ライフサイエンスコーパス: evolutionary rate

1 nce and of the corresponding fast phenotypic evolutionary rate.

2 lular variability may significantly increase evolutionary rate.

3 nomes and with a significantly elevated gene evolutionary rate.

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

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

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

7 heory sufficiently accounts for the elevated evolutionary rate.

8 was not associated with the increase in the evolutionary rate.

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

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

11 cannot fully explain the observed changes in evolutionary rate.

12 erize the infectious agent and determine its evolutionary rate.

13 traits are the primary factors of molecular evolutionary rates.

14 ytogenetic markers because they display high evolutionary rates.

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

16 rrelated with increased or decreased protein evolutionary rates.

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

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

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

20 tributions will improve our understanding of evolutionary rates.

21 d niche data to examine temporal patterns of evolutionary rates.

22 ign and damaging are predicted by positional evolutionary rates.

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

24 h ORF3 and ORF5 having the highest intrahost evolutionary rates.

25 evolutionary process with identical genomic evolutionary rates.

26 ariation in Saccharomyces cerevisiae protein evolutionary rates.

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

28 nces of different phylogenetic distances and evolutionary rates.

29 s by modulating their silent and replacement evolutionary rates.

30 oldspots changes correlated only weakly with evolutionary rates.

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

32 The evolutionary rate acceleration observed in most endosymb

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

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

35 Surprisingly, they exhibit constant evolutionary rates across the entire Cambrian, for all a

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

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

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

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

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

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

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

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

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

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

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

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

48 However, evolutionary rate analyses estimated no greater than thr

49 uman coronavirus genomes, including per-base evolutionary rate analysis.

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

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

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

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

54 Bayesian evolutionary rate and divergence date estimates were sho

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

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

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

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

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

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

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

62 Evolutionary rate and selection were estimated for each

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

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

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

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

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

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

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

70 Because of their comparatively rapid evolutionary rates and consequent high taxonomic resolut

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

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

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

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

75 A comparison of evolutionary rates and morphological disparity of basal

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

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

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

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

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

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

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

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

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

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

90 These evolutionary rates are considerably higher than the ones

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

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

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

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

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

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

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

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

99 We found marked heterogeneity in the evolutionary rate at the level of both individual residu

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

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

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

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

104 The evolutionary rate based approach was coupled with a conv

105 nd for two different prior specifications of evolutionary rates based on HCoV-OC43 and MERS-CoV.

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

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

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

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

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

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

112 ollowed by increases in niche and phenotypic evolutionary rates by ~5 Mya; all rates increase exponen

113 Evolutionary rates can be decoupled into gene-specific a

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

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

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

117 Do trait evolutionary rates coincide with rates of diversificatio

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

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

120 Evolutionary rate covariation (ERC) is a phylogenetic si

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

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

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

124 is on the lethality phenotype, as well as an evolutionary rate covariation analysis, generated lists

125 properties are tightly coupled with protein evolutionary rate, depending on whether and how gene dup

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

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

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

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

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

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

132 OROV that encompasses phylogenetic analysis, evolutionary rate estimates, inference of natural select

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

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

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

136 o display elevated disparity relative to the evolutionary rate for bones associated with feeding, whe

137 ylogenetic analysis demonstrated a molecular evolutionary rate for the Boende strain 4 to 10x slower

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

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

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

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

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

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

144 Molecular evolutionary rates for viruses belonging to different sp

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

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

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

148 rding the coupling between these fundamental evolutionary rates has been difficult due to the inconsi

149 oson exchanges that equilibrate genome size, evolutionary rate heterogeneities and positive selection

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

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

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

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

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

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

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

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

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

161 es in reserve mass rather than coat mass, as evolutionary rates in reserve mass significantly outpace

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

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

164 Evolutionary rates in the hypervariable region 1 (HVR1)

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

166 ements across vertebrates and compared their evolutionary rates in the thylacine and wolf, revealing

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

184 the genus Hanseniaspora exhibited very high evolutionary rates, low Guanine-Cytosine (GC) content, s

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

186 artifact is prompted by the faster molecular evolutionary rate observed within the Acoelomorpha.

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

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

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

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

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

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

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

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

195 The evolutionary rate of coding DNA in the catarrhine clade

196 panning 29 placental mammals to estimate the evolutionary rate of functional changes among orthologs.

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 olution are consistent with the lower global evolutionary rate of IBV.IMPORTANCE The evolution of inf

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

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

202 The evolutionary rate of minicircle and plastid-transferred

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

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

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

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

207 The evolutionary rate of proteins involved in obligate prote

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

209 As the evolutionary rate of rearrangements in lepidopteran geno

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

231 Evolutionary rates of functionally related proteins tend

232 which tests for association between relative evolutionary rates of genes and the evolution of traits

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

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

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

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

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

238 The evolutionary rates of proteins vary over several orders

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

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

241 Evolutionary rates of sites can be independent of one an

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

243 We estimated the evolutionary rates of the complementarity determining re

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

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

246 s, the role of preexisting immunity, and the evolutionary rates of the virus.

247 The evolutionary rates of these gene categories were compare

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

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

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

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

252 r chronological gaps between periods of high evolutionary rates (phenotypic and molecular) and expans

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

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

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

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

257 Genomic Evolutionary Rate Profiling mammalian conservation score

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

259 Overall evolutionary rates (ranging from 9.92 x 10(-3) to 4.1 x

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 of female-specific gene expression and lower evolutionary rates relative to autosome associated genes

263 e genes, leading to signatures of convergent evolutionary rate shifts at these genes.

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

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

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

267 tic framework coupled with biogeographic and evolutionary rate studies.

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

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

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

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

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

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

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

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

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

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

284 lyses including the use of a novel model for evolutionary rate variation across residues to predict c

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

286 Analysis of EDS1-family evolutionary rate variation and heterodimer structure-gu

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

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 an explosion, after which normal Phanerozoic evolutionary rates were established.

295 Significantly different evolutionary rates were observed in envelope versus none

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

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

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

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

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

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