Distribution and Frequency of Tandem Duplications of the rII Region of Bacteriophage T4d

Genetic analyses of 49 duplications of the rII region of bacteriophage T4D suggests that there is a non-random relationship between the end points of duplicated segments, that relaxed packaging restrictions have little if any effect on the distribution of duplications, that segregation is 3–4 times more frequent than normal recombination for the same interval, and that non-tandem duplications are rare. Extrapolation of the r1231 x rJ101 cross data suggests that the minimum frequency of duplications/genome is 1.7 x 10^-6, but possibly 3.4 x 10^-4.     

Genetic Mechanisms of Rare Matings of the Yeast SACCHAROMYCES CEREVISIAE Heterozygous for Mating Type

Yeast heterozygous for mating type lacks the ability to conjugate as judged by the mass-mating technique and accordingly is designated "non-mater". However, the non-mater shows rare mating ability with a frequency of less than 10^-6. In the present study, the RD auxotroph mating method was mainly employed with the intention of examining the rare mating ability of various non-maters, using lactate ethanol minimal medium as a selective medium for hybridization. Crosses of aα x a, aα x a, aaα x a, aαα x a, etc. resulted in the production of respective hybrids with a relatively high frequency of about 10^-6 to 10^-7, whereas crosses of aaα x a, aαα x α, aaαα x a, aaαα x α, etc. resulted in hybrids with an extremely low frequency of about less than 10^-8. Genetic analyses revealed that the rare matings were mostly caused by the presence of cells derived from the non-maters in which mating type had converted to a homozygous genotype. Mitotic recombination was shown to be a likely explanation for most of the conversion, judging from associated exchange of an outside marker, thr4. By successive employment of the RD auxotroph mating method, it was possible to produce a series of polyploid yeasts, triploids to octoploids. The DNA content and the cell volume were observed to increase parallel to the elevated ploidy states.     

Frequency of gamma-Ray Induced Specific Locus and Recessive Lethal Mutations in Mature Germ Cells of the Zebrafish, BRACHYDANIO RERIO

Specific locus and recessive lethal mutations are induced by γ-rays with approximately first order kinetics in the zebrafish (Brachydanio rerio) with frequencies of 4 x 10^-5 r^-1 and 4 x 10^-3 r^-1, respectively. The surprisingly low ratio (100:1) of recessive lethals to specific locus mutations may be due to the induction of large deficiencies by γ-rays.     

Mutation Rates for Enzyme and Morphological Loci in Barley ( HORDEUM VULGARE L.)

Spontaneous mutation rates were estimated by assaying 84,126 seedlings of a highly homozygous barley line (isogenic line 2025) for five enzyme loci. No mutants were observed in 841,260 allele replications. This result excludes, at probability level 0.95, a spontaneous mutation rate larger than 3.56 x 10^-6/locus/gamete/generation for these enzyme loci. Isogenic line 2025 also was scored for mutants at four loci governing morphological variants. No mutants were observed in 3,386,850 allele replications which indicates that the upper bound for the mutation rate for these loci is 8.85 x 10^-7. It was concluded that, even though spontaneous mutation has been important in creating variability in the barley species at the loci scored, the rate is too low to have much affect on the short-term dynamics of barley populations.     

A Comparison of Mutation Rates for Specific Loci and Chromosome Regions in Dysgenic Hybrid Males of DROSOPHILA MELANOGASTER

The mutation rates of specific loci and chromosome regions were estimated for two types of dysgenic hybrid males. These came from crosses between P or Q males and M females in the P-M system of hybrid dysgenesis. The M x P hybrids were the more mutable for each of the loci and chromosome regions tested. The Beadex locus was highly mutable in these hybrids but did not mutate at all in the sample of gametes from the M x Q hybrids. The singed locus had 75% of the mutability of Beadex in the M x P hybrids; it was also mutable in the M x Q hybrids. The white locus was only slightly mutable in the M x P hybrids and not at all mutable in the M x Q hybrids. The mutations in singed and white probably arose from the insertion of P elements into these loci; the mutations at Beadex probably involved the action of a P element located near this locus on the X chromosome of the P strain that was used in the experiments. Mutations in two chromosome regions, one including the zeste-white loci and the other near the miniature locus, were much more frequent in the M x P hybrids than in the M x Q hybrids. These mutations also probably arose from P element insertions. The implication is that insertion mutations occur infrequently in the M x Q hybrids, possibly because most of the P elements they carry are defective. In M x P hybrids, there is variation among loci with respect to P elements mutagenesis, indicating that P elements possess a degree of insertional specificity.     

An unstable nuclear gene in phycomyces

A gentic instability in Phycomyces is described that appears to be associated with a single nuclear gene, dar. The wild type is able to take up riboflavin and its toxic analogue, deaza-riboflavin, from nanomolar concentrations in the medium. The mutants are unable to take up riboflavin and are resistant to deaza-riboflavin. Forward and reverse mutation rates are estimated to be 4 x 10^-5 and 2 x 10^-3 per nuclear division. Independently arisen dar mutants do not complement in heterokaryons. The mutant alleles are almost completely recessive. The phenotype of spores is not determined cell-autonomously, but is strongly influenced by the allele ratio among the nuclei in the sporangium of origin.     

Evolutionary Relationships among Five Subspecies of MUS MUSCULUS Based on Restriction Enzyme Cleavage Patterns of Mitochondrial DNA

The intra- and intersubspecific genetic distances between five subspecies of Mus musculus were estimated from restriction enzyme cleavage patterns or maps of mitochondrial DNA (mtDNA). The European subspecies, M. m. domesticus and Asian subspecies, M. m. bactrianus, M. m. castaneus, M. m. molossinus and M. m. urbanus were examined. For each subspecies, except M. m. urbanus, at least two local races from widely separated localities were examined. Intrasubspecific heterogeneity was found in the mtDNA cleavage patterns of M. m. bactrianus and M. m. castaneus. M. m. molossinus and M. m. domesticus, however, revealed no intrasubspecific heterogeneity. Four of the subspecies had distinct cleavage patterns. The fifth, M. m. urbanus, had cleavage patterns identical to those of M. m. castaneus with several enzymes. Estimates of genetic distances between the various races and subspecies were obtained by comparing cleavage maps of the mtDNAs with various restriction enzymes. Nucleotide sequence divergences of mtDNA between local races were estimated to be less than 0.4% in M. m. bactrianus and less than 0.3% in M. m. castaneus. The times of divergence of both subspecies were calculated to be 0.1–0.2 x 10⁶ years. These values suggest that the intrasubspecific divergence began some 0.1–0.2 x 10⁶ years ago. On the other hand, nucleotide sequence divergences between European subspecies M. m. domesticus and Asian subspecies M. m. bactrianus and M. m. castaneus were 7.1% and 5.8%, respectively. The times of divergence were calculated to be 2.1–2.6 x 10⁶ years. Further, the nucleotide sequence divergence and time of divergence between M. m. molossinus and the other two Asian subspecies were comparable to those between M. m. molossinus and M. m. domesticus (about 3% and 1 x 10⁶ years, respectively). These results suggest that M. m. molossinus is situated in a unique evolutionary position among Asian subspecies.     

The genetic system controlling recombination in the silkworm

The nature of recombination modifiers was investigated in Bombyx mori lines selected for high (H) and low (L) recombination rates between the p^S and Y loci in chromosome 2. Since the mean recombination rates for the H x L and L x H F₁ crosses were approximately intermediate between those of high and low lines, the cytoplasmic maternal effect and difference in the activity of recombination modifiers between marked and unmarked second chromosomes were not detected. The H x (L x H), H x (H x L), L x (L x H) and L x (H x L) backcrosses indicated the presence of additive and dominance effects of marked and unmarked second chromosomes and the remaining chromosomes.——Recombination rates between the p^S and Y loci in chromosome 2 and half-nonrecombination rates between the pe and re loci in chromosome 5 of high and low lines indicated that these recombination modifiers caused changes in the recombination frequency between p^S and Y in chromosome 2, but not between pe and re in chromosome 5.——There were no differences in viability between individuals having the second chromosomes of the recombinant types [p^S +, p^Y (H); p^S +, + Y (L)] and those of the nonrecombinant types [p^S Y, p + (H); p^S Y, + + (L)] in both high and low lines. Mean recombination rates measured in cis [p^S Y/p + (H); p^S Y/+ + (L)] and trans [p^S +/p Y (H); p^S +/+ Y (L)] males were the same in the high but not in the low line. No segregation of a single recombination modifier was indicated by the distribution of recombination rates measured in trans males [p^S +/p Y (H); p^S +/+ Y (L)] of high and low lines. Accordingly, the recombination modifiers distributed on chromosome 2 in the heterozygous condition were not gross chromosomal aberrations, but polygenic factors in the low line.     

Odorant-binding proteins OBP57d and OBP57e affect taste perception and host-plant preference in Drosophila sechellia

Despite its morphological similarity to the other species in the Drosophila melanogaster species complex, D. sechellia has evolved distinct physiological and behavioral adaptations to its host plant Morinda citrifolia, commonly known as Tahitian Noni. The odor of the ripe fruit of M. citrifolia originates from hexanoic and octanoic acid. D. sechellia is attracted to these two fatty acids, whereas the other species in the complex are repelled. Here, using interspecies hybrids between D. melanogaster deficiency mutants and D. sechellia, we showed that the Odorant-binding protein 57e (Obp57e) gene is involved in the behavioral difference between the species. D. melanogaster knock-out flies for Obp57e and Obp57d showed altered behavioral responses to hexanoic acid and octanoic acid. Furthermore, the introduction of Obp57d and Obp57e from D. simulans and D. sechellia shifted the oviposition site preference of D. melanogaster Obp57d/e^KO flies to that of the original species, confirming the contribution of these genes to D. sechellia's specialization to M. citrifolia. Our finding of the genes involved in host-plant determination may lead to further understanding of mechanisms underlying taste perception, evolution of plant–herbivore interactions, and speciation.     

Genetic Effects of Acute Spermatogonial X-Irradiation of the Laboratory Rat

The genetic effects of one generation of spermatogonial X-irradiation in rats, by a single dose of 600r in one experiment and by a fractionated dose of 450r in another, were measured in three generations of their descendants. Estimates of dominant lethal mutation rates—(2 to 3) x 10 ^-4/gamete/r—from litter size differences between irradiated and nonirradiated stock were consistent with previous estimates from rats and mice. Similar consistency was found for estimates of sex-linked recessive mutation rates—(1 to 2) x 10^-4 chromosome/r—from male proportions within strains; however, when measured in crossbreds the proportion of males was higher in the irradiated than in the nonirradiated lines. This inconsistency in results is in keeping with the contradictory results reported for recessive sex-linked lethal mutation rates in mice. The effects used to estimate recessive lethal mutation rates which were unusually high—(2 to 14) x 10^-4/gamete/r—were not significant. Other factors that could have contributed to the observed effects are postulated.     

Requirement for Cell Dispersion Prior to Selection of Induced Azaguanine-Resistant Colonies of Chinese Hamster Cells

With V79 Chinese hamster cell cultures treated with a mutagen, the maximum frequency of colonies resistant to 8-azaguanine (AZG) was attained when the cells were dispersed after a suitable expression time before adding the selection medium. V79–4 cells were exposed to 500 µM MMS, 7 µM AFAA, or 10 µM MNNG and allowed to multiply before being reseeded at 4 x 10⁴ cells/60 mm dish and selected with 10 µg/ml AZG. Maximum frequencies of 4 x 10^-5, 4 x 10^-4, and 2.4 x 10^-3 were obtained about 100, 130, and 200 hrs after exposure to MMS, AFAA, and MNNG, respectively. The maximum frequencies following MMS or MNNG treatments were about 10-fold greater than those obtained when induction and selection of AZG-resistant colonies were performed in the same culture dish. The reseeding of treated cells eliminated the possibility of metabolic cooperation within mosaic colonies of wild-type and mutant cells and achieved expression of the induced changes before intercolony crossfeeding reduced the frequency of resistant colonies.—AZG-resistant colonies were selected in medium containing dialyzed fetal bovine serum, and the selection medium was replaced at least twice. Both serum dialysis and selection medium replacement were necessary for consistent achievement of background frequencies of resistant colonies near 10^-6. Reconstruction experiments with AZG-resistant V79 lines showed that the efficiency of recovery of resistant cells in the selection medium was constant over a range of 0–20 colonies observed/dish. A mixed population of V79 and AZG-resistant cells was also correctly analyzed by the procedure used in mutagenesis studies.     

Complete Mitochondrial Genome and Phylogeny of Pleistocene MammothMammuthus primigenius

Phylogenetic relationships between the extinct woolly mammoth(Mammuthus primigenius), and the Asian(Elephas maximus) and African savanna(Loxodonta africana) elephants remain unresolved. Here, we report the sequence of the complete mitochondrial genome (16,842 base pairs) of a woolly mammoth extracted from permafrost-preserved remains from the Pleistocene epoch—the oldest mitochondrial genome sequence determined to date. We demonstrate that well-preserved mitochondrial genome fragments, as long as ~1,600–1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests thatM. primigenius andE. maximus are sister species that diverged soon after their common ancestor split from theL. africana lineage. Low nucleotide diversity found between independently determined mitochondrial genomic sequences of woolly mammoths separated geographically and in time suggests that north-eastern Siberia was occupied by a relatively homogeneous population ofM. primigenius throughout the late Pleistocene.     

Asymmetrical reinforcement and Wolbachia infection in Drosophila

Reinforcement refers to the evolution of increased mating discrimination against heterospecific individuals in zones of geographic overlap and can be considered a final stage in the speciation process. One the factors that may affect reinforcement is the degree to which hybrid matings result in the permanent loss of genes from a species' gene pool. Matings between females of Drosophila subquinaria and males of D. recens result in high levels of offspring mortality, due to interspecific cytoplasmic incompatibility caused by Wolbachia infection of D. recens. Such hybrid inviability is not manifested in matings between D. recens females and D. subquinaria males. Here we ask whether the asymmetrical hybrid inviability is associated with a corresponding asymmetry in the level of reinforcement. The geographic ranges of D. recens and D. subquinaria were found to overlap across a broad belt of boreal forest in central Canada. Females of D. subquinaria from the zone of sympatry exhibit much stronger levels of discrimination against males of D. recens than do females from allopatric populations. In contrast, such reproductive character displacement is not evident in D. recens, consistent with the expected effects of unidirectional cytoplasmic incompatibility. Furthermore, there is substantial behavioral isolation within D. subquinaria, because females from populations sympatric with D. recens discriminate against allopatric conspecific males, whereas females from populations allopatric with D. recens show no discrimination against any conspecific males. Patterns of general genetic differentiation among populations are not consistent with patterns of behavioral discrimination, which suggests that the behavioral isolation within D. subquinaria results from selection against mating with Wolbachia-infected D. recens. Interspecific cytoplasmic incompatibility may contribute not only to post-mating isolation, an effect already widely recognized, but also to reinforcement, particularly in the uninfected species. The resulting reproductive character displacement not only increases behavioral isolation from the Wolbachia-infected species, but may also lead to behavioral isolation between populations of the uninfected species. Given the widespread occurrence of Wolbachia among insects, it thus appears that there are multiple ways by which these endosymbionts may directly and indirectly contribute to reproductive isolation and speciation.     

Intraspecific Variation of Ribosomal Gene Redundancy in ZEA MAYS

Ribosomal genes in eukaryotes are highly redundant. Considerable variation in the level of redundancy among species, especially in higher plants, has been reported; but except for deletion and duplication mutants, it is generally accepted that intraspecific variability in redundancy level is small. We have examined the level of redundancy in several lines of maize by DNA-rRNA saturation hybridization. The amount of nuclear DNA which hybridizes with rRNA in the ten lines examined varied from 0.24% to 0.50%. The number of rRNA genes per diploid genome thus ranges from 1.12 x 10⁴ to 2.32 x 10⁴. Results also indicate that the level of redundancy is genetically transmitted.     

Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting

The phylogenetic relationship of the now fully sequenced species Drosophila erecta and D. yakuba with respect to the D. melanogaster species complex has been a subject of controversy. All three possible groupings of the species have been reported in the past, though recent multi-gene studies suggest that D. erecta and D. yakuba are sister species. Using the whole genomes of each of these species as well as the four other fully sequenced species in the subgenus Sophophora, we set out to investigate the placement of D. erecta and D. yakuba in the D. melanogaster species group and to understand the cause of the past incongruence. Though we find that the phylogeny grouping D. erecta and D. yakuba together is the best supported, we also find widespread incongruence in nucleotide and amino acid substitutions, insertions and deletions, and gene trees. The time inferred to span the two key speciation events is short enough that under the coalescent model, the incongruence could be the result of incomplete lineage sorting. Consistent with the lineage-sorting hypothesis, substitutions supporting the same tree were spatially clustered. Support for the different trees was found to be linked to recombination such that adjacent genes support the same tree most often in regions of low recombination and substitutions supporting the same tree are most enriched roughly on the same scale as linkage disequilibrium, also consistent with lineage sorting. The incongruence was found to be statistically significant and robust to model and species choice. No systematic biases were found. We conclude that phylogenetic incongruence in the D. melanogaster species complex is the result, at least in part, of incomplete lineage sorting. Incomplete lineage sorting will likely cause phylogenetic incongruence in many comparative genomics datasets. Methods to infer the correct species tree, the history of every base in the genome, and comparative methods that control for and/or utilize this information will be valuable advancements for the field of comparative genomics.     

Killer Phenomenon in USTILAGO MAYDIS: The Organization of the Viral Genome

The double-stranded RNA content, the production of inactive killer protein, and the presence of virus-like particles were examined in induced nonkiller mutants and nonkiller progeny from a cross between a killer strain and a sensitive strain. A correlation between the loss of the 0.7 x 10⁶ daltons dsRNA of the Ustilago maydis P6 virus and the lack of synthesis of the killer protein was established. In vitro and in vivo complementation between nonkiller strains provide additional support for the suggestion that the 0.7 x 10⁶ daltons dsRNA is related to the killer function. The coding capacity of the various species of dsRNA is discussed in relation to their possible function.     

Genetic Map of the Lactose Repressor Gene (i) of ESCHERICHIA COLI

39 tonB i^- deletions were used to map 57 independently isolated i gene mutants. Methods selective for i⁺ recombinants from various types of i mutants are described. i⁺ recombination frequencies of 6 x 10^-6 to 6 x 10^-7 can be detected in the different selective systems. Twenty i^s mutations and 12 i^-d mutations map in distinct but different regions of the gene. i^-_sus mutations are scattered over the gene.     

The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics

The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same chromosome number and genome sizes, and they occupy the same ecological niche. To explore the basis for this striking conservation of structure and function, we have sequenced the C. briggsae genome to a high-quality draft stage and compared it to the finished C. elegans sequence. We predict approximately 19,500 protein-coding genes in the C. briggsae genome, roughly the same as in C. elegans. Of these, 12,200 have clear C. elegans orthologs, a further 6,500 have one or more clearly detectable C. elegans homologs, and approximately 800 C. briggsae genes have no detectable matches in C. elegans. Almost all of the noncoding RNAs (ncRNAs) known are shared between the two species. The two genomes exhibit extensive colinearity, and the rate of divergence appears to be higher in the chromosomal arms than in the centers. Operons, a distinctive feature of C. elegans, are highly conserved in C. briggsae, with the arrangement of genes being preserved in 96% of cases. The difference in size between the C. briggsae (estimated at approximately 104 Mbp) and C. elegans (100.3 Mbp) genomes is almost entirely due to repetitive sequence, which accounts for 22.4% of the C. briggsae genome in contrast to 16.5% of the C. elegans genome. Few, if any, repeat families are shared, suggesting that most were acquired after the two species diverged or are undergoing rapid evolution. Coclustering the C. elegans and C. briggsae proteins reveals 2,169 protein families of two or more members. Most of these are shared between the two species, but some appear to be expanding or contracting, and there seem to be as many as several hundred novel C. briggsae gene families. The C. briggsae draft sequence will greatly improve the annotation of the C. elegans genome. Based on similarity to C. briggsae, we found strong evidence for 1,300 new C. elegans genes. In addition, comparisons of the two genomes will help to understand the evolutionary forces that mold nematode genomes.     

Adaptive gene expression divergence inferred from population genomics

Detailed studies of individual genes have shown that gene expression divergence often results from adaptive evolution of regulatory sequence. Genome-wide analyses, however, have yet to unite patterns of gene expression with polymorphism and divergence to infer population genetic mechanisms underlying expression evolution. Here, we combined genomic expression data—analyzed in a phylogenetic context—with whole genome light-shotgun sequence data from six Drosophila simulans lines and reference sequences from D. melanogaster and D. yakuba. These data allowed us to use molecular population genetics to test for neutral versus adaptive gene expression divergence on a genomic scale. We identified recent and recurrent adaptive evolution along the D. simulans lineage by contrasting sequence polymorphism within D. simulans to divergence from D. melanogaster and D. yakuba. Genes that evolved higher levels of expression in D. simulans have experienced adaptive evolution of the associated 3′ flanking and amino acid sequence. Concomitantly, these genes are also decelerating in their rates of protein evolution, which is in agreement with the finding that highly expressed genes evolve slowly. Interestingly, adaptive evolution in 5′ cis-regulatory regions did not correspond strongly with expression evolution. Our results provide a genomic view of the intimate link between selection acting on a phenotype and associated genic evolution.     

Selective Recombination System in Bombyx mori. I. Chromosome Specificity of the Modification Effect

The effect of modifiers on recombination frequency between Ze and lem loci on chromosome 3 to elucidate the chromosome specificity of modification and the distribution of modifiers using Bombyx mori lines selected for high (H) and low (L) recombination rates between the p^S and Y loci in chromosome 2 was investigated. By crossing to the Z (Ze lem/++) line, the recombination rate between the p^S and Y loci in chromosome 2 was decreased from 28.18 to 23.33 in the H line and was increased from 4.92 to 16.05 in the L line. On the other hand, the recombination rate between the Ze and lem loci in chromosome 3 was increased from 16.21 to 20.21 in the Z line by crossing to the H line, but also increased to 19.02 by crossing to the L line. The significant correlation observed between the transformed recombination rates of chromosomes 2 and 3 in the (Z x L) x L backcross indicated that there were common factors modifying recombination frequency in chromosomes 2 and 3 or different factors linked to the same chromosomes. In the family of L x [(Z x L) x L] backcross, the distribution of transformed recombination rates indicated that there were several factors in the remaining chromosomes which were modifying recombination frequency in chromosome 2 but not in chromosome 3. It was also indicated that these factors were linked to different chromosomes than are the factors modifying recombination frequency in chromosome 3. In order to interpret these results, one genetic system model controlling recombination that consists of general and local recombination modifiers was proposed. The evolution of dynamic genetic systems that would effectively reduce recombinational load without reducing the advantage of recombination was discussed.