ライフサイエンスコーパス: genealogy

1 ion for a specific prior distribution of the genealogy).

2 a population are often related by an unknown genealogy.

3 nts lead to a mosaic of segments with shared genealogy.

4 have led to some confusion concerning strain genealogy.

5 oth genes are copies of the same gene in the genealogy.

6 the transmission of chromosomes through that genealogy.

7 for a founder population with a large, known genealogy.

8 haplotypes, from which we constructed a gene genealogy.

9 n mapping mutations on a phylogeny or a gene genealogy.

10 function of a mapping of mutations on a gene genealogy.

11 d to the branch lengths of the reconstructed genealogy.

12 nastomose, connected strictly via historical genealogy.

13 le, we have been unable to identify a common genealogy.

14 Utah DARCC subjects were linked to the UPDB genealogy.

15 decline based on the shape of the resulting genealogy.

16 ly reflect species phylogeny, or simply gene genealogy.

17 orting effect on the shape of the underlying genealogy.

18 forensics, population genetics, and genetic genealogy.

19 population dynamics or the shape of the gene genealogy.

20 of forward mutations mapped on the sequence genealogy.

21 of forward mutations mapped on the sequence genealogy.

22 infection of another host in a pathogen gene genealogy.

23 on the structure of the simulated coalescent genealogy.

24 ing medical genetics, forensics, and genetic genealogy.

25 fidence recombination events in their shared genealogy.

26 in addition to sampled genetic sequences and genealogies.

27 tions, and importance sampling of coalescent genealogies.

28 ance polymorphism has a genomewide impact on genealogies.

29 rees while accommodating uncertainty in gene genealogies.

30 selection has surprisingly little effect on genealogies.

31 tree, which in most cases confirmed existing genealogies.

32 ecursively linked to faculty mentors to form genealogies.

33 to date, providing evidence for ancient gene genealogies.

34 n and verification of pedigrees within large genealogies.

35 h different forms of population structure to genealogies.

36 ion dynamics and demographic parameters from genealogies.

37 fitting stochastic epidemiological models to genealogies.

38 3 through identity-by-descent analysis in 17 genealogies.

39 ns commonly insert migration events into the genealogies.

40 rfectly linked sites alters the structure of genealogies.

41 lutionary scenarios but which cannot produce genealogies.

42 has prevented the reconstruction of stallion genealogies [1, 2].

43 Authors who were members of 2 genealogies (14% of key authors) contributed to 38% of a

44 information contained in the distribution of genealogies across the genome.

45 n the ancestral recombination graph to infer genealogies across the length of the human X chromosome

46 Therefore, comparisons of gene genealogies allow inferences about the genetic architect

47 ration of the shattered coalescent model for genealogies, allowing for multiple founding mutations at

48 ion with biotic entities registered in mtDNA genealogies alone.

49 proposed for characterizing the structure of genealogies among alleles that regulate self-incompatibi

50 The lack of concordance among gene genealogies among isolates in one of the clades (group I

51 listing all the ancestral configurations and genealogies and computing the exact probability of data.

52 Positive selection distorts the structure of genealogies and hence alters patterns of genetic variati

53 Genealogies and population assignments are sampled from

54 esearchers to easily sample and analyze gene genealogies and related data from populations evolving u

55 We apply the multi-stage model to HIV genealogies and show that the proposed method can be use

56 higher than the number expected for neutral genealogies and similar sample sizes and is more consist

57 n about population structure is contained in genealogies and what sample sizes are necessary to relia

58 EFHC2 shows genealogy and extended LD consistent with directional se

59 nificantly modify the branch lengths of an S genealogy and may be ubiquitous to recognition systems.

60 Correlations between genealogy and publication result were examined.

61 RECSIM takes a general genealogy and simulates the transmission of chromosomes

62 nd for uncertainty about the true underlying genealogy and the makeup of ancestral marker haplotypes.

63 the trade-off between the complexity of the genealogy and the power lost due to the additional multi

64 oalescent model for the sampled individuals' genealogy and then integrating over all possible genealo

65 han lanosterol (characteristic of the fungal genealogy) and the chirality of the C-24 alkyl group is

66 s inferred from primary-metabolism (PM) gene genealogies, and FUM cluster types are not trans-specifi

67 simulation, REJECTOR generates numerous gene genealogies, and hence simulated data, under a model of

68 coalescent is a convenient way to model such genealogies, and in this paper we set out the theory beh

69 than among rates estimated from phylogenies, genealogies, and pedigrees.

70 n for HGGs is influenced by medical academic genealogies, and that articles contributed by authors of

71 These gene genealogies are accompanied by deviations from neutralit

72 Although these genealogies are equivocal regarding the mode of origin,

73 Furthermore, if large numbers of genealogies are imputed from the genotypes, the power of

74 across patients, we conclude that empirical genealogies are more asymmetric than expected if evoluti

75 h theory, TMRCA is significantly reduced and genealogies are significantly more imbalanced in coding

76 heritance, and show that its effects on gene genealogies are similar to partial self-fertilization.

77 d to cross the habitat, deep branches in the genealogy are longer than would be expected under the st

78 sions of the pedigree connection problem for genealogies as well as other pedigree analysis problems.

79 computing the expected overall length of the genealogy as a function of the individual birth rate gam

80 sequence data, which treats mutations in the genealogy as missing data.

81 ential applications in forensics and genetic genealogy, assessed the ability to differentiate between

82 Posterior distributions of HIV-1 genealogies assuming a Bayesian relaxed molecular clock

83 then used to generate a null distribution of genealogies assuming neutrality, with the null and empir

84 mator" of T(MRCA) that derives from the star genealogy assumption has bias of 10-50%.

85 ence times and migration rates from inferred genealogies at many neutrally evolving loci across the g

86 id increase of a selected allele affects the genealogy at partially linked sites, which under fairly

87 ses at unlinked loci are correlated with the genealogy at the selected locus; i.e., fecundity varianc

88 r of articles from the same medical academic genealogy (authors with shared training history and/or m

89 etailed reconstruction of human Y chromosome genealogy based on several tens to even hundreds of thes

90 The present symbiont genealogy, based on bacterial small subunit (16S) rDNA s

91 quences, was closely congruent with the host genealogy, based on clam mitochondrial cytochrome oxidas

92 orresponding to cell types related by a tree-genealogy, based on only a few samples from each cell ty

93 We suggest a new genealogy-based approach, CAMP (coalescent-based associa

94 In this paper, we develop a scalable genealogy-based method to detect candidate signatures of

95 Genealogy-based methods were used to estimate migration

96 empirical distributions compared using four genealogy-based summary statistics sensitive to nonneutr

97 may produce significant distortions in gene genealogies, but few studies have sought to quantify thi

98 The Y chromosome directly reflects male genealogies, but the extremely low Y chromosome sequence

99 In particular, we show that the GF of genealogies can be decomposed into a set of equivalence

100 At the same time, this variation in genealogies can be exploited to gain insight into the na

101 y shown that the generating function (GF) of genealogies can be used to analytically compute likeliho

102 imple cladogenetic theory suggests that gene genealogies can be used to detect mixis in a population

103 xtremely long time scales, such that allelic genealogies can shed insight into long-term demographic

104 In particular, local genealogies can vary considerably across loci, which can

105 Genealogy can illuminate the evolutionary path of import

106 which manifests itself in the form of a gene genealogy, causes the structure of G to be nonuniform in

107 nique users, mainly from the general genetic genealogy community, have already used DNA Compass, demo

108 e coalescence times of the intraallelic gene genealogy conditioned on the number of copies.

109 The resulting genealogy, constructed by using the highly conserved PKS

110 ntial challenge, as current methods to store genealogies consume a great deal of space, are slow to p

111 of the study might decrease if these imputed genealogies create an additional multiple-hypothesis tes

112 contains >2 million individual records with genealogy data and 250,000 linked death certificates.

113 PedHunter uses a relational database of genealogy data, with tables in specified format, for all

114 are illustrated by examples using the Amish Genealogy Database (AGDB), which was created for the Old

115 Here we show, by using a genealogy database and automated pedigree software, that

116 dy included an enlargement of the Anabaptist Genealogy Database to 539,822 individuals, which will be

117 software query system was used on the Amish Genealogy Database to correct the previous pedigree, der

118 Using a genealogy database, automated pedigree software, and lin

119 e (Y-STRs) and querying recreational genetic genealogy databases.

120 distribution of mutations on the rooted gene genealogies demonstrate that the oldest mutations in P.

121 Allelic genealogies derived from different parts of the coding s

122 Consistent with previous molecular data the genealogies do not, however, support the division of Zea

123 ulation are already in equilibrium, then the genealogy does not differ much from the neutral case.

124 the signal of negative selection in the gene genealogy enhanced by their recurrence.

125 mutating locus and an incompletely resolved genealogy, enumerates mutation histories with a minimum

126 or, less efficiently, by conditioning on one genealogy estimated from the sequence data.

127 thods prove useful for probing fragmentation genealogies, evaluating the structures of lower mass fra

128 in these statistics because of variation in genealogy even among neutral loci, and values at pairs o

129 In FUM gene genealogies, evolutionary relationships between fusaria

130 e salvage and de novo synthesis, we inferred genealogies for each enzymatic domain in the latter path

131 The likelihood is approximated based on the genealogies for each subinterval.

132 Genealogies for five gene regions are discordant, and on

133 lso possible to obtain a posterior sample of genealogies for the data using this method.

134 A coalescent genealogy for the reference haplotype data is sampled fr

135 leotide polymorphisms, we have constructed a genealogy for these three lines.

136 ity, allowed us to construct a comprehensive genealogy for Toxoplasma gondii that incorporates sexual

137 constant size (for which I = 0) or to a star genealogy (for which I = 1).

138 dies of human evolution, population history, genealogy, forensics and male medical genetics.

139 rchives, FamilySearch and Sorenson Molecular Genealogy Foundation, I was able to discern the likely h

140 ts entire geographic range, we have compared genealogies from fragments of five nuclear genes.

141 Genealogies from rapidly growing populations have approx

142 nging, however, because the inference of the genealogy from the genotypes is a computationally intens

143 enetic simulator that allows for sampling of genealogies, genetic data and many population parameters

144 racters, as well as concordance of four gene genealogies, H. capsulatum could be considered to harbor

145 Species-specific gene genealogies have longer terminal branches than expected,

146 from which the founders of the individuals' genealogy have been randomly selected.

147 s restrict themselves to perfectly tree-like genealogies (i.e. regions with no observed recombination

148 ards this goal, we explore the properties of genealogies in a model of continual adaptation in asexua

149 eography examines the distribution of allele genealogies in an explicit geographical context.

150 sing diverse populations with different gene genealogies in gene-association studies.

151 r assertions, a rigorous analysis of allelic genealogies in this gene family cannot be used to justif

152 Here we use nuclear and chloroplast gene genealogies in two species of Silene to show the histori

153 Leveraging the genealogy in association studies is challenging, however

154 A 10-species genealogy including S-RNases from a pair of congeners fr

155 Extensive incompatibilities between gene genealogies indicate frequent recombination between unli

156 ndem mass spectrometry experiments to obtain genealogy information about product ions present in mass

157 ng knowledge of genetics and accumulation of genealogy information, pedigree data is becoming increas

158 To obtain genealogy information, STEP ratios are calculated by com

159 tical methodology would attempt to take this genealogy into account.

160 eep coalescence event when fitting the mtDNA genealogy into the species tree, which is not unexpected

161 Without selection, the genealogy is described by Kingman's well-known coalescen

162 When we assume that such a genealogy is known, the coalescent model, equipped with

163 of related individuals, provided that their genealogy is known.

164 n outbred stock of mice for which the entire genealogy is known.

165 The total length of the genealogy is shown to be maximized when gamma = mu.

166 roposed that describes the extent to which a genealogy is similar to one from a population of constan

167 probability distribution, then a coalescent genealogy is simulated which extends the sampled genealo

168 d death rates and the shape of the resulting genealogy is studied.

169 orensic studies and, in the form of 'genetic genealogy', is an area of rapidly growing interest for t

170 d an authorship contribution from the second genealogy, it was less likely to support maximal resecti

171 ed an authorship contribution from the first genealogy, its results were more likely to support maxim

172 l valvular diseases using a population-based genealogy linked to death records.

173 Incongruent gene genealogies manifest genetic exchange among distantly re

174 While nuclear gene genealogies may have limited applications in phylogeogra

175 s indicate that much of the combined allelic genealogy may be explained by lineage sorting and phylog

176 cal training and that this "medical academic genealogy" may influence the landscape of the peer-revie

177 s showed that a virus time-scaled phylogeny (genealogy) may be substantially different from the betwe

178 ts one in the past, it is necessary to build genealogy models that directly relate the two.

179 These analyses suggest that the genealogies of all living humans overlap in remarkable w

180 Coalescent-based genealogies of all loci were congruent and demonstrate t

181 rom the posterior distribution of coalescent genealogies of all the sampled chromosomes without regar

182 The genealogies of different genetic loci vary in depth.

183 tropolis-Hastings sampling of fully resolved genealogies of entire nucleotide sequences.

184 hat our approach can efficiently reconstruct genealogies of isolates in situations where classical ph

185 Furthermore, gene genealogies of most loci with an excess of low frequency

186 The mitochondrial genealogies of several species of whale lice (Amphipoda:

187 ce of incomplete lineage sorting so that the genealogies of SNPs do not all conform to a single topol

188 to the two reference loci, and the inferred genealogies of the division 5D/6 genes show patterns con

189 A measure of the correlation between the genealogies of two nucleotides on two sequences is intro

190 ordant with inbreeding loops apparent in the genealogy of 11 affected horses.

191 we used a phylogenetic approach to obtain a genealogy of 148 NTPase genes and reconstruct a scenario

192 We introduce the genealogy of a random sample of genes taken from a large

193 Therefore, the genealogy of a region that contains a mobile element is

194 A stochastic model for the genealogy of a sample of recombining sequences containin

195 ne model has a more pronounced effect on the genealogy of a sample.

196 A genealogy of adenylation domains was utilized to identif

197 opose an estimator that considers the entire genealogy of all of the sampled genes and infers admixtu

198 By considering the genealogy of all sequences rather than pairs of sequence

199 igration-only models studied previously, the genealogy of any sample includes two phases: a brief sam

200 construction of a new and robust phylogenic genealogy of BCG strains.

201 A genealogy of CCR5 haplotypes had deep branch lengths des

202 mmary statistics, migration analyses and the genealogy of current populations of P. infestans for bot

203 the important features of this approach on a genealogy of HIV-1 envelope (env) partial sequences.

204 erful tools for reconstructing the worldwide genealogy of human Y chromosomes and for illuminating pa

205 have used these data to study the ancestral genealogy of human Y chromosomes.

206 The effect of the obstacle on the genealogy of individuals at the front is characterized b

207 distinct differentiation pathways and to the genealogy of mature hematopoietic cells under physiologi

208 Here, we resolve the first Y chromosome genealogy of modern horses by screening 1.46 Mb of the m

209 The genealogy of Muslim missionaries within the settled agri

210 erical simulation indicated that the allelic genealogy of one species appeared consistent with the sy

211 l that defines a probability density for the genealogy of randomly sampled individuals from the popul

212 nucleotide sequence data and a reconstructed genealogy of sequences obtained over time.

213 leles relate to properties of the underlying genealogy of sequences.

214 To correlate phenotypes with the age and genealogy of single cells over time, we developed a micr

215 ize that incorporates the uncertainty in the genealogy of such temporally spaced sequences by using M

216 nservative founder assumptions and the exact genealogy of the 411 couples.

217 A brief genealogy of the archived strains is also recorded.

218 t is useful first to consider the underlying genealogy of the chromosomes.

219 wever, SNPs are correlated by the unobserved genealogy of the population, and a more powerful statist

220 In the selective case, the genealogy of the sample is embedded in a graph with a co

221 quences permits a compact description of the genealogy of the sample.

222 these loci, many recombination events in the genealogy of the sampled alleles can be inferred and the

223 en requires Monte Carlo integration over the genealogy of the samples.

224 However, the allelic genealogy of the second species showed unusually long te

225 ects of linkage to the selected sites on the genealogy of the surrounding chromosomal region.

226 -type II parent of type III, making the full genealogy of the type III clonotype known.

227 as examined using a resource consisting of a genealogy of the Utah population linked to death certifi

228 Here we examine an allele genealogy of the Waxy locus to trace the evolutionary an

229 Gene genealogies offer a powerful context for inferences abou

230 a surprisingly accurate description of gene genealogies on a fixed pedigree.

231 in gene codon 129M and were not connected by genealogy or microsatellite haplotype background to the

232 might represent either a distinct erythroid genealogy, or an "end-stage" of normal and SS RBCs.

233 utation and genetic transmission through the genealogy, or population pedigree, of the species.

234 ted samples i.e., the set of highly probable genealogies out of the infinite set of possible genealog

235 entor trains-using data from the Mathematics Genealogy Project, which tracks the mentorship record of

236 ned on an ensemble of histories (a forest of genealogies), rather than a single tree.

237 r the inference of demographic history using genealogies reconstructed from gene sequence data.

238 tes of the scaled indices were obtained from genealogies reconstructed from nucleotide sequences of s

239 Excluding one hybrid strain, all six genealogies recovered the same seven biogeographically s

240 "Academic genealogy" refers to the linking of scientists and schol

241 ating longer terminal branches in the S gene genealogy relative to the congener Physalis crassifolia.

242 of the coalescence probability density of a genealogy requires a product over all time periods betwe

243 Utah Population Database, a population-based genealogy resource linked to electronic medical records

244 Gene genealogies reveal trans-species polymorphisms at csd bu

245 ur likelihood-based Markov chain Monte Carlo genealogy sampler LAMARC and compared the two versions f

246 resent a Markov chain Monte Carlo coalescent genealogy sampler, LAMARC 2.0, which estimates populatio

247 Coalescence-based genealogy samplers also indicated that P. triticina on A

248 We propose a genealogy-sampling algorithm, Sequential Markov Ancestra

249 at articles contributed by authors of select genealogies share common results.

250 The five genealogies show multiple incompatibilities indicative o

251 Well-supported gene genealogies show that mitochondrial and nuclear gene seq

252 can data) selects regions of the genome with genealogies similar to those expected under models of re

253 in coefficients that do not explode when the genealogy size increases.

254 ny approach which estimates growth rate from genealogy structure.

255 entiation in light of the reconstructed gene genealogy suggests that the mbuna may be of considerably

256 Observed gene genealogies support a model of secondary contact for the

257 the mode of origin, several aspects of these genealogies support an autotetraploid origin.

258 information for inferences on the population genealogy than simple summary statistics such as the ave

259 Because genealogies that contain polymorphic mobile elements are

260 ealogies out of the infinite set of possible genealogies that describe the sampled sequences.

261 the second speciation event and lead to gene genealogies that do not match the species phylogeny.

262 An efficient tool for mining complex inbred genealogies that identify clusters of individuals sharin

263 Rather, it is the depth of the entire genealogy that differs markedly in the two families, wit

264 to jointly simulate MLST data and the clonal genealogy that gave rise to the sample.

265 Europeans show an unusual haplotype genealogy that is dominated by two common haplotypes dif

266 The deeper the genealogy, the greater the chance that it will include a

267 Though originally defined in terms of genealogy, the modern version of relatedness accommodate

268 Here, we use the generating function of genealogies to derive the probability of mutational conf

269 diversity in the two species, we constructed genealogies to infer the evolutionary origin of Z. peren

270 nd records from approximately 4000 ascending genealogies to select individuals whose ancestors lived

271 oach to this test, in which we use the known genealogy to derive a correction factor for the case-con

272 alogy is simulated which extends the sampled genealogy to include new haplotype data.

273 ths of trans-specific alleles on the allelic genealogy to infer phylogenetic relationship among speci

274 Gene genealogies trace the evolutionary relationships among h

275 tools are available that allow for producing genealogies under arbitrarily complex selective and demo

276 da is a software package that simulates gene genealogies under multiple merger and Kingman's coalesce

277 tor of Kelleher et al. (2014) that simulates genealogies under the continuum model, with an approxima

278 he likelihood of the observed central RRM2P4 genealogy under two alternative views of human evolution

279 The method explicitly models the genealogy underlying a sample of case chromosomes in the

280 ed only weakly despite the shared underlying genealogy, underscoring the importance of divergent muta

281 at is orthogonal to the bonds of kinship and genealogy usually examined by evolutionary biologists.

282 However, fitting epidemiological models to genealogies via coalescent models remains a challenging

283 alogy and then integrating over all possible genealogies via Monte Carlo or, less efficiently, by con

284 erior (empirical) distribution of coalescent genealogies was estimated using Markov chain Monte Carlo

285 Then, averaging across genealogies, we estimate the likelihood of the phenotype

286 escence theory to interpret modern haplotype genealogy, we estimate the origin of the CCR5-Delta32-co

287 possible reconstructions of the recombinant genealogy, weighting according to their posterior probab

288 , is panmictic throughout its range, allelic genealogies were constructed from six single-copy nuclea

289 stent with this recent divergence, some gene genealogies were reciprocally monophyletic between these

290 kelihood methods (designed to handle complex genealogies) were used to determine the heritability of

291 ions are used to integrate over the space of genealogies, whereas other parameters are integrated out

292 AUGIST (accomodating uncertainty in genealogies while inferring species tress) is a new soft

293 oductive isolation is often incomplete, gene genealogies will be discordant, and most regions of the

294 large genetic distance, but share MRCA, the genealogies will show only little correlation.

295 ch subjects and individuals pursuing genetic genealogy will be accessible online, this type of triang

296 Monte Carlo approach to investigate possible genealogies with branch lengths and with migration event

297 escence, as well as the likelihood of a gene genealogy with heterochronous sampling and labeled taxa,

298 rder to compare their substitution rates and genealogy with those of Witheringia maculata and two spe

299 ess of intermediate-frequency alleles, and a genealogy with two common haplotypes separated by deep b

300 differences in the depths of the underlying genealogies within these subpopulations.

301 A coalescent theory of the gene genealogy within an allelic class that arises by a uniqu