ライフサイエンスコーパス: phylogeny

1 le putatively extinct clade in the Y. pestis phylogeny.

2 hese findings by analysing a large molecular phylogeny.

3 ly place these species within the Plasmodium phylogeny.

4 duplication events, molecular structure, and phylogeny.

5 amental aspect of metabolism spanning all of phylogeny.

6 from mutated genomes simulated under a known phylogeny.

7 hed and applied to reconstruction of species phylogeny.

8 athway phylogenomic profiles given a species phylogeny.

9 relationships with environmental factors and phylogeny.

10 ession of defenses in Inga is independent of phylogeny.

11 primary sequences of organism to build their phylogeny.

12 e to climate are predictable on the basis of phylogeny.

13 unding effects of environment, tree size and phylogeny.

14 ures were largely congruent with the species phylogeny.

15 hical clustering analysis were mapped to the phylogeny.

16 zes antigenic data on a continuously updated phylogeny.

17 vided into four subgroups (I to IV) based on phylogeny.

18 at incorporate both epidemiologic data and a phylogeny.

19 tal genes and sex chromosomes onto the snake phylogeny.

20 le data by using a high-resolution SNP-based phylogeny.

21 did not correlate with putative function or phylogeny.

22 ole-genome duplications was found across the phylogeny.

23 somes, we establish and date a detailed hg N phylogeny.

24 d to determine serotypes, sequence types and phylogeny.

25 ersification shifts could be mapped onto the phylogeny.

26 isingly, these were independent of microbial phylogeny.

27 cation of this clade using a time-calibrated phylogeny.

28 om autosomes many times across the eukaryote phylogeny.

29 nge size, habitat breadth, life history, and phylogeny.

30 UTR isoform expression across the Drosophila phylogeny.

31 civorous plesiosaurs through time and across phylogeny.

32 dence between transmission history and virus phylogeny.

33 has not been assessed across the angiosperm phylogeny.

34 f ancestral threats across both ontogeny and phylogeny.

35 evolve via random walk along branches of the phylogeny.

36 lade, and trichomes have diverged across the phylogeny.

37 e near-basal position of the Archaea in rRNA phylogenies.

38 s model leads to improved inference of tumor phylogenies.

39 tal niches had consistent relationships with phylogenies.

40 o construct complete sequence alignments and phylogenies.

41 ver, this is in persistent conflict with DNA phylogenies.

42 s of novel MSY variants and defines unbiased phylogenies.

43 s were identified in subtype A1, B and C pol phylogenies.

44 ncertainty of the underlying time-calibrated phylogenies.

45 ow compared to those inferred from molecular phylogenies.

46 favor hundreds if not thousands of competing phylogenies.

47 thout the need for fossil data, or molecular phylogenies.

48 the nuclear, chloroplast, and mitochondrial phylogenies.

49 For our sampled phylogeny, 11 of the 12 included families remained intac

50 ata is fundamental to recovering an accurate phylogeny [16-20], our results strongly support sponges

51 hich (1) are distinct from those observed in phylogeny, (2) invalidate a traditional neuroimaging met

52 Despite recent advancements in aculeate phylogeny [4-11], considerable uncertainty remains regar

53 There was no correlation with phylogeny, a result consistent with our observations tha

54 I present an algorithm that rapidly computes phylogenies according to a compatibility criterion.

55 In silico benchmarking on simulated tumour phylogenies across a wide range of sample purities (15-9

56 ed data that PASTRI outperforms other cancer phylogeny algorithms in terms of runtime and accuracy.

57 Host habitat, diet and phylogeny all contribute to variation in marine mammal d

58 extinction is not discernible from molecular phylogenies alone, and not predicted by most previously

59 perature responses were not predictable from phylogeny alone, indicating that temperature responses a

60 A binding domains, named QCIGP, results from phylogeny analysis of their protein sequences but is not

61 that we reconstruct very accurate and robust phylogenies and ancestors.

62 omated computational pipeline to reconstruct phylogenies and ancestral genomes for two high-resolutio

63 Molecular phylogenies and morphology support that caecilians are t

64 groups were used to coestimate time-resolved phylogenies and relative genetic diversity to infer viru

65 The maximum-likelihood phylogenies and topology tests across homeologous groups

66 Most existing genome level phylogeny and ancestor reconstruction methods can only p

67 This manuscript reviews the phylogeny and biological roles of the T6SS in plant-asso

68 Finally, we compared the phylogeny and defenses of Inga to phylogenies for the ma

69 m solitary to eusocial life, we inferred the phylogeny and divergence times of all major lineages of

70 Here, we present a highly supported eudicot phylogeny and diversification rate shifts using 31 newly

71 elated to produce 'syndromes' resulting from phylogeny and environmental variation.

72 materials provide critical insight into the phylogeny and evolution of biomineralization in the Demo

73 and diversity, mechanisms of adaptation, and phylogeny and evolutionary history.

74 lysed population trends and relationships to phylogeny and habitat.

75 Their phylogeny and historical biogeography resulting in a dis

76 ddlefish was recently validated by molecular phylogeny and Hox genes analyses.

77 sequencing (WGS) was performed to produce a phylogeny and identify multilocus sequence types (MLST),

78 and extinction) for every branch of a study phylogeny and infers the number and location of diversif

79 NTT5, with its unusual transport properties, phylogeny and localization, can be taken as further evid

80 Here we show that host phylogeny and major dietary shifts have affected the dis

81 congruence analyses of each group's complete phylogeny and microbiota dendrogram reveal significant d

82 rx superfamily members are widespread across phylogeny and multiple methods have been developed to cl

83 Lycopersicon), we infer the species phylogeny and patterns of genetic diversity in this grou

84 f the HIV-1 reservoir and characterize viral phylogeny and phenotypic changes in immune cells.

85 These light responses are linked to phylogeny and pigmentation.

86 hylogenomic studies now resolve hymenopteran phylogeny and provide scenarios for the evolution of maj

87 By integrating linkage mapping, polyploid phylogeny and sex-determining region (SDR) in a unified

88 the rather limited knowledge concerning the phylogeny and structural and functional roles of an unus

89 tions in using ITS marker for reconstructing phylogeny and studying hybridization.

90 nome analysis provided new insights into the phylogeny and taxonomy of ascaridomorph nematodes.

91 ion trees simultaneously consistent with the phylogeny and the epidemiologic data on person, place, a

92 aset is the largest assembled for echinoderm phylogeny and transcriptomics.

93 Bacterial phylogeny and virome profile analyses of fecal samples f

94 able for identifying species, reconstructing phylogenies, and studying population genetic structures.

95 documented patterns of cerebellar scaling in phylogeny, and (3) cerebellar organization is modified i

96 Our results allow a re-definition of the K1 phylogeny, and indicate that the K1f haplogroup is absen

97 nt in terms of the inferred likelihood-based phylogenies; and we also describe how it is used to effi

98 In seasonally dry tropical forests (SDTFs), phylogenies are geographically structured and multiple i

99 nts of the 28S rRNA gene did not clarify the phylogeny at the genus level.

100 Phylogeny based on rRNA genes as well as conserved singl

101 netic implications, with the background of a phylogeny based on transcriptomes.

102 A Bayesian dated phylogeny, based on the 13 mitochondrial protein-coding

103 these on the phylogeny using either BLAST or phylogeny-based approaches, and then use the displayed t

104 subfamilies of FXYDs and propose a revised, phylogeny-based FXYD classification that is consistent a

105 th of information and the lack of a coherent phylogeny-based nomenclature of these proteins can lead

106 In this study, we develop a phylogeny-based statistical approach to address this que

107 (CLL) patient, we show that a simple linear phylogeny better explains the data the complex branching

108 ontact, showing that a reticulate population phylogeny between P. maniculatus and P. leucopus was a b

109 f1, ycf1-rps15) fragments to reconstruct the phylogeny, biogeographic history, and patterns of divers

110 is approach to comprehensive bird and mammal phylogenies, body size data for 9,465 extant species, an

111 a correlation between karyotype changes and phylogeny branch lengths.

112 IM computes environmental "weights" for each phylogeny branch, which represent the degree to which th

113 ree inference consistently returned the same phylogeny, but gene tree discordance was high: 37% of ge

114 These artifacts can skew phylogenies by creating illusory tumour heterogeneity am

115 rovide(s) the best approximation to the real phylogeny by analysing a simulated epidemic (created as

116 However, inferences drawn from molecular phylogenies can be limited owing to the challenge of acc

117 in medicinal plant uses have suggested that phylogeny can be used as predictive tool.

118 In the presence of gene flow, a phylogeny cannot be described by a tree but is instead a

119 Our phylogeny cements the early branching in complex thalloi

120 A star-like phylogeny, coalescing similarly to other Ashkenazi pater

121 The resulting global phylogeny confirms that the Late Pleistocene mammoth pop

122 Analysis of chromosomal location, phylogeny, conserved domain and physical properties show

123 nship systems shaped their gene and language phylogenies: Consistently following a postmarital reside

124 The evolved phylogeny consists of 19 operational taxonomic units (le

125 The regions of phylogenies containing fluoroquinolone-resistant isolate

126 Bulk water bacterial phylogeny correlated with ARG profiles while sediment ph

127 al simulations and examined if the resulting phylogeny could recover different types of contact netwo

128 hout BSSVS, and highlight the differences in phylogenies created by each.

129 ruction, there has yet to be a comparison of phylogenies created by the two methods.

130 pectrometry-based metabolomics and molecular phylogeny data were used to identify a metabolically pro

131 Our highly resolved phylogeny demonstrates sympatric parallel diversificatio

132 eported in packaged bacteriophages and their phylogeny, distribution and sequence diversity imply lat

133 A highly supported eudicot phylogeny divided Pentapetalae into two groups: one with

134 Cross-species comparison within a single MSY phylogeny emphasizes the low human diversity, and reveal

135 fungal network structure was related to host phylogeny, environmental and sampling properties.

136 well understood due to the lack of a robust phylogeny, especially at deeper nodes.

137 te parameters of these models from molecular phylogenies, even when species sampling is incomplete.

138 dels including only geographic proximity and phylogeny explained 5-40% of the variation in four key m

139 y morphological analyses, but many molecular phylogenies fail to recover this relationship.

140 asing demand for constructing alignments and phylogenies for a given loci from thousands of available

141 Constructing alignments and phylogenies for a given locus from large genome sequenci

142 utility of phylogenomic data to infer robust phylogenies for a lineage of closely related lichen-form

143 We constructed phylogenies for both plants and insects and quantified h

144 We have applied pHMM-tree to build phylogenies for CAZyme (carbohydrate active enzyme) clas

145 ta can effectively be used to provide robust phylogenies for closely related lichen-forming fungal li

146 s for enabling the statistical estimation of phylogenies for large and potentially heterogeneous data

147 mpared the phylogeny and defenses of Inga to phylogenies for the major lepidopteran clades.

148 flora by analysing a comprehensive regional phylogeny for 39 000 species alongside information on

149 Using a dated phylogeny for the same tree species, we found that spine

150 ties across Amazonia using a newly developed phylogeny for the species-rich neotropical tree genus In

151 We constructed the largest time-calibrated phylogeny for the subfamily to date, reconstructed ances

152 ds to accurately dissect subclones and their phylogenies from noisy and impure bulk tumour samples at

153 ose a statistical inference method for tumor phylogenies from noisy single-cell sequencing data under

154 simulations showed that a virus time-scaled phylogeny (genealogy) may be substantially different fro

155 Host phylogeny, geographic isolation and coevolution with sym

156 llow for a more targeted approach for future phylogeny-guided drug discovery at an early screening st

157 If all individuals in a phylogeny had the same phenotype distribution, measured

158 lthough congruence between host and pathogen phylogenies has been extensively investigated, the congr

159 anzee subspecies: The western chimpanzee MSY phylogeny has a TMRCA of only 13.2 (10.8-15.8) thousand

160 zed in terms of deduced amino acid sequence, phylogeny, homology modeling and docking simulation.

161 the ecology of chytrids, their life cycles, phylogeny, host specificity and range.

162 e empirical model combining biomass density, phylogeny (i.e., angiosperm, gymnosperm), and the intera

163 sequencing (WGS) was performed to produce a phylogeny, identify multilocus sequence types (MLST), mu

164 Our phylogenies illustrate that the body plan of the colossa

165 contribute to the core microbiome, and host phylogeny impacts complexity rather than composition of

166 ce alignments are increasingly used to infer phylogenies in order to better understand the processes

167 ssion confound chloroplast and mitochondrial phylogenies in relation to the species tree as a result

168 Until recently, deep-level phylogeny in Lepidoptera, the largest single radiation o

169 soil type, and evaluated the general role of phylogeny in mediating patterns of canopy traits within

170 sequences were isolated and used to infer a phylogeny in which ungulate malaria parasites form a mon

171 selection across all branches of the primate phylogeny including many novel findings.

172 ing two unparalleled, densely sampled orchid phylogenies (including more than 400 newly generated DNA

173 , are important for understanding seed plant phylogeny, including the evolution of the angiosperm car

174 atterns of cancer dissemination using tumour phylogenies inferred from genome-wide copy-number profil

175 pon this element alone largely recapitulates phylogenies inferred from much larger genomic sequence d

176 Ontogeny does not recapitulate phylogeny; instead, differential outgrowth determines fi

177 s for classifying viruses and studying their phylogeny is complicated.

178 a The position of Eocaecilia within tetrapod phylogeny is controversial, as it already acquired the s

179 Conversely, correlation with host phylogeny is mostly seen among more recently diverged ba

180 Their internal phylogeny is still not fully resolved, and the position

181 We recovered near-complete genomes, whose phylogeny matched those of the principal biodegrading ta

182 hich seed mass changes across the angiosperm phylogeny may also be linked to diversification by incre

183 h to problems such as sequence alignment and phylogeny, more rigorous approaches that work directly w

184 -dimensions the relationship among competing phylogenies obtained from gene partitions found in three

185 Summarizing and comparing phylogenies obtained from multi-source data sets using c

186 Here, we analyse detailed phylogenies of amniote clades, paleontological data and

187 certain applications, such as reconstructing phylogenies of closely-related bacteria on the basis of

188 Phylogenies of mitogenomes and cox1+rbcL sequences clari

189 We review taxonomies and phylogenies of other large savannah mammals, illustratin

190 o overcome the difficulties of inferring the phylogenies of recently diverged taxa.

191 Recent phylogenies of the arthropods, based on fossil and molec

192 Molecular phylogenies of the legume-associated Ascochyta/Phoma spe

193 yielding numerous, additional, well-sampled phylogenies of TRF lineages.

194 Reconstruction of the phylogenies of zoonotic genotypes demonstrates significa

195 nd nuclear ribosomal genes, we constructed a phylogeny of 5036 species of Caryophyllales, representin

196 Based on the phylogeny of 7,554 LRR-RLK genes from 31 fully sequenced

197 In its initial form, T-BAS v1.0 uses a core phylogeny of 979 taxa (including 23 outgroup taxa, as we

198 opy, a method for inferring the evolutionary phylogeny of a tumor using both somatic copy number alte

199 el of modern human origins predicts that the phylogeny of ancestries exhibits bifurcating, tree-like

200 ange, and trait evolution to the first dated phylogeny of Andean bellflowers (Campanulaceae: Lobelioi

201 ncestral flowers at the deepest nodes in the phylogeny of angiosperms, using the largest data set of

202 The resulting gene family phylogeny of CMT transcripts from the most diverse sampl

203 In conclusion, molecular phylogeny of complete genomic sequences proved a monophy

204 The output will be a pHMM phylogeny of different protein families delineating thei

205 chthyan origins, add robust structure to the phylogeny of early crown group gnathostomes, reveal prec

206 The current distribution and molecular phylogeny of Espeletia suggest the influence of Andean g

207 Here we examined the deep phylogeny of eukaryotic CS converter gene families and i

208 tural evidence to trace their evolution in a phylogeny of extinct tetrapods.

209 rongly support several major branches of the phylogeny of insects-for instance, Cercophora, Dicondyli

210 The phylogeny of isolates and their virulence-associated gen

211 ycophyte/fern distinction is mirrored in the phylogeny of KNOX-interacting BELL proteins, in that a g

212 h type that have been used for inferring the phylogeny of mammals, we find that on average morphologi

213 a tool, called Treeomics, to reconstruct the phylogeny of metastases and map subclones to their anato

214 ographical patterns, host relationships, and phylogeny of Microgastrinae as a stimulus and foundation

215 Important concepts in the phylogeny of neuroimmunity, enteric neuronal and glial r

216 fast in speed and accurate for inferring the phylogeny of organisms.

217 Here we explored the idea of building a phylogeny of protein families using the distance matrix

218 iptomes (370 loci) to stabilize the backbone phylogeny of Reduvioidea, revealing the position of majo

219 g datasets result in the first well-resolved phylogeny of Reduvioidea.

220 variants (SNVs) were used to reconstruct the phylogeny of sequenced isolates, and epidemiologic data

221 we reconstructed a fully resolved and dated phylogeny of terrestrial isopods.

222 Phylogeny of the 141 sequences revealed a high genetic d

223 cross the tree of life, we reconstructed the phylogeny of the arsM gene that encodes the As(III) S-ad

224 morphological characters to generate a dated phylogeny of the butterfly genus Pteronymia (Nymphalidae

225 We present a complete generic-level phylogeny of the complex thalloid liverworts, a lineage

226 This paper explores the phylogeny of the delphacid subfamily Delphacinae based o

227 We present a comprehensive phylogeny of the genus Schistocerca, which contains both

228 e interest in understanding the ontogeny and phylogeny of the human language system, yet, neurobiolog

229 A comprehensive molecular phylogeny of the montium subgroup supports multiple orig

230 We present a fossil calibrated phylogeny of the new world sand dollar genus Encope, bas

231 , used maximum-likelihood methods to infer a phylogeny of the NTPase domains of R-proteins, and recon

232 Our results present a highly supported phylogeny of the stinging wasps.

233 However, the phylogeny of these medically relevant enzymes remains un

234 Here we characterize the biophysics and phylogeny of this enzyme and report the 1.86-A resolutio

235 ion describing how viral load evolves on the phylogeny of whole-genome viral sequences.

236 A phylogeny of Wolbachia and of mtDNA suggest a recent ori

237 s were linked to geography by projecting the phylogeny on a virtual globe and produced a transmission

238 te the application of SeqKernel to inferring phylogeny on RNA polymerases and show that it performs a

239 and suggest that vulnerability may depend on phylogeny or associated anatomical/physiological attribu

240 that is not readily detected using molecular phylogenies, or without a rich fossil record.

241 l three-domain structure of diTPSs, sequence phylogeny places the enzyme with two-domain TPSs of mono

242 model how climate, geographic proximity and phylogeny predicted population performance.

243 distribution of specialists correlated with phylogeny, protease and trichomes.

244 Dated phylogenies rarely include the divergence times of siste

245 , and have further applied this heuristic to phylogeny reconstruction.

246 formation derived from functional traits and phylogenies remain underdeveloped.

247 However, its internal phylogeny remains insufficiently investigated.

248 Yet, its internal phylogeny remains unresolved owing to limited sampling.

249 The leaves of the phylogeny represent sampled pathogens, which have known

250 Analysis of the C. gallinacea ompA phylogeny revealed at least 13 well segregated variants

251 ogametic systems onto the terrestrial isopod phylogeny revealed between 3 and 13 transitions of sex d

252 In addition, the phylogeny revealed that discrimination toward tRNA(Asp)

253 mplications for the interpretation of what a phylogeny reveals about the underlying epidemic contact

254 This phylogeny reveals patterns of raptorial leg evolution ac

255 nscriptomes revealed a well-resolved eudicot phylogeny, sequential separation of major core eudicot l

256 Gene phylogenies show multiple Hodgkinia lineages in the comm

257 Moreover, the phylogeny showed two different epidemic introductions in

258 Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy,

259 l 3CL(pro)'s from the same alpha-coronavirus phylogeny shows that the overall structures and active s

260 Here we summarize progress on lepidopteran phylogeny since 1975, emphasizing the superfamily level,

261 Procrustes analysis revealed that microbial phylogeny structured the antibiotic resistome.

262 d analysis of scientifically rigorous tumour phylogeny studies.

263 The time-scaled phylogeny suggested that K. pneumoniae strains isolated

264 ave, however, shifted their positions across phylogeny, suggesting that changes in location do not al

265 A mitochondrial phylogeny suggests that blue eggs originated in Asia and

266 Whole-genome molecular phylogenies supported a Tardigrada+Nematoda relationship

267 COI-based phylogeny supported the delineation of four recently des

268 fully identifies cell populations and infers phylogenies that are in concordance with existing knowle

269 ll sequencing enables the inference of tumor phylogenies that provide insights on intra-tumor heterog

270 es, and an unbiased and calibrated molecular phylogeny that has unprecedented detail.

271 tter explains the data the complex branching phylogeny that was previously reported.

272 This phylogeny - the largest of its kind to include plant fos

273 asets, which are most commonly used in coral phylogenies to date, were less informative and contradic

274 evolutionary studies, ranging from building phylogenies to predicting functional gene annotations.

275 ntly, biologists typically rely on molecular phylogenies to study the diversity dynamics of clades, u

276 of survival analysis and algorithms linking phylogenies to transmission trees is a rigorous but flex

277 f four vector species spanning the Anopheles phylogeny to explore the genomic and evolutionary proper

278 and used this to infer a strongly supported phylogeny to map major morphological and molecular trans

279 pplied to problems ranging from whole-genome phylogeny to the classification of protein families, ide

280 Here we describe the phylogeny, ultrastructure and subcellular location of 'C

281 parsing to generate accurate alignments and phylogenies using all the individuals from the 1000 Geno

282 We reconstructed a dated phylogeny using 12 genes, to investigate the biogeograph

283 esenting unknown taxa and place these on the phylogeny using either BLAST or phylogeny-based approach

284 Here we build an experimental phylogeny using the gene of a single red fluorescent pro

285 correlated with ARG profiles while sediment phylogeny varied along the river's anthropogenic gradien

286 Character mapping on the phylogeny was conducted to identify evolutionary changes

287 A time-calibrated maximum likelihood phylogeny was inferred and analyzed with bioclimatic, so

288 f enzymes sharing these sequence motifs; the phylogeny was instead dominated by bacterial taxonomy.

289 xonomic annotation of these reads, including phylogeny, was based on a combination of automated pipel

290 Placing these sequences into a global phylogeny, we found that all ciprofloxacin-resistant S.

291 HIV phylogenies were reconstructed using maximum likelihood

292 Site, individuality, and phylogeny were all determinants of stability.

293 phenotype distribution on the branches of a phylogeny, which is different from ancestral state recon

294 s a powerful framework for inferring species phylogenies while accounting for ancestral polymorphism

295 SERAPHIM can be applied to any phylogeny whose nodes are annotated with spatial and tem

296 sions the relationship among these competing phylogenies will help practitioners diagnose the limits

297 tions and a range of simulations using model phylogenies with a single reticulation.

298 oncatenate/coalesce these results to a final phylogeny with maximum support.

299 FL1 and CorAP1 expression co-occurred on the phylogeny with the morphological changes underpinning in

300 ine (DA) regulates multiple behaviors across phylogeny, with disrupted DA signaling in humans associa