Non-equilibrium allele frequency spectra via spectral methods

A major challenge in the analysis of population genomics data consists of isolating signatures of natural selection from background noise caused by random drift and gene flow. Analyses of massive amounts of data from many related populations require high-performance algorithms to determine the likelihood of different demographic scenarios that could have shaped the observed neutral single nucleotide polymorphism (SNP) allele frequency spectrum. In many areas of applied mathematics, Fourier Transforms and Spectral Methods are firmly established tools to analyze spectra of signals and model their dynamics as solutions of certain Partial Differential Equations (PDEs). When spectral methods are applicable, they have excellent error properties and are the fastest possible in high dimension; see Press et al. (2007). In this paper we present an explicit numerical solution, using spectral methods, to the forward Kolmogorov equations for a Wright–Fisher process with migration of K populations, influx of mutations, and multiple population splitting events.     

Variation in aggressive behaviour in the poeciliid fish Brachyrhaphis episcopi: Population and sex differences

Aggression is often positively correlated with other behavioural traits such as boldness and activity levels. Comparisons across populations can help to determine factors that promote the evolution of such traits. We quantified these behaviours by testing the responses of wild-caught poeciliid fish, Brachyrhaphis episcopi, to mirror image stimuli. This species occurs in populations that experience either high or low levels of predation pressure. Previous studies have shown that B. episcopi from low predation environments are less bold than those that occur with many predators. We therefore predicted that fish from high predation populations would be more aggressive and more active than fish from low predation populations. However, we found the opposite - low predation fish approached a mirror and a novel object more frequently than high predation fish suggesting that ‘boldness’ and aggression were higher in low predation populations, and that population-level boldness measures may vary depending on context. When tested individually, low predation fish inspected their mirror image more frequently. Females, but not males, from low predation sites were also more aggressive towards their mirror image. Variation in female aggression may be driven by a trade-off between food availability and predation risk. This suggests that the relationship between aggression and boldness has been shaped by adaptation to environmental conditions, and not genetic constraints.     

Follow up estimation of Aedes aegypti entomological parameters and mathematical modellings

The dengue virus is a vector-borne disease transmitted by mosquito Aedes aegypti and the incidence is strongly influenced by temperature and humidity which vary seasonally. To assess the effects of temperature on dengue transmission, mathematical models are developed based on the population dynamics theory. However, depending on the hypotheses of the modelling, different outcomes regarding to the risk of epidemics are obtained. We address this question comparing two simple models supplied with model's parameters estimated from temperature-controlled experiments, especially the entomological parameters regarded to the mosquito's life cycle in different temperatures. Once obtained the mortality and transition rates of different stages comprising the life cycle of mosquito and the oviposition rate, we compare the capacity of vector reproduction (the basic offspring number) and the risk of infection (basic reproduction number) provided by two models. The extended model, which is more realistic, showed that both mosquito population and dengue risk are situated at higher values than the simplified model, even that the basic offspring number is lower.     

内蒙古赛罕乌拉自然保护区狼的数量分布和食物组成

2006年1月至2008年12月,在内蒙古赛罕乌拉国家级自然保护区运用样线法和粪便分析法,对狼(Canis lupus)的生态分布和食物组成开展了研究。研究结果:保护区狼的数量至少7只,密度为(4.18±2.88)只/100km2,主要分布于保护区的圣山和庆云山核心区。在圣山主要活动于山脊、道路和沟谷;在庆云山主要活动于山脊。草兔(Lepus capensis)和植物在狼的食物组成中出现率最高,其食物组成在年度间存在显著差异(P<0.01),冬春与夏秋季节间差异不显著(P>0.05)。     

黑颈鹤在新疆罗布泊和昆仑山分布及种群状况

黑颈鹤(Grus nigricollis)俗称"吐尔那",在新疆罕见,主要分布在与西藏和青海接壤的阿尔金山、昆仑山、喀喇昆仑山区.作者1985～2010年间在若羌(祁曼塔格、东昆仑山、阿尔金山)、且末(吐拉牧场、车尔臣河流域)、和田(阿克赛钦湖)、墨玉、皮山(喀拉喀什河流域)、叶城(叶尔羌河流域)等地记录到黑颈鹤.采用...     

Crystal structures exploring the origins of the broader specificity of escherichia coli heat-labile enterotoxin compared to cholera toxin

Cholera toxin (CT) and Escherichia coli heat-labile enterotoxin (LT) are structurally and functionally related and share the same primary receptor, the GM1 ganglioside. Despite their extensive similarities, these two toxins exhibit distinct ligand specificities, with LT being more promiscuous than CT. Here, we have attempted to rationalize the broader binding specificity of LT and the subtle differences between the binding characteristics of LTs from human and porcine origins (mediated by their B subunit pentamers, hLTB and pLTB, respectively). The analysis is based on two crystal structures of pLTB in complexes with the pentasaccharide of its primary ligand, GM1, and with neolactotetraose, the carbohydrate determinant of a typical secondary ligand of LTs, respectively. Important molecular determinants underlying the different binding specificities of LTB and CTB are found to be contributed by Ser95, Tyr18 and Thr4 (or Ser4 of hLTB), which together prestabilize the binding site by positioning Lys91, Glu51 and the adjacent loop region (50-61) containing Ile58 for ligand binding. Glu7 and Ala1 may also play an important role. Many of these residues are closely connected with a recently identified second binding site, and there appears to be cross-talk between the two sites. Binding to N-acetyllactosamine-terminated receptors is further augmented by Arg13 (present in pLT and some hLT variants), as previously predicted.     

Congeneric but still distinct: how closely related trypsin ligands exhibit different thermodynamic and structural properties

A congeneric series of benzamidine-type ligands with a central proline moiety and a terminal cycloalkyl group—linked by a secondary amine, ether, or methylene bridge—was synthesized as trypsin inhibitors. This series of inhibitors was investigated by isothermal titration calorimetry, crystal structure analysis in two crystal forms, and molecular dynamics simulations. Even though all of these congeneric ligands exhibited essentially the same affinity for trypsin, their binding profiles at the structural, dynamic, and thermodynamic levels are very distinct. The ligands display a pronounced enthalpy/entropy compensation that results in a nearly unchanged free energy of binding, even though individual enthalpy and entropy terms change significantly across the series. Crystal structures revealed that the secondary amine-linked analogs scatter over two distinct conformational families of binding modes that occupy either the inside or of the outside the protein's S3/S4 specificity pocket. In contrast, the ether-linked and methylene-linked ligands preferentially occupy the hydrophobic specificity pocket. This also explains why the latter ligands could only be crystallized in the conformationally restricting closed crystal form whereas the derivative with the highest residual mobility in the series escaped our attempts to crystallize it in the closed form; instead, a well-resolved structure could only be achieved in the open form with the ligand in disordered orientation. These distinct binding modes are supported by molecular dynamics simulations and correlate with the shifting enthalpic/entropic signatures of ligand binding. The examples demonstrate that, at the molecular level, binding modes and thermodynamic binding signatures can be very different even for closely related ligands. However, deviating binding profiles provide the opportunity to optimally address a given target.     

Transitions of interaction outcomes in a uni-directional consumer-resource system

A uni-directional consumer-resource system of two species is analyzed. Our aim is to understand the mechanisms that determine how the interaction outcomes depend on the context of the interaction; that is, on the model parameters. The dynamic behavior of the model is described and, in particular, it is demonstrated that no periodic orbits exist. Then the parameter (factor) space is shown to be divided into four regions, which correspond to the four forms of interaction outcomes; i.e. mutualism, commensalism, parasitism and amensalism. It is shown that the interaction outcomes of the system transition smoothly among these four forms when the parameters of the system are varied continuously. Varying each parameter individually or varying pairs of parameters can also lead to smooth transitions between the interaction outcomes. The analysis leads to both conditions for which each species achieves its maximal density, and situations in which periodic oscillations of the interaction outcomes emerge.     

Minimal models of growth and decline of microbial populations

Dynamics of growth and decline of microbial populations were analysed and respective models were developed in this investigation. Analysis of the dynamics was based on general considerations concerning the main properties of microorganisms and their interactions with the environment which was supposed to be affected by the activity of the population. Those considerations were expressed mathematically by differential equations or systems of the equations containing minimal sets of parameters characterizing those properties. It has been found that: (1) the factors leading to the decline of the population have to be considered separately, namely, accumulation of metabolites (toxins) in the medium and the exhaustion of resources; the latter have to be separated again into renewable (‘building materials’) and non-renewable (sources of energy); (2) decline of the population is caused by the exhaustion of sources of energy but no decline is predicted by the model because of the exhaustion of renewable resources; (3) the model determined by the accumulation of metabolites (toxins) in the medium does not suggest the existence of a separate ‘stationary phase’; (4) in the model determined by the exhaustion of energy resources the ‘stationary’ and ‘decline’ phases are quite discernible; and (5) there is no symmetry in microbial population dynamics, the decline being slower than the rise. Mathematical models are expected to be useful in getting insight into the process of control of the dynamics of microbial populations. The models are in agreement with the experimental data.     

A three-species model explaining cyclic dominance of Pacific salmon

The four-year oscillations of the number of spawning sockeye salmon (Oncorhynchus nerka) that return to their native stream within the Fraser River basin in Canada are a striking example of population oscillations. The period of the oscillation corresponds to the dominant generation time of these fish. Various—not fully convincing—explanations for these oscillations have been proposed, including stochastic influences, depensatory fishing, or genetic effects. Here, we show that the oscillations can be explained as an attractor of the population dynamics, resulting from a strong resonance near a Neimark Sacker bifurcation. This explains not only the long-term persistence of these oscillations, but also reproduces correctly the empirical sequence of salmon abundance within one period of the oscillations. Furthermore, it explains the observation that these oscillations occur only in sockeye stocks originating from large oligotrophic lakes, and that they are usually not observed in salmon species that have a longer generation time.