Peter D. Jarvis

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We explore model-based techniques of phylogenetic tree inference exercising Markov invariants. Markov invariants are group invariant polynomials and are distinct from what is known in the literature as phylogenetic invariants, although we establish a commonality in some special cases. We show that the simplest Markov invariant forms the foundation of the(More)
Recent work has discussed the importance of multiplicative closure for the Markov models used in phylogenetics. For continuous-time Markov chains, a sufficient condition for multiplicative closure of a model class is ensured by demanding that the set of rate-matrices belonging to the model class form a Lie algebra. It is the case that some well-known Markov(More)
The general time-reversible (GTR) model (Tavaré, 1986) has been the workhorse of molecular phylogenetics for the last decade. GTR sits at the top of the ModelTest hierarchy of models (Posada & Crandall, 1998) and, usually with the addition of invariant sites and a gamma distribution of rates across sites, is currently by far the most commonly selected model(More)
A 2-year retrospective review of 238 cases of acute scrotal pain encountered in a children's hospital emergency department is presented. The incidences of testicular torsion, torsion of a testicular appendage, and epididymitis were 16%, 46%, and 35%, respectively. Testicular salvage was critically dependent on the interval between onset of pain and surgical(More)
It is possible to consider stochastic models of sequence evolution in phylogenetics in the context of a dynamical tensor description inspired from physics. Approaching the problem in this framework allows for the well developed methods of mathematical physics to be exploited in the biological arena. We present the tensor description of the homogeneous(More)
It is known that the Kimura 3ST model of sequence evolution on phylogenetic trees can be extended quite naturally to arbitrary split systems. However, this extension relies heavily on mathematical peculiarities of the associated Hadamard transformation, and providing an analogous augmentation of the general Markov model has thus far been elusive. In this(More)
The purpose of this article is to show how the isotropy subgroup of leaf permutations on binary trees can be used to systematically identify tree-informative invariants relevant to models of phylogenetic evolution. In the quartet case, we give an explicit construction of the full set of representations and describe their properties. We apply these results(More)
Continuous-time Markov chains are a standard tool in phylogenetic inference. If homogeneity is assumed, the chain is formulated by specifying time-independent rates of substitutions between states in the chain. In applications, there are usually extra constraints on the rates, depending on the situation. If a model is formulated in this way, it is possible(More)
PURPOSE Bladder resistance to bacterial infection after gastrocystoplasty, ileocystoplasty and cecocystoplasty was investigated in the rat. MATERIALS AND METHODS Bladders were infected with Escherichia coli 6 to 13 months after augmentation and urine culture was obtained weekly for 3 months. RESULTS No differences were observed in the number of infected(More)