Horizontal transmission, vertical inactivation, and stochastic loss of mariner-like transposable elements

Horizontal transmission has been well documented as a major mechanism for the dissemination of mariner-like elements (MLEs) among species. Less well understood are mechanisms that limit vertical transmission of MLEs resulting in the "spotty" or discontinuous distribution observed in closely related species. In this article we present evidence that the genome of the common ancestor of the melanogaster species subgroup of Drosophila contained an MLE related to the mellifera (honey bee) subfamily. Horizontal transmission, approximately 3-10 MYA, is strongly suggested by the observation that the sequence of the MLE in Drosophila erecta is 97% identical in nucleotide sequence with that of an MLE in the cat flea, Ctenocephalides felis. The D. erecta MLE has a spotty distribution among species in the melanogaster subgroup. The element has a high copy number in D. erecta and D. orena, a moderate copy number in D. teissieri and D. yakuba, and was apparently lost ("stochastic loss") in the lineage leading to D. melanogaster, D. simulans, D. mauritiana, and D. sechellia. In D. erecta, most copies are concentrated in the heterochromatin. Two copies from D. erecta, denoted De12 and De19, were cloned and sequenced, and they appear to be nonfunctional ("vertical inactivation"). It therefore appears that the predominant mode of MLE evolution is vertical inactivation and stochastic loss balanced against occasional reinvasion of lineages by horizontal transmission.      

Evolution of the Transposable Element Mariner in Drosophila Species

The distribution of the transposable element mariner was examined in the genus Drosophila. Among the eight species comprising the melanogaster species subgroup, the element is present in D. mauritiana, D. simulans, D. sechellia, D. yakuba and D. teissieri, but it is absent in D. melanogaster, D. erecta and D. orena. Multiple copies of mariner were sequenced from each species in which the element occurs. The inferred phylogeny of the elements and the pattern of divergence were examined in order to evaluate whether horizontal transfer among species or stochastic loss could better account for the discontinuous distribution of the element among the species. The data suggest that the element was present in the ancestral species before the melanogaster subgroup diverged and was lost in the lineage leading to D. melanogaster and the lineage leading to D. erecta and D. orena. This inference is consistent with the finding that mariner also occurs in members of several other species subgroups within the overall melanogaster species group. Within the melanogaster species subgroup, the average divergence of mariner copies between species was lower than the coding region of the alcohol dehydrogenase (Adh) gene. However, the divergence of mariner elements within species was as great as that observed for Adh. We conclude that the relative sequence homogeneity of mariner elements within species is more likely a result of rapid amplification of a few ancestral elements than of concerted evolution. The mariner element may also have had unequal mutation rates in different lineages.     

Local changes in GC/AT substitution biases and in crossover frequencies on Drosophila chromosomes

I present here evidence of remarkable local changes in GC/AT substitution biases and in crossover frequencies on Drosophila chromosomes. The substitution pattern at 10 loci in the telomeric region of the X chromosome was studied for four species of the Drosophila melanogaster species subgroup. Drosophila orena and Drosophila erecta are clearly the most closely related species pair (the erecta complex) among the four species studied; however, the overall data at the 10 loci revealed a clear dichotomy in the silent substitution patterns between the AT-biased- substitution melanogaster and erecta lineages and the GC-biased-substitution yakuba and orena lineages, suggesting two or more independent changes in GC/AT substitution biases. More importantly, the results indicated a between- loci heterogeneity in GC/AT substitution bias in this small region independently in the yakuba and orena lineages. Indeed, silent substitutions in the orena lineage were significantly biased toward G and C at the consecutive yellow, lethal of scute, and asense loci, but they were significantly biased toward A and T at sta. The substitution bias toward G and C was centered in different areas in yakuba (significantly biased at EG:165H7.3, EG:171D11.2, and suppressor of sable). The similar silent substitution patterns in coding and noncoding regions, furthermore, suggested mutational biases as a cause of the substitution biases. On the other hand, previous study reveals that Drosophila yakuba has about 20-fold higher crossover frequencies in the telomeric region of the X chromosome than does D. melanogaster; this study revealed that the total genetic map length of the yakuba X chromosome was only about 1.5 times as large as that of melanogaster and that the map length of the X-telomeric y-sta region did not differ between Drosophila yakuba and D. erecta. Taken together, the data strongly suggested that an approximately 20- fold reduction in the X-telomeric crossover frequencies occurred in the ancestral population of D. melanogaster after the melanogaster-yakuba divergence but before the melanogaster-simulans divergence.     

Phylogenetic incongruence in the Drosophila melanogaster species group

Drosophila melanogaster and its close relatives are used extensively in comparative biology. Despite the importance of phylogenetic information for such studies, relationships between some melanogaster species group members are unclear due to conflicting phylogenetic signals at different loci. In this study, we use twelve nuclear loci (eleven coding and one non-coding) to assess the degree of phylogenetic incongruence in this model system. We focus on two nodes: (1) the node joining the Drosophila erecta-Drosophila orena, Drosophila melanogaster-Drosophila simulans, and Drosophila yakuba-Drosophila teissieri lineages, and (2) the node joining the lineages leading to the melanogaster, takahashii, and eugracilis subgroups. We find limited evidence for incongruence at the first node; our data, as well as those of several previous studies, strongly support monophyly of a clade consisting of D. erecta-D. orena and D. yakuba-D. teissieri. By contrast, using likelihood based tests of congruence, we find robust evidence for topological incongruence at the second node. Different loci support different relationships among the melanogaster, takahashii, and eugracilis subgroups, and the observed incongruence is not easily attributable to homoplasy, non-equilibrium base composition, or positive selection on a subset of loci. We argue that lineage sorting in the common ancestor of these three subgroups is the most plausible explanation for our observations. Such lineage sorting may lead to biased estimation of tree topology and evolutionary rates, and may confound inferences of positive selection.     

Mitochondrial DNA evolution in themelanogaster species subgroup ofDrosophila

Detailed restriction maps (40 cleavage sites on average) of mitochondrial DNAs (mtDNAs) from the eight species of the melanogaster species subgroup of Drosophila were established. Comparison of the cleavage sites allowed us to build a phylogenetic tree based on the matrix of nucleotide distances and to select the most parsimonious network. The two methods led to similar results, which were compared with those in the literature obtained from nuclear characters. The three chromosomally homosequential species D. simulans, D. mauritiana, and D. sechellia are mitochondrially very related, but exhibit complex phylogenetic relationships. D. melanogaster is their closest relative, and the four species form a monophyletic group (the D. melanogaster complex), which is confirmed by the shared unusual length of their mt genomes (18-19 kb). The other four species of the subgroup (D. yakuba, D. teissieri, D. erecta, and D. orena) are characterized by a much shorter mt genome (16-16.5 kb). The monophyletic character of the D. yakuba complex, however, is questionable. Two species of this complex, D. yakuba and D. teissieri, are mitochondrially indistinguishable (at the level of our investigation) in spite of their noticeable allozymic and chromosomal divergence. Finally, mtDNA distances were compared with the nuclear-DNA distances thus far established. These sequences seem to evolve at rather similar rates, the mtDNA rate being barely double that of nuclear DNA.     

Divergence and heterogeneity of the histone gene repeating units in the Drosophila melanogaster species subgroup

The repeating units of the histone gene cluster containing the H1, H2A, H2B and H4 genes were amplified by PCR from the Drosophila melanogaster species subgroup, i.e., D. yakuba, D. erecta, D. sechellia, D. mauritiana, D. teissieri and D. orena. The PCR products were cloned and their nucleotide sequences of about 4.6-4.8kbp were determined to elucidate the mechanism of molecular evolution of the histone gene family. The heterogeneity among the histone gene repeating units was 0.6% and 0.7% for D. yakuba and D. sechellia, respectively, indicating the same level of heterogeneity as in the H3 gene region of D. melanogaster. Divergence of the genes among species even in the most closely related ones was much greater than the heterogeneity among family members, indicating a concerted mode of evolution for the histone gene repeating units. Among the species in the D. melanogaster species subgroup, the histone gene regions as well as 3rd codon position of the coding region showed nearly the same GC contents. These results suggested that the previous conclusion on analysis of the H3 gene regions, the gene family evolution in a concerted fashion, holds true for the whole histone gene repeating unit.     

DNA from Drosophila melanogaster region 61C7/C8 has high evolution rate

The results of a comparative study of cloned DNA fragments of Drosophila simulans, D. mauritiana, D. teissieri, and D. erecta are presented. The fragments were amplified in PCR with primers specified to the region of D. melanogaster interband 61C7/C8. The uniqueness of all cloned fragments in the genomes of these species was confirmed. A comparative analysis of nucleotide sequences revealed that the rate of evolution of DNA from D. melanogaster interband 61C7/C8 is close to the rate of neutral evolution in the genus Drosophila.     

Local recombination and mutation effects on molecular evolution in Drosophila.

I studied the cause of the significant difference in the synonymous-substitution pattern found in the achaete-scute complex genes in two Drosophila lineages, higher codon bias in Drosophila yakuba, and lower bias in D. melanogaster. Besides these genes, the functionally unrelated yellow gene showed the same substitution pattern, suggesting a region-dependent phenomenon in the X-chromosome telomere. Because the numbers of A/T --> G/C substitutions were not significantly different from those of G/C --> A/T in the yellow noncoding regions of these species, a AT/GC mutational bias could not completely account for the synonymous-substitution biases. In contrast, we did find an approximately 14-fold difference in recombination rates in the X-chromosome telomere regions between the two species, suggesting that the reduction of recombination rates in this region resulted in the reduction of the efficacy of selection in D. melanogaster. In addition, the D. orena yellow showed a 5% increase in the G + C content at silent sites in the coding and noncoding regions since the divergence from D. erecta. This pattern was significantly different from those at the orena Adh and Amy loci. These results suggest that local changes in recombination rates and mutational pressures are contributing to the irregular synonymous-substitution patterns in Drosophila.     

An intron loss of Dfak gene in species of the Drosophila melanogaster subgroup and phylogenetic analysis

Drosophila focal adhesion kinase (Dfak) gene is a single-copy nuclear gene. Previous study revealed that Drosophila melanogaster and Drosophila simulans had lost an intron precisely within the tyrosine kinase (TyK) domain of this gene. However, this did not happen in several other Drosophila species, including Drosophila elegans, Drosophila ficusphila, Drosophila biarmipes, Drosophila jambulina, Drosophila prostipennis, Drosophila takahashii, and Drosophila pseudoobscura. In the current study, homologous sequences of Drosophila sechellia, Drosophila mauritiana, Drosophila yakuba, Drosophila teissieri, Drosophila santomea, and Drosophila erecta were amplified by polymerase chain reaction, and further sequencing analysis indicated that these species were missing a TyK domain intron, indicating they were closely related. The relationship of the D. melanogaster species group was reconstructed using TyK domain nucleotide sequences. The resulting phylogenetic tree revealed that these 8 species were the most related species in the melanogaster group. These results strongly support previously proposed classifications based on morphological and molecular data.     

Evolutionary relationships to parasitism by seven species of the Drosophila melanogaster subgroup

Parasitic wasps are an important component of the niche of Drosophila species. The susceptibility to the Cynipid Leptopilina boulardi was estimated in the seven sibling species of Drosophila belonging to the melanogaster subgroup. Three categories of Hies can be distinguished, according to the level of cellular immune reaction and success of parasitism. Drosophila melanogaster and D. mauritiana belong to the category 1, specified by no encapsulative reaction and a high rate of successful parasitism. Category 2, characterized by a moderate encapsulation rate and a high mortality include D. simulans.5, D. erecta and D. orena . Category 3, with D. yakuba and D. tcissien , is specified by a very low rate or absence of successful parasitism due to a highly efficient immune cellular reaction. This classification parallels the phylogenic relationship based upon polytene chromosome banding sequences. Such specific ditferences in susceptibility to parasites may plan an important role in the competition between these species in Africa.     

The developments between gametogenesis and fertilization: ovulation and female sperm storage in Drosophila melanogaster

In animals with internal fertilization, ovulation and female sperm storage are essential steps in reproduction. While these events are often required for successful fertilization, they remain poorly understood at the developmental and molecular levels in many species. Ovulation involves the regulated release of oocytes from the ovary. Female sperm storage consists of the movement of sperm into, maintenance within, and release from specific regions of the female reproductive tract. Both ovulation and sperm storage elicit important changes in gametes: in oocytes, ovulation can trigger changes in the egg envelopes and the resumption of meiosis; for sperm, storage is a step in their transition from being "movers" to "fertilizers." Ovulation and sperm storage both consist of timed and directed cell movements within a morphologically and chemically complex environment (the female reproductive tract), culminating with gamete fusion. We review the processes of ovulation and sperm storage for Drosophila melanogaster, whose requirements for gamete maturation and sperm storage as well as powerful molecular genetics make it an excellent model organism for study of these processes. Within the female D. melanogaster, both processes are triggered by male factors during and after mating, including sperm and seminal fluid proteins. Therefore, an interplay of male and female factors coordinates the gametes for fertilization.     

Evolutionary novelties in islands: Drosophila santomea, a new melanogaster sister species from São Tomé

The finding of new melanogaster sister species may help us in understanding more about how the emergence of genetic novelties, particularly in insular habitats, can result in speciation. Here we report on the discovery of Drosophila santomea, which is the first melanogaster sibling found off West-equatorial Africa, on São Tomé, one of the Gulf of Guinea islands. Although the eight other melanogaster sister species are remarkably conservative in their morphology except for their terminalia, the new find has a morphological trait distinguishing it from all of these: a pure yellow body coloration of both sexes without the normal black abdominal banding. Evidence from the terminalia, polytene and mitotic chromosomes, period gene and allozymes are provided indicating that it is nonetheless the nearest relative of Drosophila yakuba with which it coexists on the island. The new find is a clear-cut taxon as shown by the production of sterile male hybrids, eventually with developmental defects, in both directions of cross with yakuba and by the existence of an altitudinal divide accompanied by a hybrid zone at mid-elevation on the island. Molecular and karyotypic data further support this conclusion. In contrast to the significant divergence of their nuclear DNAs, an intriguing similarity in their cytochrome b sequences was observed indicating a recent coalescence common to santomea, yakuba and also teissieri cytoplasms. These were shown to harbour the same Wolbachia endosymbiotic bacteria which could possibly be responsible for mitochondrial DNA hitchhiking across the species barrier.     

Induced Dominant Lethal Mutations and Cytotoxic Effects in Germ Cells of DROSOPHILA MELANOGASTER with Trenimon, Pdmt and Sodium Monofluorophosphate

Male and female Drosophila melanogaster with special sex chromosome or special autosome constitutions were fed with the mutagenic chemicals Trenimon (2,3,5-trisethyleneimino-1,4-benzoquinone) and PDMT (1-phenyl-3, 3-dimethyltriazene) and with the toxic substance Na2PO3F (sodium monofluorophosphate). The frequency of dominant lethality was recorded among the progeny. The results clearly show that dominant lethality is dose dependent for Trenimon- or PDMT-treated chromosomes in mature sperm and mature oocytes, and an increased amount of chromosomal material per nucleus yields an enhanced lethality. In contrast, a pure toxic effect of Na2PO3F on mature oocytes was demonstrated with one type of female. --With the stocks of Drosophila used, it is possible to distinguish between mutagenic and toxic effects of chemicals on the germ cells. Therefore, dominant lethality can be used as a simple and quick screening test for chemical mutagens.     

Identical satellite DNA sequences in sibling species of Drosophila

The evolution of simple satellite DNAs was examined by DNA-DNA hybridization of ten Drosophila melanogaster satellite sequences to DNAs of the sibling species, Drosophila simulans and Drosophila erecta. Seven of these repeat types are present in tandem arrays in D. simulans and each of the ten sequences is repeated in D. erecta. In thermal melts, six of the seven satellite sequences in D. simulans and seven of the ten sequences in D. erecta melted within 1 deg.C of the corresponding values in D. melanogaster. The remaining sequences melted within 3 deg.C of the homologous hybrids. Therefore, there is little or no alteration in those satellite sequences held in common, despite a period of about ten million years since the divergence of D. melanogaster and D. simulans from a common ancestor. Simple satellite sequences appear to be more highly conserved than coding regions of the genome, on a per nucleotide basis. Since multiple copies of three satellite sequences could not be detected in D. simulans yet are present in D. erecta, a species more distantly related to D. melanogaster than is D. simulans, these sequences show discontinuities in evolution. There were major quantitative variations between species, showing that satellite DNAs are prone to massive amplification or diminution events over timespans as short as those separating sibling species. In D. melanogaster, these sequences amount to 21% of the genome but only 5% in D. simulans and 0.4% in D. erecta. There was a general trend of lower abundance with evolutionary distance for most satellites, suggesting that the amounts of different satellite sequences do not vary independently during evolution.     

Heterospecific combinations of germ cells and gonadal soma betweenDrosophila melanogaster,D. mauritiana andD. ananassae

Summary We transplanted pole cells betweenDrosophila melanogaster, D. mauritiana andD. ananassae to investigate the ability of germ cells to develop in the gonad of a heterospecific host, and to study the interaction between somatic follicle cells and the cells of the germ line in producing the species-specific chorion. FemaleD. mauritiana germ cells in aD. melanogaster ovary produced functional eggs with normal development potential. The same is true for the reciprocal combination. FemaleD. ananassae pole cells in aD. melanogaster host only developed to a very early stage and degenerated afterwards. None of the interspecific combinations of male pole cells led to functional sperm. We could not determine at what stage the transplanted male pole cells were arrested. The cooperation of follicle cells and the oocyte-nurse cell complex in producing the chorion was studied using the germ-line-dependent mutationfs(1) K10 ofD. melanogaster, which causes fused respiratory appendages and an abnormal chorion morphology. Wild-type femaleD. mauritiana germ cells in a mutantfs(1) K10 D. melanogaster ovary led to the production of wild-type eggs withD. melanogaster-specific, short respiratory appendages. On the other hand,D. melanogaster fs(1) K10 germ cells in aD. mauritiana ovary induced the formation of eggs with mutant fused appendages which were, however, typicallyD. mauritiana in length. When.D. mauritiana pole cells developed in aD. melanogaster ovary, the chorion exhibited a new imprint pattern that differs from both species-specific patterns.     

Intra- and interspecies variation among Bari-1 elements of the melanogaster species group.

We have investigated the distribution of sequences homologous to Bari-1, a Tc1-like transposable element first identified in Drosophila melanogaster, in 87 species of the Drosophila genus. We have also isolated and sequenced Bari-1 homologues from D. simulans, D. mauritiana, and D. sechellia, the species constituting with D. melanogaster the melanogaster complex, and from D. diplacantha and D. erecta, two phylogenetically more distant species of the melanogaster group. Within the melanogaster complex the Bari-1 elements are extremely similar to each other, showing nucleotide identity values of at least 99.3%. In contrast, Bari-1-like elements from D. diplacantha and D. erecta are on average only 70% similar to D. melanogaster Bari-1 and are usually defective due to nucleotide deletions and/or insertions in the ORFs encoding their transposases. In D. erecta the defective copies are all located in the chromocenter and on chromosome 4. Surprisingly, while D. melanogaster Bari-1 elements possess 26-bp inverted terminal repeats, their D. diplacantha and D. erecta homologues possess long inverted terminal repeats similar to the terminal structures observed in the S elements of D. melanogaster and in several other Tc1-like elements of different organisms. This finding, together with the nucleotide and amino acid identity level between D. diplacantha and D. erecta elements and Bari-1 of D. melanogaster, suggests a common evolutionary origin and a rapid diversification of the termini of these Drosophila Tc1-like elements.     

A novel system of fertility rescue in Drosophila hybrids reveals a link between hybrid lethality and female sterility

Hybrid daughters of crosses between Drosophila melanogaster females and males from the D. simulans species clade are fully viable at low temperature but have agametic ovaries and are thus sterile. We report here that mutations in the D. melanogaster gene Hybrid male rescue (Hmr), along with unidentified polymorphic factors, rescue this agametic phenotype in both D. melanogaster/D. simulans and D. melanogaster/D. mauritiana F(1) female hybrids. These hybrids produced small numbers of progeny in backcrosses, their low fecundity being caused by incomplete rescue of oogenesis as well as by zygotic lethality. F(1) hybrid males from these crosses remained fully sterile. Hmr(+) is the first Drosophila gene shown to cause hybrid female sterility. These results also suggest that, while there is some common genetic basis to hybrid lethality and female sterility in D. melanogaster, hybrid females are more sensitive to fertility defects than to lethality.     

Study of the organization of polytene chromosomes in the nuclei of Drosophila melanogaster pseudonurse cells with the use of the DNA library of the Drosophila orena chromocenter

The location of the Drosophila orena chromocenter in polytene chromosomes of pseudonurse cells of the D. melanogaster ovaries (the otu11 mutation) and salivary glands has been studied. Numerous sites of location of the D. orena chromocenter DNA have been found throughout the length of D. melanogaster chromosomes. The specific distribution of the binding sites for the DNA probe has made it possible to identify chromosomes and analyze their mutual positions in the three-dimensional space of the nuclei of pseudonurse cells. The mutual positions of chromosomes have been found to vary, the pericentromeric regions of different chromosomes differing from one another in associative ratios.