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Rousselle M, Faivre N, Ballenghien M, Galtier N, Nabholz B. Hemizygosity Enhances Purifying Selection: Lack of Fast-Z Evolution in Two Satyrine Butterflies. Genome Biol Evol 2016; 8:3108-3119. [PMID: 27590089 PMCID: PMC5174731 DOI: 10.1093/gbe/evw214] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The fixation probability of a recessive beneficial mutation is increased on the X or Z chromosome, relative to autosomes, because recessive alleles carried by X or Z are exposed to selection in the heterogametic sex. This leads to an increased dN/dS ratio on sex chromosomes relative to autosomes, a pattern called the “fast-X” or “fast-Z” effect. Besides positive selection, the strength of genetic drift and the efficacy of purifying selection, which affect the rate of molecular evolution, might differ between sex chromosomes and autosomes. Disentangling the complex effects of these distinct forces requires the genome-wide analysis of polymorphism, divergence and gene expression data in a variety of taxa. Here we study the influence of hemizygosity of the Z chromosome in Maniola jurtina and Pyronia tithonus, two species of butterflies (Lepidoptera, Nymphalidae, Satyrinae). Using transcriptome data, we compare the strength of positive and negative selection between Z and autosomes accounting for sex-specific gene expression. We show that M. jurtina and P. tithonus do not experience a faster, but rather a slightly slower evolutionary rate on the Z than on autosomes. Our analysis failed to detect a significant difference in adaptive evolutionary rate between Z and autosomes, but comparison of male-biased, unbiased and female-biased Z-linked genes revealed an increased efficacy of purifying selection against recessive deleterious mutations in female-biased Z-linked genes. This probably contributes to the lack of fast-Z evolution of satyrines. We suggest that the effect of hemizygosity on the fate of recessive deleterious mutations should be taken into account when interpreting patterns of molecular evolution in sex chromosomes vs. autosomes.
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Affiliation(s)
- Marjolaine Rousselle
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France
| | - Nicolas Faivre
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France
| | - Marion Ballenghien
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France
| | - Nicolas Galtier
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France
| | - Benoit Nabholz
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France
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Delph LF, Demuth JP. Haldane’s Rule: Genetic Bases and Their Empirical Support. J Hered 2016; 107:383-91. [DOI: 10.1093/jhered/esw026] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/27/2016] [Indexed: 11/14/2022] Open
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Mank JE, Nam K, Ellegren H. Faster-Z Evolution Is Predominantly Due to Genetic Drift. Mol Biol Evol 2009; 27:661-70. [DOI: 10.1093/molbev/msp282] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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Singh ND, Arndt PF, Clark AG, Aquadro CF. Strong evidence for lineage and sequence specificity of substitution rates and patterns in Drosophila. Mol Biol Evol 2009; 26:1591-605. [PMID: 19351792 DOI: 10.1093/molbev/msp071] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Rates of single nucleotide substitution in Drosophila are highly variable within the genome, and several examples illustrate that evolutionary rates differ among Drosophila species as well. Here, we use a maximum likelihood method to quantify lineage-specific substitutional patterns and apply this method to 4-fold degenerate synonymous sites and introns from more than 8,000 genes aligned in the Drosophila melanogaster group. We find that within species, different classes of sequence evolve at different rates, with long introns evolving most slowly and short introns evolving most rapidly. Relative rates of individual single nucleotide substitutions vary approximately 3-fold among lineages, yielding patterns of substitution that are comparatively less GC-biased in the melanogaster species complex relative to Drosophila yakuba and Drosophila erecta. These results are consistent with a model coupling a mutational shift toward reduced GC content, or a shift in mutation-selection balance, in the D. melanogaster species complex, with variation in selective constraint among different classes of DNA sequence. Finally, base composition of coding and intronic sequences is not at equilibrium with respect to substitutional patterns, which primarily reflects the slow rate of the substitutional process. These results thus support the view that mutational and/or selective processes are labile on an evolutionary timescale and that if the process is indeed selection driven, then the distribution of selective constraint is variable across the genome.
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Affiliation(s)
- Nadia D Singh
- Department of Molecular Biology and Genetics, Cornell University.
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Parsch J, Zhang Z, Baines JF. The influence of demography and weak selection on the McDonald-Kreitman test: an empirical study in Drosophila. Mol Biol Evol 2009; 26:691-8. [PMID: 19126864 DOI: 10.1093/molbev/msn297] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The McDonald-Kreitman (MK) test, which compares the ratio of polymorphism to divergence at nonsynonymous and synonymous sites, is frequently used to detect adaptive evolution in protein-coding sequences. Because the two classes of sites share a common evolutionary history, the MK test is thought to be robust to most demographic factors. However, weak selection on nonsynonymous sites can bias the MK test, especially when a species' effective population size has not been constant. Here, we present an empirical analysis of the influence of demography on the MK test by comparing test results for a common set of 136 genes, including a set of sex-biased genes that shows a strong signal of adaptive evolution, in two Drosophila melanogaster populations: an ancestral population from Africa and a derived population from Europe. The latter has undergone a relatively recent bottleneck, which has reduced its effective population size. We find that the MK test has less power to detect positive selection in the European population for two reasons. First, the overall reduced level of standing variation decreases the statistical power of the test. Second, the segregation of slightly deleterious nonsynonymous mutations biases the MK test away from detecting positive selection. The latter effect is stronger for X-linked genes, which have experienced the greatest reduction in effective population size outside of Africa, and also leads to the underestimation of rates of adaptive protein evolution by multilocus implementations of the MK test. Interestingly, a subset of autosomal female-biased genes shows an increased signal of adaptive evolution in the European population. This is inconsistent with currently accepted demographic scenarios and may reflect female-specific changes in selective constraint following the colonization of non-African habitats.
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Affiliation(s)
- John Parsch
- Department of Biology, University of Munich, Germany.
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Takahashi KH, Tanaka K, Itoh M, Takano-Shimizu T. Reduced X-linked rare polymorphism in males in comparison to females of Drosophila melanogaster. J Hered 2008; 100:97-105. [PMID: 18836147 DOI: 10.1093/jhered/esn078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Natural selection is assumed to act more strongly on X-linked loci than on autosomal loci because the fitness effect of a recessive mutation on the X chromosome is fully expressed in hemizygous males. Therefore, selection is expected to fix or remove recessive mutations on the X chromosome more efficiently than those on autosomes. However, the assumption that hemizygosity of the X chromosome selectively accelerates changes in allele frequency has not been confirmed directly. To examine this assumption, we investigated current natural selection on X-linked chemoreceptor genes in a natural population of Drosophila melanogaster by comparing nucleotide diversity, linkage disequilibrium (LD), and departure from the neutrality in 4 chemoreceptor genes on 100 X chromosomes each from female and male flies. The general pattern of nucleotide diversity and LD for the genes investigated was similar in females and males. In contrast, males harbored significantly fewer rare polymorphisms defined as singletons and doubletons. When all the gene sequences were concatenated, Tajima's D showed a significant departure from the neutrality in both females and males, whereas Fu and Li's F* value revealed departure only in males. These results suggest that some rare polymorphisms on the X chromosome from females are recessively deleterious and are removed by stronger purifying selection when transferred to hemizygous males.
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Affiliation(s)
- Kazuo H Takahashi
- Department of Population Genetics, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
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Baines JF, Sawyer SA, Hartl DL, Parsch J. Effects of X-linkage and sex-biased gene expression on the rate of adaptive protein evolution in Drosophila. Mol Biol Evol 2008; 25:1639-50. [PMID: 18477586 DOI: 10.1093/molbev/msn111] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Patterns of polymorphism and divergence in Drosophila protein-coding genes suggest that a considerable fraction of amino acid differences between species can be attributed to positive selection and that genes with sex-biased expression, that is, those expressed predominantly in one sex, have especially high rates of adaptive evolution. Previous studies, however, have been restricted to autosomal sex-biased genes and, thus, do not provide a complete picture of the evolutionary forces acting on sex-biased genes across the genome. To determine the effects of X-linkage on sex-biased gene evolution, we surveyed DNA sequence polymorphism and divergence in 45 X-linked genes, including 17 with male-biased expression, 13 with female-biased expression, and 15 with equal expression in the 2 sexes. Using both single- and multilocus tests for selection, we found evidence for adaptive evolution in both groups of sex-biased genes. The signal of adaptive evolution was particularly strong for X-linked male-biased genes. A comparison with data from 91 autosomal genes revealed a "fast-X" effect, in which the rate of adaptive evolution was greater for X-linked than for autosomal genes. This effect was strongest for male-biased genes but could be seen in the other groups as well. A genome-wide analysis of coding sequence divergence that accounted for sex-biased expression also uncovered a fast-X effect for male-biased and unbiased genes, suggesting that recessive beneficial mutations play an important role in adaptation.
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Affiliation(s)
- John F Baines
- Section of Evolutionary Biology, Department of Biology, University of Munich, 82152 Munich, Germany
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Macholán M, Munclinger P, Sugerková M, Dufková P, Bímová B, Bozíková E, Zima J, Piálek J. Genetic analysis of autosomal and X-linked markers across a mouse hybrid zone. Evolution 2007; 61:746-71. [PMID: 17439609 DOI: 10.1111/j.1558-5646.2007.00065.x] [Citation(s) in RCA: 169] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
In this paper, we present results of the first comprehensive study of the introgression of both autosomal and sex-chromosome markers across the central European portion of the hybrid zone between two house mouse subspecies, Mus musculus musculus and M. m. domesticus. More than 1800 individuals sampled from 105 sites were analyzed with a set of allozyme loci (hopefully representing neutral or nearly neutral markers) and X-linked loci (which are assumed to be under selection). The zone center is best modeled as a single straight line independent of fine-scale local geographic or climatic conditions, being maintained by a balance between dispersal and selection against hybrids. The width (w) of the multilocus autosomal cline was estimated as 9.6 km whereas the estimate for the compound X-chromosome cline was about 4.6 km only. As the former estimate is comparable to that of the Danish portion of the zone (assumed to be much younger than the central European one), zone width does not appear to be related to its age. The strength (B) of the central barrier was estimated as about 20 km; with dispersal (sigma) of about 1 km/gen(1/2), this means effective selection (s*) is approximately 0.06-0.09 for autosomal loci and about 0.25 for X-linked loci. The number of loci under selection was estimated as N= 56-99 for autosomes and about 380 for X-linked loci. Finally, we highlight some potential pitfalls in hybrid zone analyses and in comparisons of different transects. We suggest that conclusions about parts of the mouse genome involved in reproductive isolation and speciation should be drawn with caution and that analytical approaches always providing some estimates should not be used without due care regarding the support or confidence of such estimates, especially if conclusions are based on the difference between these estimates. Finally, we recommend that analysis in two-dimensional space, dense sampling, and rigorous treatment of data, including inspection of likelihood profiles, are essential for hybrid zone studies.
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Affiliation(s)
- Milos Macholán
- Laboratory of Mammalian Evolutionary Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, 60200 Brno, Czech Republic.
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Mank JE, Axelsson E, Ellegren H. Fast-X on the Z: rapid evolution of sex-linked genes in birds. Genes Dev 2007; 17:618-24. [PMID: 17416747 PMCID: PMC1855182 DOI: 10.1101/gr.6031907] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2006] [Accepted: 03/06/2007] [Indexed: 01/08/2023]
Abstract
Theoretical work predicts natural selection to be more efficient in the fixation of beneficial mutations in X-linked genes than in autosomal genes. This "fast-X effect" should be evident by an increased ratio of nonsynonymous to synonymous substitutions (dN/dS) for sex-linked genes; however, recent studies have produced mixed support for this expectation. To make an independent test of the idea of fast-X evolution, we focused on birds, which have female heterogamety (males ZZ, females ZW), where analogous arguments would predict a fast-Z effect. We aligned 2.8 Mb of orthologous protein-coding sequence of zebra finch and chicken from 172 Z-linked and 4848 autosomal genes. Zebra finch data were in the form of EST sequences from brain cDNA libraries, while chicken genes were from the draft genome sequence. The dN/dS ratio was significantly higher for Z-linked (0.110) than for all autosomal genes (0.085; P=0.002), as well as for genes linked to similarly sized autosomes 1-10 (0.0948; P=0.04). This pattern of fast-Z was evident even after we accounted for the nonrandom distribution of male-biased genes. We also examined the nature of standing variation in the chicken protein-coding regions. The ratio of nonsynonymous to synonymous polymorphism (pN/pS) did not differ significantly between genes on the Z chromosome (0.104) and on the autosomes (0.0908). In conjunction, these results suggest that evolution proceeds more quickly on the Z chromosome, where hemizygous exposure of beneficial nondominant mutations increases the rate of fixation.
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Affiliation(s)
- Judith E. Mank
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, SE 752 36 Uppsala, Sweden
| | - Erik Axelsson
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, SE 752 36 Uppsala, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, SE 752 36 Uppsala, Sweden
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Thornton K, Bachtrog D, Andolfatto P. X chromosomes and autosomes evolve at similar rates in Drosophila: no evidence for faster-X protein evolution. Genes Dev 2006; 16:498-504. [PMID: 16520459 PMCID: PMC1457026 DOI: 10.1101/gr.4447906] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Accepted: 12/21/2005] [Indexed: 01/07/2023]
Abstract
Recent data from Drosophila suggest that a substantial fraction of amino acid substitutions observed between species are beneficial. If these beneficial mutations are on average partially recessive, then the rate of protein evolution is predicted to be faster for X-linked genes compared to autosomal genes (the "faster-X" hypothesis). We test this prediction by comparing rates of protein substitutions between orthologous genes, taking advantage of variations in chromosome fusions within the genus Drosophila. In members of the Drosophila melanogaster species group, the chromosomal arm 3L segregates as an ordinary autosome (i.e., two homologous copies in both males and females). However, in the Drosophila pseudoobscura species group, this chromosomal arm has become fused to the ancestral X chromosome and is hemizygous in males. The faster-X hypothesis predicts that protein evolution should be faster for genes on this chromosomal arm in the D. pseudoobscura lineage, relative to the D. melanogaster lineage. Here we combine new sequence data for 202 gene fragments in Drosophila miranda (in the pseudoobscura species group) with the completed genomes of D. melanogaster, D. pseudoobscura, and Drosophila yakuba to show that there are no detectable differences in rates of amino acid evolution for orthologous X-linked and autosomal genes. Our results imply that the contribution of the faster-X (if any) to the large-X effect on reproductive isolation in Drosophila is not due to a generally faster rate of protein evolution. The lack of a detectable faster-X effect in these species suggests either that beneficial amino acids are not partially recessive on average, or that adaptive evolution does not often use newly arising amino acid mutations.
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Affiliation(s)
- Kevin Thornton
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.
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Slotman M, Torre AD, Powell JR. FEMALE STERILITY IN HYBRIDS BETWEEN ANOPHELES GAMBIAE AND A. ARABIENSIS, AND THE CAUSES OF HALDANE'S RULE. Evolution 2005. [DOI: 10.1111/j.0014-3820.2005.tb01040.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Lu J, Wu CI. Weak selection revealed by the whole-genome comparison of the X chromosome and autosomes of human and chimpanzee. Proc Natl Acad Sci U S A 2005; 102:4063-7. [PMID: 15728731 PMCID: PMC554819 DOI: 10.1073/pnas.0500436102] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The effect of weak selection driving genome evolution has attracted much attention in the last decade, but the task of measuring the strength of such selection is particularly difficult. A useful approach is to contrast the evolution of X-linked and autosomal genes in two closely related species in a whole-genome analysis. If the fitness effect of mutations is recessive, X-linked genes should evolve more rapidly than autosomal genes when the mutations are advantageous, and they should evolve more slowly than autosomal genes when the mutations are deleterious. We found synonymous substitutions on the X chromosome of human and chimpanzee to be less frequent than those on the autosomes. When calibrated against substitutions in the intergenic regions and pseudogenes to filter out the differences in the mutation rate and ancestral population size between X chromosomes and autosomes, X-linked synonymous substitutions are still 10% less frequent. At least 90% of the synonymous substitutions in human and chimpanzee are estimated to be deleterious, but the fitness effect is weaker than the effect of genetic drift. However, X-linked nonsynonymous substitutions are approximately 30% more frequent than autosomal ones, suggesting the fixation of advantageous mutations that are recessive.
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Affiliation(s)
- Jian Lu
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
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