Multiple events of horizontal transfer of the Minos transposable element between Drosophila species

In this study the Minos element was analyzed in 26 species of the repleta group and seven species of the saltans group of the genus Drosophila. The PCR and Southern blot analysis showed a wide occurrence of the Minos transposable element among species of the repleta and the saltans groups and also a low number of insertions in both genomes. Three different analyses, nucleotide divergence, historical associations, and comparisons between substitution rates (d(N) and d(S)) of Minos and Adh host gene sequences, suggest the occurrence of horizontal transfer between repleta and saltans species. These data reinforce and extend the Arca and Savakis [Genetica 108 (2000) 263] results and suggest five events of horizontal transfer to explain the present Minos distribution: between D. saltans and the ancestor of the mulleri and the mojavensis clusters; between D. hydei and the ancestor of the mulleri and the mojavensis clusters; between D. mojavensis and D. aldrichi; between D. buzzatii and D. serido; and between D. spenceri and D. emarginata. An alternative explanation would be that repeated events of horizontal transfer involving D. hydei, which is a cosmopolitan species that diverged from the others repleta species as long as 14Mya, could have spread Minos within the repleta group and to D. saltans. The data presented in this article support a model in which distribution of Minos transposon among Drosophila species is determined by horizontal transmission balanced by vertical inactivation and extinction.     

Molecular analysis of the rDNA ITS-1 intergenic spacer in Drosophila mulleri,D. arizonae,and their hybrids

We analyzed the ITS-1 spacer region of the rDNA in Drosophila mulleri and D. arizonae, two sibling species belonging to the mulleri complex (repleta group) and in hybrids obtained in both cross directions. In spite of several previous studies showing the incompatibility of crosses involving D. arizonae females and D. mulleri males, we were able to obtain hybrids in this direction. Complete ITS-1 region was amplified using primers with homology at the 3'-end of the 18S rDNA and the 5'-end of the 5.8S rDNA genes. Our data demonstrated that D. mulleri and D. arizonae can be differentiated as they present a difference in length for the ITS-1 region. The amplified fragment for this region in D. mulleri has a length of 600 bp, whereas in D. arizonae this fragment is about 500 bp. It was also observed that male and female hybrids obtained in both cross directions present two amplified fragments, confirming the location of the ribosomal cistrons in the X chromosomes and microchromosomes of both parental species.     

Identification of Two Subfamilies of micropia Transposable Element in Species of the repleta Group of Drosophila

The occurrence, number of insertion sites and antisense RNA expression of micropia transposable element were studied in 26 species that belong to three subgroups (mercatorum, mulleri and hydei) of repleta group of Drosophila. Under high specific PCR, micropia sequences were detected in 11 species, but under less stringent condition, this retrotransposon was detected in all species. The widespread distribution of micropia suggests that this element was already present at the common ancestor of the repleta group of Drosophila. Southern blot analysis showed a variation from 0 to 17 different insertion sites and the occurrence of male-specific sequences. We found that the expression of the 1.0 kb micropia antisense RNA is variable among the species and tissues (soma and testis), which suggests that more than one mechanism regulates transposition in these species. Variation of amplification by PCR and of antisense RNA expression, as well as divergence of nucleotide sequences among the species allow us to suggest that at least two subfamilies of micropia transposable element are harbored by the genome of this species group.     

Molecular phylogeny of the Drosophila virilis section (Diptera: Drosophilidae) based on mitochondrial and nuclear sequences

Regardless of the well-documented virilis species group, most groups of the Drosophila virilis section have not been completely studied at molecular level since it was suggested. Therefore, phylogenetic relationships among and within species groups of the virilis section are generally unknown. In present paper, the complete mitochondrial ND2 gene and fragment of COI gene in combination with a nuclear gene, Adh coding region, were used to derive the most extensive molecular phylogeny to date for the Drosophila virilis section. A total of 111 individuals covering 61 species were sampled in this study. Novel phylogenetic findings included (1) support for the paraphyly of the melanica and robusta species group and at least two subgroups of the robusta species group, the lacertosa and okadai subgroups, were distinguished as paraphyletic taxa. In addition, (2) present results revealed the sister relationship between D. moriwakii and the robusta subgroup, conflicting with current taxonomy regarding D. moriwakii, which was shifted from the robusta species group to the melanica group. (3) In contrast to the robusta and melanica species groups, monophyly of the polychaeta species group, the angor group and the virilis group was confirmed, respectively. However, the monophyletic quadrisetata species group was resolved with uncertainty. (4) Our analyses of combined data set suggested close relationship between the quadrisetata species group and the unpublished clefta group, and the okadai subgroup is sister to the clade comprising of the quadrisetata and clefta species groups. Within the virilis section, D. fluvialis and three tropical species groups, the polychaeta group, the angor group and the repleta group, are found to branch off earlier than other ingroup taxa. This suggests that the virilis section might have originated in the Old World tropics. Besides, the derived status of the close affinities of the quadrisetata group, the clefta group, and the melanica and robusta groups is probably the result of their adaptation to forests between subtropical and cool-temperate climate. Based on the consideration of the phylogenetic placement of the species of the virilis section, we suggest that at least five independent migrations occurred from the Old World to the New World.     

The structure of the Adh locus of Drosophila mettleri: an intermediate in the evolution of the Adh locus in the repleta group of Drosophila.

Members of species of the mulleri and hydei subgroups of the repleta group of Drosophila have duplicate Adh genes. The Adh regions of D. mojavensis, D. mulleri, and D. hydei contain three genes--a pseudogene, Adh-2, and Adh-1--arranged 5' to 3'. To understand the evolution of the triplicate Adh structure, we have cloned and sequenced the Adh locus of D. mettleri. This region consists of a 5' pseudogene and a 3' functional Adh gene. On the basis of the structure and nucleotide sequence comparisons of Adh genes of D. mettleri and other species, we propose that an initial duplication of the ancestral Adh gene generated two Adh genes arranged in tandem. The more 5' Adh gene became a pseudogene, while the more 3' gene remained functional through all the developmental stages. A second duplication of this 3' gene resulted in Adh regions with three genes--a pseudogene, Adh-2, and Adh-1.     

New evidence for nucleolar dominance in hybrids of Drosophila arizonae and Drosophila mulleri

Drosophila mulleri (MU) and D. arizonae (AR) are cryptic species of the mulleri complex, mulleri subgroup, repleta group. Earlier cytogenetic studies revealed that these species have different regulatory mechanisms of nucleolar organizing activity. In these species, nucleolar organizing regions are found in both the X chromosome and the microchromosome. In the salivary glands of hybrids between MU females and AR males, there is an interspecific dominance of the regulatory system of the D. arizonae nucleolar organizer involving, in males, amplification and activation of the nucleolar organizer from the microchromosome. The authors who reported these findings obtained hybrids only in that cross-direction. More recently, hybrids in the opposite direction, i.e., between MU males and AR females, have been obtained. The purpose of the present study was to evaluate, in these hybrids, the association of the nucleoli with the chromosomes inherited from parental species in order to cytogenetically confirm the dominance patterns previously described. Our results support the proposed dominance of the AR nucleolar organizer activity over that of MU, regardless of cross-direction.     

胡枝了属根瘤菌的多相分类研究

采用数值分类,全细胞可溶性蛋白电泳分析,ＤＮＡ,Ｇ＋Ｃｍｏｌ％和ＤＮＡ相关性的测定以及１６ＳｒＤＮＡＰＣＲ－ＲＦＬ分析等多相分类技术对来源于不同地区的１６种寄主的胡枝子根瘤菌进行了系统的分类研究,数值分类的结果表明,在６７％的相似性水平上,全部供试菌可以为快生型根瘤菌和慢性型根瘤菌两大群,在８０％的相似性水平上又可分为两个亚群。在此基础上,对各亚群的胡枝子根瘤菌进行了ＤＮＡ相关性的测定,以进一步证     

以ND4L和ND4基因为标记探讨黑腹果蝇种组的系统发育关系

多年来的形态学、染色体组学以及DNA序列几个方面的研究均没有很好地阐明黑腹果蝇种组内的系统发育关系。本实验测定了33个样品的ND4和31个样品的ND4L基因序列,以D．obscuroides为外群,用最大简约法和Bayesian法分别构建进化树。结果表明两种方法构建的拓扑结构一致,而且大部分支系的支持率较高。整个黑腹果蝇种组分成三大谱系：1）montium种亚组;2）ananssae种亚组;3）Oriental种亚组（melanogaster、ficsphila、eugracilis、elegans、suzukii、takahashii）。montium是最早分化的种亚组。在第三谱系中,melanogaster分化得最早;然后依次是ficsphila,eugracilis,elegans;suzukii与takahashii为姐妹种亚组,最后分化。     

西藏根瘤菌新表观群的DNA同源性及16S rDNA全序列分析

在前期数值分类工作的基础上,对7株与Rhizobium关系较密切的分离自西藏部分地区豆科植物Trigonellaspp.和Astragalusspp.的根瘤菌所形成的独立表观群,通过DNA同源性测定及16S rDNA全序列分析进行了分类地位的进一步确定。结果表明:该独立表观群菌株的(G C)mol%为59.5%~63.3%,群内菌株间DNA同源性在74.3%~92.3%之间,中心菌株XZ2-3与相关Rhizobium种之间的DNA同源性在0%~47.4%之间,是不同于Rhizobium内各种的新DNA同源群。另外,16S rDNA全序列分析结果也表明,中心菌株XZ2-3占居Rhizobium系统发育分支中的一个独立亚分支,其与临近R.leguminosarumUSDA2370T和R.etliCFN42T之间的序列相似性分别为96.55%和96.62%。根据国际系统细菌学委员会提出的细菌种属分类标准,该独立表观群构成了一个不同于Rhizobium内各种的新种群。该研究结果丰富了现有根瘤菌分类系统,将为国际上现有Rhizobium的14个种中再增添一个新的分类单元。     

Monophyly, divergence times, and evolution of host plant use inferred from a revised phylogeny of the Drosophila repleta species group

We present a revised molecular phylogeny of the Drosophila repleta group including 62 repleta group taxa and nine outgroup species based on four mitochondrial and six nuclear DNA sequence fragments. With ca. 100 species endemic to the New World, the repleta species group represents one of the major species radiations in the genus Drosophila. Most repleta group species are associated with cacti in arid or semiarid regions. Contrary to previous results, maximum likelihood and Bayesian phylogenies of the 10-gene dataset strongly support the monophyly of the repleta group. Several previously described subdivisions in the group were also recovered, despite poorly resolved relationships between these clades. Divergence time estimates suggested that the repleta group split from its sister group about 21millionyears ago (Mya), although diversification of the crown group began ca. 16Mya. Character mapping of patterns of host plant use showed that flat leaf Opuntia use is common throughout the phylogeny and that shifts in host use from Opuntia to the more chemically complex columnar cacti occurred several times independently during the history of this group. Although some species retained the use of Opuntia after acquiring the use of columnar cacti, there were multiple, phylogenetically independent instances of columnar cactus specialization with loss of Opuntia as a host. Concordant with our proposed timing of host use shifts, these dates are consistent with the suggested times when the Opuntioideae originated in South America. We discuss the generally accepted South American origin of the repleta group.     

Phylogeny of the Asian spiny frog tribe Paini (Family Dicroglossidae) sensu Dubois

The anuran tribe Paini, family Dicroglossidae, is known in this group only from Asia. The phylogenetic relationships and often the taxonomic recognition of species are controversial. In order to stabilize the classification, we used approximately 2100 bp of nuclear (rhodopsin, tyrosinase) and mitochondrial (12S, 16S rRNA) DNA sequence data to infer the phylogenetic relationships of these frogs. Phylogenetic trees reconstructed using Bayesian inference and maximum parsimony methods supported a monophyletic tribe Paini. Two distinct groups (I,II) were recovered with the mtDNA alone and the total concatenated data (mtDNA+nuDNA). The recognition of two genera, Quasipaa and Nanorana, was supported. Group I, Quasipaa, is widespread east of the Hengduan Mountain Ranges and consists of taxa from relatively low elevations in southern China, Vietnam and Laos. Group II, Nanorana, contains a mix of species occurring from high to low elevation predominantly in the Qinghai-Tibetan Plateau and Hengduan Mountain Ranges. The occurrence of frogs at high elevations appears to be a derived ecological condition. The composition of some major species groups based on morphological characteristics strongly conflicts with the molecular analysis. Some possible cryptic species are indicated by the molecular analyses. The incorporation of genetic data from type localities helped to resolve some of the taxonomic problems, although further combined analyses of morphological data from type specimens are required. The two nuDNA gene segments proved to be very informative for resolving higher phylogenetic relationships and more nuclear data should be explored to be more confident in the relationships.     

Molecular and morphological data reveal cryptic taxonomic diversity in the terrestrial slug complex Arion subfuscus/fuscus (Mollusca, Pulmonata, Arionidae) in continental north-west Europe

The importance and abundance of cryptic species among invertebrate taxa is well documented. Nowadays, taxonomic, phylogenetic and conservation biological studies frequently use molecular markers to delineate cryptic taxa. Such studies, however, often face the problem of the differential resolution of the molecular markers and techniques involved. This issue is explored in the present study of cryptic taxa within the terrestrial slug complex Arion subfuscus/fuscus in continental north-west Europe. To this end, morphological, allozyme and mitochondrial 16S rDNA sequence data have been jointly evaluated. Using allozyme data and gonad type, two distinct groups were consistently delineated, even under sympatric conditions. The 16S rDNA data strongly supported both those groups and even suggested the presence of three distinct taxa within one of them. However, in view of: (1) the allopatric distribution of three OTUs, (2) the lack of allozyme or morphological differentiation, and (3) the extremely high degree of intraspecific mtDNA variation reported in pulmonate gastropods, they are, for the time being, not regarded as valid species under the biological species concept. By means of 16S rDNA and allozyme data, the position of type and topotype material of A. subfuscus s.s. and A. fuscus relative to the newly defined OTUs was determined, thus clarifying the nomenclature of this species complex. Additionally, gonad type proved to be a useful character for distinguishing the two species in north-west Europe.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 23–38.     

Phylogenetic structure of the Sphaeriinae, a global clade of freshwater bivalve molluscs, inferred from nuclear (ITS-1) and mitochondrial (16S) ribosomal gene sequences

The Sphaeriidae represent one of the primary molluscan radiations into freshwater environments. We have reconstructed phylogenetic relationships of the Sphaeriinae, a cosmopolitan sphaeriid subfamily, using variation in nuclear ribosomal first internal transcribed spacer (ITS-1) and mitochondrial large ribosomal subunit (16S) gene fragments. A total of 38 New World, Eurasian and Antipodean taxa were characterized, including all primary taxonomic groupings except for Neopisidium , and members of the sister clade Euperinae were employed as outgroups. Phylogenetic analyses of individual and combined (16S + ITS1) datasets all recovered a paraphyletic Pisidium and a derived clade of asynchronous brooding Sphaerium / Musculium taxa. Maximum parsimony as well as maximum likelihood analyses of combined data yielded largely congruent and well-resolved topologies, and robustly supported clades were utilized to revise current sphaeriine taxonomy. Instead of the traditionally accepted three cosmopolitan genera, Pisidium s.l. , Musculium , and Sphaerium , five major monophyletic lineages, Afropisidium , Odhneripisidium , Pisidium , Cyclocalyx and Sphaerium , were recognized at the generic level. In addition, a number of subgeneric level groups were recovered in Sphaerium : Herringtonium , Sphaerium s . s ., Sphaerinova , Amesoda , and Musculium , together with one unassigned species, S. transversum .     

Identification of rays through DNA barcoding: an application for ecologists

DNA barcoding potentially offers scientists who are not expert taxonomists a powerful tool to support the accuracy of field studies involving taxa that are diverse and difficult to identify. The taxonomy of rays has received reasonable attention in Australia, although the fauna in remote locations such as Ningaloo Reef, Western Australia is poorly studied and the identification of some species in the field is problematic. Here, we report an application of DNA-barcoding to the identification of 16 species (from 10 genera) of tropical rays as part of an ecological study. Analysis of the dataset combined across all samples grouped sequences into clearly defined operational taxonomic units, with two conspicuous exceptions: the Neotrygon kuhlii species complex and the Aetobatus species complex. In the field, the group that presented the most difficulties for identification was the spotted whiptail rays, referred to as the 'uarnak' complex. Two sets of problems limited the successful application of DNA barcoding: (1) the presence of cryptic species, species complexes with unresolved taxonomic status and intra-specific geographical variation, and (2) insufficient numbers of entries in online databases that have been verified taxonomically, and the presence of lodged sequences in databases with inconsistent names. Nevertheless, we demonstrate the potential of the DNA barcoding approach to confirm field identifications and to highlight species complexes where taxonomic uncertainty might confound ecological data.     

THE USE OF PROTEIN-SEROLOGICAL CHARACTERS IN THE SYSTEMATICS OF THE FAMILY OLEACEAE

Serological analyses of soluble seed proteins of 12 representative taxa of the family Oleaceae by the techniques of Ouchterlony, presaturation, and immunoelectrophoresis (IEP) yielded complementary taxonomic information. Ouchterlony reactions differentiated among protein extracts of three species, and the combined serological techniques permitted the detection of protein differences of respective taxa of the two subfamilies Jasminoideae and Oleoideae. IEP enabled the separation of the 12 taxa investigated and the distribution into the two subfamilies, by the differential electrophoretic positions of precipitin arcs, which were consistent with members of each of the two subfamilies. Presaturation data, when analyzed by two cluster analysis computer programs, were taxonomically significant. One program, which calculated amalgamation distances from the presaturation data, clustered the 12 taxa into subgroups which corresponded to tribes, and within two groups, which corresponded to two subfamilies. A monothetic clustering program provided theoretical information on evolution of taxa within the family Oleaceae based on serological correspondences obtained from the presaturation data; the subfamily Jasminoideae was found phylogenetically primitive and the subfamily Oleoideae was advanced. Additionally, IEP data supported those theories suggesting that taxa of the Oleoideae evolved from taxa of the Jasminoideae. The groupings of taxa and different information obtained from the cluster analyses of data and all serological techniques reinforced each other, as well as contemporary taxonomic and phylogenetic treatments of taxa of the family Oleaceae. This research demonstrated the taxonomic value of protein-serological data, particularly as applied to the taxonomy of the Oleaceae.     

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 ΔT_m of 6.5°C can form hybrids whereas species separated by a ΔT_m 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 ΔT_m 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.