Santa Fe Institute

About: Santa Fe Institute is a nonprofit organization based out in Santa Fe, New Mexico, United States. It is known for research contribution in the topics: Population & Context (language use). The organization has 558 authors who have published 4558 publications receiving 396015 citations. The organization is also known as: SFI.

Evolution and emergence of plant viruses

Abstract: Viruses are common agents of plant infectious diseases. During last decades, worldwide agriculture production has been compromised by a series of epidemics caused by new viruses that spilled over from reservoir species or by new variants of classic viruses that show new pathogenic and epidemiological properties. Virus emergence has been generally associated with ecological change or with intensive agronomical practices. However, the complete picture is much more complex since the viral populations constantly evolve and adapt to their new hosts and vectors. This chapter puts emergence of plant viruses into the framework of evolutionary ecology, genetics, and epidemiology. We will stress that viral emergence begins with the stochastic transmission of preexisting genetic variants from the reservoir to the new host, whose fate depends on their fitness on each hosts, followed by adaptation to new hosts or vectors, and finalizes with an efficient epidemiological spread.

A latent capacity for evolutionary innovation through exaptation in metabolic systems

Abstract: Some evolutionary innovations may originate non-adaptively as exaptations, or pre-adaptations, which are by-products of other adaptive traits. Examples include feathers, which originated before they were used in flight, and lens crystallins, which are light-refracting proteins that originated as enzymes. The question of how often adaptive traits have non-adaptive origins has profound implications for evolutionary biology, but is difficult to address systematically. Here we consider this issue in metabolism, one of the most ancient biological systems that is central to all life. We analyse a metabolic trait of great adaptive importance: the ability of a metabolic reaction network to synthesize all biomass from a single source of carbon and energy. We use novel computational methods to sample randomly many metabolic networks that can sustain life on any given carbon source but contain an otherwise random set of known biochemical reactions. We show that when we require such networks to be viable on one particular carbon source, they are typically also viable on multiple other carbon sources that were not targets of selection. For example, viability on glucose may entail viability on up to 44 other sole carbon sources. Any one adaptation in these metabolic systems typically entails multiple potential exaptations. Metabolic systems thus contain a latent potential for evolutionary innovations with non-adaptive origins. Our observations suggest that many more metabolic traits may have non-adaptive origins than is appreciated at present. They also challenge our ability to distinguish adaptive from non-adaptive traits.

Stability analysis of financial contagion due to overlapping portfolios

Abstract: Common asset holdings are widely believed to have been the primary vector of contagion in the recent financial crisis. We develop a network approach to the amplification of financial contagion due to the combination of overlapping portfolios and leverage, and we show how it can be understood in terms of a generalized branching process. By studying a stylized model we estimate the circumstances under which systemic instabilities are likely to occur as a function of parameters such as leverage, market crowding, diversification, and market impact. Although diversification may be good for individual institutions, it can create dangerous systemic effects, and as a result financial contagion gets worse with too much diversification. Under our model there is a critical threshold for leverage; below it financial networks are always stable, and above it the unstable region grows as leverage increases. The financial system exhibits "robust yet fragile" behavior, with regions of the parameter space where contagion is rare but catastrophic whenever it occurs. Our model and methods of analysis can be calibrated to real data and provide simple yet powerful tools for macroprudential stress testing.

Topology and evolution of technology innovation networks.

Abstract: The web of relations linking technological innovation can be fairly described in terms of patent citations. The resulting patent citation network provides a picture of the large-scale organization of innovations and its time evolution. Here we study the patterns of change of patents registered by the U.S. Patent and Trademark Office. We show that the scaling behavior exhibited by this network is consistent with a preferential attachment mechanism together with a Weibull-shaped aging term. Such an attachment kernel is shared by scientific citation networks, thus indicating a universal type of mechanism linking ideas and designs and their evolution. The implications for evolutionary theory of innovation are discussed.

Disease transmission in territorial populations: the small-world network of Serengeti lions

Abstract: Territoriality in animal populations creates spatial structure that is thought to naturally buffer disease invasion. Often, however, territorial populations also include highly mobile, non-residential individuals that potentially serve as disease superspreaders. Using long-term data from the Serengeti Lion Project, we characterize the contact network structure of a territorial wildlife population and address the epidemiological impact of nomadic individuals. As expected, pride contacts are dominated by interactions with neighbouring prides and interspersed by encounters with nomads as they wander throughout the ecosystem. Yet the pride–pride network also includes occasional long-range contacts between prides, making it surprisingly small world and vulnerable to epidemics, even without nomads. While nomads increase both the local and global connectivity of the network, their epidemiological impact is marginal, particularly for diseases with short infectious periods like canine distemper virus. Thus, territoriality in Serengeti lions may be less protective and non-residents less important for disease transmission than previously considered.