ライフサイエンスコーパス: phylogeny

1 in 26 species, independent of body weight or phylogeny.

2 ture and removes spurious covariation due to phylogeny.

3 ore, it seems that LCH may be independent of phylogeny.

4 eting activities that did not track based on phylogeny.

5 MMs in separate branches of the Pristionchus phylogeny.

6 atterns that generalize across the mammalian phylogeny.

7 of plants, and a time-calibrated angiosperm phylogeny.

8 in the context of a robust, time-calibrated phylogeny.

9 related taxa, we develop a fossil-calibrated phylogeny.

10 tal filtering and landscape, but not by host phylogeny.

11 ak genome that are broadly informative about phylogeny.

12 gression and phylogenetic support across the phylogeny.

13 d morphology (mass, embryo : seed ratio) and phylogeny.

14 nfluenced by a combination of physiology and phylogeny.

15 l for survival and development across animal phylogeny.

16 text of a calibrated worldwide Y-chromosomal phylogeny.

17 ided into four subtypes (A-D) based on Cas13 phylogeny.

18 es more emphasis on the shallow parts of the phylogeny.

19 across the coalescent and integrated nuclear phylogeny.

20 pendently occur in different branches of the phylogeny.

21 nd monocot families that span the angiosperm phylogeny.

22 by niche signaling is a common theme across phylogeny.

23 genome duplications, during early vertebrate phylogeny.

24 investigate decapod mitogenome diversity and phylogeny.

25 that agree with our understanding of protist phylogeny.

26 species are dispersed across the land plant phylogeny.

27 e, CITUP, Treeomics to reconstruct the tumor phylogeny.

28 nuous phenotypes across the entire mammalian phylogeny.

29 mechanistic insights likely apply throughout phylogeny.

30 past introgression across a time-calibrated phylogeny.

31 and clarifies hypotheses concerning hominin phylogeny.

32 ylogenies, but in conflict with the plastome phylogeny.

33 autotrophic Fe(II) oxidizers based on their phylogeny.

34 an historical context within the established phylogeny.

35 in) ), and matched it with global seed plant phylogenies.

36 such processes is limited without multigene phylogenies.

37 in the Cenozoic than predicted by molecular phylogenies.

38 identify a large solution space of plausible phylogenies.

39 ps between the overall network structure and phylogenies.

40 ed for mosses and liverworts using published phylogenies.

41 s for MCMCtree analysis and plot time-scaled phylogenies.

42 g of the macroevolutionary patterns in plant phylogenies.

43 parative analyses alongside songbird genetic phylogenies.

44 histories, as represented by their congruent phylogenies.

45 ore likely to be incorrect than reproducible phylogenies.

46 temporal information contained in molecular phylogenies(10) proves a powerful approach to reveal the

47 acivermis was poorly supported in a previous phylogeny [6], partially due to incomplete understanding

48 between distant loci, incongruent haplotype phylogenies across the genome, and evidence for hybridiz

49 The resulting phylogeny agrees with and extends the published results

50 difficult to predict feedback outcomes from phylogeny alone, other than to say that more closely rel

51 Our phylogeny also addresses controversies over the affiniti

52 r evolution; suggesting that development and phylogeny also limit possible structural solutions to se

53 hism (SNP) analyses were used to construct a phylogeny among 21 Mycobacterium isolates at the FDA.

54 Molecular phylogeny analyses indicate that vertebrate TIMP genes a

55 ibe a framework that integrates spectra with phylogenies and apply it to a global dataset of over 16

56 valuable information, composed of candidate phylogenies and associated clonal prevalence.

57 artly owing to discordance between molecular phylogenies and fossils(2,4).

58 nships inconsistent with both sequence-based phylogenies and previous morphological analysis.

59 he clonal populations is modeled by a clonal phylogeny and a finite-site model of evolution to accoun

60 upport multi-strain infections given a timed phylogeny and additional epidemiological data.

61 ape of the humerus are driven by ecology and phylogeny and are associated with functional trade-offs

62 onserved structure throughout the Drosophila phylogeny and carries motifs for binding of certain chro

63 among decay rates, mycorrhizal association, phylogeny and climate.

64 lly tighter connection between the community phylogeny and composition was observed in rare (R(2) = 0

65 c trees to previous estimates of mammal-wide phylogeny and divergence times, finding that (1) node ag

66 milar microbiomes, or if differences in host phylogeny and environmentally driven microhabitats withi

67 morphology and systematics but also for the phylogeny and evolution.

68 r resolve the groups identified through gene phylogeny and exon/intron phase analysis.

69 is is to uncover the links between microbial phylogeny and function in order to access ecosystem func

70 xamined the roles of plant species identity, phylogeny and functional traits in shaping rhizosphere f

71 Importantly, we provide evidence from phylogeny and genome architecture that these capstones,

72 e, life stage, habitat, latitude, elevation, phylogeny and International Union for Conservation of Na

73 Thus, irrespective of phylogeny and kinetic properties, kinesin-2 motors work

74 ceps) sperm whales to examine the effects of phylogeny and life stage on microbiome composition and d

75 Both phylogeny and life stage shaped community composition an

76 e genotypes that allow the so-called perfect phylogeny and maximize the likelihood of the genotypes.

77 hat trophic guilds can be predicted based on phylogeny and maximum body size.

78 In the context of an updated organismal phylogeny and newly inferred pigment reconstructions, we

79 important resolution of conchiferan mollusc phylogeny and offer new insights into ancestral characte

80 he organism and its ecology in the course of phylogeny and ontogeny, human memory is also profoundly

81 Its placement in the phylogeny and our synthesis point toward the existence o

82 Further, the phylogeny and predicted structural analyses of the nine

83 Host phylogeny and sociality were not significantly associate

84 heir results arise from using an implausible phylogeny and sparse sequence sampling.

85 hese flies and were limited by a provisional phylogeny and the available comparative methods.

86 n significantly impacts the estimates of the phylogeny and the evolutionary process.

87 us remains to be fully elucidated, its basal phylogeny and the in vivo infection model will allow SFV

88 elevations and microhabitats accounting for phylogeny and then ask how vulnerability varies under fo

89 the TFF superfamily by determining a global phylogeny and using it to infer an evolutionary pathway.

90 R strain was classified as MRV-3 based on S1 phylogeny and was closely related to porcine Asian strai

91 traits, including the abundance, diversity, phylogeny, and co-occurrence interactions in soil microb

92 sociations between antimicrobial resistance, phylogeny, and epidemiology.

93 ne annotation to characterize the structure, phylogeny, and expression profile of the NLR gene family

94 e for simultaneous inference of homology and phylogeny, and find strong evidence for the latter hypot

95 ur results emphasize that spatial variation, phylogeny, and life history are important considerations

96 tly estimate birth-death process parameters, phylogeny, and nuisance parameters in a Bayesian framewo

97 cranial hyperossification across the anuran phylogeny, and tested for relationships between ecology,

98 ophysical factors, as well as land use, host phylogeny, and trophic level/diet.

99 iew insights on their domestication from new phylogenies, archaeology and genomic studies.

100 Big, time-scaled phylogenies are fundamental to connecting evolutionary p

101 accurately summarize such a set T of cancer phylogenies are imperative.

102 simulations further show that irreproducible phylogenies are more likely to be incorrect than reprodu

103 These clone phylogenies are used to infer mutation order and clone o

104 f these methods in correctly inferring clone phylogenies are yet to consistently assessed.

105 The availability of a well supported phylogeny as well as reference genomes from several spec

106 similar to others seen across the Y. pestis phylogeny, associated with the Second and Third Pandemic

107 the presence of tree structure, we propose a phylogeny-aware detection procedure.

108 broad range of other flatworms and provide a phylogeny-aware interface that makes evolutionary specie

109 vide the basis for a highly resolved, genome phylogeny-based and digital prokaryotic taxonomy.

110 Phylogeny-based bipartite network analysis showed that N

111 cing in support of a highly resolved, genome phylogeny-based digital taxonomy.

112 r ten years, and analyse these archaea using phylogeny-based fluorescence analyses, proteogenomics an

113 the ground truth is unknown, we introduce a phylogeny-based measure for identifying potentially erro

114 ch outperforms Enhanced Phylogenetic Tree, a phylogeny-based method, and use the tool to reconstruct

115 r than ECM litters, with litter nitrogen and phylogeny best explaining variation in litter decay.

116 ) this spectrum were not obviously driven by phylogeny, body size, digestive strategy, or diet compos

117 ades in the genus based on consensus nuclear phylogenies, but in conflict with the plastome phylogeny

118 of these underlying assumptions on molecular phylogeny, but none have systematically analyzed their i

119 Phylogeny, but not plant traits, explained patterns of s

120 Isolates clustered on the phylogeny by patient sexual behavior (p&0.001) and race/

121 However, mitochondrial phylogenies can be misled by hybridization [9], incomple

122 al changes occurring along the branches of a phylogeny can manifest in subsequent changes in the rate

123 ANKA by presenting a detailed MCR/ACR-based phylogeny, compare their metabolic pathways and discuss

124 er extreme of resolution, it scales to large phylogenies comprising >17,000 microbial species.

125 l tribes to establish a robust Cucurbitaceae phylogeny containing eight highly resolved major clades.

126 The strong support for the phylogeny contrasts with high genomic heterogeneity in p

127 We reconstructed the gonococcal phylogeny, defined transmission clusters using a 10 non-

128 enitor cells allows the reconstruction of MF phylogeny demonstrating loss of heterozygosity and paral

129 esolve the deepest divergences in the legume phylogeny despite lack of phylogenetic signal across all

130 somal RNA genes could be inferred across the phylogeny, direct inference of phylogeny from rearrangem

131 We inferred their phylogeny, dispersal history and rates of change in seed

132 Across the entire 8,400-species phylogeny, diversification rates of ectomycorrhizal line

133 ins largely hypothetical or inferred through phylogeny due to the rarity of meaningful fossils.

134 is approach by reconstructing the artificial phylogeny emerging in three rounds of directed evolution

135 mingbird species, without accounting for the phylogeny, estimated that the DEE-body mass relationship

136 Our phylogeny, estimated using data from 2389 genomic region

137 le distribution patterns in the Streptomyces phylogeny, even among very closely related strains.

138 rences for 4,813 species and dated molecular phylogenies for 21 clades endemic to the CFR.

139 tection of clones and the inference of clone phylogenies for all methods tested.

140 Nuclear and organellar phylogenies for B. napus and its progenitors reveal vary

141 the construction of standardized and robust phylogenies for disparate types of projects, we have dev

142 We have constructed rooted phylogenies for over 1,550 representatives of the DMSOR

143 these questions, we combine a deeply sampled phylogeny for a major flowering plant clade-Saxifragales

144 ian frameworks, we reconstructed a hard tick phylogeny for the nuclear genome.

145 es of interest, it reconstructs strain-level phylogenies from among the closest species using clade-s

146 st computational approach that infers tumour phylogenies from combined single-cell and bulk sequencin

147 Many computational methods produce clone phylogenies from population bulk sequencing data collect

148 There is growing interest in reconstructing phylogenies from the copious amounts of genome sequencin

149 ing probabilities, aids in the derivation of phylogenies from ultra-low-coverage single-cell DNA sequ

150 We constructed a time-resolved phylogeny from 546 CTVT exomes and describe the lineage'

151 7 additional Erysimum species to construct a phylogeny from 9868 orthologous genes, revealing several

152 ed across the phylogeny, direct inference of phylogeny from rearrangement data in MLGO resulted in a

153 a new tool, gpps, that reconstructs a tumor phylogeny from Single Cell Sequencing data, allowing eac

154 four historical HAI outbreaks to compare the phylogenies generated using cgMLST to those of other mea

155 Molecular phylogeny grouped Clytia MIHR with a subset of bilateria

156 Culp and coworkers recently utilized a phylogeny-guided approach to mine the genomes of Actinom

157 Mass spectrometry and phylogeny-guided biochemical analyses further reveal tha

158 Such phylogeny-guided prevention is efficient under both sing

159 ents one such group where network-structured phylogeny has hampered the development of diagnostic met

160 In certain cases, these reticulated phylogenies have resulted in phenotypic and molecular ov

161 Seed mass, embryo size and phylogeny have strong constraining effects on germinatio

162 ty is present, and 2) to pinpoint where in a phylogeny high-level spread is occurring.

163 r with their associated sequence alignments, phylogenies, HMM models and functional descriptors.

164 s are best explained by host factors such as phylogeny/immune complexity and trophic level/diet, plus

165 We infer detailed reconstructions of tumor phylogenies in ten prostate cancer patients with fatal d

166 einae taxa was supported by all the inferred phylogenies in this study using, for the first time, the

167 mutations, which returned the optimal tumor phylogeny in <4 h.

168 ther cDNA-like sequences existing throughout phylogeny, including intron-less genes and inactive germ

169 location for most internal nodes of the VZV phylogeny, including the ancestor of clade 5 strains.

170 Genome analyses across the plant phylogeny indicated that the prevalent plant ICA genes e

171 tosomal genomes and mirror mitochondrial DNA phylogenies, indicating replacement of both the mitochon

172 ies interact correlated with the drosophilid phylogeny, indicating that behavioral elements of SINs h

173 Our new findings on the phylogeny, infectivity, and immunoreactivity of HBoV1 ca

174 urrent sequencing technology, current cancer phylogeny inference methods identify a large solution sp

175 We introduce PhISCS-BnB (phylogeny inference using SCS via branch and bound), a b

176 Available computational methods for tumor phylogeny inference via single-cell sequencing (SCS) dat

177 KIT, we examined the accuracy and support of phylogenies inferred from 14 different alignment trimmin

178 Phylogenies inferred from ClipKIT-trimmed alignments are

179 Notably, coalescent-based ASTRAL species phylogenies inferred from Run1 and Run2 sets of individu

180 enomic datasets, whereas concatenation-based phylogenies inferred twice from the same supermatrix are

181 Here, we present a phylogeny-informed proteomics approach to facilitate dia

182 Although the inference of tumor phylogenies is rapidly becoming standard practice in can

183 Bmp gene phylogeny is largely congruent with the Pseudoalteromona

184 A time-calibrated phylogeny is presented that offers insights into the fac

185 ally verified distribution datasets and mega-phylogenies lead to an improved understanding of tropica

186 We applied phylogeny-led genome mining, metabolite analyses and bio

187 However, current cancer phylogeny methods infer large solution spaces of plausib

188 lete material or that another factor such as phylogeny might impact size estimates and comparisons.

189 The robust phylogeny obtained revealed how the domain diversity in

190 an oil-reservoir specific clade based on the phylogenies of both 16S rRNA genes and ribosomal protein

191 The current congruence among phylogenies of both nuclear and chloroplast analyses len

192 Time-calibrated phylogenies of extant species (referred to here as 'exta

193 s providing tentative empirical evidence for phylogenies of human dance.

194 fossil morphotaxa (phena) into reconstructed phylogenies of lineages (species) by expanding the latte

195 We generated a time-calibrated phylogeny of 105 species of Neotropical Phlegmariurus an

196 id and nuclear ribosomal markers, we built a phylogeny of 448 Allium species, representing 46% of the

197 ruct metabolic models for the ancestors of a phylogeny of 53 Escherichia coli strains, linking genoty

198 Similarly, a global phylogeny of 64 CNSC genomes showed a diverse population

199 petency in prey killing, as well as with the phylogeny of A. oligospora natural strains, calculated a

200 Here, by reconstructing a large phylogeny of all currently described cichlid species, we

201 Here we make use of the phylogeny of biosynthetic genes along with the lack of k

202 Uncertainties in the phylogeny of birds (Avialae) and their closest relatives

203 Our findings provide insights into the phylogeny of Chinese indigenous pig breeds and benefit g

204 event relative to the emergence of BAT, the phylogeny of CHKB-CPT1B synteny, and the insufficiency o

205 We inferred a fossil-calibrated phylogeny of Dictyostelia, which showed that its two maj

206 A phylogeny of DOG1 haplotypes revealed ancient divergence

207 By placing the Philippine isolates within a phylogeny of global M. tuberculosis (n > 17,000), we est

208 ned for Lisboa3 and Q1 and comparison with a phylogeny of global strain-types (n = 28 385) revealed t

209 e involved developmental pathways across the phylogeny of land plants.

210 inferring the most comprehensive time-scaled phylogeny of lichen-forming fungi (LFF) to date (over 3,

211 Structure-guided phylogeny of MCP suggests that Yaravirus groups together

212 placed as a progenitor/ancestor for MCR-8 in phylogeny of MCR members.

213 Here, we reconstruct a comprehensive phylogeny of microbial expansin genes.

214 e investigated the community composition and phylogeny of rare (relative abundance <0.1%) and abundan

215 ) than that of the abundant (80%), while the phylogeny of rare bacteria (36%) was more explained than

216 The phylogeny of rare bacteria was equally explained by loca

217 A phylogeny of RbcS was used to compare the protein sequen

218 resence of synonymous substitutions across a phylogeny of related Pseudomonads suggests these mutatio

219 hylinid fossils being discovered, the robust phylogeny of Staphylininae inferred by our research will

220 ata in GenBank, we generated a well-resolved phylogeny of Staphylininae with all deep nodes (intertri

221 An updated phylogeny of the CsTPS gene family showed three cannabis

222 nical respiratory samples, reconstructed the phylogeny of the infecting viruses, and detected differe

223 ent from each other. Here we reconstruct the phylogeny of the Sino-Tibetan language family, using Bay

224 ability of sequence data for honey bees, the phylogeny of the species remains a subject of controvers

225 equence so as to confidently reconstruct the phylogeny of the tumor.

226 We inferred a phylogeny of the two species using DNA sequence data fro

227 0 Quercus species to infer a time-calibrated phylogeny of the world's oaks.

228 Here, we investigated the taxonomy and phylogeny of these two species to determine whether or n

229 Time-calibrated phylogenies offer an additional tool for dating the spre

230 The drosophilid phylogeny offered no value to predicting species' differ

231 ng users to visualize microbial function and phylogeny on a single plot and compare datasets across t

232 algorithm to compute the most likely perfect phylogeny on an input genotype matrix extracted from an

233 To quantify the influence of host phylogeny on infection status, we applied Bayesian phylo

234 ce of climate, landscape, geography and host phylogeny on regional parasite community assembly.

235 nging to retrace evolution by sequence-based phylogeny or ancestral sequence reconstruction.

236 Despite numerous discoveries regarding MTB phylogeny over the last decades, this diversity is still

237 This phylogeny places ancestral Cimicidae to 115 mya as hemat

238 This new phylogeny places the fossil taxon within the hagfish cro

239 tations, we introduce the optimal subperfect phylogeny problem which asks to integrate SCS data with

240 new progression model to the field of cancer phylogeny reconstruction on Single Cell data.

241 Principled approaches to tumor phylogeny reconstruction via SCS data are typically base

242 untime and demonstrate its applicability for phylogeny reconstruction.

243 hile being comparable in its applications to phylogeny reconstruction.

244 The NYC gonococcal phylogeny reflected global diversity with isolates from

245 Recent molecular phylogenies rejected monophyly of Staphylininae and rega

246 In this context, the reconstruction of the phylogeny representing the evolutionary history presents

247 atures and gene neighborhoods information to phylogeny, researchers need to prepare all the necessary

248 An analysis of the phylogeny revealed a set of ~200 SNPs that are specific

249 Our RNAP phylogeny revealed that the Caudovirales RNAP forms a cl

250 eotide identity (ANI) analysis and core gene phylogeny revealed that the M. salmoniphilum-like strain

251 Pathogen timetrees are phylogenies scaled to time.

252 Molecular phylogeny showed a secondary loss as color vision was sh

253 Whole genome phylogeny showed that most of the strains are distribute

254 The microbial expansin phylogeny shows evidence of multiple horizontal gene tra

255 -specific antibodies and tested whether host phylogeny, sociality, or diet influence viral prevalence

256 The phylogeny, structure and composition of EVE indicates th

257 SHMT gene family members, including synteny, phylogeny, subcellular localizations, haplotypes, protei

258 New phylogenies suggest a closer affinity to simpler pond sc

259 stral state reconstructions on our preferred phylogeny suggest that bunolophodont molars are plesiomo

260 rom Myanmar and divergence within our global phylogeny suggest that the original introduction of B. p

261 Previous mitochondrial DNA phylogenies suggested that it was a highly divergent sis

262 d emm types were disseminated throughout the phylogeny, suggesting they belong to various genetic bac

263 congruent with the Pseudoalteromonas species phylogeny, suggesting vertical inheritance within the ge

264 tumor enables the inference of high-fidelity phylogenies that form the input to many important downst

265 divergence emerging from populations of gene phylogenies that reflect histories of introgression, lin

266 of accuracy, while also continuing to infer phylogenies that were equivalent or close to the true tr

267 urrence records to 1) identify clades in the phylogeny that are characterized by either an overrepres

268 We infer an Africa-wide phylogeny that features widespread admixture and three p

269 On a global phylogeny, the BA viruses from different countries form

270 PathFinder uses the clone phylogeny, the number of mutational differences among cl

271 importance of linking microbial function to phylogeny there are currently no visualization tools tha

272 We use ribosomal RNA (rRNA) encoding gene phylogenies to demonstrate that NCLC1 is a distinct bran

273 stimation on the most complete Cucurbitaceae phylogeny to date suggests that an annual life cycle may

274 Meltos leverages the tumor phylogeny tree built on somatic single nucleotide varian

275 ally aim to identify the most likely perfect phylogeny tree satisfying the infinite sites assumption

276 arily the same as SNVs, we show that a tumor phylogeny tree using high-quality somatic SNVs can act a

277 idence validated SV calls on a refined tumor phylogeny tree.

278 ss the challenging problem of building tumor phylogeny trees using somatic structural variants (SVs)

279 lignment based methods for reconstruction of phylogeny trees.

280 icient software for simulating reconstructed phylogenies under time-dependent BD models in backward t

281 of the number of species or the portion of a phylogeny unique to a site - showed stronger, more consi

282 Here, we inferred a Brassicaceae phylogeny using newly generated targeted enrichment sequ

283 ation rates and their relationship along the phylogeny using trait-dependent diversification models.

284 fication of pathogen groups with reticulated phylogenies, using Bcc as an example.

285 al regions most strongly associated with the phylogeny vary among lineages.

286 Phylogeny was a strong driver of species-specific microb

287 Despite well-supported phylogenies, we recovered strong evidence of a reticulat

288 hK-like1 is conserved throughout sea anemone phylogeny, we conclude that the two paralogs originated

289 ing these functional data to an updated DODA phylogeny, we then explored the evolution of l-DOPA 4,5-

290 the need for additional study of reticulate phylogenies when investigating species boundaries and ev

291 y to diverge in patterns recapitulating host phylogeny when hosts undergo allopatric speciation, limi

292 ools that exist scale poorly to large modern phylogenies, which can comprise thousands or even millio

293 uencing experiments that yield high-fidelity phylogenies, which will improve downstream analyses aime

294 place more emphasis on the deep parts of the phylogeny, while unweighted Unifrac places more emphasis

295 Although the phylogeny will continue developing, our current results

296 ioli whole-genome assemblies, we constructed phylogenies with explicit representation of inferred int

297 or tip dating, and (2) species-level "patch" phylogenies with nonoverlapping in-groups that each corr

298 The results show a highly resolved phylogeny with broad agreement among the three distinct

299 nces by both 16S rRNA fractional content and phylogeny, with the former dominated by ANME-1 archaea (

300 Clone phylogenies within patients provide a means of tracing t