ライフサイエンスコーパス: substitution rate

1 ple evolutionary concepts: mutation rate and substitution rate.

2 tion for regional differences in the neutral substitution rate.

3 tion rate Ks reflects the neutral nucleotide substitution rate.

4 random and can be measured by the synonymous substitution rate.

5 the non-synonymous as well as the synonymous substitution rate.

6 onymous substitution rate and the synonymous substitution rate.

7 els") occur at approximately 5% of the point substitution rate.

8 the large acceleration in associative ligand substitution rate.

9 can increase or decrease the effective local substitution rate.

10 y size and mass-specific metabolic rate with substitution rate.

11 a negative correlation between body size and substitution rate.

12 lding a direct estimate of the mitochondrial substitution rate.

13 rage are 3.5-fold higher than the Acc intron substitution rates.

14 ecies ecology or lineage specific nucleotide substitution rates.

15 and the inaccuracy of estimates of specific substitution rates.

16 f any influence of body size on invertebrate substitution rates.

17 cient to explain the variation of nucleotide substitution rates.

18 a preponderance of conservative nor radical substitution rates.

19 odified alcohol content even at higher juice substitution rates.

20 y signals significantly constrain synonymous substitution rates.

21 ion of the tree topology, branch lengths and substitution rates.

22 n preferences and patterns of variation with substitution rates.

23 derlie the extensive variation in synonymous substitution rates.

24 impanzee and bonobo, experienced accelerated substitution rates.

25 there exists substantial variation in yearly substitution rates.

26 the wild type due to increased nonsynonymous substitution rates.

27 breakpoints, molecular adaptation and codon substitution rates.

28 orizontally transferred genes and changes in substitution rates.

29 ociation between mass-specific metabolic and substitution rates.

30 iversification does not require "virus-like" substitution rates.

31 ty (HPD): 22,000-47,100 years ago (estimated substitution rate: 2.2 x 10(-6) ; 95% HPD: 1.5-3.0 x 10(

32 s into Mali, and we show that the nucleotide substitution rate (9.6 x 10(-4) substitutions per site p

33 nd correlates of such drastic differences in substitution rates across a diverse and significant clad

34 aximum-likelihood estimates of nonsynonymous substitution rates across Buchnera species are strikingl

35 ysis, from inferring phylogeny to estimating substitution rates across different lineages.

36 y simple and naturally accommodates variable substitution rates across different sites, without requi

37 ere was extreme heterogeneity in the plastid substitution rates across the commelinid orders indicate

38 The relative substitution rates across the protein structure and at t

39 Synonymous substitution rates also are greatly reduced in the centr

40 Genes with above-average substitution rates also exhibit significant, though some

41 cularly serious if there is variation in the substitution rate among sites brought about by variation

42 expansion/contraction on plastid nucleotide substitution rates among closely related species remains

43 Further, there is considerable variation in substitution rates among loci as some protein-coding dom

44 and reveals large variability of nucleotide substitution rates among plant nuclear genomes.

45 tribute to the large variation in nucleotide substitution rates among RNA viruses remains unclear.

46 sses; they may be confounded by variation in substitution rates among sites and changes in evolutiona

47 th variation in synonymous and nonsynonymous substitution rates among sites and found evidence for di

48 Because of variability in DNA substitution rates among taxa and genes, deviation from

49 aviruses have some of the highest nucleotide substitution rates among viruses, but there have been no

50 hanges, alternative splicing (AS), and codon substitution rates among wheat and model grass genomes.

51 Synonymous substitution rate analyses of the multicopy MSY genes in

52 ip was further supported by phylogenetic and substitution rate analyses, which suggest that the linea

53 ry distance estimation, phylogeny inference, substitution rate and pattern estimation, tests of natur

54 We find a simple relation between the substitution rate and the rate of change of the optimal

55 ositively correlated with both nonsynonymous substitution rate and the sample specificity of DNA meth

56 from a comparison between the nonsynonymous substitution rate and the synonymous substitution rate.

57 iability in extraction dynamics according to substitution rate and type of blending component.

58 vious signs of temporal inhomogeneity in the substitution rates and concluded that the conserved inte

59 alyses reveal wide variation among estimated substitution rates and divergence times made with differ

60 ne's nonsynonymous and synonymous nucleotide substitution rates and dN/dS ratios were determined.

61 acea were obtained in order to compare their substitution rates and genealogy with those of Withering

62 tatherian X chromosomes have elevated silent substitution rates and high G+C contents in comparison w

63 ositive correlations were identified between substitution rates and measures of genomic rearrangement

64 ide analysis of synonymous and nonsynonymous substitution rates and others.

65 id adaptation, including elevated nucleotide substitution rates and regulatory motifs absent in other

66 evolutionary dynamics, including nucleotide substitution rates and selection pressures, using 14 IAV

67 as the ratio of nonsynonymous to synonymous substitution rates, and microbial genome size.

68 ences in diversity, nonsynonymous/synonymous substitution rates, and recombination rates between HSV-

69 s with physical distance and synonymous (Ks) substitution rates, and WGDs show lower divergence than

70 In vertebrate mitochondrial genomes, substitution rates are affected by a gradient along the

71 In fact, substitution rates are biased in favor of dominant sex d

72 s (d(S)) and nonsynonymous (d(N)) nucleotide substitution rates are both negatively correlated with m

73 Accurate estimates of mitochondrial substitution rates are central to molecular studies of h

74 d the genes with the most similar synonymous substitution rates are enriched for regulatory functions

75 d in endosymbionts for which mutation and/or substitution rates are greatly elevated over those of E.

76 evated divergence in Plantago, implying that substitution rates are highly accelerated throughout the

77 It is understood that DNA and amino acid substitution rates are highly sequence context-dependent

78 vations from a recent vaccine trial that VP1 substitution rates are increased for Sabin-like isolates

79 that short-term mutation rates and long-term substitution rates are related by a monotonic decline fr

80 ated compositional heterogeneity or elevated substitution rates are ruled out.

81 Interestingly, substitution rates are similar for leading and lagging s

82 We find that substitution rates are up to 64% higher in lineages lead

83 land plants and demonstrate that synonymous substitution rates are, on average, 3.7 times slower in

84 io of nonsynonymous to synonymous nucleotide substitution rate, are characterized by very few paralle

85 les with distinct functions, phenotypes, and substitution rates as compared with control sets of rand

86 is algorithm to estimate neighbour-dependent substitution rates, as well as rates for dinucleotide su

87 a relationship between average body size and substitution rate at both interspecies and interfamily c

88 lation-genetic model that elucidates how the substitution rate at conditionally neutral sites depends

89 a model of neutral DNA evolution that allows substitution rates at a site to depend on the two flanki

90 We inferred structure-dependent substitution rates at each amino acid site of the highly

91 n mammalian red cells show higher nucleotide substitution rates at nonsynonymous codon positions than

92 Substitution rates at synonymous sites vary substantiall

93 long branch length, with the human-platypus substitution rate being on average 55% greater than that

94 y lost "out of Africa" and the difference in substitution rate between Africans and non-Africans.

95 ingly, we observed a positive correlation in substitution rates between homologous X and homologous Y

96 By comparing the amino acid substitution rates between mammalian protein surfaces an

97 ars too weak to account for the variation in substitution rates between the mitochondrial genomes of

98 ate was initially higher than the synonymous substitution rate but decreased over time from 3.3 x 10(

99 ecies also appears to have an elevated mtDNA substitution rate, but previous studies did not provide

100 an (marsupial) mammals have evolved high CpG substitution rates, but this is apparently a convergence

101 We examined the neutral base substitution rate by measuring the sequence divergence o

102 UFA4) had significantly increased amino acid substitution rates by both PAML and Z-test, suggesting t

103 A systematic increase of substitution rates by tert-butylamine on alpha-bromoprop

104 arge systematic differences in mitochondrial substitution rates can also contribute to asymmetries.

105 volution, we show that the special nature of substitution rates can lead to a severe loss of power fo

106 and exclude those data from which changes in substitution rate cannot be reliably inferred.

107 ts in all aerobic eukaryotes, despite a high substitution rate, clonal propagation and little evidenc

108 tle evidence of diversifying selection, with substitution rates comparable across structural versus n

109 nderwent a genome-wide slowdown in molecular substitution rates compared to tropical and desert-adapt

110 unctional elements as regions having reduced substitution rates, comparison of genome sequences can a

111 ienced a dramatic acceleration in synonymous substitution rates, consistent with the hypothesis of ge

112 These substitution rates correspond to a wide range of Pareto-

113 h species exhibited a high median synonymous substitution rate (d(S) = 1.02), thereby explaining the

114 ed the ratios of nonsynonymous-to-synonymous substitution rates (d (N)/d (S)) in protein-coding genes

115 Substitution rate differs from most traits studied in th

116 e ratio between nonsynonymous and synonymous substitution rates) displays distinct profiles along the

117 s with ratios of nonsynonymous to synonymous substitution rates (dN/dS) highly suggestive of strong p

118 on the ratio of non-synonymous to synonymous substitution rates (dN/dS) on X-chromosome genes.

119 f the medians of nonsynonymous to synonymous substitution rates (dN/dS) that is used as a measure of

120 ik: The ratio of nonsynonymous to synonymous substitution rates (dN/dS) was 0.534 before the MRCA but

121 the ratio of non-silent to silent nucleotide substitution rates (dN/dS).

122 timated for HIV-1 and the overall nucleotide substitution rate estimated during HCV infection.

123 Through substitution rate estimation between bat and human, 32 g

124 and yn00) and KaKs_Calculator (including 10 substitution rate estimation methods).

125 (speciation) rate of the Yule process to the substitution rate exceeds the value 4.

126 The substitution rate for products labelled on the market as

127 validating the order of magnitude of genomic substitution rate for protein-coding regions.

128 h R2 RT error rate, the long-term nucleotide substitution rate for R2 is not significantly above that

129 The substitution rate for the 2014 EBOV was estimated to be

130 sequences also revealed a surprisingly high substitution rate for threonine residues, resulting in a

131 Our analyses showed that nucleotide substitution rates for 11 of the 14 evaluated subtypes t

132 Analysis of nucleotide substitution rates for 72 plastid genes for 47 angiosper

133 We also inferred substitution rates for attenuating nucleotides and confi

134 have disappeared although they have similar substitution rates for epizootic outbreaks.

135 decreases in gene expression and synonymous substitution rates for Gm15, for instance, a 38% increas

136 or proteins and accelerated lineage-specific substitution rates for non-coding regions are considered

137 The nucleotide substitution rates for the individual open reading frame

138 ondrial genomes from 177 humans, we estimate substitution rates for various data partitions by using

139 n of recombination, molecular adaptation and substitution rates from coding sequences using approxima

140 these studies have estimated the nucleotide substitution rates from genome sequence alignments acros

141 e DNA level is usually detected by analysing substitution rates from multiple-species comparisons.

142 f reliable methods to estimate site-specific substitution rates from sequence alignments.

143 e-stranded circular DNA genomes, showed high substitution rates (>10(-5) per nucleotide each day), so

144 Although gene losses and increased substitution rates have been characterized for parasitic

145 ral shifts in genomic structure and elevated substitution rates have important implications for the e

146 Here we present the first rigorous test of substitution rate heterogeneity in the Drosophila melano

147 ated commelinids represent a classic case of substitution rate heterogeneity that has not been invest

148 assigned to the parameter scaling molecular substitution rate heterogeneity.

149 work suggests large variability in molecular substitution rates, however, we still do not know whethe

150 is positively correlated with the synonymous substitution rate in all exon positions.

151 will it also have a high (or low) synonymous substitution rate in another mammalian species?

152 ase composition and also with the synonymous substitution rate in corresponding coding regions.

153 First, the synonymous substitution rate in DMY is 1.73 times that in DMRT1, co

154 ed a significant reduction of the nucleotide substitution rate in flanks of alternatively spliced exo

155 ps, despite a generally higher nonsynonymous substitution rate in humans.

156 n that a gene has a high (or low) synonymous substitution rate in one mammalian species, will it also

157 The Ebola virus (EBOV) genome substitution rate in the Makona strain has been estimate

158 We find that a gene's synonymous substitution rate in the rat-mouse branch of the phyloge

159 ng the spatial autocorrelation of nucleotide substitution rates in ancestral repeats.

160 nces reveal 10- to 50-fold faster amino acid substitution rates in Blochmannia compared to related ba

161 5N2, and H6N2 exhibited significantly higher substitution rates in East Asia than in North America.

162 e detected comparable accelerated amino acid substitution rates in FIS2 and MEA but not in their para

163 We applied gKaKs to estimate the genome-wide substitution rates in five pairs of closely related spec

164 , the puzzlingly low X-to-autosome ratios of substitution rates in humans and chimpanzees and differe

165 Furthermore, we show that substitution rates in INE-1 elements are not associated

166 Substitution rates in intergenic regions consisting prim

167 Using base substitution rates in intronic regions as a calibrator f

168 os of nonsynonymous to synonymous nucleotide substitution rates in known antigenic regions compared t

169 s and screened for reduced single nucleotide substitution rates in large genomic data sets from untre

170 is the ratio of nonsynonymous to synonymous substitution rates in lineage i.

171 We have observed, on average, 10-15% lower substitution rates in linker regions than in nucleosomal

172 eration time has a major influence on yearly substitution rates in mammals but only a subtle one in h

173 tes will be affected by the heterogeneity of substitution rates in neutral sequence across the genome

174 ion, as indicated by significantly different substitution rates in noncoding, silent, and replacement

175 Synonymous substitution rates in plant mitochondrial genomes vary b

176 ding and protein-coding regions, we compared substitution rates in primate and rodent lineages and an

177 oding and non-coding DNA by standardizing to substitution rates in putatively unconstrained sequences

178 divergence estimates suggest that synonymous substitution rates in the basal angiosperms are less tha

179 is lineage-specific difference in synonymous substitution rates in the central region of the domains

180 Examination of nucleotide substitution rates in the viral genome indicated an incr

181 re is a tight correlation between amino acid substitution rates inclpP1 and the nuclear-encoded Clp s

182 for several different measures of synonymous substitution rate, including corrections for base compos

183 -cytosine isochore structure, and nucleotide substitution rates indicate major shifts in the structur

184 re, analysis of nonsynonymous and synonymous substitution rates indicated that divergence of the dupl

185 ian skyline plot analyses with two different substitution rates indicated that N. tenuis might follow

186 Analysis of synonymous base substitution rates indicated that the triplicated Brassi

187 onship between effective population size and substitution rate indicates that as the efficacy of sele

188 io of nonsynonymous (Ka) and synonymous (Ks) substitution rates indicates that a considerable number

189 teins, the oncogenes E7 and E6 had increased substitution rates indicative of higher selection pressu

190 ement in proteins is context-dependent, with substitution rates influenced by local structure, functi

191 s in the genome, and (2) stochastic noise in substitution rates inherent to short lineages such as th

192 Substitution rate is consistently greater in Africans th

193 In personal genomes, the single-nucleotide substitution rate is higher near sites of structural alt

194 This substitution rate is higher than in many other mammals,

195 ta points, can have the opposite effect when substitution rate is involved.

196 lowly expressed genes; and (iii) amino acid substitution rate is negatively correlated with mRNA fol

197 we find some evidence of positive selection, substitution rate is negatively correlated with variance

198 The substitution rate is surprisingly high for a DNA virus,

199 mutation rates estimated from pedigrees into substitution rates is not as straightforward as it may s

200 exhibit some of the slowest known synonymous substitution rates, it is generally believed that they e

201 the ratio of the nonsynonymous to synonymous substitution rate (K(A)/K(S)) is commonly used.

202 es the ratio of non-synonymous to synonymous substitution rates (K(A)/K(S)) between a pair of protein

203 igh rate, as evidenced by the initially high substitution rates (K(s) and K(a)), as well as the SNP d

204 ons and premature stop codons to compute the substitution rates (Ka, Ks and Ka/Ks) between a well-ann

205 plants and among the lowest spontaneous base-substitution rates known in eukaryotes.

206 substitutions, assuming that the synonymous substitution rate Ks reflects the neutral nucleotide sub

207 ucleotide fraction and synonymous nucleotide substitution rates (Ks) across dog and human genomes.

208 The nucleotide substitution rate matrix is a key parameter of molecular

209 a global picture of change in the nucleotide substitution rate matrix on a genomewide scale across th

210 This low substitution rate may be the reason behind the clinicall

211 Their higher nucleotide substitution rates may be related to the central role pl

212 re frequently at CpG sites and that cysteine substitution rates may depend on support of the context

213 in death to donation after circulatory death substitution rate observed was 8%; however due to mitiga

214 ence that marked increases of non-synonymous substitution rates occurred in anthropoid ETC genes that

215 und to evolve even more rapidly, with a mean substitution rate of approximately 1.56 x 10(-3) subs/si

216 tions and polymorphisms showed that the high substitution rate of guanine in human mtDNA is largest i

217 Further, while the estimated nucleotide substitution rate of JCV has large confidence intervals

218 The mean substitution rate of the G ectodomain for the Kilifi dat

219 t we observe a significantly faster per site substitution rate of unpreferred changes in D. melanogas

220 This study explored patterns of nucleotide substitution rates of diatom plastids across the entire

221 Finally, we used this data to calculate the substitution rates of DNA transposons for each category

222 Analyses of synonymous and nonsynonymous substitution rates of these conserved peptides show that

223 Mechanisms of base substitution, rates of accumulation, and the amount of v

224 the overall highest nonsynonymous/synonymous substitution rate (omega) ratio (M3 = 0.7965).

225 m cnidarians to chordates, and evaluated the substitution rates (omega) at individual codons to ident

226 The ratio of synonymous-to-nonsynonymous substitution rates (omega) was estimated for eight pseud

227 e duplication with vastly increased accepted substitution rates or that they represent ancestral type

228 alculated with autocorrelated or independent substitution rates over clades agreed in placing the ori

229 d Pauling, but that it "ticks" at a constant substitution rate per unit of mass-specific metabolic en

230 The nucleotide substitution rate per year for SA EEEV (1.2 x 10(-4)) wa

231 These lower substitution rates permit inference of older duplication

232 deaths occurred in genomic regions with high substitution rates, protomicrosatellite content, and L1

233 in comparing the nonsynonymous-to-synonymous substitution rate ratio (omega = dN/dS) between two gene

234 asured by using the nonsynonymous/synonymous substitution rate ratio (omega = dN/dS).

235 The non-synonymous to synonymous nucleotide substitution rate ratio (omega=dN/dS) in these genes was

236 te/region has a non-synonymous to synonymous substitution rates ratio omega greater than one.

237 and HPV18/45/97 had nonsynonymous/synonymous substitution rate ratios (d(N)/d(S)) over 1 indicative o

238 The high nonsynonymous/synonymous substitution rate ratios (K(a)/K(s)) for both the beta a

239 Overall, annual substitution rates reached 10% of total demand.

240 Whereas short-term substitution rates reflect the accumulation of tolerated

241 tion can increase, rather than decrease, the substitution rate relative to levels of polymorphism.

242 nzee 1536) at week 216, while the synonymous substitution rate remained steady at approximately 1 x 1

243 With high mutation and genomic substitution rates, RNA and single-stranded DNA (ssDNA)

244 s to make obtaining genome-wide estimates of substitution rates, selective constraints and other mole

245 Our estimate for the neutral point substitution rate separating the two rodents is 0.196 su

246 In contrast, substitution rates show little or no elevation in Planta

247 The ratio of non-synonymous to synonymous substitution rates showed a more relaxed selection press

248 We resolve whether such synonymous substitution rate similarities exist using 7462 ortholog

249 hese mutations are recurrent with nucleotide substitution rates substantially greater than the genome

250 y regime, with relatively high nonsynonymous substitution rates, suggesting that ABP might play a sim

251 last matK gene has nucleotide and amino acid substitution rates suggestive of progression toward a ps

252 The ratio of nonsynonymous and synonymous substitution rates suggests the Ag recognition site of M

253 A comparison of the nonsynonymous substitution rate/synonymous substitution rate was made

254 ce for a significantly higher non-synonymous substitution rate than synonymous rate in ESX1 between h

255 A genes studied have a higher non-synonymous substitution rate than the corresponding genes in either

256 human lineages showed much slower nucleotide substitution rates than tenrec and mouse lineages but mo

257 racellular domains have higher nonsynonymous substitution rates than the intracellular domains, consi

258 tissues at 9 months showed higher synonymous substitution rates than WT and nucleotide substitutions

259 lism have lower synonymous and nonsynonymous substitutions rates than those involved in transcription

260 ns in modern humans have suggested a nuclear substitution rate that is approximately half that of pre

261 Methods for detecting nucleotide substitution rates that are faster or slower than expect

262 Based on the synonymous substitution rate, the E. albertii-Shigella B13 lineage

263 Based on non-synonymous nucleotide substitution rates, the calcyon genes appear to be under

264 Notably, these substitution rates, the first reported for a plant DNA v

265 Our analysis yielded data on viral substitution rates, the time to common ancestry, and ele

266 zes the juxtaposition of forward and reverse substitution rates to determine the relative importance

267 However, the use of synonymous substitution rates to infer mutation rates depends on th

268 ub-Saharan Africa may have resulted in lower substitution rates to maintain a successful coping strat

269 comparisons of synonymous and nonsynonymous substitution rates to test for evidence of divergent sel

270 Surprisingly, low synonymous substitution rates underpin more incidences than do high

271 e show that neutral evolution and nucleotide substitution rates up to forty-fold faster than observed

272 tion of the context dependence of nucleotide substitution rates using baboon, chimpanzee, and human g

273 ed the divergence times and lineage-specific substitution rates using Bayesian-skyline models.

274 Substitution rates varied regionally among introns seque

275 en called into question by observations that substitution rates vary widely between lineages.

276 The median substitution rate was 0 substitutions/site/year (95% con

277 le HPV45 E1 was highly conserved (amino acid substitution rate was 0.77%).

278 The mean genomic substitution rate was estimated to be 2.88 x 10(-4) nucl

279 Male mutation bias was evident: substitution rate was higher for a Y chromosome intron t

280 The nonsynonymous substitution rate was initially higher than the synonymo

281 The highest substitution rate was lineage-specific within the araphi

282 e nonsynonymous substitution rate/synonymous substitution rate was made at various time points to ana

283 ersistence preceding disease, the nucleotide substitution rate was not measurable within up to 15-yea

284 Synonymous and nonsynonymous nucleotide substitution rates were greatest during the first 8 week

285 in the plastid genome (plastome), nucleotide substitution rates were previously shown to be lower in

286 Relative substitution rates were quantified in diverse humans usi

287 HIV-1 synonymous substitution rates were significantly lower in LRPs than

288 ws a significant increase in their effective substitution rate when compared with unique genomic sequ

289 e neutral mutation rate is equal to the base substitution rate when the latter is not affected by nat

290 nant primary producer yielded the nucleotide substitution rate, which we used to show that proliferat

291 cales for both synonymous and non-synonymous substitution rates, which is only compatible with the 's

292 We use island ages to calibrate DNA substitution rates, which vary substantially among gene

293 how that power can be increased by comparing substitution rate with the time average of the predictor

294 Analysis of nucleotide substitution rates with Mtb homologs suggest overall str

295 the duplicative nature of the IR reduces the substitution rate within this region.

296 Analysis of synonymous base substitution rates within modeled genes revealed a relat

297 ctivity of copy-dependent repair to suppress substitution rates within repeats.

298 V18 and HPV16 genomes had similar amino acid substitution rates within the E1 ORF (2.89% and 3.24%, r

299 obust to allow exceptionally high amino acid substitution rates without compromising organismal fitne

300 In the face of very high or very low substitution rates without horizontal gene transfers, su