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Kuo A. Tardat M. Iizuka M. Burke T. Stedman W. Regulation of replication licensing by acetyltransferase Hbo1. Hbo1 Links pdependent stress signaling to DNA replication licensing. Miotto B. HBO1 histone acetylase is a coactivator of the replication licensing factor Cdt1. Role for Plk1 phosphorylation of Hbo1 in regulation of replication licensing.

Jr, Fukusato T. Histone acetyltransferase Hbo1: catalytic activity, cellular abundance, and links to primary cancers. Mantiero D. Limiting replication initiation factors execute the temporal programme of origin firing in budding yeast. Calvi B. DePamphilis ML, editor. Claycomb J. Developmental gene amplification: insights into DNA replication and gene expression. Trends Genet. Spradling A. The organization and amplification of two chromosomal domains containing Drosophila chorion genes. Kim J. Integrative analysis of gene amplification in Drosophila follicle cells: parameters of origin activation and repression.

Cell cycle control of chorion gene amplification. Austin R. Royzman I. Liu J. Analysis of model replication origins in Drosophila reveals new aspects of the chromatin landscape and its relationship to origin activity and the prereplicative complex. Aggarwal B.

Chromatin regulates origin activity in Drosophila follicle cells. Hartl T. Developmentally regulated histone modifications in Drosophila follicle cells: initiation of gene amplification is associated with histone H3 and H4 hyperacetylation and H1 phosphorylation. McConnell K. Beall E. Lewis P. A cyclin-dependent kinase inhibitor, Dacapo, is necessary for timely exit from the cell cycle during Drosophila embryogenesis. Flores O. Roy S. Gilchrist D. Rastogi P. Integrated sequence analysis for the Macintosh. Methods Mol. Negre N. A cis-regulatory map of the Drosophila genome.

Henikoff J. Epigenome characterization at single base-pair resolution. Floer M. Tims H. Dynamics of nucleosome invasion by DNA binding proteins. Drysdale R. FlyBase : a database for the Drosophila research community. FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations.

Delidakis C. Amplification enhancers and replication origins in the autosomal chorion gene cluster of Drosophila. Orr-Weaver T. The role of ACE3 in Drosophila chorion gene amplification. Heck M. Multiple replication origins are used during Drosophila chorion gene amplification. Zhang H. Sequence requirements for function of the Drosophila chorion gene locus ACE3 replicator and ori-beta origin elements. Swimmer C. Amplification-control element ACE-3 is important but not essential for autosomal chorion gene amplification.

Fenerjian M. Evolution of the autosomal chorion cluster in Drosophila. Chorion gene expression and sequence comparisons of the s16 and s19 genes in evolutionarily distant species. Comparison of the s18 gene in evolutionarily distant species and heterospecific control of chorion gene amplification. Parks S. Replication and expression of an X-linked cluster of Drosophila chorion genes. Amplification of the X-linked Drosophila chorion gene cluster requires a region upstream from the s38 chorion gene. Lane M. Dacapo, a cyclin-dependent kinase inhibitor, stops cell proliferation during Drosophila development.

Gene amplification as a developmental strategy: isolation of two developmental amplicons in Drosophila. Hua B. The role of transcription in the activation of a Drosophila amplification origin. Analysis of a Drosophila amplicon in follicle cells highlights the diversity of metazoan replication origins. Xie F. Isolation of a Drosophila amplification origin developmentally activated by transcription.

Clapier C. The biology of chromatin remodeling complexes. Macalpine D. Coordination of replication and transcription along a Drosophila chromosome. Segal E. A genomic code for nucleosome positioning. Kaplan N. The DNA-encoded nucleosome organization of a eukaryotic genome. Valouev A. Determinants of nucleosome organization in primary human cells.

Localization of a cis-acting element responsible for the developmentally regulated amplification of Drosophila chorion genes. A transcriptional insulator element, the su Hw binding site, protects a chromosomal DNA replication origin form position effects. Liu S. DNA replication and transcription programs respond to the same chromatin cues. Flanagan J. Alexiadis V. Avolio-Hunter T. Epstein-Barr nuclear antigen 1 binds and destabilizes nucleosomes at the viral origin of latent DNA replication. Sugimoto N. Chromatin remodeler sucrose nonfermenting 2 homolog SNF2H is recruited onto DNA replication origins through interaction with Cdc10 protein-dependent transcript 1 Cdt1 and promotes pre-replication complex formation.

Mito Y. Genome-scale profiling of histone H3. Deal R. Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones. Jin C. Nucleosome stability mediated by histone variants H3. Henikoff S. Labile H3. Poly dA:dT tracts: major determinants of nucleosome organization. Rein T. Active mammalian replication origins are associated with a high-density cluster of mCpG dinucleotides. Antequera F. CpG islands as genomic footprints of promoters that are associated with replication origins. Gimenes F. Intrinsically bent DNA sites in the Drosophila melanogaster third chromosome amplified domain.

Genomics: MGG. Gaczynska M. Atomic force microscopic analysis of the binding of the Schizosaccharomyces pombe origin recognition complex and the spOrc4 protein with origin DNA. Clarey M. Sun J. Bleichert F. Crystal structure of the eukaryotic origin recognition complex. Dueber E. Molecular determinants of origin discrimination by Orc1 initiators in archaea. Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex.

Marilley M. Structure-function relationships in replication origins of the yeast Saccharomyces cerevisiae: higher-order structural organization of DNA in regions flanking the ARS consensus sequence. Snyder M. Bent DNA at a yeast autonomously replicating sequence. Hertz G. Analysis of the intrinsic bend in the M13 origin of replication by atomic force microscopy. Zahn K. Direct evidence for DNA bending at the lambda replication origin. Ohyama T. Study on the function of the bent DNA within adenovirus type 2 EIA enhancer: analysis using an in vitro transcription system. Nucleic Acids Symp.

It has been found by Seyster '19 and Krafka '20a that temperature affects the facet number of bar and ultra-bar stocks. Increase in temperature decreases facet-number. Since this character can be rapidly and accurately determined on a strict nurherical basis, it has been used by several investigators in selection experiments. MacDowell '15, '17, '20 studied the number of dorsocentral modifying factors and selection 47 bristles in a race derived from wild stock.

The normal number of these bristles is four; 48 generations of selection, with brother-sister matings, brought the mean to from 8 to 9. This result was practically gained in the first 8 generations of selection; after that time selection was not successful in altering the mean, in either the plus or the minus direction. After the 48th generation MacDowell reared 4 more generations on a large scale without selection, and determined the parent-offspring correlation for the last two of these generations. Modifiers were not specifically located, but the data leave no doubt that several were present.

Payne '18 studied the number of scutellar bristles, also normally four. The mean was raised to 9 after 38 generations of selection, the effect being prolonged through about 18 generations, with another increase from the 25th to the 29th. Payne's environmental control was not very accurate, and his experiments show that temperature does affect bristle number; furthermore he did not always use brother-sister matings. These two facts may account in part for the long-continued effects of selection, but it seems probable that new mutations affecting bristle-number also appeared in his experiments.

Linkage tests showed the existence of extra-bristle genes in chromosomes I and III. In the 6th generation of this experiment occurred a mutation that reduced the number of scutellar bristles. The new type, called "reduced" by Payne, is evidently an allelomorph of "scute", a sex-liriked recessive. Payne '20 also selected this mutant stock, both for increased and for decreased numbers of scutellar bristles. Sixty generations of plus selection brought the mean to about 3. In both cases the change was practically complete after 18 generations, though there may have been a further change in the plus line about the 45th generation.

Linkage tests showed the plus line carried not only the scute gene, but also plus modifiers in chromosomes I, II, and III. The minus line did not differ markedly from the not-scute stocks chosen for the linkage tests, though there is a suggestion that a modifier was present in chromosome III.

Payne also showed that low temperature produces a slight increase in bristle-number in scute flies. Linkage tests showed that the various lines tested differed in modifying genes located in chromosomes II and III. Dichaete a and its allelomorph Extended b. Dichaete lacks certain bristles from the thorax. Unpublished data show that the number of dorsocentrals or of scutellars in these hybrids is largely determined by the stock from which the melanogaster mother came, though all the parent stocks used in the study have 4 dorsocentrals and 4 scutellars, with only the usual slight variations from these numbers.

That is, there are specific modifiers for hybrid-bristle-number. It appears also that there is no correlation between these modifiers and those for dichaete. Of five stocks tested. In accordance with this result is the fact that the pattern of bristle reduction is very different in the hybrids from that in dichaete; incomplete evidence also suggests that bristle number is very differently affected by environmental influences in the two types.

Lines with a high percentage of extra veins, and others with decreased venation, were quickly established. These results leave little doubt that modifying genes were concerned; but the case cannot now be analyzed, as the methods necessary for such analysis had not been developed when Lutz's experiments were completed. The male of melanogaster or of simulans has a comb-like row of short stiff bristles on the basal tarsal joint of each front leg. The variability in number of "teeth" in this sex-comb has been studied by Castle, Carpenter, Clark, Mast and Barrows '06 and by Hoge ' The number varies from 7 to 14 in individual sex-combs, the average being between 9.

Carpenter and Barrows showed that the number of teeth is dependent in part on culture conditions, being greater in the larger flies produced by favorable conditions. Measurements of the length of the right hind tibia were taken as an index of the size of the fly. These results show clearly that a large part of the variability in number of teeth is due to environmental causes, and even that much of it is due to causes operating differently on the two legs of the same individual.

That there are genetic factors concerned in the variability was shown by Hoge, who isolated both "plus" and "minus" lines by selection. From a wild stock with an average of 10 teeth per sex-comb she obtained one line with an average of about No further analysis of the genetic factors concerned is on record. Warren '24 has studied the variations in egg-length found in various stocks. The range in length observed was from 0. A general survey of numerous stocks showed that there is no "normal" egg-length; the two wild stocks reported were near the upper Bibliographia Genetica II 4 50 the genetics of drosophila and the lower limits, respectively, of the series.

The data also show that in general the egg-length is affected by special modifiers rather than by the mutant genes producing ordinary characters in the imagines. The data of Mohr '22a show, however, that the gene causing "singed" bristles also causes the singed females to lay short deformed eggs. AU the investigators mentioned above are agreed that low productivity may occur in inbred strains but it is not a necessary result of inbreeding.

It is clear that inbreeding reduces the variability in productivity, but that the average productivity of a given inbred line may be high, medium, or low. If selection is practiced, it is easy to estabUsh highly productive inbred lines. Hyde '17, Anat. He also reports that when two unrelated inbred stocks are crossed the percentage rises above that of either parent race; while when related inbred stocks are crossed the percentage commonly rises only to about that of the higher parent.

This result appears inconsistent with the statement above that it is easy to select a highly productive inbred line. It should, however, be pointed out that "highly productive" is here used to describe a line in which a given pair modifying factors and selection 51 gives a large progeny. Clearly many factors enter into this result besides percentage of eggs laid that give rise to adults—namely, any factors that influence number of eggs laid.

Also, productivity in this sense has not been measured as accurately as Hyde has measured the more specific variable that he uses. Pearl and others have published a series of studies of the genetic and environmental factors influencing duration of adult hfe. Pearl, Parker, and Gonzalez '23 found that clipping off the wings somewhat decreased the duration of hfe. Hyde '13 showed that length of hfe depends in part on inheritance, and presented some data on the result of crossing different strains. Pearl and Parker '22 found that offspring of separate pairs from a given stock might show significant differences in average length of hfe; and when the descendants of the separate pairs were bred as separate unselected stocks, later tests showed that the initial differences between the lines persisted.

Evidently the original stocks were heterogenous for modifiers affecting length of hfe. Various combinations of Fi and Pi individuals were mated, and duration of hfe was determined for the resulting offspring. There is also evidence that other genetic differences were present. Numerous studies have shown that this variability is in part due to environmental causes, in part to genetic ones. It was shown by Bridges '15 that crossing over in the middle portion of chromosome II is less frequent in old females than in young ones. This result was verified by Plough '17 who also showed that crossing over in the same region is increased by temperatures either above or below the usual range of room temperatures.

As shown by Plough '21 and by unpublished data, both the age and temperature changes are specific, CKXurring only in certain regions of certain chromosomes. Another environmental effect has been reported by Mavor '23 and by Mavor and Swenson '23 , due to X-rays. The treatment given decreased crossing over in chromosome I, increased it in chromosome II. These results make it clear that striking differences in cross-over values are sometimes brought about by genetic causes, and also that relatively slight differences are sometimes inherited.

Several mutant characters besides those already discussed have been shown to be modifiable by environmental conditions. The latter result has been verified in unpublished experiments carried on in he Columbia laboratory. Abnormal abdomen. Morgan '15c showed that this character is modifying factors and selection 53 most extreme in flies reared under moist conditions, and that it practically disappears in flies reared in dry conditions.

Reduplicated legs. Hoge '15 found that this character was much more marked, and appeared in a much higher percentage of the flies, if the cultures were kept at a low temperature. Bent melanogaster and virilis. Variable eye hydei. Hyde '22 found that this character was extremely variable in appearance, and was most extreme in flies reared under warm and dry conditions. Muller '16 kept a number of recessive genes in heterozygous condition for many generations.

One of these, dachs, was then r-ecovered from the stock, and the extracted homozygous dachs flies wer e compared with fhes from a stock that had been kept homozygous for dachs. It was found that the extracted fhes showed the dachs character in a slightly more extreme form than did those from the homozygous dachs stock. It seems likely that this often happens in stocks of variable mutant characters. This weakness may express itself in various Fig. Rotated abdomen. The abdomens of both sexes twisted to the left through 60 to 90 degrees; both sexes unable to mate.

At present we can only ascribe viability and lethals 55 these changes to effects of the mutant gene upon internal structures over and beyond the particular visible somatic effects produced. On the other hand, such a principle does not always apply. The vestigial race is as viable as certain other types of wing modifications truncate or rudimentary, for example where the wing is less obviously altered.

In a few stocks semi-lethal types appear, i. Lethal Bridges '17a and lethal and dwarfwarped are such semilethals. Lethal and lemon are not so extreme. Mohr '23a has described a sex-linked mutant that he calls chlorotic which he locates at 0. Cleft venation, showing projections from the lethals or semi-lethals. The females are entirely sterile in dwarf Fig. The viability and lethals 57 males are sterile in rose, parted, rotated-penis, cleft Fig. Lozenge is largely female-sterile.

This also holds for fused Fig. It is this. At one extreme are those cases when the embryo dies before hatching, then those that die as larvae, then those that die in the pupa stage, then those that emerge only rarely semi-lethals and the graded series of mutant stocks some of which live only a few days, others that live longer but are relatively weak in constitution, and lastly those that can scarcely be said to be weaker than normal fhes. We speak of the inviability of those stocks in which the number of resulting individuals is below Standard, limiting the use of the word lethal to cases where the adult stages are not reached because of death in the egg, larva, or pupal stages.

When one recalls that in the normal development a great many genes Fig. Enough is known, however, to indicate that some lethals bring about their effects in the pupal, others in the larval stages and others in the embryo before it hatches from the egg. No-wings, showing type of wings, of balancer and of scutellar bristles. Many of these mutant races would die out if left to themselves under natural conditions. Two corollaries follow from these considerations. First, it is erroneous to conclude that mutation involves only superficial characters or trivia!

It is true that these are the ones that are most worked with in plants and animals. They are used because of their survival value, not because they differ in kind from other mutations that involve essential characters. Second, it would also be erroneous to conclude, because most changes in the germ material produce deleterious or injurious results, that all mutations must be of this kind. It can be demonstrated that wild stocks often carry different factors that modify one or another part, and that are inherited as any other Mendelian character. Sex-linked Lethals To certain kinds of genes the term lethal has been applied.

These genes are supposed to destroy the individual, not necessarily because the lethal gene makes a poisonous substance, but more likely because it brings about some change, either in the germ-cells or in the embryo, that interferes with normal development. When the effect is on the germ-cell it is spoken of as a gametic lethal. When on the embryo i. No gametic lethals are known in Drosophila, but several kinds of zygotic lethals have been recorded. The simplest cases are recessive lethals in the X-chromosome, and these were in fact the first recorded. Here a change has taken place in a normal gene of such a kind that any male the male has but one X-chromosome dies if the gene is present.

In other cases the lethal effect may be due to the absence of a whole chromosome, or to the occurrence of extra chromosomes; to the absence of a part of a chromosome, or to the presence of an extra section of chromosome. The effect of these and of other kinds of lethals can best be described in connection with an account of their occurrence. The earliest work on Drosophila in which a change in the sex-ratio was observed that depended on the presence of a lethal was that of Rawls ' The demonstration that these unusual sex-ratios were due to a gene in the sex-chromosome was made by Morgan '12 with Rawls' material.

Rawls found one female that gave daughters to sons, and another female that gave daughters to sons. Of the daughters 63 were mated separately to their brothers. Twenty-six pairs had high ratios and thifty-seven had normal ratios. This equality of normal and of aberrant cultures, as we now know, is expected on the basis of a sex-linked lethal.

The few males that came through we now explain as due to crossing-over. The demonstration that the deficiency in males is to be accounted for by the hypothesis of a lethal factor was as follows Morgan ' Some of the pairs gave a 2 : 1 ratio. Crossing-over also breaks the apparent but superficial purity of such a line. Suchjoccurrences might have been put down as due to atavism before we came to understand what atavism may mean.

In fact it seems not improbable, as Muller pointed out, that some of de Vries' mutant types of Oenothera were mutant types released by crossing-over. When one balanced stock is crossed to another balanced stock twin hybrids are produced that may or may not be constant. A similar situation was found in another stock called truncate Altenburg and Muller ' When the list of dominant mutations of Drosophila is wnpared with the list of recessive mutations, the much higher proportion of lethals amongst the dominants is at once apparent.

The first impression is that there is something peculiar to dominants that makes them lethal. In fact, this relation had let to an interpretation that put dominants in a class apart from other mutations; but a closer examination of the evidence removes the mystery. In the first place, it is to be remembered that the distinction between a dominant and a recessive factor is largely an arbitrary one, depending to a great extent upon the line of demarkation in the F2 grouping of the three classes of AA, AA', and A'A'. In the second place, Muller has pointed out that lethal mutations are more numerous than any other kind of mutations, but very few of them are ever seen as mutant characters since they are usually discovered only by changes in the ratios of the classes.

On the other hand a lethal mutation that affects some visible part of the body when in a heterozygous condition is readily observed and kept as a mutant, and only later, as a rule, is it discovered that the homozygous condition is lethal. In other words since the known dominant lethals affect some visible character they are discovered in far greater numbers than are recessive lethals which are usually overlooked.

Since we have no reliable census of the frequency of the two kinds of lethals there are no compelling arguments in favor of the view that a lethal effect is more often associated with dominants than with recessives.

Sex determination in drosophila

The fact that some dominant characters, are not lethal is also to be kept in mind. The following dominants belong to this group. Most of these have been met with more than once, and some of them occur frequently. There is no certain rule by which such modifications can be distinguished from mutations. A very high percentage of these aberrant types is found persistently in certain mutant stocks, and may in part be looked upon here as one of the by-products of the mutant gene.

It is impossible, therefore, to completely exclude many of these abnormalities from the heritable characters; but whenever they can not be made to reappear in considerable numbers of the offspring by breeding from parents that show such modifications, or have not been produced by special environmental conditions, they may be looked upon as accidents of development.

It is rational to suppose that certain conditions of development may increase the chance of such accidents happening more often in certain mutant types than in other types. Expressed in another way, it may be said that the modifications characteristic of certain types make it more possible for the machinery of development to run off the beaten track. For purposes of easy identification, the material is arranged according to the organs in which the abnormalities occur. Antennae doubled a , or replacing eyes h.

Extra palpie in many Figs. It would also be quite difficult to carry this plan through systematicaUy. The terminal portions only, may be doubled. In these cases the duplicated part is a mirror figure of the antenna of the same side. Rarely an additional antenna Fig. It shows a serial homology with the antenna of its side i. These additional antennae are frequent in the eyeless stock. Very rarely two additional antennae are present on the same side in place of the eye and these are mirror figures of each other.

Not infrequently when both eyes are absent an additional antenna is found on each side. There is another frequent modification associated with these additional antennae of eyeless. At the lower edge of the empty eye-space, a palpus is present Fig. Examination m other animals has yielded suggestive pictures.

These four strands are often disposed m such a Ctha breaking and transjunction seems to have occurred between Jtwo inner strands. In subsequent stages the r mentioned has been so great that there has been little chance of failure to exclude the experiments in which they were present from the data to be used m constructing a "standard" map of the third-chromosome. One of these modifiers increases the hairy-scarlet value from about 14 to about The other decreases the Dichaete-scarlet value from about 3. In the experiments upon which the foregoing account is based approximately 10,, fhes have been raised in pedigreed cultures, carefully exarnined, classified, and recorded.

We are now in position to lay hold of any new abnormal situation that arises, to breed the flies in such a way as to keep the abnormality from being lost, and then at our leisure to analyze its basis. It should be borne in mind that while these new types are usually referred to as "aberrations", in each case a new and selfconsistent system of heredity comes to be established, with specific laws conforrning to the new physical basis — the derived chromosome group. The general classification and plan of treatment of chromosome aberrations that follows is based on the unit of change, which may be a whole chromosome, or a section of chromosome, or a group ra of chromosomes i.

It is simpler to deal first with the changes in which a single whole chromosome is the unit of change, and then to examine similar pro- i See paper by Bridges '23b for extended classification of chromosome aberrations. IV sperm of the bent father. That the deficiency phenomena and the exceptions were alike due to loss of one of the fourth chromosomes of Diminished was proved by direct cytological examination of some seventy-five Diminished females in which satisfactory figures were found.

The situation in the fourth chromosome is now comparable to that in the first, with haploidy for the fourth chromosome giving the Diminished type and pseudo-dominance of fourth-group recessives, while haploidy for the first chromosome gives the male type and pseudo-dominance of firstgroup recessives. Females heterozygous for bent and for eyeless were crosses to Diminished males, and the offspring furnished the equivalent of 17 recombinations in a total of , or 0. The positive identification of the small round chromosome as the carrier of the genes of the fourth-group mutants, extends to autosomal characters the proof of the chromosome theory of heredity.

Thetriph-IV It is evident that the same non-disjunctional process that gives rise to nullo-IV gametes and to Diminished individuals haplo-IV's should as frequently give rise to diplo-IV gametes and hence to triplo-IV zygotes. The frequency of the production of haplo-IV gametes is roughly one in In spife of a close watch no individual was found whose somatic appearance or breeding pecuharities agreed with those expected for a triplo-IV individual.

Presently a class of fhes was distinguished that possessed these characters, however, in slight degree. This type of flies was isolated and bred, and the complex of slight differences was found to be inherited as a unit and as a dominant, as it should be if due to the presence of an extra fourth chromosome.

The ratio of not-eyeless to eyeless in those results, instead of being the usual , was approximately 5 : 1. As seen in the diagram of Fig. When Ft "triplo-IV" flies were bred to each other the ratio of not-eyeless to eyeless was approximately 26 : 1, and not 3 : 1. Also, the fact that the ratio was found to be approximately 26 : 1 and not approximately 36 : 1 is interpreted as due to the death of the tetra-IV type.

The death of the tetra-IV type is also indicated by the fact that when triplo-IV were inbred, no type was found that conformed to expectation for a tetraIV somatic type, viz. Good figures were found in about ten such females; and in each case it was found that there was present an extra, small, round chromosome see Fig. Since the male is normally smaller throughoutthanthefemale Fig. All these features show in the specimen drawn in Fig. In some cases a quarter only is maie, or even a still smaller region.

More rarely the gynandromorphs are "fore-and-aft", e. The gynandromorph drawn in Fig. A gynandromorph whose left side is female throughout, and shows the dominant character Notch, and whose right side is male throughout and shows scute broad echinus ruby tan and forked. The left side shows the dominant character Notch its mother was Notch and right side shows the sex linked recessive characters, scute, broad wing, echinus eye, ruby eye, tan body color and antenna color and forked bristles all of which entered from the father.

On the other hand, autosomal characters appear in the two sides without distinction. This suggests that the cause of the gynandromorph is tobesoughtin an aberration of the X-chromosome alone. It is supposed that this type of gynandromorph starts as a female, and that the male parts arise through loss of one of the two X-chromosomes. For example, the gynandromorph of Fig. The female parts are those expected to be present in the hybrid from the cross, viz. But at an early cleavage division, probably the first Fig.

This left a cell that had only one X-chromosome, the paternal eosinminiature X. All the parts descended from this cell should be male, since they have but one X, and should show the paternal characters eosin and rniniature, corresponding to the X that was retained. Moreover, when the abdomen and genitalia are male, the gynandromorph is found to be sterile, which is expected from the XO nature of the male cells in these gynandromorphs. The frequency with which gynandromorphs are found in the Droso. The frequency of elirnination of the patemally derived X is the same as that for the maternally derived X; for, the male parts show sex-linked characters derived from the mother as frequently as from the father.

If the ehmihation occurs at the first cieavage division the gynandromorph is expected to be bilateral except for deviations due to subsequent wandering of the cells. That such wandeling occurs is evidenced by the large number of cases in which the line, especially in the head, is shifted to one side or takes an irregular course- In bilateral gynandromorphs the two gonads have nearly always been found to be the same, i. However, exceptions have occurred, and the cytological work of Huettner '22 has shown that several nuclei of the embryo give rise to the primordial Fig. A striking fact with regard to these gynandromorphs is that the male and female parts and their sex-linked characters are strictly self-determiningi , each part developing according to its own genetic constitution.

No matter how large or small the region may be, it is not interferred with by influences coming from neighboring parts, nor is it overruled by the action of the gonads. Bridges, unpublished. In crosses free from Diminished, probably more than a dozen flies, Fig. A male cut that is haplo-IV on the right side and normal on the left. Some of those may be really somatic mutations to a Minute, but certainly the majority must be due to elimination of one of the two fourth-chromosomes at an early cleavage division. If the classification was correct, this fly can be interpreted as one that started as a normal heterozygote for eyeless, and in which Fig.

A female that is eyeless and haplo-IV on the right side and wild-type on the left. Hence, when mosaics are found that involve second or third-chromosomal characters some other explanatiorl than. Among the progeny, a female occurred Fig. A double-nucleus mosaic, whose left side was pink III-chromosome and shaven IV-chromosome and whose right side was wild-type.

All of the abdomen belonged with the Dichaete, peach, sooty, side. The two sides differed in six characters. Each of these pronuclei was fertilized by a separate X-bearing sperm both sides female of the multiple recessive father. A mosaic in which certainly two different sperms, and probably two female pronuclei, were involved, occurred in the Ft of a cross between two second-chromosome recessives, vestigial and speek.

The mosaic was vestigial and male on the left side and speek and female on the right side The left side, accordingly, came from a pronucleus carrying the second-chromosome with speek and from an X-sperm carrying the speek second-chromosome. The right side came from a pronucleus carrying the vestigial second-chromosome and from a X-sperm with the vestigialsecond-chromosome.

Thus, two different pairs of chromosomes, the X and the second, were demonstrably involved. In another mosaic one side was pink and shaven and the other side not-pink and notshaven Fig. In this case, then, there is evidence that the thirdand the fourth-chromosomes were involved simultaneously. It is only rarely that a cross involving characters in different groups is made, and the definite demonstration that all four chromosomes are simultaneously involved in the mosaics interpreted as due to two pronuclei and two sperms must come from a cross specifically desdgned to check all four chromosomes.

Bridges '21c. The "intersexes," which are easily distinguished from males and from females, are large-bodied, coarse-bristled fhes with large, roughish eyes and scalloped wing margins. They show marked fluctuation in all characters; and, in addition, apparently form a bimodal group with respect to the more strictly sexual characters — on the one hand a more "female-type", and, on the other, a more "male-type".

In the "female-type" Fig. Spermathecae are present. The gonads are typically rudimentary ovaries; but the tissue in the terminal chambers of the ovaries resembles spermatogonial tissue more closely than oogonial tissue. Occasionally a gonad is mainly ovarian in appearance, but with a testicular bud. Sometimes also one gonad is a rudimentary testis and the other a rudimentary ovary. Sexcombs, a male character, are almost invariably present on the"tarsi of the forelegs, although they are sometimes absent from one tarsus or reduced in size.

In the "male-type" Fig. Sex-combs are always present. Both types of intersexes have been found entirely sterile. In addition the group to the left had a Y. The culture that produced the intersexes showed other striking pecuharities; for example, the females and males showed three, instead of two large classes representing original combinations.

These classes were plexus speek, plexus brown, and brown speek. Extensive breeding tests were made of these flies, and each was found to have received from the father, a second-chromosome carrying the three recessives plexus, brown and speek, which agreed with expectation. But from the mother each had received one of three different chromosomes; namely a plexus speek, a plexus brown, or a brown speek chromosome. That is, the mother of the intersexes had carried three second-chromosomes instead of two.

A condition of triploidy for certain sections of chromosome had been met with in the previous unpublished studies on duplications and on Fig. Male-type intersex with ventral view to the left, and a ventral view of an intermediate specimen above. The chromosome groups show two X's, three seconds, three thirds, and usually only two fourths, and not three as shown here. Not only were the second-and third-chromosomes involved, but the X as well, as was shown by specific tests with sex-linked charaqters. The chromosomes of the intersexes consisted of two sets of three V's the two sets differing in the size of the V's of a pair of rods, of three or two small round chromosomes, and usually of a J-shaped chromosome.

That is, all intersexes possessed the second- and the third-chromosomes in triplicate and the X in duplicate, but they might lack one of the expected three fourth-chromosomes and have or lack a Y-chromosome. Thus four sub-types of intersex constitution were found Figs. The 3N females About ten percent of the daughters from the original intersexproducing culture, when tested, in turn produced intersexes and further disturbances of the ratios. These females were, by rnference, tn- ploid Fig for all the chromosomes except the fourth, which might be present in duplicate.

It was then discovered that these intersex-producing females could be identified by their somatic characters which together constitute a distinct type. They are most readily identified by large, coarse-textured eyes, and, secondly, by large body-size and stocky build. The sexual characters are completely female. Genetic tests of these intersex-producers show that they possess in tnpheate the loei for a large variety of first, second, and third group mutants.

This genetic proof of triploidy was checked by direct cytological exarnination, and it was found that the intersex-producers were 3N m constitution. This finding extends the direct proof of the chromosome theory of heredity to specific second and third group mutants and corresponding specific V-shaped chromosomes. They are shifted out of the female class by the presence of an extra set of autosomes, and thereby the autosomes are proved to play a positive role in the production of sex. Since the intersexes differ from females by the assumption of certain male characters, this effect of the autosomes is due to an internal preponderance of "male-tendency" genes.

We may now reformulate the sex-relations as follows: both sexes are due to the simultaneous action of two opposed sets of genes, one set tending to produce the characters called female and the other to produce the characters called male. When, in a diploidzygete, therelative effectiveness of the female-tendency genes is lowered by the absence of one X, the male-tendency genes outweigh the female, and the result is the normal male.

When the two sets of genes are acting in a ratio between these two extremes, as is the case in the ratio of 2X : 3 sets of autosomes, the result is a sex-intermediate — the intersex. The Supersexes The phenomenon of intersexuality might be expected to have a reciprocal phase, namely, supersexes.

If the intersexes result from an intermediate ratio of X to autosomes, then when the normal female ratio of X to autosomes is exceeded, a superfemale might be expected to result ; and, by increasing the relative number of autosomes, a corresponding supermale might be produced. Diploid individuals possessing an extra X have been identified as a distinct somatic type that is ordinar, ily lethal. This type resembles the female, but hasabnormal ovaries and is sterile. Conversely, individuals with one X-chromosome and an extra set of autosomes have been identified.

These resemble the males, but form a distinct type, and are sterile. At first it was surrmsed that FiK 57 a triplo-X, or Superfemale, with two chromosome groups showing 6' the extra X-chromosome. More recent results have shown that usually the female-type has three IV-chromosomes and the male type two Table 7.

Table 7. A Supermale. Recent cytological examination shows one X and three of each autosomes. The Gametic Series in 3N Females Since each kind of chromosome exists in triphcate in the 3N female, the gametes with respect to a given chromosome C are expected to be 2C and IC with equal frequency.

Thus, half the gametes should be haplo-X and half diplo-X. If the reductions in the different kinds of chromosomes are independent of one another, then, among the haplo-X gametes, half are haplo-II and half are diplo-II, and so on for chromosomes III and IV. Disregarding the fourth chromosome, there should be eight types of gametes, including the extremes, N and 2N.

These are fertilized by two types of sperm, the X- and the Y-sperm. Thus, an Negg by an N-sperm X-sperm results in a 2N-female. By such a mating the frequency of the various types of gametes can be investigated. Table 8 gives the results of a recent cross of this type carried out by Bridges unpublished.

Table 8. From this type of reduction thVre result two kinds of mature eggs, equally numerous N tad 2N In the other type of maturation, two sets of autosomes and "efpassto one pole, oleset of autosomes and Xs to the other. In the intersexes and 3N ttTthe mortality is considerable. The ratio of : is 1 : 6. The character is quite complex in all three species, and the pecuharities agree in considerable detail. Ruby - melanogaster 7.

This locus has mutated three times in melanogaster, twice in simulans. The character is practically identical in appearance with garnet see below , and with several autosomal characters. Among the sex-linked characters it may be compared with sepia 0 and magenta 67 of virilis and with peach 40 and orange 83 of willistoni. For the reasons stated in the discussion of prune, these comparisons are not very satisfactory.

Crossveinless—melanogaster The mutation has been found once in each of the species named. Lozenge - melanogaster The characters in question are called lozenge in melanogaster, rugose with allelomorphs glazed and wax in virilis, glazed in obscura, morula in willistoni. All the types have abnormal surfaces to the compound eyes, often suggesting the presence of moisture.

In melanogaster and in virilis three allelomorphs are known that differ in the extent of eye modification, and in each species two of these have sterile females. Singed and forked - melanogaster sn, These two mutant types are considered together, since 'the characters are closely similar. The symbols used refer only to the accepted names, and are not to be taken as identifications of corresponding genes except in the case of melanogaster and simulans.

The females are sterile in both forked aUelomorphs but not in stubby of wilhstoni, and in singed of obscura. None of the other types under discussion has sterile females. Cut — melanogaster This is one of the frequently recurring mutations in melanogaster, where several different aUelomorphs are known. The character is one that is approximated by mutant types dependent on several other genes, so that the case is not a good one for establishing paraUelism.

The mutation is one of the most frequently recurring ones in melanogaster. The character is, however, nearly duplicated by the third-chromosome type scarlet of melanogaster, simulans, and obscura , and by the melanogaster types cardinal chromosome III and cinnabar chromosome II. Miniature and dusky—melanogaster m, These characters are as difficult to distinguish as are forked and singed, and are therefore here treated in the same way as were those.

Garnet — melanogaster Two aUelomorphs are known in melanogaster, and the corresponding simulans type is intermediate between the two. For possible parallels in other species see discussion under ruby. Inflated — melanogaster 53 , funebris The character, known as bubble in funebris, belongs to a rather common type of modification.

It was first compared by Weinstein '20 to vesiculated, to which it bears some resemblance. Rudimentary — melanogaster Fused melanogaster Two mutant aUelomorphs are known in melanogaster. These are the terminal loci of their respective maps, and crosses have shown them to be corresponding. Vesiculated—simulans 21 , virihs The character is very poor for linkage purposes as in both species it overlaps wild-type. It is also unsatisfactory as a parallel because it is so similar to numerous other characters. Short — virihs 86 , obscura Aside from this the character a shortening of the 5th and sometimes of other veins is of too common occurrence to be altogether satisfactory as a parallel.

Beaded, Bd. III, Wing margin scalloped. Lethal when hom. For example, there were 30 time point measurements during the egg stage; we used the average expression over those 30 time points. We repeated this for larvae, metamorph, adult female, and adult male stages. Each gene was provisionally designated as having biased expression for the stage with the maximum average expression, which we will call the biased stage. For each gene, we calculated the average difference between the biased stage expression value and the other stage expression values.

This generated a distribution of differences for each comparison of stages. A gene was finally determined to have biased expression if the average difference between the biased stage and the other stages fell into top half for that stage distribution. This procedure resulted in , , , , and stage-biased genes for egg, larvae, metamorph, adult male, and adult female stages, respectively.

We calculated the proportion of genes in a group e. We tested whether pairs of proteins that interact with one another were more likely to show evidence of adaptive protein divergence than random pairs of proteins with no evidence of interaction. Data were from Giot et al. We considered pairs of genes to have a significant interaction if the probability of interaction was greater than 0. We compared this proportion to the distribution of proportion generated from permuted datasets generated by randomly drawing pairs of genes without replacement from the Giot et al.

However, given the small sample size here and the genomic scale of the data, we used an analogous statistic for polymorphisms and fixations on the D. First, the average proportion of segregating sites in D. Only sites for which unambiguous, parsimony-inferred D. These were defined as the regions bounded by the first and last position on each chromosomes arm for which the proportion of segregating sites was greater than or equal to the chromosome arm average in a kbp window. While this makes deviations in the centromere and telomere proximal regions appear greater, it removes the obvious bias toward positive deviations i.

Minimum values for the expected numbers of segregating and fixed sites were one unless otherwise indicated. Expected nucleotide heterozygosity and polarized divergence were calculated for kb and kb nonoverlapping windows spanning each chromosome arm as described above. For each arm, autocorrelation between successive windows was calculated as: where there are n windows along an arm, and x t represents the value of nucleotide heterozyogsity or divergence for the t- th window.

Significance of r for all arms for both polymorphism and divergence was calculated by permutation. We set out to find putative selective sweeps that occurred concomitantly with migration by D. The method described here addresses the issue of autocorrelated loci. Adjacent kb windows were averaged weighted by coverage to obtain kb windows. There were no gaps in the kb window data longer than three consecutive windows in either population.

Maximum likelihood estimates of first-order coefficients of autocorrelation for each of the chromosome arms were found all were significant. Variance and estimated first-order autocorrelation of the simulations were similar to those of the empirical data without altering this procedure. Significance of runs of windows below this threshold was determined by comparison to the distribution of the run lengths in 10, Monte Carlo simulation runs for each chromosome arm, performed as described above.

P -values for each arm were corrected for multiple comparisons conservatively via Bonferroni correction Dunn-Sidak corrections did not result in an increased number of significant sweeps. Parsimony was used to infer D.

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Only codons with one synonymous variant among the three species were included in these analyses. The preferred codon set was defined following Akashi [ ]. For some analyses, preferred and unpreferred substitution rates were determined by dividing the number of substitutions of each type by the number of ancestral codons of the appropriate ancestral state unpreferred ancestors for the preferred substitution rate and preferred ancestors for the unpreferred substitution rate , all inferred by parsimony.

In principle, excess unpreferred polymorphisms at synonymous sites could erroneously lead one to infer directional selection on other sites. However, the ratio of preferred-to-unpreferred polymorphisms is not significantly different pooled across genes or gene-by-gene for UTRs that had significant versus nonsignificant MK tests in contrasts of synonymous and UTR sites.

For introns that showed a significant MK test versus synonymous sites, there was a slightly larger ratio of unpreferred-to-preferred polymorphisms compared to the ratio for introns that were not significant. However, this was seen only in the pooled analysis and not in the gene-by-gene analysis. Overall, these data suggest that most of the highly significant MK tests of noncoding DNA are not explained by excess unpreferred polymorphisms or coverage variation. Base composition analyses on noncoding DNA were carried out in a similar fashion, with parsimony being used to infer the D.

Only unambiguous parsimony-inferred sites were used in these analyses. All X -linked genes for which Flybase reported genetic and physical locations first nucleotide of the gene in Flybase annotation of D. Mean physical and genetic distances per interval were 1. The physical location of the interval was defined as the midpoint between physical locations of the first and last gene. For analyses investigating correlations of kb windows of polymorphism and divergence with crossing-over, midpoints were rounded to the nearest 50, If multiple intervals were rounded to the same number, the distal interval was used in the analyses.

Cloned elements. The coordinates are slightly rounded to facilitate finding duplicates slightly off in alignment. Clustered elements. This analysis used plasmid clones for which only one mate pair mapped uniquely and unambiguously to the genome according to the method described previously. The other mate pair was compared to the D. The estimated location begins at the end of the mate pair read and ends 10 kb away in the appropriate direction determined by the direction of the alignment.

Transposable elements from the same family located within 5 kb of each other in the same D. Coordinates reflect D. P and U are preferred and unpreferred, respectively e. The dashed olive lines are the regression lines of TEs numbers on position bp , with the outliers orange masked from the data. Note the gapped scales for total TEs on the right.

Average divergence on the D. GC content in D. The numbers of each TE family in the D. The lower-left panel is an enlargement of the lower ranges. Positive correlations for 2L , 3L , and X , and negative correlations for 2R and 3R indicate increasing values closer to centromeres. Inv 3R was used for D. Trimmed data indicates analyses for which regions of low heterozygosity were removed Materials and Methods.

X -linked polymorphic GC variants occur at higher frequency than autosomal polymorphic GC variants coverage-six polymorphisms from intergenic and intron DNA. Statistics presented are for the whole-genome assembly before it was anchored using alignments to D. The melanogaster TEs are those annotated in release 4.

The ratio of the means is also shown lower in last column. Chinwalla, Holland Cordum, Lucinda A.

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Fulton, Robert S. Fulton, Elaine M. Clifton for her role in shepherding this project. Barbash and H. Lindfors provided assistance in the laboratory at UC-Davis. Anderson alerted us to the possibility that the sim4 and sim6 libraries could be cross-contaminated and also provided many useful comments on the paper. We also thank M. Noor, T. Mitchell-Olds, and three anonymous reviewers for comments.

KS created the D. An early version of the D. Abstract The population genetic perspective is that the processes shaping genomic variation can be revealed only through simultaneous investigation of sequence polymorphism and divergence within and between closely related species. Author Summary Population genomics, the study of genome-wide patterns of sequence variation within and between closely related species, can provide a comprehensive view of the relative importance of mutation, recombination, natural selection, and genetic drift in evolution. Introduction Given the long history of Drosophila as a central model system in evolutionary genetics beginning with the origins of empirical population genetics in the s, it is unsurprising that Drosophila data have inspired the development of methods to test population genetic theories using DNA variation within and between closely related species [ 1 — 4 ].

General Patterns of Polymorphism and Divergence Nucleotide variation. Download: PPT. Figure 1. Figure 2. Variation near centromeres and telomeres. X versus Autosome Divergence Faster- X divergence. Greater X -linked deletion divergence. Chromosomal Gradients of Divergence One of the main goals of large-scale investigations of sequence divergence is to characterize the many biological factors influencing variation in substitution rates throughout the genome.

Fluctuations in Polymorphism and Divergence along Chromosome Arms There was considerable variance of polymorphism and divergence across chromosome arms, even when regions of severely reduced heterozygosity near centromeres and telomeres were excluded. Correlations between recombination rates and sequence variation.

Figure 3. Figure 4. Correlated levels of nucleotide and indel polymorphism. Hitchhiking Effects in D. Unusual genomic regions and the biology of recent selection. Figure 5. Regions of strong linkage disequilibrium. Reduced polymorphism associated with colonization. Lineage Effects on Divergence Several factors can generate lineage differences in divergence. Adaptive Protein Evolution A decades-old issue in population genetics is the extent to which directional selection determines protein divergence.

Population genetic analysis of recurrent adaptive protein evolution. Adaptive protein evolution and gene function. Adaptive protein evolution and gene expression. Adaptive evolution and protein—protein interactions. Proteins showing increased divergence. Accelerated protein divergence and gene function. Adaptive Evolution of Noncoding Elements The same logic originally proposed in the MK test using nonsynonymous and synonymous variation can be extended to any setting in which variant types can be categorized, a priori.

Whole-Genome Analysis of Polymorphic and Fixed Variants Up to this point, our analyses have investigated various attributes of polymorphism and divergence based on windows or genes. Base Composition Evolution Determining the relative contributions of various mutational and population genetic processes to base composition variation and inferring the biological basis of selection on base composition remain difficult problems.

Synonymous sites. Noncoding sites. Conclusions and Prospects The genomic analysis of polymorphism and divergence based on alignments to a reference sequence is poised to become a central component of biological research. Materials and Methods Drosophila stocks. DNA extraction.

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Empirical validation of syntenic assembly. Alignment of D. Heterochromatic regions. Consensus and quality scores. Filtering of high-quality discrepancies within lines. Inversion on the D. Defining the D. Insertions and deletions. Estimation and inferences. MK tests unpolarized and polarized. Rate variation. GO by MK permutations. GO by dN permutations. GO clustering.

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Gene expression. Protein—protein interactions. Polymorphism versus divergence. Autocorrelation of nucleotide heterozygosity and divergence. Reduced variation associated with colonization. Transposable elements. Supporting Information. Dataset S1. Dataset S2. Dataset S3. Dataset S4. Dataset S5. Dataset S6. Dataset S7. Estimates of Polymorphism and Divergence for kb Windows. Dataset S8. Dataset S9. Dataset S Figure S1.

Figure S2. Figure S3. Figure S4. Figure S5. Table S1. Coding and Noncoding Nucleotide Heterozygosity in D. Table S2. Table S3. Comparisons of D. Table S4. Table S5. Table S6. Autocorrelations of D. Table S7. Table S8. Table S9. Table S Read and Trim Statistics for D. Comparison of Expected D. Text S1. References 1. Genetics — View Article Google Scholar 2. View Article Google Scholar 3. View Article Google Scholar 4. Nature — View Article Google Scholar 5. Kimura M The neutral theory of molecular evolution.

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Li WH, Wu CI, Luo CC A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol 2: — Duret L, Mouchiroud D Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis , Drosophila , and Arabidopsis. BMC Evol Biol 2: Genome Biol 6: R Nature 82— Genet Res — Ashburner M Drosophila : A laboratory handbook and manual. Avery PJ The population genetics of haplodiploids and X-linked genes. Nat Rev Genet 7: — Am Nat — Thornton K, Bachtrog D, Andolfatto P X chromosomes and autosomes evolve at similar rates in Drosophila : no evidence for faster-X protein evolution.

Presgraves DC Intron length evolution in Drosophila. Genes Dev — Mol Cell — Genet Res 8: — Curr Opin Cell Biol — J Biol 5: 3. Mukherjee AS, Beermann W Synthesis of ribonucleic acid by the X-chromosomes of Drosophila melanogaster and the problem of dosage compensation. Chromosoma — Begun DJ The frequency distribution of nucleotide variation in Drosophila simulans. Evolution Int J Org Evolution — Hahn MW Accurate inference and estimation in population genomics. Birky CW Jr.

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Dynamic equilibrium between mutational and selective forces. Hey J, Kliman RM Interactions between natural selection, recombination and gene density in the genes of Drosophila. Contrasting levels of naturally occurring DNA restriction map variation and divergence. Hawley RS Chromosomal sites necessary for normal levels of meiotic recombination in Drosophila melanogaster.

Evidence for and mapping of the sites. Nucleic Acids Res — Nat Genet — Hudson RR Estimating the recombination parameter of a finite population model without selection. Kim Y, Nielsen R Linkage disequilibrium as a signature of selective sweeps. Hamblin MT, Veuille M Population structure among African and derived populations of Drosophila simulans : evidence for ancient subdivision and recent admixture. Biochem Genet 27— Schofl G, Schlotterer C Patterns of microsatellite variability among X chromosomes and autosomes indicate a high frequency of beneficial mutations in non-African D.

Schofl G, Schlotterer C Microsatellite variation and differentiation in African and non-African populations of Drosophila simulans. Mol Ecol — Trends Genet Akashi H Inferring the fitness effects of DNA mutations from polymorphism and divergence data: statistical power to detect directional selection under stationarity and free recombination. Nielsen R Molecular signatures of natural selection. Annu Rev Genet — Curr Biol — PLoS Biol 2: E Dev Genes Evol — Int J Dev Biol — Coyne JA Genetic basis of differences in genital morphology among the three sibling species of Drosophila.

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Weir BS Genetic data analysis.