Obscura Subgroup Research Articles

An excess of gene expression divergence on the X chromosome in Drosophila embryos: implications for the faster-X hypothesis.

The X chromosome is present as a single copy in the heterogametic sex, and this hemizygosity is expected to drive unusual patterns of evolution on the X relative to the autosomes. For example, the hemizgosity of the X may lead to a lower chromosomal effective population size compared to the autosomes, suggesting that the X might be more strongly affected by genetic drift. However, the X may also experience stronger positive selection than the autosomes, because recessive beneficial mutations will be more visible to selection on the X where they will spend less time being masked by the dominant, less beneficial allele—a proposal known as the faster-X hypothesis. Thus, empirical studies demonstrating increased genetic divergence on the X chromosome could be indicative of either adaptive or non-adaptive evolution. We measured gene expression in Drosophila species and in D. melanogaster inbred strains for both embryos and adults. In the embryos we found that expression divergence is on average more than 20% higher for genes on the X chromosome relative to the autosomes; but in contrast, in the inbred strains, gene expression variation is significantly lower on the X chromosome. Furthermore, expression divergence of genes on Muller's D element is significantly greater along the branch leading to the obscura sub-group, in which this element segregates as a neo-X chromosome. In the adults, divergence is greatest on the X chromosome for males, but not for females, yet in both sexes inbred strains harbour the lowest level of gene expression variation on the X chromosome. We consider different explanations for our results and conclude that they are most consistent within the framework of the faster-X hypothesis.

Molecular phylogeny of the Drosophila obscura species group, with emphasis on the Old World species

BackgroundSpecies of the Drosophila obscura species group (e.g., D. pseudoobscura, D. subobscura) have served as favorable models in evolutionary studies since the 1930's. Despite numbers of studies conducted with varied types of data, the basal phylogeny in this group is still controversial, presumably owing to not only the hypothetical 'rapid radiation' history of this group, but also limited taxon sampling from the Old World (esp. the Oriental and Afrotropical regions). Here we reconstruct the phylogeny of this group by using sequence data from 6 loci of 21 species (including 16 Old World ones) covering all the 6 subgroups of this group, estimate the divergence times among lineages, and statistically test the 'rapid radiation' hypothesis.ResultsPhylogenetic analyses indicate that each of the subobscura, sinobscura, affinis, and pseudoobscura subgroups is monophyletic. The subobscura and microlabis subgroups form the basal clade in the obscura group. Partial species of the obscura subgroup (the D. ambigua/D. obscura/D. tristis triad plus the D. subsilvestris/D. dianensis pair) forms a monophyletic group which appears to be most closely related to the sinobscura subgroup. The remaining basal relationships in the obscura group are not resolved by the present study. Divergence times on a ML tree based on mtDNA data are estimated with a calibration of 30–35 Mya for the divergence between the obscura and melanogaster groups. The result suggests that at least half of the current major lineages of the obscura group originated by the mid-Miocene time (~15 Mya), a time of the last developing and fragmentation of the temperate forest in North Hemisphere.ConclusionThe obscura group began to diversify rapidly before invading into the New World. The subobscura and microlabis subgroups form the basal clade in this group. The obscura subgroup is paraphyletic. Partial members of this subgroup (D. ambigua, D. obscura, D. tristis, D. subsilvestris, and D. dianensis) form a monophyletic group which appears to be most closely related to the sinobscura subgroup.

Distribution of gypsy sequences in Drosophila species of the obscura subgroup.

Eight Drosophila species of the obscura subgroup were screened for sequences homologous to the gypsy retrotransposon of D. melanogaster. Molecular characterization of gypsy sequences was first approached through digesting genomic DNAs from these obscura species with appropriate restriction enzymes and subjecting them to Southern blot analysis. The results of this analysis indicate that gypsy-homologous sequences are well conserved among species of the obscura subgroup. With the exception of D. guanche, all other species bear a 7 kb Xho I fragment that represents the complete element in D. melanogaster. Lower molecular weight fragments that could be deleted elements, are shared by different species. Both types of element probably existed before the divergence of this subgroup. Two different species clusters could be established on the basis of hybridization patterns, one represented by D. subobscura and its relative species D. guanche and D. madeirensis, and the other, in which D. obscura, D. tristis and D. subsilvestris are included.

Morphometrical evolution in a Drosophila clade: theDrosophila obscuragroup

Five morphometrical traits (wing and thoraxlength, ovariole number, and thoracic and female abdomen pigmentation) were investigated in laboratory stocks of 20 species belonging to the Drosophila obscura group (subgenus Sophophora). These species originated from four biogeographical regions and represent all five of the presently recognized, taxonomic subgroups. Size-related traits (wing and thorax length) were highly variable across species, and interspecific variation explained more than 90% of total variability. In both traditional and phylogenetic analyses, wing size was positively correlated with latitude of origin. These interspecific correlations were however notably weaker than those for intraspecific correlations. Wing/thoraxratio, which may be related to flight capacity, showed little variation. Ovariole number was highly variabl e (range 27–53) both within and between species, and was positively correlated with the wing/thoraxratio, suggesting that species with relatively large ovaries have relatively low wing loading. Although many species are completely dark, 11 had some regions of light coloration. A light thoraxwith a median darkening was observed in sixspecies. A variable pigmentation of abdominal tergites, in females only, was found in nine species, belonging to three subgroups only. With respect to both molecular phylogeny and morphometrical evolution, the D. obscura subgroup is probably now the best investigated clade in Drosophila.

Ancient and recent horizontal invasions of drosophilids by P elements.

P elements of two different subfamilies designated as M- and O-type are thought to have invaded host species in the Drosophila obscura group via horizontal transmission from external sources. Sequence comparisons with P elements isolated from other species suggested that the horizontal invasion by the O-type must have been a rather recent event, whereas the M-type invasion should have occurred in the more distant past. To trace the phylogenetic history of O-type elements, additional taxa were screened for the presence of O- and M-type elements using type-specific PCR primers. The phylogeny deduced from the sequence data of a 927-bp section (14 taxa) indicate that O-type elements have undergone longer periods of regular vertical transmission in the lineages of the saltans and willistoni groups of Drosophila. However, starting from a species of the D. willistoni group they were transmitted horizontally into other lineages. First the lineage of the D. affinis subgroup was infected, and finally, in a more recent wave of horizontal spread, species of three different genera were invaded by O-type elements from the D. affinis lineage: Scaptomyza, Lordiphosa, and the sibling species D. bifasciata/D. imaii of the Drosophila obscura subgroup. The O-type elements isolated from these taxa are almost identical (sequence divergence <1%). In contrast, no such striking similarities are observed among M-type elements. Nevertheless, the sequence phylogeny of M-type elements is also not in accordance with the phylogeny of their host species, suggesting earlier horizontal transfer events. The results imply that P elements cross species barriers more frequently than previously thought but require a particular genomic environment and thus seem to be confined to a rather narrow spectrum of host species. Consequently, different P element types acquired by successive horizontal transmission events often coexist within the same genome.

Characterization and molecular analysis of Adh retrosequences in species of the Drosophila obscura group

Retrosequences, genes, and pseudogenes originated by retrotranscription are frequent components of vertebrate genomes, but they have only occasionally been described in invertebrates. In Drosophila, very few retrosequences have been reported, among them those of alcohol dehydrogenase (Adh) and phosphoglyceromutase (Pglym). Although 52 Adh gene sequences are available for comparison, Adh retrosequences have been described only in the sibling species D. teissieri and D. yakuba (melanogaster subgroup) and in D. subobscura (obscura subgroup). Here, we report the presence of Adh retrosequences in two closely related species of D. subobscura: D. madeirensis and D. guanche. Extensive sequence comparisons with their functional paralogs suggest separate retrotranscriptional events: one in the melanogaster subgroup in the ancestor of D. teissieri and D. yakuba, and the other in the obscura subgroup before the radiation of the lineages leading to D. subobscura, D. madeirensis, and D. guanche. In the former, the Adh retrotranscript originated a new expressed gene, named jingwei. However, in the obscura Adh retrosequences, retention of codon bias and higher Ks than Ka values, both distinctive evolutionary features supporting functionality, have to be considered together with a frameshift, premature stop codons, and other nucleotide substitutions, which, added to the lack of the original promoter elements, suggest that they are pseudogenes. At least two different Adh retrosequences have been characterized in each of the obscura species, and their phylogenetic analysis indicates that paralogs and their flanking genomic regions share a higher degree of similarity than orthologous sequences. Two alternative hypotheses could explain this current organization and structure: either a multiplication event occurred independently in each species, or gene conversion events should be invoked after a single duplication in the species ancestor. The significance of retrotranscriptional events in the evolution of invertebrate genomes is discussed.

The Drosophila montium subgroup species. Phylogenetic relationships based on mitochondrial DNA analysis.

Mitochondrial DNA (mtDNA) restriction site maps for three Drosophila montium subgroup species of the melanogaster species group, inhabiting Indian and Afrotropical montium subgroup territories, were established. Taking into account previous mtDNA data concerning six oriental montium species, a phylogeny was established using distance-matrix and parsimony methods. Both genetic diversity and mtDNA size variations were found to be very narrow, suggesting close phylogenetic relationships among all montium species studied. The phylogenetic trees that were constructed revealed three main lineages for the montium subgroup species studied: one consisting of the Afrotropical species Drosophila seguyi, which is placed distantly from the other species, one comprising the north-oriental (Palearctic) species, and one comprising the southwestern (south-oriental, Australasian, Indian, and Afrotropical) species. The combination of the mtDNA data presented here with data from other species belonging to the melanogaster and obscura subgroups revealed two major clusters: melanogaster and obscura. The melanogaster cluster is further divided into two compact lineages, comprising the montium subgroup species and the melanogaster complex species; the species of the other complex of the melanogaster subgroup, yakuba, disperse among the obscura species. The above grouping is in agreement with the mtDNA size variations of the species. Overall, among all subgroups studied, the species of the montium subgroup seem to be the most closely related.

Phylogeny of the Drosophila obscura species group deduced from mitochondrial DNA sequences.

Approximately 2 kb corresponding to different regions of the mtDNA of 14 different species of the obscura group of Drosophila have been sequenced. In spite of the uncertainties arising in the phylogenetic reconstruction due to a restrictive selection toward a high mtDNA A+T content, all the phylogenetic analysis carried out clearly indicate that the obscura group is formed by, at least, four well-defined lineages that would have appeared as the consequence of a rapid phyletic radiation. Two of the lineages correspond to monophyletic subgroups (i.e., affinis and pseudoobscura), whereas the obscura subgroup remains heterogeneous assemblage that could be reasonably subdivided into at least two complexes (i.e., subobscura and obscura).

Phylogenetic reconstruction of the Drosophila obscura group, on the basis of mitochondrial DNA.

We have constructed restriction-site maps of the mtDNAs in 13 species and one subspecies of the Drosophila obscura group. The traditional division of this group into two subgroups (affinis and obscura) does not correspond to the phylogeny of the group, which shows two well-defined clusters (the Nearctic affinis and pseudoobscura subgroups) plus a very heterogeneous set of anciently diverged species (the Palearctic obscura subgroup). The mtDNA of Drosophila exhibits a tendency to evolve toward high A+T values. This leads to a "saturation" effect that (1) begets an apparent decrease in the rate of evolution as the time since the divergence of taxa increases and (2) reduces the value that mtDNA restriction analysis has for the phylogenetic reconstruction of Drosophila species that are not closely related.

EVOLUTIONARY IMPLICATIONS OF DNA DIVERGENCE IN THE DROSOPHILA OBSCURA GROUP.

Using DNA-DNA hybridization, we have determined the degree of single-copy DNA (scDNA) divergence among eight species of the Drosophila obscura group. These include Old World and New World species as well as members of two subgroups. Contrary to classical systematics, members of the affinis subgroup are more closely related to American members of the obscura subgroup than are Old World species. The Old World species are not a monophyletic group. The degree of scDNA divergence among species is not necessarily correlated with morphology, chromosomal divergence, or ability to form hybrids. A unique pattern of hybrid formation was found: species separated by a ΔTm of 6.5°C can form hybrids whereas species separated by a ΔTm of 2.5°C cannot. As with other groups of Drosophila, the obscura group has discrete parts of the genome evolving at very different rates. The slow evolving fraction of the nuclear genome is evolving at about the same rate as mitochondrial DNA. The additional scDNA divergence accompanying the step from partial reproductive isolation (between North American pseudoobscura and the isolated Bogotà population) to full isolation is very small. The resolution of the technique was challenged by five closely related taxa with a maximum ΔTm of 2.5°C separating them; the taxa were unambiguously resolved and the "correct" phylogeny recovered. Finally, there is some indication that scDNA in the obscura group may be evolving considerably slower than in the melanogaster subgroup.

Mitochondrial DNA evolution in theobscura species subgroup ofDrosophila

Mitochondrial DNA (mtDNA) restriction site maps for nine species of the Drosophila obscura subgroup and for Drosophila melanogaster were established. Taking into account all restriction enzymes (12) and strains (45) analyzed, a total of 105 different sites were detected, which corresponds to a sample of 3.49% of the mtDNA genome. Based on nucleotide divergences, two phylogenetic trees were constructed assuming either constant or variable rates of evolution. Both methods led to the same relationships. Five differentiated clusters were found for the obscura subgroup species, one Nearctic, represented by Drosophila pseudoobscura, and four Palearctic, two grouping the related triads of species Drosophila subobscura, Drosophila madeirensis, Drosophila obscura, Drosophila subsilvestris, and two more represented by one species each, Drosophila bifasciata, and Drosophila tristis. The different Palearctic clusters are as distant between themselves as with the Nearctic one. For the related species D. subobscura, D. madeirensis, and D. guanche, the pair D. subobscura-D. madeirensis is the closest one. The relationships found by nucleotide divergence were confirmed by differences in mitochondrial genome size, with related species sharing similar genome lengths and differing from the distant ones. The total mtDNA size range for the obscura subgroup species was from 15.5 kb for D. pseudoobscura to 17.1 for D. tristis.

Mitochondrial DNA evolution in the Drosophila obscura group.

We report a restriction-site study of the mitochondrial DNA (mtDNA) of seven species of the Drosophila obscura group. One species (D. azteca) belongs to the affinis subgroup; the other six species are classified in the obscura subgroup, three of them being from the old-world species (D. obscura, D. ambigua, and D. subobscura) and three from the new-world species (D. pseudoobscura, D. persimilis, and D. miranda). The mtDNA patterns suggest that the phylogeny of the group needs to be revised. The Nearctic obscura species appear as more closely related to D. azteca (affinis subgroup) than to the Palearctic species. The three Palearctic species are, in turn, a very heterogeneous group, with D. obscura no more closely related to D. subobscura and D. ambigua than to D. affinis or the Nearctic obscura species. The rates of mtDNA evolution are variable: some lineages have evolved at rates two or three times greater than others. If an average rate of 0.5% nucleotide substitutions/Myr is assumed, the divergence among the four main lineages in the phylogeny would have occurred 12-15 Myr ago, during the Miocene, which is consistent with biogeographic information.

Colonization of North America by the European Species, Drosophila subobscura and D. ambigua

Two European species, Drosophila subobscura and D. ambigua, have been found in the Pacific Northwest. Drosophila subobscura occurs from central California, N to southwestern British Columbia. Drosophila ambigua has been found only in the southwestern mainland of British Columbia. These species can be distinguished from the endemic obscura-subgroup species, D. pseudoobscura, D. persimilis and C. miranda, by sex comb, vaginal plate and wing bristle morphology, by allozymic differences and by differences in the polytene chromosomes. INTRODUCTION Students of the North American Drosophila obscura species group are not accustomed to viewing members of the group as cosmopolitan entities. The usual methods of species identification (Anderson et al., 1977; Crumpacker, 1973) simply provide means of distinguishing among the known endemic species. Thus difficulties arise when distinct species previously unknown from this continent begin appearing in collections. Two such species appeared in collections from the Pacific coastal region, from northern California to southern British Columbia. After ruling out the known North American representatives, analysis of metaphase chromosome configurations and hybridization results with D. pseudoobscura, D. miranda and D. persimilis suggested that the new residents are the widespread European species, D. subobscura and D. ambigua. Subsequent crosses to known European strains of these species verified the identifications. This colonization is not the first for Drosophila subobscura. In February 1978, it was found in Puerto Montt, Chile, and has since spread in South America to include a region from 29 ?-53 S lat (Budnik and Brncic, 1982). It has also spread eastward into Argentina (Prevosti et al., 1983). Its Old World range includes Europe from southern Scandinavia S to northern Africa and the Canary Islands, eastward to Iran, and westward to the Azores Islands (Prevosti, 1978). Drosophila ambigua occurs from southern Finland, S to the Iberian Peninsula and E to Greece (Lakovaara and Saura, 1982). The purpose of this paper is to report the apparently successful colonization by these two species in the Pacific Northwest. Morphological, allozymic and chromosomal means of distinguishing them from the indigenous Drosophila obscura subgroup species are presented, along with the presently known North American ranges of each. MATERIALS AND METHODS Collections were made at buckets of fermenting bananas. Females were immediately isolated individually into vials of standard medium of corn meal, yeast and sugars. In most collections, the species were identified by analyzing polytene chromosomes from third instar larvae from each female. The three indigenous species were identified by third and XL chromosomes (Anderson et al., 1977). The polytenes of Drosophila subobscura and D. ambigua bear little resemblance to one another or to those of any member of

GENETIC DISTANCE AND EVOLUTIONARY RELATIONSHIPS IN THE DROSOPHILA OBSCURA GROUP.

The Drosophila obscura species group extends throughout the temperate zone of the Northern Hemisphere. Within it two subgroups are distinguished, affinis and obscura, with different numbers of representatives in the Old and New Worlds. Eight species of the affinis subgroup have been found in the Nearctic (D. affinis, D. algonquin, D. athabasca, D. azteca, D. narraganset, D. seminole, D. tolteca and D. dobzhanskii) and only one in the Palearctic (D. helvetica), while in the obscura subgroup 12 species are now known in the Old World (D. alpina, D. ambigua, D. bifasciata, D. eskoi, D. guanche, D. imaii, D. madeirensis, D. obscura, D. seguyi, D. subobscura, D. subsilvestris, and D. tristis) as compared with only five in the New World (D. frolovae, D. lowei, D. miranda, D. persimilis and D. pseudoobscura). This group, especially some species of the obscura subgroup, is one of the most comprehensively studied at all levels. Morphological, cytological, ethological and molecular, and phylogenetic relationships have been proposed within several clusters of species within the group (BuzzatiTraverso and Scossiroli, 1952; Clayton and Wheeler, 1975; Dobzhansky and Powell, 1975; Throckmorton, 1975 among others). However, a phylogeny including all or at least the great majority of the species of the group was not available until Lakovaara et al. (1972, 1976) constructed two phylogenetic hypotheses, first for the obscura subgroup and subsequently for the whole group. Based on genetic distances between species, these trees were constructed using enzymatic and other protein variants as taxonomic characters and assuming that the overall rate of evolutionary divergence is approximately homogeneous over all phyletic lines. Their results are, in general, in agreement with previous studies: the European species of the obscura subgroup were shown to be more closely related to each other than to their relatives in the New World, and similarly the species of the affinis subgroup of the New World were shown to be more closely related to each other than to those of the obscura subgroup, both of the Old as well as the New World. However, using the data of Lakovaara et al. (1972) but using methods which do not assume constant evolutionary rates for the species, Farris (1974) constructed a tree in which one of the Palearctic species, D. bifasciata, appears to be more closely related to the New World species of the subgroup than to those of the Old World. More recently, Marinkovic et al. (1978) established phylogenetic relationships among some of the American and European species of the obscura subgroup and found a European species, D. subobscura, to be apparently more closely related to American species of the subgroup than to other European species. It is of interest, therefore, to determine if these proposed close relationships between some American and European species of the obscura subgroup are consistent since it would greatly contribute to our understanding of the evolutionary history of the subgroup. The present work is an attempt to establish the relationships between a Nearctic species, D. pseudoobscura, and four Palearctic species, two of which have a wide geographical distribution, D. subobscura and D. ambigua. The other two are recently discovered species which are endemic to some of the Maccaronesian Islands, D. guanche Monclus (Monclus,

The Use of Isoenzymes in Tracing Evolution and in Classifying Drosophilidae

AbstractLakovaara, S. (Department of Genetics, University of Oulu, SF‐90100 Oulu 10, Finland), Saura, A., Lankinen, P., Pohjola, Liisa and Lokki, J. The use of isoenzymes in tracing evolution and in classifying Drosophilidae. Zool. Scr. 5 (3–4): 173–179, 1976.—Studies on the genetic constitution of natural populations of organisms have shown that these populations are extensively polymorphic at gene loci coding for enzymes. Much of this polymorphism detected by electrophoresing enzyme proteins is, however, not useful in classifying organisms, even though in general species differ from each other more than populations within a species. Good diagnostic characters are monomorphic species‐specific genes and their products. Finding these characters requires a thorough study of many populations of the species being studied. Once these characters have been found they can be used in assigning single individuals into different taxa. Electrophoresis of enzymes and allozyme differences between species can also be used in tracing the evolution of organisms. On the basis of allozymes a new phylogeny is proposed for the Drosophila obscura species group. Traditionally this group has been divided into two subgroups, obscura and affinis. Genetic characters divide this species group into three evolutionary lineages. The first lineage comprises the Eurasian obscura subgroup, the second the American affinis subgroup and the third the American obscura subgroup. D. alpina and D, helvetica, which belong to the obscura and affinis subgroups, respectively, are not appreciably related to any other species.

Drosophila lowei, a New American Member of the Obscura Species Group1,2

A new species, Drosophila lowei (Diptera: Drosophilidae), from the mountains of Arizona and Colorado, is described. The species is of particular interest because it is the 5th American species to be described in the Obscura subgroup of the Obscura Fallen species-group, subgenus Sophophora, and is clearly related to D. pseudoobscura Frolowa and D. persimilis Dobzhansky & Epling. D. lowei may usually be distinguished from D. pseudoobscura, with which it is sympatric, by its smaller size, proportionately longer wings, and its darker eye color. The chromosomes of D. lowei differ from those of D. pseudoobscura by a pericentric inversion in chromosome II. Hybrids between the 2 species are sterile. Ecologically D. lowei prefers the more temperate and cooler habitats above 7000 feet elevation and has its population peak in late summer and fall. There is evidence that the species undergoes a reproductive diapause at that time.