A model study of the behaviour of steep excavated rock slopes

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Dynamics of transcription factor binding site evolution

Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ~10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of "pre-sites" or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genetics.Comment: 28 pages, 15 figure

Evolution of new regulatory functions on biophysically realistic fitness landscapes

Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous avoidance of deleterious "crosstalk" with non-cognate molecules? Although physical models of molecular interactions provide a framework in which co-evolution of network components can be analyzed, most theoretical studies have focused on the evolution of individual alleles, neglecting the network. In contrast, we study the elementary step in the evolution of gene regulatory networks: duplication of a transcription factor followed by selection for TFs to specialize their inputs as well as the regulation of their downstream genes. We show how to coarse grain the complete, biophysically realistic genotype-phenotype map for this process into macroscopic functional outcomes and quantify the probability of attaining each. We determine which evolutionary and biophysical parameters bias evolutionary trajectories towards fast emergence of new functions and show that this can be greatly facilitated by the availability of "promiscuity-promoting" mutations that affect TF specificity

Does hybridisation influence speciation?

Hybridization is an almost inevitable component of speciation, and its study can tell us much about that process. However, hybridization itself may have a negligible influence on the origin of species: on the one hand, universally favoured alleles spread readily across hybrid zones, whilst on the other, spatially heterogeneous selection causes divergence despite gene flow. Thus, narrow hybrid zones or occasional hybridisation may hardly affect the process of divergence

Recombination and sex

Sex and recombination are among the most striking features of the living world, and they play a crucial role in allowing the evolution of complex adaptation. The sharing of genomes through the sexual union of different individuals requires elaborate behavioral and physiological adaptations. At the molecular level, the alignment of two DNA double helices, followed by their precise cutting and rejoining, is an extraordinary feat. Sex and recombination have diverse—and often surprising—evolutionary consequences: distinct sexes, elaborate mating displays, selfish genetic elements, and so on

Recognising institutional context in simulating and generalising exchange values for monetary ecosystem accounts

The paper argues that monetary valuation of ecosystem services for ecosystem accounting needs to be sensitive to institutional context, when simulating markets to generate exchange values where none was available previously and when conducting value generalisation that extrapolates exchange values from specific sites to the whole acounting area. The same ecosystem type can contain different governance regimes or, conversely, a single governance regime may be present in many ecosystem types. Governance regimes are, in part, determined by ecosystem type and condition, but also by ecosystem access characteristics which vary over urban-rural gradients. An ecosystem service will not have a single price if costs of supply and transaction vary in space. This is generally true for all accounting compatible valuation methods if they are extrapolated across different market contexts, but require particular attention if markets are simulated for specific locations and then assumed to be generally valid for the accounting area. The paper exemplifies this for different institutional settings for exchange values of recreation services exploring the general recommendation in SEEA EA for making valuation methods sensitive to institutional context. Stated preference methods simulate markets for ecosystem services. The paper then reviews non-market stated preference valuation studies that have been sensitive to institutional design. Findings on institutional design are, therefore, specifically relevant for simulation of market exchange values for the purpose of compiling monetary ecosystem accounts. The paper finds that disregard for the institutional context in valuation for ecosystem accounting can lead to: (i) errors of generalisation/aggregation and (ii) downward ‘bias’ in simulated accounting prices (relative to the status quo of the institutional context). simulated exchange value (SEV), recreation services, System of Environmental and Economic Accounts Ecosystem Accounts (SEEA EA), value transfer, value generalisation, stated preference, non-market valuation, monetary accountspublishedVersio