Nutritional upgrading for omnivorous carpenter ants by the endosymbiont Blochmannia

<p>Abstract</p> <p>Background</p> <p>Carpenter ants (genus <it>Camponotus</it>) are considered to be omnivores. Nonetheless, the genome sequence of <it>Blochmannia floridanus</it>, the obligate intracellular endosymbiont of <it>Camponotus floridanus</it>, suggests a function in nutritional upgrading of host resources by the bacterium. Thus, the strongly reduced genome of the endosymbiont retains genes for all subunits of a functional urease, as well as those for biosynthetic pathways for all but one (arginine) of the amino acids essential to the host.</p> <p>Results</p> <p>Nutritional upgrading by <it>Blochmannia </it>was tested in 90-day feeding experiments with brood-raising in worker-groups on chemically defined diets with and without essential amino acids and treated or not with antibiotics. Control groups were fed with cockroaches, honey water and Bhatkar agar. Worker-groups were provided with brood collected from the queenright mother-colonies (45 eggs and 45 first instar larvae each). Brood production did not differ significantly between groups of symbiotic workers on diets with and without essential amino acids. However, aposymbiotic worker groups raised significantly less brood on a diet lacking essential amino acids. Reduced brood production by aposymbiotic workers was compensated when those groups were provided with essential amino acids in their diet. Decrease of endosymbionts due to treatment with antibiotic was monitored by qRT-PCR and FISH after the 90-day experimental period. Urease function was confirmed by feeding experiments using ¹⁵N-labelled urea. GC-MS analysis of ¹⁵N-enrichment of free amino acids in workers revealed significant labelling of the non-essential amino acids alanine, glycine, aspartic acid, and glutamic acid, as well as of the essential amino acids methionine and phenylalanine.</p> <p>Conclusion</p> <p>Our results show that endosymbiotic <it>Blochmannia </it>nutritionally upgrade the diet of <it>C. floridanus </it>hosts to provide essential amino acids, and that it may also play a role in nitrogen recycling via its functional urease. <it>Blochmannia </it>may confer a significant fitness advantage via nutritional upgrading by enhancing competitive ability of <it>Camponotus </it>with other ant species lacking such an endosymbiont. Domestication of the endosymbiont may have facilitated the evolutionary success of the genus <it>Camponotus</it>.</p

Maximum likelihood models and algorithms for gene tree evolution with duplications and losses

<p>Abstract</p> <p>Background</p> <p>The abundance of new genomic data provides the opportunity to map the location of gene duplication and loss events on a species phylogeny. The first methods for mapping gene duplications and losses were based on a parsimony criterion, finding the mapping that minimizes the number of duplication and loss events. Probabilistic modeling of gene duplication and loss is relatively new and has largely focused on birth-death processes.</p> <p>Results</p> <p>We introduce a new maximum likelihood model that estimates the speciation and gene duplication and loss events in a gene tree within a species tree with branch lengths. We also provide an, in practice, efficient algorithm that computes optimal evolutionary scenarios for this model. We implemented the algorithm in the program DrML and verified its performance with empirical and simulated data.</p> <p>Conclusions</p> <p>In test data sets, DrML finds optimal gene duplication and loss scenarios within minutes, even when the gene trees contain sequences from several hundred species. In many cases, these optimal scenarios differ from the lca-mapping that results from a parsimony gene tree reconciliation. Thus, DrML provides a new, practical statistical framework on which to study gene duplication.</p

A Post-Synaptic Scaffold at the Origin of the Animal Kingdom

The evolution of complex sub-cellular structures such as the synapse requires the assembly of multiple proteins, each conferring added functionality to the integrated structure. Tracking the early evolution of synapses has not been possible without genomic information from the earliest branching animals. As the closest extant relatives to the Eumetazoa, Porifera (sponges) represent a pivotal group for understanding the evolution of nervous systems, because sponges lack neurons with clearly recognizable synapses, in contrast to eumetazoan animals.We show that the genome of the demosponge Amphimedon queenslandica possesses a nearly complete set of post-synaptic protein homologs whose conserved interaction motifs suggest assembly into a complex structure. In the critical synaptic scaffold gene, dlg, residues that make hydrogen bonds and van der Waals interactions with the PDZ ligand are 100% conserved between sponge and human, as is the motif organization of the scaffolds. Expression in Amphimedon of multiple post-synaptic gene homologs in larval flask cells further supports the existence of an assembled structure. Among the few post-synaptic genes absent from Amphimedon, but present in Eumetazoa, are receptor genes including the entire ionotropic glutamate receptor family.Highly conserved protein interaction motifs and co-expression in sponges of multiple proteins whose homologs interact in eumetazoan synapses indicate that a complex protein scaffold was present at the origin of animals, perhaps predating nervous systems. A relatively small number of crucial innovations to this pre-existing structure may represent the founding changes that led to a post-synaptic element

Immunological Change in a Parasite-Impoverished Environment: Divergent Signals from Four Island Taxa

Dramatic declines of native Hawaiian avifauna due to the human-mediated emergence of avian malaria and pox prompted an examination of whether island taxa share a common altered immunological signature, potentially driven by reduced genetic diversity and reduced exposure to parasites. We tested this hypothesis by characterizing parasite prevalence, genetic diversity and three measures of immune response in two recently-introduced species (Neochmia temporalis and Zosterops lateralis) and two island endemics (Acrocephalus aequinoctialis and A. rimitarae) and then comparing the results to those observed in closely-related mainland counterparts. The prevalence of blood parasites was significantly lower in 3 of 4 island taxa, due in part to the absence of certain parasite lineages represented in mainland populations. Indices of genetic diversity were unchanged in the island population of N. temporalis; however, allelic richness was significantly lower in the island population of Z. lateralis while both allelic richness and heterozygosity were significantly reduced in the two island-endemic species examined. Although parasite prevalence and genetic diversity generally conformed to expectations for an island system, we did not find evidence for a pattern of uniformly altered immune responses in island taxa, even amongst endemic taxa with the longest residence times. The island population of Z. lateralis exhibited a significantly reduced inflammatory cell-mediated response while levels of natural antibodies remained unchanged for this and the other recently introduced island taxon. In contrast, the island endemic A. rimitarae exhibited a significantly increased inflammatory response as well as higher levels of natural antibodies and complement. These measures were unchanged or lower in A. aequinoctialis. We suggest that small differences in the pathogenic landscape and the stochastic history of mutation and genetic drift are likely to be important in shaping the unique immunological profiles of small isolated populations. Consequently, predicting the impact of introduced disease on the many other endemic faunas of the remote Pacific will remain a challenge

Detection and Characterization of Wolbachia Infections in Natural Populations of Aphids: Is the Hidden Diversity Fully Unraveled?

Aphids are a serious threat to agriculture, despite being a rather small group of insects. The about 4,000 species worldwide engage in highly interesting and complex relationships with their microbial fauna. One of the key symbionts in arthropods is Wolbachia, an α-Proteobacterium implicated in many important biological processes and believed to be a potential tool for biological control. Aphids were thought not to harbour Wolbachia; however, current data suggest that its presence in aphids has been missed, probably due to the low titre of the infection and/or to the high divergence of the Wolbachia strains of aphids. The goal of the present study is to map the Wolbachia infection status of natural aphids populations, along with the characterization of the detected Wolbachia strains. Out of 425 samples from Spain, Portugal, Greece, Israel and Iran, 37 were found to be infected. Our results, based mainly on 16S rRNA gene sequencing, indicate the presence of two new Wolbachia supergroups prevailing in aphids, along with some strains belonging either to supergroup B or to supergroup A

Combining Next-Generation Sequencing Strategies for Rapid Molecular Resource Development from an Invasive Aphid Species, Aphis glycines

Aphids are one of the most important insect taxa in terms of ecology, evolutionary biology, genetics and genomics, and interactions with endosymbionts. Additionally, many aphids are serious pest species of agricultural and horticultural plants. Recent genetic and genomic research has expanded molecular resources for many aphid species, including the whole genome sequencing of the pea aphid, Acrythosiphon pisum. However, the invasive soybean aphid, Aphis glycines, lacks in any significant molecular resources.Two next-generation sequencing technologies (Roche-454 and Illumina GA-II) were used in a combined approach to develop both transcriptomic and genomic resources, including expressed genes and molecular markers. Over 278 million bp were sequenced among the two methods, resulting in 19,293 transcripts and 56,688 genomic sequences. From this data set, 635 SNPs and 1,382 microsatellite markers were identified. For each sequencing method, different soybean aphid biotypes were used which revealed potential biotype specific markers. In addition, we uncovered 39,822 bp of sequence that were related to the obligatory endosymbiont, Buchnera aphidicola, as well as sequences that suggest the presence of Hamiltonella defensa, a facultative endosymbiont.Molecular resources for an invasive, non-model aphid species were generated. Additionally, the power of next-generation sequencing to uncover endosymbionts was demonstrated. The resources presented here will complement ongoing molecular studies within the Aphididae, including the pea aphid whole genome, lead to better understanding of aphid adaptation and evolution, and help provide novel targets for soybean aphid control

Caratterizzazione di alcuni siti della rete accelerometrica nazionale al fine di individuare la risposta sismica locale

Le indagini geotecniche finalizzate alla stima della risposta sismica locale si limitano molto spesso ai primi 30 m di profondità, valore che è diventato uno standard per la classificazione delle caratteristiche di un sito. Negli anni ’90 Borcherdt (1994) e Martin e Dobry (1994) suggerirono 30 m come la profondità standard di indagine per la verifica delle strutture. Boore et al. (1993, 1994, 1997) e Boore e Joyner (1997) basarono le regressioni per il calcolo delle leggi predittive del moto del suolo sullo stesso parametro. Nel 1997 negli Stati Uniti il National Earthquake Hazards Reduction Program (NEHRP) nella stesura delle norme tecniche per le costruzioni in zona sismica (FEMA, 1997) utilizza per la prima volta il parametro Vs30 come indice per la classificazione dei suoli, con lo scopo di definirne l’amplificazione. Le norme tecniche per le costruzioni in zona sismica della comunità Europea, EC8 (ENV, 1998) ente da dati provenienti dagli Stati Uniti occidentali e, utilizzando dati provenienti dalla stessa regione, Wald & Mori (2000) segnalano che le VS,30 non sono molto ben correlate con l’entità dell’amplificazione, in quanto esiste una forte dispersione dei dati. La figura 1.1 mostra il rapporto tra le amplificazioni, mediate sull’intervallo di frequenza compreso tra 3-5 Hz. raccomandano lo stesso parametro per suddividere i terreni, anche se le classi differiscono in parte dalla classificazione NEHRP. Infine, anche in Italia, le Norme Tecniche per le Costruzioni (Normative Tecniche per le Costruzioni, Gazzetta Ufficiale del 14/01/2008) adottano la stessa suddivisione dei terreni adottata dall’EC8.L’attendibilità della velocità delle onde di taglio nei primi 30 m (VS,30) come estimatore della risposta sismica di un sito, in termini di frequenza e amplificazione, è tuttavia molto discussa.Innanzitutto il parametro è stato ricavato unicamente da dati provenienti dagli Stati Uniti occidentali e, utilizzando dati provenienti dalla stessa regione, Wald & Mori (2000) segnalano che le Vs30 non sono molto ben correlate con l’entità dell’amplificazione, in quanto esiste una forte dispersione dei dati. La figura 1.1 mostra il rapporto tra le amplificazioni, mediate sull’intervallo di frequenza compreso tra 3-5 Hz. I valori risultano effettivamente molto dispersi, ma questo risultato può essere spiegato col fatto che non tutte le classi di sito hanno frequenza di risonanza compreso in questo intervallo di frequenza. Perciò per alcuni siti la media è stata calcolata nell’intorno della frequenza di risonanza (sulle amplificazioni massime), mentre per altri è stata calcolata sulle armoniche superiori, che hanno ampiezze minori. Lavori eseguiti con dati provenienti da altre regioni sottolineano come le Vs30 non siano buoni estimatori per la predizione di amplificazioni in bacini profondi (Park & Hashash, 2004), per la stima delle amplificazioni in altre regioni (Stewart et al., 2003) o in presenza di inversioni di velocità (Di Giacomo et al., 2005). Uno studio recente, eseguito su dati giapponesi (Zhao et al., 2006) si è evitato l’uso della Vs30 perché strati spessi di terreno rigido posti sopra il substrato roccioso amplificano il moto di lungo periodo, mentre gli strati sottili e soffici tendono ad amplificare il moto di corto periodo: ciò significa che la VS,30 non può rappresentare il periodo predominante del sito, dato che si basa solo sugli strati superficiali. Secondo Mucciarelli e Gallipoli (2006) il confronto tra l’amplificazione sismica al sito e la Vs30 mostra che quest’ultimo parametro non è adeguato per spiegare gli effetti di sito osservati in Italia a causa delle situazioni geologiche particolari che sono diffuse nel nostro paese. La figura 1.2 mostra la distribuzione dell’ampiezza rispetto alla classe di sito, in cui si vede che le classi sono mal discriminate e le mediane delle classi A e B (indicate dalla linea nera) sono uguali. È però necessario notare che questo grafico è stato costruito utilizzando le ampiezze ricavate col metodo dei rapporti spettrali H/V, ma in letteratura (Bard, 1999) è dimostrato che tali rapporti spettrali permettono di stimare la frequenza di risonanza, ma falliscono nella stima del valore di amplificazione. In particolare la Vs30 sottostima gli effetti locali ai siti con inversione di velocità e li sovrastima in siti con bacini profondi. La Vs30 sembra fornire dei buoni risultati solo in siti che abbiano un profilo di velocità monotono, crescente con la profondità e un forte contrasto di impedenza nella prima decina di metri. Questo studio si propone di verificare l’attendibilità della velocità delle onde di taglio valutate nei primi 30 m come estimatore della risposta sismica di un sito. Per questo scopo sono state selezionate 45 stazioni della Rete Accelerometrica Nazionale, di cui si conoscono i profili stratigrafici e i profili di velocità delle onde di taglio e di compressione. Inoltre sono state raccolte le registrazioni strong motion relative ai terremoti registrati da queste stazioni. Gli effetti di sito sono stati valutati in due modi: · Le registrazioni sono state utilizzate per calcolare i rapporti spettrali H/V per ricavare la frequenza fondamentale propria di ciascun sito (f0) e il relativo valore di amplificazione; · I profili di velocità delle onde di taglio sono serviti per ricavare il modello teorico monodimensionale per il calcolo della funzione di trasferimento del sito, eseguito per mezzo del modello proposto da Haskell e Thomson (Haskell, 1953, Thomson 1950), da cui ricavare la f0 e l’amplificazione. I valori ottenuti con i due metodi sono stati poi confrontati per verificare la congruenza dei risultati. I profili di velocità hanno permesso di classificare le stazioni utilizzando la velocità media delle onde di taglio nei primi 30 m (Vs30), secondo la normativa italiana. I risultati ottenuti dalla valutazione della risposta di ciascun sito, espressi in termini di frequenza fondamentale e amplificazione, sono stati correlati con la rispettiva classe di sito per verificare l’attendibilità del parametro delle Vs30 come estimatore degli effetti di sito

Highly repetitive DNA sequences provide evidence for a lack of gene flow between morphological forms of Herdmania momus (Ascidiacea: Stolidobranchia).

The genomic structure of two morphological forms of the pyurid ascidian Herdmania momus — H. momus forma curvata and H. momus forma grandis—are compared using a rapidly evolving highly repetitive element isolated from the genome of H. momus forma curvata. A 663 bp (base pair) Cla I satellite sequence is present only in the genome of H. momus forma curvata, and hence can be used as a form-specific marker. Low-stringency Southern blot analyses, using the Cla I satellite as a probe, revealed that the genomes of H. momus forma grandis and another pyurid ascidian, Pyura stolonifera, do not contain similar sequences to the H. momus forma curvata repetitive element. In addition to this genomic dissimilarity, there are a number of significant reproductive and developmental differences between the two H. momus forms, and interform fertilisation rates are significantly lower than intraform rates. The molecular, reproductive and developmental differences between H. momus forma curvata and H. momus forma grandis indicate the presence of strong barriers to gene flow