Fine-scale phylogenetic architecture of a complex bacterial community

Although molecular data have revealed the vast scope of microbial diversity, two fundamental questions remain unanswered even for well-defined natural microbial communities: how many bacterial types co-exist, and are such types naturally organized into phylogenetically discrete units of potential ecological significance? It has been argued that without such information, the environmental function, population biology and biogeography of microorganisms cannot be rigorously explored. Here we address these questions by comprehensive sampling of two large 16S ribosomal RNA clone libraries from a coastal bacterioplankton community. We show that compensation for artefacts generated by common library construction techniques reveals fine-scale patterns of community composition. At least 516 ribotypes (unique rRNA sequences) were detected in the sample and, by statistical extrapolation, at least 1,633 co-existing ribotypes in the sampled population. More than 50% of the ribotypes fall into discrete clusters containing less than 1% sequence divergence. This pattern cannot be accounted for by interoperon variation, indicating a large predominance of closely related taxa in this community. We propose that such microdiverse clusters arise by selective sweeps and persist because competitive mechanisms are too weak to purge diversity from within them.     

The binary progenitor of Tycho Brahe's 1572 supernova

The brightness of type Ia supernovae, and their homogeneity as a class, makes them powerful tools in cosmology, yet little is known about the progenitor systems of these explosions. They are thought to arise when a white dwarf accretes matter from a companion star, is compressed and undergoes a thermonuclear explosion. Unless the companion star is another white dwarf (in which case it should be destroyed by the mass-transfer process itself), it should survive and show distinguishing properties. Tycho's supernova is one of only two type Ia supernovae observed in our Galaxy, and so provides an opportunity to address observationally the identification of the surviving companion. Here we report a survey of the central region of its remnant, around the position of the explosion, which excludes red giants as the mass donor of the exploding white dwarf. We found a type G0-G2 star, similar to our Sun in surface temperature and luminosity (but lower surface gravity), moving at more than three times the mean velocity of the stars at that distance, which appears to be the surviving companion of the supernova.     

Population density drives the local evolution of a threshold dimorphism

Evolution can favour more than one reproductive tactic among conspecifics of the same sex. Under the conditional evolutionarily stable strategy, individuals adopt the tactic that generates the highest fitness return for their status: large males guard females, whereas small males sneak copulations. Tactics change at the status at which fitness benefits switch from favouring one tactic to favouring the alternative. This 'switchpoint' is expressed in many species as a threshold between divergent morphologies. Environmental and demographic parameters that influence the relative fitness of male tactics are predicted to determine a population's switchpoint and consequently whether the population is monomorphic or dimorphic. Here we show threshold evolution in the forceps dimorphism of the European earwig Forficula auricularia and document the transition from completely monomorphic to classical male-dimorphic populations over a distance of only 40 km. Because the superior fighting ability of the dominant morph will be more frequently rewarded at high encounter rates, population density is likely to be a key determinant of the relative fitness of the alternative tactics, and consequently the threshold. We show that, as predicted, population density correlates strongly with the shift in threshold, and that this factor drives the local evolution of the male dimorphism in these island populations. Our data provide evidence for the origin of phenotypic diversity within populations, through the evolution of a switchpoint in a conditional strategy that has responded to local population density.     

The DNA sequence and analysis of human chromosome 13

Chromosome 13 is the largest acrocentric human chromosome. It carries genes involved in cancer including the breast cancer type 2 (BRCA2) and retinoblastoma (RB1) genes, is frequently rearranged in B-cell chronic lymphocytic leukaemia, and contains the DAOA locus associated with bipolar disorder and schizophrenia. We describe completion and analysis of 95.5 megabases (Mb) of sequence from chromosome 13, which contains 633 genes and 296 pseudogenes. We estimate that more than 95.4% of the protein-coding genes of this chromosome have been identified, on the basis of comparison with other vertebrate genome sequences. Additionally, 105 putative non-coding RNA genes were found. Chromosome 13 has one of the lowest gene densities (6.5 genes per Mb) among human chromosomes, and contains a central region of 38 Mb where the gene density drops to only 3.1 genes per Mb.     

Surface transfer doping of diamond

The electronic properties of many materials can be controlled by introducing appropriate impurities into the bulk crystal lattice in a process known as doping. In this way, diamond (a well-known insulator) can be transformed into a semiconductor, and recent progress in thin-film diamond synthesis has sparked interest in the potential applications of semiconducting diamond. However, the high dopant activation energies (in excess of 0.36 eV) and the limitation of donor incorporation to (111) growth facets only have hampered the development of diamond-based devices. Here we report a doping mechanism for diamond, using a method that does not require the introduction of foreign atoms into the diamond lattice. Instead, C60 molecules are evaporated onto the hydrogen-terminated diamond surface, where they induce a subsurface hole accumulation and a significant rise in two-dimensional conductivity. Our observations bear a resemblance to the so-called surface conductivity of diamond seen when hydrogenated diamond surfaces are exposed to air, and support an electrochemical model in which the reduction of hydrated protons in an aqueous surface layer gives rise to a hole accumulation layer. We expect that transfer doping by C60 will open a broad vista of possible semiconductor applications for diamond.     

Sirtuin activators mimic caloric restriction and delay ageing in metazoans

Caloric restriction extends lifespan in numerous species. In the budding yeast Saccharomyces cerevisiae this effect requires Sir2 (ref. 1), a member of the sirtuin family of NAD+-dependent deacetylases. Sirtuin activating compounds (STACs) can promote the survival of human cells and extend the replicative lifespan of yeast. Here we show that resveratrol and other STACs activate sirtuins from Caenorhabditis elegans and Drosophila melanogaster, and extend the lifespan of these animals without reducing fecundity. Lifespan extension is dependent on functional Sir2, and is not observed when nutrients are restricted. Together these data indicate that STACs slow metazoan ageing by mechanisms that may be related to caloric restriction.     

Palaeontology: pterosaur egg with a leathery shell

The recent discovery of a pterosaur egg with embryonic skeleton and soft tissues from the Yixian Formation confirmed that the flying pterosaurs were oviparous. Here we describe another pterosaur egg whose exquisite preservation indicates that the shell structure was soft and leathery.     

Collapse and rapid resumption of Atlantic meridional circulation linked to deglacial climate changes

The Atlantic meridional overturning circulation is widely believed to affect climate. Changes in ocean circulation have been inferred from records of the deep water chemical composition derived from sedimentary nutrient proxies, but their impact on climate is difficult to assess because such reconstructions provide insufficient constraints on the rate of overturning. Here we report measurements of 231Pa/230Th, a kinematic proxy for the meridional overturning circulation, in a sediment core from the subtropical North Atlantic Ocean. We find that the meridional overturning was nearly, or completely, eliminated during the coldest deglacial interval in the North Atlantic region, beginning with the catastrophic iceberg discharge Heinrich event H1, 17,500 yr ago, and declined sharply but briefly into the Younger Dryas cold event, about 12,700 yr ago. Following these cold events, the 231Pa/230Th record indicates that rapid accelerations of the meridional overturning circulation were concurrent with the two strongest regional warming events during deglaciation. These results confirm the significance of variations in the rate of the Atlantic meridional overturning circulation for abrupt climate changes.     

Origin of AIDS: contaminated polio vaccine theory refuted

Despite strong evidence to the contrary, speculation continues that the AIDS virus, human immunodeficiency virus type 1 (HIV-1), may have crossed into humans as a result of contamination of the oral polio vaccine (OPV). This 'OPV/AIDS theory' claims that chimpanzees from the vicinity of Stanleyville--now Kisangani in the Democratic Republic of Congo--were the source of a simian immunodeficiency virus (SIVcpz) that was transmitted to humans when chimpanzee tissues were allegedly used in the preparation of OPV. Here we show that SIVcpz is indeed endemic in wild chimpanzees of this region but that the circulating virus is phylogenetically distinct from all strains of HIV-1, providing direct evidence that these chimpanzees were not the source of the human AIDS pandemic.