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.

Risk for Transportation of Coronavirus Disease from Wuhan to Other Cities in China.

Abstract: On January 23, 2020, China quarantined Wuhan to contain coronavirus disease (COVID-19). We estimated the probability of transportation of COVID-19 from Wuhan to 369 other cities in China before the quarantine. Expected COVID-19 risk is >50% in 130 (95% CI 89-190) cities and >99% in the 4 largest metropolitan areas.

Future of the human climate niche.

Abstract: All species have an environmental niche, and despite technological advances, humans are unlikely to be an exception. Here, we demonstrate that for millennia, human populations have resided in the same narrow part of the climatic envelope available on the globe, characterized by a major mode around ∼11 °C to 15 °C mean annual temperature (MAT). Supporting the fundamental nature of this temperature niche, current production of crops and livestock is largely limited to the same conditions, and the same optimum has been found for agricultural and nonagricultural economic output of countries through analyses of year-to-year variation. We show that in a business-as-usual climate change scenario, the geographical position of this temperature niche is projected to shift more over the coming 50 y than it has moved since 6000 BP. Populations will not simply track the shifting climate, as adaptation in situ may address some of the challenges, and many other factors affect decisions to migrate. Nevertheless, in the absence of migration, one third of the global population is projected to experience a MAT >29 °C currently found in only 0.8% of the Earth’s land surface, mostly concentrated in the Sahara. As the potentially most affected regions are among the poorest in the world, where adaptive capacity is low, enhancing human development in those areas should be a priority alongside climate mitigation.

Low-dose rectal inoculation of rhesus macaques by SIVsmE660 or SIVmac251 recapitulates human mucosal infection by HIV-1

Abstract: We recently developed a novel strategy to identify transmitted HIV-1 genomes in acutely infected humans using single-genome amplification and a model of random virus evolution. Here, we used this approach to determine the molecular features of simian immunodeficiency virus (SIV) transmission in 18 experimentally infected Indian rhesus macaques. Animals were inoculated intrarectally (i.r.) or intravenously (i.v.) with stocks of SIVmac251 or SIVsmE660 that exhibited sequence diversity typical of early-chronic HIV-1 infection. 987 full-length SIV env sequences (median of 48 per animal) were determined from plasma virion RNA 1–5 wk after infection. i.r. inoculation was followed by productive infection by one or a few viruses (median 1; range 1–5) that diversified randomly with near starlike phylogeny and a Poisson distribution of mutations. Consensus viral sequences from ramp-up and peak viremia were identical to viruses found in the inocula or differed from them by only one or a few nucleotides, providing direct evidence that early plasma viral sequences coalesce to transmitted/founder viruses. i.v. infection was >2,000-fold more efficient than i.r. infection, and viruses transmitted by either route represented the full genetic spectra of the inocula. These findings identify key similarities in mucosal transmission and early diversification between SIV and HIV-1, and thus validate the SIV–macaque mucosal infection model for HIV-1 vaccine and microbicide research.

Cooperation, social networks, and the emergence of leadership in a prisoner's dilemma with adaptive local interactions.

Abstract: Cooperative behavior among a group of agents is studied assuming adaptive interactions. Each agent plays a Prisoner's Dilemma game with its local neighbors, collects an aggregate payoff, and imitates the strategy of its best neighbor. Agents may punish or reward their neighbors by removing or sustaining the interactions, according to their satisfaction level and strategy played. An agent may dismiss an interaction, and the corresponding neighbor is replaced by another randomly chosen agent, introducing diversity and evolution to the network structure. We perform an extensive numerical and analytical study, extending results in M. G. Zimmermann, V. M. Eguiluz, and M. San Miguel, Phys. Rev. E 69, 065102(R) (2004). We show that the system typically reaches either a full-defective state or a highly cooperative steady state. The latter equilibrium solution is composed mostly by cooperative agents, with a minor population of defectors that exploit the cooperators. It is shown how the network adaptation dynamics favors the emergence of cooperators with the highest payoff. These "leaders" are shown to sustain the global cooperative steady state. Also we find that the average payoff of defectors is larger than the average payoff of cooperators. Whenever "leaders" are perturbed (e.g., by addition of noise), an unstable situation arises and global cascades with oscillations between the nearly full defection network and the fully cooperative outcome are observed.

On the Origin of Species by Natural and Sexual Selection

Abstract: Ecological speciation is considered an adaptive response to selection for local adaptation. However, besides suitable ecological conditions, the process requires assortative mating to protect the nascent species from homogenization by gene flow. By means of a simple model, we demonstrate that disruptive ecological selection favors the evolution of sexual preferences for ornaments that signal local adaptation. Such preferences induce assortative mating with respect to ecological characters and enhance the strength of disruptive selection. Natural and sexual selection thus work in concert to achieve local adaptation and reproductive isolation, even in the presence of substantial gene flow. The resulting speciation process ensues without the divergence of mating preferences, avoiding problems that have plagued previous models of speciation by sexual selection.