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New and Exciting in PLoS ONE

There are 23 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the day – you go and look for your own favourites:

The Emergence of Predators in Early Life: There was No Garden of Eden:

Eukaryote cells are suggested to arise somewhere between 0.85~2.7 billion years ago. However, in the present world of unicellular organisms, cells that derive their food and metabolic energy from larger cells engulfing smaller cells (phagocytosis) are almost exclusively eukaryotic. Combining these propositions, that eukaryotes were the first phagocytotic predators and that they arose only 0.85~2.7 billion years ago, leads to an unexpected prediction of a long period (~1-3 billion years) with no phagocytotes – a veritable Garden of Eden. We test whether such a long period is reasonable by simulating a population of very simple unicellular organisms – given only basic physical, biological and ecological principles. Under a wide range of initial conditions, cellular specialization occurs early in evolution; we find a range of cell types from small specialized primary producers to larger opportunistic or specialized predators. Both strategies, specialized smaller cells and phagocytotic larger cells are apparently fundamental biological strategies that are expected to arise early in cellular evolution. Such early predators could have been ‘prokaryotes’, but if the earliest cells on the eukaryote lineage were predators then this explains most of their characteristic features.

Effects of Global Warming on Ancient Mammalian Communities and Their Environments:

Current global warming affects the composition and dynamics of mammalian communities and can increase extinction risk; however, long-term effects of warming on mammals are less understood. Dietary reconstructions inferred from stable isotopes of fossil herbivorous mammalian tooth enamel document environmental and climatic changes in ancient ecosystems, including C3/C4 transitions and relative seasonality. Here, we use stable carbon and oxygen isotopes preserved in fossil teeth to document the magnitude of mammalian dietary shifts and ancient floral change during geologically documented glacial and interglacial periods during the Pliocene (~1.9 million years ago) and Pleistocene (~1.3 million years ago) in Florida. Stable isotope data demonstrate increased aridity, increased C4 grass consumption, inter-faunal dietary partitioning, increased isotopic niche breadth of mixed feeders, niche partitioning of phylogenetically similar taxa, and differences in relative seasonality with warming. Our data show that global warming resulted in dramatic vegetation and dietary changes even at lower latitudes (~28°N). Our results also question the use of models that predict the long term decline and extinction of species based on the assumption that niches are conserved over time. These findings have immediate relevance to clarifying possible biotic responses to current global warming in modern ecosystems.

Coping with Commitment: Projected Thermal Stress on Coral Reefs under Different Future Scenarios:

Periods of anomalously warm ocean temperatures can lead to mass coral bleaching. Past studies have concluded that anthropogenic climate change may rapidly increase the frequency of these thermal stress events, leading to declines in coral cover, shifts in the composition of corals and other reef-dwelling organisms, and stress on the human populations who depend on coral reef ecosystems for food, income and shoreline protection. The ability of greenhouse gas mitigation to alter the near-term forecast for coral reefs is limited by the time lag between greenhouse gas emissions and the physical climate response. This study uses observed sea surface temperatures and the results of global climate model forced with five different future emissions scenarios to evaluate the “committed warming” for coral reefs worldwide. The results show that the physical warming commitment from current accumulation of greenhouse gases in the atmosphere could cause over half of the world’s coral reefs to experience harmfully frequent (p≥0.2 year−1) thermal stress by 2080. An additional “societal” warming commitment, caused by the time required to shift from a business-as-usual emissions trajectory to a 550 ppm CO2 stabilization trajectory, may cause over 80% of the world’s coral reefs to experience harmfully frequent events by 2030. Thermal adaptation of 1.5°C would delay the thermal stress forecast by 50-80 years. The results suggest that adaptation – via biological mechanisms, coral community shifts and/or management interventions – could provide time to change the trajectory of greenhouse gas emissions and possibly avoid the recurrence of harmfully frequent events at the majority (97%) of the world’s coral reefs this century. Without any thermal adaptation, atmospheric CO2 concentrations may need to be stabilized below current levels to avoid the degradation of coral reef ecosystems from frequent thermal stress events.

The Alliance Hypothesis for Human Friendship:

Exploration of the cognitive systems underlying human friendship will be advanced by identifying the evolved functions these systems perform. Here we propose that human friendship is caused, in part, by cognitive mechanisms designed to assemble support groups for potential conflicts. We use game theory to identify computations about friends that can increase performance in multi-agent conflicts. This analysis suggests that people would benefit from: 1) ranking friends, 2) hiding friend-ranking, and 3) ranking friends according to their own position in partners’ rankings. These possible tactics motivate the hypotheses that people possess egocentric and allocentric representations of the social world, that people are motivated to conceal this information, and that egocentric friend-ranking is determined by allocentric representations of partners’ friend-rankings (more than others’ traits). We report results from three studies that confirm predictions derived from the alliance hypothesis. Our main empirical finding, replicated in three studies, was that people’s rankings of their ten closest friends were predicted by their own perceived rank among their partners’ other friends. This relationship remained strong after controlling for a variety of factors such as perceived similarity, familiarity, and benefits. Our results suggest that the alliance hypothesis merits further attention as a candidate explanation for human friendship.

Trophic Garnishes: Cat-Rat Interactions in an Urban Environment:

Community interactions can produce complex dynamics with counterintuitive responses. Synanthropic community members are of increasing practical interest for their effects on biodiversity and public health. Most studies incorporating introduced species have been performed on islands where they may pose a risk to the native fauna. Few have examined their interactions in urban environments where they represent the majority of species. We characterized house cat (Felis catus) predation on wild Norway rats (Rattus norvegicus), and its population effects in an urban area as a model system. Three aspects of predation likely to influence population dynamics were examined; the stratum of the prey population killed by predators, the intensity of the predation, and the size of the predator population. Predation pressure was estimated from the sizes of the rat and cat populations, and the characteristics of rats killed in 20 alleys. Short and long term responses of rat population to perturbations were examined by removal trapping. Perturbations removed an average of 56% of the rats/alley but had no negative long-term impact on the size of the rat population (49.6±12.5 rats/alley and 123.8±42.2 rats/alley over two years). The sizes of the cat population during two years (3.5 animals/alley and 2.7 animals/alley) also were unaffected by rat population perturbations. Predation by cats occurred in 9/20 alleys. Predated rats were predominantly juveniles and significantly smaller (144.6 g±17.8 g) than the trapped rats (385.0 g±135.6 g). Cats rarely preyed on the larger, older portion of the rat population. The rat population appears resilient to perturbation from even substantial population reduction using targeted removal. In this area there is a relatively low population density of cats and they only occasionally prey on the rat population. This occasional predation primarily removes the juvenile proportion of the rat population. The top predator in this urban ecosystem appears to have little impact on the size of the prey population, and similarly, reduction in rat populations doesn’t impact the size of the cat population. However, the selected targeting of small rats may locally influence the size structure of the population which may have consequences for patterns of pathogen transmission.

Explaining the Evolution of Warning Coloration: Secreted Secondary Defence Chemicals May Facilitate the Evolution of Visual Aposematic Signals:

Several pathways have been postulated to explain the evolution of warning coloration, which is a perplexing phenomenon. Many of these attempt to circumvent the problem of naïve predators by inferring kin selection or neophobia. Through a stochastic model, we show that a secreted secondary defence chemical can provide selective pressure, on the individual level, towards developing warning coloration. Our fundamental assumption is that increased conspicuousness will result in longer assessment periods and divergence from the predators’ searching image, thus reducing the probability of a predator making mistakes. We conclude that strong olfactory signaling by means of chemical secretions can lead to the evolution of warning coloration.

Paleo-Immunology: Evidence Consistent with Insertion of a Primordial Herpes Virus-Like Element in the Origins of Acquired Immunity:

The RAG encoded proteins, RAG-1 and RAG-2 regulate site-specific recombination events in somatic immune B- and T-lymphocytes to generate the acquired immune repertoire. Catalytic activities of the RAG proteins are related to the recombinase functions of a pre-existing mobile DNA element in the DDE recombinase/RNAse H family, sometimes termed the “RAG transposon”. Novel to this work is the suggestion that the DDE recombinase responsible for the origins of acquired immunity was encoded by a primordial herpes virus, rather than a “RAG transposon.” A subsequent “arms race” between immunity to herpes infection and the immune system obscured primary amino acid similarities between herpes and immune system proteins but preserved regulatory, structural and functional similarities between the respective recombinase proteins. In support of this hypothesis, evidence is reviewed from previous published data that a modern herpes virus protein family with properties of a viral recombinase is co-regulated with both RAG-1 and RAG-2 by closely linked cis-acting co-regulatory sequences. Structural and functional similarity is also reviewed between the putative herpes recombinase and both DDE site of the RAG-1 protein and another DDE/RNAse H family nuclease, the Argonaute protein component of RISC (RNA induced silencing complex). A “co-regulatory” model of the origins of V(D)J recombination and the acquired immune system can account for the observed linked genomic structure of RAG-1 and RAG-2 in non-vertebrate organisms such as the sea urchin that lack an acquired immune system and V(D)J recombination. Initially the regulated expression of a viral recombinase in immune cells may have been positively selected by its ability to stimulate innate immunity to herpes virus infection rather than V(D)J recombination Unlike the “RAG-transposon” hypothesis, the proposed model can be readily tested by comparative functional analysis of herpes virus replication and V(D)J recombination.

Virtual Partner Interaction (VPI): Exploring Novel Behaviors via Coordination Dynamics:

Inspired by the dynamic clamp of cellular neuroscience, this paper introduces VPI–Virtual Partner Interaction–a coupled dynamical system for studying real time interaction between a human and a machine. In this proof of concept study, human subjects coordinate hand movements with a virtual partner, an avatar of a hand whose movements are driven by a computerized version of the Haken-Kelso-Bunz (HKB) equations that have been shown to govern basic forms of human coordination. As a surrogate system for human social coordination, VPI allows one to examine regions of the parameter space not typically explored during live interactions. A number of novel behaviors never previously observed are uncovered and accounted for. Having its basis in an empirically derived theory of human coordination, VPI offers a principled approach to human-machine interaction and opens up new ways to understand how humans interact with human-like machines including identification of underlying neural mechanisms.