The ‘interval timer’ and photoperiod in the determination of parthenogenetic and sexual morphs in the aphid, Drepanosiphum platanoides

The ability of the sycamore aphid to produce sexuales (males and females) is regulated by a timing mechanism (‘interval timer’) which restrains the appearance of these morphs in the spring under short day conditions. In this species there are two ‘interval timers’: one, sensitive to day-length and controlling the production of sexual females, and another insensitive to day-length and controlling the production of males. In the production of sexual females day-length acts directly on the aphid and not through the host plant.     

Kinetics of the Multistep Rupture of Fibrin ‘A-a’ Polymerization Interactions Measured Using Atomic Force Microscopy

Fibrin, the structural scaffold of blood clots, spontaneously polymerizes through the formation of ‘A-a’ knob-hole bonds. When subjected to external force, the dissociation of this bond is accompanied by two to four abrupt changes in molecular dimension observable as rupture events in a force curve. Herein, the configuration, molecular extension, and kinetic parameters of each rupture event are examined. The increases in contour length indicate that the D region of fibrinogen can lengthen by ∼50% of the length of a fibrin monomer before rupture of the ‘A-a’ interaction. The dependence of the dissociation rate on applied force was obtained using probability distributions of rupture forces collected at different pull-off velocities. These distributions were fit using a model in which the effects of the shape of the binding potential are used to quantify the kinetic parameters of forced dissociation. We found that the weak initial rupture (i.e., event 1) was not well approximated by these models. The ruptured bonds comprising the strongest ruptures, events 2 and 3, had kinetic parameters similar to those commonly found for the mechanical unfolding of globular proteins. The bonds ruptured in event 4 were well described by these analyses, but were more loosely bound than the bonds in events 2 and 3. We propose that the first event represents the rupture of an unknown interaction parallel to the ‘A-a’ bond, events 2 and 3 represent unfolding of structures in the D region of fibrinogen, and event 4 is the rupture of the ‘A-a’ knob-hole bond weakened by prior structural unfolding. Comparison of the activation energy obtained via force spectroscopy measurements with the thermodynamic free energy of ‘A-a’ bond dissociation indicates that the ‘A-a’ bond may be more resistant to rupture by applied force than to rupture by thermal dissociation.     

Crystal structure of the human tRNA microhelix isoacceptor G9990 at 1.18 Å resolution

The tRNA^Gly/Glycyl-tRNA synthetase system belongs to the so called ‘class II’ in which tRNA identity elements consist of relative few and simple motifs, as compared to ‘class I’ where the tRNA determinants are more complicated and spread over different parts of the tRNA, mostly including the anticodon. The determinants from ‘class II’ although, are located in the aminoacyl stem and sometimes include the discriminator base. There exist predominant structure differences for the Glycyl-tRNA-synthetases and for the tRNA^Gly identity elements comparing eucaryotic/archaebacterial and eubacterial systems.We focus on comparative X-ray structure analysis of tRNA^Gly acceptor stem microhelices from different organisms. Here, we report the X-ray structure of the human tRNA^Gly microhelix isoacceptor G9990 at 1.18 Å resolution. Superposition experiments to another human tRNA^Gly microhelix and a detailed comparison of the RNA hydration patterns show a great number of water molecules with identical positions in both RNAs. This is the first structure comparison of hydration layers from two isoacceptor tRNA microhelices with a naturally occurring base pair exchange.     

Conspicuous males suffer higher predation risk: visual modelling and experimental evidence from lizards

Colour pattern variation is a striking and widespread phenomenon. Differential predation risk between individuals is often invoked to explain colour variation, but empirical support for this hypothesis is equivocal. We investigated differential conspicuousness and predation risk in two species of Australian rock dragons, Ctenophorus decresii andC. vadnappa . To humans, the coloration of males of these species varies between ‘bright’ and ‘dull’. Visual modelling based on objective colour measurements and the spectral sensitivities of avian visual pigments showed that dragon colour variants are differentially conspicuous to the visual system of avian predators when viewed against the natural background. We conducted field experiments to test for differential predation risk, using plaster models of ‘bright’ and ‘dull’ males. ‘Bright’ models were attacked significantly more often than ‘dull’ models suggesting that differential conspicuousness translates to differential predation risk in the wild. We also examined the influence of natural geographical range on predation risk. Results from 22 localities suggest that predation rates vary according to whether predators are familiar with the prey species. This study is among the first to demonstrate both differential conspicuousness and differential predation risk in the wild using an experimental protocol. Copyright 2003 Published by Elsevier Ltd on behalf of The Association for the Study of Animal Behaviour.      

Multiscale analysis of collective motion and decision-making in swarms: An advection-diffusion equation with memory approach

We propose a (time) multiscale method for the coarse-grained analysis of collective motion and decision-making in self-propelled particle models of swarms comprising a mixture of ‘naïve’ and ‘informed’ individuals. The method is based on projecting the particle configuration onto a single ‘meta-particle’ that consists of the elongation of the flock together with the mean group velocity and position. We find that the collective states can be associated with the transient and asymptotic transport properties of the random walk followed by the meta-particle, which we assume follows a continuous time random walk (CTRW). These properties can be accurately predicted at the macroscopic level by an advection-diffusion equation with memory (ADEM) whose parameters are obtained from a mean group velocity time series obtained from a single simulation run of the individual-based model.     

Quantum biology at the cellular level—Elements of the research program

Quantum biology is emerging as a new field at the intersection between fundamental physics and biology, promising novel insights into the nature and origin of biological order. We discuss several elements of QBCL (quantum biology at cellular level) – a research program designed to extend the reach of quantum concepts to higher than molecular levels of biological organization. We propose a new general way to address the issue of environmentally induced decoherence and macroscopic superpositions in biological systems, emphasizing the ‘basis-dependent’ nature of these concepts. We introduce the notion of ‘formal superposition’ and distinguish it from that of Schroedinger's cat (i.e., a superposition of macroscopically distinct states). Whereas the latter notion presents a genuine foundational problem, the former one contradicts neither common sense nor observation, and may be used to describe cellular ‘decision-making’ and adaptation. We stress that the interpretation of the notion of ‘formal superposition’ should involve non-classical correlations between molecular events in a cell. Further, we describe how better understanding of the physics of Life can shed new light on the mechanism driving evolutionary adaptation (viz., ‘Basis-Dependent Selection’, BDS). Experimental tests of BDS and the potential role of synthetic biology in closing the ‘evolvability mechanism’ loophole are also discussed.     

Is 'hand preference' coded in the hominin skeleton? An in-vivo study of bilateral morphological variation

The presumed link between bilateral asymmetry and lateralized habitual activity in extinct hominins is the basis upon which inferences of ‘hand preference’ often derive. While this presumption is reasonable, in-vivo comparisons of skeletal asymmetries and self-reported handedness are rare, and as a result the accuracy of these inferences is questionable. To assess this relationship in living humans, reported ‘handedness’ was compared against peripheral quantitative computed tomography (pQCT) derived bilateral measurements of humeral, ulnar, and tibial midshaft cortical area (CA) and torsional rigidity (J). Significant bilateral differences were found in the humerus for all groups, and in the ulna for the cricketer and field hockey sub-samples. Additionally, cricketers’ non-dominant tibiae were more robust than their dominant tibiae. An assessment of ‘Dominance Asymmetry’ revealed that measures of CA and J were higher in the dominant humeri in ∼90% of participants; in the ulna this was true in ∼75% of cases, and in the tibia CA and J were higher in the dominant limb less than 50% of the time. Comparisons of (self)‘Reported’ hand preference against ‘Predicted’ hand preference (based on the calculation of % Directional Asymmetry) revealed a low level of error for predictions based on both humeral (∼4-5% error) and ulnar (6-11% error) asymmetry. Error was decreased with the exclusion of individuals displaying less than 2.5-5% asymmetry. Contrarily, predictions based on tibial analyses had a much higher level of ‘error’ (∼45%). Overall, the results support currently accepted approaches for inferring ‘hand preference’ from measures of upper limb geometric asymmetry in the hominin skeleton.     

A multi‐method approach for analyzing hierarchical genetic structures: a case study with cougars Puma concolor

Genetic data are increasingly used to describe the structure of wildlife populations and to infer landscape influences on functional connectivity. To accomplish this, genetic structure can be described with a multitude of methods that vary in their assumptions, advantages and limitations. While some methods discriminate distinct subpopulations separated by sharp genetic boundaries (i.e. barrier detection or clustering methods), other methods estimate gradient genetic structures using individual‐based genetic distances. We present an analytical framework based on individual ancestry values that combines these different approaches and can be used to a) test for local barriers to gene flow and b) evaluate effects of landscape gradients through individual‐based genetic distances that account for hierarchical genetic structure. We illustrate the approach with a data set of 371 cougars Puma concolor from a 217 000 km² study area in Idaho and western Montana (USA) that were genotyped at 12 microsatellite loci. Results suggest that cougars in the region show a complex, hierarchical genetic structure that is influenced by a local barrier to gene flow (an urban population cluster connected by high traffic volumes), different landscape features (the Snake River Plain, forested habitat), and geographic distance. Our novel approach helped to elucidate the relative influence of these factors on different hierarchical levels of population structure, which was not possible when using either clustering methods or standard genetic distances. Results obtained with our analytical framework highlight the need for multi‐scale management of cougars in the region and show that landscape heterogeneity can create complex genetic structures, even in generalist species with high dispersal capabilities.     

Agility and search and rescue training differently affects pet dogs’ behaviour in socio-cognitive tasks

Both genetic factors and life experiences appear to be important in shaping dogs’ responses in a test situation. One potentially highly relevant life experience may be the dog's training history, however few studies have investigated this aspect so far. This paper briefly reviews studies focusing on the effects of training on dogs’ performance in cognitive tasks, and presents new, preliminary evidence on trained and untrained pet dogs’ performance in an ‘unsolvable task’. Thirty-nine adult dogs: 13 trained for search and rescue activities (S&R group), 13 for agility competition (Agility group) and 13 untrained pets (Pet group) were tested. Three ‘solvable’ trials in which dogs could obtain the food by manipulating a plastic container were followed by an ‘unsolvable’ trial in which obtaining the food became impossible. The dogs’ behaviours towards the apparatus and the people present (owner and researcher) were analysed. Both in the first ‘solvable’ and in the ‘unsolvable’ trial the groups were comparable on actions towards the apparatus, however differences emerged in their human-directed gazing behaviour. In fact, results in the ‘solvable’ trial, showed fewer S&R dogs looking back at a person compared to agility dogs, and the latter alternating their gaze between person and apparatus more frequently than pet dogs. In the unsolvable trial no difference between groups emerged in the latency to look at the person however agility dogs looked longer at the owner than both pet and S&R dogs; whereas S&R dogs exhibited significantly more barking (always occurring concurrently to looking at the person or the apparatus) than both other groups. Furthermore, S&R dogs alternated their gaze between person and apparatus more than untrained pet dogs, with agility dogs falling in between these two groups. Thus overall, it seems that the dogs’ human-directed communicative behaviours are significantly influenced by their individual training experiences.     

Not my brother's keeper: A thought experiment for Hamilton's rule

The now popular ‘selfish gene’ view defines evolutionary fitness at the gene level - in terms of the number of gene copies residing in future generations (or propelled from previous generations). Yet, most current biology textbooks still apply the concept of fitness to the individual, where it is defined more traditionally as the number of descendants residing in future generations. The existing literature remains ambiguous regarding whether one of these concepts is more meaningful than the other, or whether they both represent legitimate, functional definitions of fitness. In support of the latter view, I present a composite perspective that recognizes the gene as evolutionarily ‘selfish’, but also the individual as a ‘selfish vehicle’ for resident genes. Hamilton's rule explains, based on genetic relatedness, why natural selection has favoured behaviours that compel individuals (as ‘donors’ of help) to act for the good of copies of their genes residing in close kin (‘recipients’). I propose however, that natural selection should particularly favour helping behaviours directed at those recipient kin who have the highest relative probability of being the vehicle for a remarkably adaptive newly mutant gene, weighted by the proportion of genes shared with the donor. According to this ‘adaptive-genetic-novelty-rescue’ (AGNR) hypothesis, these favoured vehicles for shared gene copies are more likely to involve direct descendants (e.g. offspring) than other close kin from one's collateral lineage (e.g. siblings), even when the donor (e.g. a father) shares fewer genes with an offspring (e.g. a son) than with a sibling (e.g. a brother).     

Origins of learned reciprocity in solitary ciliates searching grouped ‘courting’ assurances at quantum efficiencies

Learning to reciprocate socially valued actions, such as cheating and cooperation, marks evolutionary advances in animal intelligence thought unequalled by even colonial microbes known to secure respective individual or group fitness tradeoffs through genetic and epigenetic processes. However, solitary ciliates, unique among microbes for their emulation of simple Hebbian-like learning contingent upon feedback between behavioral output and vibration-activated mechanosensitive Ca²⁺ channels, might be the best candidates to learn to reciprocate necessary preconjugant touches perceived during complex ‘courtship rituals’. Testing this hypothesis here with mock social trials involving an ambiguous vibration source, the large heterotrich ciliate Spirostomum ambiguum showed it can indeed learn to modify emitted signals about mating fitness to encourage paired reproduction. Ciliates, improving their signaling expertise with each felt vibration, grouped serial escape strategies gesturing opposite ‘courting’ assurances of playing ‘harder to get’ or ‘easier to get’ into separate, topologically invariant computational networks. Stored strategies formed patterns of action or heuristics with which ciliates performed fast, quantum-like distributed modular searches to guide future replies of specific fitness content. Heuristic-guided searches helped initial inferior repliers, ciliates with high initial reproductive costs, learn to sensitize their behavioral output and opportunistically compete with presumptive mating ‘rivals’ advertising higher quality fitness. Whereas, initial superior repliers, ciliates with low initial reproductive costs, learned with the aid of heuristics to habituate their behavioral output and sacrifice net reproductive payoffs to cooperate with presumptive ‘suitors’, a kind of learned altruism only before attributed to animal social intelligences. The present findings confirm that ciliates are highly competent decision makers capable of achieving paired fitness goals through learning.     

Muscle proteins — their actions and interactions

Muscle contracts by the myosin cross-bridges ‘rowing’ the actin filaments past the myosin filaments. In the past year many structural details of this mechanism have become clear. Structural studies indicate distinct states for myosin S1 in the rigor, ATP or ‘down’ conformation and in the products complex (ADP·P_i) or ‘up’ state. Crystallographic studies substantiate this classification and yield details of the transformation. The isomerization ‘up’ to ‘down’ is the power stroke of muscle. This consists in the main of large changes of angle of the ‘lever arm’ (at the distal part of the myosin head) which can account for an 11 nm power stroke.     

The effect of female presence on spermiation, and of male sexual activity on ‘ready’ sperm in the male guppy

This study examines the effect of female presence on the amount of ‘strippable’ sperm, and the relationship between male sexual activity and the amount of ‘ready’ sperm in the male guppy Poecilia reticulata. The amount of strippable sperm was greater in males paired for one week with females than in isolated males. We separated these ‘paired’ males from females by a clear partition and thus exposed males to visual and possibly olfactory stimuli. In the second experiment, control males spent more time attending females and performed more sexual acts during a 15-min test period than males previously stripped of spermatophores. These results indicate that females play an important role in stimulating sperm availability in males and that the amount of ready sperm influences male sexual behaviour. Copyright 2003 The Association for the Study of Animal Behaviour. Published by Elsevier Science Ltd. All rights reserved.      

Reconstructing pedigrees: a stochastic perspective

A pedigree is a directed graph that describes how individuals are related through ancestry in a sexually-reproducing population. In this paper we explore the question of whether one can reconstruct a pedigree by just observing sequence data for present day individuals. This is motivated by the increasing availability of genomic sequences, but in this paper we take a more theoretical approach and consider what models of sequence evolution might allow pedigree reconstruction (given sufficiently long sequences). Our results complement recent work that showed that pedigree reconstruction may be fundamentally impossible if one uses just the degrees of relatedness between different extant individuals. We find that for certain stochastic processes, pedigrees can be recovered up to isomorphism from sufficiently long sequences.     

Factors affecting colour change in ‘white’ western rock lobsters, Panulirus cygnus

At 4-5 years old, western rock lobsters migrate offshore to the fishery, soon after their colouring has changed from red to a pale pink colour. Although a large number of these animals (known as ‘whites’) are landed by the commercial fishery during November to January each year, they are less popular with consumers in the Japanese market, and so have a lower market value than the ‘red’ nonmigrating recruits. ‘White’ rock lobsters darken in colour without moulting, so that by February, virtually all are classified as ‘reds.’ This study examined methods of increasing the value of the catch by speeding up their change back to red while held live in tanks after being caught. The first experiment tested the effect of background colour (three treatments) and diet (six treatments); the second tested the effect of colour of incident light (three treatments), period of light exposure (two treatments), and light intensity (two treatments). In both experiments, tanks kept in total darkness were used as controls. Changes in lobster colouration over the experiment were recorded in Munsell Colour Notation, using a colorimeter. The classification tree method was used to define the colour represented by different colour components, making up production categories of ‘white,’ ‘coral,’ and ‘red’ lobsters. Treatments were gauged in terms of their ability to speed up the natural colour change from white to red. Few of the treatment combinations were successful in producing ‘red’ lobsters and, except for those held on a white background, the lobsters darkened in colour from a white to a coral colour. The rate of change within a moult was no different from the rate in the field, although field lobsters generally attain the more sought-after red rather than coral colour. Of the treatments tested, a dark background with high light intensity levels produced the most optimally (red) coloured lobsters. Most of the experimental treatments (14 of 16) recorded a further progression towards a red colouration after moulting. While the intermoult durations of the lobsters held under most treatments were similar, those held under high light intensity (5-30 mmol quantum m⁻¹ s⁻¹) had significantly shorter intermoult periods (P<0.01). However, none of the treatments produced red lobsters more quickly than in the wild, and the research did not therefore produce commercial benefits.     

Certain heptapeptide and large sequences representing an entire helix, strand or coil conformation in proteins are associated as chameleon sequences

Helices, strands and coils in proteins of known three-dimensional structure, corresponding to heptapeptide and large sequences (‘probe’ peptides), were scanned against peptide sequences of variable length, comprising seven or more residues that correspond to a different conformation (‘target’ peptides) in protein crystal structures available from the Protein Data Bank (PDB). Where the ‘probe’ and ‘target’ peptide sequences exactly match, they correspond to ‘chameleon’ sequences in protein structures. We observed ∼548 heptapeptide and large chameleon sequences that included peptides in the coil conformation from 53,794 PDB files that were analyzed. However, after excluding several chameleon peptides based on the quality of protein structure data, redundancy and peptides associated with cloning artifacts, such as, histidine-tags, we observed only ten chameleon peptides in structurally different proteins and the maximum length comprised seven amino acid residues. Our analysis suggests that the quality of protein structure data is important for identifying possibly, the ‘true chameleons’ in PDB. Majority of the chameleon sequences correspond to an entire strand in one protein that is observed as part of helix sequence in another protein. The heptapeptide chameleons are characterized with a high propensity of alanine, leucine and valine amino acid residues. The total hydropathy values range between −11.2 and 22.9, the difference in solvent accessibility between 2.0 Å² and 373 Å² units and the difference in total number of residue neighbor contacts between 0 and 7 residues. Our work identifies for the first time heptapeptide and large sequences that correspond to a single complete helix, strand or coil, which adopt entirely different secondary structures in another protein.     

Measuring European population stratification with microarray genotype data

A proper understanding of population genetic stratification--differences in individual ancestry within a population--is crucial in attempts to find genes for complex traits through association mapping. We report on genomewide typing of approximately 10,000 single-nucleotide polymorphisms in 297 individuals, to explore population structure in Europeans of known and unknown ancestry. The results reveal the presence of several significant axes of stratification, most prominently in a northern-southeastern trend, but also along an east-west axis. We also demonstrate the selection and application of EuroAIMs (European ancestry informative markers) for ancestry estimation and correction. The Coriell Caucasian and CEPH (Centre d'Etude du Polymorphisme Humain) Utah sample panels, often used as proxies for European populations, are found to reflect different subsets of the continent's ancestry.     

Who made the Aurignacian and other early Upper Paleolithic industries?

The Aurignacian is typically taken as a marker of the spread of anatomically modern humans into Europe. However, human remains associated with this industry are frustratingly sparse and often limited to teeth. Some have suggested that Neandertals may, in fact, be responsible for the Aurignacian and the earliest Upper Paleolithic industries. Although dental remains are frequently considered to be taxonomically undiagnostic in this context, recent research shows that Neandertals possess a distinct dental pattern relative to anatomically modern humans. Even so, it is rare to find mandibles or maxillae that preserve all or most of their teeth; and, the probability of correctly identifying individuals represented by only a few teeth or a single tooth is unknown. We present a Bayesian statistical approach to classifying individuals represented exclusively by teeth into two possible groups. The classification is based on dental trait frequencies and sample sizes for ‘known’ samples of 95 Neandertals and 63 Upper Paleolithic modern humans. In a cross validation test of the known samples, 89% of the Neandertals and 89% of the Upper Paleolithic modern humans were classified correctly. We then classified an ‘unknown’ sample of 52 individuals: 34 associated with Aurignacian or other (non-Châtelperronian) early Upper Paleolithic industries, 15 associated with the Châtelperronian, and three unassociated. Of the 34 early Upper Paleolithic-associated individuals, 29 were assigned to modern humans, which is well within the range expected (95% of the time 26-33) with an 11% misclassification rate for an entirely modern human sample. These results provide some of the strongest evidence that anatomically modern humans made the Aurignacian and other (non-Châtelperronian) early Upper Paleolithic industries.     

The evolution of senescence in multi-component systems

Actuarial senescence is characterized by an increase in mortality rate with increasing chronological age. The reliability theory of senescence proposes that organisms’ vital functions can be modelled as a suite of damageable, irreplaceable elements (typically genes or their products) that protect their bearer from condition-dependent death so long as at least one of the elements remains intact. Current incarnations of the reliability theory of senescence are continuous-time models with no explicit evolutionary component. Here, we use elementary probability theory and evolutionary dynamics analysis to derive a discrete-time version of the reliability theory of senescence. We include three variations on this theme: the ‘Series’ model in which damage to any of n elements results in death, the ‘Parallel’ model, in which damage accumulates in random order and damage to all n elements results in death, and the ‘Cascade’ (multi-stage) model, which is like the Parallel model, except the irreparable damage necessarily follows a strict sequence. For simplicity, we refer to the state of having multiple elements as ‘redundancy’, but this does not imply that the elements are necessarily identical. We show that redundancy leads to actuarial senescence in the Parallel and Cascade models but not in the Series model. We further demonstrate that in the Parallel and Cascade models, lifetime reproductive output (a potential proxy for fitness in populations with discrete generations) is a positive but decelerating function of redundancy. The positive nature of the fitness function leads to the prediction that redundancy and senescence should evolve from non-redundant, non-senescing ancestral populations; however, the deceleration of the fitness function leads to the prediction that this evolution towards increased redundancy will eventually be limited by mutation-selection balance. Using evolutionary dynamics analysis involving the discrete-generation quasispecies equation, we confirm these two predictions. Finally, we show that a population's equilibrium redundancy is sensitive to the environmental conditions that prevailed during its evolution, such as the rate of extrinsic mortality.