ライフサイエンスコーパス: D. simulans

1 D. simulans and D. mauritiana are both highly polymorphi

2 D. simulans and D. mauritiana Hmr+ partially complement

3 D. simulans appears to be intermediate both in terms of

4 D. simulans is thought to have colonized New World habit

5 D. simulans shows substantial linkage phase structuring

6 D. simulans, together with two additional sister species

7 studied in 50 Drosophila melanogaster and 12 D. simulans lines.

8 mosome that cause hybrid male sterility in a D. simulans background.

9 ila mauritiana that were introgressed into a D. simulans background.

10 na third chromosome were introgressed into a D. simulans genetic background and tested as homozygotes

11 hen the D. melanogaster X is replaced with a D. simulans X.

12 ainst D. simulans males, three QTL affecting D. simulans male traits against which D. mauritiana fema

13 ion in the same genomic region in an African D. simulans population revealed no evidence for a high-f

14 fornia population is not found in an African D. simulans population sample and may be a result of nov

15 crimination of D. mauritiana females against D. simulans males, three QTL affecting D. simulans male

16 lite variability in North and South American D. simulans populations than for an African population.

17 by Hmr and the rescue mutations In(1)AB and D. simulans Lhr.

18 of Drosophila melanogaster (five genes) and D. simulans (four genes) to characterize the homogenizin

19 ibute to ecological isolation between it and D. simulans.

20 in crosses between Drosophila mauritiana and D. simulans was investigated to gain insight into the ev

21 differences in trn between D. mauritiana and D. simulans, but differences in the expression of this g

22 ifferences between Drosophila mauritiana and D. simulans.

23 es in samples of Drosophila melanogaster and D. simulans (Acp29AB, Acp32CD, Acp33A, Acp36DE, Acp53Ea,

24 otide divergence between D. melanogaster and D. simulans (Jukes-Cantor distance = 0.149 +/- 0.150) wa

25 valley variation between D. melanogaster and D. simulans [5, 6].

26 (Sr-C's) between Drosophila melanogaster and D. simulans and between each of these species and D. yak

27 specific crosses between D. melanogaster and D. simulans and compare them with intraspecific control

28 f rescue lines from both D. melanogaster and D. simulans can restore hybrid fitness.

29 amples from wild Drosophila melanogaster and D. simulans collected from a variety of natural substrat

30 what could be a natural D. melanogaster and D. simulans core microbiome.

31 adaptive evolution after D. melanogaster and D. simulans diverged and, consequently, is not a speciat

32 ly become feasible after D. melanogaster and D. simulans extended their distributions into the Americ

33 The ran-like gene of D. melanogaster and D. simulans has undergone recurrent positive selection.

34 Comparison of the D. melanogaster and D. simulans hsp70 genes reveals whole-family fixed diffe

35 cement fixations between D. melanogaster and D. simulans in the Sr-C's, but tests of polymorphic site

36 crosses between Drosophila melanogaster and D. simulans is due to a failure in dosage compensation,

37 uence divergence between D. melanogaster and D. simulans is greater at regulatory sites than expected

38 nonymous polymorphism in D. melanogaster and D. simulans populations.

39 Although D. melanogaster and D. simulans share common allozyme mobility alleles, we f

40 intron sequences between D. melanogaster and D. simulans suggest that D. melanogaster has undergone a

41 the Pgm gene in Drosophila melanogaster and D. simulans to investigate the role that protein polymor

42 nt of divergence between D. melanogaster and D. simulans when the pseudogene data are compared to the

43 s of these parameters in D. melanogaster and D. simulans will benefit future studies in population an

44 telomere of the Drosophila melanogaster and D. simulans X chromosome at two loci, erect wing (ewg) a

45 ated Drosophila species, D. melanogaster and D. simulans, and show functional cis-regulatory differen

46 f these species, Drosophila melanogaster and D. simulans, have previously been described, while this

47 compatibilities separate D. melanogaster and D. simulans, indicating extensive functional divergence

48 d between populations of D. melanogaster and D. simulans, our data appear more consistent with the op

49 ese and other hybrids of D. melanogaster and D. simulans, resulting in an advanced understanding of s

50 coding regions; in both D. melanogaster and D. simulans, same-cluster paralogues are virtually ident

51 D. melanogaster and D. simulans, share many transcript models and long-read

52 since the separation of D. melanogaster and D. simulans, suggesting adaptive evolution.

53 d D. virilis and 27 from D. melanogaster and D. simulans, we show considerable variation between amin

54 h its generalist cousins D. melanogaster and D. simulans.

55 these proteins are from D. melanogaster and D. simulans.

56 ruitfly species, Drosophila melanogaster and D. simulans.

57 b of the gene ankyrin in D. melanogaster and D. simulans.

58 ruses are shared between D. melanogaster and D. simulans.

59 a cross between Drosophila melanogaster and D. simulans.

60 0-65 MYA), as well as in D. melanogaster and D. simulans.

61 sibling species, Drosophila melanogaster and D. simulans.

62 as actually two species: D. melanogaster and D. simulans.

63 osome in hybrids between D. melanogaster and D. simulans.

64 tion on the tip of 3L in D. melanogaster and D. simulans.

65 ation of such effects in D. melanogaster and D. simulans.

66 rocal crosses of Drosophila melanogaster and D. simulans.

67 duced divergence between D. melanogaster and D. simulans; these regions of psiEst-6 could be involved

68 Drosophila sechellia (8 ovarioles/ovary) and D. simulans (15 ovarioles/ovary) identified a major QTL

69 rage, very weak in both D. pseudoobscura and D. simulans (magnitude of NS approximately 1).

70 e in egg production between D. sechellia and D. simulans appears to be a polygenic trait.

71 autosomal region from both D. sechellia and D. simulans, Suppressor of hlx [Su(hlx)].

72 e in egg production between D. sechellia and D. simulans.

73 nd its two sibling species, D. sechellia and D. simulans.

74 Acp's from D. mauritiana, D. sechellia, and D. simulans.

75 sophila (D. melanogaster vs. D. simulans and D. simulans vs. D. sechellia).

76 tional CHCs that differ in abundance between D. simulans and D. sechellia females.

77 he QTL for interspecific differences between D. simulans and D. mauritiana.

78 e that appear to exhibit differences between D. simulans and D. sechellia in their regulation of sex

79 , the two major female CHs differing between D. simulans and D. sechellia.

80 osophila simulans and the divergence between D. simulans and D. melanogaster.

81 o been reported in the hybridization between D. simulans and its closer relative D. sechellia, implyi

82 nsation, caused by incompatibilities between D. simulans dosage compensation proteins and the D. mela

83 with QTL affecting sexual isolation between D. simulans and D. mauritiana and with QTL affecting dif

84 ecifically by D. melanogaster Hmr but not by D. simulans or D. mauritiana Hmr.

85 tim cDNA and corresponds to the one used by D. simulans and D. yakuba.

86 to: (i) species origin of the Y chromosome (D. simulans or D. sechellia); (ii) location of the intro

87 onships within the Drosophila simulans clade-D. simulans, D. sechellia, and D. mauritiana-and their r

88 , and this is especially true for the closer D. simulans vs. D. sechellia comparison.

89 hila simulans are introgressed into a common D. simulans genetic background.

90 for the Drosophila simulans species complex (D. simulans, D. mauritiana, and D. sechellia), which spe

91 We find that the divergent D. simulans Nicknack protein can still localize to D. me

92 n California, and Dulzura kangaroo rat (DKR, D. simulans, 2N = 60) to the south, with a suspected sym

93 Two closely related species of Drosophila, D. simulans and D. mauritiana, differ markedly in morpho

94 n two pairs of sister species of Drosophila: D. simulans and D. mauritiana; and D. yakuba and D. sant

95 tive to synonymous substitutions within each D. simulans haplotype.

96 seudoobscura genes and five alleles of eight D. simulans genes.

97 The European D. simulans population has a similar mutation rate to Eu

98 el of DNA sequence variation was typical for D. simulans autosomal genes and showed no departure from

99 or using different genetic backgrounds from D. simulans.

100 zed 56 genes in which polymorphism data from D. simulans are compared with divergence from a referenc

101 Data from D. simulans Cyp6g1 are paralleled in many respects by da

102 a from a single highly inbred line each from D. simulans, D. mauritiana, and D. sechellia.

103 erious and are removed more effectively from D. simulans due to its larger effective population size.

104 anogaster and a 458-bp Lcp psi fragment from D. simulans was also sequenced.

105 Several genes from D. simulans appear to be subject to recent selection on

106 ximately 50% higher than the same genes from D. simulans.

107 hese genomes to variation among genomes from D. simulans suggests that many targets of directional se

108 en shown that a mitochondrial haplotype from D. simulans (simw(501) ) is incompatible with a nuclear

109 lanogaster and a hybrid rescue mutation from D. simulans, I measured the viability of hybrid males th

110 extensive similarity of the R2 ribozyme from D. simulans to that of HDV was a result of convergent ev

111 A comparison was made with sequence from D. simulans.

112 lines of D. melanogaster and sequences from D. simulans and D. yakuba.

113 Possibly following hybridization, D. simulans infected the island endemic species D. mauri

114 In D. simulans we observed a significant excess of intermed

115 In D. simulans, analysis of the homologous region reveals u

116 In D. simulans, we find that preferred changes per "site" a

117 In D. simulans, where the novel gene does not exist, the pa

118 detection) of the 52 D. melanogaster ACPs in D. simulans, D. yakuba, and D. pseudoobscura.

119 roach by mapping a dominant marker allele in D. simulans to within 105 kb of its true position using

120 for higher skew with higher CO rates, as in D. simulans, will be explored elsewhere.

121 meric heterochromatin of the X chromosome in D. simulans and D. mauritiana, which we call heterochrom

122 ze and sequence of this exon is conserved in D. simulans and putative alternative exons of different

123 Interestingly, the lower TE content in D. simulans compared to D. melanogaster correlates with

124 A-seq to investigate splicing differences in D. simulans, D. sechellia, and three strains of D. melan

125 showed significantly less differentiation in D. simulans than in D. melanogaster.

126 (s), at least some of which have diverged in D. simulans and D. sechellia but not in D. mauritiana.

127 ts show even deeper interslope divergence in D. simulans than in D. melanogaster, with extensive sign

128 tochondrial DNA (mtDNA) and autosomal DNA in D. simulans.

129 The early death effect in D. simulans attenuated only slightly and was comparable

130 P-elements in D. simulans appear to have been acquired recently from D

131 g evidence for adaptive protein evolution in D. simulans, but not in D. melanogaster.

132 rs contribute to variation for expression in D. simulans with the preponderance of effects being tran

133 , initiation of cellularization is faster in D. simulans by 15 min, 42 s; and initiation of morphogen

134 and initiation of morphogenesis is faster in D. simulans by 18 min, 7 s.

135 of the Winters sex-ratio genes are fixed in D. simulans, and at all loci we find ancestral alleles,

136 ed insertion state at very high frequency in D. simulans.

137 The synonymous site diversity was greater in D. simulans than in D. melanogaster, but the diversity b

138 nd significantly less silent polymorphism in D. simulans on the X chromosome than on 3R, but no diffe

139 expression is accelerated by 13 min, 48 s in D. simulans and retarded by 24 min in D. pseudoobscura.

140 n of hairy is accelerated by 13 min, 48 s in D. simulans.

141 A previous evolutionary EST screen in D. simulans identified partial cDNAs for 57 new candidat

142 Mean heterozygosity at replacement sites in D. simulans was 0.0074 for Acp genes and 0.0013 for a se

143 igher in the D. melanogaster lineage than in D. simulans in 14 genes for which outgroup sequences are

144 sizes are larger in D. melanogaster than in D. simulans in the 34 genes compared between the two spe

145 s are more divergent in D. sechellia than in D. simulans-despite their similar phylogenetic distance

146 resent more often in D. melanogaster than in D. simulans.

147 ith the excess of high-frequency variants in D. simulans is inconsistent with the hitchhiking and bac

148 level of infertility when introgressed into D. simulans.

149 ess the bwD allele from D. melanogaster into D. simulans, which lacks the AAGAG on the autosomes.

150 sed from D. mauritiana and D. sechellia into D. simulans and tested for their homozygous effects on h

151 evidence that the P-element has also invaded D. simulans.

152 980s, while both Shellder and Spoink invaded D. simulans in the 1990s.

153 We successfully mapped D. simulans introgression regions in a small mapping pop

154 males of its sibling species D. mauritiana, D. simulans, and D. sechellia.

155 In C. elegans, Z. mays, D. melanogaster, D. simulans and H. sapiens, alternative exons were obser

156 s generalist sister species D. melanogaster, D. simulans, and D. mauritiana.

157 hree species of Drosophila, D. melanogaster, D. simulans, and D. pseudoobscura.

158 sion levels for 31 genes in D. melanogaster, D. simulans, and their F1 hybrid.

159 om four Drosophila species (D. melanogaster, D. simulans, D. erecta, and D. virilis) and performed co

160 d in the common ancestor of D. melanogaster, D. simulans, D. sechellia, and D. mauritiana, within the

161 ng five Drosophila species: D. melanogaster, D. simulans, D. subobscura, D. mojavensis, and D. virili

162 anogaster subgroup species (D. melanogaster, D. simulans, D. teissieri, D. yakuba, D. erecta, and D.

163 species-restricted genes in D. melanogaster, D. simulans, D. yakuba, D. ananassae, D. pseudoobscura,

164 h male-biased expression on D. melanogaster, D. simulans, D. yakuba, D. ananassae, D. virilis and D.

165 body, and testis in Drosophila melanogaster, D. simulans, and D. yakuba.

166 on level samples of Drosophila melanogaster, D. simulans, and D. yakuba.

167 male adult heads of Drosophila melanogaster, D. simulans, and their F1 hybrids.

168 d in data sets from Drosophila melanogaster, D. simulans, and Zea mays.

169 pecies pairs relative to the D. melanogaster-D. simulans-D. mauritiana-D. sechellia species complex.

170 In certain Drosophila melanogaster-D. simulans hybrids, hybrid male sterility is caused by

171 Sturtevant's description of D. melanogaster/D. simulans hybrid sterility, we have discovered a strai

172 isappointed to find that the D. melanogaster/D. simulans hybridization resulted only in unisexual ste

173 javensis/D. arizonae than in D. melanogaster/D. simulans.

174 We therefore detected no D. simulans chromosome regions causing unconditional hyb

175 distribution of indel variation in Ifc-2h of D. simulans and D. mauritiana revealed a significant seq

176 aspers with more bristles than the allele of D. simulans Therefore, we have identified a gene underly

177 ing with the heterochromatic Y chromosome of D. simulans, whereas D. simulans OdsH (OdsHsim) does not

178 the variation along the fourth chromosome of D. simulans.

179 melanogaster but on the third chromosome of D. simulans.

180 nated in the common ancestor of the clade of D. simulans, D. mauritiana, and D. sechellia.

181 Hmr were observed in the reciprocal cross of D. simulans females to D. melanogaster males.

182 The reciprocal cross of D. simulans mothers by D. melanogaster males exhibits un

183 s of Drosophila melanogaster and one each of D. simulans and D. sechellia, within two closely linked

184 olving quickly, since the larval exudates of D. simulans, the sister species of D. melanogaster, are

185 referred or unpreferred for several genes of D. simulans and D. melanogaster.

186 ental genomic background (three genotypes of D. simulans).

187 s of Drosophila melanogaster and one line of D. simulans and used a variety of tests to determine whe

188 e P-element is processed in the germ line of D. simulans, and genomic data show an enrichment of P-el

189 s of Drosophila melanogaster and one line of D. simulans.

190 hondrial genomes of three isofemale lines of D. simulans (siI, -II, and -III), two of D. melanogaster

191 11 lines of D. melanogaster and 10 lines of D. simulans found only a single silent polymorphism in t

192 triction survey of an additional 28 lines of D. simulans revealed strong linkage disequilibrium over

193 osomal and X-linked genome that is mostly of D. simulans origin.

194 trains of Drosophila melanogaster and one of D. simulans.

195 D. melanogaster and a European population of D. simulans Across 89 flies, we observe 58 single-nucleo

196 segregating mutations in this population of D. simulans.

197 ons of D. melanogaster and one population of D. simulans.

198 mitochondrial DNA (mtDNA) in populations of D. simulans from Zimbabwe, Malawi, Tanzania, and Kenya.

199 alleles observed in New World populations of D. simulans than seen in a similar survey of D. melanoga

200 These are the first known populations of D. simulans that do not exhibit reduced mtDNA variation.

201 hic history of North American populations of D. simulans.

202 id sterility, we have discovered a strain of D. simulans that produces fertile female hybrids in cros

203 of Drosophila melanogaster, three strains of D. simulans and a total of 78 genes.

204 e compare infected and uninfected strains of D. simulans for (1) sperm production, (2) male fertility

205 r to the one they observed in two strains of D. simulans from Italy, could account for the observed m

206 ymorphism data from 14 loci in 16 strains of D. simulans, finding that the test retains 80% power eve

207 strains of D. melanogaster and 5 strains of D. simulans.

208 ations of Drosophila melanogaster and two of D. simulans.

209 nced on D. ananassae and least pronounced on D. simulans and D. erecta terminal lineages.

210 rid males hemizygous for a D. mauritiana (or D. simulans) X chromosome are viable, the lethality of d

211 D. sechellia, which closely resembled other D. simulans sequences.

212 American populations of D. melanogaster, our D. simulans sample shows a marked reduction in the numbe

213 Overall, D. simulans shows the earliest expression, followed by D

214 are sexually dimorphic between the parental D. simulans and D. mauritiana strains, suggesting that p

215 dely colonized D. melanogaster (and possibly D. simulans) to temperate climates and that natural sele

216 of the D. sechellia X chromosome into a pure D. simulans genetic background and found that males carr

217 Lhr(2) is a rare D. simulans allele that has the ancestral deletion state

218 ween D. melanogaster and the closely related D. simulans.

219 between D. sechellia and its close relative D. simulans show that each of the five major chromosome

220 melanogaster, but not in its close relatives D. simulans and D. yakuba.

221 om 6 of these in the closely related species D. simulans and D. yakuba.

222 of the sequences, or in the sibling species D. simulans and D. mauritiana.

223 sophila melanogaster and its sibling species D. simulans have very different cuticular hydrocarbons,

224 ion on codon usage, while its sister species D. simulans experiences only half the selection pressure

225 ed for genomic regions in the sister species D. simulans that could cause lethality when hemizygous o

226 hism arose in parallel in the sister species D. simulans, by independent mutation with equivalent phe

227 stribution range and in their sister species D. simulans, indicating widespread and evolutionarily pe

228 associated with CENP-A in the sister species D. simulans, revealing an unexpected conservation despit

229 F1 hybrids between it and its sister species D. simulans.

230 cent gene flow between the mainland species (D. simulans) and the two island endemic species (D. maur

231 an allele from one of the parental species (D. simulans) is consistently overexpressed.

232 la simulans clade--the cosmopolitan species, D. simulans, and the two island endemic species, D. maur

233 comparisons of TEs from two related species, D. simulans and D. yakuba.

234 istory of the three closely related species, D. simulans, D. mauritiana and D. sechellia.

235 . Sturtevant discovered its sibling species, D. simulans.

236 hybrids when crossed to its sister species, D. simulans, D. sechellia, and D. mauritiana.

237 sechellia and its generalist sister species, D. simulans.

238 Strikingly, D. simulans is also segregating deletions that cause mth

239 Drosophila melanogaster evolves faster than D. simulans at all annotated classes of sites, including

240 which develops smaller posterior lobes than D. simulans.

241 We find that D. simulans bwD associates with 2h, which lacks the AAGA

242 ther recent results, these data suggest that D. simulans and D. sechellia are much more closely relat

243 The D. simulans alleles on the left arm of chromosome 3 are

244 The D. simulans Y chromosome also modulated gene expression

245 Drosophila lineages were evident: along the D. simulans lineage we consistently found evidence of ad

246 e divergence between D. melanogaster and the D. simulans clade, indicating that centromere machinery

247 le is consistently overexpressed on both the D. simulans and D. mauritiana backcross genomic backgrou

248 However, the genotypes carrying the D. simulans mtDNA were not consistently short-lived, as

249 such that if either were homozygous for the D. simulans allele, the fly was similar to D. simulans i

250 autosomes is the better explanation for the D. simulans data.

251 , its three closest sibling species from the D. simulans species complex, and two obscura clade speci

252 have since diversified in morphology in the D. simulans clade, in particular, over the last 240,000

253 s relative to the neutral expectation in the D. simulans sample and some populations of D. melanogast

254 of the Drosophila sechellia genome into the D. simulans genome.

255 Ablation of the D. simulans allele of this gene is sufficient to rescue

256 neously hemizygous for a small region of the D. simulans autosomal genome and hemizygous for the D. m

257 A screen of approximately 70% of the D. simulans autosomal genome reveals 20 hybrid-lethal an

258 w has occurred throughout the genomes of the D. simulans clade species despite considerable geographi

259 We find that at least 15% of the D. simulans complex species genomes fail to align unique

260 A survey of roughly 50% of the D. simulans genome (114 chromosome regions) revealed onl

261 In a region of 5% of the D. simulans genome introgressed into D. melanogaster, we

262 osome during the evolutionary history of the D. simulans lineage.

263 he introgressed D. mauritiana segment on the D. simulans third chromosome, and (iii) grandparental ge

264 ine if MH and 359bp coevolve, we swapped the D. simulans version of MH ("MH[sim]") into D. melanogast

265 F(1) male lethality is suppressed when the D. simulans Lhr(1) hybrid rescue strain is used.

266 Relationships within the D. simulans complex are not addressed.

267 relative to silent mutations than have their D. simulans orthologs.

268 s sequence alignment that includes all three D. simulans clade species as well as the D. melanogaster

269 In this study, we focus on three D. simulans immunity loci, Hmu, Sr-CI/Sr-CIII, and Tehao

270 We found six loci contributing to D. simulans food preference, one of which overlaps a pre

271 cross of Drosophila melanogaster females to D. simulans males typically produces lethal F(1) hybrid

272 e D. simulans allele, the fly was similar to D. simulans in phenotype, with a low level of 7,11-HD.

273 mapping more than 400 previously unassembled D. simulans contigs to linkage groups and by evaluating

274 Using an unusual D. simulans Lhr hybrid rescue allele, Lhr(2), we here id

275 mparisons of Drosophila (D. melanogaster vs. D. simulans and D. simulans vs. D. sechellia).

276 vs. chimpanzees, Drosophila melanogaster vs. D. simulans, and sheep vs. cattle.

277 ellia is sexually dimorphic in CHCs, whereas D. simulans is not.

278 romatic Y chromosome of D. simulans, whereas D. simulans OdsH (OdsHsim) does not.

279 ting D. mauritiana male traits against which D. simulans females discriminate.

280 is also highly conserved in comparison with D. simulans and D. pseudoobscura.

281 aster and use interspecific comparisons with D. simulans, D. pseudoobscura and D.virilis to explore t

282 complete absence of fixed replacements with D. simulans.

283 Dox loci are functionally polymorphic within D. simulans, such that both nmy-associated sex ratio bia