Drosophila Obscura Species Group Research Articles

Complex Evolutionary History of the Y Chromosome in Flies of the Drosophila obscura Species Group.

The Drosophila obscura species group shows dramatic variation in karyotype, including transitions among sex chromosomes. Members of the affinis and pseudoobscura subgroups contain a neo-X chromosome (a fusion of the X with an autosome), and ancestral Y genes have become autosomal in species harboring the neo-X. Detailed analysis of species in the pseudoobscura subgroup revealed that ancestral Y genes became autosomal through a translocation to the small dot chromosome. Here, we show that the Y-dot translocation is restricted to the pseudoobscura subgroup, and translocation of ancestral Y genes in the affinis subgroup likely followed a different route. We find that most ancestral Y genes have translocated to unique autosomal or X-linked locations in different taxa of the affinis subgroup, and we propose a dynamic model of sex chromosome formation and turnover in the obscura species group. Our results suggest that Y genes can find unique paths to escape unfavorable genomic environments that form after sex chromosome–autosome fusions.

Chromosome-Level Assembly of Drosophila bifasciata Reveals Important Karyotypic Transition of the X Chromosome

The Drosophila obscura species group is one of the most studied clades of Drosophila and harbors multiple distinct karyotypes. Here we present a de novo genome assembly and annotation of D. bifasciata, a species which represents an important subgroup for which no high-quality chromosome-level genome assembly currently exists. We combined long-read sequencing (Nanopore) and Hi-C scaffolding to achieve a highly contiguous genome assembly approximately 193 Mb in size, with repetitive elements constituting 30.1% of the total length. Drosophila bifasciata harbors four large metacentric chromosomes and the small dot, and our assembly contains each chromosome in a single scaffold, including the highly repetitive pericentromeres, which were largely composed of Jockey and Gypsy transposable elements. We annotated a total of 12,821 protein-coding genes and comparisons of synteny with D. athabasca orthologs show that the large metacentric pericentromeric regions of multiple chromosomes are conserved between these species. Importantly, Muller A (X chromosome) was found to be metacentric in D. bifasciata and the pericentromeric region appears homologous to the pericentromeric region of the fused Muller A-AD (XL and XR) of pseudoobscura/affinis subgroup species. Our finding suggests a metacentric ancestral X fused to a telocentric Muller D and created the large neo-X (Muller A-AD) chromosome ∼15 MYA. We also confirm the fusion of Muller C and D in D. bifasciata and show that it likely involved a centromere-centromere fusion.

Discovery of three new species of Drosophila obscura species group (Diptera: Drosophilidae) from Mount Kinabalu in Borneo

AbstractWe describe three new species of the Drosophila obscura species group, D. hypercephala, D. hideakii and D. quadrangula Gao & Toda, spp. nov., all discovered from high altitudes (>1500 m) on Mt Kinabalu, Sabah, Malaysia. These are the southernmost distribution records of the D. obscura group in the Oriental Region. The three new species are each morphologically similar to different species of the Old World D. obscura species subgroup. This suggests that they are descendants of different founder species that independently colonized the tropics from the subtropical or temperate zones during the glacial ages. The new species D. hypercephala is hypercephalic not only in males but also, although less distinct, in females, unlike other hypercephalic drosophilid species in which only males are hypercephalic. This new finding of a hypercephalic species from the subgenus Sophophora, of which species are relatively easy to culture in the laboratory and include the model species such as D. melanogaster and D. pseudoobscura, will promote genetic analyses on the development and the evolution of hypercephaly.

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.

Domesticated P Elements in the Drosophila montium Species Subgroup Have a New Function Related to a DNA Binding Property

Molecular domestication of a transposable element is defined as its functional recruitment by the host genome. To date, two independent events of molecular domestication of the P transposable element have been described: in the Drosophila obscura species group and in the Drosophila montium species subgroup. These P neogenes consist of stationary, nonrepeated sequences, potentially encoding 66-kDa repressor-like (RL) proteins. Here we investigate the function of the montium P neogenes. We provide evidence for the presence of RL proteins in two montium species (D. tsacasi and D. bocqueti) specifically expressed in adult and larval brain and gonads. We tested the hypothesis that the montium P neogenes' function is related to the repression of the transposition of distantly related mobile P elements which coexist in the genome. Our results strongly suggest that the montium P neogenes are not recruited to downregulate the P element transposition. Given that all the proteins encoded by mobile or stationary P homologous sequences show a strong conservation of the DNA binding domain, we tested the capacity of the RL proteins to bind DNA in vivo. Immunostaining of polytene chromosomes in D. melanogaster transgenic lines strongly suggests that montium P neogenes encode proteins that bind DNA in vivo. RL proteins show multiple binding to the chromosomes. We suggest that the property recruited in the case of the montium P neoproteins is their DNA binding property. The possible functions of these neogenes are discussed.

Recurrent exon shuffling between distant P-element families.

Two independent stationary P-related neogenes had been previously described in the Drosophila obscura species group and in the Drosophila montium species subgroup. In Drosophila melanogaster, P-transposable elements can encode an 87 kDa transposase and a 66 kDa repressor, but the P-neogenes have only conserved the capacity to encode a 66 kDa repressor-like protein specified by the first three exons. We have previously analyzed the genomic modifications associated with the transition of a P-element into the montium P-neogene, the coding capacity of which has been conserved for around 20 Myr ( Nouaud, D., and D. Anxolabéhère. 1997. Mol. Biol. Evol. 14:1132-1144). Here we show that the P-neogene of some species of the montium subgroup presents a new structure involving the capture of an additional exon from a very distant P-element subfamily. This additional exon is inserted either upstream or downstream of the first exon of the P-neogene. As a result of alternative splicing, these modified neogenes can produce, in addition to the repressor-like protein, a new protein which differs only by the NH2-terminal region. We hypothesize that this protein diversity within an organism results in a functional diversification due to the selective advantage associated with the domestication of the P-neogene in these species. Moreover, the autonomous P-element which provides the additional exons is still present in the genome. Its nucleotide sequence is more than 45% distant from the previously defined P-type element (M-type, O-type, T-type) and defines a new P-type element subfamily referred to as the K-type.

Distribution of the bilbo non-LTR retrotransposon in Drosophilidae and its evolution in the Drosophila obscura species group.

The bilbo element is a non-LTR retrotransposon isolated from Drosophila subobscura. We conducted a distribution survey by Southern blot for 52 species of the family Drosophilidae, mainly from the obscura and melanogaster groups. Most of the analyzed species bear sequences homologous to bilbo from D. subobscura. In the obscura group, species from the same species subgroup also share similar Southern blot patterns. To investigate the phylogenetic relationship among these elements, we analyzed eight copies of a short sequence of the element from several species of the obscura group. The obtained phylogram agrees with the phylogeny of the species, which suggests vertical transmission of the element.

Evolutionary dynamics of the SGM transposon family in the Drosophila obscura species group.

SGM (Drosophila subobscura, Drosophila guanche, and Drosophila madeirensis) transposons are a family of transposable elements (TEs) in Drosophila with some functional and structural similarities to miniature inverted-repeat transposable elements (MITEs). These elements were recently active in D. subobscura and D. madeirensis (1-2 MYA), but in D. guanche (3-4 MYA), they gave rise to a species-specifically amplified satellite DNA making up approximately 10% of its genome. SGM elements were already active in the common ancestor of all three species, giving rise to the A-type specific promoter section of the P:-related neogene cluster. SGM sequences are similar to elements found in other obscura group species, such as the ISY elements in D. miranda and the ISamb elements in Drosophila ambigua. SGM elements are composed of different sequence modules, and some of them, i.e., LS and LS-core, are found throughout the Drosophila and Sophophora radiation with similarity to more distantly related TEs. The LS-core module is highly enriched in the noncoding sections of the Drosophila melanogaster genome, suggesting potential regulatory host gene functions. The SGM elements can be considered as a model system elucidating the evolutionary dynamics of mobile elements in their arms race with host-directed silencing mechanisms and their evolutionary impact on the structure and composition of their respective host genomes.

DROSOPHILA MAYA, A NEW NEOTROPICAL MEMBER OF THE DROSOPHILA OBSCURA SPECIES GROUP (DIPTERA: DROSOPHILIDAE)

A new Neotropical member of the Drosophila obscura species group from El Salvador and Honduras, Drosophila maya, is described. This species belongs to the New World pseudoobscura subgroup and, based on a variety of internal and external morphological characters, is most closely related to D. lowei. This species is distinguished from other members of the pseudoobscura subgroup by the shape of the hypandrium and by having fewer teeth on the sex combs. Ecologically, D. maya inhabits cloud forests at elevations around 2,000 m in El Salvador and Honduras. A key to eight members of the obscura species group which have been recorded in and near the Neotropical region is presented.

Evolution of overwintering strategies in Eurasian species of the Drosophila obscura species group

Abstract The phylogenetic relationship of Eurasian species of the Drosophila obscura species group remains ambiguous in spite of intensive analyses based on morphology, allozymes and DNA sequences. The present analysis based on sequence data for cytochrome oxidase subunit I (COI) and α-glycerophosphate dehydrogenase ( Gpdh ) suggests that the phylogenetic position of D. alpina is also ambiguous. These ambiguities have been considered to be attributable to rapid phyletic radiation in this group at an early stage of its evolution. Overwintering strategies are diversified among these species D. alpina and D. subsilvestris pass the winter in pupal diapause, D. bifasciata and D. obscura in reproductive diapause, and D. subobscura and D. guanche without entering diapause. This diversity may also suggest rapid radiation at an early phase of adaptations to temperate climates. On the other hand, adult tolerance of cold was closely related to overwintering strategy and distribution D. obscura and D. bifasciata with reproductive diapause were very tolerant D. alpina and D. subsilvestris which pass the winter in pupal diapause were less tolerant D. subobscura having no diapause was moderately tolerant and D. guanche occurring in the Canary Islands was rather susceptible. Tolerance of high temperature at the preimaginal stages seemed to be also associated with overwintering strategy; i.e. lower in the species with pupal diapause than in those with reproductive diapause or without diapause mechanism.

Evolution of overwintering strategies in Eurasian species of the Drosophila obscura species group

The phylogenetic relationship of Eurasian species of the Drosophila obscura species group remains ambiguous in spite of intensive analyses based on morphology, allozymes and DNA sequences. The present analysis based on sequence data for cytochrome oxidase subunit I (COI) and α-glycerophosphate dehydrogenase (Gpdh) suggests that the phylogenetic position of D. alpina is also ambiguous. These ambiguities have been considered to be attributable to rapid phyletic radiation in this group at an early stage of its evolution. Overwintering strategies are diversified among these speciesD. alpina and D. subsilvestris pass the winter in pupal diapause, D. bifasciata and D. obscura in reproductive diapause, and D. subobscura and D. guanche without entering diapause. This diversity may also suggest rapid radiation at an early phase of adaptations to temperate climates. On the other hand, adult tolerance of cold was closely related to overwintering strategy and distribution D. obscura and D. bifasciata with reproductive diapause were very tolerant D. alpina and D. subsilvestris which pass the winter in pupal diapause were less tolerant D. subobscura having no diapause was moderately tolerant and D. guanche occurring in the Canary Islands was rather susceptible. Tolerance of high temperature at the preimaginal stages seemed to be also associated with overwintering strategy; i.e. lower in the species with pupal diapause than in those with reproductive diapause or without diapause mechanism.

Reevaluation of Phylogeny in the Drosophila obscura Species Group Based on Combined Analysis of Nucleotide Sequences

The Drosophila obscura species group has served as an important model system in many evolutionary and population genetic studies. Despite the amount of study this group has received, some phylogenetic relationships remain unclear. While individual analysis of different nuclear, mitochondrial, allozyme, restriction fragment, and morphological data partitions are able to discern relationships among closely related species, they are unable to resolve relationships among the five obscura species subgroups. A combined analysis of several nucleotide data sets is able to provide resolution and support for some nodes not seen or well supported in analyses of individual loci. A phylogeny of the obscura species group based on combined analysis of nucleotide sequences from six mitochondrial and five nuclear loci is presented here. The results of several different combined analyses indicate that the Old World obscura and subobscura subgroups form a monophyletic clade, although they are unable to resolve the relationships among the major lineages within the obscura species group.

Molecular evolution of P transposable elements in the Genus drosophila. II. The obscura species group.

A phylogenetic analysis of P transposable elements in the Drosophila obscura species group is described. Multiple P sequences from each of 10 species were obtained using PCR primers that flank a conserved region of exon 2 of the transposase gene. In general, the P element phylogeny is congruent with the species phylogeny, indicating that the dominant mode of transmission has been vertical, from generation to generation. One manifestation of this is the distinction of P elements from the Old World obscura and subobscura subgroups from those of the New World affinis subgroup. However, the overall distribution of elements within the obscura species group is not congruent with the phylogenetic relationships of the species themselves. There are at least four distinct subfamilies of P elements, which differ in sequence from each other by as much as 34%, and some individual species carry sequences belonging to different subfamilies. P sequences from D. bifasciata are particularly interesting. These sequences belong to two subfamilies and both are distinct from all other P elements identified in this survey. Several mechanisms are postulated to be involved in determining phylogenetic relationships among P elements in the obscura group. In addition to vertical transmission, these include retention of ancestral polymorphisms and horizontal transfer by an unknown mating-independent mechanism.

The length of the sperm nucleus in Drosophila obscura group species is depending on the total length of the sperm

Summary Males of the Drosophila obscura species group develop sperm of more than one length class. Also the lengths of the nuclei are different. When the total sperm length and the nucleus length were subject to a cluster analysis, it was shown that in D. subobscura and in D. affinis two classes of sperm exist. In D. azteca three classes were found. In the analyzed species the lengths of short sperm are more similar than the lengths of long ones. For example, the short sperm of D. subobscura and D. affinis have the same length while the long sperm of the two species are significantly different. This fact supports the idea that in evolution there is a tendency towards an increase in the length of sperm. But according to our data, in species with sperm heteromorphism preferentially the length of the long class is increased. In the two species D. subobscura and D. affinis, the size of the sperm nuclei corresponded to the total length of sperm. Long sperm had longer nuclei than short sperm. In D. azteca only for the length classes of short and medium sperm the same was found, but in the class of the longest sperm of D. azteca the lengths of nucleus and sperm were not correlated. In this class the total length of sperm varied while the length of the nuclei was rather constant with a mean value of 495 μm and a maximum of 631 μm. We assume therefore that the longest nuclei in this class have reached their upper limit of elongation.

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).

"Sex ratio" meiotic drive in Drosophila testacea.

We document the occurrence of "sex ratio" meiotic drive in natural populations of Drosophila testacea. "Sex ratio" males sire greater than 95% female offspring. Genetic analysis reveals that this effect is due to a meiotically driven X chromosome, as in other species of Drosophila in which "sex ratio" has been found. In contrast to other drosophilids, the "sex ratio" and standard chromosomes of D. testacea do not differ in gene arrangement, implying that the effect may be due to a single genetic factor in this species. In all likelihood, the "sex ratio" condition has evolved independently in D. testacea and in the Drosophila obscura species group, as the loci responsible for the effect occur on different chromosomal elements. An important ecological consequence of "sex ratio" is that natural populations of D. testacea exhibit a strong female bias. Because D. testacea mates, oviposits, and feeds as adults and larvae on mushrooms, this species provides an excellent opportunity to study the selective factors in nature that prevent "sex ratio" chromosomes from increasing to fixation and causing the extinction of the species.

New African species in the Drosophila obscura species group: genetic variation, differentiation and evolution

New African species in the Drosophila obscura species group: genetic variation, differentiation and evolution

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.