Statistics of Certain Models of Evolution

In a recent paper, Newman surveys the literature on power law spectra in evolution, self-organised criticality and presents a model of his own to arrive at a conclusion that self-organised criticality is not necessary for evolution. Not only did he miss a key model (Ecolab) that has a clear self-organised critical mechanism, but also Newman's model exhibits the same mechanism that gives rise to power law behaviour as does Ecolab. Newman's model is, in fact, a ``mean field'' approximation of a self-organised critical system. In this paper, I have also implemented Newman's model using the Ecolab software, removing the restriction that the number of species remains constant. It turns out that the requirement of constant species number is non-trivial, leading to a global coupling between species that is similar in effect to the species interactions seen in Ecolab. In fact, the model must self-organise to a state where the long time average of speciations balances that of the extinctions, otherwise the system either collapses or explodes. In view of this, Newman's model does not provide the hoped-for counter example to the presence of self-organised criticality in evolution, but does provide a simple, almost analytic model that can used to understand more intricate models such as Ecolab.Comment: accepted in Phys Rev E.; RevTeX; See http://parallel.hpc.unsw.edu.au/rks/ecolab.html for more informatio

Fully Bayesian tests of neutrality using genealogical summary statistics

<p>Abstract</p> <p>Background</p> <p>Many data summary statistics have been developed to detect departures from neutral expectations of evolutionary models. However questions about the neutrality of the evolution of genetic loci within natural populations remain difficult to assess. One critical cause of this difficulty is that most methods for testing neutrality make simplifying assumptions simultaneously about the mutational model and the population size model. Consequentially, rejecting the null hypothesis of neutrality under these methods could result from violations of either or both assumptions, making interpretation troublesome.</p> <p>Results</p> <p>Here we harness posterior predictive simulation to exploit summary statistics of both the data and model parameters to test the goodness-of-fit of standard models of evolution. We apply the method to test the selective neutrality of molecular evolution in non-recombining gene genealogies and we demonstrate the utility of our method on four real data sets, identifying significant departures of neutrality in human influenza A virus, even after controlling for variation in population size.</p> <p>Conclusion</p> <p>Importantly, by employing a full model-based Bayesian analysis, our method separates the effects of demography from the effects of selection. The method also allows multiple summary statistics to be used in concert, thus potentially increasing sensitivity. Furthermore, our method remains useful in situations where analytical expectations and variances of summary statistics are not available. This aspect has great potential for the analysis of temporally spaced data, an expanding area previously ignored for limited availability of theory and methods.</p

IL-10 transcription is negatively regulated by BAF180, a component of the SWI/SNF chromatin remodeling enzyme

<p>Abstract</p> <p>Background</p> <p>SWI/SNF chromatin remodeling enzymes play a critical role in the development of T helper lymphocytes, including Th2 cells, and directly program chromatin structure at Th2 cytokine genes. Different versions of SWI/SNF complexes, including BAF and PBAF, have been described based on unique subunit composition. However, the relative role of BAF and PBAF in Th cell function and cytokine expression has not been reported.</p> <p>Results</p> <p>Here we examine the role of the PBAF SWI/SNF complex in Th cell development and gene expression using mice deficient for a PBAF-specific component, BAF180. We find that T cell development in the thymus and lymphoid periphery is largely normal when the BAF180 gene is deleted late in thymic development. However, BAF180-deficient Th2 cells express high levels of the immunoregulatory cytokine IL-10. BAF180 binds directly to regulatory elements in the Il-10 locus but is replaced by BAF250 BAF complexes in the absence of BAF180, resulting in increased histone acetylation and CBP recruitment to the IL-10 locus.</p> <p>Conclusions</p> <p>These results demonstrate that BAF180 is a repressor of IL-10 transcription in Th2 cells and suggest that the differential recruitment of different SWI/SNF subtypes can have direct consequences on chromatin structure and gene transcription.</p

Complex Interplay of Evolutionary Forces in the ladybird Homeobox Genes of Drosophila melanogaster

Tandemly arranged paralogous genes lbe and lbl are members of the Drosophila NK homeobox family. We analyzed population samples of Drosophila melanogaster from Africa, Europe, North and South America, and single strains of D. sechellia, D. simulans, and D. yakuba within two linked regions encompassing partial sequences of lbe and lbl. The evolution of lbe and lbl is highly constrained due to their important regulatory functions. Despite this, a variety of forces have shaped the patterns of variation in lb genes: recombination, intragenic gene conversion and natural selection strongly influence background variation created by linkage disequilibrium and dimorphic haplotype structure. The two genes exhibited similar levels of nucleotide diversity and positive selection was detected in the noncoding regions of both genes. However, synonymous variability was significantly higher for lbe: no nonsynonymous changes were observed in this gene. We argue that balancing selection impacts some synonymous sites of the lbe gene. Stability of mRNA secondary structure was significantly different between the lbe (but not lbl) haplotype groups and may represent a driving force of balancing selection in epistatically interacting synonymous sites. Balancing selection on synonymous sites may be the first, or one of a few such observations, in Drosophila. In contrast, recurrent positive selection on lbl at the protein level influenced evolution at three codon sites. Transcription factor binding-site profiles were different for lbe and lbl, suggesting that their developmental functions are not redundant. Combined with our previous results on nucleotide variation in esterase and other homeobox genes, these results suggest that interplay of balancing and directional selection may be a general feature of molecular evolution in Drosophila and other eukaryote genomes

Population genetics from 1966 to 2016

We describe the astonishing changes and progress that have occurred in the field of population genetics over the past 50 years, slightly longer than the time since the first Population Genetics Group (PGG) meeting in January 1968. We review the major questions and controversies that have preoccupied population geneticists during this time (and were often hotly debated at PGG meetings). We show how theoretical and empirical work has combined to generate a highly productive interaction involving successive developments in the ability to characterise variability at the molecular level, to apply mathematical models to the interpretation of the data and to use the results to answer biologically important questions, even in nonmodel organisms. We also describe the changes from a field that was largely dominated by UK and North American biologists to a much more international one (with the PGG meetings having made important contributions to the increased number of population geneticists in several European countries). Although we concentrate on the earlier history of the field, because developments in recent years are more familiar to most contemporary researchers, we end with a brief outline of topics in which new understanding is still actively developing