Genetic recombination and adaptation to fluctuating environments: selection for geotaxis in Drosophila melanogaster

Heritable variation in fitness is the fuel of adaptive evolution, and sex can generate new adaptive combinations of alleles. If the generation of beneficial combinations drives the evolution of recombination, then the level of recombination should result in changes in the response to selection. Three types of lines of Drosophila melanogaster varying in their level of genetic recombination were selected over 38 generations for geotaxis. The within-chromosome recombination level of these lines was controlled for 60% of the genome: chromosome X and chromosome II. The full recombination lines had normal, unmanipulated levels of recombination on these two chromosomes. Conversely, nonrecombination lines had recombination effectively eliminated within the X and second chromosomes. Finally, partial recombination lines had the effective rate of within-chromosome recombination lowered to 10% of natural levels for these two chromosomes. The rate of response to selection was measured for continuous negative geotaxis and for a fluctuating environment (alternating selection for negative and positive geotaxis). All selected Drosophila lines responded to selection and approximately 36% of the response to selection was because of the X and second chromosomes. However, recombination did not accelerate adaptation during either directional or fluctuating selection for geotaxis.     

Double crossing over: elementary events and the sequence of their occurrence

Analysis of the crossing over increment in the structurally normal chromosome of Drosophila caused by a rearrangement in nonhomologous chromosome (interchromosomal effect on crossing over, IEC) was carried out based on the author's personal and literature data. The IEC in the left arm of chromosome 2 caused by inversions in chromosomes X and 3, as well as the IEC in X chromosome caused by inversions in chromosomes 2 and 3, were examined. The IEC-induced increment of crossing over results from the increase of the number of double exchanges under the constant or reduced number of single exchanges. Tetrad analysis showed that the given alternation of the crossing over processes could occur only in the case of conversion of the tetrads with single exchanges into the tetrads with double exchanges. In other words, the events leading to the formation of double exchanges occur consecutively. The borders of the IEC-induced double exchanges can be seen all over the chromosome body. However, the IEC-induced increase of chromosome recombination length occurs only in the proximal region (in rare cases, in proximal and distal regions) of the chromosome arm. This means that a double exchange is formed when the first event with predominant location in the middle of the arm is supplemented with the second event predominantly localized at the arm T end, most frequently in the proximal region. The pattern of the IEC-induced double exchange formation can be satisfactorily described in terms of the contact model of the crossing over. According to the model, an elementary crossing-over event is the local contact between the homologues. Neither single exchange nor a double-stranded DNA break can serve as an elementary event in the process of any multiple exchange formation.     

An Analysis of Male-Recombination Elements in a Natural Population of DROSOPHILA MELANOGASTER in South Texas

Genomes from a group of Drosophila melanogaster collected from a natural population at San Benito, South Texas, in March of 1975 were analyzed for the presence of male-recombination elements. All three autosomes and both sex chromosomes were examined, with emphasis placed on the two major autosomes, the second and third chromosomes. In samples of 16 second and 16 third chromosomes, at least half, but not all, of each were found to carry male-recombination elements. It is suggested, although the data are not conclusive, that some of the fourth, X, and Y chromosomes might also be associated with male-recombination elements.—When a male-recombination element, or elements, was located in the second chromosome, relatively more male recombination was induced in the second than in the third chromosome. This situation was reversed when the element(s) was located in the third chromosome.—Distortion of transmission frequency, one of the characteristics of previously studied second chromosome lines associated with male recombination, was confirmed for these second chromosomes that carried male-recombination elements. Similar, but less pronounced, distortion was observed for the third chromosome lines that carried male-recombination elements.     

Genetical Analysis of Chromosomal Interaction Effects on the Activities of the Glucose 6-Phosphate and 6-Phosphogluconate Dehydrogenases in DROSOPHILA MELANOGASTER

By combining ten second and ten third chromosomes, we investigated chromosomal interaction with respect to the action of the modifier factors on G6PD and 6PGD activities in Drosophila melanogaster. Analysis of variance revealed that highly significant chromosomal interaction exists for both enzyme activities. From the estimated variance components, it was concluded that the variation in enzyme activity attributed to the interaction is as great as the variation attributed to the second chromosome but less than attributed to the third chromosome. The interaction is not explained by the variation of body size (live weight). The interaction is generated from both the lack of correlation of second chromosomes for third chromosome backgrounds and the heterogeneous variance of second chromosomes for different third chromosome backgrounds. Large and constant correlation between G6PD and 6PGD activities were found for third chromosomes with any second chromosome background, whereas the correlations for second chromosomes were much smaller and varied considerably with the third chromosome background. This result suggests that the activity modifiers on the second chromosome are under the influence of third chromosome factors.     

The Effect of Recombination-Defective Meiotic Mutants on Fourth-Chromosome Crossing over in DROSOPHILA MELANOGASTER

Crossing over was measured on the normally achiasmate fourth chromosome in females homozygous for one of our different recombination-defective meiotic mutants. Under the influence of those meiotic mutants that affect the major chromosomes by altering the spatial distribution of exchanges, meiotic fourth-chromosome recombinants were recovered irrespective of whether or not the meiotic mutant decreases crossing over on the other chromosomes. No crossing over, on the other hand, was detected on chromosome 4 in either wild type or in the presence of a meiotic mutant that decreases the frequency, but does not affect the spatial distribution, of exchange on the major chromosomes. It is concluded from these observations that (a) in wild type there are regional constraints on exchange that can be attenuated or eliminated by the defects caused by recombination-defective meiotic mutants; [b] these very constraints account for the absence of recombination on chromosome 4 in wild type; and [c] despite being normally achiasmate, chromosome 4 responds to recombination-defective meiotic mutants in the same way as do the other chromosomes.     

Interchromosomal Effects of Heterochromatic Deletions on Recombination in DROSOPHILA MELANOGASTER

It is now known that partial deletions of the satellite sequences in X-chromosome heterochromatin result in a significant decrease in intrachromosomal recombination in the proximal region of the X chromosome of D. melanogaster (YAMAMOTO and MIKLOS 1978). It is important to ask then if the loss or gain of heterochromatin on the X also alters recombination in other chromosomes of the genome (interchromosomal effects). I have looked for such alterations by measuring recombination in chromosome 3. The results clearly indicate that the partial loss of X-chromosome heterochromatin not only decreases crossing over in the proximal region of the X chromosome itself, but also increases the frequency in chromosome 3, especially in the euchromatic regions around the centromere. Furthermore, the greater the deficiency of X heterochromatin, the higher is recombination in chromosome 3. This finding not only provides further evidence in support of the hypothesis that heterochromatin, in this case mainly composed of satellite DNA, regulates the recombination system, but it demonstrates that when the satellite content of one chromosome of the D. melanogaster genome is altered, there is an alteration in the crossover characteristics of other chromosomes in the same complement. If the amount of satellite DNA in a genome is being continuously altered, then one can predict that the recombination system is also being continually perturbed. Thus, the changing gene combinations produced indirectly by increases or decreases of heterochromatin are among the components available to organisms to break up or form new gene combinations upon which selection can act.     

The mitotic, polytene, and meiotic chromosomes of Drosophila ananassae.

The mitotic chromosome complement of D. ananassae consists of four structurally distinguishable submetacentric pairs and all four have been identified with their linkage groups. For the polytene chromosome complement of six arms representing the X, second and third chromosomes, an improved reference map has been constructed and used to describe selected cytogenetically useful rearrangements. In meiotic prophase of spermatocytes, chromosomes 2 and 3 form pachytene-diplotene bivalents whose arms may be associated by chiasmata in postdiplotene stages, but the X, Y and fourth chromosomes participate in a complex multivalent. No correlation was detected between meiotic chromosome behavior and specific genes that regulate crossing over in males. In male inversion heterozygotes having high levels of genetically monitored crossing over, no unequivocal evidence was found for formation of either pachytene inversion loops or anaphase bridges and fragments.     

Meiotic recombination at the ends of chromosomes in Saccharomyces cerevisiae

Meiotic reciprocal recombination (crossing over) was examined in the outermost 60-80 kb of almost all Saccharomyces cerevisiae chromosomes. These sequences included both repetitive gene-poor subtelomeric heterochromatin-like regions and their adjacent unique gene-rich euchromatin-like regions. Subtelomeric sequences underwent very little crossing over, exhibiting approximately two- to threefold fewer crossovers per kilobase of DNA than the genomic average. Surprisingly, the adjacent euchromatic regions underwent crossing over at twice the average genomic rate and contained at least nine new recombination "hot spots." These results prompted an analysis of existing genetic mapping data, which showed that meiotic reciprocal recombination rates were on average greater near chromosome ends exclusive of the subtelomeres. Thus, the distribution of crossovers in S. cerevisiae appears to resemble that found in several higher eukaryotes where the outermost chromosomal regions show increased crossing over.     

A Cis-Acting Locus That Promotes Crossing over between X Chromosomes in Caenorhabditis Elegans

This study reports the characterization of a cis-acting locus on the Caenorhabditis elegans X chromosome that is crucial for promoting normal levels of crossing over specifically between the X homologs and for ensuring their proper disjunction at meiosis I. The function of this locus is disrupted by the mutation me8, which maps to the extreme left end of the X chromosome within the region previously implicated by studies of X;A translocations and X duplications to contain a meiotic pairing site. Hermaphrodites homozygous for a deletion of the locus (Df/Df) or heterozygous for a deletion and the me8 mutation (me8/Df) exhibit extremely high levels of X chromosome nondisjunction at the reductional division; this is correlated with a sharp decrease in crossing over between the X homologs as evidenced both by reductions in genetic map distances and by the presence of achiasmate chromosomes in cytological preparations of oocyte nuclei. Duplications of the wild-type region that are unlinked to the X chromosome cannot complement the recombination and disjunction defects in trans, indicating that this region must be present in cis to the X chromosome to ensure normal levels of crossing over and proper homolog disjunction. me8 homozygotes exhibit an altered distribution of crossovers along the X chromosome that suggests a defect in processivity along the X chromosome of an event that initiates at the chromosome end. Models are discussed in which the cis-acting locus deleted by the Dfs functions as a meiotic pairing center that recruits trans-acting factors onto the chromosomes to nucleate assembly of a crossover-competent complex between the X homologs. This pairing center might function in the process of homolog recognition, or in the initiation of homologous synapsis.     

mus309 mutation, defective in DNA double-strand break repair, affects intergenic but not intragenic meiotic recombination in Drosophila melanogaster

The effect was investigated of the hypomorphic DNA double-strand break repair, notably synthesis-dependent strand annealing, deficient mutation mus309 on the third chromosome of Drosophila melanogaster on intergenic and intragenic meiotic recombination in the X chromosome. The results showed that the mutation significantly increases the frequency of intergenic crossing over in two of three gene intervals of the X chromosome studied. Interestingly the increase was most prevalent in the tip of the X chromosome where crossovers normally are least frequent per physical map unit length. In particular crossing over interference was also affected, indicating that the effect of the mus309 mutation involves preconditions of crossing over but not the event of crossing over itself. On the other hand, the results also show that most probably the mutation does not have any effect on intragenic recombination, i.e. gene conversion. These results are fully consistent with the present molecular models of meiotic crossing over initiated by double-strand breaks of DNA followed by formation of a single-end-invasion intermediate, or D-loop, which is subsequently processed to generate either crossover or non-crossover products involving formation of a double Holliday junction. In particular the results suggest that the mus309 gene is involved in resolution of the D-loop, thereby affecting the choice between double-strand-break repair (DSBR) and synthesis-dependent strand annealing (SDSA) pathways of meiotic recombination.     

Distribution of Nonstructural Variation between Wheat Cultivars along Chromosome Arm 6Bp: Evidence from the Linkage Map and Physical Map of the Arm

Metaphase I (MI) pairing of homologous chromosomes in wheat intercultivar hybrids (heterohomologous chromosomes) is usually reduced relative to that within the inbred parental cultivars (euhomologous chromosomes). It was proposed elsewhere that this phenomenon is caused by polymorphism in nucleotide sequences (nonstructural chromosome variation) among wheat cultivars. The distribution of this polymorphism along chromosome arm 6Bp (=6BS) of cultivars Chinese Spring and Cheyenne was investigated. A population of potentially recombinant chromosomes derived from crossing over between telosome 6Bp of Chinese Spring and Cheyenne chromosome 6B was developed in the isogenic background of Chinese Spring. The approximate length of the Chinese Spring segment present in each of these chromosomes was assessed by determining for each chromosome the interval in which crossing over occurred (utilizing the rRNA gene region, a distal C-band and the gliadin gene region as markers). The MI pairing frequencies of these chromosomes (only the complete chromosomes were used) with the normal Chinese Spring telosome 6Bp were determined. These were directly proportional to the length of the euhomologous segment. The longer the incorporated euhomologous segment the better was the MI pairing. This provided evidence that the heterohomologous chromosomes are differentiated from each other in numerous sites distributed throughout the arm.—The comparison of the physical map of arm 6Bp with the linkage map showed a remarkable distortion of the linkage map; no crossing over was detected in the proximal 68% of the arm. A population of 49 recombinant chromosomes was assayed for recombination within the rRNA gene region, but none was detected. No new length variants of the nontranscribed spacer separating the 18S and 26S rRNA genes were detected either.     

Patterns of meiotic recombination in human fetal oocytes

Abnormal patterns of meiotic recombination (i.e., crossing-over) are believed to increase the risk of chromosome nondisjunction in human oocytes. To date, information on recombination has been obtained using indirect, genetic methods. Here we use an immunocytological approach, based on detection of foci of a DNA mismatch-repair protein, MLH1, on synaptonemal complexes at prophase I of meiosis, to provide the first direct estimate of the frequency of meiotic recombination in human oocytes. At pachytene, the stage of maximum homologous chromosome pairing, we found a mean of 70.3 foci (i.e., crossovers) per oocyte, with considerable intercell variability (range 48-102 foci). This mean equates to a genetic-map length of 3,515 cM. The numbers and positions of foci were determined for chromosomes 21, 18, 13, and X. These chromosomes yielded means of 1.23 foci (61.5 cM), 2.36 foci (118 cM), 2.5 foci (125 cM), and 3.22 foci (161 cM), respectively. The foci were almost invariably located interstitially and were only occasionally located close to chromosome ends. These data confirm the large difference, in recombination frequency, between human oocytes and spermatocytes and demonstrate a clear intersex variation in distribution of crossovers. In a few cells, chromosomes 21 and 18 did not have any foci (i.e., were presumptively noncrossover); however, configurations that lacked foci were not observed for chromosomes 13 and X. For the latter two chromosome pairs, the only instances of absence of foci were observed in abnormal cells that showed chromosome-pairing errors affecting these chromosomes. We speculate that these abnormal fetal oocytes may be the source of the nonrecombinant chromosomes 13 and X suggested, by genetic studies, to be associated with maternally derived chromosome nondisjunction.     

Fine-Scale Heterogeneity in Crossover Rate in the garnet-scalloped Region of the Drosophila melanogaster X Chromosome

Homologous recombination affects myriad aspects of genome evolution, from standing levels of nucleotide diversity to the efficacy of natural selection. Rates of crossing over show marked variability at all scales surveyed, including species-, population-, and individual-level differences. Even within genomes, crossovers are nonrandomly distributed in a wide diversity of taxa. Although intra- and intergenomic heterogeneities in crossover distribution have been documented in Drosophila, the scale and degree of crossover rate heterogeneity remain unclear. In addition, the genetic features mediating this heterogeneity are unknown. Here we quantify fine-scale heterogeneity in crossover distribution in a 2.1-Mb region of the Drosophila melanogaster X chromosome by localizing crossover breakpoints in 2500 individuals, each containing a single crossover in this specific X chromosome region. We show 90-fold variation in rates of crossing over at a 5-kb scale, place this variation in the context of several aspects of genome evolution, and identify several genetic features associated with crossover rates. Our results shed new light on the scale and magnitude of crossover rate heterogeneity in D. melanogaster and highlight potential features mediating this heterogeneity.     

Chromosome Rearrangements in CAENORHABDITIS ELEGANS

A method for selecting unlinked duplications of a part of the X chromosome of C. elegans is described. Five such duplications have been identified. One of them, Dp (X;V)1, is translocated to linkage group V, where it suppresses crossing over along the left half of linkage group V. Dp(X;V)1 homozygotes grow slowly and are sterile. The other four duplications are associated with chromosome fragments, as observed cytologically by fluorescence microscopy, and tend to be lost. Their frequency of loss is higher in strains homozygous for a mutation that promotes nondisjunction of X chromosomes. The recombination frequencies between two of these duplications and the X have been measured: the frequencies are at least 50 times less than for X-X recombination in the same region. The duplications may prove useful as balancers of recessive lethal mutations.     

Meiotic Recombination on Artificial Chromosomes in Yeast

We have examined the meiotic recombination characteristics of artificial chromosomes in Saccharomyces cerevisiae. Our experiments were carried out using minichromosome derivatives of yeast chromosome III and yeast artificial chromosomes composed primarily of bacteriophage lambda DNA. Tetrad analysis revealed that the artificial chromosomes exhibit very low levels of meiotic recombination. However, when a 12.5-kbp fragment from yeast chromosome VIII was inserted into the right arm of the artificial chromosome, recombination within that arm mimicked the recombination characteristics of the fragment in its natural context including the ability of crossovers to ensure meiotic disjunction. Both crossing over and gene conversion (within the ARG4 gene contained within the fragment) were measured in the experiments. Similarly, a 55-kbp region from chromosome III carried on a minichromosome showed crossover behavior indistinguishable from that seen when it is carried on chromosome III. We discuss the notion that, in yeast, meiotic recombination behavior is determined locally by small chromosomal regions that function free of the influence of the chromosome as a whole.     

Caenorhabditis briggsae recombinant inbred line genotypes reveal inter-strain incompatibility and the evolution of recombination

The nematode Caenorhabditis briggsae is an emerging model organism that allows evolutionary comparisons with C. elegans and exploration of its own unique biological attributes. To produce a high-resolution C. briggsae recombination map, recombinant inbred lines were generated from reciprocal crosses between two strains and genotyped at over 1,000 loci. A second set of recombinant inbred lines involving a third strain was also genotyped at lower resolution. The resulting recombination maps exhibit discrete domains of high and low recombination, as in C. elegans, indicating these are a general feature of Caenorhabditis species. The proportion of a chromosome's physical size occupied by the central, low-recombination domain is highly correlated between species. However, the C. briggsae intra-species comparison reveals striking variation in the distribution of recombination between domains. Hybrid lines made with the more divergent pair of strains also exhibit pervasive marker transmission ratio distortion, evidence of selection acting on hybrid genotypes. The strongest effect, on chromosome III, is explained by a developmental delay phenotype exhibited by some hybrid F2 animals. In addition, on chromosomes IV and V, cross direction-specific biases towards one parental genotype suggest the existence of cytonuclear epistatic interactions. These interactions are discussed in relation to surprising mitochondrial genome polymorphism in C. briggsae, evidence that the two strains diverged in allopatry, the potential for local adaptation, and the evolution of Dobzhansky-Muller incompatibilities. The genetic and genomic resources resulting from this work will support future efforts to understand inter-strain divergence as well as facilitate studies of gene function, natural variation, and the evolution of recombination in Caenorhabditis nematodes.     

Chromosome size-dependent control of meiotic reciprocal recombination in Saccharomyces cerevisiae: the role of crossover interference.

In the yeast Saccharomyces cerevisiae, small chromosomes undergo meiotic reciprocal recombination (crossing over) at rates (centimorgans per kilobases) greater than those of large chromosomes, and recombination rates respond directly to changes in the total size of a chromosomal DNA molecule. This phenomenon, termed chromosome size-dependent control of meiotic reciprocal recombination, has been suggested to be important for ensuring that homologous chromosomes cross over during meiosis. The mechanism of this regulation was investigated by analyzing recombination in identical genetic intervals present on different size chromosomes. The results indicate that chromosome size-dependent control is due to different amounts of crossover interference. Large chromosomes have high levels of interference while small chromosomes have much lower levels of interference. A model for how crossover interference directly responds to chromosome size is presented. In addition, chromosome size-dependent control was shown to lower the frequency of homologous chromosomes that failed to undergo crossovers, suggesting that this control is an integral part of the mechanism for ensuring meiotic crossing over between homologous chromosomes.     

The Meiotic Behavior of an Inversion in Caenorhabditis Elegans

The rearrangement hIn1(I) was isolated as a crossover suppressor for the right end of linkage group (LG) I. By inducing genetic markers on this crossover suppressor and establishing the gene order in the homozygote, hIn1(I) was demonstrated to be the first genetically proven inversion in Caenorhabditis elegans. hIn1(I) extensively suppresses recombination in heterozygotes in the right arm of chromosome I from unc-75 to unc-54. This suppression is associated with enhancement of recombination in other regions of the chromosome. The enhancement observed maintains the normal distribution of events but does not extend to other chromosomes. The genetic distance of chromosome I in inversion heterozygotes approaches 50 map units (m.u.), approximately equal to one chiasma per meiosis. This value is maintained in hIn1(I)/szT1(I;X) heterozygotes indicating that small homologous regions can pair and recombine efficiently. hIn1(I)/hT2(I;III) heterozygotes share no uninverted homologous regions and segregate randomly, suggesting the importance of chiasma formation in proper segregation of chromosomes. The genetic distance of chromosome I in these heterozygotes is less that 1 m.u., indicating that crossing over can be suppressed along an entire chromosome. Since one of our goals was to develop an efficient balancer for the right end of LGI, the effectiveness of hIn1(I) as a balancer was tested by isolating and maintaining lethal mutations. The meiotic behaviour of hIn1(I) is consistent with other genetic and cytogenetic data suggesting the meiotic chromosomes are monocentric. Rare recombinants bearing duplications and deficiencies of chromosome I were recovered from hIn1(I) heterozygotes, leading to the proposal the inversion was paracentric.     

Two Types of Sites Required for Meiotic Chromosome Pairing in Caenorhabditis Elegans

Previous studies have shown that isolated portions of Caenorhabditis elegans chromosomes are not equally capable of meiotic exchange. These results led to the proposal that a homolog recognition region (HRR), defined as the region containing those sequences enabling homologous chromosomes to pair and recombine, is localized near one end of each chromosome. Using translocations and duplications we have localized the chromosome I HRR to the right end. Whereas the other half of chromosome I did not confer any ability for homologs to pair and recombine, deficiencies in this region dominantly suppressed recombination to the middle of the chromosome. These deletions may have disrupted pairing mechanisms that are secondary to and require an HRR. Thus, the processes of pairing and recombination appear to utilize at least two chromosomal elements, the HRR and other pairing sites. For example, terminal sequences from other chromosomes increase the ability of free duplications to recombine with their normal homologs, suggesting that telomere-associated sequences, homologous or nonhomologous, play a role in facilitating meiotic exchange. Recombination can also initiate at internal sites separated from the HRR by chromosome rearrangement, such as deletions of the unc-54 region of chromosome I. When crossing over was suppressed in a region of chromosome I, compensatory increases were observed in other regions. Thus, the presence of the HRR enabled recombination to occur but did not determine the distribution of the crossover events. It seems most likely that there are multiple initiation sites for recombination once homolog recognition has been achieved.     

Molecular population genetics of Drosophila subtelomeric DNA

DNA sequence surveys in yeast and humans suggest that the forces shaping telomeric polymorphism and divergence are distinctly more dynamic than those in the euchromatic, gene-rich regions of the chromosomes. However, the generality of this pattern across outbreeding, multicellular eukaryotes has not been determined. To characterize the structure and evolution of Drosophila telomeres, we collected and analyzed molecular population genetics data from the X chromosome subtelomere in 58 lines of North American Drosophila melanogaster and 29 lines of African D. melanogaster. We found that Drosophila subtelomeres exhibit high levels of both structural and substitutional polymorphism relative to linked euchromatic regions. We also observed strikingly different patterns of variation in the North American and African samples. Moreover, our analyses of the polymorphism data identify a localized hotspot of recombination in the most-distal portion of the X subtelomere. While the levels of polymorphism decline sharply and in parallel with rates of crossing over per physical length over the distal first euchromatic megabase pairs of the X chromosome, our data suggest that they rise again sharply in the subtelomeric region (approximately 80 kbp). These patterns of historical recombination and geographic differentiation indicate that, similar to yeast and humans, Drosophila subtelomeric DNA is evolving very differently from euchromatic DNA.