Frequency-dependent survival in natural guppy populations

The maintenance of genetic variation in traits under natural selection is a long-standing paradox in evolutionary biology. Of the processes capable of maintaining variation, negative frequency-dependent selection (where rare types are favoured by selection) is the most powerful, at least in theory; however, few experimental studies have confirmed that this process operates in nature. One of the most extreme, unexplained genetic polymorphisms is seen in the colour patterns of male guppies (Poecilia reticulata). Here we manipulated the frequencies of males with different colour patterns in three natural populations to estimate survival rates, and found that rare phenotypes had a highly significant survival advantage compared to common phenotypes. Evidence from humans and other species implicates frequency-dependent survival in the maintenance of molecular, morphological and health-related polymorphisms. As a controlled manipulation in nature, this study provides unequivocal support for frequency-dependent survival--an evolutionary process capable of maintaining extreme polymorphism.     

Independent evolution of bitter-taste sensitivity in humans and chimpanzees

It was reported over 65 years ago that chimpanzees, like humans, vary in taste sensitivity to the bitter compound phenylthiocarbamide (PTC). This was suggested to be the result of a shared balanced polymorphism, defining the first, and now classic, example of the effects of balancing selection in great apes. In humans, variable PTC sensitivity is largely controlled by the segregation of two common alleles at the TAS2R38 locus, which encode receptor variants with different ligand affinities. Here we show that PTC taste sensitivity in chimpanzees is also controlled by two common alleles of TAS2R38; however, neither of these alleles is shared with humans. Instead, a mutation of the initiation codon results in the use of an alternative downstream start codon and production of a truncated receptor variant that fails to respond to PTC in vitro. Association testing of PTC sensitivity in a cohort of captive chimpanzees confirmed that chimpanzee TAS2R38 genotype accurately predicts taster status in vivo. Therefore, although Fisher et al.'s observations were accurate, their explanation was wrong. Humans and chimpanzees share variable taste sensitivity to bitter compounds mediated by PTC receptor variants, but the molecular basis of this variation has arisen twice, independently, in the two species.     

Prediction intervals for exponential smoothing using two new classes of state space models

Three general classes of state space models are presented, using the single source of error formulation. The first class is the standard linear model with homoscedastic errors, the second retains the linear structure but incorporates a dynamic form of heteroscedasticity, and the third allows for non‐linear structure in the observation equation as well as heteroscedasticity. These three classes provide stochastic models for a wide variety of exponential smoothing methods. We use these classes to provide exact analytic (matrix) expressions for forecast error variances that can be used to construct prediction intervals one or multiple steps ahead. These formulas are reduced to non‐matrix expressions for 15 state space models that underlie the most common exponential smoothing methods. We discuss relationships between our expressions and previous suggestions for finding forecast error variances and prediction intervals for exponential smoothing methods. Simpler approximations are developed for the more complex schemes and their validity examined. The paper concludes with a numerical example using a non‐linear model. Copyright © 2005 John Wiley & Sons, Ltd.     

Crystal structure of a self-splicing group I intron with both exons

The discovery of the RNA self-splicing group I intron provided the first demonstration that not all enzymes are proteins. Here we report the X-ray crystal structure (3.1-A resolution) of a complete group I bacterial intron in complex with both the 5'- and the 3'-exons. This complex corresponds to the splicing intermediate before the exon ligation step. It reveals how the intron uses structurally unprecedented RNA motifs to select the 5'- and 3'-splice sites. The 5'-exon's 3'-OH is positioned for inline nucleophilic attack on the conformationally constrained scissile phosphate at the intron-3'-exon junction. Six phosphates from three disparate RNA strands converge to coordinate two metal ions that are asymmetrically positioned on opposing sides of the reactive phosphate. This structure represents the first splicing complex to include a complete intron, both exons and an organized active site occupied with metal ions.     

Changes in fisheries discard rates and seabird communities

It is clear that discards from commercial fisheries are a key food resource for many seabird species around the world. But predicting the response of seabird communities to changes in discard rates is problematic and requires historical data to elucidate the confounding effects of other, more 'natural' ecological processes. In the North Sea, declining stocks, changes in technical measures, changes in population structure and the establishment of a recovery programme for cod (Gadus morhua) will alter the amount of fish discarded. This region also supports internationally important populations of seabirds, some of which feed extensively, but facultatively, on discards, in particular on undersized haddock (Melanogrammus aeglefinus) and whiting (Merlangius merlangus). Here we use long-term data sets from the northern North Sea to show that there is a direct link between discard availability and discard use by a generalist predator and scavenger--the great skua (Stercorarius skua). Reduced rates of discarding, particularly when coupled with reduced availability of small shoaling pelagic fish such as sandeel (Ammodytes marinus), result in an increase in predation by great skuas on other birds. This switching of prey by a facultative scavenger presents a potentially serious threat to some seabird communities.     

A 'snowball Earth' climate triggered by continental break-up through changes in runoff

Geological and palaeomagnetic studies indicate that ice sheets may have reached the Equator at the end of the Proterozoic eon, 800 to 550 million years ago, leading to the suggestion of a fully ice-covered 'snowball Earth'. Climate model simulations indicate that such a snowball state for the Earth depends on anomalously low atmospheric carbon dioxide concentrations, in addition to the Sun being 6 per cent fainter than it is today. However, the mechanisms producing such low carbon dioxide concentrations remain controversial. Here we assess the effect of the palaeogeographic changes preceding the Sturtian glacial period, 750 million years ago, on the long-term evolution of atmospheric carbon dioxide levels using the coupled climate-geochemical model GEOCLIM. In our simulation, the continental break-up of Rodinia leads to an increase in runoff and hence consumption of carbon dioxide through continental weathering that decreases atmospheric carbon dioxide concentrations by 1,320 p.p.m. This indicates that tectonic changes could have triggered a progressive transition from a 'greenhouse' to an 'icehouse' climate during the Neoproterozoic era. When we combine these results with the concomitant weathering effect of the voluminous basaltic traps erupted throughout the break-up of Rodinia, our simulation results in a snowball glaciation.