51
|
Lisachov AP, Trifonov VA, Giovannotti M, Ferguson-Smith MA, Borodin PM. Immunocytological analysis of meiotic recombination in two anole lizards (Squamata, Dactyloidae). COMPARATIVE CYTOGENETICS 2017; 11:129-141. [PMID: 28919954 PMCID: PMC5599703 DOI: 10.3897/compcytogen.v11i1.10916] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/16/2017] [Indexed: 05/13/2023]
Abstract
Although the evolutionary importance of meiotic recombination is not disputed, the significance of interspecies differences in the recombination rates and recombination landscapes remains under-appreciated. Recombination rates and distribution of chiasmata have been examined cytologically in many mammalian species, whereas data on other vertebrates are scarce. Immunolocalization of the protein of the synaptonemal complex (SYCP3), centromere proteins and the mismatch-repair protein MLH1 was used, which is associated with the most common type of recombination nodules, to analyze the pattern of meiotic recombination in the male of two species of iguanian lizards, Anolis carolinensis Voigt, 1832 and Deiroptyx coelestinus (Cope, 1862). These species are separated by a relatively long evolutionary history although they retain the ancestral iguanian karyotype. In both species similar and extremely uneven distributions of MLH1 foci along the macrochromosome bivalents were detected: approximately 90% of crossovers were located at the distal 20% of the chromosome arm length. Almost total suppression of recombination in the intermediate and proximal regions of the chromosome arms contradicts the hypothesis that "homogenous recombination" is responsible for the low variation in GC content across the anole genome. It also leads to strong linkage disequilibrium between the genes located in these regions, which may benefit conservation of co-adaptive gene arrays responsible for the ecological adaptations of the anoles.
Collapse
Affiliation(s)
- Artem P. Lisachov
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, Russia
| | - Vladimir A. Trifonov
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Massimo Giovannotti
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | | |
Collapse
|
52
|
Higher rates of sex evolve during adaptation to more complex environments. Proc Natl Acad Sci U S A 2017; 114:534-539. [PMID: 28053226 DOI: 10.1073/pnas.1604072114] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A leading hypothesis for the evolutionary maintenance of sexual reproduction proposes that sex is advantageous because it facilitates adaptation. Changes in the environment stimulate adaptation but not all changes are equivalent; a change may occur along one or multiple environmental dimensions. In two evolution experiments with the facultatively sexual rotifer Brachionus calyciflorus, we test how environmental complexity affects the evolution of sex by adapting replicate populations to various environments that differ from the original along one, two, or three environmental dimensions. Three different estimates of fitness (growth, lifetime reproduction, and population density) confirmed that populations adapted to their new environment. Growth measures revealed an intriguing cost of complex adaptations: populations that adapted to more complex environments lost greater amounts of fitness in the original environment. Furthermore, both experiments showed that B. calyciflorus became more sexual when adapting to a greater number of environmental dimensions. Common garden experiments confirmed that observed changes in sex were heritable. As environments in nature are inherently complex these findings help explain why sex is maintained in natural populations.
Collapse
|
53
|
Abascal F, Corvelo A, Cruz F, Villanueva-Cañas JL, Vlasova A, Marcet-Houben M, Martínez-Cruz B, Cheng JY, Prieto P, Quesada V, Quilez J, Li G, García F, Rubio-Camarillo M, Frias L, Ribeca P, Capella-Gutiérrez S, Rodríguez JM, Câmara F, Lowy E, Cozzuto L, Erb I, Tress ML, Rodriguez-Ales JL, Ruiz-Orera J, Reverter F, Casas-Marce M, Soriano L, Arango JR, Derdak S, Galán B, Blanc J, Gut M, Lorente-Galdos B, Andrés-Nieto M, López-Otín C, Valencia A, Gut I, García JL, Guigó R, Murphy WJ, Ruiz-Herrera A, Marques-Bonet T, Roma G, Notredame C, Mailund T, Albà MM, Gabaldón T, Alioto T, Godoy JA. Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx. Genome Biol 2016; 17:251. [PMID: 27964752 PMCID: PMC5155386 DOI: 10.1186/s13059-016-1090-1] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 10/25/2016] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and a unique example of a species on the brink of extinction. RESULTS We generate the first annotated draft of the Iberian lynx genome and carry out genome-based analyses of lynx demography, evolution, and population genetics. We identify a series of severe population bottlenecks in the history of the Iberian lynx that predate its known demographic decline during the 20th century and have greatly impacted its genome evolution. We observe drastically reduced rates of weak-to-strong substitutions associated with GC-biased gene conversion and increased rates of fixation of transposable elements. We also find multiple signatures of genetic erosion in the two remnant Iberian lynx populations, including a high frequency of potentially deleterious variants and substitutions, as well as the lowest genome-wide genetic diversity reported so far in any species. CONCLUSIONS The genomic features observed in the Iberian lynx genome may hamper short- and long-term viability through reduced fitness and adaptive potential. The knowledge and resources developed in this study will boost the research on felid evolution and conservation genomics and will benefit the ongoing conservation and management of this emblematic species.
Collapse
Affiliation(s)
- Federico Abascal
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - André Corvelo
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Fernando Cruz
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
- Department of Integrative Ecology, Doñana Biological Station (EBD), Spanish National Research Council (CSIC), C/ Americo Vespucio, s/n, 41092, Sevilla, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - José L Villanueva-Cañas
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Anna Vlasova
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Marina Marcet-Houben
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Begoña Martínez-Cruz
- Department of Integrative Ecology, Doñana Biological Station (EBD), Spanish National Research Council (CSIC), C/ Americo Vespucio, s/n, 41092, Sevilla, Spain
| | - Jade Yu Cheng
- Bioinformatics Research Centre, Aarhus University, C.F. Møllers Allé 8, 8000, Aarhus, Denmark
| | - Pablo Prieto
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Víctor Quesada
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006, Oviedo, Spain
| | - Javier Quilez
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, 08003, Barcelona, Spain
| | - Gang Li
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Francisca García
- Servei de Cultius Cel.lulars (SCC, SCAC), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Miriam Rubio-Camarillo
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Leonor Frias
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Paolo Ribeca
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Salvador Capella-Gutiérrez
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - José M Rodríguez
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
- National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Francisco Câmara
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Ernesto Lowy
- Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Luca Cozzuto
- Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Ionas Erb
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Michael L Tress
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Jose L Rodriguez-Ales
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Jorge Ruiz-Orera
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Ferran Reverter
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Mireia Casas-Marce
- Department of Integrative Ecology, Doñana Biological Station (EBD), Spanish National Research Council (CSIC), C/ Americo Vespucio, s/n, 41092, Sevilla, Spain
| | - Laura Soriano
- Department of Integrative Ecology, Doñana Biological Station (EBD), Spanish National Research Council (CSIC), C/ Americo Vespucio, s/n, 41092, Sevilla, Spain
| | - Javier R Arango
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006, Oviedo, Spain
| | - Sophia Derdak
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Beatriz Galán
- Department of Environmental Biology, Center for Biological Research (CIB), Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Belen Lorente-Galdos
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, 08003, Barcelona, Spain
| | - Marta Andrés-Nieto
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006, Oviedo, Spain
| | - Alfonso Valencia
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
- National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - José L García
- Department of Environmental Biology, Center for Biological Research (CIB), Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Roderic Guigó
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Computational Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Aurora Ruiz-Herrera
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain
- Departament de Biologia Cel.lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain
| | - Tomas Marques-Bonet
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, 08003, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Guglielmo Roma
- Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Cedric Notredame
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Thomas Mailund
- Bioinformatics Research Centre, Aarhus University, C.F. Møllers Allé 8, 8000, Aarhus, Denmark
| | - M Mar Albà
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Tyler Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - José A Godoy
- Department of Integrative Ecology, Doñana Biological Station (EBD), Spanish National Research Council (CSIC), C/ Americo Vespucio, s/n, 41092, Sevilla, Spain.
| |
Collapse
|
54
|
Koch H, Becks L. The consequences of facultative sex in a prey adapting to predation. J Evol Biol 2016; 30:210-220. [DOI: 10.1111/jeb.12987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 09/28/2016] [Accepted: 09/29/2016] [Indexed: 10/20/2022]
Affiliation(s)
- H. Koch
- Community Dynamics Group; Department Evolutionary Ecology; Max Planck Institute for Evolutionary Biology; Plön Germany
| | - L. Becks
- Community Dynamics Group; Department Evolutionary Ecology; Max Planck Institute for Evolutionary Biology; Plön Germany
| |
Collapse
|
55
|
The Nonstationary Dynamics of Fitness Distributions: Asexual Model with Epistasis and Standing Variation. Genetics 2016; 204:1541-1558. [PMID: 27770037 DOI: 10.1534/genetics.116.187385] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 10/10/2016] [Indexed: 11/18/2022] Open
Abstract
Various models describe asexual evolution by mutation, selection, and drift. Some focus directly on fitness, typically modeling drift but ignoring or simplifying both epistasis and the distribution of mutation effects (traveling wave models). Others follow the dynamics of quantitative traits determining fitness (Fisher's geometric model), imposing a complex but fixed form of mutation effects and epistasis, and often ignoring drift. In all cases, predictions are typically obtained in high or low mutation rate limits and for long-term stationary regimes, thus losing information on transient behaviors and the effect of initial conditions. Here, we connect fitness-based and trait-based models into a single framework, and seek explicit solutions even away from stationarity. The expected fitness distribution is followed over time via its cumulant generating function, using a deterministic approximation that neglects drift. In several cases, explicit trajectories for the full fitness distribution are obtained for arbitrary mutation rates and standing variance. For nonepistatic mutations, especially with beneficial mutations, this approximation fails over the long term but captures the early dynamics, thus complementing stationary stochastic predictions. The approximation also handles several diminishing returns epistasis models (e.g., with an optimal genotype); it can be applied at and away from equilibrium. General results arise at equilibrium, where fitness distributions display a "phase transition" with mutation rate. Beyond this phase transition, in Fisher's geometric model, the full trajectory of fitness and trait distributions takes a simple form; robust to the details of the mutant phenotype distribution. Analytical arguments are explored regarding why and when the deterministic approximation applies.
Collapse
|
56
|
Genomics of Natural Populations: How Differentially Expressed Genes Shape the Evolution of Chromosomal Inversions in Drosophila pseudoobscura. Genetics 2016; 204:287-301. [PMID: 27401754 PMCID: PMC5012393 DOI: 10.1534/genetics.116.191429] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/05/2016] [Indexed: 01/13/2023] Open
Abstract
Chromosomal rearrangements can shape the structure of genetic variation in the genome directly through alteration of genes at breakpoints or indirectly by holding combinations of genetic variants together due to reduced recombination. The third chromosome of Drosophila pseudoobscura is a model system to test hypotheses about how rearrangements are established in populations because its third chromosome is polymorphic for >30 gene arrangements that were generated by a series of overlapping inversion mutations. Circumstantial evidence has suggested that these gene arrangements are selected. Despite the expected homogenizing effects of extensive gene flow, the frequencies of arrangements form gradients or clines in nature, which have been stable since the system was first described >80 years ago. Furthermore, multiple arrangements exist at appreciable frequencies across several ecological niches providing the opportunity for heterokaryotypes to form. In this study, we tested whether genes are differentially expressed among chromosome arrangements in first instar larvae, adult females and males. In addition, we asked whether transcriptional patterns in heterokaryotypes are dominant, semidominant, overdominant, or underdominant. We find evidence for a significant abundance of differentially expressed genes across the inverted regions of the third chromosome, including an enrichment of genes involved in sensory perception for males. We find the majority of loci show additivity in heterokaryotypes. Our results suggest that multiple genes have expression differences among arrangements that were either captured by the original inversion mutation or accumulated after it reached polymorphic frequencies, providing a potential source of genetic variation for selection to act upon. These data suggest that the inversions are favored because of their indirect effect of recombination suppression that has held different combinations of differentially expressed genes together in the various gene arrangement backgrounds.
Collapse
|
57
|
Battagin M, Gorjanc G, Faux AM, Johnston SE, Hickey JM. Effect of manipulating recombination rates on response to selection in livestock breeding programs. Genet Sel Evol 2016; 48:44. [PMID: 27335010 PMCID: PMC4917950 DOI: 10.1186/s12711-016-0221-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 06/07/2016] [Indexed: 11/10/2022] Open
Abstract
Background In this work, we performed simulations to explore the potential of manipulating recombination rates to increase response to selection in livestock breeding programs. Methods We carried out ten replicates of several scenarios that followed a common overall structure but differed in the average rate of recombination along the genome (expressed as the length of a chromosome in Morgan), the genetic architecture of the trait under selection, and the selection intensity under truncation selection (expressed as the proportion of males selected). Recombination rates were defined by simulating nine different chromosome lengths: 0.10, 0.25, 0.50, 1, 2, 5, 10, 15 and 20 Morgan, respectively. One Morgan was considered to be the typical chromosome length for current livestock species. The genetic architecture was defined by the number of quantitative trait variants (QTV) that affected the trait under selection. Either a large (10,000) or a small (1000 or 500) number of QTV was simulated. Finally, the proportions of males selected under truncation selection as sires for the next generation were equal to 1.2, 2.4, 5, or 10 %. Results Increasing recombination rate increased the overall response to selection and decreased the loss of genetic variance. The difference in cumulative response between low and high recombination rates increased over generations. At low recombination rates, cumulative response to selection tended to asymptote sooner and the genetic variance was completely eroded. If the trait under selection was affected by few QTV, differences between low and high recombination rates still existed, but the selection limit was reached at all rates of recombination. Conclusions Higher recombination rates can enhance the efficiency of breeding programs to turn genetic variation into response to selection. However, to increase response to selection significantly, the recombination rate would need to be increased 10- or 20-fold. The biological feasibility and consequences of such large increases in recombination rates are unknown. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0221-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Mara Battagin
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK
| | - Anne-Michelle Faux
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK
| | - Susan E Johnston
- Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - John M Hickey
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK.
| |
Collapse
|
58
|
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].
Collapse
|
59
|
Conserved Genetic Architecture Underlying Individual Recombination Rate Variation in a Wild Population of Soay Sheep (Ovis aries). Genetics 2016; 203:583-98. [PMID: 27029733 PMCID: PMC4858801 DOI: 10.1534/genetics.115.185553] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/11/2016] [Indexed: 02/06/2023] Open
Abstract
Meiotic recombination breaks down linkage disequilibrium (LD) and forms new haplotypes, meaning that it is an important driver of diversity in eukaryotic genomes. Understanding the causes of variation in recombination rate is important in interpreting and predicting evolutionary phenomena and in understanding the potential of a population to respond to selection. However, despite attention in model systems, there remains little data on how recombination rate varies at the individual level in natural populations. Here we used extensive pedigree and high-density SNP information in a wild population of Soay sheep (Ovis aries) to investigate the genetic architecture of individual autosomal recombination rates. Individual rates were high relative to other mammal systems and were higher in males than in females (autosomal map lengths of 3748 and 2860 cM, respectively). The heritability of autosomal recombination rate was low but significant in both sexes (h2 = 0.16 and 0.12 in females and males, respectively). In females, 46.7% of the heritable variation was explained by a subtelomeric region on chromosome 6; a genome-wide association study showed the strongest associations at locus RNF212, with further associations observed at a nearby ∼374-kb region of complete LD containing three additional candidate loci, CPLX1, GAK, and PCGF3. A second region on chromosome 7 containing REC8 and RNF212B explained 26.2% of the heritable variation in recombination rate in both sexes. Comparative analyses with 40 other sheep breeds showed that haplotypes associated with recombination rates are both old and globally distributed. Both regions have been implicated in rate variation in mice, cattle, and humans, suggesting a common genetic architecture of recombination rate variation in mammals.
Collapse
|
60
|
Abstract
Evolution and maintenance of genetic recombination and its relation to the mutational process is a long-standing, fundamental problem in evolutionary biology that is linked to the general problem of evolution of evolvability. We explored a stochastic model of the evolution of recombination using additive fitness and infinite allele assumptions but no assumptions on the sign or magnitude of the epistasis and the distribution of mutation effects. In this model, fluctuating negative epistasis and predominantly deleterious mutations arise naturally as a consequence of the additive fitness and a reservoir from which new alleles arrive with a fixed distribution of fitness effects. Analysis of the model revealed a nonmonotonic effect of recombination intensity on fitness, with an optimal recombination rate value which maximized fitness in steady state. The optimal recombination rate depended on the mutation rate and was evolvable, that is, subject to selection. The predictions of the model were compatible with the observations on the dependence between genome rearrangement rate and gene flux in microbial genomes.
Collapse
Affiliation(s)
- Alexander E Lobkovsky
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland
| |
Collapse
|
61
|
Aggarwal DD, Rashkovetsky E, Michalak P, Cohen I, Ronin Y, Zhou D, Haddad GG, Korol AB. Experimental evolution of recombination and crossover interference in Drosophila caused by directional selection for stress-related traits. BMC Biol 2015; 13:101. [PMID: 26614097 PMCID: PMC4661966 DOI: 10.1186/s12915-015-0206-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 10/27/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Population genetics predicts that tight linkage between new and/or pre-existing beneficial and deleterious alleles should decrease the efficiency of natural selection in finite populations. By decoupling beneficial and deleterious alleles and facilitating the combination of beneficial alleles, recombination accelerates the formation of high-fitness genotypes. This may impose indirect selection for increased recombination. Despite the progress in theoretical understanding, interplay between recombination and selection remains a controversial issue in evolutionary biology. Even less satisfactory is the situation with crossover interference, which is a deviation of double-crossover frequency in a pair of adjacent intervals from the product of recombination rates in the two intervals expected on the assumption of crossover independence. Here, we report substantial changes in recombination and interference in three long-term directional selection experiments with Drosophila melanogaster: for desiccation (~50 generations), hypoxia, and hyperoxia tolerance (>200 generations each). RESULTS For all three experiments, we found a high interval-specific increase of recombination frequencies in selection lines (up to 40-50% per interval) compared to the control lines. We also discovered a profound effect of selection on interference as expressed by an increased frequency of double crossovers in selection lines. Our results show that changes in interference are not necessarily coupled with increased recombination. CONCLUSIONS Our results support the theoretical predictions that adaptation to a new environment can promote evolution toward higher recombination. Moreover, this is the first evidence of selection for different recombination-unrelated traits potentially leading, not only to evolution toward increased crossover rates, but also to changes in crossover interference, one of the fundamental features of recombination.
Collapse
Affiliation(s)
| | | | - Pawel Michalak
- Virginia Bioinformatics Institute, Virginia Tech, Washington Street, MC 0477, Blacksburg, VA, 24061-0477, USA
| | - Irit Cohen
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel
| | - Yefim Ronin
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel
| | - Dan Zhou
- University of California, San Diego, USA
| | - Gabriel G Haddad
- University of California, San Diego, USA
- Rady Children's Hospital, San Diego, USA
| | - Abraham B Korol
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel.
| |
Collapse
|
62
|
Williams JL, Hall SJ, Del Corvo M, Ballingall KT, Colli L, Ajmone Marsan P, Biscarini F. Inbreeding and purging at the genomic Level: the Chillingham cattle reveal extensive, non-random SNP heterozygosity. Anim Genet 2015; 47:19-27. [DOI: 10.1111/age.12376] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2015] [Indexed: 11/29/2022]
Affiliation(s)
- J. L. Williams
- PTP Science Park; Via Einstein - Loc. Cascina Codazza 26900 Lodi Italy
| | - S. J.G. Hall
- School of Life Sciences; University of Lincoln; Brayford Pool Lincoln LN6 7TS UK
| | - M. Del Corvo
- PTP Science Park; Via Einstein - Loc. Cascina Codazza 26900 Lodi Italy
| | - K. T. Ballingall
- Moredun Research Institute; Pentlands Science Park; Bush Loan Penicuik Midlothian EH26 0PZ UK
| | - L. Colli
- Università Cattolica del Sacro Cuore; via Emilia Parmense 84 29122 Piacenza Italy
| | - P. Ajmone Marsan
- Università Cattolica del Sacro Cuore; via Emilia Parmense 84 29122 Piacenza Italy
| | - F. Biscarini
- PTP Science Park; Via Einstein - Loc. Cascina Codazza 26900 Lodi Italy
| |
Collapse
|
63
|
Bomblies K, Higgins JD, Yant L. Meiosis evolves: adaptation to external and internal environments. THE NEW PHYTOLOGIST 2015; 208:306-23. [PMID: 26075313 DOI: 10.1111/nph.13499] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 05/03/2015] [Indexed: 05/23/2023]
Abstract
306 I. 306 II. 307 III. 312 IV. 317 V. 318 319 References 319 SUMMARY: Meiosis is essential for the fertility of most eukaryotes and its structures and progression are conserved across kingdoms. Yet many of its core proteins show evidence of rapid or adaptive evolution. What drives the evolution of meiosis proteins? How can constrained meiotic processes be modified in response to challenges without compromising their essential functions? In surveying the literature, we found evidence of two especially potent challenges to meiotic chromosome segregation that probably necessitate adaptive evolutionary responses: whole-genome duplication and abiotic environment, especially temperature. Evolutionary solutions to both kinds of challenge are likely to involve modification of homologous recombination and synapsis, probably via adjustments of core structural components important in meiosis I. Synthesizing these findings with broader patterns of meiosis gene evolution suggests that the structural components of meiosis coevolve as adaptive modules that may change in primary sequence and function while maintaining three-dimensional structures and protein interactions. The often sharp divergence of these genes among species probably reflects periodic modification of entire multiprotein complexes driven by genomic or environmental changes. We suggest that the pressures that cause meiosis to evolve to maintain fertility may cause pleiotropic alterations of global crossover rates. We highlight several important areas for future research.
Collapse
Affiliation(s)
- Kirsten Bomblies
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - James D Higgins
- Department of Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Levi Yant
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| |
Collapse
|
64
|
Smukowski Heil CS, Ellison C, Dubin M, Noor MAF. Recombining without Hotspots: A Comprehensive Evolutionary Portrait of Recombination in Two Closely Related Species of Drosophila. Genome Biol Evol 2015; 7:2829-42. [PMID: 26430062 PMCID: PMC4684701 DOI: 10.1093/gbe/evv182] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2015] [Indexed: 12/12/2022] Open
Abstract
Meiotic recombination rate varies across the genome within and between individuals, populations, and species in virtually all taxa studied. In almost every species, this variation takes the form of discrete recombination hotspots, determined in some mammals by a protein called PRDM9. Hotspots and their determinants have a profound effect on the genomic landscape, and share certain features that extend across the tree of life. Drosophila, in contrast, are anomalous in their absence of hotspots, PRDM9, and other species-specific differences in the determination of recombination. To better understand the evolution of meiosis and general patterns of recombination across diverse taxa, we present a truly comprehensive portrait of recombination across time, combining recently published cross-based contemporary recombination estimates from each of two sister species with newly obtained linkage-disequilibrium-based historic estimates of recombination from both of these species. Using Drosophila pseudoobscura and Drosophila miranda as a model system, we compare recombination rate between species at multiple scales, and we suggest that Drosophila replicate the pattern seen in human-chimpanzee in which recombination rate is conserved at broad scales. We also find evidence of a species-wide recombination modifier(s), resulting in both a present and historic genome-wide elevation of recombination rates in D. miranda, and identify broad scale effects on recombination from the presence of an inversion. Finally, we reveal an unprecedented view of the distribution of recombination in D. pseudoobscura, illustrating patterns of linked selection and where recombination is taking place. Overall, by combining these estimation approaches, we highlight key similarities and differences in recombination between Drosophila and other organisms.
Collapse
Affiliation(s)
- Caiti S Smukowski Heil
- Biology Department, Duke University Genome Sciences Department, University of Washington
| | - Chris Ellison
- Department of Integrative Biology, University of California, Berkeley
| | | | | |
Collapse
|
65
|
Havird JC, Hall MD, Dowling DK. The evolution of sex: A new hypothesis based on mitochondrial mutational erosion: Mitochondrial mutational erosion in ancestral eukaryotes would favor the evolution of sex, harnessing nuclear recombination to optimize compensatory nuclear coadaptation. Bioessays 2015. [PMID: 26201475 DOI: 10.1002/bies.201500057] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The evolution of sex in eukaryotes represents a paradox, given the "twofold" fitness cost it incurs. We hypothesize that the mutational dynamics of the mitochondrial genome would have favored the evolution of sexual reproduction. Mitochondrial DNA (mtDNA) exhibits a high-mutation rate across most eukaryote taxa, and several lines of evidence suggest that this high rate is an ancestral character. This seems inexplicable given that mtDNA-encoded genes underlie the expression of life's most salient functions, including energy conversion. We propose that negative metabolic effects linked to mitochondrial mutation accumulation would have invoked selection for sexual recombination between divergent host nuclear genomes in early eukaryote lineages. This would provide a mechanism by which recombinant host genotypes could be rapidly shuffled and screened for the presence of compensatory modifiers that offset mtDNA-induced harm. Under this hypothesis, recombination provides the genetic variation necessary for compensatory nuclear coadaptation to keep pace with mitochondrial mutation accumulation.
Collapse
Affiliation(s)
- Justin C Havird
- Deptartment of Biological Sciences, Auburn University, Auburn, AL, USA.,Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Matthew D Hall
- School of Biological Sciences, Monash University, Victoria, Australia
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Victoria, Australia
| |
Collapse
|
66
|
Carranza J, Polo V. Sexual reproduction with variable mating systems can resist asexuality in a rock-paper-scissors dynamics. ROYAL SOCIETY OPEN SCIENCE 2015; 2:140383. [PMID: 26587254 PMCID: PMC4632567 DOI: 10.1098/rsos.140383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 06/18/2015] [Indexed: 06/05/2023]
Abstract
While sex can be advantageous for a lineage in the long term, we still lack an explanation for its maintenance with the twofold cost per generation. Here we model an infinite diploid population where two autosomal loci determine, respectively, the reproductive mode, sexual versus asexual and the mating system, polygynous (costly sex) versus monogamous (assuming equal contribution of parents to offspring, i.e. non-costly sex). We show that alleles for costly sex can spread when non-costly sexual modes buffer the interaction between asexual and costly sexual strategies, even without twofold benefit of recombination with respect to asexuality. The three interacting strategies have intransitive fitness relationships leading to a rock-paper-scissors dynamics, so that alleles for costly sex cannot be eliminated by asexuals in most situations throughout the parameter space. Our results indicate that sexual lineages with variable mating systems can resist the invasion of asexuals and allow for long-term effects to accumulate, thus providing a solution to the persisting theoretical question of why sex was not displaced by asexuality along evolution.
Collapse
Affiliation(s)
- Juan Carranza
- Department of Zoology, CRCP Research Center, University of Córdoba, Córdoba 14071, Spain
- Biology and Ethology Unit, University of Extremadura, Cáceres 10071, Spain
| | - Vicente Polo
- Departamento de Biología y Geología del Área de Biodiversidad y Conservación, Escuela Superior de Ciencias Experimentales y Tecnología (ESCET), Universidad Rey Juan Carlos, Madrid, Spain
| |
Collapse
|
67
|
Kleiman M, Hadany L. The evolution of obligate sex: the roles of sexual selection and recombination. Ecol Evol 2015; 5:2572-83. [PMID: 26257871 PMCID: PMC4523354 DOI: 10.1002/ece3.1516] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/20/2015] [Accepted: 04/23/2015] [Indexed: 11/20/2022] Open
Abstract
The evolution of sex is one of the greatest mysteries in evolutionary biology. An even greater mystery is the evolution of obligate sex, particularly when competing with facultative sex and not with complete asexuality. Here, we develop a stochastic simulation of an obligate allele invading a facultative population, where males are subject to sexual selection. We identify a range of parameters where sexual selection can contribute to the evolution of obligate sex: Especially when the cost of sex is low, mutation rate is high, and the facultative individuals do not reproduce sexually very often. The advantage of obligate sex becomes larger in the absence of recombination. Surprisingly, obligate sex can take over even when the population has a lower mean fitness as a result. We show that this is due to the high success of obligate males that can compensate the cost of sex.
Collapse
Affiliation(s)
- Maya Kleiman
- Department of Chemistry, Ben-Gurion University of the Negev Be'er-Sheva, 8410501, Israel
| | - Lilach Hadany
- Department of Molecular Biology and Ecology of Plants, Faculty of Life Sciences, Tel Aviv University Ramat Aviv, 69978, Israel
| |
Collapse
|
68
|
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.
Collapse
|
69
|
Abstract
Eukaryotes were born of a chimeric union between two prokaryotes--the progenitors of the mitochondrial and nuclear genomes. Early in eukaryote evolution, most mitochondrial genes were lost or transferred to the nucleus, but a core set of genes that code exclusively for products associated with the electron transport system remained in the mitochondrion. The products of these mitochondrial genes work in intimate association with the products of nuclear genes to enable oxidative phosphorylation and core energy production. The need for coadaptation, the challenge of cotransmission, and the possibility of genomic conflict between mitochondrial and nuclear genes have profound consequences for the ecology and evolution of eukaryotic life. An emerging interdisciplinary field that I call "mitonuclear ecology" is reassessing core concepts in evolutionary ecology including sexual reproduction, two sexes, sexual selection, adaptation, and speciation in light of the interactions of mitochondrial and nuclear genomes.
Collapse
|
70
|
Evolution in changing environments: modifiers of mutation, recombination, and migration. Proc Natl Acad Sci U S A 2014; 111:17935-40. [PMID: 25427794 DOI: 10.1073/pnas.1417664111] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The production and maintenance of genetic and phenotypic diversity under temporally fluctuating selection and the signatures of environmental changes in the patterns of this variation have been important areas of focus in population genetics. On one hand, periods of constant selection pull the genetic makeup of populations toward local fitness optima. On the other, to cope with changes in the selection regime, populations may evolve mechanisms that create a diversity of genotypes. By tuning the rates at which variability is produced--such as the rates of recombination, mutation, or migration--populations may increase their long-term adaptability. Here we use theoretical models to gain insight into how the rates of these three evolutionary forces are shaped by fluctuating selection. We compare and contrast the evolution of recombination, mutation, and migration under similar patterns of environmental change and show that these three sources of phenotypic variation are surprisingly similar in their response to changing selection. We show that the shape, size, variance, and asymmetry of environmental fluctuation have different but predictable effects on evolutionary dynamics.
Collapse
|
71
|
Gibson AK, Fuentes JA. A phylogenetic test of the Red Queen Hypothesis: outcrossing and parasitism in the Nematode phylum. Evolution 2014; 69:530-40. [PMID: 25403727 DOI: 10.1111/evo.12565] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 11/06/2014] [Indexed: 01/04/2023]
Abstract
Sexual outcrossing is costly relative to selfing and asexuality, yet it is ubiquitous in nature, a paradox that has long puzzled evolutionary biologists. The Red Queen Hypothesis argues that outcrossing is maintained by antagonistic interactions between host and parasites. Most tests of this hypothesis focus on the maintenance of outcrossing in hosts. The Red Queen makes an additional prediction that parasitic taxa are more likely to be outcrossing than their free-living relatives. We test this prediction in the diverse Nematode phylum using phylogenetic comparative methods to evaluate trait correlations. In support of the Red Queen, we demonstrate a significant correlation between parasitism and outcrossing in this clade. We find that this correlation is driven by animal parasites, for which outcrossing is significantly enriched relative to both free-living and plant parasitic taxa. Finally, we test hypotheses for the evolutionary history underlying the correlation of outcrossing and animal parasitism. Our results demonstrate that selfing and asexuality are significantly less likely to arise on parasitic lineages than on free-living ones. The findings of this study are consistent with the Red Queen Hypothesis. Moreover, they suggest that the maintenance of genetic variation is an important factor in the persistence of parasitic lineages.
Collapse
|
72
|
Muñoz-Fuentes V, Marcet-Ortega M, Alkorta-Aranburu G, Linde Forsberg C, Morrell JM, Manzano-Piedras E, Söderberg A, Daniel K, Villalba A, Toth A, Di Rienzo A, Roig I, Vilà C. Strong artificial selection in domestic mammals did not result in an increased recombination rate. Mol Biol Evol 2014; 32:510-23. [PMID: 25414125 DOI: 10.1093/molbev/msu322] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Recombination rates vary in intensity and location at the species, individual, sex and chromosome levels. Despite the fundamental biological importance of this process, the selective forces that operate to shape recombination rate and patterns are unclear. Domestication offers a unique opportunity to study the interplay between recombination and selection. In domesticates, intense selection for particular traits is imposed on small populations over many generations, resulting in organisms that differ, sometimes dramatically, in morphology and physiology from their wild ancestor. Although earlier studies suggested increased recombination rate in domesticates, a formal comparison of recombination rates between domestic mammals and their wild congeners was missing. In order to determine broad-scale recombination rate, we used immunolabeling detection of MLH1 foci as crossover markers in spermatocytes in three pairs of closely related wild and domestic species (dog and wolf, goat and ibex, and sheep and mouflon). In the three pairs, and contrary to previous suggestions, our data show that contemporary recombination rate is higher in the wild species. Subsequently, we inferred recombination breakpoints in sequence data for 16 genomic regions in dogs and wolves, each containing a locus associated with a dog phenotype potentially under selection during domestication. No difference in the number and distribution of recombination breakpoints was found between dogs and wolves. We conclude that our data indicate that strong directional selection did not result in changes in recombination in domestic mammals, and that both upper and lower bounds for crossover rates may be tightly regulated.
Collapse
Affiliation(s)
- Violeta Muñoz-Fuentes
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana EBD-CSIC, Sevilla, Spain Department of Population and Conservation Biology, Uppsala University, Uppsala, Sweden
| | - Marina Marcet-Ortega
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain Cytology and Histology Unit, Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | | | | | - Jane M Morrell
- Division of Reproduction, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Arne Söderberg
- Department of Pathology and Wildlife Diseases, National Veterinary Institute (SVA), Uppsala, Sweden
| | - Katrin Daniel
- Institute of Physiological Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Adrian Villalba
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain Cytology and Histology Unit, Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Attila Toth
- Institute of Physiological Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Anna Di Rienzo
- Department of Human Genetics, Cummings Life Science Center, University of Chicago
| | - Ignasi Roig
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain Cytology and Histology Unit, Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Carles Vilà
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana EBD-CSIC, Sevilla, Spain
| |
Collapse
|
73
|
Godfrey RM, Johnson MTJ. Effects of functionally asexual reproduction on quantitative genetic variation in the evening primroses (Oenothera, Onagraceae). AMERICAN JOURNAL OF BOTANY 2014; 101:1906-14. [PMID: 25366856 DOI: 10.3732/ajb.1400226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
PREMISE OF THE STUDY It has long been predicted that a loss of sexual reproduction leads to decreased heritable variation within populations and increased differentiation between populations. Despite an abundance of theory, there are few empirical tests of how sex affects genetic variation in phenotypic traits, especially for plants. Here we test whether repeated losses of two critical components of sex (recombination and segregation) in the evening primroses (Oenothera L., Onagraceae) affect quantitative genetic variation within and between populations. METHODS We sampled multiple genetic families from 3-5 populations from each of eight Oenothera species, which represented four independent transitions between sexual reproduction and a functionally asexual genetic system called "permanent translocation heterozygosity." We used quantitative genetics methods to partition genetic variation within and between populations for eight plant traits related to growth, leaf physiology, flowering, and resistance to herbivores. KEY RESULTS Heritability was, on average, 74% higher in sexual Oenothera populations than in functionally asexual populations, with plant growth rate, specific leaf area, and the percentage of leaf water content showing the strongest differences. By contrast, genetic differentiation among populations was 2.8× higher in functionally asexual vs. sexual Oenothera species. This difference was particularly strong for specific leaf area. Sexual populations tended to exhibit higher genetic correlations among traits, but this difference was weakly supported. CONCLUSIONS These results support the prediction that sexual reproduction maintains higher genetic variation within populations, which may facilitate adaptive evolution. We also found partial support for the prediction that a loss of sex leads to greater population differentiation, which may elevate speciation rates.
Collapse
Affiliation(s)
- Ryan M Godfrey
- Department of Biology, University of Toronto-Mississauga, Mississauga, Ontario, L5L 1C6, Canada
| | - Marc T J Johnson
- Department of Biology, University of Toronto-Mississauga, Mississauga, Ontario, L5L 1C6, Canada
| |
Collapse
|
74
|
Stewart EL, McDonald BA. Measuring quantitative virulence in the wheat pathogen Zymoseptoria tritici using high-throughput automated image analysis. PHYTOPATHOLOGY 2014; 104:985-92. [PMID: 24624955 DOI: 10.1094/phyto-11-13-0328-r] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Zymoseptoria tritici, causal agent of Septoria tritici blotch on wheat, produces pycnidia in chlorotic and necrotic lesions on infected leaves. A high-throughput phenotyping method was developed based on automated digital image analysis that accurately measures the percentage of leaf area covered by lesions (PLACL) as well as pycnidia size and number. A seedling inoculation assay was conducted using 361 Z. tritici isolates originating from a controlled cross and two different winter wheat cultivars. Pycnidia size and density were found to be quantitative traits that showed a continuous distribution in the progeny. There was a weak correlation between pycnidia density and size (r = -0.27) and between pycnidia density and PLACL (r = 0.37). There were significant differences in PLACL and pycnidia density on resistant and susceptible cultivars. In all, >20% of the offspring exhibited significantly different pycnidia density on the two cultivars, consistent with host specialization. Automated image analysis provided greater accuracy and precision compared with traditional visual estimates of virulence. These results show that digital image analysis provides a powerful tool for measuring differences in quantitative virulence among strains of Z. tritici.
Collapse
|
75
|
Arnaud-Haond S, Moalic Y, Barnabé C, Ayala FJ, Tibayrenc M. Discriminating micropathogen lineages and their reticulate evolution through graph theory-based network analysis: the case of Trypanosoma cruzi, the agent of Chagas disease. PLoS One 2014; 9:e103213. [PMID: 25148574 PMCID: PMC4141739 DOI: 10.1371/journal.pone.0103213] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 06/28/2014] [Indexed: 12/02/2022] Open
Abstract
Micropathogens (viruses, bacteria, fungi, parasitic protozoa) share a common trait, which is partial clonality, with wide variance in the respective influence of clonality and sexual recombination on the dynamics and evolution of taxa. The discrimination of distinct lineages and the reconstruction of their phylogenetic history are key information to infer their biomedical properties. However, the phylogenetic picture is often clouded by occasional events of recombination across divergent lineages, limiting the relevance of classical phylogenetic analysis and dichotomic trees. We have applied a network analysis based on graph theory to illustrate the relationships among genotypes of Trypanosoma cruzi, the parasitic protozoan responsible for Chagas disease, to identify major lineages and to unravel their past history of divergence and possible recombination events. At the scale of T. cruzi subspecific diversity, graph theory-based networks applied to 22 isoenzyme loci (262 distinct Multi-Locus-Enzyme-Electrophoresis -MLEE) and 19 microsatellite loci (66 Multi-Locus-Genotypes -MLG) fully confirms the high clustering of genotypes into major lineages or "near-clades". The release of the dichotomic constraint associated with phylogenetic reconstruction usually applied to Multilocus data allows identifying putative hybrids and their parental lineages. Reticulate topology suggests a slightly different history for some of the main "near-clades", and a possibly more complex origin for the putative hybrids than hitherto proposed. Finally the sub-network of the near-clade T. cruzi I (28 MLG) shows a clustering subdivision into three differentiated lesser near-clades ("Russian doll pattern"), which confirms the hypothesis recently proposed by other investigators. The present study broadens and clarifies the hypotheses previously obtained from classical markers on the same sets of data, which demonstrates the added value of this approach. This underlines the potential of graph theory-based network analysis for describing the nature and relationships of major pathogens, thereby opening stimulating prospects to unravel the organization, dynamics and history of major micropathogen lineages.
Collapse
Affiliation(s)
- Sophie Arnaud-Haond
- IFREMER (Institut Français de Recherche pour l'Exploitation de la Mer) - Département Ecosystèmes Marins Exploités, Sète, France
| | - Yann Moalic
- IFREMER (Institut Français de Recherche pour l'Exploitation de la Mer) - Département Ecosystèmes Marins Exploités, Sète, France
| | - Christian Barnabé
- Interactions hôte-vecteur-parasite dans les maladies dues aux Trypanosomatidés, INTERTRYP (IRD-CIRAD), Montpellier, France
| | - Francisco José Ayala
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, United States of America
| | - Michel Tibayrenc
- Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle, MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), Montpellier, France
| |
Collapse
|
76
|
Moradigaravand D, Kouyos R, Hinkley T, Haddad M, Petropoulos CJ, Engelstädter J, Bonhoeffer S. Recombination accelerates adaptation on a large-scale empirical fitness landscape in HIV-1. PLoS Genet 2014; 10:e1004439. [PMID: 24967626 PMCID: PMC4072600 DOI: 10.1371/journal.pgen.1004439] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 04/30/2014] [Indexed: 01/18/2023] Open
Abstract
Recombination has the potential to facilitate adaptation. In spite of the substantial body of theory on the impact of recombination on the evolutionary dynamics of adapting populations, empirical evidence to test these theories is still scarce. We examined the effect of recombination on adaptation on a large-scale empirical fitness landscape in HIV-1 based on in vitro fitness measurements. Our results indicate that recombination substantially increases the rate of adaptation under a wide range of parameter values for population size, mutation rate and recombination rate. The accelerating effect of recombination is stronger for intermediate mutation rates but increases in a monotonic way with the recombination rates and population sizes that we examined. We also found that both fitness effects of individual mutations and epistatic fitness interactions cause recombination to accelerate adaptation. The estimated epistasis in the adapting populations is significantly negative. Our results highlight the importance of recombination in the evolution of HIV-I. One of the most challenging issues in evolutionary biology concerns the question of why most organisms exchange genetic material with each other, e.g. during sexual reproduction. Gene shuffling can create genetic diversity that facilitates adaptation to new environments, but theory shows that this effect is highly dependent on how different genes interact in determining the fitness of an organism. Using a large data set of fitness values based on HIV-1, we provide evidence that shuffling of genetic material indeed raises the level of genetic diversity, and as a result accelerates adaptation. Our results also propose genetic shuffling as a mechanism utilized by HIV to accelerate the evolution of multi-drug-resistant strains.
Collapse
Affiliation(s)
- Danesh Moradigaravand
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland
- * E-mail: (DM); (SB)
| | - Roger Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zürich, Zürich, Switzerland
| | - Trevor Hinkley
- WestCHEM, School of Chemistry, The University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Mojgan Haddad
- Monogram Biosciences, South San Francisco, California, United States of America
| | | | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Sebastian Bonhoeffer
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- * E-mail: (DM); (SB)
| |
Collapse
|
77
|
Roze D. Selection for sex in finite populations. J Evol Biol 2014; 27:1304-22. [DOI: 10.1111/jeb.12344] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 01/07/2014] [Accepted: 01/20/2014] [Indexed: 11/28/2022]
Affiliation(s)
- D. Roze
- CNRS; UMI 3614; Evolutionary Biology and Ecology of Algae; Roscoff France
- Sorbonne Universités; UPMC Université Paris VI; Roscoff France
| |
Collapse
|
78
|
Moray C, Lanfear R, Bromham L. Domestication and the mitochondrial genome: comparing patterns and rates of molecular evolution in domesticated mammals and birds and their wild relatives. Genome Biol Evol 2014; 6:161-9. [PMID: 24459286 PMCID: PMC3914681 DOI: 10.1093/gbe/evu005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2013] [Indexed: 11/14/2022] Open
Abstract
Studies of domesticated animals have led to the suggestion that domestication could have significant effects on patterns of molecular evolution. In particular, analyses of mitochondrial genome sequences from domestic dogs and yaks have yielded higher ratios of non-synonymous to synonymous substitutions in the domesticated lineages than in their wild relatives. These results are important because they imply that changes to selection or population size operating over a short timescale can cause significant changes to the patterns of mitochondrial molecular evolution. In this study, our aim is to test whether the impact on mitochondrial genome evolution is a general feature of domestication or whether it is specific to particular examples. We test whether domesticated mammals and birds have consistently different patterns of molecular evolution than their wild relatives for 16 phylogenetically independent comparisons of mitochondrial genome sequences. We find no consistent difference in branch lengths or dN/dS between domesticated and wild lineages. We also find no evidence that our failure to detect a consistent pattern is due to the short timescales involved or low genetic distance between domesticated lineages and their wild relatives. However, removing comparisons where the wild relative may also have undergone a bottleneck does reveal a pattern consistent with reduced effective population size in domesticated lineages. Our results suggest that, although some domesticated lineages may have undergone changes to selective regime or effective population size that could have affected mitochondrial evolution, it is not possible to generalize these patterns over all domesticated mammals and birds.
Collapse
Affiliation(s)
- Camile Moray
- Centre for Macroevolution and Macroecology, Division of Evolution Ecology and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Robert Lanfear
- Centre for Macroevolution and Macroecology, Division of Evolution Ecology and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
- National Evolutionary Synthesis Center, Durham, NC
| | - Lindell Bromham
- Centre for Macroevolution and Macroecology, Division of Evolution Ecology and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| |
Collapse
|
79
|
Hansen TF. Why epistasis is important for selection and adaptation. Evolution 2013; 67:3501-11. [PMID: 24299403 DOI: 10.1111/evo.12214] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 07/04/2013] [Indexed: 12/16/2022]
Abstract
Organisms are built from thousands of genes that interact in complex ways. Still, the mathematical theory of evolution is dominated by a gene-by-gene perspective in which genes are assumed to have the same effects regardless of genetic background. Gene interaction, or epistasis, plays a role in some theoretical developments such as the evolution of recombination, reproductive isolation, and canalization, but is strikingly missing from our standard accounts of phenotypic adaptation. This absence is most puzzling within the field of quantitative genetics, which, despite its polygenic perspective and elaborate statistical representation of epistasis, has not found a single important role for gene interaction in evolution. To the contrary, there is a widespread consensus that epistasis is evolutionary inert, and that all we need to know to predict evolutionary dynamics is the additive component of the genetic variance. This view may have roots in convenience, but also in theoretical results showing that the response to selection derived from epistatic variance components is not permanent and will decay when selection is relaxed. I show that these results are tied to a conceptual confusion, and are misleading as general statements about the significance of epistasis for the selection response and adaptation.
Collapse
Affiliation(s)
- Thomas F Hansen
- Department of Biology, University of Oslo, CEES, P.O. Box 1066, Blindern, N-0316 Oslo, Norway.
| |
Collapse
|
80
|
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.
Collapse
|
81
|
Abstract
The evolution of sex is one of the most important and controversial problems in evolutionary biology. Although sex is almost universal in higher animals and plants, its inherent costs have made its maintenance difficult to explain. The most famous of these is the twofold cost of males, which can greatly reduce the fecundity of a sexual population, compared to a population of asexual females. Over the past century, multiple hypotheses, along with experimental evidence to support these, have been put forward to explain widespread costly sex. In this review, we outline some of the most prominent theories, along with the experimental and observational evidence supporting these. Historically, there have been 4 classes of theories: the ability of sex to fix multiple novel advantageous mutants (Fisher-Muller hypothesis); sex as a mechanism to stop the build-up of deleterious mutations in finite populations (Muller's ratchet); recombination creating novel genotypes that can resist infection by parasites (Red Queen hypothesis); and the ability of sex to purge bad genomes if deleterious mutations act synergistically (mutational deterministic hypothesis). Current theoretical and experimental evidence seems to favor the hypothesis that sex breaks down selection interference between new mutants, or it acts as a mechanism to shuffle genotypes in order to repel parasitic invasion. However, there is still a need to collect more data from natural populations and experimental studies, which can be used to test different hypotheses.
Collapse
Affiliation(s)
- Matthew Hartfield
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | |
Collapse
|
82
|
Zhan J, McDonald BA. Experimental measures of pathogen competition and relative fitness. ANNUAL REVIEW OF PHYTOPATHOLOGY 2013; 51:131-53. [PMID: 23767846 DOI: 10.1146/annurev-phyto-082712-102302] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Competition among pathogen strains for limited host resources can have a profound effect on pathogen evolution. A better understanding of the principles and consequences of competition can be useful in designing more sustainable disease management strategies. The competitive ability and relative fitness of a pathogen strain are determined by its intrinsic biological properties, the resistance and heterogeneity of the corresponding host population, the population density and genetic relatedness of the competing strains, and the physical environment. Competitive ability can be inferred indirectly from fitness components, such as basic reproduction rate or transmission rate. However, pathogen strains that exhibit higher fitness components when they infect a host alone may not exhibit a competitive advantage when they co-infect the same host. The most comprehensive measures of competitive ability and relative fitness come from calculating selection coefficients in a mixed infection in a field setting. Mark-release-recapture experiments can be used to estimate fitness costs associated with unnecessary virulence and fungicide resistance.
Collapse
Affiliation(s)
- Jiasui Zhan
- Key Lab for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | | |
Collapse
|
83
|
Rohde C, Valente VLS. Three decades of studies on chromosomal polymorphism of Drosophila willistoni and description of fifty different rearrangements. Genet Mol Biol 2012; 35:966-79. [PMID: 23411997 PMCID: PMC3571430 DOI: 10.1590/s1415-47572012000600012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Drosophila willistoni (Insecta, Diptera) is considered a paradigm for evolutionary studies. Their chromosomes are characterized by multiple paracentric inversions that make it hard to identify and describe chromosomal polymorphisms. In the present report we attempted to systematize the description of all the 50 inversions found in the last three decades, since we have been studying the chromosomes of several individuals of 30 different populations, including the one used in the genome sequencing project (Gd-H4-1). We present the photographic register of 11 arrangements in the left arm of the X chromosome (XL), eight in the right arm (XR), 10 in the left arm of chromosome II (IIL), eight in its right arm (IIR) and 13 in chromosome III. This information also includes their breakpoints on the reference photomap. A clear geographic difference was detected in XL and XR, with different fixed arrangements depending on the origin of the population studied. Through the comparison of all X arrangements it was possible to infer the putative ancestral arrangements, i.e., those related to all the remaining arrangements through the small number of inversions that occurred in the past, which we will call XL-A and XR-A. In the autosomes (IIL/IIR and III), fixed inversions were detected, but most are segregating in different frequencies along the geographical distribution of the D. willistoni populations.
Collapse
Affiliation(s)
| | - Vera Lúcia S. Valente
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| |
Collapse
|
84
|
Abstract
Pathogens adapt to antibody surveillance through amino acid replacements in targeted protein regions, or epitopes, that interfere with antibody binding. However, such escape mutations may exact a fitness cost due to impaired protein function. Here, it is hypothesized that the recurring generation of specific neutralizing antibodies to an epitope region as it evolves in response to antibody selection will cause amino acid reversions by releasing early escape mutations from immune selection. The plausibility of this hypothesis was tested with stochastic simulation of adaptation at the molecular sequence level in finite populations. Under the conditions of strong selection and weak mutation, the rates of allele fixation and amino acid reversion increased with population size and selection coefficients. These rates decreased with population size, however, if mutation became strong, because clonal interference reduced the rate of adaptation. The model successfully predicts the rate of reversion per allele fixation for an important human immunodeficiency virus type 1 (HIV-1) antibody epitope region. Therefore, antibody selection may generate complex adaptive dynamics.
Collapse
Affiliation(s)
- Jack da Silva
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, South Australia 5005, Australia.
| |
Collapse
|
85
|
Cattani MV, Kingan SB, Presgraves DC. Cis
‐
and
trans
‐acting genetic factors contribute to heterogeneity in the rate of crossing over between the
D
rosophila simulans
clade species. J Evol Biol 2012; 25:2014-2022. [DOI: 10.1111/j.1420-9101.2012.02578.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 06/25/2012] [Accepted: 06/26/2012] [Indexed: 12/19/2022]
Affiliation(s)
- M. V. Cattani
- Department of Biology University of Rochester Rochester NY USA
| | - S. B. Kingan
- Department of Biology University of Rochester Rochester NY USA
| | | |
Collapse
|
86
|
Escudero M, Hipp AL, Hansen TF, Voje KL, Luceño M. Selection and inertia in the evolution of holocentric chromosomes in sedges (Carex, Cyperaceae). THE NEW PHYTOLOGIST 2012; 195:237-47. [PMID: 22489934 DOI: 10.1111/j.1469-8137.2012.04137.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
• Changes in chromosome number as a result of fission and fusion in holocentrics have direct and immediate effects on the recombination rate. We investigate the support for the classic hypothesis that environmental stability selects for increased recombination rates. • We employed a phylogenetic and cytogenetic data set from one of the most diverse angiosperm genera in the world, which has the largest nonpolyploid chromosome radiation (Carex, Cyperaceae; 2n = 12-124; 2100 spp.). We evaluated alternative Ornstein-Uhlenbeck models of chromosome number adaptation to the environment in an information-theoretic framework. • We found moderate support for a positive influence of lateral inflorescence unit size on chromosome number, which may be selected in a stable environment in which resources for reproductive investment are larger. We found weak support for a positive influence on chromosome number of water-saturated soils and among-month temperature constancy, which would be expected to be negatively select for pioneering species. Chromosome number showed a strong phylogenetic signal. • We argue that our finding of small but significant effects of life history and ecology is compatible with our original hypothesis regarding selection of optima in recombination rates: low recombination rate is optimal when inmediate fitness is required. By contrast, high recombination rate is optimal when stable environments allow for evolutionary innovation.
Collapse
Affiliation(s)
- Marcial Escudero
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Seville, Spain.
| | | | | | | | | |
Collapse
|
87
|
Weissman DB, Barton NH. Limits to the rate of adaptive substitution in sexual populations. PLoS Genet 2012; 8:e1002740. [PMID: 22685419 PMCID: PMC3369949 DOI: 10.1371/journal.pgen.1002740] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 04/16/2012] [Indexed: 12/31/2022] Open
Abstract
In large populations, many beneficial mutations may be simultaneously available and may compete with one another, slowing adaptation. By finding the probability of fixation of a favorable allele in a simple model of a haploid sexual population, we find limits to the rate of adaptive substitution, Λ, that depend on simple parameter combinations. When variance in fitness is low and linkage is loose, the baseline rate of substitution is Λ₀ = 2NU , where N is the population size, U is the rate of beneficial mutations per genome, and is their mean selective advantage. Heritable variance v in log fitness due to unlinked loci reduces Λ by e⁻⁴(v) under polygamy and e⁻⁸ (v) under monogamy. With a linear genetic map of length R Morgans, interference is yet stronger. We use a scaling argument to show that the density of adaptive substitutions depends on s, N, U, and R only through the baseline density: Λ/R = F (Λ₀/R). Under the approximation that the interference due to different sweeps adds up, we show that Λ/R ~(Λ₀/R) / (1 +2Λ₉/R) , implying that interference prevents the rate of adaptive substitution from exceeding one per centimorgan per 200 generations. Simulations and numerical calculations confirm the scaling argument and confirm the additive approximation for Λ₀/R ~ 1; for higher Λ₀/R , the rate of adaptation grows above R/2, but only very slowly. We also consider the effect of sweeps on neutral diversity and show that, while even occasional sweeps can greatly reduce neutral diversity, this effect saturates as sweeps become more common-diversity can be maintained even in populations experiencing very strong interference. Our results indicate that for some organisms the rate of adaptive substitution may be primarily recombination-limited, depending only weakly on the mutation supply and the strength of selection.
Collapse
Affiliation(s)
- Daniel B Weissman
- Institute of Science and Technology Austria, Klosterneuburg, Austria.
| | | |
Collapse
|
88
|
Kermany AR, Lessard S. Effect of epistasis and linkage on fixation probability in three-locus models: an ancestral recombination-selection graph approach. Theor Popul Biol 2012; 82:131-45. [PMID: 22634384 DOI: 10.1016/j.tpb.2012.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 05/07/2012] [Accepted: 05/09/2012] [Indexed: 10/28/2022]
Abstract
We study the probability of ultimate fixation of a single new mutant arising in an individual chosen at random at a locus linked to two other loci carrying previously arisen mutations. This is done using the Ancestral Recombination-Selection Graph (ARSG) in a finite population in the limit of a large population size, which is also known as the Ancestral Influence Graph (AIG). An analytical expansion of the fixation probability with respect to population-scaled recombination rates and selection intensities is obtained. The coefficients of the expansion are expressed in terms of the initial state of the population and the epistatic interactions among the selected loci. Under the assumption of weak selection at tightly linked loci, the sign of the leading term, which depends on the signs of epistasis and initial linkage disequilibrium, determines whether an increase in recombination rates increases the chance of ultimate fixation of the new mutant. If mutants are advantageous, this is the case when epistasis is positive or null and the initial linkage disequilibrium is negative, which is an expected state in a finite population under directional selection. Moreover, this is also the case for a neutral mutant modifier coding for higher recombination rates if the same conditions hold at the selected loci. Under the same conditions, deleterious mutants are disfavored for ultimate fixation and neutral modifiers for higher recombination rates still favored. The recombination rates between the modifier locus and the selected loci do not come into play in the leading terms of the approximation for the fixation probability, but they do in higher-order terms.
Collapse
Affiliation(s)
- Amir R Kermany
- Département de mathématiques et de statistique, Université de Montréal, Montréal (Québec) H3C 3J7, Canada.
| | | |
Collapse
|
89
|
Becks L, Agrawal AF. The evolution of sex is favoured during adaptation to new environments. PLoS Biol 2012; 10:e1001317. [PMID: 22563299 PMCID: PMC3341334 DOI: 10.1371/journal.pbio.1001317] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 03/20/2012] [Indexed: 11/18/2022] Open
Abstract
Both theory and experiments have demonstrated that sex can facilitate adaptation, potentially yielding a group-level advantage to sex. However, it is unclear whether this process can help solve the more difficult problem of the maintenance of sex within populations. Using experimental populations of the facultatively sexual rotifer Brachionus calyciflorus, we show that rates of sex evolve to higher levels during adaptation but then decline as fitness plateaus. To assess the fitness consequences of genetic mixing, we directly compare the fitnesses of sexually and asexually derived genotypes that naturally occur in our experimental populations. Sexually derived genotypes are more fit than asexually derived genotypes when adaptive pressures are strong, but this pattern reverses as the pace of adaptation slows, matching the pattern of evolutionary change in the rate of sex. These fitness assays test the net effect of sex but cannot be used to disentangle whether selection on sex arises because highly sexual lineages become associated with different allele combinations or with different allele frequencies than less sexual lineages (i.e., "short-" or "long-term" effects, respectively). We infer which of these mechanisms provides an advantage to sex by performing additional manipulations to obtain fitness distributions of sexual and asexual progeny arrays from unbiased parents (rather than from naturally occurring, and thereby evolutionarily biased, parents). We find evidence that sex breaks down adaptive gene combinations, resulting in lower average fitness of sexual progeny (i.e., a short-term disadvantage to sex). As predicted by theory, the advantage to sex arises because sexually derived progeny are more variable in fitness, allowing for faster adaptation. This "long-term advantage" builds over multiple generations, eventually resulting in higher fitness of sexual types.
Collapse
Affiliation(s)
- Lutz Becks
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.
| | | |
Collapse
|
90
|
Kouyos RD, Leventhal GE, Hinkley T, Haddad M, Whitcomb JM, Petropoulos CJ, Bonhoeffer S. Exploring the complexity of the HIV-1 fitness landscape. PLoS Genet 2012; 8:e1002551. [PMID: 22412384 PMCID: PMC3297571 DOI: 10.1371/journal.pgen.1002551] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 01/07/2012] [Indexed: 11/19/2022] Open
Abstract
Although fitness landscapes are central to evolutionary theory, so far no biologically realistic examples for large-scale fitness landscapes have been described. Most currently available biological examples are restricted to very few loci or alleles and therefore do not capture the high dimensionality characteristic of real fitness landscapes. Here we analyze large-scale fitness landscapes that are based on predictive models for in vitro replicative fitness of HIV-1. We find that these landscapes are characterized by large correlation lengths, considerable neutrality, and high ruggedness and that these properties depend only weakly on whether fitness is measured in the absence or presence of different antiretrovirals. Accordingly, adaptive processes on these landscapes depend sensitively on the initial conditions. While the relative extent to which mutations affect fitness on their own (main effects) or in combination with other mutations (epistasis) is a strong determinant of these properties, the fitness landscape of HIV-1 is considerably less rugged, less neutral, and more correlated than expected from the distribution of main effects and epistatic interactions alone. Overall this study confirms theoretical conjectures about the complexity of biological fitness landscapes and the importance of the high dimensionality of the genetic space in which adaptation takes place. Evolutionary adaptation can be understood as populations moving uphill on landscapes, in which height corresponds to evolutionary fitness. Although such fitness landscapes are central to evolutionary theory, there is currently a lack of biologically realistic examples. Here we analyze large-scale fitness landscapes derived from in vitro fitness measurements of HIV-1. We find that these landscapes are very rugged and that, accordingly, adaptive processes on these landscapes depend sensitively on the initial conditions. Moreover, the landscapes contain large networks along which fitness changes only minimally. While the relative extent to which mutations affect fitness on their own or in combination with other mutations is a strong determinant of these properties, the fitness landscape of HIV-1 is considerably less rugged than expected from the individual and pair-wise effects of mutations. Overall this study confirms theoretical conjectures about the complexity of biological fitness landscapes and the importance of the high dimensionality of the genetic space in which adaptation takes place.
Collapse
Affiliation(s)
- Roger D. Kouyos
- ETH Zürich, Institute of Integrative Biology, Zürich, Switzerland
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- * E-mail: (SB); (RDK)
| | | | - Trevor Hinkley
- ETH Zürich, Institute of Integrative Biology, Zürich, Switzerland
| | - Mojgan Haddad
- Monogram Biosciences, South San Francisco, California, United States of America
| | | | | | - Sebastian Bonhoeffer
- ETH Zürich, Institute of Integrative Biology, Zürich, Switzerland
- * E-mail: (SB); (RDK)
| |
Collapse
|
91
|
Kerstes NAG, Bérénos C, Schmid-Hempel P, Wegner KM. Antagonistic experimental coevolution with a parasite increases host recombination frequency. BMC Evol Biol 2012; 12:18. [PMID: 22330615 PMCID: PMC3293731 DOI: 10.1186/1471-2148-12-18] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 02/13/2012] [Indexed: 11/10/2022] Open
Abstract
Background One of the big remaining challenges in evolutionary biology is to understand the evolution and maintenance of meiotic recombination. As recombination breaks down successful genotypes, it should be selected for only under very limited conditions. Yet, recombination is very common and phylogenetically widespread. The Red Queen Hypothesis is one of the most prominent hypotheses for the adaptive value of recombination and sexual reproduction. The Red Queen Hypothesis predicts an advantage of recombination for hosts that are coevolving with their parasites. We tested predictions of the hypothesis with experimental coevolution using the red flour beetle, Tribolium castaneum, and its microsporidian parasite, Nosema whitei. Results By measuring recombination directly in the individuals under selection, we found that recombination in the host population was increased after 11 generations of coevolution. Detailed insights into genotypic and phenotypic changes occurring during the coevolution experiment furthermore helped us to reconstruct the coevolutionary dynamics that were associated with this increase in recombination frequency. As coevolved lines maintained higher genetic diversity than control lines, and because there was no evidence for heterozygote advantage or for a plastic response of recombination to infection, the observed increase in recombination most likely represented an adaptive host response under Red Queen dynamics. Conclusions This study provides direct, experimental evidence for an increase in recombination frequency under host-parasite coevolution in an obligatory outcrossing species. Combined with earlier results, the Red Queen process is the most likely explanation for this observation.
Collapse
Affiliation(s)
- Niels A G Kerstes
- ETH Zürich, Institute of Integrative Biology, Experimental Ecology, CH-8092 Zürich, Switzerland.
| | | | | | | |
Collapse
|
92
|
Hodgson EE, Otto SP. The red queen coupled with directional selection favours the evolution of sex. J Evol Biol 2012; 25:797-802. [PMID: 22320180 DOI: 10.1111/j.1420-9101.2012.02468.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Why sexual reproduction has evolved to be such a widespread mode of reproduction remains a major question in evolutionary biology. Although previous studies have shown that increased sex and recombination can evolve in the presence of host-parasite interactions (the 'Red Queen hypothesis' for sex), many of these studies have assumed that multiple loci mediate infection vs. resistance. Data suggest, however, that a major locus is typically involved in antigen presentation and recognition. Here, we explore a model where only one locus mediates host-parasite interactions, but a second locus is subject to directional selection. Even though the effects of these genes on fitness are independent, we show that increased rates of sex and recombination are favoured at a modifier gene that alters the rate of genetic mixing. This result occurs because of selective interference in finite populations (the 'Hill-Robertson effect'), which also favours sex. These results suggest that the Red Queen hypothesis may help to explain the evolution of sex by contributing a form of persistent selection, which interferes with directional selection at other loci and thereby favours sex and recombination.
Collapse
Affiliation(s)
- E E Hodgson
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | | |
Collapse
|
93
|
Webster MT, Hurst LD. Direct and indirect consequences of meiotic recombination: implications for genome evolution. Trends Genet 2011; 28:101-9. [PMID: 22154475 DOI: 10.1016/j.tig.2011.11.002] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 11/08/2011] [Accepted: 11/09/2011] [Indexed: 12/23/2022]
Abstract
There is considerable variation within eukaryotic genomes in the local rate of crossing over. Why is this and what effect does it have on genome evolution? On the genome scale, it is known that by shuffling alleles, recombination increases the efficacy of selection. By contrast, the extent to which differences in the recombination rate modulate the efficacy of selection between genomic regions is unclear. Recombination also has direct consequences on the origin and fate of mutations: biased gene conversion and other forms of meiotic drive promote the fixation of mutations in a similar way to selection, and recombination itself may be mutagenic. Consideration of both the direct and indirect effects of recombination is necessary to understand why its rate is so variable and for correct interpretation of patterns of genome evolution.
Collapse
Affiliation(s)
- Matthew T Webster
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
| | | |
Collapse
|
94
|
Smukowski CS, Noor MAF. Recombination rate variation in closely related species. Heredity (Edinb) 2011; 107:496-508. [PMID: 21673743 PMCID: PMC3242630 DOI: 10.1038/hdy.2011.44] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Revised: 03/21/2011] [Accepted: 04/27/2011] [Indexed: 11/09/2022] Open
Abstract
Despite their importance to successful meiosis and various evolutionary processes, meiotic recombination rates sometimes vary within species or between closely related species. For example, humans and chimpanzees share virtually no recombination hotspot locations in the surveyed portion of the genomes. However, conservation of recombination rates between closely related species has also been documented, raising an apparent contradiction. Here, we evaluate how and why conflicting patterns of recombination rate conservation and divergence may be observed, with particular emphasis on features that affect recombination, and the scale and method with which recombination is surveyed. Additionally, we review recent studies identifying features influencing fine-scale and broad-scale recombination patterns and informing how quickly recombination rates evolve, how changes in recombination impact selection and evolution in natural populations, and more broadly, which forces influence genome evolution.
Collapse
Affiliation(s)
- C S Smukowski
- Department of Biology, Duke University, Durham, NC 27708, USA.
| | | |
Collapse
|
95
|
Fixation probability in a two-locus model by the ancestral recombination-selection graph. Genetics 2011; 190:691-707. [PMID: 22095080 DOI: 10.1534/genetics.111.136309] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We use the ancestral influence graph (AIG) for a two-locus, two-allele selection model in the limit of a large population size to obtain an analytic approximation for the probability of ultimate fixation of a single mutant allele A. We assume that this new mutant is introduced at a given locus into a finite population in which a previous mutant allele B is already segregating with a wild type at another linked locus. We deduce that the fixation probability increases as the recombination rate increases if allele A is either in positive epistatic interaction with B and allele B is beneficial or in no epistatic interaction with B and then allele A itself is beneficial. This holds at least as long as the recombination fraction and the selection intensity are small enough and the population size is large enough. In particular this confirms the Hill-Robertson effect, which predicts that recombination renders more likely the ultimate fixation of beneficial mutants at different loci in a population in the presence of random genetic drift even in the absence of epistasis. More importantly, we show that this is true from weak negative epistasis to positive epistasis, at least under weak selection. In the case of deleterious mutants, the fixation probability decreases as the recombination rate increases. This supports Muller's ratchet mechanism to explain the accumulation of deleterious mutants in a population lacking recombination.
Collapse
|
96
|
Abstract
Anisogamy is known to generate an important cost for sexual reproduction (the famous "twofold cost of sex"). However, male-female differences may have other consequences on the evolution of sex, due to the fact that selective pressures may differ among the sexes. On the one hand, intralocus sexual conflict should favor asexual females, which can fix female-beneficial, male-detrimental alleles. On the other hand, it has been suggested repeatedly that sexual selection among males may help to purge the mutation load, providing an advantage to sexual females. However, no analytical model has computed the strength of selection acting on a modifier gene affecting the frequency of sexual reproduction when selection differs between the sexes. In this article, we analyze a two-locus model using two approaches: a quasi-linkage-equilibrium (QLE) analysis and a local stability analysis, whose predictions are verified using a multilocus simulation. We find that costly sex can be maintained when selection is stronger in males than in females, but acts in the same direction in both. Complete asexuality, however, evolves under any other form of selection. Finally, we discuss how experimental measurements of fitness variances and covariances between sexes could be used to determine the overall direction and strength on selection for sex arising from differences in selection between males and females.
Collapse
Affiliation(s)
- Denis Roze
- CNRS, UMR 7144, Adaptation et Diversité en Milieu Marin, 29682 Roscoff, France.
| | | |
Collapse
|
97
|
Fledel-Alon A, Leffler EM, Guan Y, Stephens M, Coop G, Przeworski M. Variation in human recombination rates and its genetic determinants. PLoS One 2011; 6:e20321. [PMID: 21698098 PMCID: PMC3117798 DOI: 10.1371/journal.pone.0020321] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 04/23/2011] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Despite the fundamental role of crossing-over in the pairing and segregation of chromosomes during human meiosis, the rates and placements of events vary markedly among individuals. Characterizing this variation and identifying its determinants are essential steps in our understanding of the human recombination process and its evolution. STUDY DESIGN/RESULTS Using three large sets of European-American pedigrees, we examined variation in five recombination phenotypes that capture distinct aspects of crossing-over patterns. We found that the mean recombination rate in males and females and the historical hotspot usage are significantly heritable and are uncorrelated with one another. We then conducted a genome-wide association study in order to identify loci that influence them. We replicated associations of RNF212 with the mean rate in males and in females as well as the association of Inversion 17q21.31 with the female mean rate. We also replicated the association of PRDM9 with historical hotspot usage, finding that it explains most of the genetic variance in this phenotype. In addition, we identified a set of new candidate regions for further validation. SIGNIFICANCE These findings suggest that variation at broad and fine scales is largely separable and that, beyond three known loci, there is no evidence for common variation with large effects on recombination phenotypes.
Collapse
Affiliation(s)
- Adi Fledel-Alon
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Ellen Miranda Leffler
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Yongtao Guan
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Department of Statistics, University of Chicago, Chicago, Illinois, United States of America
| | - Matthew Stephens
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Department of Statistics, University of Chicago, Chicago, Illinois, United States of America
| | - Graham Coop
- Department of Evolution and Ecology and Center for Population Biology, University of California Davis, Davis, California, United States of America
| | - Molly Przeworski
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
- Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, United States of America
| |
Collapse
|
98
|
Abstract
Although very closely related species can differ in their fine-scale patterns of recombination hotspots, variation in the average genomic recombination rate among recently diverged taxa has rarely been surveyed. We measured recombination rates in eight species that collectively represent several temporal scales of divergence within a single rodent family, Muridae. We used a cytological approach that enables in situ visualization of crossovers at meiosis to quantify recombination rates in multiple males from each rodent group. We uncovered large differences in genomic recombination rate between rodent species, which were independent of karyotypic variation. The divergence in genomic recombination rate that we document is not proportional to DNA sequence divergence, suggesting that recombination has evolved at variable rates along the murid phylogeny. Additionally, we document significant variation in genomic recombination rate both within and between subspecies of house mice. Recombination rates estimated in F(1) hybrids reveal evidence for sex-linked loci contributing to the evolution of recombination in house mice. Our results provide one of the first detailed portraits of genomic-scale recombination rate variation within a single mammalian family and demonstrate that the low recombination rates in laboratory mice and rats reflect a more general reduction in recombination rate across murid rodents.
Collapse
|
99
|
Abstract
We examine the behavior of sexual and asexual populations in modular multipeaked fitness landscapes and show that sexuals can systematically reach different, higher fitness adaptive peaks than asexuals. Whereas asexuals must move against selection to escape local optima, sexuals reach higher fitness peaks reliably because they create specific genetic variants that "skip over" fitness valleys, moving from peak to peak in the fitness landscape. This occurs because recombination can supply combinations of mutations in functional composites or "modules," that may include individually deleterious mutations. Thus when a beneficial module is substituted for another less-fit module by sexual recombination it provides a genetic variant that would require either several specific simultaneous mutations in an asexual population or a sequence of individual mutations some of which would be selected against. This effect requires modular genomes, such that subsets of strongly epistatic mutations are tightly physically linked. We argue that such a structure is provided simply by virtue of the fact that genomes contain many genes each containing many strongly epistatic nucleotides. We briefly discuss the connections with "building blocks" in the evolutionary computation literature. We conclude that there are conditions in which sexuals can systematically evolve high-fitness genotypes that are essentially unevolvable for asexuals.
Collapse
Affiliation(s)
- Richard A Watson
- Natural Systems group, School of Electronics and Computer Science, University of Southampton, Southampton SO17 1BJ, United Kingdom.
| | | | | |
Collapse
|
100
|
Hiruta C, Nishida C, Tochinai S. Abortive meiosis in the oogenesis of parthenogenetic Daphnia pulex. Chromosome Res 2010; 18:833-40. [PMID: 20949314 DOI: 10.1007/s10577-010-9159-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 09/22/2010] [Accepted: 09/28/2010] [Indexed: 11/24/2022]
Abstract
Most daphnid species adopt parthenogenesis and sexual reproduction differentially in response to varied environmental cues, resulting in the production of diploid progenies in both cases. Previous studies have reportedly suggested that daphnids produce their parthenogenetic eggs via apomixis; the nuclear division of mature oocytes should be an equational division similar to somatic mitosis. However, it seems premature to conclude that this has been unequivocally established in any daphnids. Therefore, the objective of our research was to precisely reveal the process and mechanism of parthenogenetic oogenesis and maintenance of diploidy in Daphnia pulex through histology, karyology, and immunohistochemistry. We found that, when a parthenogenetic egg entered the first meiosis, division was arrested in the early first anaphase. Then, two half-bivalents, which were dismembered from each bivalent, moved back to the equatorial plate and assembled to form a diploid equatorial plate. Finally, the sister chromatids were separated and moved to opposite poles in the same manner as the second meiotic division followed by the extrusion of one extremely small daughter cell (resembling a polar body). These results suggest that parthenogenetic D. pulex do not adopt typical apomixis. We hypothesize that D. pulex switches reproductive mode depending on whether the egg is fertilized or not.
Collapse
Affiliation(s)
- Chizue Hiruta
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan.
| | | | | |
Collapse
|