RCA: 306] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 12/14/2022]
Affiliation(s)
- M. Ravinet
- Centre for Ecological and Evolutionary Synthesis; University of Oslo; Oslo Norway
- National Institute of Genetics; Mishima Shizuoka Japan
| | - R. Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO, Laboratório Associado; Universidade do Porto; Vairão Portugal
- Department of Experimental and Health Sciences; IBE, Institute of Evolutionary Biology (CSIC-UPF); Pompeu Fabra University; Barcelona Spain
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
| | - R. K. Butlin
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
- Department of Marine Sciences; Centre for Marine Evolutionary Biology; University of Gothenburg; Gothenburg Sweden
| | - J. Galindo
- Department of Biochemistry, Genetics and Immunology; University of Vigo; Vigo Spain
| | - N. Bierne
- CNRS; Université Montpellier; ISEM; Station Marine Sète France
| | - M. Rafajlović
- Department of Physics; University of Gothenburg; Gothenburg Sweden
| | | | - B. Mehlig
- Department of Physics; University of Gothenburg; Gothenburg Sweden
| | - A. M. Westram
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
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70
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Lawson LP, Petren K. The adaptive genomic landscape of beak morphology in Darwin's finches. Mol Ecol 2017; 26:4978-4989. [DOI: 10.1111/mec.14166] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 04/26/2017] [Accepted: 04/27/2017] [Indexed: 01/02/2023]
Affiliation(s)
- Lucinda P. Lawson
- Department of Biological Sciences; University of Cincinnati; Cincinnati OH USA
| | - Kenneth Petren
- Department of Biological Sciences; University of Cincinnati; Cincinnati OH USA
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71
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Abstract
Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data.
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72
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Kokko H, Chaturvedi A, Croll D, Fischer MC, Guillaume F, Karrenberg S, Kerr B, Rolshausen G, Stapley J. Can Evolution Supply What Ecology Demands? Trends Ecol Evol 2017; 32:187-197. [DOI: 10.1016/j.tree.2016.12.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/09/2016] [Accepted: 12/13/2016] [Indexed: 11/26/2022]
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73
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Dukić M, Berner D, Roesti M, Haag CR, Ebert D. A high-density genetic map reveals variation in recombination rate across the genome of Daphnia magna. BMC Genet 2016; 17:137. [PMID: 27737627 PMCID: PMC5064971 DOI: 10.1186/s12863-016-0445-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 10/04/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recombination rate is an essential parameter for many genetic analyses. Recombination rates are highly variable across species, populations, individuals and different genomic regions. Due to the profound influence that recombination can have on intraspecific diversity and interspecific divergence, characterization of recombination rate variation emerges as a key resource for population genomic studies and emphasises the importance of high-density genetic maps as tools for studying genome biology. Here we present such a high-density genetic map for Daphnia magna, and analyse patterns of recombination rate across the genome. RESULTS A F2 intercross panel was genotyped by Restriction-site Associated DNA sequencing to construct the third-generation linkage map of D. magna. The resulting high-density map included 4037 markers covering 813 scaffolds and contigs that sum up to 77 % of the currently available genome draft sequence (v2.4) and 55 % of the estimated genome size (238 Mb). Total genetic length of the map presented here is 1614.5 cM and the genome-wide recombination rate is estimated to 6.78 cM/Mb. Merging genetic and physical information we consistently found that recombination rate estimates are high towards the peripheral parts of the chromosomes, while chromosome centres, harbouring centromeres in D. magna, show very low recombination rate estimates. CONCLUSIONS Due to its high-density, the third-generation linkage map for D. magna can be coupled with the draft genome assembly, providing an essential tool for genome investigation in this model organism. Thus, our linkage map can be used for the on-going improvements of the genome assembly, but more importantly, it has enabled us to characterize variation in recombination rate across the genome of D. magna for the first time. These new insights can provide a valuable assistance in future studies of the genome evolution, mapping of quantitative traits and population genetic studies.
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Affiliation(s)
- Marinela Dukić
- University of Basel, Zoological Institute, Vesalgasse 1, Basel, CH-4051, Switzerland.
| | - Daniel Berner
- University of Basel, Zoological Institute, Vesalgasse 1, Basel, CH-4051, Switzerland
| | - Marius Roesti
- University of Basel, Zoological Institute, Vesalgasse 1, Basel, CH-4051, Switzerland.,Biodiversity Research Centre and Zoology Department, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Christoph R Haag
- Centre d'Ecologie Fonctionnelle et Evolutive - CEFE UMR 5175, CNRS - Université de Montpellier - Université Paul-Valéry Montpellier - EPHE, campus CNRS, 1919, route de Mende, 34293, Montpellier Cedex 5, France.,Department of Biology, Ecology and Evolution, University of Fribourg, Chemin du Muśee 10, 1700, Fribourg, Switzerland
| | - Dieter Ebert
- University of Basel, Zoological Institute, Vesalgasse 1, Basel, CH-4051, Switzerland
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74
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Su J, Han B, Rao Y, Feng X, Su J. Functional characterizations and expression profiles of ADAR2 gene, responsible for RNA editing, in response to GCRV challenge in grass carp (Ctenopharyngodon idella). FISH & SHELLFISH IMMUNOLOGY 2016; 56:534-542. [PMID: 27514783 DOI: 10.1016/j.fsi.2016.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 07/21/2016] [Accepted: 08/07/2016] [Indexed: 06/06/2023]
Abstract
ADAR (adenosine deaminases acting on RNA)-mediated adenosine-to-inosine (A-to-I) editing to double-stranded RNA (dsRNA) is a critical arm of the antiviral response. The present study focused on the structural and functional characterizations of grass carp (Ctenopharyngodon idella) ADAR2 (CiADAR2) gene. The complete genomic sequence of CiADAR2 is 150,458 bp in length, containing 12 exons and 11 introns. The open reading frame (ORF) of 2100 bp encodes a polypeptide of 699 amino acids (aa) which contains three highly conservative domains - two N-terminal dsRNA binding domains (dsRBDs) and one C-terminal deaminase domain. The predicted crystal structure of CiADAR2 deaminase domain suggested a catalytic center form in the enzyme active site. CiADAR2 mRNA was ubiquitously expressed in the fifteen tested tissues, and was induced post GCRV challenge in spleen and head kidney and C. idella kidney (CIK) cells. The ex vivo expression of CiADAR2 protein was verified by the Flag (tag)-based western blot assay. Antiviral activity assay of CiADAR2 was manifested by the delayed appearance of cytopathic effect (CPE) and inhibition of GCRV yield at 48 h post infection. Furthermore, in CiADAR2 overexpression cells, mRNA expression levels of CiIFN1, CiTLR7 and CiTLR8 were facilitated at different time points after GCRV infection, comparing to those in control group. Taken together, it was indicated that ADAR2 was an antiviral cytokine against GCRV and anti-GCRV function mechanism might involve in the TLR7/8-regulated IFN-signaling. These findings suggested that CiADAR2 was a novel member engaging in antiviral innate immune defense in C. idella, which laid a foundation for the further mechanism research of ADAR2 in fishes.
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Affiliation(s)
- Juanjuan Su
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Baoquan Han
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Youliang Rao
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China
| | - Xiaoli Feng
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jianguo Su
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China.
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75
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Estimating the Effective Population Size from Temporal Allele Frequency Changes in Experimental Evolution. Genetics 2016; 204:723-735. [PMID: 27542959 PMCID: PMC5068858 DOI: 10.1534/genetics.116.191197] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 07/30/2016] [Indexed: 01/22/2023] Open
Abstract
The effective population size (Ne) is a major factor determining allele frequency changes in natural and experimental populations. Temporal methods provide a powerful and simple approach to estimate short-term Ne. They use allele frequency shifts between temporal samples to calculate the standardized variance, which is directly related to Ne. Here we focus on experimental evolution studies that often rely on repeated sequencing of samples in pools (Pool-seq). Pool-seq is cost-effective and often outperforms individual-based sequencing in estimating allele frequencies, but it is associated with atypical sampling properties: Additional to sampling individuals, sequencing DNA in pools leads to a second round of sampling, which increases the variance of allele frequency estimates. We propose a new estimator of Ne, which relies on allele frequency changes in temporal data and corrects for the variance in both sampling steps. In simulations, we obtain accurate Ne estimates, as long as the drift variance is not too small compared to the sampling and sequencing variance. In addition to genome-wide Ne estimates, we extend our method using a recursive partitioning approach to estimate Ne locally along the chromosome. Since the type I error is controlled, our method permits the identification of genomic regions that differ significantly in their Ne estimates. We present an application to Pool-seq data from experimental evolution with Drosophila and provide recommendations for whole-genome data. The estimator is computationally efficient and available as an R package at https://github.com/ThomasTaus/Nest.
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76
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An Evolving Genetic Architecture Interacts with Hill-Robertson Interference to Determine the Benefit of Sex. Genetics 2016; 203:923-36. [PMID: 27098911 DOI: 10.1534/genetics.116.186916] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 04/06/2016] [Indexed: 02/05/2023] Open
Abstract
Sex is ubiquitous in the natural world, but the nature of its benefits remains controversial. Previous studies have suggested that a major advantage of sex is its ability to eliminate interference between selection on linked mutations, a phenomenon known as Hill-Robertson interference. However, those studies may have missed both important advantages and important disadvantages of sexual reproduction because they did not allow the distributions of mutational effects and interactions (i.e., the genetic architecture) to evolve. Here we investigate how Hill-Robertson interference interacts with an evolving genetic architecture to affect the evolutionary origin and maintenance of sex by simulating evolution in populations of artificial gene networks. We observed a long-term advantage of sex-equilibrium mean fitness of sexual populations exceeded that of asexual populations-that did not depend on population size. We also observed a short-term advantage of sex-sexual modifier mutations readily invaded asexual populations-that increased with population size, as was observed in previous studies. We show that the long- and short-term advantages of sex were both determined by differences between sexual and asexual populations in the evolutionary dynamics of two properties of the genetic architecture: the deleterious mutation rate ([Formula: see text]) and recombination load ([Formula: see text]). These differences resulted from a combination of selection to minimize [Formula: see text] which is experienced only by sexuals, and Hill-Robertson interference experienced primarily by asexuals. In contrast to the previous studies, in which Hill-Robertson interference had only a direct impact on the fitness advantages of sex, the impact of Hill-Robertson interference in our simulations was mediated additionally by an indirect impact on the efficiency with which selection acted to reduce [Formula: see text].
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77
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Jo BS, Choi SS. Introns: The Functional Benefits of Introns in Genomes. Genomics Inform 2015; 13:112-8. [PMID: 26865841 PMCID: PMC4742320 DOI: 10.5808/gi.2015.13.4.112] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 12/14/2015] [Accepted: 12/21/2015] [Indexed: 01/12/2023] Open
Abstract
The intron has been a big biological mystery since it was first discovered in several aspects. First, all of the completely sequenced eukaryotes harbor introns in the genomic structure, whereas no prokaryotes identified so far carry introns. Second, the amount of total introns varies in different species. Third, the length and number of introns vary in different genes, even within the same species genome. Fourth, all introns are copied into RNAs by transcription and DNAs by replication processes, but intron sequences do not participate in protein-coding sequences. The existence of introns in the genome should be a burden to some cells, because cells have to consume a great deal of energy to copy and excise them exactly at the correct positions with the help of complicated spliceosomal machineries. The existence throughout the long evolutionary history is explained, only if selective advantages of carrying introns are assumed to be given to cells to overcome the negative effect of introns. In that regard, we summarize previous research about the functional roles or benefits of introns. Additionally, several other studies strongly suggesting that introns should not be junk will be introduced.
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Affiliation(s)
- Bong-Seok Jo
- Department of Medical Biotechnology, College of Biomedical Science, and Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon 24341, Korea
| | - Sun Shim Choi
- Department of Medical Biotechnology, College of Biomedical Science, and Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon 24341, Korea
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78
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Castellano D, Coronado-Zamora M, Campos JL, Barbadilla A, Eyre-Walker A. Adaptive Evolution Is Substantially Impeded by Hill-Robertson Interference in Drosophila. Mol Biol Evol 2015; 33:442-55. [PMID: 26494843 PMCID: PMC4794616 DOI: 10.1093/molbev/msv236] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Hill-Robertson interference (HRi) is expected to reduce the efficiency of natural selection when two or more linked selected sites do not segregate freely, but no attempt has been done so far to quantify the overall impact of HRi on the rate of adaptive evolution for any given genome. In this work, we estimate how much HRi impedes the rate of adaptive evolution in the coding genome of Drosophila melanogaster. We compiled a data set of 6,141 autosomal protein-coding genes from Drosophila, from which polymorphism levels in D. melanogaster and divergence out to D. yakuba were estimated. The rate of adaptive evolution was calculated using a derivative of the McDonald-Kreitman test that controls for slightly deleterious mutations. We find that the rate of adaptive amino acid substitution at a given position of the genome is positively correlated to both the rate of recombination and the mutation rate, and negatively correlated to the gene density of the region. These correlations are robust to controlling for each other, for synonymous codon bias and for gene functions related to immune response and testes. We show that HRi diminishes the rate of adaptive evolution by approximately 27%. Interestingly, genes with low mutation rates embedded in gene poor regions lose approximately 17% of their adaptive substitutions whereas genes with high mutation rates embedded in gene rich regions lose approximately 60%. We conclude that HRi hampers the rate of adaptive evolution in Drosophila and that the variation in recombination, mutation, and gene density along the genome affects the HRi effect.
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Affiliation(s)
- David Castellano
- Genomics, Bioinformatics and Evolution Group, Institut de Biotecnologia i de Biomedicina (IBB) and Department de Genètica i Microbiologia, Campus Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Marta Coronado-Zamora
- Genomics, Bioinformatics and Evolution Group, Institut de Biotecnologia i de Biomedicina (IBB) and Department de Genètica i Microbiologia, Campus Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Jose L Campos
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Antonio Barbadilla
- Genomics, Bioinformatics and Evolution Group, Institut de Biotecnologia i de Biomedicina (IBB) and Department de Genètica i Microbiologia, Campus Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Adam Eyre-Walker
- Centre for the Study of Evolution, School of Life Sciences, University of Sussex, Brighton, United Kingdom
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79
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Influences of dominance and evolution of sex in finite diploid populations. PLoS One 2015; 10:e0128459. [PMID: 26011082 PMCID: PMC4444274 DOI: 10.1371/journal.pone.0128459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 04/27/2015] [Indexed: 11/19/2022] Open
Abstract
Most eukaryotes reproduce sexually. Although the benefits of sex in diploids mainly stem from recombination and segregation, the relative effects of recombination and segregation are relatively less known. In this study, we adopt an infinite loci model to illustrate how dominance coefficient of mutations affects the above-mentioned genetic events. However, we assume mutational effects to be independent and also ignore the effects of epistasis within loci. Our simulations show that with different levels of dominance, segregation and recombination may play different roles. In particular, recombination more commonly has a major impact on the evolution of sex when deleterious mutations are partially recessive. In contrast, when deleterious mutations are dominant, segregation becomes more important than recombination, a finding that is consistent with previous studies stating that segregation, rather than recombination, is more likely to drive the evolution of sex. Moreover, beneficial mutations alone remarkably increases the effects of recombination. We also note that populations favor sexual reproduction when deleterious mutations become more dominant or beneficial mutations become more recessive. Overall, these results illustrate that the existence of dominance is an important mechanism that affects the evolution of sex.
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80
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Massey SE. Genetic code evolution reveals the neutral emergence of mutational robustness, and information as an evolutionary constraint. Life (Basel) 2015; 5:1301-32. [PMID: 25919033 PMCID: PMC4500140 DOI: 10.3390/life5021301] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/02/2015] [Accepted: 04/03/2015] [Indexed: 01/09/2023] Open
Abstract
The standard genetic code (SGC) is central to molecular biology and its origin and evolution is a fundamental problem in evolutionary biology, the elucidation of which promises to reveal much about the origins of life. In addition, we propose that study of its origin can also reveal some fundamental and generalizable insights into mechanisms of molecular evolution, utilizing concepts from complexity theory. The first is that beneficial traits may arise by non-adaptive processes, via a process of "neutral emergence". The structure of the SGC is optimized for the property of error minimization, which reduces the deleterious impact of point mutations. Via simulation, it can be shown that genetic codes with error minimization superior to the SGC can emerge in a neutral fashion simply by a process of genetic code expansion via tRNA and aminoacyl-tRNA synthetase duplication, whereby similar amino acids are added to codons related to that of the parent amino acid. This process of neutral emergence has implications beyond that of the genetic code, as it suggests that not all beneficial traits have arisen by the direct action of natural selection; we term these "pseudaptations", and discuss a range of potential examples. Secondly, consideration of genetic code deviations (codon reassignments) reveals that these are mostly associated with a reduction in proteome size. This code malleability implies the existence of a proteomic constraint on the genetic code, proportional to the size of the proteome (P), and that its reduction in size leads to an "unfreezing" of the codon - amino acid mapping that defines the genetic code, consistent with Crick's Frozen Accident theory. The concept of a proteomic constraint may be extended to propose a general informational constraint on genetic fidelity, which may be used to explain variously, differences in mutation rates in genomes with differing proteome sizes, differences in DNA repair capacity and genome GC content between organisms, a selective pressure in the evolution of sexual reproduction, and differences in translational fidelity. Lastly, the utility of the concept of an informational constraint to other diverse fields of research is explored.
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Affiliation(s)
- Steven E Massey
- Biology Department, PO Box 23360, University of Puerto Rico-Rio Piedras, San Juan, PR 00931, USA.
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81
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Gossmann TI, Santure AW, Sheldon BC, Slate J, Zeng K. Highly variable recombinational landscape modulates efficacy of natural selection in birds. Genome Biol Evol 2015; 6:2061-75. [PMID: 25062920 PMCID: PMC4231635 DOI: 10.1093/gbe/evu157] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Determining the rate of protein evolution and identifying the causes of its variation across the genome are powerful ways to understand forces that are important for genome evolution. By using a multitissue transcriptome data set from great tit (Parus major), we analyzed patterns of molecular evolution between two passerine birds, great tit and zebra finch (Taeniopygia guttata), using the chicken genome (Gallus gallus) as an outgroup. We investigated whether a special feature of avian genomes, the highly variable recombinational landscape, modulates the efficacy of natural selection through the effects of Hill-Robertson interference, which predicts that selection should be more effective in removing deleterious mutations and incorporating beneficial mutations in high-recombination regions than in low-recombination regions. In agreement with these predictions, genes located in low-recombination regions tend to have a high proportion of neutrally evolving sites and relaxed selective constraint on sites subject to purifying selection, whereas genes that show strong support for past episodes of positive selection appear disproportionally in high-recombination regions. There is also evidence that genes located in high-recombination regions tend to have higher gene expression specificity than those located in low-recombination regions. Furthermore, more compact genes (i.e., those with fewer/shorter introns or shorter proteins) evolve faster than less compact ones. In sum, our results demonstrate that transcriptome sequencing is a powerful method to answer fundamental questions about genome evolution in nonmodel organisms.
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Affiliation(s)
- Toni I Gossmann
- Department of Animal and Plant Sciences, University of Sheffield, United Kingdom
| | - Anna W Santure
- Department of Animal and Plant Sciences, University of Sheffield, United KingdomSchool of Biological Sciences, University of Auckland, New Zealand
| | - Ben C Sheldon
- Edward Grey Institute, Department of Zoology, University of Oxford, United Kingdom
| | - Jon Slate
- Department of Animal and Plant Sciences, University of Sheffield, United Kingdom
| | - Kai Zeng
- Department of Animal and Plant Sciences, University of Sheffield, United Kingdom
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82
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Complex trait architecture: the pleiotropic model revisited. Sci Rep 2015; 5:9351. [PMID: 25792462 PMCID: PMC4366851 DOI: 10.1038/srep09351] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 02/20/2015] [Indexed: 01/30/2023] Open
Abstract
There is currently much debate about how much the genetic heritability of complex traits is due to very rare alleles. This issue is important because it determines sampling strategies for genetic association studies. Several recent theoretical papers based on a pleiotropic model for trait evolution suggest that it is possible that a large proportion of the genetic variance could be explained by rare alleles. This model assumes that mutations with a large effect on fitness also tend to have large positive or negative effects on phenotypic traits. We show that conclusions based on standard diffusion results are generally applicable to simulations of whole genomes with overlapping generations in a finite population, although the variance contribution of rare alleles is somewhat smaller than theoretical predictions. We show that under many scenarios the pleiotropic model predicts trait distributions that are unrealistically leptokurtic. We argue that this imposes a limit on the relationship between fitness and trait effects.
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83
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Couce A, Tenaillon OA. The rule of declining adaptability in microbial evolution experiments. Front Genet 2015; 6:99. [PMID: 25815007 PMCID: PMC4356158 DOI: 10.3389/fgene.2015.00099] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 02/24/2015] [Indexed: 11/25/2022] Open
Abstract
One of the most recurrent observations after two decades of microbial evolution experiments regards the dynamics of fitness change. In a given environment, low-fitness genotypes are recurrently observed to adapt faster than their more fit counterparts. Since adaptation is the main macroscopic outcome of Darwinian evolution, studying its patterns of change could potentially provide insight into key issues of evolutionary theory, from fixation dynamics to the genetic architecture of organisms. Here, we re-analyze several published datasets from experimental evolution with microbes and show that, despite large differences in the origin of the data, a pattern of inverse dependence of adaptability with fitness clearly emerges. In quantitative terms, it is remarkable to observe little if any degree of idiosyncrasy across systems as diverse as virus, bacteria and yeast. The universality of this phenomenon suggests that its emergence might be understood from general principles, giving rise to the exciting prospect that evolution might be statistically predictable at the macroscopic level. We discuss these possibilities in the light of the various theories of adaptation that have been proposed and delineate future directions of research.
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84
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Hussin JG, Hodgkinson A, Idaghdour Y, Grenier JC, Goulet JP, Gbeha E, Hip-Ki E, Awadalla P. Recombination affects accumulation of damaging and disease-associated mutations in human populations. Nat Genet 2015; 47:400-4. [DOI: 10.1038/ng.3216] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 01/14/2015] [Indexed: 01/17/2023]
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85
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The evolution of selfing is accompanied by reduced efficacy of selection and purging of deleterious mutations. Genetics 2014; 199:817-29. [PMID: 25552275 DOI: 10.1534/genetics.114.172809] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The transition from outcrossing to selfing is predicted to reduce the genome-wide efficacy of selection because of the lower effective population size (Ne) that accompanies this change in mating system. However, strongly recessive deleterious mutations exposed in the homozygous backgrounds of selfers should be under strong purifying selection. Here, we examine estimates of the distribution of fitness effects (DFE) and changes in the magnitude of effective selection coefficients (Nes) acting on mutations during the transition from outcrossing to selfing. Using forward simulations, we investigated the ability of a DFE inference approach to detect the joint influence of mating system and the dominance of deleterious mutations on selection efficacy. We investigated predictions from our simulations in the annual plant Eichhornia paniculata, in which selfing has evolved from outcrossing on multiple occasions. We used range-wide sampling to generate population genomic datasets and identified nonsynonymous and synonymous polymorphisms segregating in outcrossing and selfing populations. We found that the transition to selfing was accompanied by a change in the DFE, with a larger fraction of effectively neutral sites (Nes < 1), a result consistent with the effects of reduced Ne in selfers. Moreover, an increased proportion of sites in selfers were under strong purifying selection (Nes > 100), and simulations suggest that this is due to the exposure of recessive deleterious mutations. We conclude that the transition to selfing has been accompanied by the genome-wide influences of reduced Ne and strong purifying selection against deleterious recessive mutations, an example of purging at the molecular level.
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86
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On the unfounded enthusiasm for soft selective sweeps. Nat Commun 2014; 5:5281. [DOI: 10.1038/ncomms6281] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 09/17/2014] [Indexed: 11/09/2022] Open
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87
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Jackson BC, Campos JL, Zeng K. The effects of purifying selection on patterns of genetic differentiation between Drosophila melanogaster populations. Heredity (Edinb) 2014; 114:163-74. [PMID: 25227256 PMCID: PMC4270736 DOI: 10.1038/hdy.2014.80] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 06/16/2014] [Accepted: 07/22/2014] [Indexed: 01/21/2023] Open
Abstract
Using the data provided by the Drosophila Population Genomics Project, we investigate factors that affect the genetic differentiation between Rwandan and French populations of D. melanogaster. By examining within-population polymorphisms, we show that sites in long introns (especially those >2000 bp) have significantly lower π (nucleotide diversity) and more low-frequency variants (as measured by Tajima's D, minor allele frequencies, and prevalence of variants that are private to one of the two populations) than short introns, suggesting a positive relationship between intron length and selective constraint. A similar analysis of protein-coding polymorphisms shows that 0-fold (degenerate) sites in more conserved genes are under stronger purifying selection than those in less conserved genes. There is limited evidence that selection on codon bias has an effect on differentiation (as measured by FST) at 4-fold (degenerate) sites, and 4-fold sites and sites in 8–30 bp of short introns ⩽65 bp have comparable FST values. Consistent with the expected effect of purifying selection, sites in long introns and 0-fold sites in conserved genes are less differentiated than those in short introns and less conserved genes, respectively. Genes in non-crossover regions (for example, the fourth chromosome) have very high FST values at both 0-fold and 4-fold degenerate sites, which is probably because of the large reduction in within-population diversity caused by tight linkage between many selected sites. Our analyses also reveal subtle statistical properties of FST, which arise when information from multiple single nucleotide polymorphisms is combined and can lead to the masking of important signals of selection.
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Affiliation(s)
- B C Jackson
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - J L Campos
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - K Zeng
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
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88
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Charlesworth B, Campos JL. The relations between recombination rate and patterns of molecular variation and evolution in Drosophila. Annu Rev Genet 2014; 48:383-403. [PMID: 25251853 DOI: 10.1146/annurev-genet-120213-092525] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetic recombination affects levels of variability and the efficacy of selection because natural selection acting at one site affects evolutionary processes at linked sites. The variation in local recombination rates across the Drosophila genome provides excellent material for testing hypotheses concerning the evolutionary consequences of recombination. The current state of knowledge from studies of Drosophila genomics and population genetics is reviewed here. Selection at linked sites has influenced the relations between recombination rates and patterns of molecular variation and evolution, such that higher rates of recombination are associated with both higher levels of variability and a greater efficacy of selection. It seems likely that background selection against deleterious mutations is a major factor contributing to these patterns in genome regions in which crossing over is rare or absent, whereas selective sweeps of positively selected mutations probably play an important role in regions with crossing over.
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Affiliation(s)
- Brian Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom; , ,
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Background selection as baseline for nucleotide variation across the Drosophila genome. PLoS Genet 2014; 10:e1004434. [PMID: 24968283 PMCID: PMC4072542 DOI: 10.1371/journal.pgen.1004434] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 04/28/2014] [Indexed: 11/21/2022] Open
Abstract
The constant removal of deleterious mutations by natural selection causes a reduction in neutral diversity and efficacy of selection at genetically linked sites (a process called Background Selection, BGS). Population genetic studies, however, often ignore BGS effects when investigating demographic events or the presence of other types of selection. To obtain a more realistic evolutionary expectation that incorporates the unavoidable consequences of deleterious mutations, we generated high-resolution landscapes of variation across the Drosophila melanogaster genome under a BGS scenario independent of polymorphism data. We find that BGS plays a significant role in shaping levels of variation across the entire genome, including long introns and intergenic regions distant from annotated genes. We also find that a very large percentage of the observed variation in diversity across autosomes can be explained by BGS alone, up to 70% across individual chromosome arms at 100-kb scale, thus indicating that BGS predictions can be used as baseline to infer additional types of selection and demographic events. This approach allows detecting several outlier regions with signal of recent adaptive events and selective sweeps. The use of a BGS baseline, however, is particularly appropriate to investigate the presence of balancing selection and our study exposes numerous genomic regions with the predicted signature of higher polymorphism than expected when a BGS context is taken into account. Importantly, we show that these conclusions are robust to the mutation and selection parameters of the BGS model. Finally, analyses of protein evolution together with previous comparisons of genetic maps between Drosophila species, suggest temporally variable recombination landscapes and, thus, local BGS effects that may differ between extant and past phases. Because genome-wide BGS and temporal changes in linkage effects can skew approaches to estimate demographic and selective events, future analyses should incorporate BGS predictions and capture local recombination variation across genomes and along lineages. The removal of deleterious mutations from natural populations has potential consequences on patterns of variation across genomes. Population genetic analyses, however, often assume that such effects are negligible across recombining regions of species like Drosophila. We use simple models of purifying selection and current knowledge of recombination rates and gene distribution across the genome to obtain a baseline of variation predicted by the constant input and removal of deleterious mutations. We find that purifying selection alone can explain a major fraction of the observed variance in nucleotide diversity across the genome. The use of a baseline of variation predicted by linkage to deleterious mutations as null expectation exposes genomic regions under other selective regimes, including more regions showing the signature of balancing selection than would be evident when using traditional approaches. Our study also indicates that most, if not all, nucleotides across the D. melanogaster genome are significantly influenced by the removal of deleterious mutations, even when located in the middle of highly recombining regions and distant from genes. Additionally, the study of rates of protein evolution confirms previous analyses suggesting that the recombination landscape across the genome has changed in the recent history of D. melanogaster. All these reported factors can skew current analyses designed to capture demographic events or estimate the strength and frequency of adaptive mutations, and illustrate the need for new and more realistic theoretical and modeling approaches to study naturally occurring genetic variation.
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90
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Evidence that natural selection on codon usage in Drosophila pseudoobscura varies across codons. G3-GENES GENOMES GENETICS 2014; 4:681-92. [PMID: 24531731 PMCID: PMC4059240 DOI: 10.1534/g3.114.010488] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Like other species of Drosophila, Drosophila pseudoobscura has a distinct bias toward the usage of C- and G-ending codons. Previous studies have indicated that this bias is due, at least in part, to natural selection. Codon bias clearly differs among amino acids (and other codon classes) in Drosophila, which may reflect differences in the intensity of selection on codon usage. Ongoing natural selection on synonymous codon usage should be reflected in the shapes of the site frequency spectra of derived states at polymorphic positions. Specifically, regardless of other demographic effects on the spectrum, it should be shifted toward higher values for changes from less-preferred to more-preferred codons, and toward lower values for the converse. If the intensity of natural selection is increased, shifts in the site frequency spectra should be more pronounced. A total of 33,729 synonymous polymorphic sites on Chromosome 2 in D. pseudoobscura were analyzed. Shifts in the site frequency spectra are consistent with differential intensity of natural selection on codon usage, with stronger shifts associated with higher codon bias. The shifts, in general, are greater for polymorphic synonymous sites than for polymorphic intron sites, also consistent with natural selection. However, unlike observations in D. melanogaster, codon bias is not reduced in areas of low recombination in D. pseudoobscura; the site frequency spectrum signal for selection on codon usage remains strong in these regions. However, diversity is reduced, as expected. It is possible that estimates of low recombination reflect a recent change in recombination rate.
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91
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Campos JL, Halligan DL, Haddrill PR, Charlesworth B. The relation between recombination rate and patterns of molecular evolution and variation in Drosophila melanogaster. Mol Biol Evol 2014; 31:1010-28. [PMID: 24489114 PMCID: PMC3969569 DOI: 10.1093/molbev/msu056] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Genetic recombination associated with sexual reproduction increases the efficiency of natural selection by reducing the strength of Hill–Robertson interference. Such interference can be caused either by selective sweeps of positively selected alleles or by background selection (BGS) against deleterious mutations. Its consequences can be studied by comparing patterns of molecular evolution and variation in genomic regions with different rates of crossing over. We carried out a comprehensive study of the benefits of recombination in Drosophila melanogaster, both by contrasting five independent genomic regions that lack crossing over with the rest of the genome and by comparing regions with different rates of crossing over, using data on DNA sequence polymorphisms from an African population that is geographically close to the putatively ancestral population for the species, and on sequence divergence from a related species. We observed reductions in sequence diversity in noncrossover (NC) regions that are inconsistent with the effects of hard selective sweeps in the absence of recombination. Overall, the observed patterns suggest that the recombination rate experienced by a gene is positively related to an increase in the efficiency of both positive and purifying selection. The results are consistent with a BGS model with interference among selected sites in NC regions, and joint effects of BGS, selective sweeps, and a past population expansion on variability in regions of the genome that experience crossing over. In such crossover regions, the X chromosome exhibits a higher rate of adaptive protein sequence evolution than the autosomes, implying a Faster-X effect.
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Affiliation(s)
- José L Campos
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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92
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Abstract
Self-fertilization is generally seen to be disadvantageous in the long term. It increases genetic drift, which subsequently reduces polymorphism and the efficiency of selection, which also challenges adaptation. However, high selfing rates can increase the fixation probability of recessive beneficial mutations, but existing theory has generally not accounted for the effect of linked sites. Here, we analyze a model for the fixation probability of deleterious mutants that hitchhike with selective sweeps in diploid, partially selfing populations. Approximate analytical solutions show that, conditional on the sweep not being lost by drift, higher inbreeding rates increase the fixation probability of the deleterious allele, due to the resulting reduction in polymorphism and effective recombination. When extending the analysis to consider a distribution of deleterious alleles, as well as the average fitness increase after a sweep, we find that beneficial alleles generally need to be more recessive than the previously assumed dominance threshold (h < 1/2) for selfing to be beneficial from one-locus theory. Our results highlight that recombination aiding the efficiency of selection on multiple loci amplifies the fitness benefits of outcrossing over selfing, compared to results obtained from one-locus theory. This effect additionally increases the parameter range under which obligate outcrossing is beneficial over partial selfing.
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93
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Zhao M, Du J, Lin F, Tong C, Yu J, Huang S, Wang X, Liu S, Ma J. Shifts in the evolutionary rate and intensity of purifying selection between two Brassica genomes revealed by analyses of orthologous transposons and relics of a whole genome triplication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:211-22. [PMID: 23869625 DOI: 10.1111/tpj.12291] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 06/28/2013] [Accepted: 07/04/2013] [Indexed: 05/23/2023]
Abstract
Recent sequencing of the Brassica rapa and Brassica oleracea genomes revealed extremely contrasting genomic features such as the abundance and distribution of transposable elements between the two genomes. However, whether and how these structural differentiations may have influenced the evolutionary rates of the two genomes since their split from a common ancestor are unknown. Here, we investigated and compared the rates of nucleotide substitution between two long terminal repeats (LTRs) of individual orthologous LTR-retrotransposons, the rates of synonymous and non-synonymous substitution among triplicated genes retained in both genomes from a shared whole genome triplication event, and the rates of genetic recombination estimated/deduced by the comparison of physical and genetic distances along chromosomes and ratios of solo LTRs to intact elements. Overall, LTR sequences and genic sequences showed more rapid nucleotide substitution in B. rapa than in B. oleracea. Synonymous substitution of triplicated genes retained from a shared whole genome triplication was detected at higher rates in B. rapa than in B. oleracea. Interestingly, non-synonymous substitution was observed at lower rates in the former than in the latter, indicating shifted densities of purifying selection between the two genomes. In addition to evolutionary asymmetry, orthologous genes differentially regulated and/or disrupted by transposable elements between the two genomes were also characterized. Our analyses suggest that local genomic and epigenomic features, such as recombination rates and chromatin dynamics reshaped by independent proliferation of transposable elements and elimination between the two genomes, are perhaps partially the causes and partially the outcomes of the observed inter-specific asymmetric evolution.
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Affiliation(s)
- Meixia Zhao
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China; Department of Agronomy, Purdue University, West Lafayette, 47907, IN, USA
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94
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Tucker AE, Ackerman MS, Eads BD, Xu S, Lynch M. Population-genomic insights into the evolutionary origin and fate of obligately asexual Daphnia pulex. Proc Natl Acad Sci U S A 2013; 110:15740-5. [PMID: 23959868 PMCID: PMC3785735 DOI: 10.1073/pnas.1313388110] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Despite much theoretical work, the molecular-genetic causes and evolutionary consequences of asexuality remain largely undetermined. Asexual animal species are rare, evolutionarily short-lived, and thought to suffer mutational meltdown as a result of lack of recombination. Whole-genome analysis of 11 sexual and 11 asexual genotypes of Daphnia pulex indicates that current asexual lineages are in fact very young, exhibit no signs of purifying selection against accumulating mutations, and have extremely high rates of gene conversion and deletion. The reconstruction of chromosomal haplotypes in regions containing SNP markers associated with asexuality (chromosomes VIII and IX) indicates that introgression from a sister species, Daphnia pulicaria, underlies the origin of the asexual phenotype. Silent-site divergence of the shared chromosomal haplotypes of asexuals indicates that the spread of asexuality is as recent as 1,250 y, although the origin of the meiosis-suppressing element or elements could be substantially older. In addition, using previous estimates of the gene conversion rate from Daphnia mutation accumulation lines, we are able to age each asexual lineage. Although asexual lineages originate from wide crosses that introduce elevated individual heterozygosities on clone foundation, they also appear to be constrained by the inbreeding-like effect of loss of heterozygosity that accrues as gene conversion and hemizygous deletion expose preexisting recessive deleterious alleles of asexuals, limiting their evolutionary longevity. Our study implies that the buildup of newly introduced deleterious mutations (i.e., Muller's ratchet) may not be the dominant force imperiling nonrecombining populations of D. pulex, as previously proposed.
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Affiliation(s)
| | | | - Brian D. Eads
- Department of Biology, Indiana University, Bloomington, IN 47405
| | - Sen Xu
- Department of Biology, Indiana University, Bloomington, IN 47405
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, IN 47405
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95
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Relative effects of segregation and recombination on the evolution of sex in finite diploid populations. Heredity (Edinb) 2013; 111:505-12. [PMID: 23900397 DOI: 10.1038/hdy.2013.72] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Revised: 05/19/2013] [Accepted: 06/18/2013] [Indexed: 11/08/2022] Open
Abstract
The mechanism of reproducing more viable offspring in response to selection is a major factor influencing the advantages of sex. In diploids, sexual reproduction combines genotype by recombination and segregation. Theoretical studies of sexual reproduction have investigated the advantage of recombination in haploids. However, the potential advantage of segregation in diploids is less studied. This study aimed to quantify the relative contribution of recombination and segregation to the evolution of sex in finite diploids by using multilocus simulations. The mean fitness of a sexually or asexually reproduced population was calculated to describe the long-term effects of sex. The evolutionary fate of a sex or recombination modifier was also monitored to investigate the short-term effects of sex. Two different scenarios of mutations were considered: (1) only deleterious mutations were present and (2) a combination of deleterious and beneficial mutations. Results showed that the combined effects of segregation and recombination strongly contributed to the evolution of sex in diploids. If deleterious mutations were only present, segregation efficiently slowed down the speed of Muller's ratchet. As the recombination level was increased, the accumulation of deleterious mutations was totally inhibited and recombination substantially contributed to the evolution of sex. The presence of beneficial mutations evidently increased the fixation rate of a recombination modifier. We also observed that the twofold cost of sex was easily to overcome in diploids if a sex modifier caused a moderate frequency of sex.
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96
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Purifying selection causes widespread distortions of genealogical structure on the human X chromosome. Genetics 2013; 194:485-92. [PMID: 23589459 DOI: 10.1534/genetics.113.152074] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The extent to which selective forces shape patterns of genetic and genealogical variation is unknown in many species. Recent theoretical models have suggested that even relatively weak purifying selection may produce significant distortions in gene genealogies, but few studies have sought to quantify this effect in humans. Here, we employ a reconstruction method based on the ancestral recombination graph to infer genealogies across the length of the human X chromosome and to examine time to most recent common ancestor (TMRCA) and measures of tree imbalance at both broad and very fine scales. In agreement with theory, TMRCA is significantly reduced and genealogies are significantly more imbalanced in coding regions and introns when compared to intergenic regions, and these effects are increased in areas of greater evolutionary constraint. These distortions are present at multiple scales, and chromosomal regions as broad as 5 Mb show a significant negative correlation in TMRCA with exon density. We also show that areas of recent TMRCA are significantly associated with the disease-causing potential of site as measured by the MutationTaster prediction algorithm. Together, these findings suggest that purifying selection has significantly distorted human genealogical structure on both broad and fine scales and that few chromosomal regions escape selection-induced distortions.
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97
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Genomic signatures of selection at linked sites: unifying the disparity among species. Nat Rev Genet 2013; 14:262-74. [PMID: 23478346 DOI: 10.1038/nrg3425] [Citation(s) in RCA: 315] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Population genetics theory supplies powerful predictions about how natural selection interacts with genetic linkage to sculpt the genomic landscape of nucleotide polymorphism. Both the spread of beneficial mutations and the removal of deleterious mutations act to depress polymorphism levels, especially in low-recombination regions. However, empiricists have documented extreme disparities among species. Here we characterize the dominant features that could drive differences in linked selection among species--including roles for selective sweeps being 'hard' or 'soft'--and the concealing effects of demography and confounding genomic variables. We advocate targeted studies of closely related species to unify our understanding of how selection and linkage interact to shape genome evolution.
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98
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Choi SS, Hannenhalli S. Three independent determinants of protein evolutionary rate. J Mol Evol 2013; 76:98-111. [PMID: 23400388 DOI: 10.1007/s00239-013-9543-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 01/16/2013] [Indexed: 12/15/2022]
Abstract
One of the most widely accepted ideas related to the evolutionary rates of proteins is that functionally important residues or regions evolve slower than other regions, a reasonable outcome of which should be a slower evolutionary rate of the proteins with a higher density of functionally important sites. Oddly, the role of functional importance, mainly measured by essentiality, in determining evolutionary rate has been challenged in recent studies. Several variables other than protein essentiality, such as expression level, gene compactness, protein-protein interactions, etc., have been suggested to affect protein evolutionary rate. In the present review, we try to refine the concept of functional importance of a gene, and consider three factors-functional importance, expression level, and gene compactness, as independent determinants of evolutionary rate of a protein, based not only on their known correlation with evolutionary rate but also on a reasonable mechanistic model. We suggest a framework based on these mechanistic models to correctly interpret the correlations between evolutionary rates and the various variables as well as the interrelationships among the variables.
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Affiliation(s)
- Sun Shim Choi
- Department of Medical Biotechnology, College of Biomedical Science, and Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon, South Korea.
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99
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100
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Irisarri I, San Mauro D, Abascal F, Ohler A, Vences M, Zardoya R. The origin of modern frogs (Neobatrachia) was accompanied by acceleration in mitochondrial and nuclear substitution rates. BMC Genomics 2012; 13:626. [PMID: 23153022 PMCID: PMC3551647 DOI: 10.1186/1471-2164-13-626] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 11/04/2012] [Indexed: 01/20/2023] Open
Abstract
Background Understanding the causes underlying heterogeneity of molecular evolutionary rates among lineages is a long-standing and central question in evolutionary biology. Although several earlier studies showed that modern frogs (Neobatrachia) experienced an acceleration of mitochondrial gene substitution rates compared to non-neobatrachian relatives, no further characterization of this phenomenon was attempted. To gain new insights on this topic, we sequenced the complete mitochondrial genomes and nine nuclear loci of one pelobatoid (Pelodytes punctatus) and five neobatrachians, Heleophryne regis (Heleophrynidae), Lechriodus melanopyga (Limnodynastidae), Calyptocephalella gayi (Calyptocephalellidae), Telmatobius bolivianus (Ceratophryidae), and Sooglossus thomasseti (Sooglossidae). These represent major clades not included in previous mitogenomic analyses, and most of them are remarkably species-poor compared to other neobatrachians. Results We reconstructed a fully resolved and robust phylogeny of extant frogs based on the new mitochondrial and nuclear sequence data, and dated major cladogenetic events. The reconstructed tree recovered Heleophryne as sister group to all other neobatrachians, the Australasian Lechriodus and the South American Calyptocephalella formed a clade that was the sister group to Nobleobatrachia, and the Seychellois Sooglossus was recovered as the sister group of Ranoides. We used relative-rate tests and direct comparison of branch lengths from mitochondrial and nuclear-based trees to demonstrate that both mitochondrial and nuclear evolutionary rates are significantly higher in all neobatrachians compared to their non-neobatrachian relatives, and that such rate acceleration started at the origin of Neobatrachia. Conclusions Through the analysis of the selection coefficient (ω) in different branches of the tree, we found compelling evidence of relaxation of purifying selection in neobatrachians, which could (at least in part) explain the observed higher mitochondrial and nuclear substitution rates in this clade. Our analyses allowed us to discard that changes in substitution rates could be correlated with increased mitochondrial genome rearrangement or diversification rates observed in different lineages of neobatrachians.
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Affiliation(s)
- Iker Irisarri
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain
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