Robust information from phylogenetic trees?

Traditional information criteria approaches can lead to misleading model choice in comparative phylogenetics. I present both these weaknesses and a more robust comparison by likelihood ratio. I then discuss a new class of models to capture the transition process between evolutionary regimes

Early warning signals: The charted and uncharted territories

The realization that complex systems such as ecological communities can collapse or shift regimes suddenly and without rapid external forcing poses a serious challenge to our understanding and management of the natural world. The potential to identify early warning signals that would allow researchers and managers to predict such events before they happen has therefore been an invaluable discovery that offers a way forward in spite of such seemingly unpredictable behavior. Research into early warning signals has demonstrated that it is possible to define and detect such early warning signals in advance of a transition in certain contexts. Here we describe the pattern emerging as research continues to explore just how far we can generalize these results. A core of examples emerges that shares three properties: the phenomenon of rapid regime shifts, a pattern of 'critical slowing down' that can be used to detect the approaching shift, and a mechanism of bifurcation driving the sudden change. As research has expanded beyond these core examples, it is becoming clear that not all systems that show regime shifts exhibit critical slowing down, or vice versa. Even when systems exhibit critical slowing down, statistical detection is a challenge. We review the literature that explores these edge cases and highlight the need for (a) new early warning behaviors that can be used in cases where rapid shifts do not exhibit critical slowing down, (b) the development of methods to identify which behavior might be an appropriate signal when encountering a novel system; bearing in mind that a positive indication for some systems is a negative indication in others, and (c) statistical methods that can distinguish between signatures of early warning behaviors and noise

After the games are over: life-history trade-offs drive dispersal attenuation following range expansion.

Increased dispersal propensity often evolves on expanding range edges due to the Olympic Village effect, which involves the fastest and fittest finding themselves together in the same place at the same time, mating, and giving rise to like individuals. But what happens after the ranges leading edge has passed and the games are over? Although empirical studies indicate that dispersal propensity attenuates following range expansion, hypotheses about the mechanisms driving this attenuation have not been clearly articulated or tested. Here, we used a simple model of the spatiotemporal dynamics of two phenotypes, one fast and the other slow, to propose that dispersal attenuation beyond preexpansion levels is only possible in the presence of trade-offs between dispersal and life-history traits. The Olympic Village effect ensures that fast dispersers preempt locations far from the ranges previous limits. When trade-offs are absent, this preemptive spatial advantage has a lasting impact, with highly dispersive individuals attaining equilibrium frequencies that are strictly higher than their introduction frequencies. When trade-offs are present, dispersal propensity decays rapidly at all locations. Our models results about the postcolonization trajectory of dispersal evolution are clear and, in principle, should be observable in field studies. We conclude that empirical observations of postcolonization dispersal attenuation offer a novel way to detect the existence of otherwise elusive trade-offs between dispersal and life-history traits

Unidirectional Movement Fibres from A Proprioceptive Organ of the Crab, Carcinus Maenas

1. The proprioceptive organ of the shore crab Carcinus maenas, which signals all proprioceptive sensation from the joint between propodite and dactylopodite, has been shown to contain sense cells receptive to position as well as to movement. 2. Certain cells of the organ increase their discharge frequency in response to greater degrees of flexion, while other endings respond to greater degrees of extension. Movement has little effect on the frequency of the position fibres. 3. Cells responding to movement in one direction only are present, certain ones signalling fiexion and others extension. The most sensitive undirectional movement fibres are almost completely independent of position and velocity. They provide the crab with an extremely sensitive movement sense not as yet reported in other proprioceptive mechanisms. 4. Both position-sensitive and movement-sensitive cells show a wide range of thresholds. 5. Cells which cannot be strictly classified as either position or movement sensitive have also been found. 6. By tracing the origin of the signals to the cell bodies, it appears that movement fibres have on the whole larger cell bodies than position fibres and are more proximally located. 7. Flexor and extensor movement cells appear to lie on different sides of elastic strand. 8. The question of how unidirectional sensitivity may be achieved is discussed

Managing Intellectual Property to Foster Agricultural Development

Over the past decades, consideration of IPRs has become increasingly important in many areas of agricultural development, including foreign direct investment, technology transfer, trade, investment in innovation, access to genetic resources, and the protection of traditional knowledge. The widening role of IPRs in governing the ownership of—and access to—innovation, information, and knowledge makes them particularly critical in ensuring that developing countries benefit from the introduction of new technologies that could radically alter the welfare of the poor. Failing to improve IPR policies and practices to support the needs of developing countries will eliminate significant development opportunities. The discussion in this note moves away from policy prescriptions to focus on investments to improve how IPRs are used in practice in agricultural development. These investments must be seen as complementary to other investments in agricultural development. IPRs are woven into the context of innovation and R&D. They can enable entrepreneurship and allow the leveraging of private resources for resolving the problems of poverty. Conversely, IPRs issues can delay important scientific advancements, deter investment in products for the poor, and impose crippling transaction costs on organizations if the wrong tools are used or tools are badly applied. The central benefit of pursuing the investments outlined in this note is to build into the system a more robust capacity for strategic and flexible use of IPRs tailored to development goals

RNeXML: a package for reading and writing richly annotated phylogenetic, character, and trait data in R

NeXML is a powerful and extensible exchange standard recently proposed to better meet the expanding needs for phylogenetic data and metadata sharing. Here we present the RNeXML package, which provides users of the R programming language with easy-to-use tools for reading and writing NeXML documents, including rich metadata, in a way that interfaces seamlessly with the extensive library of phylogenetic tools already available in the R ecosystem

Reading the Secrets of Biological Fluctuations

I explore tools and applications of the van Kampen expansion of the stochastic master equation in several areas of population biology. I highlight fluctuation-dissipation and fluctuation-enhancement regimes, using information from noise to help model choice, and examples where noise changes the macroscopic dynamics of a system

Enforcing public data archiving policies in academic publishing: A study of ecology journals

To improve the quality and efficiency of research, groups within the scientific community seek to exploit the value of data sharing. Funders, institutions, and specialist organizations are developing and implementing strategies to encourage or mandate data sharing within and across disciplines, with varying degrees of success. Academic journals in ecology and evolution have adopted several types of public data archiving policies requiring authors to make data underlying scholarly manuscripts freely available. Yet anecdotes from the community and studies evaluating data availability suggest that these policies have not obtained the desired effects, both in terms of quantity and quality of available datasets. We conducted a qualitative, interview-based study with journal editorial staff and other stakeholders in the academic publishing process to examine how journals enforce data archiving policies. We specifically sought to establish who editors and other stakeholders perceive as responsible for ensuring data completeness and quality in the peer review process. Our analysis revealed little consensus with regard to how data archiving policies should be enforced and who should hold authors accountable for dataset submissions. Themes in interviewee responses included hopefulness that reviewers would take the initiative to review datasets and trust in authors to ensure the completeness and quality of their datasets. We highlight problematic aspects of these thematic responses and offer potential starting points for improvement of the public data archiving process.Comment: 35 pages, 1 figure, 1 tabl