Microsatellite-based species identification method for Drosophila virilis group species

Species of the D. virilis group are widely used in evolutionary research, but the individuals of different species are difficult to distinguish from each other morphologically. We constructed a fast and easy microsatellite-based identification method for the species of the group occurring sympatrically in northern Europe. The neighbor joining tree based on 14 microsatellite loci also gave a good resolution of the species divergence pattern in the whole group.     

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.     

Basal relationships in the Drosophila melanogaster species group

The Drosophila melanogaster species group is a popular model for evolutionary studies due to its morphological and ecological diversity and its inclusion of the model species D. melanogaster. However, phylogenetic relationships among major lineages within this species group remain controversial. In this report, the phylogeny of 10 species representing each of the well-supported monophyletic clades in the melanogaster group was studied using the sequences of 14 loci that together comprise 9493 nucleotide positions. Combined Bayesian analysis using gene-specific substitution models produced a 100% credible set of two trees. In the strict consensus of these trees, the ananassae subgroup branches first in the melanogaster species group, followed by the montium subgroup. The remaining lineages form a monophyletic clade in which D. ficusphila and D. elegans branch first, followed by D. biarmipes, D. eugracilis, and the melanogaster subgroup. This strongly supported phylogeny resolves most basal relationships in the melanogaster species group, and provides a framework that can be extended in the future to encompass more species.     

The Drosophila flavopilosa species group (Diptera,Drosophilidae)

The D. flavopilosa group encompasses an ecologically restricted set of species strictly adapted to hosting flowers of Cestrum (Solanaceae). This group presents potential to be used as a model to the study of different questions regarding ecologically restricted species macro and microevolutionary responses, geographical vs. ecological speciation and intra and interspecific competition. This review aims to revisit and reanalyze the patterns and processes that are subjacent to the interesting ecological and evolutionary properties of these species. Biotic and abiotic niche properties of some species were reanalyzed in face of ecological niche modeling approaches in order to get some insights into their ecological evolution. A test of the potential of DNA-Barcoding provided evidences that this technology may be a way of overcoming difficulties related to cryptic species differentiation. The new focus replenishes the scenario with new questions, presenting a case where neither geographical nor ecological speciation may be as yet suggested.     

Ongoing hybridization obscures phylogenetic relationships in the Drosophila subquinaria species complex

Inferring evolutionary relationships among recently diverged lineages is necessary to understand how isolating barriers produce independent lineages. Here, we investigate the phylogenetic relationships between three incompletely isolated and closely related mushroom‐feeding Drosophila species. These species form the Drosophila subquinaria species complex and consist of one Eurasian species (D. transversa) and two widespread North American species (D. subquinaria and D. recens) that are sympatric in central Canada. Although patterns of pre‐ and post‐mating isolation among these species are well characterized, previous work on their phylogenetic relationships is limited and conflicting. In this study, we generated a multi‐locus data set of 29 loci from across the genome sequenced in a population sample from each species, and then, we inferred species relationships and patterns of introgression. We find strong statistical support that D. subquinaria is paraphyletic, showing that samples from the geographic region sympatric with D. recens are most closely related to D. recens, whereas samples from the geographic region allopatric with D. recens are most closely related to D. transversa. We present several lines of evidence that both incomplete lineage sorting and gene flow are causing phylogenetic discordance. We suggest that ongoing gene flow primarily from D. recens into D. subquinaria in the sympatric part of their ranges causes phylogenetic uncertainty in the evolutionary history of these species. Our results highlight how population genetic data can be used to disentangle the sources of phylogenetic discordance among closely related species.     

Radiation of the Drosophila nannoptera species group in Mexico

The Drosophila nannoptera species group, a taxon of Mexican cactophilic flies, is an excellent model system to study the influence of abiotic and biotic factors on speciation, the genetic causes of ecological specialization and the evolution of unusual reproductive characters. However, the phylogenetic relationships in the nannoptera species group and its position within the virilis‐repleta phylogeny have not been thoroughly investigated. Using a multilocus data set of gene coding regions of eight nuclear and three mitochondrial genes, we found that the four described nannoptera group species diverged rapidly, with very short internodes between divergence events. Phylogenetic analysis of repleta group lineages revealed that D. inca and D. canalinea are sister to all other repleta group species, whereas the annulimana species D. aracataca and D. pseudotalamancana are sister to the nannoptera and bromeliae species groups. Our divergence time estimates suggest that the nannoptera species group radiated following important geological events in Central America. Our results indicate that a single evolutionary transition to asymmetric genitalia and to unusual sperm storage may have occurred during evolution of the nannoptera group.     

中国黑腹果蝇种组40种果蝇的核型多样性研究

通过传统的敲片、Giemsa染色的方法制片对中国黑腹果蝇种组(Drosophilamelanogasterspeciesgroup)8个种亚组40种果蝇的染色体进行了分析,共发现18种核型,即A、A′′、C、C′、C′′、C′′′、C′′′′、D、D′、D′′、E、E′、E′′、F、F′、G、H和I,其中A、A′′、C′′′、C′′′′、D′′和F′为新发现的核型。8个种亚组的基本核型分别是:嗜凤梨果蝇种亚组(D.ananassaesubgroup)的核型为F、F′、G和H型;牵牛花果蝇种亚组(D.eleganssubgroup)的核型为A和A′′型;细针果蝇种亚组(D.eugracilissubgroup)的核型为C型;嗜榕果蝇种亚组(D.ficusphilasubgroup)的核型为C′型;黑腹果蝇种亚组(D.melanogastersubgroup)的核型为C和C′型;山果蝇种亚组(D.montiumsubgroup)的核型为C、C′、C′′、D、D′、D′′、E、E′、E′′和I型;铃木氏果蝇种亚组(D.suzukiisubgroup)的核型为C′′′和C′′′′型;高桥氏果蝇种亚组(D.takahashiisubgroup)的核型为C、C′′′和C′′′′型。透明翅果蝇(D.lucipennis)雌性核型2n=8,雄性核型2n=7,雄性Ⅳ号染色体为染色体单体。此外还发现,吉川氏果蝇(D.kikkawai)、林氏果蝇(D.lini)、奥尼氏果蝇(D.ogumai)、拟嗜凤梨果蝇(D.pseudoananassae)和叔白颜果蝇(D.triauraria)5种果蝇有B染色体。本文确定了D.sp.likeelegans、D.sp.likenyinyii、D.sp.liketrapezifrons1、D.sp.liketakahashii、D.sp.liketrapezifrons2和D.sp.likeauraria等6个未描述种的核型和1个新记录种吉里果蝇(D.giriensis)的核型。本研究证明了在黑腹果蝇种组内、亚组内、种内和单雌系内的核型多样性,为果蝇遗传和进化提供了进一步的细胞学证据。     

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 a-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. subsihestris 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.     

Patterns of inversion polymorphism in three species of the Drosophila melanogaster species group

In Drosophila, chromosomal polymorphism due to paracentric inversions is very common and constitutes an adaptive character. The degree of chromosomal variability varies in different species and also in different populations of the same species. Chromosomal polymorphism in Indian natural populations of three species, D. melaonogaster, D. ananassae and D. bipectinata which belong to the melanogaster species group has been studied and the quantitative data on frequency of inversions have been reported. Behaviour of chromosome inversions has also been studied in laboratory conditions. The present review summarises the work done on inversion polymorphism in Indian populations of three species which clearly demonstrates that these three species vary in their patterns of inversion polymorphism and have evolved different mechanisms for adjustment to their environments although they belong to the same species group.     

The Adh in Drosophila: Chromosomal location and restriction analysis in species with different phylogenetic relationships

Restriction analysis of the genomic region containing the Adh gene and in situ hybridization assays were performed in six Drosophila species belonging to three different subgenera: D. ambigua, D. subobscura, D. madeirensis and D. guanche (sg. Sophophora); D. immigrans (sg. Drosophila); and D. lebanonensis (sg. Pholadoris). In agreement with previous observations, comparison of restriction maps of the Adh region shows that D. subobscura and D. madeirensis are very closely related. Partial homology is also observed with the rest of the obscura group species. Nevertheless, no resemblance at the restriction map level is detected when more distantly related species are compared. In D. ambigua, D. immigrans and D. lebanonensis in situ hybridization assays reveal a single chromosomal location for Adh, which in D. lebanonensis appears to be sex linked. In contrast, in D. subobscura, D. madeirensis and D. guanche multiple sites of hybridization with homologous and heterologous probes are observed. For example, in D. subobscura and D. madeirensis the functional Adh gene is located on the U chromosome and additional homologous retrosequences are found on the E chromosome.by H. Jäckle     

Genetic variation and phylogenetic relationships of a pantropical species group in Polystachya (Orchidaceae)

Amplified fragment length polymorphism (AFLP) markers were used to investigate the relationships among Polystachya accessions from a group of closely related pantropical tetraploids. Before starting with the fingerprinting analyses, the polyploid accessions were first included in a phylogenetic analysis using low‐copy nuclear DNA data to establish their relationships, which confirmed that they belonged to a species group of closely related allotetraploids. Neo‐ and Palaeotropical polyploid accessions formed two hybrid clades with apparently independent origins. Sampling for the AFLP analyses included single accessions from much of the range of the genus and populations from Costa Rica (CR) and Sri Lanka (SL) to compare population structure and genetic diversity in these two areas in more detail. A splits graph of the complete AFLP data showed three major clusters corresponding to three sources of population sampling (P. concreta, SL; P. foliosa, CR; P. masayensis, CR), with individual accessions from Africa and Indian Ocean islands showing a closer relationship to P. concreta from SL than to the two CR species. Individual accessions from the Neotropics occurred in more isolated positions in the splits network, with little resolution. Some P. foliosa accessions clustered with P. masayensis, suggesting some hybridization between the two species, and this was confirmed by Bayesian structure analysis. However, the splits network, structure and analyses of molecular variance indicated a generally high level of genetic divergence between the two CR species, despite their recent hybrid origin, occurrence in largely the same localities and occasional hybridization. Polystachya foliosa from CR had a higher degree of population‐level genetic structure (Φ_ST = 0.291) than P. masayensis from CR (Φ_ST = 0.161) and P. concreta from SL (Φ_ST = 0.138), possibly because of its occurrence within a larger and more environmentally diverse continuous range than the other two species. Genetic divergence between Neo‐ and Palaeotropical members of the pantropical tetraploid group of Polystachya and the nonmonophyly of P. concreta suggested that P. concreta s.l. should be split and the use of this epithet should be confined to the Neotropics (the type is from Martinique). Other names should be used in Africa and the Asian tropics. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 165 , 235–250.     

Principles of genome evolution in the Drosophila melanogaster species group

That closely related species often differ by chromosomal inversions was discovered by Sturtevant and Plunkett in 1926. Our knowledge of how these inversions originate is still very limited, although a prevailing view is that they are facilitated by ectopic recombination events between inverted repetitive sequences. The availability of genome sequences of related species now allows us to study in detail the mechanisms that generate interspecific inversions. We have analyzed the breakpoint regions of the 29 inversions that differentiate the chromosomes of Drosophila melanogaster and two closely related species, D. simulans and D. yakuba, and reconstructed the molecular events that underlie their origin. Experimental and computational analysis revealed that the breakpoint regions of 59% of the inversions (17/29) are associated with inverted duplications of genes or other nonrepetitive sequences. In only two cases do we find evidence for inverted repetitive sequences in inversion breakpoints. We propose that the presence of inverted duplications associated with inversion breakpoint regions is the result of staggered breaks, either isochromatid or chromatid, and that this, rather than ectopic exchange between inverted repetitive sequences, is the prevalent mechanism for the generation of inversions in the melanogaster species group. Outgroup analysis also revealed evidence for widespread breakpoint recycling. Lastly, we have found that expression domains in D. melanogaster may be disrupted in D. yakuba, bringing into question their potential adaptive significance.     

Phylogeny of the Oriental Drosophila melanogaster species group: a multilocus reconstruction

The melanogaster species group of Drosophila (subgenus Sophophora) has long been a favored model for evolutionary studies because of its morphological and ecological diversity and wide geographic distribution. However, phylogenetic relationships among species and subgroups within this lineage are not well understood. We reconstructed the phylogeny of 17 species representing 7 "oriental" species subgroups, which are especially closely related to D. melanogaster. We used DNA sequences of four nuclear and two mitochondrial loci in an attempt to obtain the best possible estimate of species phylogeny and to assess the extent and sources of remaining uncertainties. Comparison of trees derived from single-gene data sets allowed us to identify several strongly supported clades, which were also consistently seen in combined analyses. The relationships among these clades are less certain. The combined data set contains data partitions that are incongruent with each other. Trees reconstructed from the combined data set and from internally homogenous data sets consisting of three or four genes each differ at several deep nodes. The total data set tree is fully resolved and strongly supported at most nodes. Statistical tests indicated that this tree is compatible with all individual and combined data sets. Therefore, we accepted this tree as the most likely model of historical relationships. We compared the new molecular phylogeny to earlier estimates based on morphology and chromosome structure and discuss its taxonomic and evolutionary implications.     

The Drosophila melanogaster hybrid male rescue gene causes inviability in male and female species hybrids

The Drosophila melanogaster mutation Hmr rescues inviable hybrid sons from the cross of D. melanogaster females to males of its sibling species D. mauritiana, D. simulans, and D. sechellia. We have extended previous observations that hybrid daughters from this cross are poorly viable at high temperatures and have shown that this female lethality is suppressed by Hmr and the rescue mutations In(1)AB and D. simulans Lhr. Deficiencies defined here as Hmr(-) also suppressed lethality, demonstrating that reducing Hmr(+) activity can rescue otherwise inviable hybrids. An Hmr(+) duplication had the opposite effect of reducing the viability of female and sibling X-male hybrid progeny. Similar dose-dependent viability effects of Hmr were observed in the reciprocal cross of D. simulans females to D. melanogaster males. Finally, Lhr and Hmr(+) were shown to have mutually antagonistic effects on hybrid viability. These data suggest a model where the interaction of sibling species Lhr(+) and D. melanogaster Hmr(+) causes lethality in both sexes of species hybrids and in both directions of crossing. Our results further suggest that a twofold difference in Hmr(+) dosage accounts in part for the differential viability of male and female hybrid progeny, but also that additional, unidentified genes must be invoked to account for the invariant lethality of hybrid sons of D. melanogaster mothers. Implications of our findings for understanding Haldane's rule-the observation that hybrid breakdown is often specific to the heterogametic sex-are also discussed.     

Testing nested phylogenetic and phylogeographic hypotheses in the Plethodon vandykei species group

Mesic forests in the North American Pacific Northwest occur in two disjunct areas: along the coastal and Cascade ranges of Oregon, Washington, and British Columbia as well as the Northern Rocky Mountains of Idaho, Montana, and British Columbia. Over 150 species or species complexes have disjunct populations in each area, and a priori hypotheses based on phytogeography and geology potentially explain the disjunction via either dispersal or vicariance. Here, we test these hypotheses in the disjunct salamander complex Plethodon vandykei and P. idahoensisby collecting genetic data (669 bp of Cyt b) from 262 individuals. Maximum likelihood analysis indicated reciprocal monophyly of these species, supporting the ancient vicariance hypothesis, whereas parametric bootstrap and Bayesian hypothesis testing allow rejection of the dispersal hypothesis. The coalescent estimate of the time since population divergence (estimated using MDIV) is 3.75 x 106 years, and the 95%credibility interval of this value overlaps with the geological estimate of vicariance, but not the hypothesized dispersal. These results are congruent with the pattern seen in other mesic forest amphibian lineages and suggest disjunction in amphibians may be a concerted response to a geological/climatological event. WithinP. idahoensis, we tested the corollary hypothesis of an inland Pleistocene refugium in the Clearwater drainage with nested clade analysis and coalescent estimates of population growth rate (g). Both analyses support post-Pleistocene expansion from the Clearwater refugium. We corroborated this result by calculating Tajima's Dand mismatch distribution within each drainage, showing strong evidence for recent population expansion within most drainages. This work demonstrates the utility of statistical phylogeography and contributes two novel analytical tools: tests of stationarity with respect to topology in the Bayesian estimation, and the use of coalescent simulations to test the significance of the population growth-rate parameter.