Local Recombination and Mutation Effects on Molecular Evolution in Drosophila

Genetics ◽  
1999 ◽  
Vol 153 (3) ◽  
pp. 1285-1296 ◽  
Author(s):  
Toshiyuki Takano-Shimizu
Keyword(s):  
Molecular Evolution ◽  
X Chromosome ◽  
Codon Bias ◽  
Synonymous Substitution ◽  
Mutational Bias ◽  
Recombination Rates ◽  
Substitution Pattern ◽  
Noncoding Regions ◽  
Significant Difference ◽  
Drosophila Yakuba

Abstract I studied the cause of the significant difference in the synonymous-substitution pattern found in the achaete-scute complex genes in two Drosophila lineages, higher codon bias in Drosophila yakuba, and lower bias in D. melanogaster. Besides these genes, the functionally unrelated yellow gene showed the same substitution pattern, suggesting a region-dependent phenomenon in the X-chromosome telomere. Because the numbers of A/T → G/C substitutions were not significantly different from those of G/C → A/T in the yellow noncoding regions of these species, a AT/GC mutational bias could not completely account for the synonymous-substitution biases. In contrast, we did find an ~14-fold difference in recombination rates in the X-chromosome telomere regions between the two species, suggesting that the reduction of recombination rates in this region resulted in the reduction of the efficacy of selection in D. melanogaster. In addition, the D. orena yellow showed a 5% increase in the G + C content at silent sites in the coding and noncoding regions since the divergence from D. erecta. This pattern was significantly different from those at the orena Adh and Amy loci. These results suggest that local changes in recombination rates and mutational pressures are contributing to the irregular synonymous-substitution patterns in Drosophila.

scholarly journals Runaway GC Evolution in Gerbil Genomes

2020 ◽  
Vol 37 (8) ◽  
pp. 2197-2210 ◽  
Author(s):  
Rodrigo Pracana ◽  
Adam D Hargreaves ◽  
John F Mulley ◽  
Peter W H Holland
Keyword(s):  
Rapid Evolution ◽  
Gc Content ◽  
Synonymous Substitution ◽  
Genomic Region ◽  
Recombination Rates ◽  
Substitution Pattern ◽  
Substitution Rates ◽  
Protein Coding ◽  
Murine Rodents ◽  
Genomic Regions

Abstract Recombination increases the local GC-content in genomic regions through GC-biased gene conversion (gBGC). The recent discovery of a large genomic region with extreme GC-content in the fat sand rat Psammomys obesus provides a model to study the effects of gBGC on chromosome evolution. Here, we compare the GC-content and GC-to-AT substitution patterns across protein-coding genes of four gerbil species and two murine rodents (mouse and rat). We find that the known high-GC region is present in all the gerbils, and is characterized by high substitution rates for all mutational categories (AT-to-GC, GC-to-AT, and GC-conservative) both at synonymous and nonsynonymous sites. A higher AT-to-GC than GC-to-AT rate is consistent with the high GC-content. Additionally, we find more than 300 genes outside the known region with outlying values of AT-to-GC synonymous substitution rates in gerbils. Of these, over 30% are organized into at least 17 large clusters observable at the megabase-scale. The unusual GC-skewed substitution pattern suggests the evolution of genomic regions with very high recombination rates in the gerbil lineage, which can lead to a runaway increase in GC-content. Our results imply that rapid evolution of GC-content is possible in mammals, with gerbil species providing a powerful model to study the mechanisms of gBGC.

scholarly journals A multispecies approach for comparing sequence evolution of X-linked and autosomal sites in Drosophila

2008 ◽  
Vol 90 (5) ◽  
pp. 421-431 ◽  
Author(s):  
BEATRIZ VICOSO ◽  
PENELOPE R. HADDRILL ◽  
BRIAN CHARLESWORTH
Keyword(s):  
Positive Selection ◽  
X Chromosome ◽  
Codon Bias ◽  
Purifying Selection ◽  
Drosophila Pseudoobscura ◽  
Sequence Evolution ◽  
Strong Positive Selection ◽  
Effective Selection ◽  
Efficient Selection ◽  
Drosophila Yakuba

SummaryPopulation genetics models show that, under certain conditions, the X chromosome is expected to be under more efficient selection than the autosomes. This could lead to ‘faster-X evolution’, if a large proportion of mutations are fixed by positive selection, as suggested by recent studies in Drosophila. We used a multispecies approach to test this: Muller's element D, an autosomal arm, is fused to the ancestral X chromosome in Drosophila pseudoobscura and its sister species, Drosophila affinis. We tested whether the same set of genes had higher rates of non-synonymous evolution when they were X-linked (in the D. pseudoobscura/D. affinis comparison) than when they were autosomal (in Drosophila melanogaster/Drosophila yakuba). Although not significant, our results suggest this may be the case, but only for genes under particularly strong positive selection/weak purifying selection. They also suggest that genes that have become X-linked have higher levels of codon bias and slower synonymous site evolution, consistent with more effective selection on codon usage at X-linked sites.

scholarly journals Natural Selection on Synonymous Sites Is Correlated With Gene Length and Recombination in Drosophila

Genetics ◽  
1999 ◽  
Vol 151 (1) ◽  
pp. 239-249 ◽  
Author(s):  
Josep M Comeron ◽  
Martin Kreitman ◽  
Montserrat Aguadé
Keyword(s):  
Natural Selection ◽  
Codon Bias ◽  
Synonymous Substitution ◽  
Small Scale ◽  
Evolutionary Analysis ◽  
Coding Region ◽  
Weak Selection ◽  
Recombination Rates ◽  
Synonymous Mutations ◽  
Synonymous Sites

AbstractEvolutionary analysis of codon bias in Drosophila indicates that synonymous mutations are not neutral, but rather are subject to weak selection at the translation level. Here we show that the effectiveness of natural selection on synonymous sites is strongly correlated with the rate of recombination, in accord with the nearly neutral hypothesis. This correlation, however, is apparent only in genes encoding short proteins. Long coding regions have both a lower codon bias and higher synonymous substitution rates, suggesting that they are affected less efficiently by selection. Therefore, both the length of the coding region and the recombination rate modulate codon bias. In addition, the data indicate that selection coefficients for synonymous mutations must vary by a minimum of one or two orders of magnitude. Two hypotheses are proposed to explain the relationship among the coding region length, the codon bias, and the synonymous divergence and polymorphism levels across the range of recombination rates in Drosophila. The first hypothesis is that selection coefficients on synonymous mutations are inversely related to the total length of the coding region. The second hypothesis proposes that interference among synonymous mutations reduces the efficacy of selection on these mutations. We investigated this second hypothesis by carrying out forward simulations of weakly selected mutations in model populations. These simulations show that even with realistic recombination rates, this interference, which we call the “small-scale” Hill-Robertson effect, can have a moderately strong influence on codon bias.

Protein Evolution and Codon Usage Bias on the Neo-Sex Chromosomes of Drosophila miranda

Genetics ◽  
2003 ◽  
Vol 165 (3) ◽  
pp. 1221-1232
Author(s):  
Doris Bachtrog
Keyword(s):  
Amino Acid ◽  
Molecular Evolution ◽  
Y Chromosome ◽  
Protein Evolution ◽  
Sex Chromosomes ◽  
Codon Bias ◽  
Mutational Bias ◽  
Significant Heterogeneity ◽  
Synonymous Mutations ◽  
Ideal System

Abstract The neo-sex chromosomes of Drosophila miranda constitute an ideal system to study the effects of recombination on patterns of genome evolution. Due to a fusion of an autosome with the Y chromosome, one homolog is transmitted clonally. Here, I compare patterns of molecular evolution of 18 protein-coding genes located on the recombining neo-X and their homologs on the nonrecombining neo-Y chromosome. The rate of protein evolution has significantly increased on the neo-Y lineage since its formation. Amino acid substitutions are accumulating uniformly among neo-Y-linked genes, as expected if all loci on the neo-Y chromosome suffer from a reduced effectiveness of natural selection. In contrast, there is significant heterogeneity in the rate of protein evolution among neo-X-linked genes, with most loci being under strong purifying selection and two genes showing evidence for adaptive evolution. This observation agrees with theory predicting that linkage limits adaptive protein evolution. Both the neo-X and the neo-Y chromosome show an excess of unpreferred codon substitutions over preferred ones and no difference in this pattern was observed between the chromosomes. This suggests that there has been little or no selection maintaining codon bias in the D. miranda lineage. A change in mutational bias toward AT substitutions also contributes to the decline in codon bias. The contrast in patterns of molecular evolution between amino acid mutations and synonymous mutations on the neo-sex-linked genes can be understood in terms of chromosome-specific differences in effective population size and the distribution of selective effects of mutations.

scholarly journals Patterns of DNA Variability at X-Linked Loci in Mus domesticus

Genetics ◽  
1997 ◽  
Vol 147 (3) ◽  
pp. 1303-1316
Author(s):  
Michael W Nachman
Keyword(s):  
Drosophila Melanogaster ◽  
X Chromosome ◽  
House Mouse ◽  
Recombination Rate ◽  
Nucleotide Diversity ◽  
Mus Domesticus ◽  
Substantial Variation ◽  
Intraspecific Polymorphism ◽  
Recombination Rates ◽  
Interspecific Divergence

Introns of four X-linked genes (Hprt, Plp, Glra2, and Amg) were sequenced to provide an estimate of nucleotide diversity at nuclear genes within the house mouse and to test the neutral prediction that the ratio of intraspecific polymorphism to interspecific divergence is the same for different loci. Hprt and Plp lie in a region of the X chromosome that experiences relatively low recombination rates, while Glra2 and Amg lie near the telomere of the X chromosome, a region that experiences higher recombination rates. A total of 6022 bases were sequenced in each of 10 Mus domesticus and one M. caroli. Average nucleotide diversity (π) for introns within M. domesticus was quite low (π = 0.078%). However, there was substantial variation in the level of heterozygosity among loci. The two telomeric loci, Glra2 and Amg, had higher ratios of polymorphism to divergence than the two loci experiencing lower recombination rates. These results are consistent with the hypothesis that heterozygosity is reduced in regions with lower rates of recombination, although sampling of additional genes is needed to establish whether there is a general correlation between heterozygosity and recombination rate as in Drosophila melanogaster.

scholarly journals Vanishing GC-Rich Isochores in Mammalian Genomes

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1837-1847 ◽  
Author(s):  
Laurent Duret ◽  
Marie Semon ◽  
Gwenaël Piganeau ◽  
Dominique Mouchiroud ◽  
Nicolas Galtier
Keyword(s):  
Gc Content ◽  
Synonymous Substitution ◽  
Equilibrium Analysis ◽  
Large Excess ◽  
Substitution Pattern ◽  
Origin And Evolution ◽  
Evolutionary Force ◽  
Mammalian Genomes ◽  
Human Polymorphism ◽  
Probability Of Fixation

AbstractTo understand the origin and evolution of isochores—the peculiar spatial distribution of GC content within mammalian genomes—we analyzed the synonymous substitution pattern in coding sequences from closely related species in different mammalian orders. In primate and cetartiodactyls, GC-rich genes are undergoing a large excess of GC → AT substitutions over AT → GC substitutions: GC-rich isochores are slowly disappearing from the genome of these two mammalian orders. In rodents, our analyses suggest both a decrease in GC content of GC-rich isochores and an increase in GC-poor isochores, but more data will be necessary to assess the significance of this pattern. These observations question the conclusions of previous works that assumed that base composition was at equilibrium. Analysis of allele frequency in human polymorphism data, however, confirmed that in the GC-rich parts of the genome, GC alleles have a higher probability of fixation than AT alleles. This fixation bias appears not strong enough to overcome the large excess of GC → AT mutations. Thus, whatever the evolutionary force (neutral or selective) at the origin of GC-rich isochores, this force is no longer effective in mammals. We propose a model based on the biased gene conversion hypothesis that accounts for the origin of GC-rich isochores in the ancestral amniote genome and for their decline in present-day mammals.

Abstract WP325: X, but Not Y, Sex Chromosome Contributes to Stroke Sensitivity in Aged Mice

Stroke ◽  
2020 ◽  
Vol 51 (Suppl_1) ◽  
Author(s):  
Shaohua Qi ◽  
Abdullah Al Mamun ◽  
Romana Sharmeen ◽  
Conelius Ngwa ◽  
Louise D. McCullough ◽  
...  
Keyword(s):  
X Chromosome ◽  
Sex Chromosome ◽  
Elderly Women ◽  
The Elderly ◽  
Artery Occlusion ◽  
Natural Menopause ◽  
Aged Mice ◽  
Tnf Α ◽  
Significant Difference ◽  
Four Core Genotype

Introduction: Stroke is a sexually dimorphic disease. Women are protected against ischemia compared to men before menopause due to estrogen’s neuroprotection; after menopause the elderly women become vulnerable to stroke attack. Our previous studies with four core genotype mice found a chromosomal effect (either X or Y) in stroke sensitivity. Recently, we found two X-linked genes ( Kdm6a and Kdm5c ) that escape from X chromosome inactivation (XCI) are higher expressed in aged female vs. male microglia after stroke. KDM6A and KDM5C are histone demethylases that modify gene expression of inflammatory mediators. By these early studies, we hypothesized that the second X chromosome contributes to stroke sensitivity in aged mice through immune responses mediated by KDM6A and KDM5C. Methods: XY* aged (18-22 months) mice (natural menopause cohort) that have four genotypes (XO, XX, XY, XXY) were subjected to middle cerebral artery occlusion (MCAO). Another cohort of gonadectomized XY* mice were also used as the “surgical menopause” cohort. Infarct volumes and behavior deficits were quantified 3 days after MCAO. KDM6A and KDM5C localization with microglial marker TMEM119 was examined by IHC. Plasma inflammatory cytokine (IL-1β, TNF-α, IL-6, IL-4, TL-10, etc.) levels were analyzed with MultiPlex. The contribution of the second X-chromosome to stroke sensitivity was determined by comparing XX vs. XO or XXY vs. XY mice, and the effect of the Y-chromosome was evaluated by a comparison between XY vs. XO and XXY vs. XX mice. Results: In both surgical and natural menopause cohorts, XX and XXY mice showed worse stroke outcomes compared to XO or XY mice respectively; however, no significant difference was found between XX vs. XXY or XO vs. XY mice. IHC results showed higher expression of KDM6A and KDM5C in TMEM119 positive cells in mice with two vs. one copy of X chromosome. XXY mice had significantly higher levels of circulating TNF-α and IL-6 than XY mice. Conclusion: The second X chromosome contributes to stroke sensitivity in mice. Kdm6a and Kdm5c may play important roles in mediating post-stroke inflammation. Future work will genetically manipulate the expression of Kdm6a and Kdm5c in microglia to examine the roles of the two XCI escapee gene in stroke.

scholarly journals Eusociality Shapes Convergent Patterns of Molecular Evolution across Mitochondrial Genomes of Snapping Shrimps

2020 ◽  
Author(s):  
Solomon T C Chak ◽  
Juan Antonio Baeza ◽  
Phillip Barden
Keyword(s):  
Molecular Evolution ◽  
Genome Evolution ◽  
Purifying Selection ◽  
Synonymous Substitution ◽  
Mitochondrial Genomes ◽  
Comparative Genomic ◽  
Effective Population ◽  
Protein Coding ◽  
Marine Realm ◽  
Snapping Shrimps

Abstract Eusociality is a highly conspicuous and ecologically impactful behavioral syndrome that has evolved independently across multiple animal lineages. So far, comparative genomic analyses of advanced sociality have been mostly limited to insects. Here, we study the only clade of animals known to exhibit eusociality in the marine realm—lineages of socially diverse snapping shrimps in the genus Synalpheus. To investigate the molecular impact of sociality, we assembled the mitochondrial genomes of eight Synalpheus species that represent three independent origins of eusociality and analyzed patterns of molecular evolution in protein-coding genes. Synonymous substitution rates are lower and potential signals of relaxed purifying selection are higher in eusocial relative to noneusocial taxa. Our results suggest that mitochondrial genome evolution was shaped by eusociality-linked traits—extended generation times and reduced effective population sizes that are hallmarks of advanced animal societies. This is the first direct evidence of eusociality impacting genome evolution in marine taxa. Our results also strongly support the idea that eusociality can shape genome evolution through profound changes in life history and demography.

Mitochondrial genomes of Vanhornia eucnemidarum (Apocrita: Vanhorniidae) and Primeuchroeus spp. (Aculeata: Chrysididae): evidence of rearranged mitochondrial genomes within the Apocrita (Insecta: Hymenoptera)

Genome ◽  
2006 ◽  
Vol 49 (7) ◽  
pp. 752-766 ◽  
Author(s):  
Lyda Raquel Castro ◽  
Kalani Ruberu ◽  
Mark Dowton
Keyword(s):  
Molecular Evolution ◽  
Gene Duplication ◽  
Ribosomal Rna ◽  
Nucleotide Composition ◽  
Gene Organization ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Noncoding Regions ◽  
Mt Genome ◽  
Rna Genes

We sequenced most of the mitochondrial (mt) genomes of 2 apocritan taxa: Vanhornia eucnemidarum and Primeuchroeus spp. These mt genomes have similar nucleotide composition and codon usage to those of mt genomes reported for other Hymenoptera, with a total A + T content of 80.1% and 78.2%, respectively. Gene content corresponds to that of other metazoan mt genomes, but gene organization is not conserved. There are a total of 6 tRNA genes rearranged in V. eucnemidarum and 9 in Primeuchroeus spp. Additionally, several noncoding regions were found in the mt genome of V. eucnemidarum, as well as evidence of a sustained gene duplication involving 3 tRNA genes. We also report an inversion of the large and small ribosomal RNA genes in Primeuchroeus spp. mt genome. However, none of the rearrangements reported are phylogenetically informative with respect to the current taxon sample.Key words: mitochondrial genomes, molecular evolution, hymenoptera.

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