Testing the trend towards specialization in herbivore-host plant associations using a molecular phylogeny of Tomoplagia (Diptera: Tephritidae)

Herbivorous insects are abundant and diverse and insect-host plant associations tend to be specialized and evolutionarily conserved. Some authors suggested that generalist insect lineages tend to become specialists, with host specialization leading to an evolutionary dead-end for the parasite species. In this paper, we have examined this tendency using a phylogenetic tree of Tomoplagia (Diptera: Tephritidae), a parasite of asteracean plants. We have tested the trend towards specialization in different hierarchical degrees of host specialization. The topology of the tree, the inference of ancestral hosts, and the lack of directional evolution indicated that specialization does not correspond to a phylogenetic dead-end. Although most Tomoplagia species are restricted to a single host genus, specialization does not seem to limit further host range evolution. This work emphasizes the advantages of the use of different levels of specialization and the inclusion of occasional hosts to establish a more detailed scenario for the evolution of this kind of ecological association.     

Molecular evolution of Bowman-Birk type proteinase inhibitors in flowering plants

The Bowman-Birk family (BBI) of proteinase inhibitors is probably the most studied family of plant inhibitors. We describe the primary structure and the gene expression profile of 14 putative BBIs from the sugarcane expressed sequence tag database and show how we used these newly discovered sequences together with 87 previously described BBI sequences from the GenBank database to construct phylogenetic trees for the BBI family. Phylogenetic analysis revealed that BBI-type inhibitors from monocotyledonous and dicotyledonous plants could be clearly separated into different groups, while the overall topology of the BBI tree suggests a different pattern of evolution for BBI families in flowering plants. We also found that BBI proteinase inhibitors from dicotyledonous plants were well conserved, accumulating only slight differences during their evolution. In addition, we found that BBIs from monocotyledonous plants were highly variable, indicating an interesting process of evolution based on internal gene duplications and mutation events.     

Identification of 18 genes encoding necrosis-inducing proteins from the plant pathogen Phytophthora capsici (Pythiaceae: Oomycetes)

Phytophthora capsici is an aggressive plant pathogen that affects solanaceous and cucurbitaceous hosts. Necrosis-inducing Phytophthora proteins (NPPs) are a group of secreted toxins found particularly in oomycetes. Several NPPs from Phytophthora species trigger plant cell death and activate host defense gene expression. We isolated 18 P. capsici NPP genes, of which 12 were active during hypha growth from a Phytophthora stain isolated from pepper (Capsicum annuum) plants in China. The 18 predicted proteins had a sequence homology of 46.26%. The 18 Pcnpp sequences had a conserved GHRHDWE motif and fell into two groups. Eleven sequences in group 1 had two conserved cysteine residues, whereas the other seven sequences in group 2 lacked these two cysteine residues. A phylogenetic tree was constructed on the basis of the alignment of the predicted protein sequences of 52 selected NPP genes from oomycetes, fungi and bacteria from Genbank. The tree did not rigorously follow the taxonomic classification of the species; all the NPPs from oomycetes formed their own clusters, while fungal sequences were grouped into two separate clades, indicating that based on NPPs, we can separate oomycetes from fungi and bacteria, and that expansion of the NPP family was a feature of Phytophthora evolution.     

Systematic status of the genus Formosaphis Takahashi and the evolution of galls based on the molecular phylogeny of Pemphigini (Hemiptera: Aphididae: Eriosomatinae)

Abstract.  Aphids of the tribe Pemphigini (Hemiptera: Aphididae: Eriosomatinae) can induce pseudo-galls or galls on their primary host plants. Those belonging to subtribe Prociphilina often produce pseudo-galls, and those of the other subtribe, Pemphigina, can form not only pseudo-galls but also true galls. Pseudo-galls are all formed on the leaves, whereas true galls, although all similar in shape, can be located on the joint of the leaf blade and the petiole, the middle of the petiole and the branches of the host plant. From a first phylogenetic analysis of Pemphigini based on nuclear elongation factor-1α (EF-1α) sequences, no support was found for the monophyly of Pemphigini, but subtribe Pemphigina was monophyletic with robust support. Formosaphis obviously clusters with Pemphigina which has Populus as a primary host. Formosaphis belongs to Pemphigini and its unknown primary host is probably Populus. The evolution of galls in Pemphigina is discussed based on the phylogenetic tree drawn from EF-1α sequences and mitochondrial cytochrome oxidase subunit I (COI) sequences. The results suggest that, in this subtribe, the closed gall is preceded by an open pseudo-gall, and the galls move their locations from the joint of the leaf blade and the petiole to the middle of the petiole and, eventually, to the branch of the host plant. Such an evolutionary tendency may provide aphids with more protection and nutrition.     

An evaluation of the phylogenetic position of the dinoflagellateCrypthecodinium cohnii based on 5S rRNA characterization

Summary Partial nucleotide sequences for the 5S and 5.8S rRNAs from the dinoflagellateCrypthecodinium cohnii have been determined, using a rapid chemical sequencing method, for the purpose of studying dinoflagellate phylogeny. The 5S RNA sequence shows the most homology (75%) with the 5S sequences of higher animals and the least homology (< 60%) with prokaryotic sequences. In addition, it lacks certain residues which are highly conserved in prokaryotic molecules but are generally missing in eukaryotes. These findings suggest a distant relationship between dinoflagellates and the prokaryotes. Using two different sequence alignments and several different methods for selecting an optimum phylogenetic tree for a collection of 5S sequences including higher plants and animals, fungi, and bacteria in addition to theC. cohnii sequence, the dinoflagellate lineage was joined to the tree at the point of the plant-animal divergence, well above the branching point of the fungi. This result is of interest because it implies that the well-documented absence in dinoflagellates of histones and the typical nucleosomal subunit structure of eukaryotic chromatin is the result of secondary loss. and not anindication of an extremely primitive state, as was previously suggested. Computer simulations of 5S RNA evolution have been carried out in order to demonstrate that the above-mentioned phylogenetic placement is not likely to be the result of random sequence convergence.We have also constructed a phylogeny for 5.8S RNA sequences in which plants, animals, fungi and the dinoflagellates are again represented. While the order of branching on this tree is the same as in the 5S tree for the organisms represented, because it lacks prokaryotes, the 5.8S tree cannot be considered a strong independent confirmation of the 5S result. Moreover, 5.8S RNA appears to have experienced very different rates of evolution in different lineages indicating that it may not be the best indicator of evolutionary relationships.We have also considered the existing biological data regarding dinoflagellate evolution in relation to our molecular phylogenetic evidence.     

Molecular phylogeny of the actinorhizal Hamamelidae and relationships with host promiscuity towards Frankia

Several of the most studied actinorhizal symbioses involve associations between host plants in the subclass Hamamelidae of the dicots and actinomycetes of the genus Frankia. These actinorhizal plants comprise eight genera distributed among three families of ‘higher’ Hamamelidae, the Betulaceae, Myricaceae, and Casuarinaceae. Contrasting promiscuity towards Frankia is encountered among the different actinorhizal members of these families, and a better assessment of the evolutionary history of these actinorhizal taxa could help to understand the observed contrasts and their implications for the ecology and evolution of the actinorhizal symbiosis. Complete DNA sequences of the chloroplast gene coding for the large subunit of ribulose 1,5-bisphosphate carboxylase (rbcL) were obtained from taxa representative of these families and the Fagaceae. The phylogenetic relationships among and within these families were estimated using parsimony and distance-matrix approaches. All families appeared monophyletic. The Myricaceae appeared to derive first before the Betulaceae and the Casuarinaceae. In the Casuarinaceae, the genus Gymnostoma derived before the genera Casuarina and Allocasuarina, which were found closely related. The analysis of character-state changes in promiscuity along the consensus tree topology suggested a strong relationship between the evolutionary history of host plants and their promiscuity toward Frankia. Indeed, the actinorhizal taxa that diverged more recently in this group of plants were shown to be susceptible to a narrower spectrum of Frankia strains. The results also suggest that the ancestor of this group of plant was highly promiscuous, and that evolution has proceeded toward narrower promiscuity and greater specialization. These results imply that a tight relationship between the phytogenies of both symbiotic partners should not be expected, and that host promiscuity is likely to be a key determinant in the establishment of an effective symbiosis.     

Classical plant taxonomic ambiguities extend to the molecular level

Summary The molecular evolution of cytochrome c from angiosperms is compared to that from vertebrates. On the basis of a cladistic analysis from 26 plant species, compared to that from 27 vertebrate species, we find that although the vertebrate sequences yield reasonably well-defined minimal trees that are congruent with the biological tree, the plant sequences yield multiple minimal trees that are not only highly incongruent with each other, but none of which is congruent with any reasonably biological tree. That is, the plant sequence set is much more homoplastic than that of the animal. However, as judged by the relative rate test, the extent of divergence, and degree of functional constraint, cytochrome c evolution in plants does not appear to differ from that of vertebrates.     

Evolution of Internal Transcribed Spacer Region of Nuclear Ribosomal DNA in Allopolyploids of Aegilops

Hybridization with subsequent polyploidy is a prominent process in evolution of higher plants, but few data address the evolution of homeologous sequences after polyploidy. The internal transcribed spacer (ITS) of nuclear ribosomal DNA (nrDNA) from eleven allopolyploid species in Aegilops was investigated by PCR amplification and direct sequencing. The sequences obtained were used to study the evolution of ITS region in allopolyploid species. The length of ITS region varied from 599 to 606 bp and the number of variable sites was 93, i.e. 51 and 42 for ITS1 and ITS2 re spectively. Some polymorphic sites were observed in polyploid species, and this indicated that the ancestral sequences had not been homogenized completely by concerted evolution. Distance matrix analysis of diploid and polyploid species by neighbor-joining method, using Triticum monococcum as outgroup, resulted in well-resolved neighbor-joining tree indicating that the ITS regions of UUMM and UUSS genome ( sect. Vertebrata) were homogenizing toward those of UU ancestal genome. This result is in agreement with the results of ctyogenetics of Aegilops. On the other hand, the neighbor joining tree including the D-genome group species (sect. Cylindropyrum and sect. Polyeides ) com prised three clades (CC-DDCC, UU-DDMM-DDMMSS-DDMMUU and MM-DDMvMv), which sug gested that concerted evolution was homogenizing the ITS region of the polyploid derivatives to either of their ancestors.     

Ancestral state reconstruction for Dendroctonus bark beetles: evolution of a tree killer

While most bark beetles attack only dead or weakened trees, many species in the genus Dendroctonus have the ability to kill healthy conifers through mass attack of the host tree, and can exhibit devastating outbreaks. Other species in this group are able to successfully colonize trees in small numbers without killing the host. We reconstruct the evolution of these ecological and life history traits, first classifying the extant Dendroctonus species by attack type (mass or few), outbreaks (yes or no), host genus (Pinus and others), location of attacks on the tree (bole, base, etc.), whether the host is killed (yes or no), and if the larvae are gregarious or have individual galleries (yes or no). We then estimated a molecular phylogeny for a data set of cytochrome oxidase I sequences sampled from nearly all Dendroctonus species, and used this phylogeny to reconstruct the ancestral state at various nodes on the tree, employing maximum parsimony, maximum likelihood, and Bayesian methods. Our reconstructions suggest that extant Dendroctonus species likely evolved from an ancestor that killed host pines through mass attack of the bole, had individual larvae, and exhibited outbreaks. The ability to colonize a host tree in small numbers (as well as gregarious larvae and attacks at the tree base) apparently evolved later, possibly as two separate events in different clades. It is likely that tree mortality and outbreaks have been continuing features of the interaction between conifers and Dendroctonus bark beetles.     

Molecular phylogenies of plants and Frankia support multiple origins of actinorhizal symbioses

Molecular phylogenetic trees were reconstructed from nucleotide sequences of nifH and 16S rDNA for Frankia and of rbcL for actinorhizal plants. Comparison of Frankia phylogenetic trees reconstructed using nifH and 16S rDNA sequences indicated that subgroupings of both trees correspond with each other in terms of plant origins of Frankia strains. The results suggested that 16S rDNAs can be utilized for coevolution analysis of actinorhizal symbioses. Frankia and plant phylogenetic trees reconstructed using 16S rDNA and rbcL sequences were compared. The comparison by tree matching and likelihood ratio tests indicated that although branching orders of both trees do not strictly correspond with each other, subgroupings of Frankia and their host plants correspond with each other in terms of symbiotic partnership. Estimated divergence times among Frankia and plant clades indicated that Frankia clades diverged more recently than plant clades. Taken together, actinorhizal symbioses originated more than three times after the four plant clades diverged.     

A bacterial genetic screen identifies functional coding sequences of the insect mariner transposable element Famar1 amplified from the genome of the earwig, Forficula auricularia

Transposons of the mariner family are widespread in animal genomes and have apparently infected them by horizontal transfer. Most species carry only old defective copies of particular mariner transposons that have diverged greatly from their active horizontally transferred ancestor, while a few contain young, very similar, and active copies. We report here the use of a whole-genome screen in bacteria to isolate somewhat diverged Famar1 copies from the European earwig, Forficula auricularia, that encode functional transposases. Functional and nonfunctional coding sequences of Famar1 and nonfunctional copies of Ammar1 from the European honey bee, Apis mellifera, were sequenced to examine their molecular evolution. No selection for sequence conservation was detected in any clade of a tree derived from these sequences, not even on branches leading to functional copies. This agrees with the current model for mariner transposon evolution that expects neutral evolution within particular hosts, with selection for function occurring only upon horizontal transfer to a new host. Our results further suggest that mariners are not finely tuned genetic entities and that a greater amount of sequence diversification than had previously been appreciated can occur in functional copies in a single host lineage. Finally, this method of isolating active copies can be used to isolate other novel active transposons without resorting to reconstruction of ancestral sequences.     

Comparative genomics reveals genes significantly associated with woody hosts in the plant pathogen Pseudomonas syringae

The diversification of lineages within Pseudomonas syringae has involved a number of adaptive shifts from herbaceous hosts onto various species of tree, resulting in the emergence of highly destructive diseases such as bacterial canker of kiwi and bleeding canker of horse chestnut. This diversification has involved a high level of gene gain and loss, and these processes are likely to play major roles in the adaptation of individual lineages onto their host plants. In order to better understand the evolution of P. syringae onto woody plants, we have generated de novo genome sequences for 26 strains from the P. syringae species complex that are pathogenic on a range of woody species, and have looked for statistically significant associations between gene presence and host type (i.e. woody or herbaceous) across a phylogeny of 64 strains. We have found evidence for a common set of genes associated with strains that are able to colonize woody plants, suggesting that divergent lineages have acquired similarities in genome composition that may form the genetic basis of their adaptation to woody hosts. We also describe in detail the gain, loss and rearrangement of specific loci that may be functionally important in facilitating this adaptive shift. Overall, our analyses allow for a greater understanding of how gene gain and loss may contribute to adaptation in P. syringae.     

Fungal diversity associated with hawaiian Drosophila host plants

Hawaiian Drosophila depend primarily, sometimes exclusively, on specific host plants for oviposition and larval development, and most specialize further on a particular decomposing part of that plant. Differences in fungal community between host plants and substrate types may establish the basis for host specificity in Hawaiian Drosophila. Fungi mediate decomposition, releasing plant micronutrients and volatiles that can indicate high quality substrates and serve as cues to stimulate oviposition. This study addresses major gaps in our knowledge by providing the first culture-free, DNA-based survey of fungal diversity associated with four ecologically important tree genera in the Hawaiian Islands. Three genera, Cheirodendron, Clermontia, and Pisonia, are important host plants for Drosophila. The fourth, Acacia, is not an important drosophilid host but is a dominant forest tree. We sampled fresh and rotting leaves from all four taxa, plus rotting stems from Clermontia and Pisonia. Based on sequences from the D1/D2 domain of the 26S rDNA gene, we identified by BLAST search representatives from 113 genera in 13 fungal classes. A total of 160 operational taxonomic units, defined on the basis of ≥97% genetic similarity, were identified in these samples, but sampling curves show this is an underestimate of the total fungal diversity present on these substrates. Shannon diversity indices ranged from 2.0 to 3.5 among the Hawaiian samples, a slight reduction compared to continental surveys. We detected very little sharing of fungal taxa among the substrates, and tests of community composition confirmed that the structure of the fungal community differed significantly among the substrates and host plants. Based on these results, we hypothesize that fungal community structure plays a central role in the establishment of host preference in the Hawaiian Drosophila radiation.     

指环虫属的早期辐射及其与宿主鲤科鱼类的协同进化关系

本研究利用28SrDNAC1-D2区序列分析采自鲤科鱼类中6亚科宿主和寄生在花鲈、梅花鲈上的共17种指环虫的系统发育关系。同时,通过比较宿主鲤科鱼类与指环虫的系统发育树,检验指环虫与其宿主是否存在协同进化关系。结果表明:17种指环虫形成5个进化支(Clade),其中寄生在团头鲂(亚科)和鲢、鳙(鲢亚科)上的6种指环虫聚为一支(Clade1),而它们的宿主鱼类在系统发育分析中也表现为近缘关系;寄生在鲮鱼(野鲮亚科)上的D.quanfami(Clade5)位于系统树最基部,鲫鱼和鲤鱼(鲤亚科)的寄生指环虫处在系统树的次基部位置,而鲤亚科与野鲮亚科组成的姐妹群在宿主系统树上同样处在基部位置,寄生虫和宿主在进化上较为原始的地位得到了很好地相互印证。因而,本研究首次利用分子系统学手段分析指环虫属远缘物种间的系统关系,揭示了指环虫属与宿主鱼类之间存在协同进化关系。另外,本研究首次发现,野鲮亚科鱼类也可能是指环虫类的早期宿主,这与先前认为鲤亚科鱼类为指环虫类的祖先宿主的推测有所不同。     

Structure and evolution of the hAT transposon superfamily.

The maize transposon Activator (Ac) was the first mobile DNA element to be discovered. Since then, other elements were found that share similarity to Ac, suggesting that it belongs to a transposon superfamily named hAT after hobo from Drosophila, Ac from maize, and Tam3 from snapdragon. We addressed the structure and evolution of hAT elements by developing new tools for transposon mining and searching the public sequence databases for the hallmarks of hAT elements, namely the transposase and short terminal inverted repeats (TIRs) flanked by 8-bp host duplications. We found 147 hAT-related sequences in plants, animals, and fungi. Six conserved blocks could be identified in the transposase of most hAT elements. A total of 41 hAT sequences were flanked by TIRs and 8-bp host duplications and, out of these, 34 sequences had TIRs similar to the consensus determined in this work, suggesting that they are active or recently active transposons. Phylogenetic analysis and clustering of hAT sequences suggest that the hAT superfamily is very ancient, probably predating the plant-fungi-animal separation, and that, unlike previously proposed, there is no evidence that horizontal gene transfer was involved in the evolution of hAT elements.     

Intraspecific variability in host plant quality and ovipositionaI preferences in Eucheira socialis (Lepidoptera: Pieridae)

Abstract.

• 1 This study investigates interactions between Eucheira socialis (Pieridae: Lepidoptera), a strict monophagous herbivore, on Arbutus xalapensis (Ericaceae), a host plant with few herbivores. This tight association of insect on plant has many attributes conducive to reciprocal rather than diffuse evolution.
• 2 An indirect way of testing plant–insect coevolutionary theories is to test for the necessary conditions for reciprocal evolution in ecological time. Two conditions for coevolution were studied: (1) host plants vary in their suitability for larval growth and development, and (2) ovipositing insects discriminate among these plants based on their relative suitability.
• 3 Large differences in host plant suitability were found and relative differences were consistent from year to year.
• 4 There was no evidence that female insects based their ovipositional decisions on relative tree quality, which implies that factors other than host plant quality are involved in the maintenance and evolution of oviposition behaviour in Eucheira.
• 5 Of seven factors known to influence ovipositional preferences of insects among plants independent of potential larval success, the most likely causal factor in this system is the ability of females to balance a time/energy budget for finding potential oviposition sites, discriminating among them, and actually ovipositing.

     

Structure, function, and evolution of plant O-methyltransferases.

Plant O-methyltransferases (OMTs) constitute a large family of enzymes that methylate the oxygen atom of a variety of secondary metabolites including phenylpropanoids, flavonoids, and alkaloids. O-Methylation plays a key role in lignin biosynthesis, stress tolerance, and disease resistance in plants. To gain insights into the evolution of the extraordinary diversity of plant O-methyltransferases, and to develop a framework phylogenetic tree for improved prediction of the putative function of newly identified OMT-like gene sequences, we performed a comparative and phylogenetic analysis of 61 biochemically characterized plant OMT protein sequences. The resulting phylogenetic tree revealed two major groups. One of the groups included two sister clades, one comprising the caffeoyl CoA OMTs (CCoA OMTs) that methylate phenolic hydroxyl groups of hydroxycinnamoyl CoA esters, and the other containing the carboxylic acid OMTs that methylate aliphatic carboxyl groups. The other group comprised the remaining OMTs, which act on a diverse group of metabolites including hydroxycinnamic acids, flavonoids, and alkaloids. The results suggest that some OMTs may have undergone convergent evolution, while others show divergent evolution. The high number of unique conserved regions within the CCoA OMTs and carboxylic acid OMTs provide an opportunity to design oligonucleotide primers to selectively amplify and characterize similar OMT genes from many plant species.     

Ecological and evolutionary diversification of the seed beetle genus Stator (Coleoptera: Chrysomelidae: Bruchinae)

Ehrlich and Raven's (1964) hypothesis on coevolution has stimulated numerous phylogenetic studies that focus on the effects of plant defensive chemistry as the main ecological axis of phytophagous insect diversification. However, other ecological features affect host use and diet breadth and they may have very different consequences for insect evolution. In this paper, we present a phylogenetic study based on DNA sequences from mitochondrial and protein-coding genes of species in the seed beetle genus Stator, which collectively show considerable interspecific variation in host affiliation, diet breadth, and the dispersal stage of the seeds that they attack. We used comparative analyses to examine transitions in these three axes of resource use. We argue that these analyses show that diet breadth evolution is dependent upon colonizing novel hosts that are closely or distantly related to the ancestral host, and that oviposition substrate affects the evolution of host-plant affiliation, the evolution of dietary specialization, and the degree to which host plants are shared between species. The results of this study show that diversification is structured by interactions between different selective pressures and along multiple ecological axes.     

Flies on thistles: support for synchronous speciation?

Synchronous speciation of hosts and herbivorous insects predicts a congruent topology of host and insect phylogenies and similar evolutionary ages of host and insect taxa. To test these predictions for the specialized herbivorous fly genus Urophora (Diptera: Tephritidae), we used three different approaches. (i) We generated a phylogenetic tree of 11 European Urophora species from allozyme data and constructed a phylogeny of their hosts from published sources. Superimposing the Urophora tree on the host-plant tree we found no evidence for general congruence. (ii) We correlated genetic distances (Nei distances) of the host plants vs. the genetic distances of associated Urophora species. Overall, the relationship was not positive. Nevertheless, for some pairs of Urophora species and host plants genetic distances were in the same order of magnitude. (iii) We collected allozyme data for pairs of thistle taxa and pairs of herbivores on thistles together with independent time estimates. With these data we calibrated a molecular clock. There was a non-linear relationship between phylogenetic age and genetic distance, rendering the dating of deep events in thistle–insect evolution difficult. Nevertheless the derived molecular clock showed that the split of insect taxa lagged behind the split of hosts.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 775–783.     

Phylogeny of a Macaronesian radiation: host-plant use and possible cryptic speciation in Liparthrum bark beetles

The Macaronesian islands are well known for their unique endemic floras of woody plants. Many of these unusual plant groups provide important novel resources for bark and wood boring beetles which breed in dead or moribund parts of their host plants. The bark beetle genus Liparthrum exploits a wide range of unusual host plants and has its highest proportion of species living on the Macaronesian Islands. We used DNA sequences of the mitochondrial Cytochrome Oxidase I gene and the nuclear Elongation Factor 1 alpha gene, and morphological characters, to estimate the phylogenetic relationships among species endemic to these archipelagos, and to trace the evolution of host-plant use. All parsimony and Bayesian analyses of the combined data, and maximum likelihood analyses of the molecular data, showed that species associated with Euphorbia are monophyletic. We also found genetic and subtle morphological evidence for three cases of cryptic speciation in one polyphyletic species associated with different Euphorbia plants, showing that high levels of host specialisation can occur also in insects breeding in older and very dry, dead plant tissues.