Phylogenetic information complexity: Is testing a tree easier than finding it?

Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following question: is the amount of sequence data required to accurately reconstruct a tree significantly more than the amount required to test whether or not a candidate tree was the `true' tree? By `significantly', we mean that the two quantities behave the same way as a function of the number of species being considered. We prove that, for a certain type of model, the amount of information required is not significantly different; while for another type of model, the information required to test a tree is independent of the number of leaves, while that required to reconstruct it grows with this number. Our results combine probabilistic and combinatorial arguments.Comment: 15 pages, 3 figure

Adamawa primary education research: final report

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An HMM-based Comparative Genomic Framework for Detecting Introgression in Eukaryotes

One outcome of interspecific hybridization and subsequent effects of evolutionary forces is introgression, which is the integration of genetic material from one species into the genome of an individual in another species. The evolution of several groups of eukaryotic species has involved hybridization, and cases of adaptation through introgression have been already established. In this work, we report on a new comparative genomic framework for detecting introgression in genomes, called PhyloNet-HMM, which combines phylogenetic networks, that capture reticulate evolutionary relationships among genomes, with hidden Markov models (HMMs), that capture dependencies within genomes. A novel aspect of our work is that it also accounts for incomplete lineage sorting and dependence across loci. Application of our model to variation data from chromosome 7 in the mouse (Mus musculus domesticus) genome detects a recently reported adaptive introgression event involving the rodent poison resistance gene Vkorc1, in addition to other newly detected introgression regions. Based on our analysis, it is estimated that about 12% of all sites withinchromosome 7 are of introgressive origin (these cover about 18 Mbp of chromosome 7, and over 300 genes). Further, our model detects no introgression in two negative control data sets. Our work provides a powerful framework for systematic analysis of introgression while simultaneously accounting for dependence across sites, point mutations, recombination, and ancestral polymorphism

What is ‘mental action’?

There has been a resurgence of interest lately within philosophy of mind and action in the category of mental action. Against this background, the present paper aims to question the very possibility, or at least the theoretical significance, of teasing apart mental and bodily acts. After raising some doubts over the viability of various possible ways of drawing the mental act/bodily act distinction, the paper draws some lessons from debates over embodied cognition, which arguably further undermine the credibility of the distinction. The insignificance of the distinction is demonstrated in part by showing how the focus on ‘inner’ acts hampers fruitful discussion of Galen Strawson’s skepticism of mental agency. Finally, the possibility is discussed that a distinction between covert and overt action should supplant the one between mental and bodily action

Indigenous Ecology and Chicanada Coalition Building in the dramatic works of Cherríe Moraga: “Living Models” for a Sustainable Future

Abstract: This study focuses on three recent dramatic works by Cherríe Moraga’s written in the same period as her essay and poetry collection, The Last Generation. Heroes and Saints, Watsonville: Some Place Not Here, and Circle in the Dirt: El Pueblo de East Palo Alto draw from indigenous ecology and the historical archive of Chicano struggle that provide models for a sustainable future she envisions. The author shifts from poetry and essay - the lyrical, reflective mode of self-inquiry and expression for which she is so well known – to a collective dramatic dialogue allowing her to represent the diversity of perspectives that have always existed within and around Chicano communities. Through this plurality she is able to give voice to marginalized perspectives and exhibit the ingeniousness and courage behind a long tradition of Chicano coalition building that will be necessary for global alliances of collective resistance. As Chicano activist theater originated with Luis Valdez’s Teatro Campesino associated with United Farmer Workers Union and later with the Chicano Movement, Moraga’s plays are situated within the tradition of Chicano environmental political struggle. These works are infused with the author’s interpretation of an indigenous ecology that conflates her interlaced political discourses on race, sexuality, gender, community, nationalism, and art with a holistic view of the earth. Contributing to a tradition of Chicano environmental discourse and the global indigenous struggle for sovereignty, her work brings together and challenges the assumptions of ecocriticism, ecofeminism and American environmental and naturalist writing particularly in terms of race and class. In these works, Moraga prioritizes the wellbeing of those who dwell in or work the land as opposed to “pristine” open spaces perceived as untouched by human hands

Spatial patterns of tree yield explained by endogenous forces through a correspondence between the Ising model and ecology.

Spatial patterning of periodic dynamics is a dramatic and ubiquitous ecological phenomenon arising in systems ranging from diseases to plants to mammals. The degree to which spatial correlations in cyclic dynamics are the result of endogenous factors related to local dynamics vs. exogenous forcing has been one of the central questions in ecology for nearly a century. With the goal of obtaining a robust explanation for correlations over space and time in dynamics that would apply to many systems, we base our analysis on the Ising model of statistical physics, which provides a fundamental mechanism of spatial patterning. We show, using 5 y of data on over 6,500 trees in a pistachio orchard, that annual nut production, in different years, exhibits both large-scale synchrony and self-similar, power-law decaying correlations consistent with the Ising model near criticality. Our approach demonstrates the possibility that short-range interactions can lead to long-range correlations over space and time of cyclic dynamics even in the presence of large environmental variability. We propose that root grafting could be the common mechanism leading to positive short-range interactions that explains the ubiquity of masting, correlated seed production over space through time, by trees

MEGA: merger graphs of structure formation

When following the growth of structure in the Universe, we propose replacing merger trees with merger graphs, in which haloes can both merge and split into separate pieces. We show that this leads to smoother mass growth and eliminates catastrophic failures in which massive haloes have no progenitors or descendants. For those who prefer to stick with merger trees, we find that trees derived from our merger graphs have similar mass growth properties to previous methods, but again without catastrophic failures. For future galaxy formation modelling, two different density thresholds can be used to distinguish host haloes (extended galactic haloes, groups and clusters) from higher-density subhaloes: sites of galaxy formation