101
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Miller MA, Cutter AD, Yamamoto I, Ward S, Greenstein D. Clustered organization of reproductive genes in the C. elegans genome. Curr Biol 2004; 14:1284-90. [PMID: 15268860 DOI: 10.1016/j.cub.2004.07.025] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2004] [Revised: 05/30/2004] [Accepted: 06/02/2004] [Indexed: 10/26/2022]
Abstract
Defining the forces that sculpt genome organization is fundamental for understanding the origin, persistence, and diversification of species. The genomic sequences of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae provide an excellent opportunity to explore the dynamics of chromosome evolution. Extensive chromosomal rearrangement has accompanied divergence from their common ancestor, an event occurring roughly 100 million years ago (Mya); yet, morphologically, these species are nearly indistinguishable and both reproduce primarily by self-fertilization. Here, we show that genes expressed during spermatogenesis (sperm genes) are nonrandomly distributed across the C. elegans genome into three large clusters located on two autosomes. In addition to sperm genes, these chromosomal regions are enriched for genes involved in the hermaphrodite sperm/oocyte switch and in the reception of sperm signals that control fertilization. Most loci are present in single copy, suggesting that cluster formation is largely due to gene aggregation and not to tandem duplication. Comparative mapping indicates that the C. briggsae genome differs dramatically from the C. elegans genome in clustering. Because clustered genes have a direct role in reproduction and thus fitness, their aggregated pattern might have been shaped by natural selection, perhaps as hermaphroditism evolved.
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Affiliation(s)
- Michael A Miller
- Department of Cell Biology, University of Alabama at Birmingham, 35294, USA.
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102
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Cutter AD, Ward S. Sexual and Temporal Dynamics of Molecular Evolution in C. elegans Development. Mol Biol Evol 2004; 22:178-88. [PMID: 15371532 DOI: 10.1093/molbev/msh267] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Dissection of the phenotypic and molecular details of development and differentiation is a centuries-old topic in evolutionary biology. However, an adequate understanding is missing for the molecular evolution of genes that are expressed differentially throughout development-across time, tissues, and the sexes. In this study, we investigate the dynamics of gene evolution across Caenorhabditis elegans ontogeny and among genes expressed differentially between each sex and gamete type. Using gene classes identified by genome-wide gene expression developmental time series and comparative sequence analysis with the congener C. briggsae, we demonstrate that genes expressed predominantly after reproductive maturity evolve more rapidly than genes expressed earlier in development and that genes expressed transiently during embryogenesis evolve faster than other embryonic transcripts. These results are indicative of relaxed selection on genes expressed after maturity, in accord with the mutation-accumulation model of aging. Furthermore, genes involved in spermatogenesis reveal more rapid evolution than other phenotypic classes of genes. Average rates of evolution among male soma-related genes indicates that selection acts to maintain males in these androdioecious species, despite their rarity, and the rapid evolution of sperm genes suggests that sexual selection acts on sperm development and function.
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Affiliation(s)
- Asher D Cutter
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, USA.
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103
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Marais G, Charlesworth B, Wright SI. Recombination and base composition: the case of the highly self-fertilizing plant Arabidopsis thaliana. Genome Biol 2004; 5:R45. [PMID: 15239830 PMCID: PMC463295 DOI: 10.1186/gb-2004-5-7-r45] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2004] [Revised: 04/26/2004] [Accepted: 04/30/2004] [Indexed: 11/24/2022] Open
Abstract
The effects of recombination and self-fertilization on base composition were investigated both theoretically and experimentally in the Arabidopsis genome. Levels of inbreeding modulate the effect of recombination on base composition. Background Rates of recombination can vary among genomic regions in eukaryotes, and this is believed to have major effects on their genome organization in terms of base composition, DNA repeat density, intron size, evolutionary rates and gene order. In highly self-fertilizing species such as Arabidopsis thaliana, however, heterozygosity is expected to be strongly reduced and recombination will be much less effective, so that its influence on genome organization should be greatly reduced. Results Here we investigated theoretically the joint effects of recombination and self-fertilization on base composition, and tested the predictions with genomic data from the complete A. thaliana genome. We show that, in this species, both codon-usage bias and GC content do not correlate with the local rates of crossing over, in agreement with our theoretical results. Conclusions We conclude that levels of inbreeding modulate the effect of recombination on base composition, and possibly other genomic features (for example, transposable element dynamics). We argue that inbreeding should be considered when interpreting patterns of molecular evolution.
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Affiliation(s)
- G Marais
- Institute of Cell, Animal and Population Biology, University of Edinburgh, EH9 3JT Edinburgh, UK
| | - B Charlesworth
- Institute of Cell, Animal and Population Biology, University of Edinburgh, EH9 3JT Edinburgh, UK
| | - S I Wright
- Institute of Cell, Animal and Population Biology, University of Edinburgh, EH9 3JT Edinburgh, UK
- Current address: Department of Biology, York University, 4700 Keele St, Toronto, Ontario M3J 1P3, Canada
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104
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Sweigart AL, Willis JH. Patterns of nucleotide diversity in two species of Mimulus are affected by mating system and asymmetric introgression. Evolution 2004; 57:2490-506. [PMID: 14686526 DOI: 10.1111/j.0014-3820.2003.tb01494.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The evolutionary transition from outcrossing to self-fertilization has far-reaching implications for patterns of intraspecific genetic diversity and the potential for speciation. Using DNA sequence variation at two nuclear loci, we examined the divergence history of two closely related species of Mimulus. To investigate the effects of mating system and introgressive hybridization on the outcrossing M. guttatus and the selfing M. nasutus, we inspected nucleotide diversity within and between natural populations spanning the species' geographic ranges. High sequence similarity among populations of the selfing M. nasutus points to a single evolutionary origin for the species. Consistent with their distinct mating systems, all genetic variation in M. nasutus is distributed among populations, whereas M. guttatus exhibits appreciable levels of nucleotide diversity within populations. Silent genetic diversity is extensive in M. guttatus (mean theta(sil)/site = 0.077) and greatly exceeds the predicted twofold elevation in neutral variation for outcrossers relative to selfers. The finding of several M. guttatus sequences that share complete identity with sequences from M. nasutus suggests that recent asymmetric introgression may have occurred. We argue that exceptionally high nucleotide diversity in M. guttatus is consistent with a long-term history of directional introgression from M. nasutus to M. guttatus throughout the divergence of these two species.
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Affiliation(s)
- Andrea L Sweigart
- Department of Biology, Duke University, Durham, North Carolina 27708, USA.
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105
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Charlesworth B, Charlesworth D, Barton NH. The Effects of Genetic and Geographic Structure on Neutral Variation. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2003. [DOI: 10.1146/annurev.ecolsys.34.011802.132359] [Citation(s) in RCA: 189] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Brian Charlesworth
- Institute for Cell, Animal, and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom;
| | - Deborah Charlesworth
- Institute for Cell, Animal, and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom;
| | - Nicholas H. Barton
- Institute for Cell, Animal, and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom;
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106
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Abstract
A variety of models propose that the accumulation of deleterious mutations plays an important role in the evolution of breeding systems. These models make predictions regarding the relative rates of protein evolution and deleterious mutation in taxa with contrasting modes of reproduction. Here we compare available coding sequences from one obligately outcrossing and two primarily selfing species of Caenorhabditis to explore the potential for mutational models to explain the evolution of breeding system in this clade. If deleterious mutations interact synergistically, the mutational deterministic hypothesis predicts that a high genomic deleterious mutation rate (U) will offset the reproductive disadvantage of outcrossing relative to asexual or selfing reproduction. Therefore, C. elegans and C. briggsae (both largely selfing) should both exhibit lower rates of deleterious mutation than the obligately outcrossing relative C. remanei. Using a comparative approach, we estimate U to be equivalent (and < 1) among all three related species. Stochastic mutational models, Muller's ratchet and Hill-Robertson interference, are expected to cause reductions in the effective population size in species that rarely outcross, thereby allowing deleterious mutations to accumulate at an elevated rate. We find only limited support for more rapid molecular evolution in selfing lineages. Overall, our analyses indicate that the evolution of breeding system in this group is unlikely to be explained solely by available mutational models.
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Affiliation(s)
- A D Cutter
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
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107
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Wright SI, Agrawal N, Bureau TE. Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana. Genome Res 2003; 13:1897-903. [PMID: 12902382 PMCID: PMC403781 DOI: 10.1101/gr.1281503] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Transposable elements (TEs) comprise a major component of eukaryotic genomes, and exhibit striking deviations from random distribution across the genomes studied, including humans, flies, nematodes, and plants. Although considerable progress has been made in documenting these patterns, the causes are subject to debate. Here, we use the genome sequence of Arabidopsis thaliana to test for the importance of competing models of natural selection against TE insertions. We show that, despite TE accumulation near the centromeres, recombination does not generally correlate with TE abundance, suggesting that selection against ectopic recombination does not influence TE distribution in A. thaliana. In contrast, a consistent negative correlation between gene density and TE abundance, and a strong under-representation of TE insertions in introns suggest that selection against TE disruption of gene expression is playing a more important role in A. thaliana. High rates of self-fertilization may reduce the importance of recombination rate in genome structuring in inbreeding organisms such as A. thaliana and Caenorhabditis elegans.
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Affiliation(s)
- Stephen I Wright
- Institute of Cell, Animal and Population Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, Scotland EH9 3JT, UK.
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108
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Charlesworth D. Effects of inbreeding on the genetic diversity of populations. Philos Trans R Soc Lond B Biol Sci 2003; 358:1051-70. [PMID: 12831472 PMCID: PMC1693193 DOI: 10.1098/rstb.2003.1296] [Citation(s) in RCA: 290] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The study of variability within species is important to all biologists who use genetic markers. Since the discovery of molecular variability among normal individuals, data have been collected from a wide range of organisms, and it is important to understand the major factors affecting diversity levels and patterns. Comparisons of inbreeding and outcrossing populations can contribute to this understanding, and therefore studying plant populations is important, because related species often have different breeding systems. DNA sequence data are now starting to become available from suitable plant and animal populations, to measure and compare variability levels and test predictions.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Cell, Animal and Population Biology (ICAPB), University of Edinburgh, Ashworth Laboratory, King's Buildings, West Mains Road, Edinburgh EH9 3JT, UK.
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109
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Jovelin R, Ajie BC, Phillips PC. Molecular evolution and quantitative variation for chemosensory behaviour in the nematode genus Caenorhabditis. Mol Ecol 2003; 12:1325-37. [PMID: 12694294 DOI: 10.1046/j.1365-294x.2003.01805.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Caenorhabditis elegans is a model organism in biology, yet despite the tremendous information generated from genetic, genomic and functional analyses, C. elegans has rarely been used to address questions in ecological genetics. Here, we analyse genetic variation for chemosensory behaviour, an ecologically important trait that is also genetically well characterized, at both the phenotypic and molecular levels within three species of the genus Caenorhabditis. We show that the G-protein ODR-3 plays an important role in chemosensory avoidance behaviour and identify orthologues of odr-3 in C. briggsae and C. remanei. Both quantitative genetic analysis of chemosensory behaviour and molecular population genetic analysis of odr-3 show that there is little genetic variation among a worldwide collection of isolates of the primarily selfing C. elegans, whereas there is substantially more variation within a single population of the outcrossing C. remanei. Although there are a large number of substitutions at silent sites within odr-3 among the three species, molecular evolution at the protein level is extremely conserved, suggesting that odr-3 plays an important role in cell signalling during chemosensation and/or neuronal cilia development in C. remanei and in C. briggsae as it does in C. elegans. Our results suggest that C. remanei may be a more suitable subject for ecological and evolutionary genetic studies than C. elegans.
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Affiliation(s)
- R Jovelin
- Center for Ecology and Evolutionary Biology, 5289 University of Oregon, Eugene, OR 97403-5289, USA
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110
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Sivasundar A, Hey J. Population genetics of Caenorhabditis elegans: the paradox of low polymorphism in a widespread species. Genetics 2003; 163:147-57. [PMID: 12586703 PMCID: PMC1462423 DOI: 10.1093/genetics/163.1.147] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Caenorhabditis elegans has become one of the most widely used model research organisms, yet we have little information on evolutionary processes and recent evolutionary history of this widespread species. We examined patterns of variation at 20 microsatellite loci in a sample of 23 natural isolates of C. elegans from various parts of the world. One-half of the loci were monomorphic among all strains, and overall genetic variation at microsatellite loci was low, relative to most other species. Some population structure was detected, but there was no association between the genetic and geographic distances among different natural isolates. Thus, despite the nearly worldwide occurrence of C. elegans, little evidence was found for local adaptation in strains derived from different parts of the world. The low levels of genetic variation within and among populations suggest that recent colonization and population expansion might have occurred. However, the patterns of variation are not consistent with population expansion. A possible explanation for the observed patterns is the action of background selection to reduce polymorphism, coupled with ongoing gene flow among populations worldwide.
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Affiliation(s)
- Arjun Sivasundar
- Department of Genetics, Rutgers University, Piscataway, New Jersey 08854-8082, USA
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111
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Sweigart AL, Willis JH. PATTERNS OF NUCLEOTIDE DIVERSITY IN TWO SPECIES OF MIMULUS ARE AFFECTED BY MATING SYSTEM AND ASYMMETRIC INTROGRESSION. Evolution 2003. [DOI: 10.1554/02-726] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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112
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Wright SI, Lauga B, Charlesworth D. Rates and patterns of molecular evolution in inbred and outbred Arabidopsis. Mol Biol Evol 2002; 19:1407-20. [PMID: 12200469 DOI: 10.1093/oxfordjournals.molbev.a004204] [Citation(s) in RCA: 167] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The evolution of self-fertilization is associated with a large reduction in the effective rate of recombination and a corresponding decline in effective population size. If many spontaneous mutations are slightly deleterious, this shift in the breeding system is expected to lead to a reduced efficacy of natural selection and genome-wide changes in the rates of molecular evolution. Here, we investigate the effects of the breeding system on molecular evolution in the highly self-fertilizing plant Arabidopsis thaliana by comparing its coding and noncoding genomic regions with those of its close outcrossing relative, the self-incompatible A. lyrata. More distantly related species in the Brassicaceae are used as outgroups to polarize the substitutions along each lineage. In contrast to expectations, no significant difference in the rates of protein evolution is observed between selfing and outcrossing Arabidopsis species. Similarly, no consistent overall difference in codon bias is observed between the species, although for low-biased genes A. lyrata shows significantly higher major codon usage. There is also evidence of intron size evolution in A. thaliana, which has consistently smaller introns than its outcrossing congener, potentially reflecting directional selection on intron size. The results are discussed in the context of heterogeneity in selection coefficients across loci and the effects of life history and population structure on rates of molecular evolution. Using estimates of substitution rates in coding regions and approximate estimates of divergence and generation times, the genomic deleterious mutation rate (U) for amino acid substitutions in Arabidopsis is estimated to be approximately 0.2-0.6 per generation.
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Affiliation(s)
- Stephen I Wright
- Institute of Cell, Animal, and Population Biology, Ashworth Laboratories, University of Edinburgh.
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