Mitochondrial metagenomics: letting the genes out of the bottle

‘Mitochondrial metagenomics’ (MMG) is a methodology for shotgun sequencing of total DNA from specimen mixtures and subsequent bioinformatic extraction of mitochondrial sequences. The approach can be applied to phylogenetic analysis of taxonomically selected taxa, as an economical alternative to mitogenome sequencing from individual species, or to environmental samples of mixed specimens, such as from mass trapping of invertebrates. The routine generation of mitochondrial genome sequences has great potential both for systematics and community phylogenetics. Mapping of reads from low-coverage shotgun sequencing of environmental samples also makes it possible to obtain data on spatial and temporal turnover in whole-community phylogenetic and species composition, even in complex ecosystems where species-level taxonomy and biodiversity patterns are poorly known. In addition, read mapping can produce information on species biomass, and potentially allows quantification of within-species genetic variation. The success of MMG relies on the formation of numerous mitochondrial genome contigs, achievable with standard genome assemblers, but various challenges for the efficiency of assembly remain, particularly in the face of variable relative species abundance and intra-specific genetic variation. Nevertheless, several studies have demonstrated the power of mitogenomes from MMG for accurate phylogenetic placement, evolutionary analysis of species traits, biodiversity discovery and the establishment of species distribution patterns; it offers a promising avenue for unifying the ecological and evolutionary understanding of species diversity

Experimental studies of species-specificity in cecropia-ant relationships

Journal ArticleStrict coevolution requires that interactions among organisms be speciesspecific. We assessed the relative roles of host- and habitat-specificity in determining the match between a genus of myrmecophytic trees and a guild of obligate plant-ants in the moist tropical forests of Madre de Dios, Peru. Four locally coexisting but habitat-restricted Cecropia species were cultivated in screen tents until all plants had developed myrmecophytic traits. Saplings were then placed within replicate blocks of each of two habitat types: riversides and small forest light gaps. Colonization events were recorded every 3 d between June and August of 1992, and queens were later removed from stem internodes for identification and brood censuses. A similar experiment, conducted in September through November of 1993, included just two species of Cecropia hosts. Effects of host species and habitat on queen colonization rates were evaluated by log-likelihood goodness-of-fit tests and contingency table tests. For three ant species, we also conducted queen preference experiments to compare queen behaviors across a range of host plants. Differences among ants in the extent of habitat-specificity vs. host-specificity provide evidence for multiple evolutionary routes to obligate association with Cecropia. Habitat- specificity exceeded host-specificity in Azteca ovaticeps (Dolichoderinae), for which queen preference experiments revealed no significant discrimination among hosts. This extreme riverside specialist is thought to have descended from generalist live-stem nesters in secondgrowth habitats. In Azteca australis, host-specificity was strong, and in this species only, directed toward hosts where brood production was most successful. Conflicting habitat associations in the two experiments indicated the weakness or absence of a consistent habitat affiliation in Azteca australis and suggested that colonization frequencies were influenced instead by proximity to foundress sources. Close relatives of A. australis live in exposed carton nests, which may have been positioned ancestrally on key resource plants, e.g., those producing lipid- and amino-acid-rich pearl bodies. Pachycondyla luteola (Ponerinae) exhibited both strong habitat and host associations and may have undergone pairwise coevolution with its forest-gap-dwelling primary host. Queens of Camponotus balzani (Formicinae), possibly a recent and secondary associate of Cecropia, were overrepresented in forest gap habitat but were host generalists, underrepresented only on a host with extremely small internodes. Apparently greater host-specificity in C. balzani at later stages of colony establishment may be due to differential post colonization mortality on the various hosts. Attack of ant queens by parasitoid wasps was strongly concentrated in the linear riverside habitat and weak to absent in the patchily distributed forest gap habitat. Due to lower rates of either parasitoid attack or other forms of queen mortality, Camponotus balzani experienced greater success in the forest gap habitat, where it was overrepresented in colonization experiments. Historical coincidences and preadaptations appear to have strongly influenced pairings between Cecropia species and their obligate plant-ants and account for much of the "apparent" niche partitioning observed in the system. Species-specificity seems to be determined mainly by coincident habitat affiliations of ants and plants ("coordinated dispersal") and by preadapted capacities of ants to distinguish among host-plant species. Multiple mechanisms for species-specificity may be characteristic of relationships in which associates disperse separately from one another (i.e., show horizontal transmission). Our results are consistent with the view that coadaptation and co-cladogenesis are more likely in systems where dispersal of associates is tightly coupled

Ultrahigh energy neutrino scattering: an update

We update our estimates of charged and neutral current neutrino total cross sections on isoscalar nucleons at ultrahigh energies using a global (x, Q^2) fit, motivated by the Froissart bound, to the F_2 (electron-proton) structure function utilizing the most recent analysis of the complete ZEUS and H1 data sets from HERA I. Using the large Q^2, small Bjorken-x limits of the "wee" parton model, we connect the ultrahigh energy neutrino cross sections directly to the large Q^2, small-x extrapolation of our new fit, which we assume saturates the Froissart bound. We compare both to our previous work, which utilized only the smaller ZEUS data set, as well as to recent results of a calculation using the ZEUS-S based global perturbative QCD parton distributions using the combined HERA I results as input. Our new results substantiate our previous conclusions, again predicting significantly smaller cross sections than those predicted by extrapolating pQCD calculations to neutrino energies above 10^9 GeV.Comment: 8 pages, 1 figure, 3 table

A single Streptomyces symbiont makes multiple antifungals to support the fungus farming ant Acromyrmex octospinosus

Attine ants are dependent on a cultivated fungus for food and use antibiotics produced by symbiotic Actinobacteria as weedkillers in their fungus gardens. Actinobacterial species belonging to the genera Pseudonocardia, Streptomyces and Amycolatopsis have been isolated from attine ant nests and shown to confer protection against a range of microfungal weeds. In previous work on the higher attine Acromyrmex octospinosus we isolated a Streptomyces strain that produces candicidin, consistent with another report that attine ants use Streptomyces-produced candicidin in their fungiculture. Here we report the genome analysis of this Streptomyces strain and identify multiple antibiotic biosynthetic pathways. We demonstrate, using gene disruptions and mass spectrometry, that this single strain has the capacity to make candicidin and multiple antimycin compounds. Although antimycins have been known for > 60 years we report the sequence of the biosynthetic gene cluster for the first time. Crucially, disrupting the candicidin and antimycin gene clusters in the same strain had no effect on bioactivity against a co-evolved nest pathogen called Escovopsis that has been identified in similar to 30% of attine ant nests. Since the Streptomyces strain has strong bioactivity against Escovopsis we conclude that it must make additional antifungal(s) to inhibit Escovopsis. However, candicidin and antimycins likely offer protection against other microfungal weeds that infect the attine fungal gardens. Thus, we propose that the selection of this biosynthetically prolific strain from the natural environment provides A. octospinosus with broad spectrum activity against Escovopsis and other microfungal weeds.Publisher PDFPeer reviewe

iDNA from terrestrial haematophagous leeches as a wildlife surveying and monitoring tool - prospects, pitfalls and avenues to be developed

Invertebrate-derived DNA (iDNA) from terrestrial haematophagous leeches has recently been proposed as a powerful non-invasive tool with which to detect vertebrate species and thus to survey their populations. However, to date little attention has been given to whether and how this, or indeed any other iDNA-derived data, can be combined with state-of-the-art analytical tools to estimate wildlife abundances, population dynamics and distributions. In this review, we discuss the challenges that face the application of existing analytical methods such as site-occupancy and spatial capture-recapture (SCR) models to terrestrial leech iDNA, in particular, possible violations of key assumptions arising from factors intrinsic to invertebrate parasite biology. Specifically, we review the advantages and disadvantages of terrestrial leeches as a source of iDNA and summarize the utility of leeches for presence, occupancy, and spatial capture-recapture models. The main source of uncertainty that attends species detections derived from leech gut contents is attributable to uncertainty about the spatio-temporal sampling frame, since leeches retain host-blood for months and can move after feeding. Subsequently, we briefly address how the analytical challenges associated with leeches may apply to other sources of iDNA. Our review highlights that despite the considerable potential of leech (and indeed any) iDNA as a new survey tool, further pilot studies are needed to assess how analytical methods can overcome or not the potential biases and assumption violations of the new field of iDNA. Specifically we argue that studies to compare iDNA sampling with standard survey methods such as camera trapping, and those to improve our knowledge on leech (and other invertebrate parasite) physiology, taxonomy, and ecology will be of immense future value

Ultra-high energy neutrino scattering

Estimates are made of the ultra-high energy neutrino cross sections based on an extrapolation to very small Bjorken x of the logarithmic Froissart dependence in x shown previously to provide an excellent fit to the measured proton structure function F_2^p(x,Q^2) over a broad range of the virtuality Q^2. Expressions are obtained for both the neutral current and the charged current cross sections. Comparison with an extrapolation based on perturbative QCD shows good agreement for energies where both fit data, but our rates are as much as a factor of 10 smaller for neutrino energies above 10^9 GeV, with important implications for experiments searching for extra-galactic neutrinos.Comment: 4 pages, 1 figure, 1 table; Title, abstract and text changed, conclusions unchanged. Version accepted for publication in Physical Review

Efficient assembly and long-term stability of defensive microbiomes via private resources and community bistability

Understanding the mechanisms that promote the assembly and maintenance of host-beneficial microbiomes is an open problem. Empirical evidence supports the idea that animal and plant hosts can combine ‘private resources’ with the ecological phenomenon known as ‘community bistability’ to favour some microbial strains over others. We briefly review evidence showing that hosts can: (i) protect the growth of beneficial strains in an isolated habitat, (ii) use antibiotics to suppress non-beneficial, competitor strains, and (iii) provide resources that only beneficial strains are able to translate into an increased rate of growth, reproduction, or antibiotic production. We then demonstrate in a spatially explicit, individual-based model that these three mechanisms act similarly by selectively promoting the initial proliferation of preferred strains, that is, by acting as a private resource. The faster early growth of preferred strains, combined with the phenomenon of ‘community bistability,’ allows those strains to continue to dominate the microbiome even after the private resource is withdrawn or made public. This is because after a beneficial colony reaches a sufficiently large size, it can resist invasion by parasites without further private support from the host. We further explicitly model localized microbial interactions and diffusion dynamics, and we show that an intermediate level of antibiotic diffusion is the most efficient mechanism in promoting preferred strains and that there is a wide range of parameters under which hosts can promote the assembly of a self-sustaining defensive microbiome. This in turn supports the idea that hosts readily evolve to promote host-beneficial defensive microbiomes

Reply to Kiers et al.: Economic and Biological Clarity in the Theory of Mutualism

Kiers et al. (1) make three main points. First, they noted that many mutualisms involve multiple symbionts interacting with a single host. We agree, and we explained that partner fidelity feedback (PFF) can function because plants generally “limit, withdraw, or even abscise investment in shoots, flowers, and roots (or subsets of any of these) after physical damage or deficits of… resources…” (2). This “modularity” of plant hosts (3) separates the effects of different symbionts and allows the host to react to individual symbionts. Modularity is easily incorporated into our model, because (with no change in our results) principal-agent theory allows the assumption of one agent per host to be replaced …Organismic and Evolutionary Biolog

Top Quark Physics at the Tevatron

We review the field of top-quark physics with an emphasis on experimental techniques. The role of the top quark in the Standard Model of particle physics is summarized and the basic phenomenology of top-quark production and decay is introduced. We discuss how contributions from physics beyond the Standard Model could affect top-quark properties or event samples. The many measurements made at the Fermilab Tevatron, which test the Standard Model predictions or probe for direct evidence of new physics using the top-quark event samples, are reviewed here.Comment: 50 pages, 17 figures, 2 tables; version accepted by Review of Modern Physic