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Thomas R. Buckley - One of the best experts on this subject based on the ideXlab platform.
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old world and new world Phasmatodea phylogenomics resolve the evolutionary history of stick and leaf insects
Frontiers in Ecology and Evolution, 2019Co-Authors: Sabrina Simon, Harald Letsch, Thomas R. Buckley, Sarah Bank, Alexander Donath, Ryuichiro Machida, Karen Meusemann, Bernhard MisofAbstract:Phasmatodea comprises over 3,000 extant species and stands out as one of the last remaining insect orders for which a robust, higher-level phylogenetic hypothesis is lacking. New research suggests that the extant diversity is the result of a surprisingly recent and rapid radiation that has been difficult to resolve with standard Sanger sequence data. In order to resolve the early branching events of stick and leaf insects, we analyzed transcriptomes from 61 species, including 38 Phasmatodea species comprising all major clades and 23 outgroup taxa, including all other Polyneoptera orders. Using a custom-made ortholog set based on reference genomes from four species, we identified on average 2,274 orthologous genes in the sequenced transcriptomes. We generated various sub-alignments and performed maximum-likelihood analyses on several representative datasets to evaluate the effect of missing data and matrix composition on our phylogenetic estimates. Based on our new data, we are able to reliably resolve the deeper nodes between the principal lineages of extant Phasmatodea. Among EuPhasmatodea, we provide strong evidence for a basal dichotomy of AschiPhasmatodea and all remaining euPhasmatodeans, the NeoPhasmatodea. Within the latter clade, we recovered a previously unrecognized major New World and Old World lineage, for which we introduce the new names Oriophasmata tax. nov. (“Eastern phasmids”) and Occidophasmata tax. nov. (“Western phasmids”). Occidophasmata comprise Diapheromerinae, Pseudophasmatinae, and Agathemera, whereas all remaining lineages form the Oriophasmata, including Heteropterygidae, Phylliinae, Bacillus, Lonchodidae (Necrosciinae + Lonchodinae), Clitumninae, Cladomorphinae, and Lanceocercata. We furthermore performed a divergence time analysis and reconstructed the historical biogeography for stick and leaf insects. Phasmatodea either originated in Southeast Asia or in the New World. Our results suggest that the extant distribution of Phasmatodea is largely the result of dispersal events in a recently and rapidly diversified insect lineage rather than the result of vicariant processes.
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the evolution of tarsal adhesive microstructures in stick and leaf insects Phasmatodea
Frontiers in Ecology and Evolution, 2018Co-Authors: Thies H. Büscher, Thomas R. Buckley, Stanislav N Gorb, Constanze Grohmann, Sven BradlerAbstract:Insects have developed specialized structures on their feet for adhering to surfaces, with stick and leaf insects or Phasmatodea exhibiting an unexpectedly high diversity of these structures. In Phasmatodea, attachment on different substrates is achieved by two types of pads on the legs: the euplantulae on the tarsomeres and the arolium on the pretarsus. The euplantulae are adhesive structures capable of adaptability to the substrate profile and generation of the required attachment strength. The diversity of euplantular microstructures of 56 species that represent all major lineages recognized within Phasmatodea and the whole biogeographical distribution of the group are examined using scanning electron microscopy (SEM). Nine different types of attachment structures can be distinguished whereby one, the nubby type, can be further divided into three different distinct types based on the specific ratio of each conical outgrowth. We mapped the morphological data from the SEM onto a phylogenetic tree we that reconstructed based on molecular data. Previously, the evolution of different adhesive microstructures (AMs) on these pads has been suggested to reflect phylogenetic groups. However, different types of AMs are found within monophyletic groups, and our ancestral character state reconstruction suggests smooth euplantulae in the ground pattern of EuPhasmatodea and multiple independent origins of other forms. The type of AM appears to be strongly associated with ecomorphs, e.g., smooth euplantular surfaces are more frequently found in tree-dwellers than in ground-dwellers, whilst the attachment pads of ground-dwelling species primarily bear conical cuticular outgrowths (nubby euplantulae).
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Assembling large genomes: analysis of the stick insect (Clitarchus hookeri) genome reveals a high repeat content and sex-biased genes associated with reproduction
BMC Genomics, 2017Co-Authors: Chen Wu, Ross N Crowhurst, Victoria G Twort, Richard D Newcomb, Thomas R. BuckleyAbstract:Background Stick insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south. Here, we present a de novo genome assembly of a female C. hookeri and use it to detect candidate genes associated with gamete production and development in females and males. We also explore the factors underlying large genome size in stick insects. Results The C. hookeri genome assembly was 4.2 Gb, similar to the flow cytometry estimate, making it the second largest insect genome sequenced and assembled to date. Like the large genome of Locusta migratoria , the genome of C. hookeri is also highly repetitive and the predicted gene models are much longer than those from most other sequenced insect genomes, largely due to longer introns. Miniature inverted repeat transposable elements (MITEs), absent in the much smaller T. cristinae genome, is the most abundant repeat type in the C. hookeri genome assembly. Mapping RNA-Seq reads from female and male gonadal transcriptomes onto the genome assembly resulted in the identification of 39,940 gene loci, 15.8% and 37.6% of which showed female-biased and male-biased expression, respectively. The genes that were over-expressed in females were mostly associated with molecular transportation, developmental process, oocyte growth and reproductive process; whereas, the male-biased genes were enriched in rhythmic process, molecular transducer activity and synapse. Several genes involved in the juvenile hormone synthesis pathway were also identified. Conclusions The evolution of large insect genomes such as L. migratoria and C. hookeri genomes is most likely due to the accumulation of repetitive regions and intron elongation. MITEs contributed significantly to the growth of C. hookeri genome size yet are surprisingly absent from the T. cristinae genome. Sex-biased genes identified from gonadal tissues, including genes involved in juvenile hormone synthesis, provide interesting candidates for the further study of flexible reproduction in stick insects.
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de novo transcriptome analysis of the common new zealand stick insect clitarchus hookeri Phasmatodea reveals genes involved in olfaction digestion and sexual reproduction
PLOS ONE, 2016Co-Authors: Chen Wu, Ross N Crowhurst, Alice B Dennis, Victoria G Twort, Richard D Newcomb, Howard A Ross, Thomas R. BuckleyAbstract:Phasmatodea, more commonly known as stick insects, have been poorly studied at the molecular level for several key traits, such as components of the sensory system and regulators of reproduction and development, impeding a deeper understanding of their functional biology. Here, we employ de novo transcriptome analysis to identify genes with primary functions related to female odour reception, digestion, and male sexual traits in the New Zealand common stick insect Clitarchus hookeri (White). The female olfactory gene repertoire revealed ten odorant binding proteins with three recently duplicated, 12 chemosensory proteins, 16 odorant receptors, and 17 ionotropic receptors. The majority of these olfactory genes were over-expressed in female antennae and have the inferred function of odorant reception. Others that were predominantly expressed in male terminalia (n = 3) and female midgut (n = 1) suggest they have a role in sexual reproduction and digestion, respectively. Over-represented transcripts in the midgut were enriched with digestive enzyme gene families. Clitarchus hookeri is likely to harbour nine members of an endogenous cellulase family (glycoside hydrolase family 9), two of which appear to be specific to the C. hookeri lineage. All of these cellulase sequences fall into four main phasmid clades and show gene duplication events occurred early in the diversification of Phasmatodea. In addition, C. hookeri genome is likely to express γ-proteobacteria pectinase transcripts that have recently been shown to be the result of horizontal transfer. We also predicted 711 male terminalia-enriched transcripts that are candidate accessory gland proteins, 28 of which were annotated to have molecular functions of peptidase activity and peptidase inhibitor activity, two groups being widely reported to regulate female reproduction through proteolytic cascades. Our study has yielded new insights into the genetic basis of odour detection, nutrient digestion, and male sexual traits in stick insects. The C. hookeri reference transcriptome, together with identified gene families, provides a comprehensive resource for studying the evolution of sensory perception, digestive systems, and reproductive success in phasmids.
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Single origin of the Mascarene stick insects: ancient radiation on sunken islands?
BMC Evolutionary Biology, 2015Co-Authors: Sven Bradler, Nicolas Cliquennois, Thomas R. BuckleyAbstract:Background The study of islands as model systems plays a key role in understanding many evolutionary processes. Knowledge of the historical events leading to present-day island communities is pivotal for exploring fundamental mechanisms of speciation and adaptation. The remote Mascarene archipelago (Mauritius, Réunion, Rodrigues), considered to be the product of an age-progressive trend of north-to-south volcanic activity in the Indian Ocean, hosts a remarkably diverse, endemic and threatened concentration of flora and fauna that has traditionally been considered to be biogeographically related to Madagascar and Africa. To explore the evolutionary diversity of the Mascarene stick insects (Phasmatodea), we constructed a global phylogeny from approximately 2.4 kb of mitochondrial and nuclear sequence data of more than 120 species representing all major Phasmatodean lineages. Results Based on the obtained time-calibrated molecular tree we demonstrate that the current phasmid community of the Mascarene archipelago, which consists of members of four presumably unrelated traditional subfamilies, is the result of a single ancient dispersal event from Australasia and started radiating between 16–29 million years ago, significantly predating the age of Mauritius (8–10 million years). Conclusions We propose that the Mascarene stick insects diversified on landmasses now eroded away, presumably to the north of Mauritius. In consequence, ancient islands have probably persisted in the Indian Ocean until the emergence of Mauritius and not only served as stepping stones for colonisation events during sea-level lowstands, but as long-lasting cradles of evolution. These ancient landmasses most likely allowed for adaptive speciation and served as significant sources of diversity that contributed to the biomes of the Mascarene archipelago and the megadiverse Madagascar.
Matan Shelomi - One of the best experts on this subject based on the ideXlab platform.
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carausius morosus Phasmatodea homologues of human genes withelevated expression in the colon
Annals of Colorectal Research, 2019Co-Authors: Matan ShelomiAbstract:Background: Preliminary testing of novel drugs for colorectal conditions must be performed on animal models, with invertebratemodels desirable for practical reasons. The insect excretory organs, the Malpighian tubules, have been cited as models for humanrenal disease research because they differentially express several genes homologous to those differentially expressed in humankidneys. Their role in excretion and homeostasis suggests that they could be models for human colorectal disease. The insect Carausiusmorosus (Phasmatodea) has been a model organism for decades. Regarding its potential use as a colorectal disease model,it has an advantage over other insects in that excretion in Phasmatodea is split between two organs: Malpighian tubules and thePhasmatodea-specific “appendices of the midgut”.Objectives: To find homologues of human colon genes expressed in the excretory tissues of C. morosus for potential use in drugtesting and other experiments requiring an animal model.Methods: Pre-existing transcriptomics data for the excretory system of the C. morosus were examined to find genes homologous tothose known to have elevated expression in the human colon. This was done with the goal of possibly determining the excretorytissues in which they are differentially expressed.Results: Exactly sixty transcripts from the excretory system transcriptome of C. morosus showed high sequence homology withhuman colon-specific genes, with a minimum e-value of 1e-50. Examples include solute carriers, myosin, bestrophin, carbonic anhydrase,and nitric oxide synthase. Several genes were identified with prognostic value for renal, pancreatic, endometrial, liver, skin,and urothelial cancers.Conclusions: C. morosus can be used as model insect for human medical research applications, including colorectal drug testing.
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de novo transcriptome analysis of the excretory tubules of carausius morosus Phasmatodea and possible functions of the midgut appendices
PLOS ONE, 2017Co-Authors: Matan ShelomiAbstract:: The Malpighian tubules are the insect excretory organs, responsible for ion and water homeostasis and elimination of nitrogenous wastes. Post-genomic assays suggest they also metabolize and detoxify xenobiotic compounds and have antimicrobial properties. The Phasmatodea have an additional, unique set of excretory organs referred to predominantly as midgut appendices. Their function and how it compares to phasmid and other insect Malpighian tubules is unknown. Hypotheses include carbonic anhydrase activity, calcium and metal cation sequestration, and xenobiotic transport. This work presents the first comparative transcriptomic analysis of the Phasmatodean excretory organs, using the model insect Carausius morosus. I produced de novo transcriptomes of the midgut appendices, midgut wall, and Malpighian tubules, and looked for differentially expressed genes associated with putative organ functions. The appendices differentially and highly express lipid transport and metabolism proteins, and the biomineralization gene otopetrin. The Malpighian tubules differentially and highly express acid phosphatases and multiple transporter types, while appendices express fat-soluble vitamin and peptide transporters. Many defense proteins such as multidrug resistance proteins, ABC transporters, cytochrome P450's, and glutathione-S-transferases were differentially expressed in specific excretory organs. I hypothesize that the appendices and Malpighian tubules both have defensive / xenobiotic metabolism functions, but each likely target different substrates. Phasmid Malpighian tubules excrete as in other insects, while the appendices may predominantly regulate amino acids, fats, and fat-soluble compounds. Lipid metabolism in insects is poorly understood, and the Phasmatodea may thus serve as a model for studying this further.
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bergmann s and allen s rules in native european and mediterranean Phasmatodea
Frontiers in Ecology and Evolution, 2017Co-Authors: Matan Shelomi, Dirk ZeussAbstract:Bergmann’s rule states that organisms at higher latitudes should be larger and thicker than those closer to the equator to better conserve heat, and Allen’s rule states that they will have shorter and thicker limbs at higher latitudes. Alternative explanations for latitudinal size clines include plant productivity and seasonality. The rules generally hold in endotherms, but in insects different species within the same genus can respond to latitude in unpredictable ways. We present the first biogeographical analysis of these rules in stick insects (order Phasmatodea), using four European species. Their long and thin bauplan makes the Phasmatodea ideal for ecomorphological studies of body length, which could identify the evolutionary drivers of their remarkable size range (including the world’s longest insects). Using preserved specimens from collections across Europe; body segment and limb measurements were taken for both genders of the species Bacillus rossius, Clonopsis gallica, Leptynia attenuata, and Pijnackeria hispanica. Lengths and volumetric features were compared to latitude as well as annual mean temperature, net primary productivity, and annual growing degree days, using weighted linear regressions and ANOVA analyses. At lower latitudes / higher temperatures, B. rossius and L. attenuata had longer limbs [Allen clines] and were larger bodied and/or longer [converse-Bergmann clines], while the other species did not show latitudinal clines per se. This matches what was predicted based on closely related insects and the presence of large Phasmatodea in the tropics, but violates the temperature-size rule. Most variation in size could be attributed to temperature, but untested factors could also play a role Whether these ecogeographic rules hold true for tropical Phasmatodea and whether genetics or environment play are more important in determining adult length are topics for future research.
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ancestral gene duplication enabled the evolution of multifunctional cellulases in stick insects Phasmatodea
Insect Biochemistry and Molecular Biology, 2016Co-Authors: Matan Shelomi, David G Heckel, Yannick PauchetAbstract:The Phasmatodea (stick insects) have multiple, endogenous, highly expressed copies of glycoside hydrolase family 9 (GH9) genes. The purpose for retaining so many was unknown. We cloned and expressed the enzymes in transfected insect cell lines, and tested the individual proteins against different plant cell wall component poly- and oligosaccharides. Nearly all isolated enzymes were active against carboxymethylcellulose, however most could also degrade glucomannan, and some also either xylan or xyloglucan. The latter two enzyme groups were each monophyletic, suggesting the evolution of these novel substrate specificities in an early ancestor of the order. Such enzymes are highly unusual for Metazoa, for which no xyloglucanases had been reported. Phasmatodea gut extracts could degrade multiple plant cell wall components fully into sugar monomers, suggesting that enzymatic breakdown of plant cell walls by the entire Phasmatodea digestome may contribute to the Phasmatodea nutritional budget. The duplication and neofunctionalization of GH9s in the ancestral Phasmatodea may have enabled them to specialize as folivores and diverge from their omnivorous ancestors. The structural changes enabling these unprecedented activities in the cellulases require further study.
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review of the gross anatomy and microbiology of the Phasmatodea digestive tract
Journal of Orthoptera Research, 2015Co-Authors: Matan Shelomi, Irnayuli R Sitepu, Kyria Boundymills, Lynn S KimseyAbstract:Abstract The sparse descriptions of the stick insect (Phasmatodea) digestive system as reported/provided in the literature are highly contradictory. This paper describes the digestive systems of several families of Phasmatodea (Timematidae, Heteropterygidae, Diapheromeridae, Pseudophasmatidae, and Phasmatidae) plus the gut microbiome of these and one other (Phylliidae) to both verify past findings and provide a general description of the Phasmatodea alimentary canal. The constrictions imposed by this anatomy on phasmid gut microbiology, its connections to recently released Phasmatodea transcriptomes, and how it differs from the anatomy of related orders in the Polyneoptera are discussed. All Phasmatodea have ridged proventriculi lined or covered with small spines. Anterior projections of the midgut, sometimes described as gastric caeca, are only found in EuPhasmatodea and often obscure the proventriculus. We define the cardia as the complex of foregut and midgut tissue where the type II peritrophic matrix...
Sven Bradler - One of the best experts on this subject based on the ideXlab platform.
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evolution of oviposition techniques in stick and leaf insects Phasmatodea
Frontiers in Ecology and Evolution, 2018Co-Authors: Sven Bradler, J A Robertson, Michael F WhitingAbstract:Stick and leaf insects (Phasmatodea) are large, tropical, predominantly nocturnal herbivores, which exhibit extreme masquerade crypsis, whereby they morphologically and behaviorally resemble twigs, bark, lichen, moss, and leaves. Females employ a wide range of egg-laying techniques, largely corresponding to their ecological niche, including dropping or flicking eggs to the forest floor, gluing eggs to plant substrate, skewering eggs through leaves, ovipositing directly into the soil, or even producing a complex ootheca. Phasmids are the only insects with highly species-specific egg morphology across the entire order, with specific egg forms that correspond to oviposition technique. We investigate the temporal, biogeographic and phylogenetic pattern of evolution of egg-laying strategies in Phasmatodea. Our results unequivocally demonstrate that the ancestral oviposition strategy for female stick and leaf insects is to remain in the foliage and drop or flick eggs to the ground, a strategy that maintains their masquerade. Other major key innovations in the evolution of Phasmatodea include the (1) hardening of the egg capsule in EuPhasmatodea; (2) the repeated evolution of capitulate eggs (which induce ant-mediated dispersal, or myrmecochory); (3) adapting to a ground or bark dwelling microhabitat with a corresponding shift in adult and egg phenotype and egg deposition directly into the soil; and (4) adhesion of eggs in a clade of Necrosciinae that led to subsequent diversification in oviposition modes and egg types. We infer 16 independent origins of a burying/inserting eggs into soil/crevices oviposition strategy, 7 origins of gluing eggs to substrate, and a single origin each of skewering eggs through leaves and producing an ootheca. We additionally discuss the systematic implications of our phylogenetic results. Aschiphasmatinae is strongly supported as the earliest diverging extant lineage of EuPhasmatodea. Phylliinae and Diapheromerinae are both relatively early diverging euPhasmatodean taxa. We formally transfer Otocrania from Cladomorphinae to Diapheromerinae and recognize two tribes within Diapheromerinae: Diapheromerini sensu nov. and Oreophoetini sensu nov. We formally recognize the clade comprising Necrosciinae and Lonchodinae as Lonchodidae stat. rev. sensu nov.
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the evolution of tarsal adhesive microstructures in stick and leaf insects Phasmatodea
Frontiers in Ecology and Evolution, 2018Co-Authors: Thies H. Büscher, Thomas R. Buckley, Stanislav N Gorb, Constanze Grohmann, Sven BradlerAbstract:Insects have developed specialized structures on their feet for adhering to surfaces, with stick and leaf insects or Phasmatodea exhibiting an unexpectedly high diversity of these structures. In Phasmatodea, attachment on different substrates is achieved by two types of pads on the legs: the euplantulae on the tarsomeres and the arolium on the pretarsus. The euplantulae are adhesive structures capable of adaptability to the substrate profile and generation of the required attachment strength. The diversity of euplantular microstructures of 56 species that represent all major lineages recognized within Phasmatodea and the whole biogeographical distribution of the group are examined using scanning electron microscopy (SEM). Nine different types of attachment structures can be distinguished whereby one, the nubby type, can be further divided into three different distinct types based on the specific ratio of each conical outgrowth. We mapped the morphological data from the SEM onto a phylogenetic tree we that reconstructed based on molecular data. Previously, the evolution of different adhesive microstructures (AMs) on these pads has been suggested to reflect phylogenetic groups. However, different types of AMs are found within monophyletic groups, and our ancestral character state reconstruction suggests smooth euplantulae in the ground pattern of EuPhasmatodea and multiple independent origins of other forms. The type of AM appears to be strongly associated with ecomorphs, e.g., smooth euplantular surfaces are more frequently found in tree-dwellers than in ground-dwellers, whilst the attachment pads of ground-dwelling species primarily bear conical cuticular outgrowths (nubby euplantulae).
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stem group stick insects Phasmatodea in the early eocene at mcabee british columbia canada and republic washington united states of america
Canadian Entomologist, 2015Co-Authors: Bruce S Archibald, Sven BradlerAbstract:Stem-group Phasmatodea, known as the Susumanioidea, are previously established from the Jurassic through the Paleocene. Here, we extend this record to the early Eocene with five new fossils: two forewings from the Klondike Mountain Formation exposures at Republic, Washington, United States of America, and three partially complete specimens from the McAbee locality in southern British Columbia, Canada. We assign both of the Republic specimens to the new genus and species Eoprephasma hichensi new genus, new species . Two of the McAbee fossils appear to represent two further new species, which we refer to as Susumanioidea species A and B for lack of clearly preserved diagnostic species-level character states. The third might belong to one of these two species, but this is unclear. In all three, the mesothorax and metathorax are not notably extended, the forewings are not shortened, the foreleg femur is straight, and species A possesses an extended, external ovipositor with an operculum (unknown in the other specimens). These conditions are rare and never found in combination in EuPhasmatodea. All other stem-group Phasmatodea younger than the Early Cretaceous of China are only known from isolated wings.
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Single origin of the Mascarene stick insects: ancient radiation on sunken islands?
BMC Evolutionary Biology, 2015Co-Authors: Sven Bradler, Nicolas Cliquennois, Thomas R. BuckleyAbstract:Background The study of islands as model systems plays a key role in understanding many evolutionary processes. Knowledge of the historical events leading to present-day island communities is pivotal for exploring fundamental mechanisms of speciation and adaptation. The remote Mascarene archipelago (Mauritius, Réunion, Rodrigues), considered to be the product of an age-progressive trend of north-to-south volcanic activity in the Indian Ocean, hosts a remarkably diverse, endemic and threatened concentration of flora and fauna that has traditionally been considered to be biogeographically related to Madagascar and Africa. To explore the evolutionary diversity of the Mascarene stick insects (Phasmatodea), we constructed a global phylogeny from approximately 2.4 kb of mitochondrial and nuclear sequence data of more than 120 species representing all major Phasmatodean lineages. Results Based on the obtained time-calibrated molecular tree we demonstrate that the current phasmid community of the Mascarene archipelago, which consists of members of four presumably unrelated traditional subfamilies, is the result of a single ancient dispersal event from Australasia and started radiating between 16–29 million years ago, significantly predating the age of Mauritius (8–10 million years). Conclusions We propose that the Mascarene stick insects diversified on landmasses now eroded away, presumably to the north of Mauritius. In consequence, ancient islands have probably persisted in the Indian Ocean until the emergence of Mauritius and not only served as stepping stones for colonisation events during sea-level lowstands, but as long-lasting cradles of evolution. These ancient landmasses most likely allowed for adaptive speciation and served as significant sources of diversity that contributed to the biomes of the Mascarene archipelago and the megadiverse Madagascar.
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Extreme convergence in egg-laying strategy across insect orders
Scientific Reports, 2015Co-Authors: Julia Goldberg, Joachim Bresseel, Jerome Constant, Bruno Kneubühler, Fanny Leubner, Peter Michalik, Sven BradlerAbstract:The eggs of stick and leaf insects (Phasmatodea) bear strong resemblance to plant seeds and are commonly dispersed by females dropping them to the litter. Here we report a novel egg-deposition mode for Phasmatodea performed by an undescribed Vietnamese species of the enigmatic subfamily Korinninae that produces a complex egg case (ootheca), containing numerous eggs in a highly ordered arrangement. This novel egg-deposition mode is most reminiscent of egg cases produced by members of unrelated insect orders, e.g. by praying mantises (Mantodea) and tortoise beetles (Coleoptera: Cassidinae). Ootheca production constitutes a striking convergence and major transition in reproductive strategy among stick insects, viz. a shift from dispersal of individual eggs to elaborate egg concentration. Adaptive advantages of ootheca formation on arboreal substrate are likely related to protection against parasitoids and desiccation and to allocation of specific host plants. Our phylogenetic analysis of nuclear (28S, H3) and mitochondrial (COI, COII) genes recovered Korinninae as a subordinate taxon among the species-rich Necrosciinae with Asceles as sister taxon, thus suggesting that placement of single eggs on leaves by host plant specialists might be the evolutionary precursor of ootheca formation within stick insects.
Victoria G Twort - One of the best experts on this subject based on the ideXlab platform.
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Assembling large genomes: analysis of the stick insect (Clitarchus hookeri) genome reveals a high repeat content and sex-biased genes associated with reproduction
BMC Genomics, 2017Co-Authors: Chen Wu, Ross N Crowhurst, Victoria G Twort, Richard D Newcomb, Thomas R. BuckleyAbstract:Background Stick insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south. Here, we present a de novo genome assembly of a female C. hookeri and use it to detect candidate genes associated with gamete production and development in females and males. We also explore the factors underlying large genome size in stick insects. Results The C. hookeri genome assembly was 4.2 Gb, similar to the flow cytometry estimate, making it the second largest insect genome sequenced and assembled to date. Like the large genome of Locusta migratoria , the genome of C. hookeri is also highly repetitive and the predicted gene models are much longer than those from most other sequenced insect genomes, largely due to longer introns. Miniature inverted repeat transposable elements (MITEs), absent in the much smaller T. cristinae genome, is the most abundant repeat type in the C. hookeri genome assembly. Mapping RNA-Seq reads from female and male gonadal transcriptomes onto the genome assembly resulted in the identification of 39,940 gene loci, 15.8% and 37.6% of which showed female-biased and male-biased expression, respectively. The genes that were over-expressed in females were mostly associated with molecular transportation, developmental process, oocyte growth and reproductive process; whereas, the male-biased genes were enriched in rhythmic process, molecular transducer activity and synapse. Several genes involved in the juvenile hormone synthesis pathway were also identified. Conclusions The evolution of large insect genomes such as L. migratoria and C. hookeri genomes is most likely due to the accumulation of repetitive regions and intron elongation. MITEs contributed significantly to the growth of C. hookeri genome size yet are surprisingly absent from the T. cristinae genome. Sex-biased genes identified from gonadal tissues, including genes involved in juvenile hormone synthesis, provide interesting candidates for the further study of flexible reproduction in stick insects.
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de novo transcriptome analysis of the common new zealand stick insect clitarchus hookeri Phasmatodea reveals genes involved in olfaction digestion and sexual reproduction
PLOS ONE, 2016Co-Authors: Chen Wu, Ross N Crowhurst, Alice B Dennis, Victoria G Twort, Richard D Newcomb, Howard A Ross, Thomas R. BuckleyAbstract:Phasmatodea, more commonly known as stick insects, have been poorly studied at the molecular level for several key traits, such as components of the sensory system and regulators of reproduction and development, impeding a deeper understanding of their functional biology. Here, we employ de novo transcriptome analysis to identify genes with primary functions related to female odour reception, digestion, and male sexual traits in the New Zealand common stick insect Clitarchus hookeri (White). The female olfactory gene repertoire revealed ten odorant binding proteins with three recently duplicated, 12 chemosensory proteins, 16 odorant receptors, and 17 ionotropic receptors. The majority of these olfactory genes were over-expressed in female antennae and have the inferred function of odorant reception. Others that were predominantly expressed in male terminalia (n = 3) and female midgut (n = 1) suggest they have a role in sexual reproduction and digestion, respectively. Over-represented transcripts in the midgut were enriched with digestive enzyme gene families. Clitarchus hookeri is likely to harbour nine members of an endogenous cellulase family (glycoside hydrolase family 9), two of which appear to be specific to the C. hookeri lineage. All of these cellulase sequences fall into four main phasmid clades and show gene duplication events occurred early in the diversification of Phasmatodea. In addition, C. hookeri genome is likely to express γ-proteobacteria pectinase transcripts that have recently been shown to be the result of horizontal transfer. We also predicted 711 male terminalia-enriched transcripts that are candidate accessory gland proteins, 28 of which were annotated to have molecular functions of peptidase activity and peptidase inhibitor activity, two groups being widely reported to regulate female reproduction through proteolytic cascades. Our study has yielded new insights into the genetic basis of odour detection, nutrient digestion, and male sexual traits in stick insects. The C. hookeri reference transcriptome, together with identified gene families, provides a comprehensive resource for studying the evolution of sensory perception, digestive systems, and reproductive success in phasmids.
Chen Wu - One of the best experts on this subject based on the ideXlab platform.
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Assembling large genomes: analysis of the stick insect (Clitarchus hookeri) genome reveals a high repeat content and sex-biased genes associated with reproduction
BMC Genomics, 2017Co-Authors: Chen Wu, Ross N Crowhurst, Victoria G Twort, Richard D Newcomb, Thomas R. BuckleyAbstract:Background Stick insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south. Here, we present a de novo genome assembly of a female C. hookeri and use it to detect candidate genes associated with gamete production and development in females and males. We also explore the factors underlying large genome size in stick insects. Results The C. hookeri genome assembly was 4.2 Gb, similar to the flow cytometry estimate, making it the second largest insect genome sequenced and assembled to date. Like the large genome of Locusta migratoria , the genome of C. hookeri is also highly repetitive and the predicted gene models are much longer than those from most other sequenced insect genomes, largely due to longer introns. Miniature inverted repeat transposable elements (MITEs), absent in the much smaller T. cristinae genome, is the most abundant repeat type in the C. hookeri genome assembly. Mapping RNA-Seq reads from female and male gonadal transcriptomes onto the genome assembly resulted in the identification of 39,940 gene loci, 15.8% and 37.6% of which showed female-biased and male-biased expression, respectively. The genes that were over-expressed in females were mostly associated with molecular transportation, developmental process, oocyte growth and reproductive process; whereas, the male-biased genes were enriched in rhythmic process, molecular transducer activity and synapse. Several genes involved in the juvenile hormone synthesis pathway were also identified. Conclusions The evolution of large insect genomes such as L. migratoria and C. hookeri genomes is most likely due to the accumulation of repetitive regions and intron elongation. MITEs contributed significantly to the growth of C. hookeri genome size yet are surprisingly absent from the T. cristinae genome. Sex-biased genes identified from gonadal tissues, including genes involved in juvenile hormone synthesis, provide interesting candidates for the further study of flexible reproduction in stick insects.
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de novo transcriptome analysis of the common new zealand stick insect clitarchus hookeri Phasmatodea reveals genes involved in olfaction digestion and sexual reproduction
PLOS ONE, 2016Co-Authors: Chen Wu, Ross N Crowhurst, Alice B Dennis, Victoria G Twort, Richard D Newcomb, Howard A Ross, Thomas R. BuckleyAbstract:Phasmatodea, more commonly known as stick insects, have been poorly studied at the molecular level for several key traits, such as components of the sensory system and regulators of reproduction and development, impeding a deeper understanding of their functional biology. Here, we employ de novo transcriptome analysis to identify genes with primary functions related to female odour reception, digestion, and male sexual traits in the New Zealand common stick insect Clitarchus hookeri (White). The female olfactory gene repertoire revealed ten odorant binding proteins with three recently duplicated, 12 chemosensory proteins, 16 odorant receptors, and 17 ionotropic receptors. The majority of these olfactory genes were over-expressed in female antennae and have the inferred function of odorant reception. Others that were predominantly expressed in male terminalia (n = 3) and female midgut (n = 1) suggest they have a role in sexual reproduction and digestion, respectively. Over-represented transcripts in the midgut were enriched with digestive enzyme gene families. Clitarchus hookeri is likely to harbour nine members of an endogenous cellulase family (glycoside hydrolase family 9), two of which appear to be specific to the C. hookeri lineage. All of these cellulase sequences fall into four main phasmid clades and show gene duplication events occurred early in the diversification of Phasmatodea. In addition, C. hookeri genome is likely to express γ-proteobacteria pectinase transcripts that have recently been shown to be the result of horizontal transfer. We also predicted 711 male terminalia-enriched transcripts that are candidate accessory gland proteins, 28 of which were annotated to have molecular functions of peptidase activity and peptidase inhibitor activity, two groups being widely reported to regulate female reproduction through proteolytic cascades. Our study has yielded new insights into the genetic basis of odour detection, nutrient digestion, and male sexual traits in stick insects. The C. hookeri reference transcriptome, together with identified gene families, provides a comprehensive resource for studying the evolution of sensory perception, digestive systems, and reproductive success in phasmids.
