ライフサイエンスコーパス: evolutionary rate

1 lular variability may significantly increase evolutionary rate.

2 nomes and with a significantly elevated gene evolutionary rate.

3 of isolation, resulting in an abnormally low evolutionary rate.

4 in's contact density influences the domain's evolutionary rate.

5 ns expressed in adult males show an elevated evolutionary rate.

6 s to examine changes in dental disparity and evolutionary rate.

7 heory sufficiently accounts for the elevated evolutionary rate.

8 nfected for longer time tend to have a lower evolutionary rate.

9 s evaluated and correlated to the calculated evolutionary rate.

10 den orthologs in a lineage and its "average" evolutionary rate.

11 cannot fully explain the observed changes in evolutionary rate.

12 erize the infectious agent and determine its evolutionary rate.

13 rrelated with increased or decreased protein evolutionary rates.

14 icantly related to within-gene variations in evolutionary rates.

15 ge expanses of time, given their much slower evolutionary rates.

16 e first within-family meta-analysis of viral evolutionary rates.

17 tributions will improve our understanding of evolutionary rates.

18 ign and damaging are predicted by positional evolutionary rates.

19 on the role of natural selection in shaping evolutionary rates.

20 evolutionary process with identical genomic evolutionary rates.

21 ariation in Saccharomyces cerevisiae protein evolutionary rates.

22 e, and establish their functional status and evolutionary rates.

23 nces of different phylogenetic distances and evolutionary rates.

24 s by modulating their silent and replacement evolutionary rates.

25 oldspots changes correlated only weakly with evolutionary rates.

26 traits are the primary factors of molecular evolutionary rates.

27 ze is the more important factor of molecular evolutionary rates.

28 echanisms, such as protein function [10-13], evolutionary rate [14, 15], dosage [11], and dosage bala

29 The evolutionary rate acceleration observed in most endosymb

30 rst opportunity to investigate variations in evolutionary rates across a clade of closely related spe

31 This revealed uneven evolutionary rates across genomes with genes in repeat-r

32 hen there are differences in substitution or evolutionary rates across the genomes of different subty

33 We observe accelerated evolutionary rates, adaptive evolutions in homeostasis r

34 compare human-mouse and human-macaque exonic evolutionary rates against experimentally determined sin

35 ch, we quantify and find support for a lower evolutionary rate along branches that accommodate a tran

36 ves each protein a characteristic pattern of evolutionary rates along its sequence.

37 Our results show that site-specific shifted evolutionary rate (altered functional constraint) is a c

38 ilarly biased with respect to codon bias and evolutionary rate, although differing significantly in t

39 n the presence of extensive variation in the evolutionary rate among lineages or significant biases i

40 vidual clades are characterized by disparate evolutionary rates among cranial regions.

41 der the transmission model to estimate HIV-1 evolutionary rates among epidemiologically-related patie

42 DetectIng Variability in Evolutionary Rates among GEnes (DIVERGE) is a software s

43 ate process, with identical distributions of evolutionary rates among genes that are gained and genes

44 red including the invariant distributions of evolutionary rates among orthologous genes from diverse

45 simultaneously reveal striking variation in evolutionary rates among whole genomes, with nucleotide

46 However, evolutionary rate analyses estimated no greater than thr

47 Evolutionary rate analyses indicate that mammalian genes

48 Accurately estimating the evolutionary rate and age of hepatitis B virus (HBV) has

49 y, the outbreak isolates show an accelerated evolutionary rate and an atypical mutational spectrum.

50 We test this key assumption by quantifying evolutionary rate and capacity for innovation in size an

51 Both the evolutionary rate and disparity of skull modules are ass

52 bility had significant correlations with its evolutionary rate and duplication rate, as well as its c

53 thways but no particular association between evolutionary rate and gene position, suggesting that the

54 pread forest tree species can result in slow evolutionary rate and incomplete lineage sorting, compli

55 to this quantity provides insight into their evolutionary rate and indicates that additional mechanis

56 ariation in mesodermal size occurs at a fast evolutionary rate and is an important mechanism to defin

57 ration of traits is also associated with low evolutionary rate and low disparity.

58 pattern of evolution, with a slow underlying evolutionary rate and occasional sustained bursts of rap

59 We set out to assess the evolutionary rate and pattern of experimentally characte

60 Evolutionary rate and selection were estimated for each

61 rther analyses assessing the effects of gene evolutionary rate and targeted taxon exclusion support R

62 sion level is the main predictor of a gene's evolutionary rate and that more highly expressed genes e

63 hile recombination affects estimates of both evolutionary rate and tMRCA, in no case was this suffici

64 important contributor to the differences in evolutionary rate and to an increased susceptibility of

65 elling and the node height test reveal rapid evolutionary rates and a predominance of rapid shifts am

66 ttractive therapeutic targets to limit tumor evolutionary rates and adaptation.

67 cate intragenomic differences in regulation, evolutionary rates and coalescent effective population s

68 sian analyses were performed to estimate the evolutionary rates and dates of appearance of the genoty

69 oint produced greatly different estimates of evolutionary rates and divergence times for both genes,

70 refore, it is important to consider position evolutionary rates and EPAs when interpreting the conseq

71 ported, to comprehensively examine molecular evolutionary rates and estimate dates of common ancestry

72 urs as a whole is characterized by declining evolutionary rates and increasing disparity, suggesting

73 A comparison of evolutionary rates and morphological disparity of basal

74 ong-branch attraction effects due to unequal evolutionary rates and mutational saturation effects may

75 The differences in evolutionary rates and patterns within and between linea

76 h significant sequence similarity, for which evolutionary rates and selection (dN/dS) can be estimate

77 Evolutionary rates and selection pressure coevolve with

78 post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protei

79 s, including biased taxonomic sampling, high evolutionary rates and sequence composition bias have lo

80 the resting-stage spore may lead to very low evolutionary rates and, perhaps, to the lack of potentia

81 ationship between protein dispensability and evolutionary rate, and explains why this relationship is

82 reasing the tree size (number of sequences), evolutionary rate, and sequence length on the efficiency

83 he connection between reproductive mode, the evolutionary rate, and species diversity remains largely

84 t contact density correlates positively with evolutionary rate, and that these correlations do not se

85 s evidence that contact density can increase evolutionary rates, and that it acts similarly on the le

86 tion have a larger increase in nonsynonymous evolutionary rate; and (iv) more genes with adaptive evo

87 acellular network exhibit exceptionally fast evolutionary rates; and (iii) signatures of positive sel

88 govern where along the spectrum of potential evolutionary rates any given lineage lies.

89 ferent lineages, with a dramatic increase in evolutionary rate apparent in primates.

90 Rather, the elevated evolutionary rate appears to be mainly due to enhanced m

91 l metabolic rate is a primary determinant of evolutionary rates: approximately 10(13) J of energy flu

92 dicots than in grasses and their patterns of evolutionary rate are different.

93 less constrained than coding regions, their evolutionary rates are also associated with genomic posi

94 These evolutionary rates are considerably higher than the ones

95 We conclude that evolutionary rates are directly linked to the distributi

96 es than nonsecreted proteins, and that their evolutionary rates are highly correlated with tissue spe

97 Unexpectedly, evolutionary rates are inferred to be higher during peri

98 me since their last common ancestor, average evolutionary rates are remarkably similar for Bacteria a

99 Evolutionary rates are seen to be quite variable, both a

100 een rejected prematurely, and that long-term evolutionary rates are very much slower than short-term

101 olutionary history, followed by a decline in evolutionary rates as ecological space fills or due to i

102 a substantially slower population growth and evolutionary rates, as well as smaller spatial dispersal

103 of loci which exhibit significant (P < 0.05) evolutionary rate asymmetry, three of which exhibit elev

104 is study presents an algorithm that uses the evolutionary rate at codon sites, the dN/dS (omega) para

105 We have found a negative correlation between evolutionary rate at the protein level (as measured by d

106 viruses, consistent with our findings about evolutionary rates at amino acid positions most directly

107 to time-stamped sequences, we estimated mean evolutionary rates at the nucleotide and amino acid leve

108 This study describes the utility of an evolutionary rate based approach coupled to the BLOSUM62

109 The evolutionary rate based approach was coupled with a conv

110 cate genes is reflected in the difference in evolutionary rate because the functional change of genes

111 Inferred regional correlations in evolutionary rates between lineages and between types of

112 linositol 3-kinase (PI3K), exhibit divergent evolutionary rates between reptiles and mammals; (ii) co

113 The detection of strong correlation of evolutionary rates between SIG and RNAP genes suggests a

114 nclude biogeographic factors, differences in evolutionary rates between subgenomes, gene conversion o

115 at shifted selective constraints (or shifted evolutionary rates) between the JH1 and the JH2 domains

116 oups, suggesting that temperature influences evolutionary rates by modifying selective pressures rath

117 Evolutionary rates can be decoupled into gene-specific a

118 substantially to, but do not fully explain, evolutionary rate change for HIV-1-targeting bnAb lineag

119 This result suggests that a substantial evolutionary rate change in feeding time occurred along

120 Using a method for detecting evolutionary rate changes along the branches of phylogen

121 We further develop a way to measure evolutionary rates comparably between the two networks a

122 ain does show a distinct pattern of relative evolutionary rates compared to other CFTR domains, which

123 Evolutionary rate covariation (ERC) is a phylogenetic si

124 Such evolutionary rate covariation (ERC) is a sequence-based

125 portunity to construct gene networks via the evolutionary rate covariation (ERC) signature.

126 ng glutmatergic signal transmission, we used Evolutionary Rate Covariation (ERC), a recently develope

127 biology are how fast viruses evolve and how evolutionary rates differ among viruses and fluctuate th

128 There are evolutionary rate differences among lineages, possibly o

129 study needs to make no assumptions regarding evolutionary rates, divergence times, or phylogenetic re

130 that both factors contributed to our revised evolutionary rate estimate but continue to stand by our

131 In this study, we collected 396 viral evolutionary rate estimates across almost all viral geno

132 As viral evolutionary rate estimates become more available, it ap

133 his work provides direct evidence that viral evolutionary rate estimates decay with their measurement

134 Evolutionary rate estimates differ between loci and in s

135 s protein dispensability, which we relate to evolutionary rate estimates that are based on comparison

136 Phylogenetic analysis and evolutionary rate estimation indicate that VT-AANAT evol

137 ancestors, (iv) a variation in the molecular evolutionary rate exists between the two genomes in the

138 lation between highly connected proteins and evolutionary rate exists in the E. coli metabolic networ

139 model that assumes identical protein-family evolutionary rates for all species.

140 es, SNP rates in rice were not predictive of evolutionary rates for corresponding genes in another gr

141 ical likelihood methods detect heterogeneous evolutionary rates for segments of both molecules.

142 eukaryotes which require drastic changes in evolutionary rates for some period during the last 2 bil

143 ulatory networks leads to different observed evolutionary rates for terminal properties of the body p

144 lite is less conserved, suggesting different evolutionary rates for the two types of alpha-satellite.

145 Molecular evolutionary rates for viruses belonging to different sp

146 We present a methodology for deriving evolutionary rates from empirical data that is used to p

147 Here, we compared evolutionary rates, gene duplication, and selective patt

148 e the effects of the various determinants of evolutionary rate: generation time, mutation rate, popul

149 ationship between protein dispensability and evolutionary rate has remained unconfirmed.

150 contributing factors have been implicated in evolutionary rate heterogeneity among proteins, but thei

151 fugu and medaka per2a/per2b have asymmetric evolutionary rates, implicating that one of these duplic

152 ispensability in yeast is also predictive of evolutionary rate in a nematode worm.

153 mino acid replacement may reconcile the fast evolutionary rate in matK with conservation in protein f

154 We studied convergence in evolutionary rate in subterranean mammals in order to as

155 Therefore, the higher evolutionary rate in the meninges and temporal lobe coul

156 genomic and network-level determinants of TF evolutionary rate in yeast, and how they compare to thos

157 ntinued warming will likely be determined by evolutionary rates in both, rather than single, symbioti

158 suggests that analysis of large data sets of evolutionary rates in conjunction with the results from

159 rmone beta-subunit) showed markedly variable evolutionary rates in each case with a pattern of a slow

160 ians of log-transformed viral RNA levels and evolutionary rates in each gene of a 5'-hemigenomic ampl

161 rovide the first systematic estimates of HCV evolutionary rates in multiple genes during early infect

162 enome coevolution due to the highly elevated evolutionary rates in plastid genomes.

163 Evolutionary rates in the Cambrian have been difficult t

164 , we pay particular attention to the role of evolutionary rates in the establishment of mutualism and

165 (PRM2 and FOXP2) with significantly enhanced evolutionary rates in the hominid lineage.

166 Evolutionary rates in the hypervariable region 1 (HVR1)

167 hod, we made a genome-wide comparison of the evolutionary rates in the lineages leading to the labora

168 matched by some DNA viruses, suggesting that evolutionary rates in viruses are explained by diverse a

169 We demonstrate that a dramatic molecular evolutionary rate increase in subunit I of cytochrome c

170 onal categories; (ii) most of the synonymous evolutionary rate increases in S288c occur in genes with

171 There were four major evolutionary rate increases, the first among basal iguan

172 This last bias could systematically inflate evolutionary rates inferred from molecular data because

173 Here, we investigate how a gene's evolutionary rate is affected by its protein's contact d

174 been previously suggested that the TM's low evolutionary rate is caused by their high percentage of

175 The best predictor of evolutionary rate is expression level, for reasons that

176 Such a low evolutionary rate is in apparent contradiction with the

177 e trend relating TF regulatory in-degree and evolutionary rate is likely related to the species-speci

178 e found that CaM evolves slowly but that its evolutionary rate is substantially faster in fungi.

179 However, the impact of secretion on evolutionary rates is countered by tissue-specific const

180 fe history traits primarily affect molecular evolutionary rates is often confounded by the covariance

181 ProPhylER (Protein Phylogeny and Evolutionary Rates) is a next-generation curated proteom

182 Most importantly, the correlations between evolutionary rate (K(A)/K(S)) and degrees for TFs are si

183 d that for TFs, the dominant determinants of evolutionary rate lie in the structure of the regulatory

184 g., defense and development), display faster evolutionary rates, lie closer to transposable elements

185 an Drosophila genes, suggesting that unequal evolutionary rates may contribute to the differences in

186 the universal empirical distribution of the evolutionary rates more closely than either distribution

187 Furthermore, different evolutionary rates must have prevailed during different

188 rvations: (i) the increases in nonsynonymous evolutionary rate occur for genes in all functional cate

189 The Pf4 population diversified with an evolutionary rate of 2.43 x 10(-3) substitutions per sit

190 ks affect genetic buffering by comparing the evolutionary rate of 242 human and mouse orthologous gen

191 Additionally, the evolutionary rate of a gene sequence is correlated with

192 These studies found that the evolutionary rate of a protein is predominantly influenc

193 e maximum rate, which represents the maximum evolutionary rate of a trait within a clade.

194 lts suggest that for different proteins, the evolutionary rate of amino acid replacements correlates

195 c and heritable epigenetic changes drive the evolutionary rate of cancer progression and drug resista

196 The evolutionary rate of coding DNA in the catarrhine clade

197 tion models to test for associations between evolutionary rate of genotype and phenotype.

198 c trees simulated with the recently reported evolutionary rate of HIV-1 on ART of 6 x 10-4 substituti

199 and (ii) providing the first estimate of the evolutionary rate of JCV that is independent from the as

200 Using historical isolates, we show that the evolutionary rate of Lm from lineage I and lineage II is

201 The evolutionary rate of minicircle and plastid-transferred

202 Notably, the evolutionary rate of nonoverlapping regions of the viral

203 The high transmissibility and rapid evolutionary rate of norovirus, combined with a short-li

204 xpression level, codon adaptation index, the evolutionary rate of physical interaction partners, and,

205 from other eukaryotes, we estimate that the evolutionary rate of protein interaction is (2.6 +/- 1.6

206 The evolutionary rate of proteins involved in obligate prote

207 y, appear to have independent effects on the evolutionary rate of proteins, suggesting that proteomes

208 As the evolutionary rate of rearrangements in lepidopteran geno

209 a previously hypothesized trend, whereby the evolutionary rate of repression or loss of gene expressi

210 horizontal gene transfers, conservation and evolutionary rate of sex-related genes.

211 siae shows a linear relationship between the evolutionary rate of sites and the relative solvent acce

212 ltaG correlates with the mRNA length and the evolutionary rate of synonymous positions.

213 f the regulatory network, such as the median evolutionary rate of target genes and the fraction of sp

214 Our results therefore suggest that the high evolutionary rate of the geminiviruses is not primarily

215 Mean evolutionary rate of the global ON1 was 4.10 x 10(-3) su

216 omic change probably contributed to the high evolutionary rate of the outbreak strain and may have in

217 We report here the evolutionary rate of the tomato yellow leaf curl disease

218 focus on CDK5RAP2 and show that the protein evolutionary rate of this gene is significantly higher i

219 To this end, we estimated the evolutionary rates of >3,000 proteins in four species of

220 The evolutionary rates of amino acid replacement are signifi

221 Considerable uncertainty surrounds the evolutionary rates of and selection pressures acting on

222 ating host transmission cycles constrain the evolutionary rates of arboviruses but not their fitness

223 Variation in the evolutionary rates of bindin may reflect historic differ

224 The evolutionary rates of both the coding and noncoding chan

225 following gene duplication, and the possible evolutionary rates of change for different epitypes.

226 correlations between DNA methylation and the evolutionary rates of coding exons in different genic po

227 L performs maximum likelihood estimation for evolutionary rates of discrete characters on a provided

228 eloped as a unified R program for estimating evolutionary rates of discrete characters with no restri

229 r to molecular evolution models in which the evolutionary rates of DNA sequence at multiple loci foll

230 n a probabilistic framework, to estimate the evolutionary rates of each sequence position.

231 formation on protein sequence evolution, the evolutionary rates of early-stage developmental genes, o

232 ion, with their close relatives to study the evolutionary rates of functional genes in endosymbionts.

233 Evolutionary rates of functionally related proteins tend

234 ogy to examine the effect of taxon sampling, evolutionary rates of genes, and combined data on tree r

235 underlying causes of the variability in the evolutionary rates of intrinsically ordered and disorder

236 We analyzed the evolutionary rates of pan-eukaryotic protein families an

237 -synonymous codon substitutions for studying evolutionary rates of protein coding genes.

238 The evolutionary rates of protein-coding genes in an organis

239 ggest that the universal distribution of the evolutionary rates of protein-coding genes is a direct c

240 The evolutionary rates of proteins vary over several orders

241 increasing complexity of animal body form on evolutionary rates of proteins.

242 The molecular evolutionary rates of scombroids are primarily tied to b

243 Evolutionary rates of sites can be independent of one an

244 has proven difficult to accurately quantify evolutionary rates of such binding change or to estimate

245 We estimated the evolutionary rates of the complementarity determining re

246 The evolutionary rates of the HN and F genes were similar (0

247 ral differentiations may have influenced the evolutionary rates of the two genomes since their split

248 The evolutionary rates of these gene categories were compare

249 The evolutionary rates of this virus are estimated to be 1.3

250 The impact of evolutionary rates on the strength of such associations

251 Yet little is known about its evolutionary rate or the fraction of the methylome that

252 reover, no correlation was found between the evolutionary rate or the heterogeneity of the viral quas

253 Given C. difficile evolutionary rates, paired samples </=2 single-nucleotid

254 rmline transcription may affect both protein evolutionary rates, possibly mediated by repair processe

255 negative selection, possessing high genomic evolutionary rate profiling (GERP) and sitewise likeliho

256 of numbers of substitutions, and the genomic evolutionary rate profiling (GERP) test.

257 These results were obtained with Genomic Evolutionary Rate Profiling (GERP), a statistically rigo

258 Genomic Evolutionary Rate Profiling mammalian conservation score

259 onservation at the nucleotide level (genomic evolutionary rate profiling, PhastCons) did not perform

260 tion is decoupled from temporal variation in evolutionary rate: rates of bill evolution vary among li

261 nctional reduction process, the elevation of evolutionary rates reaches several new rate equilibria,

262 The accelerated evolutionary rates reflect not only the transition from

263 Bayesian inference of evolutionary rates shows that genotypes 3 and 4 have sig

264 ying it can alter the link between mutation, evolutionary rate, speciation and biodiversity and we su

265 absence of detectable sequence conservation, evolutionary rate studies were performed on a set of nin

266 tic framework coupled with biogeographic and evolutionary rate studies.

267 updated fossil evidence and lineage-specific evolutionary rates suggested that maize subgenome diverg

268 ranching pattern, together with estimates of evolutionary rate, suggests that relapse-associated clon

269 ry low frequency of reassortment and a lower evolutionary rate than that of influenza A virus.

270 ressed than single-copy genes and had slower evolutionary rates than unmethylated genes, suggesting t

271 ates share most other properties influencing evolutionary rate that might otherwise conceal the chape

272 Finally, the high evolutionary rate that we estimated shows how rapidly ne

273 or robust constrained Bayesian estimation of evolutionary rates that avoids overfitting independent r

274 or protein hormones than the one of constant evolutionary rates that is commonly favored.

275 ade rooting of the C branch revealed unequal evolutionary rates that seem to be correlated with ecolo

276 By comparing the evolutionary rates that we report here with differences

277 ample, Psittaciformes (parrots) exhibit high evolutionary rates throughout the skull, but their close

278 nd significantly distinct trends relating TF evolutionary rate to mRNA expression level, codon adapta

279 understanding of how fast within-host HIV-1 evolutionary rates translate to lower rates at the betwe

280 ion between Darwinian selection strength and evolutionary rate trended toward significance, especiall

281 ne evolution could reflect the existence of 'evolutionary rate units' along the chromosome.

282 ibit a more pronounced difference in protein evolutionary rates (up to three times) between the genes

283 family by detecting site-specific change in evolutionary rate using a multiple alignment of amino ac

284 GPCRs, positive selection and high levels of evolutionary rate variability are common.

285 r, and recombination rate also contribute to evolutionary rate variation among proteins.

286 The interplay between HIV-1 evolutionary rate variation and risk of progression to A

287 e loss combined with sample size effects and evolutionary rate variation provide an alternative, more

288 strength of purifying selection can explain evolutionary rate variation.

289 Evolutionary rate varies across intergenic regions of th

290 Evolutionary rate was higher in nef and gag vs. pol, and

291 substitutions/site/year) whereas the SH gene evolutionary rate was three times faster.

292 pression have significant effects on protein evolutionary rate, we cannot yet accurately estimate the

293 tly developed method for detecting shifts in evolutionary rates, we find that the rate of change in r

294 Significantly different evolutionary rates were observed in envelope versus none

295 which dominated in the Ordovician, taxonomic evolutionary rates were relatively low and the probabili

296 Estimated evolutionary rates were revised from 0.51%/year (95% con

297 d final environments lead to the increase of evolutionary rates, when the environmental complexity in

298 ain the universal log-normal distribution of evolutionary rates, with a shift toward higher rates in

299 We further show that the evolutionary rate within primates is particularly high i

300 ruses, but there have been no comparisons of evolutionary rates within this broad family.