Testing the new animal phylogeny: a phylum level molecular analysis of the animal kingdom

The new animal phylogeny inferred from ribosomal genes some years ago has prompted a number of radical rearrangements of the traditional, morphology based metazoan tree. The two main bilaterian clades, Deuterostomia and Protostomia, find strong support, but the protostomes consist of two sister groups, Ecdysozoa and Lophotrochozoa, not seen in morphology based trees. Although widely accepted, not all recent molecular phylogenetic analyses have supported the tripartite structure of the new animal phylogeny. Furthermore, even if the small ribosomal subunit (SSU) based phylogeny is correct, there is a frustrating lack of resolution of relationships between the phyla that make up the three clades of this tree. To address this issue, we have assembled a dataset including a large number of aligned sequence positions as well as a broad sampling of metazoan phyla. Our dataset consists of sequence data from ribosomal and mitochondrial genes combined with new data from protein coding genes (5139 amino acid and 3524 nucleotide positions in total) from 37 representative taxa sampled across the Metazoa. Our data show strong support for the basic structure of the new animal phylogeny as well as for the Mandibulata including Myriapoda. We also provide some resolution within the Lophotrochozoa, where we confirm support for a monophyletic clade of Echiura, Sipuncula and Annelida and surprising evidence of a close relationship between Brachiopoda and Nemertea.     

Phylogeny of the avian genus Pitohui and the evolution of toxicity in birds

Bird species in the avian genus Pitohui contain potent neurotoxic alkaloids that may be used for defense. The genus comprises multiple species that are endemic to New Guinea and were presumed to belong to the family Pachycephalidae or Colluricinclidae, within the core corvoidea, an ancient Australasian radiation of crow-like birds. In order to understand the evolution of toxicity within the genus Pitohui, we sequenced three mitochondrial and two nuclear gene segments and reconstructed a phylogeny of the genus Pitohui and its putative relatives. We show that the genus Pitohui is polyphyletic, and consists of five different lineages. Using Bayesian ancestral state reconstruction, we estimate that toxicity likely evolved multiple times within this group. Furthermore, because the morphological and behavioral similarity among these poisonous birds appears to have evolved convergently, we hypothesize that this may be a possible example of Müllerian mimicry in birds. The Morningbird of Palau, Micronesia, that has often been included in the genus Pitohui, actually belongs in the genus Pachycephala and offers an intriguing case of pronounced evolution on a remote oceanic island.     

A comparison of the polycation receptors of Paramecium tetraurelia and Tetrahymena thermophila

Chemorepellents are compounds that cause ciliated protozoans to reorient their swimming direction. A number of chemorepellents have been studied in the ciliated protozoans, Paramecium and Tetrahymena. Chemorepellents, such as polycations, cause the organism to exhibit "avoidance behavior," a swimming behavior characterized by jerky movements and other deviations from normal forward swimming, which result from ciliary reversal. One well-characterized chemorepellent pathway in Tetrahymena is that of the proposed polycation receptor that is activated by lysozyme and pituitary adenylate cyclase activating polypeptide (PACAP). In this study, we compare the response of Paramecium to the chemorepellents lysozyme, vasoactive intestinal peptide (VIP), and PACAP to the previously studied polycation response in Tetrahymena. Our results indicate that lysozyme, VIP, and PACAP are all chemorepellents in Paramecium, just as they are in Tetrahymena. However, the signaling pathways involved appear to be different. While previous pharmacological characterization indicates that G-proteins are involved in polycation signaling in Tetrahymena, we present evidence that similar reception in Paramecium involves activation of a tyrosine kinase pathway in order for lysozyme avoidance to occur. Polycation responses of both organisms are inhibited by neomycin sulfate. While PACAP is the most effective of the three chemorepellents in Tetrahymena, lysozyme is the most effective chemorepellent in Paramecium.     

Range‐wide patterns of greater sage‐grouse persistence

Aim Greater sage‐grouse (Centrocercus urophasianus), a shrub‐steppe obligate species of western North America, currently occupies only half its historical range. Here we examine how broad‐scale, long‐term trends in landscape condition have affected range contraction. Location Sagebrush biome of the western USA. Methods Logistic regression was used to assess persistence and extirpation of greater sage‐grouse range based on landscape conditions measured by human population (density and population change), vegetation (percentage of sagebrush habitat), roads (density of and distance to roads), agriculture (cropland, farmland and cattle density), climate (number of severe and extreme droughts) and range periphery. Model predictions were used to identify areas where future extirpations can be expected, while also explaining possible causes of past extirpations. Results Greater sage‐grouse persistence and extirpation were significantly related to sagebrush habitat, cultivated cropland, human population density in 1950, prevalence of severe droughts and historical range periphery. Extirpation of sage‐grouse was most likely in areas having at least four persons per square kilometre in 1950, 25% cultivated cropland in 2002 or the presence of three or more severe droughts per decade. In contrast, persistence of sage‐grouse was expected when at least 30 km from historical range edge and in habitats containing at least 25% sagebrush cover within 30 km. Extirpation was most often explained (35%) by the combined effects of peripherality (within 30 km of range edge) and lack of sagebrush cover (less than 25% within 30 km). Based on patterns of prior extirpation and model predictions, we predict that 29% of remaining range may be at risk. Main Conclusions Spatial patterns in greater sage‐grouse range contraction can be explained by widely available landscape variables that describe patterns of remaining sagebrush habitat and loss due to cultivation, climatic trends, human population growth and peripherality of populations. However, future range loss may relate less to historical mechanisms and more to recent changes in land use and habitat condition, including energy developments and invasions by non‐native species such as cheatgrass (Bromus tectorum) and West Nile virus. In conjunction with local measures of population performance, landscape‐scale predictions of future range loss may be useful for prioritizing management and protection. Our results suggest that initial conservation efforts should focus on maintaining large expanses of sagebrush habitat, enhancing quality of existing habitats, and increasing habitat connectivity.     

Expressed sequence tag-derived microsatellite markers of perennial ryegrass (Lolium perenne L.)

An expressed sequence tag (EST) library of the key grassland species perennial ryegrass (Lolium perenne L.) has been exploited as a resource for microsatellite marker development. Out of 955 simple sequence repeat (SSR) containing ESTs, 744 were used for primer design. Primer amplification was tested in eight genotypes of L. perenne and L. multiflorum representing (grand-) parents of four mapping populations and resulted in 464 successfully amplified EST-SSRs. Three hundred and six primer pairs successfully amplified products in the mapping population VrnA derived from two of the eight genotypes included in the original screening and revealed SSR polymorphisms for 143 ESTs. Here, we report on 464 EST-derived SSR primer sequences of perennial ryegrass established in laboratory assays, providing a dedicated tool for marker assisted breeding and comparative mapping within and among forage and turf grasses. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Little evidence for negative effects of an invasive alien plant on pollinator services

Many invasive alien plants occur in large populations with abundant flowers which are highly attractive to pollinators, and thus might affect pollination of co-occurring native species. This study focuses on the invasive Heracleum mantegazzianum and distance-dependent effects on pollination of Mimulus guttatus in abandoned grassland over 2 years. First, we examined pollinator abundance in yellow traps at 0, 10, 30 and 60–200 m from H. mantegazzianum. We then placed M. guttatus plants at the same distances to monitor effects of the invasive species on pollinator visitation and seed set of neighbouring plants. Finally, we conducted a garden experiment to test if deposition of H. mantegazzianum pollen reduces seed set in M. guttatus. No distance effect was found for the number of bumblebees in traps, although the invasive species attracted a diverse assemblage of insects, and visitation of M. guttatus was enhanced close to H. mantegazzianum. This positive effect was not reflected by seed set of M. guttatus, and heterospecific pollen decreased seed set in these plants. Overall there is little evidence for negative effects of the invasive species on pollination of neighbouring plants, and flower visitation even increases close to the invaded patches. The functional role of the invader and suitable control strategies need further clarification, since removal of H. mantegazzianum may actually damage local pollinator populations. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Mutants with aberrant numbers of gametic cells shed new light on old questions

In contrast to animals, plant gametes form in distinct haploid generations, termed gametophytes. The female gametophyte of Arabidopsis consists of two gametic cells, the egg and central cell, which are flanked by accessory cells. The gametic cells differ with respect to morphology, molecular attributes and, importantly, their fate: whereas the egg cell, upon fertilisation, gives rise to the embryo, the central cell forms the endosperm. To ensure correct endosperm formation, not only the egg cell but also the central cell has to fuse with a sperm cell. The respective sperm cell pair is delivered by a single pollen tube. In some plant species, the two male gametes appear to express a different bias towards the female gametes. Such a preference consequently determines their respective contribution to either embryo or endosperm development. In Arabidopsis and many other species the sperm cells are indistinguishable and it has been discussed whether they possess an inherent preference for either of the female gametes. The recent isolation of mutants that form an aberrant number of either male or female gametes stimulates discussion, albeit with different results. Furthermore, some data indicate that the central cell is competent to initiate endosperm formation without a paternal contribution. These data support the theory that the endosperm is of gametophytic rather than sporophytic origin.     

The Delta fbpA mutant derived from Mycobacterium tuberculosis H37Rv has an enhanced susceptibility to intracellular antimicrobial oxidative mechanisms, undergoes limited phagosome maturation and activates macrophages and dendritic cells

Mycobacterium tuberculosis H37Rv (Mtb) excludes phagocyte oxidase (phox) and inducible nitric oxide synthase (iNOS) while preventing lysosomal fusion in macrophages (MPhis). The antigen 85A deficient (Delta fbpA) mutant of Mtb was vaccinogenic in mice and the mechanisms of attenuation were compared with MPhis infected with H37Rv and BCG. Delta fbpA contained reduced amounts of trehalose 6, 6, dimycolate and induced minimal levels of SOCS-1 in MPhis. Blockade of oxidants enhanced the growth of Delta fbpA in MPhis that correlated with increased colocalization with phox and iNOS. Green fluorescent protein-expressing strains within MPhis or purified phagosomes were analysed for endosomal traffick with immunofluorescence and Western blot. Delta fbpA phagosomes were enriched for rab5, rab11, LAMP-1 and Hck suggesting enhanced fusion with early, recycling and late endosomes in MPhis compared with BCG or H37Rv. Delta fbpA phagosomes were thus more mature than H37Rv or BCG although, they failed to acquire rab7 and CD63 preventing lysosomal fusion. Finally, Delta fbpA infected MPhis and dendritic cells (DCs) showed an enhanced MHC-II and CD1d expression and primed immune T cells to release more IFN-gamma compared with those infected with BCG and H37Rv. Delta fbpA was thus more immunogenic in MPhis and DCs because of an enhanced susceptibility to oxidants and increased maturation.