The evolutionary origins of human patience: temporal preferences in chimpanzees, bonobos, and human adults.

To make adaptive choices, individuals must sometimes exhibit patience, forgoing immediate benefits to acquire more valuable future rewards [1-3]. Although humans account for future consequences when making temporal decisions [4], many animal species wait only a few seconds for delayed benefits [5-10]. Current research thus suggests a phylogenetic gap between patient humans and impulsive, present-oriented animals [9, 11], a distinction with implications for our understanding of economic decision making [12] and the origins of human cooperation [13]. On the basis of a series of experimental results, we reject this conclusion. First, bonobos (Pan paniscus) and chimpanzees (Pan troglodytes) exhibit a degree of patience not seen in other animals tested thus far. Second, humans are less willing to wait for food rewards than are chimpanzees. Third, humans are more willing to wait for monetary rewards than for food, and show the highest degree of patience only in response to decisions about money involving low opportunity costs. These findings suggest that core components of the capacity for future-oriented decisions evolved before the human lineage diverged from apes. Moreover, the different levels of patience that humans exhibit might be driven by fundamental differences in the mechanisms representing biological versus abstract rewards.

Eco-evolutionary dynamics: intertwining ecological and evolutionary processes in contemporary time.

Evolution occurring over contemporary time scales can have important effects on populations, communities, and ecosystems. Recent studies show that the magnitude of these effects can be large and can generate feedbacks that further shape evolution.

A dimensionless number for understanding the evolutionary dynamics of antigenically variable RNA viruses.

Antigenically variable RNA viruses are significant contributors to the burden of infectious disease worldwide. One reason for their ubiquity is their ability to escape herd immunity through rapid antigenic evolution and thereby to reinfect previously infected hosts. However, the ways in which these viruses evolve antigenically are highly diverse. Some have only limited diversity in the long-run, with every emergence of a new antigenic variant coupled with a replacement of the older variant. Other viruses rapidly accumulate antigenic diversity over time. Others still exhibit dynamics that can be considered evolutionary intermediates between these two extremes. Here, we present a theoretical framework that aims to understand these differences in evolutionary patterns by considering a virus's epidemiological dynamics in a given host population. Our framework, based on a dimensionless number, probabilistically anticipates patterns of viral antigenic diversification and thereby quantifies a virus's evolutionary potential. It is therefore similar in spirit to the basic reproduction number, the well-known dimensionless number which quantifies a pathogen's reproductive potential. We further outline how our theoretical framework can be applied to empirical viral systems, using influenza A/H3N2 as a case study. We end with predictions of our framework and work that remains to be done to further integrate viral evolutionary dynamics with disease ecology.

Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment.

BACKGROUND: Penguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an aquatic life, and some of them have successfully adapted to the hostile environments in Antarctica. To study the phylogenetic and population history of penguins and the molecular basis of their adaptations to Antarctica, we sequenced the genomes of the two Antarctic dwelling penguin species, the Adélie penguin [Pygoscelis adeliae] and emperor penguin [Aptenodytes forsteri]. RESULTS: Phylogenetic dating suggests that early penguins arose ~60 million years ago, coinciding with a period of global warming. Analysis of effective population sizes reveals that the two penguin species experienced population expansions from ~1 million years ago to ~100 thousand years ago, but responded differently to the climatic cooling of the last glacial period. Comparative genomic analyses with other available avian genomes identified molecular changes in genes related to epidermal structure, phototransduction, lipid metabolism, and forelimb morphology. CONCLUSIONS: Our sequencing and initial analyses of the first two penguin genomes provide insights into the timing of penguin origin, fluctuations in effective population sizes of the two penguin species over the past 10 million years, and the potential associations between these biological patterns and global climate change. The molecular changes compared with other avian genomes reflect both shared and diverse adaptations of the two penguin species to the Antarctic environment.

Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature.

BACKGROUND: The wealth of phenotypic descriptions documented in the published articles, monographs, and dissertations of phylogenetic systematics is traditionally reported in a free-text format, and it is therefore largely inaccessible for linkage to biological databases for genetics, development, and phenotypes, and difficult to manage for large-scale integrative work. The Phenoscape project aims to represent these complex and detailed descriptions with rich and formal semantics that are amenable to computation and integration with phenotype data from other fields of biology. This entails reconceptualizing the traditional free-text characters into the computable Entity-Quality (EQ) formalism using ontologies. METHODOLOGY/PRINCIPAL FINDINGS: We used ontologies and the EQ formalism to curate a collection of 47 phylogenetic studies on ostariophysan fishes (including catfishes, characins, minnows, knifefishes) and their relatives with the goal of integrating these complex phenotype descriptions with information from an existing model organism database (zebrafish, http://zfin.org). We developed a curation workflow for the collection of character, taxonomic and specimen data from these publications. A total of 4,617 phenotypic characters (10,512 states) for 3,449 taxa, primarily species, were curated into EQ formalism (for a total of 12,861 EQ statements) using anatomical and taxonomic terms from teleost-specific ontologies (Teleost Anatomy Ontology and Teleost Taxonomy Ontology) in combination with terms from a quality ontology (Phenotype and Trait Ontology). Standards and guidelines for consistently and accurately representing phenotypes were developed in response to the challenges that were evident from two annotation experiments and from feedback from curators. CONCLUSIONS/SIGNIFICANCE: The challenges we encountered and many of the curation standards and methods for improving consistency that we developed are generally applicable to any effort to represent phenotypes using ontologies. This is because an ontological representation of the detailed variations in phenotype, whether between mutant or wildtype, among individual humans, or across the diversity of species, requires a process by which a precise combination of terms from domain ontologies are selected and organized according to logical relations. The efficiencies that we have developed in this process will be useful for any attempt to annotate complex phenotypic descriptions using ontologies. We also discuss some ramifications of EQ representation for the domain of systematics.

The evolutionary history of ferns inferred from 25 low-copy nuclear genes.

UNLABELLED: • PREMISE OF THE STUDY: Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data.• METHODS: Here we take a curated phylogenomics approach to infer the first broad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35877 bp), along with rigorous alignment, orthology inference and model selection.• KEY RESULTS: Our phylogeny corroborates some earlier inferences and provides novel insights; in particular, we find strong support for Equisetales as sister to the rest of ferns, Marattiales as sister to leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypods. Our divergence-time analyses reveal that divergences among the extant fern orders all occurred prior to ∼200 MYA. Finally, our species-tree inferences are congruent with analyses of concatenated data, but generally with lower support. Those cases where species-tree support values are higher than expected involve relationships that have been supported by smaller plastid datasets, suggesting that deep coalescence may be reducing support from the concatenated nuclear data.• CONCLUSIONS: Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies.

Integrating simultaneous prosocial and antisocial behavior into theories of collective action.

Trust and cooperation constitute cornerstones of common-pool resource theory, showing that "prosocial" strategies among resource users can overcome collective action problems and lead to sustainable resource governance. Yet, antisocial behavior and especially the coexistence of prosocial and antisocial behaviors have received less attention. We broaden the analysis to include the effects of both "prosocial" and "antisocial" interactions. We do so in the context of marine protected areas (MPAs), the most prominent form of biodiversity conservation intervention worldwide. Our multimethod approach relied on lab-in-the-field economic experiments (n = 127) in two MPA and two non-MPA communities in Baja California, Mexico. In addition, we deployed a standardized fishers' survey (n = 544) to verify the external validity of our findings and expert informant interviews (n = 77) to develop potential explanatory mechanisms. In MPA sites, prosocial and antisocial behavior is significantly higher, and the presence of antisocial behavior does not seem to have a negative effect on prosocial behavior. We suggest that market integration, economic diversification, and strengthened group identity in MPAs are the main potential mechanisms for the simultaneity of prosocial and antisocial behavior we observed. This study constitutes a first step in better understanding the interaction between prosociality and antisociality as related to natural resources governance and conservation science, integrating literatures from social psychology, evolutionary anthropology, behavioral economics, and ecology.

The FUELGEN alternative: an evolutionary approach. The architecture

This paper introduces a few architectural concepts from FUELGEN, that generates a "cloud" of reload patterns, like the generator in the FUELCON expert system, but unlike that generator, is based on a genetic algorithm. There are indications FUELGEN may outperform FUELCON and other tools as reported in the literature, in well-researched case studies, but careful comparisons have to be carried out. This paper complements the information in two other recent papers on FUELGEN. Moreover, a sequel project is outlined.

FUELGEN: effective evolutionary design of refuellings for pressurized water reactors

The paper describes the design of an efficient and robust genetic algorithm for the nuclear fuel loading problem (i.e., refuellings: the in-core fuel management problem) - a complex combinatorial, multimodal optimisation., Evolutionary computation as performed by FUELGEN replaces heuristic search of the kind performed by the FUELCON expert system (CAI 12/4), to solve the same problem. In contrast to the traditional genetic algorithm which makes strong requirements on the representation used and its parameter setting in order to be efficient, the results of recent research results on new, robust genetic algorithms show that representations unsuitable for the traditional genetic algorithm can still be used to good effect with little parameter adjustment. The representation presented here is a simple symbolic one with no linkage attributes, making the genetic algorithm particularly easy to apply to fuel loading problems with differing core structures and assembly inventories. A nonlinear fitness function has been constructed to direct the search efficiently in the presence of the many local optima that result from the constraint on solutions.

[Book review] Psychology and Law: Truthfulness, Accuracy and Credibility

Review of: Psychology and law : truthfulness, accuracy and credibility by Amina Memon, Aldert Vrij and Ray Bull. London: McGraw-Hill, 1998.

[Book review] Psicologia Della Prova [Psychology of Proof]

Review of: Psicologia Della Prova [Psychology of Proof] edited by C. Cabras, Giuffré, Milano. 1996.

[Book review] Handbook of Psychology in Legal Contexts

Review of: Handbook of Psychology in Legal Contexts. Ray Bull and David Carson (eds.) Wiley-Blackwell. 1999.