Summary
1. Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment.

2. The focus of the package is on methods for phylogenetic comparative biology; however, it also includes tools for tree inference, phylogeny input/output, plotting, manipulation and several other tasks.

3. I describe and tabulate the major methods implemented in phytools, and in addition provide some demonstration of its use in the form of two illustrative examples.

4. Finally, I conclude by briefly describing an active web-log that I use to document present and future developments for phytools. I also note other web resources for phylogenetics in the R computational environment.

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phytools: an R package for phylogenetic comparative biology (and other things)

Associations between modifiable exposures and disease seen in observational epidemiology are sometimes confounded and thus misleading, despite our best efforts to improve the design and analysis of studies. Mendelian randomization-the random assortment of genes from parents to offspring that occurs during gamete formation and conception-provides one method for assessing the causal nature of some environmental exposures. The association between a disease and a polymorphism that mimics the biological link between a proposed exposure and disease is not generally susceptible to the reverse causation or confounding that may distort interpretations of conventional observational studies. Several examples where the phenotypic effects of polymorphisms are well documented provide encouraging evidence of the explanatory power of Mendelian randomization and are described. The limitations of the approach include confounding by polymorphisms in linkage disequilibrium with the polymorphism under study, that polymorphisms may have several phenotypic effects associated with disease, the lack of suitable polymorphisms for studying modifiable exposures of interest, and canalization-the buffering of the effects of genetic variation during development. Nevertheless, Mendelian randomization provides new opportunities to test causality and demonstrates how investment in the human genome project may contribute to understanding and preventing the adverse effects on human health of modifiable exposures.

/pdf/mendelian-randomization-can-genetic-epidemiology-contribute-vb0zjyrtxf.pdf

‘Mendelian randomization’: can genetic epidemiology contribute to understanding environmental determinants of disease?

In recent months there has been an explosion of interest in using the Web to create, assemble, and disseminate geographic information provided voluntarily by individuals. Sites such as Wikimapia and OpenStreetMap are empowering citizens to create a global patchwork of geographic information, while Google Earth and other virtual globes are encouraging volunteers to develop inter- esting applications using their own data. I review this phenomenon, and examine associated issues: what drives people to do this, how accurate are the results, will they threaten individual privacy, and how can they augment more conventional sources? I compare this new phenomenon to more traditional citizen science and the role of the amateur in geographic observation.

/pdf/citizens-as-sensors-the-world-of-volunteered-geography-phibl484h3.pdf

Citizens as sensors: the world of volunteered geography

We review the recent rapid progress in the statistical physics of evolving networks. Interest has focused mainly on the structural properties of complex networks in communications, biology, social sciences and economics. A number of giant artificial networks of this kind have recently been created, which opens a wide field for the study of their topology, evolution, and the complex processes which occur in them. Such networks possess a rich set of scaling properties. A number of them are scale-free and show striking resilience against random breakdowns. In spite of the large sizes of these networks, the distances between most of their vertices are short - a feature known as the 'small-world' effect. We discuss how growing networks self-organize into scale-free structures, and investigate the role of the mechanism of preferential linking. We consider the topological and structural properties of evolving networks, and percolation and disease spread on these networks. We present a number of models demonstrat...

/pdf/evolution-of-networks-27h4ny8xbi.pdf

Evolution of networks

Yuelong Shu1, John McCauley2 1. WHO Collaborating Center for Reference and Research on Influenza, Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China 2. WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, the Francis Crick Institute, London, United Kingdom

GISAID: Global initiative on sharing all influenza data - from vision to reality.

/pdf/and-le-monde-points-a-finger-at-the-us-1wo84rhu6n.pdf

And Le Monde points a finger at the US

/pdf/risks-of-flu-work-underrated-1gz3bs01r7.pdf

Risks of flu work underrated

The Beagle 2 Mars lander has had some unusual backers — among them British pop stars and artists. Declan Butler finds out how one researcher's publicity drive got the project off the ground.

/pdf/special-section-on-martian-exploration-are-you-on-board-4ye2aehmmk.pdf

Special section on Martian Exploration: Are you on board?

NATURE | VOL 419 | 31 OCTOBER 2002 | www.nature.com/nature 869 Declan Butler Plans by the Massachusetts Institute of Technology (MIT) look set to transform the way in which academics publish and archive their results and raw data. On 4 November, the institute will launch its DSpace electronic archive, a joint venture with technology firm Hewlett-Packard of Palo Alto, California. The ultimate goal of the system is to capture MIT’s entire intellectual output in a stable archive, and to extend it to create a seamless global network of similar archives at other research institutions. These multiple databases could be searched as if they were a single entity, and specialized collections could be built by drawing data from participating archives. More than 40 academic institutions worldwide are considering adopting DSpace, and seven universities, including the University of Cambridge in Britain, are installing and evaluating the system. The move towards such archives is in part driven by libraries, which are looking for cheaper alternatives to costly academic journals. The technology involved is not rocket science, admits MacKenzie Smith, associate director for technology at MIT Libraries and head of the DSpace project. The main innovation is in transforming the often anarchic sprawl of researchers’ websites into a professionally managed system, she says. Documents uploaded onto Dspace must be carefully tagged with ‘metadata’ codes, such as subject keywords, which will help search engines to navigate the database. DSpace should also spare MIT researchers much of the hassle of setting up and maintaining their own websites. The system supports a huge variety of file formats, allowing users to make anything from preprints to medical images available online. It also lets users attach other features to their documents, such as software that can manage access to restricted material. But Smith warns that getting busy faculty members to provide high-quality metadata on their material is a big obstacle, and could deter many would-be participants. “You find that users are not beating down your door,” says Eric Van de Velde, director of library information technology at the California Institute of Technology, who has developed a similar, smaller-scale institutional archive. To get enough data onto the system to make it useful, DSpace has grouped content around individual departments or labs that have well-organized publishing activities. The launch version of DSpace includes five of these ‘early adopter’ communities such as MIT’s Department of Ocean Engineering and MIT Press. The groups have already placed about 750 documents on the database. Smith says that a major demand from researchers is the storage of their raw data, such as medical images and other large data files. “A lot of these deserve to be managed and preserved as much as the publications that result from them,” she says. She is also talking to publishers about the possibility of linking papers in their journals to supplementary information and data stored in the DSpace network of archives. DSpace may also provide a more solid foundation for preprints than existing servers, but it can also support journals and new forms of information sharing, which could help libraries to cut down on journal subscription costs. In the long term, many academic centres feel that they need to retain control of more of what they produce, and DSpace may be a first step in that direction.■ ➧ www.dspace.org

/pdf/mit-gets-plugged-in-for-global-data-archive-1vu8d6z914.pdf

MIT gets plugged in for global data archive.

Downward trend in postgraduate enrolment stokes fears of a brain drain in the country's pipeline of promising young scientists. Downward trend in postgraduate enrolment stokes fears of a brain drain in the country's pipeline of promising young scientists.

Declan Butler

Papers

And Le Monde points a finger at the US

Risks of flu work underrated

Special section on Martian Exploration: Are you on board?

MIT gets plugged in for global data archive.

Number of EU research students in Britain drops from pre-referendum high