Optimal algorithms for comparing trees with labeled leaves

LetR _n denote the set of rooted trees withn leaves in which: the leaves are labeled by the integers in {1, ...,n}; and among interior vertices only the root may have degree two. Associated with each interior vertexv in such a tree is the subset, orcluster, of leaf labels in the subtree rooted atv. Cluster {1, ...,n} is calledtrivial. Clusters are used in quantitative measures of similarity, dissimilarity and consensus among trees. For anyk trees inR _n , thestrict consensus tree C(T ₁, ...,T _k ) is that tree inR _n containing exactly those clusters common to every one of thek trees. Similarity between treesT ₁ andT ₂ inR _n is measured by the numberS(T ₁,T ₂) of nontrivial clusters in bothT ₁ andT ₂; dissimilarity, by the numberD(T ₁,T ₂) of clusters inT ₁ orT ₂ but not in both. Algorithms are known to computeC(T ₁, ...,T _k ) inO(kn ²) time, andS(T ₁,T ₂) andD(T ₁,T ₂) inO(n ²) time. I propose a special representation of the clusters of any treeT R _n , one that permits testing in constant time whether a given cluster exists inT. I describe algorithms that exploit this representation to computeC(T ₁, ...,T _k ) inO(kn) time, andS(T ₁,T ₂) andD(T ₁,T ₂) inO(_n) time. These algorithms are optimal in a technical sense. They enable well-known indices of consensus between two trees to be computed inO(n) time. All these results apply as well to comparable problems involving unrooted trees with labeled leaves.The Natural Sciences and Engineering Research Council of Canada partially supported this work with grant A-4142.     

Criterion-referenced judgemental forecasting models

Human judgements are usually made with reference to a criteria such as cost or profit. When making a judgement model for such a decision, the ideal is for the model to yield near-optimal results in terms of the criteria. This article starts with the theory behind concave criteria and then develops a mathematical argument which gives guidance to judgemental model building. This guidance departs from the conventional wisdom of using only R-squared in model selection.     

RNASEL Arg462Gln variant is implicated in up to 13% of prostate cancer cases

RNASEL (encoding ribonuclease L) has recently been proposed as a candidate for the hereditary prostate cancer (HPC1) gene. We determined that the RNASEL variant Arg462Gln has three times less enzymatic activity than the wildtype and is significantly associated with prostate cancer risk (P = 0.007). At least one copy of the mutated allele that causes this substitution is carried by nearly 60% of the men in our study. Men that are heterozygous with respect to the mutated allele have 50% greater risk of prostate cancer than non-carriers, and homozygotes have more than double the risk.     

Communication arising. Is coral bleaching really adaptive?

From an experiment in which corals are transplanted between two depths on a Panamanian coral reef, Baker infers that bleaching may sometimes help reef corals to survive environmental change. Although Baker's results hint at further mechanisms by which reef-building corals may acclimatize to changing light conditions, we do not consider that the evidence supports his inference.     

Unsuspected diversity among marine aerobic anoxygenic phototrophs

Aerobic, anoxygenic, phototrophic bacteria containing bacteriochlorophyll a (Bchla) require oxygen for both growth and Bchla synthesis. Recent reports suggest that these bacteria are widely distributed in marine plankton, and that they may account for up to 5% of surface ocean photosynthetic electron transport and 11% of the total microbial community. Known planktonic anoxygenic phototrophs belong to only a few restricted groups within the Proteobacteria alpha-subclass. Here we report genomic analyses of the photosynthetic gene content and operon organization in naturally occurring marine bacteria. These photosynthetic gene clusters included some that most closely resembled those of Proteobacteria from the beta-subclass, which have never before been observed in marine environments. Furthermore, these photosynthetic genes were broadly distributed in marine plankton, and actively expressed in neritic bacterioplankton assemblages, indicating that the newly identified phototrophs were photosynthetically competent. Our data demonstrate that planktonic bacterial assemblages are not simply composed of one uniform, widespread class of anoxygenic phototrophs, as previously proposed; rather, these assemblages contain multiple, distantly related, photosynthetically active bacterial groups, including some unrelated to known and cultivated types.     

Inhibition of climbing fibres is a signal for the extinction of conditioned eyelid responses

A fundamental tenet of cerebellar learning theories asserts that climbing fibre afferents from the inferior olive provide a teaching signal that promotes the gradual adaptation of movements. Data from several forms of motor learning provide support for this tenet. In pavlovian eyelid conditioning, for example, where a tone is repeatedly paired with a reinforcing unconditioned stimulus like periorbital stimulation, the unconditioned stimulus promotes acquisition of conditioned eyelid responses by activating climbing fibres. Climbing fibre activity elicited by an unconditioned stimulus is inhibited during the expression of conditioned responses-consistent with the inhibitory projection from the cerebellum to inferior olive. Here, we show that inhibition of climbing fibres serves as a teaching signal for extinction, where learning not to respond is signalled by presenting a tone without the unconditioned stimulus. We used reversible infusion of synaptic receptor antagonists to show that blocking inhibitory input to the climbing fibres prevents extinction of the conditioned response, whereas blocking excitatory input induces extinction. These results, combined with analysis of climbing fibre activity in a computer simulation of the cerebellar-olivary system, suggest that transient inhibition of climbing fibres below their background level is the signal that drives extinction.     

Patterns of colonization in a metapopulation of grey seals

The colonization of a new habitat is a fundamental process in metapopulation biology, but it is difficult to study. The emigration of colonists from established populations might be induced by resource competition owing to high local population density. Migration distances are also important because they determine the frequency and scale of recolonization and hence the spatial scale of the metapopulation. Traditionally, these factors have been investigated with demographic approaches that are labour-intensive and are only possible in amenable species. In many cases, genetic differentiation is minimal, preventing traditional genetic approaches from identifying the source of colonists unambiguously. Here we present a bayesian approach that integrates genetic, demographic and geographic distance data. We apply the method to study the British metapopulation of grey seals, which has been growing at 6% per year over the last few decades. Our method reveals differential recruitment to three newly founded colonies and implicates density-dependent dispersal in metapopulation dynamics by using genetic data.     

Selective blockade by mephentermine of reserpine-induced serotonin depletion

Zusammenfassung Die kombinierte i.v. Verabreichung von Reserpin (1 mg/kg) und Mephentermin (1 mg/kg) bewirkte Erregung in Kaninchen. Diese Erregung ist verbunden mit einem Verlust an Noradrenalin (NE) im Gehirn, nicht jedoch mit einem Verlust an Serotonin (5-HT). Aus den Ergebnissen lässt sich schliessen, dass die beobachtete Erregung von einem momentanen Ungleichgewicht zwischen NE und 5-HT im Gehirn herrührt.

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This study is supported in part by Career Development Award No. K3 NB 15279-09 and Grant No. MH 11189 from the National Institutes of Health, U.S.P.H.S. The authors wish to thank Dr.A. J. Plummer of CIBA Pharmaceutical Company for supplying the reserpine phosphate and Dr.R. J. Bower of Wyeth Laboratories for the mephentermine used in this study.