What can the mitochondrial genome reveal about higher‐level phylogeny of the molluscan class Cephalopoda?

We present the first analysis of cephalopod mitochondrial gene order and construct phylogenies based on gene order using Bayesian, distance, and parsimony analysis methods. Analyses included all species of cephalopod for which the whole mitochondrial genome has been sequenced. Where resolution was obtained, these analyses supported division of Neocoleoidea, in which all recent coleoid Cephalopoda can be placed, into Octopodiformes and Decapodiformes. For the same taxa, we also constructed a phylogeny in a maximum likelihood framework based on amino‐acid coded sequence data of all mitochondrial protein coding genes. As well as supporting Octopodiformes and Decapodiformes, amino‐acid analyses established support for Teuthoidea (Oegospida and Myopsida) to the exclusion of Sepiidae, and supported a monophyletic Oegopsida. Partial mitochondrial sequences of additional higher‐level taxa for which whole genome data were not available were subsequently included in the amino‐acid analysis to provide additional information on phylogeny. Spirulida was found to be basal amongst Decapodiformes. Mapping of morphological characters onto our phylogeny and consideration of palaeontological evidence suggests that our phylogeny reflects true evolutionary relationships. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 161 , 573–586.     

Classifying the fire‐response traits of plants: How reliable are species‐level classifications?

Plant species in fire‐prone environments possess specific traits which allow them to survive fire. Species are commonly classified according to whether they survive fire and resprout or whether they are killed by fire and regenerate from seed. However, different populations of the same species have been shown to vary in their responses. Therefore, the classification of a species into a single category based on fire‐response traits may not necessarily be representative of every population under every circumstance. This study examined the extent of within‐species variation in fire‐response traits of woody plants in south‐eastern Australia after the 2003 fires. Species were then classified using two approaches: (i) using data from a field survey of fire‐response traits, taking into account within‐species variation; and (ii) using species' fire responses listed in a pre‐existing fire‐response database compiled from a variety of primary sources. Field data showed that the majority of species in the study area resprouted after fire with around one in 10 species variable in their resprouting response. Almost half of all species varied from site to site according to whether they regenerated from seed, either solely or in addition to resprouting. The numbers of species classified as resprouters and seed regenerators varied according to the classification method used. Differences were also found between the classification method when calculating the mean proportion of resprouters and seed regenerators across sites. The fire‐response traits for some species from the database were found to differ from the observed field responses. This study demonstrated that the application of a fire‐response trait, reported in a trait database, to an entire species, may not adequately represent the actual fire responses of the populations of interest. Rather than considering the fire‐response traits of a species, accurate prediction may be better achieved by considering how different populations of plants will respond to fire.     

What is the function of neuronal AP‐3?

Neurotransmission requires the proper organization and rapid recycling of synaptic vesicles. Rapid retrieval has been suggested to occur either by kiss-and-stay or kiss-and-run mechanisms, whereas classical recycling is mediated by clathrin-dependent endocytosis. Molecular coats are key components in the selection of cargos, AP-2 (adaptor protein 2) playing a prominent role in synaptic vesicle endocytosis. Another coat protein, AP-3, has been implicated in synaptic vesicle biogenesis and in the generation of secretory and lysosomal-related organelles. In the present review, we will particularly focus on the recent data concerning the recycling of synaptic vesicles and the function of AP-3 and the v-SNARE (vesicular soluble N-ethylmaleimide-sensitive fusion protein-attachment protein receptor) TI-VAMP (tetanus neurotoxin-insensitive vesicle-associated membrane protein) in these processes. We propose that AP-3 plays an important regulatory role in neurons which contributes to the basal and stimulated exocytosis of synaptic vesicles.     

An annotated update of the scale insect checklist of?Hungary (Hemiptera,Coccoidea)

The number of scale insect species (Hemiptera: Coccoidea) known from Hungary has increased in the last 10 years by 39 (16.6 %), to a total of 274 species belonging to 112 genera in10 families. The family Pseudococcidae is the most species rich, with 101 species in 34 genera; Diaspididae contains 59 species in 27 genera; Coccidae contains 54 species in 27 genera; and the Eriococcidae contains 33 species in 8 genera. The other 6 coccoid families each contain only a few species: Asterolecaniidae (7 species in 3 genera); Ortheziidae (7 species in 4 genera); Margarodidae sensu lato (5 species in 5 genera); Cryptococcidae (3 species in 2 genera); Kermesidae (4 species in 1genus); and Cerococcidae (1 species). Of the species in the check list, 224 were found in outdoor conditions, while 50 species occurred only in indoor conditions. This paper contains 22 species recorded for the first time in the Hungarian fauna.     

Dynamic models of immune responses: what is the ideal level of detail?

Background  

One of the goals of computational immunology is to facilitate the study of infectious diseases. Dynamic modeling is a powerful tool to integrate empirical data from independent sources, make novel predictions, and to foresee the gaps in the current knowledge. Dynamic models constructed to study the interactions between pathogens and hosts' immune responses have revealed key regulatory processes in the infection.     

Does phylogeny matter? Assessing the impact of phylogenetic information in ecological meta‐analysis

Meta-analysis is increasingly used in ecology and evolutionary biology. Yet, in these fields this technique has an important limitation: phylogenetic non-independence exists among taxa, violating the statistical assumptions underlying traditional meta-analytic models. Recently, meta-analytical techniques incorporating phylogenetic information have been developed to address this issue. However, no syntheses have evaluated how often including phylogenetic information changes meta-analytic results. To address this gap, we built phylogenies for and re-analysed 30 published meta-analyses, comparing results for traditional vs. phylogenetic approaches and assessing which characteristics of phylogenies best explained changes in meta-analytic results and relative model fit. Accounting for phylogeny significantly changed estimates of the overall pooled effect size in 47% of datasets for fixed-effects analyses and 7% of datasets for random-effects analyses. Accounting for phylogeny also changed whether those effect sizes were significantly different from zero in 23 and 40% of our datasets (for fixed- and random-effects models, respectively). Across datasets, decreases in pooled effect size magnitudes after incorporating phylogenetic information were associated with larger phylogenies and those with stronger phylogenetic signal. We conclude that incorporating phylogenetic information in ecological meta-analyses is important, and we provide practical recommendations for doing so.     

What is the mechanism of ParA‐mediated DNA movement?

The stable maintenance of low‐copy‐number plasmids requires active partitioning, with the most common mechanism in prokaryotes involving the ATPase ParA. ParA proteins undergo intricate spatiotemporal relocations across the nucleoid, dynamics that function to position plasmids at equally spaced intervals. This spacing naturally guarantees equal partitioning of plasmids to each daughter cell. However, the fundamental mechanism linking ParA dynamics with regular plasmid positioning has proved difficult to dissect. In this issue of Molecular Microbiology, Vecchiarelli et al. report on a time‐delay mechanism that allows a slow cycling between the nucleoid‐bound and unbound forms of ParA. The authors also propose a mechanism for plasmid movement that does not rely on ParA polymerization.     

Seed plant phylogeny: Demise of the anthophyte hypothesis?

Recent molecular phylogenetic studies indicate, surprisingly, that Gnetales are related to conifers, or even derived from them, and that no other extant seed plants are closely related to angiosperms. Are these results believable? Is this a clash between molecules and morphology?     

Can hyperparasitoids cause large‐scale outbreaks of insect herbivores?

Synchronous population fluctuations occur in many species and have large economic impacts, but remain poorly understood. Dispersal, climate and natural enemies have been hypothesized to cause synchronous population fluctuations across large areas. For example, insect herbivores cause extensive forest defoliation and have many natural enemies, such as parasitoids, that may cause landscape‐scale changes in density. Between outbreaks, parasitoid‐caused mortality of hosts/herbivores is high, but it drops substantially during outbreak episodes. Because of their essential role in regulating herbivore populations, we need to include parasitoids in spatial modelling approaches to more effectively manage insect defoliation. However, classic host‐parasitoid population models predict parasitoid density, and parasitoid density is difficult to relate to host‐level observations of parasitoid‐caused mortality. We constructed a novel model to study how parasitoids affect insect outbreaks at the landscape scale. The model represents metacommunity dynamics, in which herbivore regulation, colonisation and extinction are driven by interactions with the forest, primary parasitoids and hyperparasitoids. The model suggests that parasitoid spatial dynamics can produce landscape‐scale outbreaks. Our results propose the testable prediction that hyperparasitoid prevalence should increase just before the onset of an outbreak because of hyperparasitoid overexploitation. If verified empirically, hyperparasitoid distribution could provide a biotic indicator that an outbreak will occur.     

Which wavelength is optimal for transcranial low‐level laser stimulation?

One of the challenges in transcranial low‐level laser therapy (LLLT) is to optimally choose illumination parameters, such as wavelength. However, there is sparse study on the wavelengths comparison especially on human transcranial LLLT. Here, we employed Monte Carlo modeling and visible human phantom to compute the penetrated photon fluence distribution within cerebral cortex. By comparing the fluence distribution, penetration depth and the intensity of laser‐tissue‐interaction within brain among all candidate wavelengths, we found that 660, 810 nm performed much better than 980, 1064 nm with much stronger, deeper and wider photon penetration into cerebral tissue; 660 nm was shown to be the best and slightly better than 810 nm. Our computational finding was in a surprising accordance with previous LLLT‐neurobehavioral studies on mice. This study not only offered quantitative comparison among wavelengths in the effect of LLLT light penetration effectiveness but also anticipated a delightful possibility of online, precise and visible optimization of LLLT illumination parameters.      

On the value of Elongation factor-1α for reconstructing pterygote insect phylogeny

Pterygota are traditionally divided in two lineages, the “Palaeoptera” and Neoptera. Despite several efforts neither morphology nor molecular systematics have resolved the phylogeny of the pterygote insects. Too few markers have yet been identified for adequately tracking mesozoic-aged divergences. We tested the Elongation factor-1α for its phylogenetic value in pterygote insect systematics. This highly conserved nuclear protein-coding gene has previously been reported to be useful in other groups for phylogenetic analyses at the intraordinal level as well as at the interordinal level. The analyses suggest that EF-1α DNA sequences as well as intron positions provide informative markers for pterygote phylogenetics.     

Fear in the dark? Community‐level effects of non‐lethal predators change with light regime

The total effect of predators on prey is a combination of direct consumption, and non‐consumptive effects (NCEs), such as predator‐induced changes to prey morphology, behaviour and life history. Past research into NCEs has tended to focus on pair‐wise interactions between predators and prey, while in natural ecosystems, species exist in complex communities with several trophic levels made up of multiple autotrophic and heterotropic species. To address how predator NCEs alter the photosynthetic and heterotrophic components of communities, we exposed microbial microcosms to one of three predator treatments: live predators (full predator effect), freeze‐killed predators (NCEs only) or no predators (control), and incubated them under either 12 h:12 h light:dark conditions or continual darkness. Under 12 h:12 h light:dark conditions, NCEs‐only communities never differed from predator‐free communities, but differed from live predator communities. Under conditions of continual darkness, the structure of NCEs‐only communities differed from predator‐free controls, but not from live predator communities, suggesting NCEs can be strong enough to structure communities. Predation threat may cause certain prey to induce defences, such as reductions in movement, which make them less competitive in a community setting. This reduction in competitive ability could lead to these species being driven to extinction through interspecific competition, resulting in similar communities to those in which live predators are present. Heterotrophic species whose rates of resource acquisition depend on movement rates may be affected to a greater extent than autotrophs by predator‐induced reductions in movement, accounting for our observed differences in predator NCEs in ‘dark’ and ‘light’ communities. Our results suggest that the community‐level consequences of fear are greater in the dark. Synthesis Predators affect prey through consumptive and non‐consumptive effects (NCEs) such as alterations to prey behaviour, morphology, and life history. However, predators and prey do not exist in isolated pairs, but in complex communities where they interact with many other species. Using a long term study (>10 predator generations), we show that predator NCEs alone can alter community structure under conditions of darkness, but not in a 12h:12h light:dark cycle. Our results demonstrate for the first time that although the community‐level consequences of predator NCEs may be dramatic, they depend upon the abiotic conditions of the ecosystem.     

Trade‐offs in evolutionary immunology: just what is the cost of immunity?

It has become increasingly clear that life-history patterns among the vertebrates have been shaped by the plethora and variety of immunological risks associated with parasitic faunas in their environments. Immunological competence could very well be the most important determinant of life-time reproductive success and fitness for many species. It is generally assumed by evolutionary ecologists that providing immunological defences to minimise such risks to the host is costly in terms of necessitating trade-offs with other nutrient-demanding processes such as growth, reproduction, and thermoregulation. Studies devoted to providing assessments of such costs and how they may force evolutionary trade-offs among life-history characters are few, especially for wild vertebrate species, and their results are widely scattered throughout the literature. In this paper we attempt to review this literature to obtain a better understanding of energetic and nutritional costs for maintaining a normal immune system and examine how costly it might be for a host who is forced to up-regulate its immunological defence mechanisms. The significance of these various costs to ecology and life history trade-offs among the vertebrates is explored. It is concluded that sufficient evidence exists to support the primary assumption that immunological defences are costly to the vertebrate host.     

Out of Africa? A dated molecular phylogeny of the cicada tribe Platypleurini Schmidt (Hemiptera: Cicadidae), with a focus on African genera and the genus Platypleura Amyot & Audinet‐Serville

The Platypleurini is a large group of charismatic cicadas distributed from Cape Agulhas in South Africa, through tropical Africa, Madagascar, India and eastern Asia to Japan, with generic diversity concentrated in equatorial and southern Africa. This distribution suggests the possibility of a Gondwanan origin and dispersal to eastern Asia from Africa or India. We used a four‐gene (three mitochondrial) molecular dataset, fossil calibrations and molecular clock information to explore the phylogenetic relationships of the platypleurine cicadas and the timing and geography of their diversification. The earliest splits in the tribe were found to separate forest genera in Madagascar and equatorial Africa from the main radiation, and all of the Asian/Indian species sampled formed a younger clade nested well within the African taxa. The tribe appears to have diversified during the Cenozoic, beginning c. 50–32 Ma, with most extant African lineages originating in the Miocene or later, well after the breakup of the Gondwanan landmass. Biogeographical analysis suggests an African origin for the tribe and a single dispersal event founding the Asian platypleurines, although additional taxon sampling and genetic data will be needed to confirm this pattern because key nodes in the tree are still weakly supported. Two Platypleurini genera from Madagascar (Pycna Amyot & Audinet‐Serville, Yanga Distant) are found to have originated by late Miocene dispersal of a single lineage from Africa. The genus Platypleura is recovered as polyphyletic, with Platypleura signifera Walker from South Africa and many Asian/Indian species apparently requiring assignment to different genera, and a new Platypleura concept is proposed with the synonymization of Azanicada Villet syn.n. The genera Orapa Distant and Hamza Distant, currently listed within separate tribes but suspected of platypleurine affinity, are nested deeply within the Platypleurini radiation. The tribe Orapini syn.n . is here synonymized while the tribe Hamzini is pending a decision of the ICZN to preserve nomenclatorial stability.     

Mutation processes at the protein level: is Lamarck back?

The experimental evidence accumulated for the last half of the century clearly suggests that inherited variation is not restricted to the changes in genomic sequences. The prion model, originally based on unusual transmission of certain neurodegenerative diseases in mammals, provides a molecular mechanism for the template-like reproduction of alternative protein conformations. Recent data extend this model to protein-based genetic elements in yeast and other fungi. Reproduction and transmission of yeast protein-based genetic elements is controlled by the "prion replication" machinery of the cell, composed of the protein helpers responsible for the processes of assembly and disassembly of protein structures and multiprotein complexes. Among these, the stress-related chaperones of Hsp100 and Hsp70 groups play an important role. Alterations of levels or activity of these proteins result in "mutator" or "antimutator" affects in regard to protein-based genetic elements. "Protein mutagens" have also been identified that affect formation and/or propagation of the alternative protein conformations. Prion-forming abilities appear to be conserved in evolution, despite the divergence of the corresponding amino acid sequences. Moreover, a wide variety of proteins of different origins appear to possess the ability to form amyloid-like aggregates, that in certain conditions might potentially result in prion-like switches. This suggests a possible mechanism for the inheritance of acquired traits, postulated in the Lamarckian theory of evolution. The prion model also puts in doubt the notion that cloned animals are genetically identical to their genome donors, and suggests that genome sequence would not provide a complete information about the genetic makeup of an organism.     

Aphid‐tending ants on introduced fennel: can resources derived from non‐native plants alter the trophic position of higher‐order consumers?

1. Although plant invasions often reduce insect abundance and diversity, non‐native plants that support phytophagous insects can subsidise higher trophic levels via elevated herbivore abundance. 2. Here ant–aphid interactions on non‐native fennel on Santa Cruz Island, California are examined. Fennel hosts abundant, honeydew‐producing fennel aphids. The patchiness of fennel and the relative lack of honeydew‐producing insects on other plants at our study sites suggest that assimilation of fennel‐derived honeydew would increase the abundance and decrease the trophic position of the omnivorous, aphid‐tending Argentine ant. 3. To assess the strength of the ant–aphid interaction, a comparison of ant abundance on and adjacent to fennel prior to and 3 weeks after experimental aphid removal was performed. Compared with control plants with aphids, ants declined in abundance on and around fennel plants following aphid removal. At the habitat scale, pitfall traps in fennel‐dominated habitats captured more ants than in fennel‐free scrub habitats. 4. To determine if assimilation of aphid‐produced honeydew reduces the ant's trophic position, variation in δ¹⁵N values among ants, plants and other arthropods was analysed. Unexpectedly, δ¹⁵N values for ants in fennel‐dominated habitats were higher than those of arthropod predators from the same sites and also higher than those of ants from fennel‐free habitats. 5. Our results illustrate how introduced plants that support phytophagous insects appear to transfer energy to higher trophic levels via elevated herbivore abundance. Although assimilation of fennel‐derived honeydew did not appear to reduce consumer trophic position, spatial variation in alternative food resources might obscure contributions from honeydew.