Non-random Structure Research Articles

Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape

BackgroundThe standard genetic code table has a distinctly non-random structure, with similar amino acids often encoded by codons series that differ by a single nucleotide substitution, typically, in the third or the first position of the codon. It has been repeatedly argued that this structure of the code results from selective optimization for robustness to translation errors such that translational misreading has the minimal adverse effect. Indeed, it has been shown in several studies that the standard code is more robust than a substantial majority of random codes. However, it remains unclear how much evolution the standard code underwent, what is the level of optimization, and what is the likely starting point.ResultsWe explored possible evolutionary trajectories of the genetic code within a limited domain of the vast space of possible codes. Only those codes were analyzed for robustness to translation error that possess the same block structure and the same degree of degeneracy as the standard code. This choice of a small part of the vast space of possible codes is based on the notion that the block structure of the standard code is a consequence of the structure of the complex between the cognate tRNA and the codon in mRNA where the third base of the codon plays a minimum role as a specificity determinant. Within this part of the fitness landscape, a simple evolutionary algorithm, with elementary evolutionary steps comprising swaps of four-codon or two-codon series, was employed to investigate the optimization of codes for the maximum attainable robustness. The properties of the standard code were compared to the properties of four sets of codes, namely, purely random codes, random codes that are more robust than the standard code, and two sets of codes that resulted from optimization of the first two sets. The comparison of these sets of codes with the standard code and its locally optimized version showed that, on average, optimization of random codes yielded evolutionary trajectories that converged at the same level of robustness to translation errors as the optimization path of the standard code; however, the standard code required considerably fewer steps to reach that level than an average random code. When evolution starts from random codes whose fitness is comparable to that of the standard code, they typically reach much higher level of optimization than the standard code, i.e., the standard code is much closer to its local minimum (fitness peak) than most of the random codes with similar levels of robustness. Thus, the standard genetic code appears to be a point on an evolutionary trajectory from a random point (code) about half the way to the summit of the local peak. The fitness landscape of code evolution appears to be extremely rugged, containing numerous peaks with a broad distribution of heights, and the standard code is relatively unremarkable, being located on the slope of a moderate-height peak.ConclusionThe standard code appears to be the result of partial optimization of a random code for robustness to errors of translation. The reason the code is not fully optimized could be the trade-off between the beneficial effect of increasing robustness to translation errors and the deleterious effect of codon series reassignment that becomes increasingly severe with growing complexity of the evolving system. Thus, evolution of the code can be represented as a combination of adaptation and frozen accident.ReviewersThis article was reviewed by David Ardell, Allan Drummond (nominated by Laura Landweber), and Rob Knight.Open Peer ReviewThis article was reviewed by David Ardell, Allan Drummond (nominated by Laura Landweber), and Rob Knight.

Halfway up the trophic chain: development of parasite communities in the sparid fish Boops boops

We examined the patterns of composition and structure of parasite communities in the Mediterranean sparid fish Boops boops along a gradient of fish sizes, using a large sample from a single population. We tested the hypothesis that species forming the core of the bogue parasite fauna (i.e. species which have a wide geographical range and are responsible for recognizable community structure) appear early in the fish ontogeny. The sequential community development observed supported the prediction that core species appear in the fish population earlier than rare and stochastic species. There was also a strong correlation between the order of 'arrival' of the species and their overall prevalence. Six key species were responsible for recognizable community structure across size/age cohorts; the addition to this baseline community of key parasite species resulted in a nested structure that is linked to differential species abundance rather than fish size. Information on the life-cycles, distribution and host range of the parasites is used to explain the observed patterns of parasite community structure. We conclude that the small mouth size of B. boops coupled with suction feeding may provide a setting for passive sampling as a mechanism leading to non-random parasite community structure.

A note on non-random error structure in trawl survey abundance indices

Abstract Cordue, P. L. 2007. A note on non-random error structure in trawl survey abundance indices. – ICES Journal of Marine Science, 64: 1333–1337. Trawl survey time-series are routinely used in stock assessments to provide indices of relative abundance. There is the general assumption, for each year y, that the expected value of the trawl survey index (Xy) is related to the biomass (By) by a single proportionality constant q: E(Xy) = qBy. In reality, the constant q varies due to many factors. An important factor, which is almost always ignored, is the role that non-trawlable ground can play in the variation of q. A general formula is derived for the q of a stratified random trawl survey. When the survey area contains non-trawlable ground, strata-specific data on the proportion of non-trawlable ground and on the preference of the species for trawlable/non-trawlable ground is required to weight stratum estimates correctly. In the absence of the correct stratum weights, a shift in the spatial distribution of the stock can combine with differing proportions of non-trawlable ground to introduce non-random error and possibly spurious trends into biomass indices. Each survey and species/stock should be considered on a case-by-case basis. A stratum-specific assessment of the proportion of non-trawlable ground is a pre-requisite for the production of trawl survey biomass indices.

Influence of local and residual structures on the scaling behavior and dimensions of unfolded proteins

Although recent spectroscopic studies of chemically denatured proteins hint at significant nonrandom residual structure, the results of extensive small angle X-ray scattering studies suggest random coil behavior, calling for a coherent understanding of these seemingly contradicting observations. Here, we report the results of a Monte Carlo study of the effects of two types of local structures, alpha helix and Polyproline II (PPII) helix, on the dimensions of random coil polyalanine chains viewed as a model of highly denatured proteins. We find that although Flory's power law scaling, long regarded as a signature of random coil behavior, holds for chains containing up to 90% alpha or PPII helix, the absolute magnitude of the chain dimensions is sensitive to helix content. As residual alpha helix content increases, the chain contracts until it reaches a minimum radius at approximately 70% helix, after which the chain dimensions expand rapidly. With an alpha helix content of approximately 20%, corresponding to the Ramachandran probability of being in the helical basin, experimentally observed radii of gyration are recovered. Experimental radii are similarly recovered at an alpha helix content of approximately 87%, providing an explanation for the previously puzzling experimental finding that the dimensions of the highly helical methanol-induced unfolded state are experimentally indistinguishable from those of the helix-poor urea-unfolded state. In contrast, the radius of gyration increases monotonically with increasing PPII content, and is always more expanded than the dimensions observed experimentally. These results suggest that PPII is unlikely the sole, dominant preferred conformation for unfolded proteins.

Structural Properties of an Artificial Protein That Regulates the Nucleation of Inorganic and Organic Crystals

Technological advances have facilitated the generation of artificial proteins that possess the capabilities of recognizing and binding to inorganic solids and/or controlling nucleation processes that form inorganic solids. However, very little is known regarding the structure of these interesting polypeptides and how their structure contributes to functionality. To address this deficiency, we report structural investigations of an artificial protein, p288, that self-assembles and controls the nucleation of simple salts and organic compounds into dendrite-like crystals. Under aqueous conditions at low pH and in the presence of high salt, p288 is conformationally labile and exists primarily as a random coil conformer in equilibrium with other undefined secondary structures, including polyproline type II and beta turn. We note that p288 can fold into either a partial beta strand (at neutral pH) or a predominantly alpha helical (in the presence of TFE) conformation. Solid-state 13C-15N NMR experiments also reveal that p288 in the lyophilized, hydrated state possesses some degree of nonrandom coil structure. These results indicate that p288 is conformationally labile but can undergo conformational transitions to a more stable structure when water solvent loss/displacement occurs and protein concentrations increase. We believe that conformational instability and the ability to adopt different structures as a function of different environmental conditions represent important molecular features that impact p288 supramolecular assembly and crystal nucleation processes.

Ecological factors influence population genetic structure of European grey wolves

Although the mechanisms controlling gene flow among populations are particularly important for evolutionary processes, they are still poorly understood, especially in the case of large carnivoran mammals with extensive continuous distributions. We studied the question of factors affecting population genetic structure in the grey wolf, Canis lupus, one of the most mobile terrestrial carnivores. We analysed variability in mitochondrial DNA and 14 microsatellite loci for a sample of 643 individuals from 59 localities representing most of the continuous wolf range in Eastern Europe. We tested an array of geographical, historical and ecological factors to check whether they may explain genetic differentiation among local wolf populations. We showed that wolf populations in Eastern Europe displayed nonrandom spatial genetic structure in the absence of obvious physical barriers to movement. Neither topographic barriers nor past fragmentation could explain spatial genetic structure. However, we found that the genetic differentiation among local populations was correlated with climate, habitat types, and wolf diet composition. This result shows that ecological processes may strongly influence the amount of gene flow among populations. We suggest natal-habitat-biased dispersal as an underlying mechanism linking population ecology with population genetic structure.

The Folding Energy Landscape of the Dimerization Domain of Escherichia coli Trp Repressor: A Joint Experimental and Theoretical Investigation

Enhanced structural insights into the folding energy landscape of the N-terminal dimerization domain of Escherichia coli tryptophan repressor, [2-66] 2 TR, were obtained from a combined experimental and theoretical analysis of its equilibrium folding reaction. Previous studies have shown that the three intertwined helices in [2-66] 2 TR are sufficient to drive the formation of a stable dimer for the full-length protein, [2-107] 2 TR. The monomeric and dimeric folding intermediates that appear during the folding reactions of [2-66] 2 TR have counterparts in the folding mechanism of the full-length protein. The equilibrium unfolding energy surface on which the folding and dimerization reactions occur for [2-66] 2 TR was examined with a combination of native-state hydrogen exchange analysis, pepsin digestion and matrix-assisted laser/desorption mass spectrometry performed at several concentrations of protein and denaturant. Peptides corresponding to all three helices in [2-66] 2 TR show multi-layered protection patterns consistent with the relative stabilities of the dimeric and monomeric folding intermediates. The observation of protection exceeding that offered by the dimeric intermediate in segments from all three helices implies that a segment-swapping mechanism may be operative in the monomeric intermediate. Protection greater than that expected from the global stability for a single amide hydrogen in a peptide from the C-helix possibly and another from the A-helix may reflect non-random structure, possibly a precursor for segment swapping, in the urea-denatured state. Native topology-based model simulations that correspond to a funnel energy landscape capture both the monomeric and dimeric intermediates suggested by the HX MS data and provide a rationale for the progressive acquisition of secondary structure in their conformational ensembles.

A model-independent test for the presence of regulatory equilibrium and non-random structure in island species trajectories

Aims To test a key prevision of the dynamic equilibrium theory of island biogeography, namely that changes in species numbers on islands over time (hereafter, species trajectories) are equilibrial, and to characterize aspects of the dynamical properties of species change over time using a model-independent test. Methods We tested for regulatory equilibrium and non-random structure in species numbers through time by comparing observed correlation coefficients at lag-k for species trajectories from four true islands and two habitat islands. First, we estimated the shape of the autocorrelation function for each observed species trajectory by calculating correlation coefficients of the observed data between pairs of values Nt)k and Nt separated by lag-k (k ¼ 1, 2, …, N ) 1). Second, we tested the observed correlation coefficients at each lag against a distribution of correlation coefficients generated by randomly ordering observed numbers in the species trajectories. Results The patterns of autocorrelation functions for all but one of the observed species trajectories did not exhibit evidence of regulatory equilibrium, and, in fact, closely matched what would be expected from a non-stationary or ‘random walk’ process. The majority of the correlation coefficients generated from the observed species trajectories did not deviate significantly from correlation coefficients produced by the randomized trajectories. However, there was strong evidence of unusual positive autocorrelation at small time lags for birds on islands measured annually (2- to 4-year lags) and for arthropods on islands measured weekly (7- to 8-week lags), suggesting some degree of structure in change in species richness over time. Main conclusions The autocorrelation function patterns for all but one of the observed species trajectories showed various forms of non-stationarity. These types of patterns suggest that the numbers of species through time gradually wandered away from their initial sizes. Our model-independent test of individual correlation coefficients revealed significant structure in the observed species trajectories. These trajectories appear to be non-random at relatively short lag intervals, indicating a process with short memory.

THE PHYLOGENETIC STRUCTURE OF A NEOTROPICAL FOREST TREE COMMUNITY

Numerous ecological and evolutionary processes are thought to play a role in maintaining the high plant species diversity of tropical forests. An understanding of the phylogenetic structure of an ecological community can provide insights into the relative importance of different processes structuring that community. The objectives of this study were to measure the phylogenetic structure of Neotropical forest tree communities in the Forest Dynamics Plot (FDP) on Barro Colorado Island, Panama, to determine how the phylogenetic structure of tree communities varied among spatial scales and habitats within the FDP, and to study the effects of null-model choice on estimates of community phylogenetic structure. We measured community phylogenetic structure for tree species occurring together in quadrats ranging in size from 10 x 10 m to 100 X 100 m in the FDP. We estimated phylogenetic structure by comparing observed phylogenetic distances among species to the distribution of phylogenetic distances for null communities generated using two different null models. A null model that did not maintain observed species occurrence frequencies tended to find nonrandom community phylogenetic structure, even for random data. Using a null model that maintained observed species frequencies in null communities, the average phylogenetic structure of tree communities in the FDP was close to random at all spatial scales examined, but more quadrats than expected contained species that were phylogenetically clustered or overdispersed, and phylogenetic structure varied among habitats. In young forests and plateau habitats, communities were phylogenetically clustered, meaning that trees were more closely related to their neighbors than expected, while communities in swamp and slope habitats were phylogenetically overdispersed, meaning that trees were more distantly related to their neighbors than expected. Phylogenetic clustering suggests the importance of environmental filtering of phylogenetically conserved traits in young forests and plateau habitats, but the phylogenetic overdispersion observed in other habitats has several possible explanations, including variation in the strength of ecological processes among habitats or the phylogenetic history of niches, traits, and habitat associations. Future studies will need to include information on species traits in order to explain the variation in phylogenetic structure among habitats in tropical forests.

IN SEARCH OF QUORUM EFFECTS IN METACOMMUNITY STRUCTURE: SPECIES CO-OCCURRENCE ANALYSES

Alternative models of community assembly emphasize regional, stochastic, dispersal-based processes or local, deterministic, niche-based processes. Community ecology's historical focus on local processes implicitly assumes that local processes surpass regional processes over time or across space to derive nonrandom metacommunity structure (i.e., a quorum effect). Quorum effects are expected late in succession among nearby sites, whereas quorum effects are not expected early in succession among distant sites. I conducted a meta-analysis of zooplankton data sets encompassing time scales of one to thousands of years and spatial scales of <1 m to thousands of kilometers. Species co-occurrence analyses statistically evaluated presence/absence patterns relative to random patterns obtained with Monte Carlo null models. A series of weighted analyses was conducted and alternative randomization algorithms and null models were evaluated. Most zooplankton metacommunities were randomly structured in unweighted analyses, and the distribution of significant structure did not follow quorum effect predictions. Weighted analyses (e.g., by habitat area) revealed significant, nonrandom structure in most zooplankton metacommunities, but the distribution of significant structure still did not adhere well to quorum effect predictions. Finally, additional weighting for study scale (number of sites) nullified most significant area-weighted structure, and again, the distribution of significant structure did not follow quorum effect predictions. Overall, a quorum effect was not supported, perhaps related to zooplankton life histories and energetics and/or the quorum effect itself. Results at the presence/absence level of resolution indicated that local processes did not generally override regional processes over time or across space to drive community structure. A full integration of dispersal- and niche-based concepts in metacommunity dynamics will be most fruitful for unraveling community assembly. Species co-occurrence analyses were scale dependent (habitat area and study size). Future analyses should use weights for important factors (e.g., habitat area), and meta-analyses should include study scale as an additional factor contributing to apparent patterns.

Conformational Features of a Natural Break in the Type IV Collagen Gly-X-Y Repeat

Fibrillar collagens have an absolute requirement for Gly as every 3rd residue, whereas breaks in the Gly-X-Y repeating pattern are found normally in the triple helix domains of non-fibrillar collagens, such as type IV collagen in basement membranes. In this study, a model 30-mer peptide is designed to include the interruption GPOGAAVMGPOGPO found in the alpha5 chain of type IV collagen. The GAAVM peptide forms a stable triple helix, with Tm= 29 degrees C. When compared with a control peptide with Gly as every 3rd residue, the GAAVM peptide has a marked decrease in the 225 nm maximum of its CD spectrum and a 10 degrees C drop in stability. A 50% decrease in calorimetric enthalpy is observed, which may result from disruption of ordered water structure anchored by regularly placed backbone carbonyls. NMR studies on specific 15N-labeled residues within the GAAVM peptide indicate a normal triple helical structure for Gly-Pro-Hyp residues flanking the break. The sequence within the break is not disordered but shows altered hydrogen exchange rates and an abnormal Val chemical shift. It was previously reported that a peptide designed to model a similar kind of interruption in the peptide (Pro-Hyp-Gly)10, (GPOGPOPOGPO), is unable to form a stable triple helix, and replacement of GAA by GPO or VM by PO within the GAAVM break decreases the stability. Thus, rigid imino acids are unfavorable within a break, despite their favorable stabilization of the triple helix itself. These results suggest some non-random structure typical of this category of breaks in the Gly-X-Y repeat of the triple helix.

The Deformation and Adhesion of Randomly Rough and Patterned Surfaces

Using a surface forces apparatus (SFA) and an atomic force microscope (AFM) we have studied the effects of surface roughness (root-mean-square (RMS) roughness between 0.3 and 220 nm) on the "contact mechanics", which describes the deformations and loading and unloading adhesion forces, of various polymeric surfaces. For randomly rough, moderately stiff, elastomeric surfaces, the force-distance curves on approach and separation are nearly reversible and almost perfectly exponentially repulsive, with an adhesion on separation that decreases only slightly with increasing RMS. Additionally, the magnitude of the preload force is seen to play a large role in determining the measured adhesion. The exponential repulsion likely arises from the local compressions (fine-grained nano- or submicron-scale deformations) of the surface asperities. The resulting characteristic decay lengths of the repulsion scale with the RMS roughness and correlate very well with a simple finite element method (FEM) analysis based on actual AFM topographical images of the surfaces. For "patterned" surfaces, with a nonrandom terraced structure, no similar exponential repulsion is observed, suggesting that asperity height variability or random roughness is required for the exponential behavior. However, the adhesion force or energy between two "patterned" surfaces fell off dramatically and roughly exponentially as the RMS increased, likely owing to a significant decrease in the contact area which in turn determines their adhesion. For both types of rough surfaces, random and patterned, the coarse-grained (global, meso- or macroscopic) deformations of the initially curved surfaces appear to be Hertzian.

Conditions Under Which Function Information Attenuates Name Extension via Shape

Children often extend names to novel artifacts on the basis of overall shape rather than core properties (e.g., function). This bias is claimed to reflect the fact that nonrandom structure is a reliable cue to an object having a specific designed function. In this article, we show that information about an object's design (i.e., about its creator's intentions) is neither necessary nor sufficient for children to override the shape bias. Children extend names on the basis of any information specifying the artifact's function (e.g., information about design, current use, or possible use), especially when this information is made salient when candidate objects for extension are introduced. Possible mechanisms via which children come to rely less on easily observable cues (e.g., shape) and more on core properties (e.g., function) are discussed.

Ac-like transposons in populations of wild diploid Triticeae species: comparative analysis of chromosomal distribution

Data are presented on the intra- and interspecific differences/similarities in chromosomal patterns of Ac-like elements (hAT family) in ecologically contrasted populations of three Triticeae species - Aegilops speltoides, Triticum urartu, and Hordeum spontaneum. Application of original computer software made it possible to precisely map transposon clusters and to link them to known chromosomal markers (rDNA sites, centromeres, and heterochromatin regions). From our data we can specify the most visible features of Ac-like elements chromosomal distribution: preferential concentration in chromosomal proximal regions; high percentage of clusters on the border between euchromatin and heterochromatin; complementary chromosomal arrangement towards En/Spm transposons (CACTA); population-specific insertions into centromeres; more differences in total cluster numbers between populations of self-pollinated species than between populations of cross-pollinated species. The application of statistical simulation (Resampling) method to analysis of data indicates that ecology may play a certain role in dynamics of Ac-like elements. Comparison of real Ayala distances, as well as real chromosomal distribution of Ac-like elements in populations of two species with different mating systems with the same but randomly simulated parameters, revealed that non-random population structure in the Mediterranean floral zone suffers and becomes chaotic in the Irano-Turanian zone.

Characterization of Intra-molecular Distances and Site-specific Dynamics in Chemically Unfolded Barstar: Evidence for Denaturant-dependent Non-random Structure

The structure and dynamics of the unfolded form of a protein are expected to play critical roles in determining folding pathways. In this study, the urea and guanidine hydrochloride (GdnHCl)-unfolded forms of the small protein barstar were explored by time-resolved fluorescence techniques. Barstar was labeled specifically with thionitrobenzoate (TNB), by coupling it to the thiol side-chain of a cysteine residue at one of the following positions on the sequence: 14, 25, 40, 42, 62, 82 and 89, in single cysteine-containing mutant proteins. Seven intra-molecular distances (R(DA)) under unfolding conditions were estimated from measurements of time-resolved fluorescence resonance energy transfer between the donor Trp53 and the non-fluorescent acceptor TNB coupled to one of the seven cysteine side-chains. The unfolded protein chain expands with an increase in the concentration of the denaturants. The extent of expansion was found to be non-uniform, with different intra-molecular distances expanding to different extents. In general, shorter distances were found to expand less when compared to longer spans. The extent of expansion was higher in the case of GdnHCl when compared to urea. A comparison of the measured values of R(DA) with those derived from a model based on excluded volume, revealed that while shorter spans showed good agreement, the experimental values of R(DA) of longer spans were smaller when compared to the theoretical values. Sequence-specific flexibility of the polypeptide was determined by time-resolved fluorescence anisotropy decay measurements on acrylodan or 1,5-IAEDANS labeled single cysteine-containing proteins under unfolding conditions. Rotational dynamics derived from these measurements indicated that the level of flexibility increased with increase in the concentration of denaturants and showed a graded increase towards the C-terminal end. Taken together, these results appear to indicate the presence of specific non-random coil structures and show that the deviation from random coil structure is different for the two denaturants.

Population genetic structure ofSorex unguiculatusandSorex caecutiens(Soricidae, Mammalia) in Hokkaido, based on microsatellite DNA polymorphism

AbstractWe investigated the genetic structure ofSorex unguiculatusandSorex caecutienspopulations in Hokkaido, Japan, using hypervariable microsatellite DNA markers. We used five microsatellite loci to type 475S. unguiculatusindividuals from 20 localities on the Hokkaido mainland and four localities from each of four offshore islands (and 11 shrews from one locality in southern Sakhalin for a particular analysis). We used six microsatellite loci to type 240S. caecutiensindividuals from 13 localities on the Hokkaido mainland. Genetic variation was high in mainland populations of both species and low in the island populations ofS. unguiculatus. Allelic richness and island size were positively correlated forS. unguiculatus, suggesting that genetic drift occurred on those islands due to small population size. In addition, four insular populations ofS. unguiculatuswere genetically differentiated from the mainland populations, although clear phylogeographic clustering was not confirmed among populations on the Hokkaido mainland for eitherS. unguiculatusorS. caecutiens. Heterozygosity excess was observed in more than half of the populations including the mainland populations of the two species, suggesting recent bottleneck events in these populations. Population dynamics of the shrews might be explained by a metapopulation scheme. According to autocorrelation analysis, the extent of non‐random spatial genetic structure was approximately 100 km. Isolation by distance was observed inS. unguiculatus, but not inS. caecutiensalthough there is a positive trend. The lack of correlation forS. caecutiensmight have been due to small sample size. Thus, no obvious differences in population genetic structure were found between the two species on the Hokkaido mainland in the present study, while previous investigations using mitochondrial DNA sequences inferred that these two species might have rather different biogeographic histories.

Null models, co-occurrence patterns, and ecological modelling of a Mediterranean community of snakes

AbstractA Mediterranean community of snakes, inhabiting a hilly area in central Italy (Monterano, Tolfa Mountains) was statistically modelled to investigate whether: (i) it shows non-random structure as predicted by competition theories, (ii) there are proximate elements of the landscape that may predict the presence/absence of the various snake species at the study area, and (iii) the snakes select 'resting sites' which are relatively simple or relatively complicated in landscape structure. To investigate issue (i) we used co-occurrence pattern analyses and Monte Carlo simulations. To investigate issue (ii) we used logistic regression analysis on presence/absence data of eleven 'proximate landscape' variables around sites of presence for the snakes and around random (= absence) sites at the same study area. To investigate issue (iii), we used expected-versus-observed χ2 to test whether snake presences were associated more often than random with a combination of variables, i.e. with at least four different variables for each point of presence. The snake community was constituted by eight species, but only the five commonest species (i.e. Coluber viridiflavus, Elaphe longissima, Elaphe quatuorlineata, Natrix natrix, and Vipera aspis) were included in our models. Our modeling and simulation analyses suggested that: (i) the community structure was not competitively structured both in terms of habitat resource and in terms of 'proximate landscape' variables influencing snake presences; (ii) all five snake species were positively influenced by at least two of the eleven variables considered in the logistic regression model; (iii) four out of five species clearly selected sites with complicated structure, the only exception being Coluber viridiflavus.

Investigating Disease Spread between Two Assessment Dates with Permutation Tests on a Lattice

ABSTRACT Mapping and analyzing the disease status of individual plants within a study area at successive dates can give insight into the processes involved in the spread of a disease. We propose a permutation method to analyze such spatiotemporal maps of binary data (healthy or diseased plants) in regularly spaced plantings. It requires little prior information on the causes of disease spread and handles missing plants and censored data. A Monte Carlo test is used to assess whether the location of newly diseased plants is independent of the location of previously diseased plants. The test takes account of the significant spatial structures at each date in order to separate nonrandomness caused by the structure at one date from nonrandomness caused by the dependence between newly diseased plants and previously diseased plants. If there is a nonrandom structure at both dates, independent patterns are simulated by randomly shifting the entire pattern observed at the second date. Otherwise, independent patterns are simulated by randomly reallocating the positions of one group of diseased plants. Simulated and observed patterns of disease are then compared through distance-based statistics. The performance of the method and its robustness are evaluated by its ability to accurately identify simulated independent and dependent bivariate point patterns. Additionally, two realworld spatiotemporal maps with contrasting disease progress illustrate how the tests can provide valuable clues about the processes of disease spread. This method can supplement biological investigations and be used as an exploratory step before developing a specific mechanistic model.

Dynamic Properties of Network Motifs Contribute to Biological Network Organization

Biological networks, such as those describing gene regulation, signal transduction, and neural synapses, are representations of large-scale dynamic systems. Discovery of organizing principles of biological networks can be enhanced by embracing the notion that there is a deep interplay between network structure and system dynamics. Recently, many structural characteristics of these non-random networks have been identified, but dynamical implications of the features have not been explored comprehensively. We demonstrate by exhaustive computational analysis that a dynamical property—stability or robustness to small perturbations—is highly correlated with the relative abundance of small subnetworks (network motifs) in several previously determined biological networks. We propose that robust dynamical stability is an influential property that can determine the non-random structure of biological networks.

Spatial and temporal predictability of the parasite community structure of a benthic marine fish along its distributional range

The search for consistent patterns of organisation in parasite communities remains a central theme in parasite community ecology. However, to date, much evidence comes from studies without replication in both space and time; when replicate communities are examined, repeatable patterns are rarely observed. Here we determine, using nested subset analyses, whether the infracommunities of ectoparasites and endoparasites of a benthic marine fish ( Sebastes capensis) show non-random structure. Then we examine the spatial repeatability of parasite community structure across the host's distribution in the southern Pacific, and the temporal repeatability of ectoparasite community structure from one locality. In total, 537 fish were captured from different latitudes (between 11°S and 52°S) along the Pacific coast of South America; a further 122 specimens were captured in two other years from one of the sampling localities, Valdivia (40°S). In spite of variation in fish sizes among samples, fish size generally did not correlate with either ecto- or endoparasite species richness. The ecto- and endoparasite species richness of the component communities were also not correlated with fish sample size across the nine localities. Significant nested patterns were found in the ectoparasite communities of S. capensis at all eight localities, except at latitude 52°S. Significant nested patterns were also found in the endoparasite infracommunities of S. capensis at seven of the nine localities, the exceptions being those from latitudes 11°S and 20°S. On a temporal scale, significant nestedness was observed in the ectoparasite infracommunities of S. capensis during each of the 3 years of sampling at Valdivia. In general, the same parasite species are responsible for the repeatability of nested patterns, though their importance varies among localities. The spatial and temporal predictability of the parasite community structure in S. capensis may be associated with the fish's benthic habitat and territorial behavior, suggesting that host biology may be a key determinant of the structure of parasite communities.