Harmonic Analysis of Boolean Networks: Determinative Power and Perturbations

Consider a large Boolean network with a feed forward structure. Given a probability distribution on the inputs, can one find, possibly small, collections of input nodes that determine the states of most other nodes in the network? To answer this question, a notion that quantifies the determinative power of an input over the states of the nodes in the network is needed. We argue that the mutual information (MI) between a given subset of the inputs X = {X_1, ..., X_n} of some node i and its associated function f_i(X) quantifies the determinative power of this set of inputs over node i. We compare the determinative power of a set of inputs to the sensitivity to perturbations to these inputs, and find that, maybe surprisingly, an input that has large sensitivity to perturbations does not necessarily have large determinative power. However, for unate functions, which play an important role in genetic regulatory networks, we find a direct relation between MI and sensitivity to perturbations. As an application of our results, we analyze the large-scale regulatory network of Escherichia coli. We identify the most determinative nodes and show that a small subset of those reduces the overall uncertainty of the network state significantly. Furthermore, the network is found to be tolerant to perturbations of its inputs

ABCtoolbox: a versatile toolkit for approximate Bayesian computations

BACKGROUND: The estimation of demographic parameters from genetic data often requires the computation of likelihoods. However, the likelihood function is computationally intractable for many realistic evolutionary models, and the use of Bayesian inference has therefore been limited to very simple models. The situation changed recently with the advent of Approximate Bayesian Computation (ABC) algorithms allowing one to obtain parameter posterior distributions based on simulations not requiring likelihood computations. RESULTS: Here we present ABCtoolbox, a series of open source programs to perform Approximate Bayesian Computations (ABC). It implements various ABC algorithms including rejection sampling, MCMC without likelihood, a Particle-based sampler and ABC-GLM. ABCtoolbox is bundled with, but not limited to, a program that allows parameter inference in a population genetics context and the simultaneous use of different types of markers with different ploidy levels. In addition, ABCtoolbox can also interact with most simulation and summary statistics computation programs. The usability of the ABCtoolbox is demonstrated by inferring the evolutionary history of two evolutionary lineages of Microtus arvalis. Using nuclear microsatellites and mitochondrial sequence data in the same estimation procedure enabled us to infer sex-specific population sizes and migration rates and to find that males show smaller population sizes but much higher levels of migration than females. CONCLUSION: ABCtoolbox allows a user to perform all the necessary steps of a full ABC analysis, from parameter sampling from prior distributions, data simulations, computation of summary statistics, estimation of posterior distributions, model choice, validation of the estimation procedure, and visualization of the results

Dispersal and population structure at different spatial scales in the subterranean rodent Ctenomys australis

<p>Abstract</p> <p><b>Background</b></p> <p>The population genetic structure of subterranean rodent species is strongly affected by demographic (e.g. rates of dispersal and social structure) and stochastic factors (e.g. random genetic drift among subpopulations and habitat fragmentation). In particular, gene flow estimates at different spatial scales are essential to understand genetic differentiation among populations of a species living in a highly fragmented landscape. <it>Ctenomys australis </it>(the sand dune tuco-tuco) is a territorial subterranean rodent that inhabits a relatively secure, permanently sealed burrow system, occurring in sand dune habitats on the coastal landscape in the south-east of Buenos Aires province, Argentina. Currently, this habitat is threatened by urban development and forestry and, therefore, the survival of this endemic species is at risk. Here, we assess population genetic structure and patterns of dispersal among individuals of this species at different spatial scales using 8 polymorphic microsatellite loci. Furthermore, we evaluate the relative importance of sex and habitat configuration in modulating the dispersal patterns at these geographical scales.</p> <p>Results</p> <p>Our results show that dispersal in <it>C. australis </it>is not restricted at regional spatial scales (~ 4 km). Assignment tests revealed significant population substructure within the study area, providing support for the presence of two subpopulations from three original sampling sites. Finally, male-biased dispersal was found in the Western side of our study area, but in the Eastern side no apparent philopatric pattern was found, suggesting that in a more continuous habitat males might move longer distances than females.</p> <p>Conclusions</p> <p>Overall, the assignment-based approaches were able to detect population substructure at fine geographical scales. Additionally, the maintenance of a significant genetic structure at regional (~ 4 km) and small (less than 1 km) spatial scales despite apparently moderate to high levels of gene flow between local sampling sites could not be explained simply by the linear distance among them. On the whole, our results support the hypothesis that males disperse more frequently than females; however they do not provide support for strict philopatry within females.</p

Ichthyofauna of the River Sava System

On the survey of the recent records, the fish and lamprey fauna of the River Sava catchment consists of 74 species, 15 of which being considered alien. The indigenous species diversity, explained using the relation N = 0. 546 A 0.232, fits well into the range common for large catchments in Europe. Both taxonomic and ecological diversity, as well as the character of fish communities in streams and rivers, are strongly correlated with the stream order. On the relative abundance of species in fish communities, the upper rhithron fish communities cluster distinctly from those belonging to the middle rhithron, within which several subgroups of fish communities were distinguishable. Fish communities of the middle rhithron character in streams and small rivers stand distinctly apart from those belonging to particular sections of large rivers (e.g., the Rivers Sava, Drina, Vrbas, and Bosna), with the transitional type of middle rhithron fish community in larger rivers (e.g., those in the Rivers Una and Sana) that resemble more to the fish communities common in middle rhithron streams. Fish communities in the middle section of the River Sava in Croatia and in the bordering area with Bosnia and Herzegovina mainly belong to the lower rhithron, attaining the character of potamon in the most downstream, Serbian section. River Sava’s fish communities strongly interact with the ones occurring in the most downstream sections of their largest tributaries, e.g., the Rivers Una, Vrbas, Bosna, Drina, and Kolubara, which makes them very similar in structure in the areas of river mouths. Classification of fish communities based solely on the presence and absence of species revealed similar general pattern of fish community classification, though with the more sharp delimitation between those belonging to the upper and middle rhithron on one and to the lower rhithron and potamon on the other side. That was supported by the determination of fish communities belonging to the upper rhithron with brown trout Salmo cf. trutta, European bullhead Cottus gobio, and minnow Phoxinus phoxinus as the most common fish species. Fish communities belonging to the middle rhithron were determined mainly with chub Squalius cephalus and spirlin Alburnoides bipunctatus, whereas brook barbel Barbus balcanicus and stone loach Barbatula barbatula occurred in both upper rhithron and middle rhithron. Nase Chondrostoma nasus were associated with both middle and lower rhithron fish communities. The most common fish species that determine the lower rhithron fish communities were common bream Abramis brama, ide Idus idus, and bleak Alburnus alburnus, with the northern pike Esox lucius, Balon’s ruffe Gymnocephalus baloni, and racer goby Neogobius gymnotrachelus as significant species explaining fish communities of both lower rhithron and potamon. The level of production of fish in the River Sava varies remarkably within the sections with the similar ecological features, as well as between the sections that differ for the type of fish community. The greatest biomass and annual natural production were recorded in the sections homing the potamon and lower rhithron fish communities, especially in the flooding areas of side arms and oxbows which serve as spawning areas and nurseries. A total of 15 alien fish species was recorded in the River Sava catchment, the Prussian carp Carassius gibelio and brown bullhead Ameiurus nebulosus being assessed the most invasive in the areas with the potamon fish community. A strong impact from both long-term and recent stocking with alien hatchery-reared brown trout strains and rainbow trout in the upper rhithron fish communities was recently recognized. Mudminnow Umbra krameri and huchen (or Danube salmon) Hucho hucho are considered the two most threatened fish species of the River Sava catchment, where various types of riverbed modifications, especially the damming, were seen the most prominent threatening factors for fish diversity.Milačić R, Ščančar J, Paunović M, editors. The Sava River. Berlin, Heidelberg: Springer-Verlag; 2015. p. 361-400

Red deer mediate spatial and temporal plant heterogeneity in boreal forests

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