Constructing Phylogenetic Networks based on Trinets

Abstract The motivation of phylogenetic analysis is to discover the evolutionary relationships between species, with the broader aim of understanding the origins of life. Our understanding of the molecular character- istics of species through DNA sequencing permanently changed the approach to understanding the evolution of species. Indeed, the ad- vancement of technology has played a major role in the fast sequencing of DNA as well as the use of computers in solving biological problems in general. These evolutionary relationships are often visualised and represented using a phylogenetic tree. As a natural generalisation of phylogenetic trees, phylogenetic networks are used in biology to rep- resent evolutionary histories that contain reticulate, or non-treelike events such as recombination, hybridisation and horizontal gene trans- fer. The reconstruction of explicit phylogenetic networks from biolog- ical data is currently an active area of phylogenetics research. Here we consider the problem of constructing such networks from trinets, that is, phylogenetic networks on three leaves. More speci�cally, we present the SeqTrinet and TriLoNet methods, which form a supernet- work based approach to constructing level-1 phylogenetic networks directly from multiple sequence alignments

The Formation and Age of Leucogranitic Melt in the Garhwal Himalaya

Metamorphism during orogenic evolution results in the melting of high-grade metamorphic rocks which dramatically decreases mechanical strength, activates shear zones, and may consequently initiate exhumation. The timescales of anatexis, melt amalgamation, migration, and emplacement are the focus of active research and have critical implications for orogenic tectonic development. It is, therefore, important to recognise and distinguish between the geochemical signatures that these processes create and to delineate more precisely the relevant mechanisms and timescales leading to magma genesis. Granitic bodies and source migmatites are exposed across the Himalaya in the Greater Himalayan Sequence (GHS). Many of these granites formed as high-grade metamorphic rocks and were decompressed during the Miocene. However, exact timings of melt formation and melt mechanisms appear to vary laterally across the orogen. This thesis presents constraints on the melt reactions, sources, and timescales of melting episodes that formed the migmatites and leucogranites of the upper GHS using samples from the Alaknanda valley in the Garhwal Himalaya. Detailed petrography and geochemical characterisation of feldspars, micas, and garnet reveal melt reaction systematics through peritectic crystallisation textures and large-ion lithophile element concentrations. Samples are identified with predominately fluid-present, muscovite-dehydration, and biotite-dehydration melting contributions. Combined zircon and monazite geochronology suggests partial melting occurred over an extended period, from 35 to 14 Ma, with melt production sharply increasing around 25 Ma and reaching its peak at 21 Ma, primarily attributed to muscovite-dehydration. Zircon εHf values show little systematic variation with age, suggesting a geochemically-common source of melt. Successive episodes of melt generation around peak metamorphic conditions likely weakened the mid-crustal GHS, priming it for exhumation and subsequent decompression melting

TriLoNet: Piecing together small networks to reconstruct reticulate evolutionary histories

Phylogenetic networks are a generalisation of evolutionary trees that can be used to represent reticulate processes such as hybridisation and recombination. Here we introduce a new approach called TriLoNet to construct such networks directly from sequence alignments which works by piecing together smaller phylogenetic networks. More specifically, using a bottom up approach similar to Neighbor-Joining, TriLoNet constructs level-1 networks (networks that are somewhat more general than trees) from smaller level-1 networks on three taxa. In simulations we show that TriLoNet compares well with Lev1athan, a method for reconstructing level-1 networks from three-leaved trees. In particular, in simulations we find that Lev1athan tends to generate networks that overestimate the number of reticulate events as compared with those generated by TriLoNet. We also illustrate TriLoNet’s applicability using simulated and real sequence data involving recombination, demonstrating that it has the potential to reconstruct informative reticulate evolutionary histories. TriLoNet has been implemented in JAVA and is freely available at https://www.uea.ac.uk/computing/TriLoNet

A cubic-time algorithm for computing the trinet distance between level-1 networks

In evolutionary biology, phylogenetic networks are constructed to represent the evolution of species in which reticulate events are thought to have occurred, such as recombination and hybridization. It is therefore useful to have efficiently computable metrics with which to systematically compare such networks. Through developing an optimal algorithm to enumerate all trinets displayed by a level-1 network (a type of network that is slightly more general than an evolutionary tree), here we propose a cubic-time algorithm to compute the trinet distance between two level-1 networks. Employing simulations, we also present a comparison between the trinet metric and the so-called Robinson-Foulds phylogenetic network metric restricted to level-1 networks. The algorithms described in this paper have been implemented in JAVA and are freely available at (https://www.uea.ac.uk/computing/TriLoNet

Effects of Patellar Taping on Knee Joint Proprioception

Introduction Although patellar taping is readily used in the treatment of patients with patellofemoral pain syndrome, doubts still exist as to the mechanism for its success. Patellar instability is often an area of concern with many forms of corrective treatment being instigated. It has been proposed tha