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.

/pdf/phytools-an-r-package-for-phylogenetic-comparative-biology-yli0omoidd.pdf

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.

How Ebola-vaccine success could reshape clinical-trial policy

/pdf/laser-test-facility-will-maintain-deterrence-5ddns31sa3.pdf

Laser test facility `will maintain deterrence'

Arnold Levine has resigned as president of Rockefeller University in New York amid reports of a public and allegedly inappropriate encounter with a female graduate student. In a statement issued on 10 February, 62-year-old Levine said he was leaving to address matters affecting his health.“In light of my health issues, I regret I will not be able to continue to lead this extraordinary institution and these talented people,”he wrote. But sources at the university confirmed reports that Levine has resigned over what one of them described as an “inappropriate incident”with a female graduate student that occurred on 10 January. Various reports of the encounter have swept through Rockefeller in recent weeks. According to the sources, the encounter occurred in the university’s faculty club, a popular meeting place for researchers and graduate students. Both Levine and the participating student were intoxicated, the sources say, and she is said to have told university officials that the encounter was consensual. A male student who was in the faculty club confronted Levine during the encounter, one of the sources says, at which point Levine became angry. This student reported the incident to the Board of Trustees. Levine,who was the first to isolate the p53 tumour-suppressor protein, rushed back on 8 February from a meeting held to mark the opening of the Spanish National Cancer Centre in Madrid. Summoned by the Board of Trustees, he expressed profound regrets and said he would resign, says a source familiar with the situation.Levine was unavailable to comment on the incident. Thomas Sakmar, who works on mechanisms of cell signalling and has headed the university’s Academic Senate for the past year, has since been appointed acting president while the board sets about selecting a permanent replacement for Levine. news

/pdf/soros-offers-open-access-to-science-papers-1g8737yd9f.pdf

Soros offers open access to science papers

Predicting the number of cases of Creutzfeldt–Jakob disease (CJD) in people as a result of transmission of bovine spongiform encephalopathy (BSE) has just got more difficult. Whereas it was thought that BSE only caused a new form of the disease called variant CJD (vCJD), a study in mice from a team led by John Collinge at University College London suggests that it may also cause a disease indistinguishable from the commonest form of classical, or ‘sporadic’, CJD (E. A. Asante et al. EMBO J. 21, 6358–6366; 2002). If the group’s mouse model is relevant to the human disease, the results also suggest that the true extent of infection may be difficult to assess because of the large number of asymptomatic carriers. The latest work uses mice engineered to carry the human gene for a cell-membrane protein called PrP. Prion diseases occur when PrP is converted to the abnormal ‘prion’ form, PrP. Collinge has developed a test, based on a standard western blot for analysing proteins, to study PrP extracted from the brain. This previously showed disease caused by BSE or vCJD to give a characteristic molecular signature that is distinct from sporadic CJD (J.Collinge,K.C. L. Sidle, J. Meads, J. Ironside and A. F. Hill Nature 383, 685–690; 1996). In their latest experiments, Collinge and his team injected material from the brains of cows with BSE or people with vCJD directly into the brains of two strains of mice with a human PrP genotype known as 129MM. Almost 40% of the British population has this genotype. In one mouse strain, those that became infected showed the usual BSE pattern in the western blot. But in the other,Collinge’s team tested 11 mice infected with BSE material using the western blot.Ten of them showed a pattern consistent with sporadic CJD. The number of cases of sporadic CJD have been rising in Britain since the 1970s, and this had been attributed to better monitoring for the condition. But in July, researchers led by Adriano Aguzzi of the University Hospital Zurich reported a sudden increase in sporadic CJD figures in Switzerland in 2001,and suggested that infection with BSE might be to blame (see Nature 418, 266 ; 2002). Collinge’s new data provide worrying molecular evidence that BSE might be to blame for the rise in sporadic CJD. In previous experiments, Collinge had injected BSE and vCJD material into mice with another human PrP genotype, known as 129VV. The new data are thought to be more relevant to the transmission of BSE because all of the known human victims of vCJD have the 129MM genotype. Another worrying finding is that the 129MM mice seem to be more susceptible to developing a subclinical infection, with no obvious symptoms. If a large pool of the British population is carrying a subclinical BSE infection, this would have serious consequences for the potential transmission of the disease, for instance through contaminated surgical instruments. And although laboratory mice are short-lived, infected humans might go on to develop the disease later in life. The UK Department of Health, which has been briefed by Collinge on his findings, says that it will ask its Spongiform Encephalopathy Advisory Committee to consider the results closely at its next meeting in February. Collinge says that an urgent nationwide screening of tonsil material is needed to get a better estimate of the level of infection in the population. ■ news

/pdf/prion-data-suggest-bse-link-to-sporadic-cjd-4bvgqidaow.pdf

Prion data suggest BSE link to sporadic CJD.

/pdf/agreement-urged-on-access-to-dna-databases-cuvoiyhfs2.pdf

Declan Butler

Papers

How Ebola-vaccine success could reshape clinical-trial policy

Laser test facility `will maintain deterrence'

Soros offers open access to science papers

Prion data suggest BSE link to sporadic CJD.

Agreement urged on access to DNA databases