Homology of polytene elements between Drosophila and Zaprionus determined by in situ hybridization in Zaprionus indianus

The drosophilid Zaprionus indianus due to its economical importance as an insect pest in Brazil deserves more investigation into its genetics. Its mitotic karyotype and a line-drawing map of its polytene chromosomes are already available. This paper presents a photomap of Z. indianus polytene chromosomes, which was used as the reference map for identification of sections marked by in situ hybridization with gene probes. Hybridization signals for Hsp70 and Hsr-omega were detected, respectively, in sections 34B and 32C of chromosome V of Z. indianus, which indicates its homology to the chromosomal arm 3R of Drosophila melanogaster and, therefore, to Muller's element E. The main signal for Hsp83 gene probe hybridization was in section 17C of Z. indianus chromosome III, suggesting its homology to arm 3L of D. melanogaster and to element D of Muller. The Ubi probe hybridized in sections 10C of chromosome II and 17A of chromosome III. Probably the 17A is the polyubiquitin locus, with homology to arm 3L of D. melanogaster and to the mullerian D element, as suggested also by Hsp83 gene location. The Br-C gene was mapped in section 1D, near the tip of the X chromosome, indicating its homology to the X chromosome of D. melanogaster and to mullerian element A. The Dpp gene probe hybridized mainly in the section 32A of chromosome V and, at lower frequencies to other sections, although no signal was observed as expected in the correspondent mullerian B element. This result led to the suggestion of a rearrangement including the Dpp locus in Z. indianus, the secondary signals possibly pointing to related genes of the TGF-beta family. In conclusion, the results indicate that chromosomes X, III, V of Z. indianus are respectively correspondents to elements A, D, and E of Muller. At least chromosome V of Z. indianus seems to share synteny with the 3R arm of D. melanogaster, as indicated by the relative positions of Hsp70 and Hsr-omega, although the Dpp gene indicates a disruption of synteny in its distal region.     

Is genome size influenced by colonization of new environments in dipteran species?

Genome size differences are usually attributed to the amplification and deletion of various repeated DNA sequences, including transposable elements (TEs). Because environmental changes may promote modifications in the amount of these repeated sequences, it has been postulated that when a species colonizes new environments this could be followed by an increase in its genome size. We tested this hypothesis by estimating the genome size of geographically distinct populations of Drosophila ananassae, Drosophila malerkotliana, Drosophila melanogaster, Drosophila simulans, Drosophila subobscura, and Zaprionus indianus, all of which have known colonization capacities. There was no strong statistical differences between continents for most species. However, we found that populations of D. melanogaster from east Africa have smaller genomes than more recent populations. For species in which colonization is a recent event, the differences between genome sizes do not thus seem to be related to colonization history. These findings suggest either that genome size is seldom modified in a significant way during colonization or that it takes time for genome size of invading species to change significantly.     

极端生理耐受性导致果蝇Zaprionus indianus 在温带地区广泛分布（英文）

在过去的十年中, Zaprionus indianus这一温带适应性果蝇已经入侵印度次大陆, 并扩大了其在该地区的分布。Z. indianus能成功入侵是由于它具有很强的适应性和对极端生理条件的耐受性。对Z. indianus (温带狭域分布种类) 和黑腹果蝇Drosophila melanogaster (全球广域分布种类)在极端温度下未成熟期和成虫期发育阈值的比较研究表明, 两者的死亡率和发育起点温度存在显著差异。为了检测越冬期间未成熟期和成虫期抗逆性和存活率的变化, 以采自印度温带和热带不同地点的Z. indianus种群进行饲养实验。在温带地区的田间养虫笼中以及恒定的实验室条件下监测这些种群的卵孵化率和成虫存活率, 直至全部成虫死亡。结果表明, 由于温带地区卵孵化率和存活率高, 导致总的孵化率和存活率在不同纬度间存在显著差异。卵至成虫发育实验结果表明, 低温条件下产下的卵在温度适中时成功发育成成虫。由此可见, 这种昆虫在未成熟期具有的气候适应性以及在成虫期具有的抗逆性可为该物种提供季节性保护。考虑到气候变暖情况, 即温度增加0.6℃, 温度的少许改变都可能导致种群存活能力的显著增强和发育历期缩短。这些结果可解释Z. indianus为什么能够轻易突破障碍并适应新的环境。     

Variation at the Est3 locus and adaptability to organophosphorous compounds in Zaprionus indianus populations

Carboxylesterases are enzymes often associated with insect resistance to insecticides. The Est3 locus of Zaprionus indianus Gupta (Diptera: Drosophilidae) harbors four alleles that encode carboxylesterases with potentially detoxifying roles. In this study, we propose a model of resistance to insecticides in Z. indianus based on the adaptability of the Est3 locus inferred from the spread of its alleles over 27 generations in experimental populations, and their frequencies in field populations, which were either exposed or unexposed to the organophosphorous insecticide malathion. The increase in the frequency of this allele in experimental populations, and its high prevalence in field populations exposed to organophosphorous insecticides suggest that natural selection favors individuals with the Est3-3 allele. The low frequency of this allele in unexposed field populations, and the low productivity of Est3-3 homozygotes indicate that an adaptive cost is associated with this allele. The existence of a marker locus for insecticide resistance in Z. indianus makes it possible to use this species as a bioindicator for monitoring the excessive use of organophosphorous products and the emergence of resistance, and to devise strategies for the management of agricultural pests.     

Changes in cuticular lipids, water loss and desiccation resistance in a tropical drosophilid: analysis of variation between and within populations

We investigated within as well as between population variability in desiccation resistance, cuticular lipid mass per fly and cuticular water loss in nine geographical populations of a tropical drosophilid, Zaprionus indianus. Interestingly, the amount of cuticular lipids and desiccation resistance in this non-melanic species are significantly higher as compared with melanic Drosophila melanogaster. On the basis of isofemale line analysis, within population trait variability in cuticular lipid mass per fly is positively correlated with desiccation resistance and negatively correlated with cuticular water loss but show lack of correlation with body size. We observed geographical variation in the amount of cuticular lipid mass per fly in Zaprionus indianus but no such divergence was found in D.melanogaster. In both the species, geographical variations in desiccation resistance are negatively correlated with cuticular water loss but the underlying mechanisms for changes in cuticular permeability are quite different. Thus, we may suggest that body melanisation and cuticular lipids may represent alternative strategies for coping with dehydration stress in melanic versus non-melanic drosophilids. For both the species, desiccation resistance and cuticular water loss are correlated with regular increase in aridity in the northern subtropical localities as compared with southern peninsular humid tropical localities. The role of climatic selection is evident from multiple regression analysis with seasonal changes in temperature and humidity (Tcv and RHcv) of the sites of origin of populations of Zaprionus indianus along latitude.     

Divergent abdominal bristle patterns in two distantly related drosophilids: antero-posterior variations and sexual dimorphism in a modular trait

The number of neurosensory bristles on abdominal sternites of Drosophila is a most investigated trait for quantitative genetic studies. However, the developmental pattern expressed on successive segments in both sexes has remained so far a neglected field. We explored three aspects of this general problem with an isofemale line design: comparing two distantly related species, Drosophila melanogaster and Zaprionus indianus, investigating bristle number variation along the antero-posterior axis, and analysing the sexual dimorphism. Antero-posterior variations could be analysed from segment A2 to A7 in females, and A2-A5 in males. In D. melanogaster, males and females showed parallel changes with a consistently lower number in males. In Z. indianus females the number was quite stable along the abdomen, while in males an important antero-posterior increase was found. The sexual dimorphism was further analysed by considering the female-male correlation and the female/male ratio. The results suggest that sternite bristle number is determined by several developmental genetic systems. One is acting along the antero-posterior axis and may be associated to a gradient, since the genetic correlation decreases when more distant segments are compared. Another is acting in the same way on most segments of both sexes, since the female-male genetic correlation is similar between homologous and non-homologous segments. Finally, genes with specific sex effects are acting on A7 in females of both species, and on A5 in Z. indianus males. The overall architecture of female and male abdomen seems to be constrained by the development of reproductive organs. A large difference between species suggests, however, that the sexual dimorphism of abdominal bristle number is not evolutionarily constrained.     

Quantitative trait analysis and geographic variability of natural populations of Zaprionus indianus, a recent invader in Brazil

Five natural samples of a recent South America invader, the drosophilid Zaprionus indianus, were investigated with the isofemale line technique. These samples were compared to five African mainland populations, investigated with the same method. The results were also compared to data obtained on mass cultures of other populations from Africa and India. Three quantitative traits were measured on both sexes, wing and thorax length and sternopleural bristle number. We did not find any latitudinal trend among the American samples, while a significant increase in body size with latitude was observed in the Indian and, to a lesser degree, in the African populations. American populations were also characterized by their bigger size. Genetic variability, estimated by the intraclass correlation among isofemale lines, was similar in American and African populations. The intraline, nongenetic variability was significantly less in the American samples, suggesting a better developmental stability, the origin of which is unclear. A positive relationship was evident between intraline variability of size traits and the wing-thorax length correlation. Altogether, our data suggest that the colonizing propagule introduced to Brazil had a fairly large size, preventing any bottleneck effect being detected. The big body size of American flies suggests that they came from a high-latitude African country. The lack of a latitudinal dine in America seems to be related to the short time elapsed since introduction. The very rapid spread of Z. indianus all over South America suggests that it might rapidly invade North America.     

Zaprionus tuberculatus: chromosome map and gene mapping by DNA in situ hybridization.

The genus Drosophila has long been used as a model of karyotype evolution, demonstrating change by paracentric inversion and occasional centric fusion of an ancestral karyotype of five rod-shaped and one "dot" chromosome. This study shows, by mapping D. melanogaster probes hybridized to polytene chromosomes of Zaprionus tuberculatus, that this ancestral pattern extends beyond the genus Drosophila. A formal polytene chromosome map of Z. tuberculatus is presented.     

Complex evolution of gypsy in Drosophilid species

In an endeavor to contribute to the comprehension of the evolution of transposable elements (TEs) in the genome of host species, we investigated the phylogenetic relationships of sequences homologous to the retrotransposon gypsy of Drosophila melanogaster in 19 species of Drosophila, in Scaptodrosophila latifasciaeformis, and in Zaprionus indianus. This phylogenetic study was based on approximately 500 base pairs of the env gene. Our analyses showed considerable discrepancy between the phylogeny of gypsy elements and the relationship of their host species, and they allow us to infer a complex evolutionary pattern that could include ancestral polymorphism, vertical transmission, and several cases of horizontal transmission.     

Grafting the molecular phylogenetic tree with morphological branches to reconstruct the evolutionary history of the genus Zaprionus (Diptera: Drosophilidae)

A molecular phylogeny for the drosophilid genus Zaprionus was inferred using a mitochondrial (CO-II) and a nuclear (Amyrel) gene using 22 available species. The combined molecular tree does not support the current classification, dubbed phylogenetic, based entirely upon a morphocline of forefemoral ornamentation. For species for which DNA was not available, phylogenetic positioning was only assigned using morphological characters. In order to avoid conflict between DNA and morphology in the combined analyses (supermatrix method), we developed a new method in which few morphological characters were sampled according to an a priori homoplasy assessment on the consensus molecular tree. At each internal node of the tree, a number of synapomorphies was determined, and species with no molecular sequences were grafted thereon. Analogously to tree vocabulary, we called our method 'morphological grafting'. New species groups and complexes were then defined in the light of our findings. Further, divergence times were estimated under a relaxed molecular clock, and historical biogeography was reconstructed under a maximum likelihood model. Zaprionus appears to be of recent origin in the Oriental region during the Late Miocene ( approximately 10 MYA), and colonization of Africa started shortly after ( approximately 7 MYA) via the maritime route of the Indian Ocean Islands. Most of the morphological and ecological diversification took place, later, in Western Africa during the Quaternary cyclic climatic changes. Furthermore, some species became recent invaders, with one, Zaprionus indianus, has successfully invaded South and North America during the last decade.     

Taxonomic survey of Drosophilidae (Diptera) from mangrove forests of Santa Catarina Island, Southern Brazil

Assemblages of drosophilids have been characterised in several environments of the Brazilian territory, like the Atlantic Rain Forest, urban areas, cerrados, the Amazon Forest, and others. The present survey is the first attempt to characterise the fauna of Drosophilidae in mangrove forests, an environment typical of tropical coasts worldwide. Twenty-eight samples were collected from the three main mangrove forests of Santa Catarina Island, southern Brazil, using banana-baited traps hung in trees. Samples were taken in January (summer), April (autumn), July (winter) and October (spring) between July 2002 and July 2005. In total, 82,942 specimens of drosophilids were caught, belonging to 69 species of six genera - Amiota Loew, Drosophila Fallén, Leucophenga Mik, Scaptodrosophila Duda, Zaprionus Coquillett and Zygothrica Wiedemann. The high abundance of D. simulans Sturtevant was remarkable, with some notable peaks of D. malerkotliana Parshad & Paika in autumn samples. Other common species were Zaprionus indianus Gupta, D. mediostriata Duda and D. willistoni Sturtevant. We also collected 45,826 flies of family Curtonotidae, the sister-group of Drosophilidae virtually absent in other environments. The assemblages of drosophilids were very similar in the three mangrove forests surveyed, despite the different surrounding environments. In general, the species sampled in the mangroves were the same as those observed in the surrounding environments, but in varying abundances. This suggests that drosophilids are differently affected by environmental pressures operating in mangroves.     

Whole genome sequence resource of Indian Zaprionus indianus

This article documents the whole genome sequence information of the Indian Zaprionus indianus, a member of the fruit fly family Drosophilidae. The sequences were generated on an Illumina platform and reads and whole genome sequence submitted to NCBI to the SRA and BioProject databases, respectively. This is the first Indian Z. indianus whole genome (draft) submitted to the sequence repository with SRA reads. The details of methodology, assembly statistics and functional annotation are presented in this work.     

Variability of Wing Size and Shape in Three Populations of a Recent Brazilian Invader, Zaprionus indianus (Diptera: Drosophilidae), from Different Habitats

Zaprionus indianus (Diptera: Drosophilidae) is an African species that was introduced in Brazil near the end of the 1990’s decade. To evaluate the adaptive potential of morphological traits in natural populations of this recently introduced species, we have investigated wing size and shape variation at Rio de Janeiro populations only two years after the first record of Z. indianus in Brazil. Significant genetic differences among populations from three distinct ecological habitats were detected. The heritability and evolvability estimates show that, even with the population bottleneck that should have occurred during the invasion event, an appreciable amount of additive genetic variation for wing size and shape was retained. Our results also indicated a greater influence of environmental variation on wing size than on wing shape. The importance of quantitative genetic variability and plasticity in the successful establishment and dispersal of Z. indianus in the Brazilian territory is then discussed.     

Phylogeny of Drosophila and related genera: conflict between molecular and anatomical analyses

Drosophila species are extensively used in biological research; yet, important phylogenetic relationships within the genus and with related genera remain unresolved. The combined data for three genes (Adh, Sod, and Gpdh) statistically resolves outstanding issues. We define the genus Drosophila inclusively so as to include Scaptomyza and Zaprionus (considered distinct genera in the taxonomy of Wheeler, 1981) but excluding Scaptodrosophila. The genus Drosophila so defined is monophyletic. The subgenus Sophophora (including the melanogaster, obscura, and willistoni groups) is monophyletic and the sister clade to all other Drosophila subgenera. The Hawaiian Drosophila (including Scaptomyza) is a monophyletic group, but the subgenus Drosophila is not monophyletic, because the immigrans group is more closely related to the subgenus Hirtodrosophila than to other species of the subgenus Drosophila, such as the virilis and repleta groups.     

Scenario of the spread of the invasive species Zaprionus indianus Gupta, 1970 (Diptera, Drosophilidae) in Brazil

Zaprionus indianus was first recorded in Brazil in 1999 and rapidly spread throughout the country. We have obtained data on esterase loci polymorphisms (Est2 and Est3), and analyzed them, using Landscape Shape Interpolation and the Monmonier Maximum Difference Algorithm to discover how regional invasion occurred. Hence, it was apparent that Z. indianus, after first arriving in São Paulo state, spread throughout the country, probably together with the transportation of commercial fruits by way of the two main Brazilian freeways, BR 153, to the south and the surrounding countryside, and the BR 116 along the coast and throughout the north-east.     

Molecular phylogeny and divergence times of drosophilid species

The phylogenetic relationships and divergence times of 39 drosophilid species were studied by using the coding region of the Adh gene. Four genera--Scaptodrosophila, Zaprionus, Drosophila, and Scaptomyza (from Hawaii)--and three Drosophila subgenera--Drosophila, Engiscaptomyza, and Sophophora--were included. After conducting statistical analyses of the nucleotide sequences of the Adh, Adhr (Adh-related gene), and nuclear rRNA genes and a 905-bp segment of mitochondrial DNA, we used Scaptodrosophila as the outgroup. The phylogenetic tree obtained showed that the first major division of drosophilid species occurs between subgenus Sophophora (genus Drosophila) and the group including subgenera Drosophila and Engiscaptomyza plus the genera Zaprionus and Scaptomyza. Subgenus Sophophora is then divided into D. willistoni and the clade of D. obscura and D. melanogaster species groups. In the other major drosophilid group, Zaprionus first separates from the other species, and then D. immigrans leaves the remaining group of species. This remaining group then splits into the D. repleta group and the Hawaiian drosophilid cluster (Hawaiian Drosophila, Engiscaptomyza, and Scaptomyza). Engiscaptomyza and Scaptomyza are tightly clustered. Each of the D. repleta, D. obscura, and D. melanogaster groups is monophyletic. The splitting of subgenera Drosophila and Sophophora apparently occurred about 40 Mya, whereas the D. repleta group and the Hawaiian drosophilid cluster separated about 32 Mya. By contrast, the splitting of Engiscaptomyza and Scaptomyza occurred only about 11 Mya, suggesting that Scaptomyza experienced a rapid morphological evolution. The D. obscura and D. melanogaster groups apparently diverged about 25 Mya. Many of the D. repleta group species studied here have two functional Adh genes (Adh-1 and Adh-2), and these duplicated genes can be explained by two duplication events.      

Allozyme variability in an invasive drosophilid,Zaprionus indianus (Diptera: Drosophilidae): comparison of a recently introduced Brazilian population with Old World populations

Colonizing species often go through genetic bottlenecks when new territories are invaded. The South American continent has been recently colonized by a generalist African drosophilid, Zaprionus indianus, which has become an agricultural pest in Brazil in the last five years. In this paper we used allozyme electrophoresis to estimate levels of genetic differentiation of Z. indianus collected from sites 4 300 km apart in Brazil. We also compared the level of polymorphism of the Brazilian populations with that found in laboratory strains from Africa and Asia, to verify if a significant decrease in gene variability has taken place during the invasion process. The populations were polymorphic for three out of the 11 loci investigated. Genetic distances and F_ST indices among Brazilian populations were small and generally non significant, suggesting a colonization from one single propagule followed by a rapid demographic expansion. Ancestral and old populations from Africa and Asia were slightly more heterozygous than those from Brazil. Compared to other drosophilids, Z. indianus appears to be characterized by a low proportion (25%) of polymorphic loci. We suggest that the propagule introduced to Brazil had a sufficient size to carry almost all the polymorphism from the (unknown) origin population, although not the precise allelic frequencies.     

Tri-locus sequence data reject a “Gondwanan origin hypothesis” for the African/South Pacific crab genus Hymenosoma

Crabs of the family Hymenosomatidae are common in coastal and shelf regions throughout much of the southern hemisphere. One of the genera in the family, Hymenosoma, is represented in Africa and the South Pacific (Australia and New Zealand). This distribution can be explained either by vicariance (presence of the genus on the Gondwanan supercontinent and divergence following its break-up) or more recent transoceanic dispersal from one region to the other. We tested these hypotheses by reconstructing phylogenetic relationships among the seven presently-accepted species in the genus, as well as examining their placement among other hymenosomatid crabs, using sequence data from two nuclear markers (Adenine Nucleotide Transporter [ANT] exon 2 and 18S rDNA) and three mitochondrial markers (COI, 12S and 16S rDNA). The five southern African representatives of the genus were recovered as a monophyletic lineage, and another southern African species, Neorhynchoplax bovis, was identified as their sister taxon. The two species of Hymenosoma from the South Pacific neither clustered with their African congeners, nor with each other, and should therefore both be placed into different genera. Molecular dating supports a post-Gondwanan origin of the Hymenosomatidae. While long-distance dispersal cannot be ruled out to explain the presence of the family Hymenosomatidae on the former Gondwanan land-masses and beyond, the evolutionary history of the African species of Hymenosoma indicates that a third means of speciation may be important in this group: gradual along-coast dispersal from tropical towards temperate regions, with range expansions into formerly inhospitable habitat during warm climatic phases, followed by adaptation and speciation during subsequent cooler phases.     

Molecular phylogenies and historical biogeography of a circumtropical group of gastropods (Genus: Nerita): implications for regional diversity patterns in the marine tropics

To determine how historical processes, namely speciation, extinction, and dispersal, have contributed to regional species diversity patterns across the marine tropics, we examined the biogeographical history of a circumtropical genus of intertidal gastropods. A species-level phylogeny of Nerita, representing approximately 87% of extant species, was developed from 1608bp of mitochondrial (COI and 16S) and nuclear (ATPSalpha) markers. Phylogenetic relationships generally corresponded to prior classifications; however, comprehensive sampling revealed a number of previously undetected ESUs. Using the resulting tree as a framework, we combined geographical distributions and fossil evidence to reconstruct ancestral ranges, produce a time-calibrated chronogram, and estimate diversification rates. Analyses revealed two monophyletic eastern Pacific+Atlantic (EPA) clades, each of which likely split from an Indo-West Pacific (IWP) sister clade prior to an early Miocene Tethys Seaway closure. More recent diversification throughout the IWP appears to have been driven by both vicariance and dispersal events; EPA diversity has been further shaped by speciation across the Central American Seaway prior to its closure and dispersal across the Atlantic. Despite the latter, inter-regional dispersal has been rare, and likely contributes little to regional diversity patterns. Similarly, infrequent transitions into temperate regions combined with reduced diversification rates may explain low diversity in West and South Pacific clades. Since origination, Nerita diversification appears remarkably constant, with the exception of a lag in the late Eocene-early Oligocene and elevated rates in the late Oligocene-early Miocene. However, a comparison among regions suggested that IWP clades have experienced, on average, higher rates of speciation. Fossil evidence indicates that the EPA likely witnessed greater extinction relative to the IWP. We propose that regional differences in species diversity in Nerita have been largely shaped by differential rates of speciation and extinction.