Differences in gene regulation in a tephritid model of prezygotic reproductive isolation.

The two tephritid fruit fly pests, Bactrocera tryoni and Bactrocera neohumeralis, are unusually well suited to the study of the genetics of reproductive isolating mechanisms. Sequence difference between the species is no greater than between a pair of conspecific Drosophila melanogaster populations. The two species exist in close sympatry, yet do not hybridize in the field, apparently kept separate by a strong premating isolation mechanism involving the time of day at which mating occurs. This spurred us to search for key genes for which time of day expression is regulated differently between the species. Using replicated, quantitative transcriptomes from head tissues of males of the two species, sampled in the day and night, we identified 141 transcripts whose abundance showed a significant interaction between species and time of day, indicating a difference in gene regulation. The brain transcripts showing this interaction were enriched for genes with a neurone function and 90% of these were more abundant at night than day in B. tryoni. Features of the expression patterns suggest that there may be a difference in the regulation of sleep-wake cycles between the species. In particular several genes, which in D. melanogaster are expressed in circadian pacemaker cells, are promising candidates to further explore the genetic differentiation involved in this prezygotic reproductive isolation mechanism.

Genetic consequences of domestication and mass rearing of pest fruit fly Bactrocera tryoni (Diptera: Tephritidae).

Tephritid fruit flies, an important pest of horticulture worldwide, are increasingly targeted for control or eradication by large-scale releases of sterile flies of the same species. For each species treated, strains must be domesticated for mass rearing to provide sufficiently large numbers of individuals for releases. Increases in productivity of domesticated tephritid strains are well documented, but there have been few systematic studies of the genetic consequences of domestication in tephritids. Here, we used nine DNA microsatellite markers to monitor changes in genetic diversity during the early generations of domestication in replicated lines of the fruit fly Bactrocera tryoni (Froggatt) (Diptera: Tephritidae). The observed changes in heterozygosity and allelic richness were compared with the expected changes in heterozygosity generated by a stochastic simulation including genetic drift but not selection. The results showed that repeatable genetic bottlenecks occur in the early generations and that selection occurs in the later generations. Furthermore, using the same simulation, we show that there is inadvertent selection for increased productivity for the entire life on a mass-rearing colony, in addition to intentional selection for increased productivity. That additional selection results from the common practice of establishing the next generation of the breeding colony from a small proportion of one day's pupae collection (the pupal raffle). That selection occurs during all generations and acts only on fecundity variation. Practical methods to counter that unavoidable loss of genetic diversity during the domestication process in B. tryoni are discussed.

Pest fruit fly (Diptera: Tephritidae) in northwestern Australia: one species or two?

Since 1985, a new and serious fruit fly pest has been reported in northwestern Australia. It has been unclear whether this pest was the supposedly benign endemic species, Bactrocera aquilonis, or a recent introduction of the morphologically near-identical Queensland fruit fly, B. tryoni. B. tryoni is a major pest throughout eastern Australia but is isolated from the northwest region by an arid zone. In the present study, we sought to clarify the species status of these new pests using an extensive DNA microsatellite survey across the entire northwest region of Australia. Population differentiation tests and clustering analyses revealed a high degree of homogeneity within the northwest samples, suggesting that just one species is present in the region. That northwestern population showed minimal genetic differentiation from B. tryoni from Queensland (FST=0.015). Since 2000, new outbreaks of this pest fruit fly have occurred to the west of the region, and clustering analysis suggested recurrent migration from the northwest region rather than Queensland. Mitochondrial DNA sequencing also showed no evidence for the existence of a distinct species in the northwest region. We conclude that the new pest fruit fly in the northwest is the endemic population of B. aquilonis but that there is no genetic evidence supporting the separation of B. aquilonis and B. tryoni as distinct species.

Correlation measures for linkage disequilibrium within and between populations.

Correlation statistics can be used to measure the amount of linkage disequilibrium (LD) between two loci in subdivided populations. Within populations, the square of the correlation of gene frequencies, r2, is a convenient measure of LD. Between populations, the statistic rirj, for populations i and j, measures the relatedness of LD. Recurrence relationships for these two parameters are derived for the island model of population subdivision, under the assumptions of the linked identity-by-descent (LIBD) model in which correlation measures are equated to probability measures. The recurrence relationships closely predict the build-up of r2 and rirj following population subdivision in computer simulations. The LIBD model predicts that a steady state will be reached with r2 equal to 1/[1+4Nec(1+(k-1)rho)], where k is the number of island populations, Ne is the effective local population (island) size, and rho measures the ratio of migration (m) to recombination (c) and is equal to m/[c(k-1)+m]. For low values of m/c, rho=0, and E(r2) is equal to 1/(1+4Nec). For high values of m/c, rho=1, and E(r2) is equal to 1/(1+4kNec). The value of rirj following separation eventually settles down to a steady state whose expectation, E(rirj), is equal to E(r2) multiplied by rho. Equations predicting the change in rirj values are applied to the separation of African (Yoruba - YRI) and non-African (European - CEU) populations, using data from Hapmap. The primary data lead to an estimate of separation time of less than 1000 generations if there has been no migration, which is around one-third of minimum current estimates. Ancient rather than recent migration can explain the form of the data.

Properties of re-arranged P elements in Drosophila melanogaster.

P elements, both complete and incomplete, contain a left and right end, normally depicted as pointing away from each other. Here, we examine the properties of P elements that may be described as 're-arranged elements' or 'inside-out elements', containing inverted ends. Two such structures exist, having either ends pointing towards each other, 'head-to-head or H-H', or ends pointing in the same direction 'head-to-tail or H-T'. We show that both structures are unstable in the presence of P element transposase. For the H-H element there is a high frequency of deletion of the intervening material and almost exact rejoining of element ends with the 4 bp CATG palindromic end sequence shared by the two element ends. This result is predicted by the Beall and Rio model of P element excision. For the H-T element there is a high frequency of exact excision of the entire inverted right-end, a result again predicted by the Beall and Rio model. Both structures lead to recombination in the way expected from a normal element. The rates of recombination are, however, much lower than might be expected from the organization of ends, a result that can be explained in terms of the low likelihood of insertion into a chromosomal region lacking another P element end. We also investigate the properties of combinations of re-arranged and normal elements, and show that there is a directionality property when left and right ends are combined in trans that can be explained in terms of strand repair.

Repair of P element ends following hybrid element excision leads to recombination in Drosophila melanogaster.

P elements are thought to replicate themselves starting with the association of the left and right ends, followed by a cut-copy-paste process. An abnormal form of this process has been shown to occur when the associated left and right ends come from sister elements rather than from the same element, leading to formation of a 'hybrid element.' These ends can insert nearby in the genome to produce recombination, with associated structural changes. We have previously increased the frequency of such 'hybrid element insertion' by combining end-deleted elements in trans in a genotype with a left-end on one chromosome and a right-end on the homologous chromosome. Although many recombinants produced by this genotype have structural changes expected with insertion, nearly 50% of the predicted insertional recombinants contain no structural change. We present evidence using RFLP markers closely linked to the end-deleted elements that in these cases the P element ends dissociate before insertion, and are subsequently ligated together following a process analogous to synthesis-dependent strand annealing. The results suggest that broken ends containing P elements are resolved by the same repair process as ends not containing P elements, and that such repair from hybrid element events may occur in the majority of cases.

Genetic and molecular markers of the Queensland fruit fly, Bactrocera tryoni.

Twenty-six microsatellite markers, along with two restriction fragment length polymorphism (RFLP) markers and three morphological markers, have been mapped to five linkage groups, corresponding to the five autosomes of the Queensland fruit fly, Bactrocera tryoni. All these molecular and genetic markers were genotyped in three-generation pedigrees. Eight molecular markers were also localized to the salivary gland polytene chromosomes by in situ hybridization. This provides a substantial starting point for an integrated genetic and physical map of B. tryoni.

Inferring modes of colonization for pest species using heterozygosity comparisons and a shared-allele test.

Long-range dispersal of a species may involve either a single long-distance movement from a core population or spreading via unobserved intermediate populations. Where the new populations originate as small propagules, genetic drift may be extreme and gene frequency or assignment methods may not prove useful in determining the relation between the core population and outbreak samples. We describe computationally simple resampling methods for use in this situation to distinguish between the different modes of dispersal. First, estimates of heterozygosity can be used to test for direct sampling from the core population and to estimate the effective size of intermediate populations. Second, a test of sharing of alleles, particularly rare alleles, can show whether outbreaks are related to each other rather than arriving as independent samples from the core population. The shared-allele statistic also serves as a genetic distance measure that is appropriate for small samples. These methods were applied to data on a fruit fly pest species, Bactrocera tryoni, which is quarantined from some horticultural areas in Australia. We concluded that the outbreaks in the quarantine zone came from a heterogeneous set of genetically differentiated populations, possibly ones that overwinter in the vicinity of the quarantine zone.

Towards a male-only release system for SIT with the Queensland fruit fly, Bactrocera tryoni, using a genetic sexing strain with a temperature-sensitive lethal mutation.

Flies that are homozygous for the recessive autosomal mutation bent wings have a limited ability to fly and are less tolerant of high temperatures than normal flies in both the egg and puparial stages. The differences between the mutant and normal flies were found sufficient to be the basis of a genetic sexing strain. Genetic sexing strains were created using translocations of the autosome bearing the wild-type allele of bent wings (chromosome 2) to the Y chromosome, and crossing male flies carrying the translocation to mutant bent wings females. In the resulting strain, the females were homozygous for the bent wings mutation and the males were phenotypically normal for wing characters. Several translocations were recovered after irradiation, but only one translocation involving chromosome 2 was both stable and expressed in a stock that was vigorous enough for long-term viability. Unfortunately, all stocks containing the translocation showed high levels of temperature-dependent lethality, including, inexplicably, both males and females. Translocation stocks showing this effect included bent wings, another second chromosome mutation, white marks, and an otherwise normal stock. This phenomenon is probably rare, as it has not been reported before. It is likely that bent wings could be suitably used with another translocation.

Microsatellite analysis of the Queensland fruit fly Bactrocera tryoni (Diptera: Tephritidae) indicates spatial structuring: implications for population control.

The population structure of a tephritid pest species, the Queensland fruit fly Bactrocera tryoni (Froggatt), has been analysed over a five year period (1994-1998), using six microsatellites. Adult fly samples were collected to cover most regions of eastern and central Australia where the flies are regularly found. Tests for heterogeneity indicated that flies within geographically defined regions were homogeneous. The samples were allocated into five regions, including one very large region, Queensland, which encompasses that portion of the fly's range where breeding can occur year-round. With one exception, the collections from different regions were homogeneous between years, showing a fairly static distribution of the species. However, differences between regions were highly significant. The one case of a change in frequency between years indicated a gradual replacement of flies in a marginal region by flies from the main part of the range. The finding of stability in the distribution of a highly mobile insect is of interest, potentially also for other species which have expanded beyond their native range. It is argued that a contributing reason for this stability may be adaptation to different climatic regimes, and that strategies for control based on this hypothesis afford a reasonable chance of success.

The IEC star-mode fusion neutron source for NAA--status and next-step designs

Based on research at the University of Illinois, a commercial neutron source has been developed by Daimler Chrysler Aerospace using a small grided-type Inertial Electrostatic Confinement (IEC) plasma device (Miley and Sved, 1997) This device employs a unique "Star-Mode" deuterium plasma discharge to create ion-beam driven fusion reactions in a plasma target (Miley et al., 1997a, 1997b, 1997c; Miley, 1999). As such, it represents the first commercial application of a confined fusing plasma. The Star-Mode discharge is an essential feature of this device since it minimizes ion-grid collisions and also allows tight beam focussing.

Close genetic similarity between two sympatric species of tephritid fruit fly reproductively isolated by mating time.

Two sibling species of tephritid fruit fly, Bactrocera tryoni and B. neohumeralis, occur sympatrically throughout the range of B. neohumeralis in Australia. Isolation between the two species appears to be maintained by a difference in mating time: B. tryoni mates at dusk, whereas B. neohumeralis mates during the middle of the day. A morphological difference in humeral callus color also distinguishes the two species. Despite clear phenotypic evidence that B. tryoni and B. neohumeralis are distinct species, genetic differentiation as measured by four markers--nuclear DNA sequences from the white gene and the ribosomal internal transcribed spacer (ITS2), and mitochondrial DNA sequences from the cytochrome b (cytb) and cytochrome oxidase subunit II (COII) genes--is very small. Minor fixed differences occur in the ITS2 sequence, however, in all other cases the two species exhibit a high level of shared polymorphic variation. The close genetic similarity suggests either that speciation has occurred very rapidly and recently in the absence of any mitochondrial DNA sorting or that the sharing of polymorphisms is due to hybridization or introgression. A third species within the tryoni complex, B. aquilonis, is geographically isolated. Bactrocera aquilonis is also genetically very similar, but in this case there is clear differentiation for the mitochondrial loci. The three species form a group of considerable interest for investigation of speciation mechanisms.

Polymorphic microsatellite markers for population analysis of a tephritid pest species, Bactrocera tryoni.

To obtain a set of microsatellite markers for the Queensland fruit fly Bactrocera tryoni, a genomic library was screened with a number of simple repeat oligonucleotide probes. Sequencing recovered 22 repeat loci. The microsatellite sequences were short, with repeat numbers ranging from five to 11. Of these, 16 polymerase chain reaction (PCR) primer sets yielded amplifiable products, which were tested on 53 flies from five widely separated sites. All loci showed polymorphism in the population sample, with the number of alleles ranging from two to 16. Several dinucleotide repeats showed alleles separated by single-base differences and multiple steps, suggesting a mutation process more complex than the stepwise mutation model.

Mitotic and polytene chromosome analyses in the Queensland fruit fly, Bactrocera tryoni (Diptera: Tephritidae).

The Queensland fruit fly, Bactrocera tryoni, like the Mediterranean fruit fly, Ceratitis capitata, has a diploid complement of 12 chromosomes, including five pairs of autosomes and a XX/XY sex chromosome pair. Characteristic features of each chromosome are described. Chromosomal homology between B. tryoni and C. capitata has been determined by comparing chromosome banding pattern and in situ hybridisation of cloned genes to polytene chromosomes. Although the evidence indicates that a number of chromosomal inversions have occurred since the separation of the two species, synteny of the chromosomes appears to have been maintained.

Structure and associated mutational effects of the cysteine proteinase (CP1) gene of Drosophila melanogaster.

The complete structure of the cysteine proteinase (CP1) gene reveals two large 5' introns as well as a small third intron. Deletion studies have shown that null mutations for the locus are female sterile with partial male sterility as well as wing and pigmentation effects. Null alleles can be produced by either deletions to the left or deletions to the right of a P element insertion in the long second intron of the gene. A nearby phenylalanyl tRNA synthetase gene (Pts) was also identified.

Mitochondrial control-region sequence variation in aboriginal Australians.

The mitochondrial D-loop hypervariable segment 1 (mt HVS1) between nucleotides 15997 and 16377 has been examined in aboriginal Australian people from the Darling River region of New South Wales (riverine) and from Yuendumu in central Australia (desert). Forty-seven unique HVS1 types were identified, varying at 49 nucleotide positions. Pairwise analysis by calculation of BEPPI (between population proportion index) reveals statistically significant structure in the populations, although some identical HVS1 types are seen in the two contrasting regions. mt HVS1 types may reflect more-ancient distributions than do linguistic diversity and other culturally distinguishing attributes. Comparison with sequences from five published global studies reveals that these Australians demonstrate greatest divergence from some Africans, least from Papua New Guinea highlanders, and only slightly more from some Pacific groups (Indonesian, Asian, Samoan, and coastal Papua New Guinea), although the HVS1 types vary at different nucleotide sites. Construction of a median network, displaying three main groups, suggests that several hypervariable nucleotide sites within the HVS1 are likely to have undergone mutation independently, making phylogenetic comparison with global samples by conventional methods difficult. Specific nucleotide-site variants are major separators in median networks constructed from Australian HVS1 types alone and for one global selection. The distribution of these, requiring extended study, suggests that they may be signatures of different groups of prehistoric colonizers into Australia, for which the time of colonization remains elusive.

The accumulation of P-element-induced recombinants in the germline of male Drosophila melanogaster.

P-element-induced recombination in Drosophila melanogaster occurs premeiotically. Recombinants are therefore expected to accumulate in the stem cells of the germline of P-element-carrying males. We show that both the recombination frequency and the incidence of "clustering" increase with the age of males carrying various P-element derivatives. The combination of end-deleted elements can lead to average recombination frequencies >50% with individual instances of 100% recombination. These elements also lowered the fertility of the carriers. We investigated these features by constructing an analytical and a computer simulation model of the course of events in the germline, incorporating the recently proposed hybrid element insertion (HEI) model of P-element activity. The model is able to predict extreme recombination levels, segregation ratio biases and lowered fertility through cell death in a single analysis.

Mitochondrial D-loop diversity in Australian riverine and Australian desert Aborigines.

Population structure has been revealed in mitochondrial D-loop segment 1 (mt DLS1) sequences from Australian Aboriginal people in the Darling River region of NSW (Riverine) and from Yuendumu in central Australia (Desert). Comparison with five published global studies reveals that these Australians demonstrate greatest divergence from some Africans, least from Papua New Guinea (PNG) highlanders, and only slightly more divergence from some Pacific groups (Indonesian, Asian, Samoan, and coastal PNG). A median networks approach demonstrates that several hypervariable nucleotide sites within the DLS1 are likely to have undergone mutation independently. A comprehensive evaluation of specific nucleotide variants with the large amount of global sequence data now available has been achieved in three stages of analysis: (i) identification of key nucleotide variants (from the Cambridge reference sequence) in the Aboriginal Australian by pairwise comparison and construction of a 'local' median network, (ii) identification of key nucleotide variants in a selected global sample including Australian mtDLS1 types most different from each other, and (iii) calculation of the frequency with which these key nucleotide sites occur as variants in a greatly extended global sample. The third stage of the analysis revealed that nucleotides 16287 and 16356 are unique markers for representatives from the northern Riverine region. A 'thymine' at nucleotide 16223 is an informative signature of African and several identifiable non-African DLS1 types, whereas the 'cytosine' form is a marker for European, Pacific, and some Asian populations.

P-element-induced recombination in Drosophila melanogaster: hybrid element insertion.

It has previously been shown that the combination of two deleted P elements in trans, one containing the left functional end and the second element the right functional end, can lead to high levels of male recombination. This finding strongly suggests that P-element ends from different chromosomes can become associated, followed by "pseudo-excision". We show that two different processes are involved in resolving the pseudo-excision event: (1) the excised P-element ends continue to function as a single unit (Hybrid Element) and insert at a nearby site in the chromosome or into the element itself [Hybrid Element Insertion (HEI)] and (2) free ends that do not contain P elements repair and rejoin [(Hybrid Excision and Repair (HER)]. Both types of resolution can lead to recombination, and this paper concentrates on the HEI class. One type of HEI event predicts the exact reverse complementary duplication of an 8-bp target site, and we have confirmed the existence of such a structure in six independently derived recombinant chromosomes. There is also a high tendency for insertion events to occur within a few bases of the original 8-bp target site, including six apparent cases of insertion into the exact site.