ライフサイエンスコーパス: archaic

1 atterns in aDNA, implemented in an R package aRchaic.

2 Importantly, some archaic adaptation mechanisms appear to have reemerged a

3 enomic regions that show strong evidence for archaic adaptive introgression.

4 istory: recent African replacement (RAR) and archaic admixture (AA).

5 tter define the scope of plausible models of archaic admixture between Neandertals and anatomically m

6 owever, we do find evidence for at least one archaic admixture event in sub-Saharan Africa, with the

7 Here we search for evidence of archaic admixture from a worldwide panel of 1,667 indivi

8 In great apes, archaic admixture has been identified in chimpanzees and

9 Archaic admixture has had a substantial impact on human

10 Signals of archaic admixture have been identified through compariso

11 Our current understanding of archaic admixture in humans relies on statistical method

12 We find no evidence for archaic admixture in the Andaman Islands, as previously

13 Our results establish that archaic admixture influences disease risk in modern huma

14 and fit expectations better under a range of archaic admixture scenarios.

15 samples have pointed to several instances of archaic admixture through interbreeding between the ance

16 The locations of these putative archaic admixture tracts are weighted against functional

17 ygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population s

18 a, Biaka, and San) to test models of African archaic admixture.

19 first whole genome-level evidence of African archaic admixture.

20 lly described as an individual with possible archaic affinities, but its ancestry has been debated si

21 lly and chronologically intermediate between archaic African fossils and later anatomically modern La

22 opling of the Caribbean and the movements of Archaic Age peoples in the Americas.

23 , who first entered the Caribbean during the Archaic Age, derive from a deeply divergent population t

24 When an introgressed archaic allele has a selective advantage, even rare inte

25 aic lineages, provided that the introgressed archaic allele has risen to high frequency under positiv

26 Finally, to facilitate the exploration of archaic alleles and adaptive signals in human genomics a

27 pistatic incompatibilities between human and archaic alleles are needed to explain the degree of arch

28 This implies that many archaic alleles harmed the fitness of hybrid individuals

29 Thus, adaptive introgression of archaic alleles has significantly shaped modern human im

30 at selection acted to purge these regions of archaic alleles that disrupted their gene regulatory fun

31 se enhancers show the strongest depletion of archaic alleles, but only brain enhancers show evidence

32 Finally, the reduction of both archaic ancestries is especially pronounced on chromosom

33 s, we generate a map within human genomes of archaic ancestry and of genomic regions not shared with

34 ciated alleles in European populations using archaic, ancient and modern human samples.

35 eal orientation is intermediate between late archaic and early modern humans, the ramus is exceptiona

36 indicators of lower facial projection across archaic and modern Homo indicates that Neandertal facial

37 ability to make a direct comparison between archaic and modern human genomes.

38 The phylogenetic relationships of archaic and modern human Y chromosomes differ from the p

39 ic biases or behavioral distinctions between archaic and modern humans remains much debated.

40 tals than in the ancestral lineage common to archaic and modern humans, whereas genes involved in beh

41 ars ago) in Israel, an early contact area of archaic and modern humans.

42 -stone models, pairwise F(ST) values between archaic and present-day samples reflect both the spatial

43 phological evidence of a strong link between archaic and recent Asian H. sapiens populations.

44 es of the hominins from this site with other archaic and recent human groups.

45 lly, beta-lactamases are widely distributed, archaic, and have wide spectrum, including digesting ant

46 remain useful, letting go of what has become archaic, and introducing new concepts and methods that s

47 Proteopithecus sylviae is an archaic anthropoid from the late Eocene quarry L-41, Fay

48 However, archaic approaches, especially combinational ones, are r

49 Hence, the change from the Desert Archaic/Basketmaker to Pueblo cultures was associated wi

50 Here, we redescribe the wings of the archaic bird Archaeopteryx lithographica and the dinosau

51 ecies are identified, including 7 species of archaic bird, representing Enantiornithes, Ichthyornithe

52 In particular, it remains unclear whether archaic birds became extinct gradually over the course o

53 des strong evidence for a mass extinction of archaic birds coinciding with the Chicxulub asteroid imp

54 e evidence for the persistence of a range of archaic birds to within 300,000 y of the K-Pg boundary.

55 Sequencing DNA derived from archaic bones has enabled genetic comparison of Neandert

56 covered in a secure and undisturbed Terminal Archaic burial context at Jiskairumoko, a multicomponent

57 Archaic chaperone-usher pathway pili, the most diverse a

58 The archaic characteristics of this ancient fish lineage pla

59 ed by high, but short-lived, diversity of an archaic clade, Rhomaleosauridae.

60 lazed (BG) specimens from different periods (Archaic, Classical, Hellenistic) with laboratory reprodu

61 Here, aRchaic clearly distinguishes modern from ancient sample

62 l mosaic suggests considerable complexity in archaic contact, with modern humans interbreeding with m

63 the concept of culture and ethnicity in such archaic contexts, this paper then examines three example

64 ron microscopy structure of the prototypical archaic Csu pilus that mediates biofilm formation of Aci

65 sistent with the notion of a subcortical and archaic danger recognition system and a system detecting

66 erences among more divergent populations, as archaic Denisovans have accumulated nonsynonymous mutati

67 Thus, archaic Denisovans must have lived over an extraordinari

68 approximately 5% [1] of their ancestry from archaic Denisovans, an even larger proportion than the a

69 dence show that modern humans interbred with archaic Denisovans.

70 in evidence through the identification of an archaic-derived amino acid sequence for the collagen typ

71 in Kenya from ca. 4.1 to 1.4 Ma samples two archaic early hominin genera and records some of the ear

72 It therefore presents a mosaic of archaic, early modern human and possibly Neandertal morp

73 ntext at Jiskairumoko, a multicomponent Late Archaic-Early Formative period site in the southwestern

74 r studies reveal an evolutionarily conserved archaic embryonic program in somatic cells that can be d

75 Lycophyte plastomes include the most archaic examples among vascular plants and the most reco

76 either by outcompeting them or when the more archaic faunas suddenly became extinct.

77 Postcranial remains seem also to have archaic features.

78 hologically modern overall but displays some archaic features.

79 Here we report the complete mtDNA of an archaic femur from the Hohlenstein-Stadel (HST) cave in

80 Archaic flying insects were considered to lack metamorph

81 anatomically modern humans (AMH) and various archaic forms coexisted for much of the last 200,000 yr;

82 ve entered the population via gene flow with archaic forms in Eurasia.

83 A long-debated question concerns the fate of archaic forms of the genus Homo: did they go extinct wit

84 cally focused on the genetic contribution of archaic forms outside of Africa.

85 ra, including living taxa (lipotyphlans) and archaic fossil forms, is central to the question of high

86 Regarding archaic gene flow, we test six complex demographic model

87 Are they relics of the archaic genes, or are they results of rearrangement in g

88 ionships and population history of available archaic genomes and 25 present-day human genomes shows t

89 ty to consider how findings from ancient and archaic genomes could inform our knowledge of evolution

90 ow how integration of fossil skull data with archaic genomics and neuroimaging can suggest developmen

91 o contamination experiment, we show that the aRchaic grades of membership reflect relative levels of

92 ng gene flow into Denisovans from an unknown archaic group.

93 for exploring phenotypic differences between archaic groups from genomic information alone.

94 on depended in part on the genetic legacy of archaic groups such as the Neanderthals.

95 several migrations and possible survival of archaic groups.

96 Relative to body mass, brain mass in late archaic H. sapiens (Neanderthals) was slightly smaller t

97 Introgressed archaic haplotypes (introduced from an archaic human gen

98 on datasets to show many positively selected archaic haplotypes act as expression quantitative trait

99 analyses that identified 126 high-frequency archaic haplotypes as putative targets of adaptive intro

100 We identified high-confidence archaic haplotypes in 161 new genomes spanning 14 island

101 Denisovan and Neandertal genomes identified archaic HLA haplotypes carrying functionally distinctive

102 man genome (hg38) and appear to be unique to archaic hominids.

103 also provide insights into the evolution of archaic hominids.

104 ilable for more than 1,100 ancient human and archaic hominin (for example, Neandertal) individuals.

105 diseases, and summarise the contribution of archaic hominin admixture to present-day human SV.

106 oach to identify DNA inherited from multiple archaic hominin ancestors and applied it to whole-genome

107 to live at high altitude, was inherited from archaic hominin ancestors.

108 Existing methods detect this archaic hominin ancestry within human genomes using patt

109 phenotypic, and evolutionary significance of archaic hominin DNA that persists in present-day individ

110 ortion of their ancestry from Denisovans, an archaic hominin group from Siberia.

111 s expanded and completely replaced all other archaic hominin populations.

112 e, we review recent work that has identified archaic hominin sequence that survives in modern human g

113 A tooth from the third archaic hominin specimen (Mezmaiskaya 3) was retrieved f

114 Siberia, we have sequenced the genome of an archaic hominin to about 1.9-fold coverage.

115 Conversely, in all archaic-hominin samples the fixation for a specific H4 h

116 history of introgressive hybridization from archaic hominins (most likely Asian Homo erectus) into t

117 Genomic analyses of these haplotypes in archaic hominins and ancient human genomes suggest that

118 that HPV58 variants may have coevolved with archaic hominins and dispersed across the planet through

119 debate concerning the dietary adaptations of archaic hominins and early Homo has been fuelled by cont

120 ively suggest that large CNVs originating in archaic hominins and introgressed into modern humans hav

121 ect to the genetic constitution of these two archaic hominins and Pan troglodytes (chimpanzee).

122 ivergent selection for higher muscle mass in archaic hominins compared with humans.

123 estry and of genomic regions not shared with archaic hominins either by admixture or incomplete linea

124 archaeological and fossil evidence indicates archaic hominins had not spread as far as the Sahul cont

125 Ancient DNA from archaic hominins has revealed a rich history of admixtur

126 Our results indicate that archaic hominins occupied the Tibetan Plateau in the Mid

127 to change-containing variation acquired from archaic hominins or adaptive variants in specific popula

128 strate that hybridization between modern and archaic hominins provided an important reservoir of adva

129 Neanderthals were a group of archaic hominins that occupied most of Europe and parts

130 ptive introgression of genetic variants from archaic hominins to humans and emerging ancient genome d

131 d Denisovan sequences suggests that PRDM9 in archaic hominins was closely related to present-day huma

132 y motifs absent in other primates (including archaic hominins), with evidence for selective pressures

133 ene regulatory architecture between AMHs and archaic hominins, and provide an avenue for exploring ph

134 ow the sequencing of genomes from modern and archaic hominins, great apes and other primates is revea

135 e world, they encountered and interbred with archaic hominins, including Neanderthals and Denisovans

136 etween our direct ancestors and contemporary archaic hominins, including the Neanderthals.

137 retain DNA inherited from interbreeding with archaic hominins, such as Neandertals, yet the influence

138 dentifying divergent gene regulation between archaic hominins, such as Neanderthals, and AMH sequence

139 Genome sequences are known for two archaic hominins-Neanderthals and Denisovans-which inter

140 nst admixture similar to those described for archaic hominins.

141 actions and what led to the disappearance of archaic hominins.

142 directly compare splicing between modern and archaic hominins.

143 ns and putatively introgressed variants from archaic hominins.

144 on average are similar to those of preceding archaic Homo and principally contrast with those of rece

145 oughout the globe is the question of whether archaic Homo lineages contributed to the modern human ge

146 ility of admixture between modern humans and archaic Homo populations (Neanderthals being one possibi

147 been argued to result from the expansion of archaic Homo sapiens out of Africa.

148 rm, and suggests that Neanderthals and other archaic Homo should be excluded from H. sapiens.

149 although morphologically similar to those of archaic Homo, the Saint-Cesaire 1 femoral midshaft exhib

150 hat AMHS is a distinct species from taxa of "archaic" Homo (e.g., Homo neanderthalensis).

151 S) from those attributed to various taxa of "archaic" Homo spp. (AH) and to test hypotheses about the

152 These results suggest an archaic human diaspora early in the Middle Pleistocene.

153 ica, raises hopes for the future recovery of archaic human DNA from regions in which climatic conditi

154 The preservation of archaic human DNA in the warm coastal climate of Gibralt

155 essed archaic haplotypes (introduced from an archaic human genome into the modern human genome) might

156 ed in modern humans, the deletion is also in archaic human genomes.

157 Recent work has demonstrated that two archaic human groups (Neanderthals and Denisovans) inter

158 a result of past admixture events with these archaic human groups.

159 st in human evolution centers around whether archaic human populations (such as the Neanderthals) hav

160 ach that does not require the presence of an archaic human reference genome.

161 ferences that distinguish modern humans from archaic human species.

162 n these early modern humans met preexisting 'archaic human' populations outside of Africa.

163 Earlier (archaic) human populations were biologically similar and

164 a previously undocumented mixture related to archaic humans (p = 0.0013).

165 40 y) adult mortality distributions for late archaic humans (principally Neandertals) and two samples

166 We analyzed the APOL1 sequence in modern and archaic humans and baboons along with geographic distrib

167 Hence, admixture with archaic humans brought a functional HLA-H allele into mo

168 3 allele in west Asia through admixture with archaic humans called Denisovans, a likely sister group

169 ons and limited admixture between modern and archaic humans can be accommodated in the model while co

170 DNA predicted faces of archaic humans differ more from those of Europeans than

171 cing has revolutionised our understanding of archaic humans during the Middle and Upper Palaeolithic.

172 The Late Pleistocene archaic humans from western Eurasia (the Neandertals) ha

173 y provide immunity against diseases to which archaic humans had evolved resistance.

174 is also differentiated from western Eurasian archaic humans in aspects of its temporal, occipital, an

175 a complex intertwined history of modern and archaic humans in the Asia-Pacific region, where distinc

176 graphical spread, and eventual extinction of archaic humans outside of Africa are much debated.

177 istence of beneficial variants acquired from archaic humans that may have accelerated adaptation and

178 es have focused on vertebrates, particularly archaic humans, newer technologies allow the capture of

179 sm arose before the divergence of modern and archaic humans, segregates at intermediate to high frequ

180 d Neandertals in the Eurasian range of these archaic humans.

181 underrepresented in the genomic landscape of archaic humans.

182 ority population was also ancestral to those archaic humans.

183 d more typically found in Middle Pleistocene archaic humans.

184 d a role in the evolution of both modern and archaic humans.

185 mbian fish-trapping facilities built by Late Archaic hunter-gatherer-fishers, which continued to be u

186 According to this model, archaic introgressed alleles were somehow distinct from

187 he statistical methods developed to identify archaic introgressed fragments in the genome sequences o

188 involved in the post-hybridisation purge of archaic introgressed regions.

189 ngle-nucleotide variants, but their roles in archaic introgression and adaptation have not been syste

190 ic genetic architecture, local ancestry, and archaic introgression drive variation in gene regulation

191 We identify the fingerprint of an archaic introgression event in the sub-Saharan populatio

192 tified multiple genes putatively involved in archaic introgression events and that, especially as reg

193 We found evidence of archaic introgression in all three populations, and the

194 cover novel instances of population-specific archaic introgression in diverse populations, spanning g

195 By combining local ancestry and archaic introgression inference with eQTLs and methylQTL

196 mong African groups, as well as the putative archaic introgression of ancient hominins, have been poo

197 population structure and the possibility of archaic introgression of Y chromosomes into anatomically

198 expanding the investigation of the impact of archaic introgression on more complex adaptive responses

199 In contrast to models with archaic introgression, we predict that fossil remains fr

200 confound genetic signals from adaptation and archaic introgression.

201 ls that consider recent admixture as well as archaic introgression.

202 at the first dinosaurs quickly replaced more archaic Late Triassic faunas, either by outcompeting the

203 closely match the logic and content of those archaic laws.

204 eages and those that are only derived in one archaic lineage.

205 c lineages, those that are ancestral in both archaic lineages and those that are only derived in one

206 uestion is that low levels of admixture with archaic lineages are not expected to leave extensive tra

207 Analyses of surviving archaic lineages suggest that there were fitness costs t

208 rtunity to identify low-level admixture with archaic lineages, provided that the introgressed archaic

209 ts, including those that are derived in both archaic lineages, those that are ancestral in both archa

210 As reintroduction of the archaic LSD1 variant (AA) abolishes E9-long splicing, th

211 The evidence for Late Archaic maize has been limited, leading to the interpret

212 Discoveries of archaic Mesozoic fossil birds ('opposite' birds, or enan

213 In the context of an increasingly documented archaic-modern morphological mosaic among the earliest m

214 he majority MRSA clone suggest that it is an archaic MRSA isolate similar in features to early MRSA i

215 o those that accompanied the replacement of "archaic" Neanderthal by anatomically modern human popula

216 st approximately 100,000 years ago, the late archaic Neanderthals and the early modern Skhul/Qafzeh h

217 In addition, we document a remarkably archaic new fossil peramelemorphian taxon that inhabited

218 posure on human brain organoids carrying the archaic NOVA1 variant disrupts FOXP2 expression in corti

219 The wings of archaic Odonatoidea from the mid-Carboniferous of Argent

220 We illustrate aRchaic on data from several aDNA studies and modern ind

221 hin contemporary human genomes that may have archaic or common ancestral roots.

222 nly prior hypothesis not disproven is a late Archaic origin for BCS rock art, although our age result

223 HLA class I alleles of archaic origin may have been retained in modern humans b

224 ve scenarios of a relatively recent or super-archaic origin of Neandertal Y chromosomes.

225 ed HLA-A*11, we also show that H*02:07 is of archaic origin.

226 t HLA-B*73:01, a rare allotype with putative archaic origins, has a relatively rare peptide binding m

227 inct cultural groups, including the Maritime Archaic, Palaeoeskimo, and Beothuk.

228 portance of maize (Zea mays) during the Late Archaic period (3000-1800 B.C.) in ancient Peru.

229 tural complex in this region during the Late Archaic period between 3000 and 1800 calibrated calendar

230 ical sites from the terminal Paleoindian and Archaic periods associated with the Lake Stanley low wat

231 permits the serial founder model but not the archaic persistence model to explain the three trends ob

232 al tubes of the classical type 1 and P pili, archaic pili assemble into an ultrathin zigzag architect

233 om 'condylarths', a paraphyletic assembly of archaic placentals.

234 One of the USA300 isolates contained an archaic plasmid that encoded staphylococcal enterotoxins

235 lt of introgression from some late-surviving archaic population in the region.

236 ast a single admixture event from an unknown archaic population into the ancestors of AMH, likely wit

237 at introgressed approximately 35 kya from an archaic population that split from the ancestors of anat

238 tructure, with and without gene flow from an archaic population.

239 by around 40,000 years ago, having replaced archaic populations across Eurasia after episodes of ear

240 used to determine if dual ancestry in local archaic populations and earlier modern populations from

241 a 100,000 years ago and total replacement of archaic populations in Asia.

242 adaptive alleles may have introgressed from archaic populations into modern humans.

243 gration expands into a series of preexisting archaic populations produces nearly opposite patterns to

244 rom those expected if alleles from divergent archaic populations were maintained through multiregiona

245 an population or an amalgamation of distinct archaic populations.

246 r modern humans, with general replacement of archaic populations.

247 than evolution from or admixture with local archaic populations.

248 ica dispersal, and subsequently admixed with archaic populations.

249 or without interbreeding) of the preceding "archaic" populations in these regions.

250 This is, in part, due to the archaic practice of patients remaining nil per os postop

251 In this way archaic progenitors of G-protein-coupled chemical quanta

252 ctivity was observed in vitro for modern and archaic protein fragments identified with panCleave.

253 Additionally, representative modern and archaic protein fragments showed anti-infective efficacy

254 Together, the outputs of aRchaic provide a concise visual summary of DNA damage p

255 and temporal placement between the earliest archaic putative hominins and later hominins-including t

256 y three decades of progress in the field, an archaic regulatory framework has stymied US clinical pra

257 Archaic-related lineages were >98% replaced by a genetic

258 illustrate our results with applications to archaic samples from European human populations.

259 e compare present-day samples with a pair of archaic samples taken before and after a replacement eve

260 gnificantly improves read mapping quality in archaic samples.

261 We use these maps of archaic sequences to show that Neandertal admixture occu

262 c regions that are significantly depleted of archaic sequences, and identify signatures of adaptive i

263 otropic enhancers show stronger depletion of archaic single-nucleotide polymorphisms.

264 However, archaic species concepts and an inadequate fossil record

265 not depleted of older variants found in both archaic species.

266 Archaic-specific SAVs are enriched in genes that contrib

267 Compared to shared SAVs, archaic-specific SAVs occur in sites under weaker select

268 as propagated in DNA alongside adenine since archaic stages of evolution.

269 iroom temple, associated with the rise of an archaic state at ca. 300-100 B.C.

270 te Alban I phase (300-100 BC), the period of archaic state emergence in the region.

271 all in use during the 300-100 B.C. period of archaic state emergence.

272 ciopolitical transformation from chiefdom to archaic state in precontact Hawai'i.

273 a significant factor in the evolution of the archaic state in the northern Titicaca Basin.

274 tion of the Maui polity to form an incipient archaic state.

275 of society from hunting and gathering to the archaic state.

276 istoric accounts of late precontact Hawaiian archaic states emphasize the independence of chiefly con

277 dominant role of centralized institutions in archaic states.

278 nd resources during the rise of the Hawaiian archaic states.

279 moting the consolidation and reproduction of archaic states.

280 Eocene bat that helps bridge the gap between archaic stem bats and the hyperdiverse modern bat radiat

281 also find evidence of introgression from the archaic Taimyr wolf lineage into present-day dog breeds

282 e that accurate terminology is used and that archaic terms are avoided when vascular lesions are desc

283 rous palaeoequator with rapid replacement of archaic tetrapod groups by relatives of modern amniotes

284 he western Titicaca Basin dating to the Late Archaic to Early Formative periods ( approximately 3,400

285 me comparisons identified introgression from archaic to modern humans.

286 ntensified agriculture mark a shift from the Archaic to the Ceramic Age at around 2,500 years ago(1-3

287 n in habitual load levels from Eurasian late archaic, to Early Upper Paleolithic early modern, to Mid

288 pATOM36 is required for the assembly of the archaic translocase of the outer membrane (ATOM), the fu

289 ane space domain of the translocase subunit, archaic translocase of the outer membrane (ATOM)14, on t

290 owever, and use instead a protein termed the archaic translocase of the outer mitochondrial membrane

291 a conventional Tom40 and instead employs the archaic translocase of the outer mitochondrial membrane

292 y 'Zhelestidae' within a clade that includes archaic ungulates ('condylarths').

293 (Tribosphenomys), lagomorphs (Mimotona) and archaic ungulates (Protungulatum and Oxyprimus) strongly

294 ne or more mesonychians, a group of extinct, archaic ungulates, but molecular analyses have indicated

295 une system in early vertebrates by splitting archaic V genes with transposable elements.

296 alleles are needed to explain the degree of archaic variant depletion from foetal muscle enhancers,

297 ression process and investigation of whether archaic variants conferred an adaptive advantage to the

298 re efficient removal of slightly deleterious archaic variants have been proposed as selection-based p

299 In order to identify functionally divergent archaic variants removed in humans, we focused on mitonu

300 e infer that selection acted mainly on young archaic variation that arose in Neandertals or Denisovan