Widespread local house-sparrow extinctions

House-sparrow populations have declined sharply in Western Europe in recent decades, but the reasons for this decline have yet to be identified, despite intense public interest in the matter. Here we use a combination of field experimentation, genetic analysis and demographic data to show that a reduction in winter food supply caused by agricultural intensification is probably the principal explanation for the widespread local extinctions of rural house-sparrow populations in southern England. We show that farmland populations exhibit fine-level genetic structuring and that some populations are unable to sustain themselves (sinks), whereas others act as sources.     

The 'solar model problem' solved by the abundance of neon in nearby stars

The interior structure of the Sun can be studied with great accuracy using observations of its oscillations, similar to seismology of the Earth. Precise agreement between helioseismological measurements and predictions of theoretical solar models has been a triumph of modern astrophysics. A recent downward revision by 25-35 per cent of the solar abundances of light elements such as C, N, O and Ne (ref. 2) has, however, broken this accordance: models adopting the new abundances incorrectly predict the depth of the convection zone, the depth profiles of sound speed and density, and the helium abundance. The discrepancies are far beyond the uncertainties in either the data or the model predictions. Here we report neon-to-oxygen ratios measured in a sample of nearby solar-like stars, using their X-ray spectra. The abundance ratios are all very similar and substantially larger than the recently revised solar value. The neon abundance in the Sun is quite poorly determined. If the Ne/O abundance in these stars is adopted for the Sun, the models are brought back into agreement with helioseismology measurements.     

Convective-region geometry as the cause of Uranus' and Neptune's unusual magnetic fields

The discovery of Uranus' and Neptune's non-dipolar, non-axisymmetric magnetic fields destroyed the picture--established by Earth, Jupiter and Saturn--that planetary magnetic fields are dominated by axial dipoles. Although various explanations for these unusual fields have been proposed, the cause of such field morphologies remains unexplained. Planetary magnetic fields are generated by complex fluid motions in electrically conducting regions of the planets (a process known as dynamo action), and so are intimately linked to the structure and evolution of planetary interiors. Determining why Uranus and Neptune have different field morphologies is not only critical for studying the interiors of these planets, but also essential for understanding the dynamics of magnetic-field generation in all planets. Here we present three-dimensional numerical dynamo simulations that model the dynamo source region as a convecting thin shell surrounding a stably stratified fluid interior. We show that this convective-region geometry produces magnetic fields similar in morphology to those of Uranus and Neptune. The fields are non-dipolar and non-axisymmetric, and result from a combination of the stable fluid's response to electromagnetic stress and the small length scales imposed by the thin shell.     

The DNA sequence and biology of human chromosome 19

Chromosome 19 has the highest gene density of all human chromosomes, more than double the genome-wide average. The large clustered gene families, corresponding high G + C content, CpG islands and density of repetitive DNA indicate a chromosome rich in biological and evolutionary significance. Here we describe 55.8 million base pairs of highly accurate finished sequence representing 99.9% of the euchromatin portion of the chromosome. Manual curation of gene loci reveals 1,461 protein-coding genes and 321 pseudogenes. Among these are genes directly implicated in mendelian disorders, including familial hypercholesterolaemia and insulin-resistant diabetes. Nearly one-quarter of these genes belong to tandemly arranged families, encompassing more than 25% of the chromosome. Comparative analyses show a fascinating picture of conservation and divergence, revealing large blocks of gene orthology with rodents, scattered regions with more recent gene family expansions and deletions, and segments of coding and non-coding conservation with the distant fish species Takifugu.     

Evolutionary genetics: Ambiguous role of CCR5 in Y. pestis infection

Mecsas and colleagues suggest that a deficiency in the chemokine receptor CCR5 in humans is unlikely to confer protection against plague, based on their study of Yersinia pestis infection in Ccr5-deficient mice. They were testing the hypothesis that a mutation in the CCR5 gene, frequently found in Caucasians, may have been selected for in the past because it provided protection against (bubonic) plague; the mutation, called CCR5Delta32, is characterized by a 32-base-pair deletion. We have also tested this hypothesis by using Y. pestis infection in mice and, in addition, we have done phagocytosis experiments with macrophages from wild-type and Ccr5-deficient mice. Although, like Mecsas et al., we did not see any difference in the survival of the two groups of mice, we did find that there was a significantly reduced uptake of Y. pestis by Ccr5-deficient macrophages in vitro. Our results indicate that the role of Ccr5 in Y. pestis infection may therefore be more complex than previously thought.     

Pre-social benefits of extended parental care

The evolution of helping, in which some individuals forfeit their own reproduction and help others to reproduce, is a central problem in evolutionary biology. Recently proposed insurance-based mechanisms rely on a pre-existing life history with a long period of offspring dependency relative to the short life expectancies of adult carers: a lone mother's offspring are doomed if she dies young, whereas after a helper dies, other group members can finish rearing the offspring. A critical question, however, is how this life history could evolve in ancestral non-social populations, as offspring survival would then depend on a single, short-lived carer. Here, we resolve this paradox by focusing on the extended parental care inherent in prolonged dependency. We show experimentally that in non-social wasps, extended care can significantly reduce the impact of interspecific parasites. Under extended care, offspring are less vulnerable by the time they are exposed to parasites, and costs of parasitism are reduced because mothers have the option to terminate investment in failing offspring. By experimentally simulating aspects of extended care in a species where it is lacking, we demonstrate that neither benefit requires specialized behaviour. Such benefits could therefore offset the disadvantage of prolonged dependency in non-social species, thereby facilitating the evolution of helping.     

Vertebrate Smoothened functions at the primary cilium

The unanticipated involvement of several intraflagellar transport proteins in the mammalian Hedgehog (Hh) pathway has hinted at a functional connection between cilia and Hh signal transduction. Here we show that mammalian Smoothened (Smo), a seven-transmembrane protein essential for Hh signalling, is expressed on the primary cilium. This ciliary expression is regulated by Hh pathway activity; Sonic hedgehog or activating mutations in Smo promote ciliary localization, whereas the Smo antagonist cyclopamine inhibits ciliary localization. The translocation of Smo to primary cilia depends upon a conserved hydrophobic and basic residue sequence homologous to a domain previously shown to be required for the ciliary localization of seven-transmembrane proteins in Caenorhabditis elegans. Mutation of this domain not only prevents ciliary localization but also eliminates Smo activity both in cultured cells and in zebrafish embryos. Thus, Hh-dependent translocation to cilia is essential for Smo activity, suggesting that Smo acts at the primary cilium.     

Direct measurement of the transfer rate of chloroplast DNA into the nucleus

Gene transfer from the chloroplast to the nucleus has occurred over evolutionary time. Functional gene establishment in the nucleus is rare, but DNA transfer without functionality is presumably more frequent. Here, we measured directly the transfer rate of chloroplast DNA (cpDNA) into the nucleus of tobacco plants (Nicotiana tabacum). To visualize this process, a nucleus-specific neomycin phosphotransferase gene (neoSTLS2) was integrated into the chloroplast genome, and the transfer of cpDNA to the nucleus was detected by screening for kanamycin-resistant seedlings in progeny. A screen for kanamycin-resistant seedlings was conducted with about 250,000 progeny produced by fertilization of wild-type females with pollen from plants containing cp-neoSTLS2. Sixteen plants of independent origin were identified and their progenies showed stable inheritance of neoSTLS2, characteristic of nuclear genes. Thus, we provide a quantitative estimate of one transposition event in about 16,000 pollen grains for the frequency of transfer of cpDNA to the nucleus. In addition to its evident role in organellar evolution, transposition of cpDNA to the nucleus in tobacco occurs at a rate that must have significant consequences for existing nuclear genes.     

Motor neuron columnar fate imposed by sequential phases of Hox-c activity

The organization of neurons into columns is a prominent feature of central nervous system structure and function. In many regions of the central nervous system the grouping of neurons into columns links cell-body position to axonal trajectory, thus contributing to the establishment of topographic neural maps. This link is prominent in the developing spinal cord, where columnar sets of motor neurons innervate distinct targets in the periphery. We show here that sequential phases of Hox-c protein expression and activity control the columnar differentiation of spinal motor neurons. Hox expression in neural progenitors is established by graded fibroblast growth factor signalling and translated into a distinct motor neuron Hox pattern. Motor neuron columnar fate then emerges through cell autonomous repressor and activator functions of Hox proteins. Hox proteins also direct the expression of genes that establish motor topographic projections, thus implicating Hox proteins as critical determinants of spinal motor neuron identity and organization.