Metastable Evolutionary Dynamics: Crossing Fitness Barriers or Escaping via Neutral Paths?

We analytically study the dynamics of evolving populations that exhibit metastability on the level of phenotype or fitness. In constant selective environments, such metastable behavior is caused by two qualitatively different mechanisms. One the one hand, populations may become pinned at a local fitness optimum, being separated from higher-fitness genotypes by a {\em fitness barrier} of low-fitness genotypes. On the other hand, the population may only be metastable on the level of phenotype or fitness while, at the same time, diffusing over {\em neutral networks} of selectively neutral genotypes. Metastability occurs in this case because the population is separated from higher-fitness genotypes by an {\em entropy barrier}: The population must explore large portions of these neutral networks before it discovers a rare connection to fitter phenotypes. We derive analytical expressions for the barrier crossing times in both the fitness barrier and entropy barrier regime. In contrast with ``landscape'' evolutionary models, we show that the waiting times to reach higher fitness depend strongly on the width of a fitness barrier and much less on its height. The analysis further shows that crossing entropy barriers is faster by orders of magnitude than fitness barrier crossing. Thus, when populations are trapped in a metastable phenotypic state, they are most likely to escape by crossing an entropy barrier, along a neutral path in genotype space. If no such escape route along a neutral path exists, a population is most likely to cross a fitness barrier where the barrier is {\em narrowest}, rather than where the barrier is shallowest.Comment: 32 pages, 7 figures, 1 table; http://www.santafe.edu/projects/evca/med.ps.g

The Evolutionary Unfolding of Complexity

We analyze the population dynamics of a broad class of fitness functions that exhibit epochal evolution---a dynamical behavior, commonly observed in both natural and artificial evolutionary processes, in which long periods of stasis in an evolving population are punctuated by sudden bursts of change. Our approach---statistical dynamics---combines methods from both statistical mechanics and dynamical systems theory in a way that offers an alternative to current ``landscape'' models of evolutionary optimization. We describe the population dynamics on the macroscopic level of fitness classes or phenotype subbasins, while averaging out the genotypic variation that is consistent with a macroscopic state. Metastability in epochal evolution occurs solely at the macroscopic level of the fitness distribution. While a balance between selection and mutation maintains a quasistationary distribution of fitness, individuals diffuse randomly through selectively neutral subbasins in genotype space. Sudden innovations occur when, through this diffusion, a genotypic portal is discovered that connects to a new subbasin of higher fitness genotypes. In this way, we identify innovations with the unfolding and stabilization of a new dimension in the macroscopic state space. The architectural view of subbasins and portals in genotype space clarifies how frozen accidents and the resulting phenotypic constraints guide the evolution to higher complexity.Comment: 28 pages, 5 figure

Shifting waters - Indonesia's dynamic marine protected area policy seascape

The coastal waters of Indonesia are among the planet’s most biologically diverse. They also provide food and income for thousands of vulnerable coastal communities. These ecosystems are increasingly being degraded from overexploitation and other threats. Marine Protected Areas (MPAs) are essential for supporting the sustainable management of the country’s marine resources and contributing to the food security of coastal communities. However, these conservation initiatives suffer from chronically low levels of effectiveness. A robust policy framework is vital for creating effective natural resource management regimes. This study rigorously reviewed Indonesia’s MPA policy arrangements and examined whether they reflect contemporary theory and practice. It also examined how Indonesia’s MPA policies are being implemented in the field using the Eastern Indonesian case-study sites of Raja Ampat Islands MPA and Sawu Sea Marine National Park. With this information, the research identified policy needs and opportunities for improving MPA performance. A variety of methods were employed to collect data, including in-depth literature and policy reviews, semi-structured interviews and field visits. The research found that although Indonesia’s MPA policy arrangements capture many aspects of contemporary theory and practice, some significant issues exist. The move to ‘decentralisation’ and then ‘recentralisation’, overlapping legislative instruments and the multiplicity of management institutions have created a complex and sometimes confusing jurisdictional framework. To improve the country’s MPA performance and overcome the main policy weaknesses, the study recommended that attention be given to the five key policy areas of (i) clarification on jurisdictional and institutional overlap, (ii) institutionalisation of community-based and co-management arrangements, (iii) building legitimacy and support with local communities, (iv) tighter prescriptions for biophysical design, and (v) mainstreaming contemporary theory and practice into core policies. Many aspects of planning and management from the Raja Ampat Islands MPA can help guide the development of tighter national policy settings. The findings presented in the thesis may be used to provide a better understanding of how Indonesia’s MPA performance can be enhanced

The Genomic Context and Corecruitment of SP1 Affect ERRα Coactivation by PGC-1α in Muscle Cells

The peroxisome proliferator-activated receptor-γ coactivator 1α (PGC-1α) coordinates the transcriptional network response to promote an improved endurance capacity in skeletal muscle, eg, by coactivating the estrogen-related receptor-α (ERRα) in the regulation of oxidative substrate metabolism. Despite a close functional relationship, the interaction between these 2 proteins has not been studied on a genomic level. We now mapped the genome-wide binding of ERRα to DNA in a skeletal muscle cell line with elevated PGC-1α and linked the DNA recruitment to global PGC-1α target gene regulation. We found that, surprisingly, ERRα coactivation by PGC-1α is only observed in the minority of all PGC-1α recruitment sites. Nevertheless, a majority of PGC-1α target gene expression is dependent on ERRα. Intriguingly, the interaction between these 2 proteins is controlled by the genomic context of response elements, in particular the relative GC and CpG content, monomeric and dimeric repeat-binding site configuration for ERRα, and adjacent recruitment of the transcription factor specificity protein 1. These findings thus not only reveal a novel insight into the regulatory network underlying muscle cell plasticity but also strongly link the genomic context of DNA-response elements to control transcription factor-coregulator interactions

Risk of cardiovascular diseases after Hodgkin lymphoma treatment

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