Chloroplast and Mitochondrial DNA Variation in HORDEUM VULGARE and HORDEUM SPONTANEUM

A survey of restriction fragment polymorphism in Hordeum vulgare and Hordeum spontaneum was made using 17 and 16 hexanucleotide restriction endonucleases on chloroplast (cp) and mitochondrial (mt) DNA, respectively. The plant accessions originated from various places throughout the Fertile Cresent and Mediterranean. The types of changes in cpDNA consisted of nucleotide substitutions and insertions and deletions on the order of 100 base pairs. In contrast, mtDNA has most likely undergone larger insertions and deletions of up to 20 kilobase pairs in addition to rearrangements. Grouping of mtDNA fragment data showed that in some cases geographical affinities existed between the two species, whereas in others there were no clear affinities. Nucleotide diversity estimates derived from the restriction fragment data were used in a number of comparisons of variability. Comparisons of overall mtDNA variability (nucleotide diversity = 9.68 x 10^-4) with cpDNA variability (nucleotide diversity = 6.38 x 10^-4 ) indicated that the former are somewhat more variable. Furthermore, there was no indication that the wild H. spontaneum (cpDNA diversity = 5.57 x 10^-4; mtDNA diversity = 6.04 x 10 ^-4) was more variable than the land races of H. vulgare (cpDNA diversity = 5.88 x 10^-4; mtDNA diversity = 9.79 x 10^-4). In fact, on the basis of mtDNA diversity, H. vulgare was the more variable species. Comparison of organelle nucleotide diversity estimates with an estimate of nuclear nucleotide diversity derived from existing isozyme data provided evidence that both organelle genomes are evolving at a slower rate than the nuclear genome.     

Location of a contact zone between Mus musculus domesticus and M. m. domesticus with M. m. castaneus mtDNA in southern New Zealand

The house mouse, Mus musculus, was first introduced into New Zealand in significant numbers in the early to mid nineteenth century, with genomic components from different sources of the three subspecies M. m. domesticus, M. m. musculus and M. m. castaneus. M. m. domesticus is now widely distributed in New Zealand, with genomic and morphological evidence of M. m. musculus in a few scattered locations. M. m. domesticus/M. m. castaneus hybrids are dominant in the southern third of the South Island. We anticipated that there should be a definable southern contact zone between pure M. m. domesticus and M. m. domesticus/M. m. castaneus hybrids. We tested this hypothesis by screening 170 DNA samples from mice collected in the southern South Island, using a PCR technique which rapidly distinguishes the mitochondrial genomes of the three subspecies.All mice sampled from in or north of Lincoln (43.63° S) had only M. m. domesticus mtDNA, whereas all those from or further south than Hook (44.68° S) had M. m. castaneus mtDNA. Between the two sites, mice carrying mtDNA of both subspecies were found, sometimes in the same building. On present data, this contact zone extends approximately 50 km north to south and some 30 km inland. Classical tests with three nuclear DNA markers confirmed earlier work showing that the nuclear genomes of all mice appeared to be predominantly domesticus-like.We conclude that if purebred M. m. castaneus mice did originally reach New Zealand, extensive backcrossing with M. m. domesticus has made the castaneus nuclear genome virtually undetectable with the tests that we employ.     

The musculus-type Y Chromosome of the laboratory mouse is of Asian origin

Mus musculus domesticus, M.m. bactrianus, M. m. musculus, M.m. castaneus, and M.m. molossinus wild mice were investigated for polymorphisms of the Y Chromosome (Chr) genes Zinc finger-Y (Zfy) and Sex-determining region-Y (Sry). Zfy divided the Y Chrs of these mice into domesticus- (domesticus) and musculus-types (musculus, castaneus, molossinus). M.m. bactrianus specimens had both Y Chrs, possibly owing to the introgression of a musculus-type Y into this population. Sry identified a subpopulation of musculus-type Y chromosomes. This subpopulation, designated the molossinus-type, was found in M.m. molossinus, a M. musculus subspecies specimen from northern China (Changchun), and laboratory mice. The cumulative data suggest that M.m. musculus of northern China and Korea are subpopulation distinct from M.m. musculus of Europe and central China and that this subpopulation invaded Japan, giving rise to M.m. molossinus. Furthermore, the data suggest that the musculus-type Y of the laboratory mouse originated from this subpopulation, corroborating early historical record reporting that Chinese and Japanese mice that were imported into Europe for the pet trade contributed to the genome of the laboratory mouse.     

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.     

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.     

Detection of recombinant haplotypes in wild mice (Mus musculus) provides new insights into the origin of Japanese mice

Japanese house mice (Mus musculus molossinus) are thought to be a hybrid lineage derived from two prehistoric immigrants, the subspecies M. m. musculus of northern Eurasia and M. m. castaneus of South Asia. Mice of the western European subspecies M. m. domesticus have been detected in Japanese ports and airports only. We examined haplotype structuring of a 200 kb stretch on chromosome 8 for 59 mice from throughout Eurasia, determining short segments (≈ 370–600 bp) of eight nuclear genes (Fanca, Spire2, Tcf25, Mc1r, Tubb3, Def8, Afg3l1 and Dbndd1) which are intermittently arranged in this order. Where possible we identified the subspecies origin for individual gene alleles and then designated haplotypes for concatenated alleles. We recovered 11 haplotypes among 19 Japanese mice examined, identified either as ‘intact’ haplotypes derived from the subspecies musculus (57.9%), domesticus (7.9%), and castaneus (2.6%), or as ‘recombinant’ haplotypes (31.6%). We also detected recombinant haplotypes unique to Sakhalin. The complex nature of the recombinant haplotypes suggests ancient introduction of all three subspecies components into the peripheral part of Eurasia or complicated genomic admixture before the movement from source areas. ‘Intact’domesticus and castaneus haplotypes in other Japanese wild mice imply ongoing stowaway introductions. The method has general utility for assessing the history of genetic admixture and for disclosing ongoing genetic contamination.     

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.     

Serological survey of complement factor H in common laboratory and wild mice: a new third allotype

Antigenic specificities of complement factor H from mice were studied serologically. In addition to previously reported allotypes, referred to as H.1 and H.2, a new allotype of complement factor H, H.3, was identified in the BFM/2Ms strain derived from European wild mice. Using three different alloantisera raised against the various mouse factor H allotype, a serological survey of the common laboratory strains and wild-derived strains of Mus musculus and its relatives, Mus spretus, Mus spretoides, and Mus spicilegus was carried out. All of the common laboratory strains examined in this survey had the H.1 allotype except for STR/N which had H.2. The geographical distributions of factor H allotypes in M. musculus were specific to the subspecies. Mice derived from Mus musculus domesticus and Mus musculus castaneus had the H.1 allotype. Mice derived from M. m. musculus, Mus musculus bactrianus, and Mus musculus molossinus had the H.2 allotype. Only BFM/2Ms and BFM/1Mpl strains derived from M. m. domesticus had the novel H.3 allotype. Sera of mice from strains derived from M. spretoides and M. spicilegus cross-reacted with H.2-specific antiserum, and those from M. spretus cross-reacted with H.3-specific antiserum.     

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.     

The telocentric tandem repeat at the p-arm is not conserved in Mus musculus subspecies

Mouse chromosomes, with the exception of the Y chromosome, are telocentric. The telomere at the p-arm is separated from the centromere by the tL1 sequence and TLC tandem repeats. A previous report showed that the TLC array was also conserved in other strains of the subgenus Mus. These results suggest that the TLC arrays promote the stable evolutionary maintenance of a telocentric karyotype in the subgenus Mus. In this study, we investigated the degree of conservation of TLC arrays among a variety of wild-derived inbred strains, all of which are descendants of wild mice captured in several areas of the world. Genomic PCR analysis indicates that the sequential order of telomere-tL1 is highly conserved in all strains, whereas tL1-TLC is not. Next, Southern blot analysis of DNAs isolated from a panel of mouse subspecies showed both Mus musculus domesticus and Mus musculus castaneus subspecies possess TLC arrays. Unexpectedly, this repeat appears to be lost in almost all Mus musculus musculus and Mus musculus molossinus subspecies, which show a clear geographic divide. These results indicate that either other unknown sequences were replaced by the TLC repeat or almost all M. m. musculus and M. m. molossinus subspecies do not have any sequence between the telomere and minor satellites. Our observation suggests that the TLC array might be evolutionarily unstable and not essential for murine chromosomal conformation. This is the first example of the subspecies-specific large genome alterations in mice.     

Heterogeneity of Maize Cytoplasmic Genomes among Male-Sterile Cytoplasms

Maize mitochondrial and chloroplast DNA's were prepared from normal (fertile) lines or single crosses and from members of the T, C, and S groups of male-sterile cytoplasms. Restriction endonucleases HindIII, BamI, EcoRI, and SalI were used to restrict the DNA, and the resultant fragments were electrophoresed in agarose gels. The results show that the N (fertile), T, C, and S cytoplasms each contained distinct mitochondrial DNA (mtDNA). These distinctive patterns were unaffected by nuclear genotype. No evidence of paternal inheritance of mtDNA was observed. Chloroplast DNA (ctDNA) from the N, C, and T cytoplasms was indistinguishable by HindIII, SalI, or EcoRI endonuclease digestion. The S cytoplasm ctDNA, however, was slightly different from that of other cytoplasms, as indicated by a slight displacement of one band in HindIII digests. The molecular weight of maize ctDNA was estimated to be as high as 88 x 10⁶. Estimates of the minimum molecular weight of maize mtDNA ranged from 116–131 x 10⁶, but the patterns were to complex for an unambiguous determination. Based on HindIII data, a comparison of the molecular weight of mtDNA bands common to the N, T. C, and S cytoplasms suggests that C cytoplasm most closely resembles N cytoplasm. The T and S sources are more divergent from the C and N cytoplasms. These results indicate a possible gradation of relatedness among male-sterile cytoplasms. The marked variation in mtDNA, with apparently less variation in ctDNA, represents circumstantial, but compelling, evidence that mtDNA may be involved in the male sterility and disease susceptibility traits in maize.     

Functional divergence caused by ancient positive selection of a Drosophila hybrid incompatibility locus

Interspecific hybrid lethality and sterility are a consequence of divergent evolution between species and serve to maintain the discrete identities of species. The evolution of hybrid incompatibilities has been described in widely accepted models by Dobzhansky and Muller where lineage-specific functional divergence is the essential characteristic of hybrid incompatibility genes. Experimentally tractable models are required to identify and test candidate hybrid incompatibility genes. Several Drosophila melanogaster genes involved in hybrid incompatibility have been identified but none has yet been shown to have functionally diverged in accordance with the Dobzhansky-Muller model. By introducing transgenic copies of the X-linked Hybrid male rescue (Hmr) gene into D. melanogaster from its sibling species D. simulans and D. mauritiana, we demonstrate that Hmr has functionally diverged to cause F1 hybrid incompatibility between these species. Consistent with the Dobzhansky-Muller model, we find that Hmr has diverged extensively in the D. melanogaster lineage, but we also find extensive divergence in the sibling-species lineage. Together, these findings implicate over 13% of the amino acids encoded by Hmr as candidates for causing hybrid incompatibility. The exceptional level of divergence at Hmr cannot be explained by neutral processes because we use phylogenetic methods and population genetic analyses to show that the elevated amino-acid divergence in both lineages is due to positive selection in the distant past—at least one million generations ago. Our findings suggest that multiple substitutions driven by natural selection may be a general phenomenon required to generate hybrid incompatibility alleles.     

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.     

Incipient Genome Differentiation in Gossypium. II. Comparison of 12 Chromosomes in G. HIRSUTUM, G. MUSTELINUM and G. TOMENTOSUM Using Heterozygous Translocations

Eight homozygous translocation lines (TT) of G. hirsutum marking 3 chromosomes of the A genome and 9 chromosomes of the D genome were crossed with G. hirsutum, G. mustelinum and G. tomentosum, all homozygous for the standard end arrangements (tt). Chiasma frequencies in the G. hirsutum Tt controls were compared with those in the G. hirsutum x G. mustelinum and the G. hirsutum x G. tomentosum Tt hybrids. Both nucleus-wide and region-specific chiasma frequencies were compared.—Some genome differentiation appears to have arisen between G. hirsutum and G. mustelinum. The G. hirsutum x G. mustelinum hybrids had a 1.8 to 1.9% reduction in the nucleus-wide chiasma frequency. Four of the eight TT lines showed a 3.4 to 10.5% reduction in chiasmata in the hybrid translocation quadrivalents, suggesting that chromosomes 1, 21, 23 and 24 may have undergone localized genome differentiation. The two species may differ naturally in the end arrangement of two chromosomes, since a quadrivalent not due to experimentally introduced translocations was observed in 13% of the PMC's of two G. hirsutum x G. mustelinum hybrids.—Very little genome differentiation has occurred between G. hirsutum and G. tomentosum. In the G. hirsutum x G. tomentosum hybrids, the nucleus-wide estimates showed only a very small (0.1 to 0.2%), though statistically significant, lowering of the chiasma frequency, and there was no reduction in chiasma frequency in the more sensitive readings for specific translocation quadrivalents.     

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.     

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.     

Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans

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. Here we present a population genetic analysis of Drosophila simulans based on whole-genome shotgun sequencing of multiple inbred lines and comparison of the resulting data to genome assemblies of the closely related species, D. melanogaster and D. yakuba. We discovered previously unknown, large-scale fluctuations of polymorphism and divergence along chromosome arms, and significantly less polymorphism and faster divergence on the X chromosome. We generated a comprehensive list of functional elements in the D. simulans genome influenced by adaptive evolution. Finally, we characterized genomic patterns of base composition for coding and noncoding sequence. These results suggest several new hypotheses regarding the genetic and biological mechanisms controlling polymorphism and divergence across the Drosophila genome, and provide a rich resource for the investigation of adaptive evolution and functional variation in D. simulans.     

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.     

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.