Category Archives: Publications

Inference and informatics in a ‘sequenced’ world

Short lecture relating my recent work on real-time phylogenomics, implications for bioinformatics research and future directions of genomic/phylogenetic modelling to explicitly account for phylogeny, synteny and identity through coloured graphs.

University of Reading, 2nd August 2017

Slides [SlideShare]: cc-by-nd


Using field-based DNA sequencing to accelerate phylogenomics

Invited seminar at the Department of Zoology, Oxford University, 30th November 2016.

Summary of our field-based real-time phylogenomics (MinION DNA sequencing) experiments this year, and applicability to broad-scale tree-of-life phylogenomics and macroevolutionary biology.

Slides [SlideShare]: cc-by-nd


Single-molecule real-time (SMRT) Nanopore sequencing for Plant Pathology applications

A short presentation to the British Society for Plant Pathology’s ‘Grand Challenges in Plant Pathology’ workshop on the uses of real-time DNA/RNA sequencing technology for plant health applications.

Doctoral Training Centre, University of Oxford, 14th September 2016.

Slides [SlideShare]: cc-by-nc-nd


Application note: ‘Befi-BaTS’ version 0.10.1 – Error rate and statistical power of distance-based measures of phylogeny-trait association.

In prep.

SUMMARY

Building on work presented previously (Parker et al., 2008), we study a number of more complex measures of phylogeny-trait association (implemented in the program Befi-BaTS / BaTS v0.10.1) which take into account the branch lengths of a phylogenetic tree in addition to the topographical relationship between taxa. Extensive simulation is performed to measure the Type II error rate (statistical power) of these statistics including those introduced in Parker et al. (2008), as well as the relationship between power and tree shape. The technique is applied to an empirical hepatitis C virus data set presented by Sobesky et al. (2007); their original conclusion that compartmentalization exists between viruses sampled from tumorous and non-tumorous cirrhotic nodules and the plasma is upheld. The association index (AI), migration (PS), phylodynamic diversity (PD) and unique fraction (UF) statistics offer the best combination of Type I error and statistical power to investigate phylogeny-trait association in RNA virus data, while the maximum monophyletic clade size (MC) and nearest taxon (NT) statistics suffer from reduced power in some regions of tree space.

Keywords: BaTS, hepatitis C virus, Markov-chain Monte Carlo, Phylogeny-trait association, Phylogenetic uncertainty, simulation.

Manuscripts in progress (all rights reserved – you may not copy or distribute these files; content and conclusions subject to change; strictly embargoed until publication in a peer-reviewed journal/book):

  • v1: (): .doc
  • v2 (01/01/2014): .docx
  • v3 (16/06/2017): .pdf
  • View this project on GitHub

 

Application note: CONTEXT, a Phylogenomic Dataset Browser

In prep. (v3 – 14 Jun 2017)

Summary. The CONTEXT (COmparative Nucleotides and Trees Exploration Tool) is a phylogenomics dataset browser that consists of a Java API and an executable binary jarfile with graphical user interface (GUI) for the high-throughput analysis of phylogenomic datasets to detect convergent molecular evolution.

Motivation. Comparative genomics studies have become increasingly common, but these analyses are sensitive to the quality and heterogeneity of input datasets (multiple sequence analyses and phylogenies). Currently few tools exist to readily compute descriptive statistics, or to visualise large numbers of input datasets. CONTEXT facilitates these analyses in a lightweight application which allows any user to rapidly visualise, inspect, score, and sort input datasets to identify outlying datasets which may need additional processing or filtering.

Results. The application has been successfully implemented on a variety of infrastructures. A variety of common input data formats including FASTA, Phylip/PAML, Nexus, and Newick conventions are automatically read and parsed.

 

Manuscripts in progress (all rights reserved – you may not copy or distribute these files; content and conclusions subject to change; strictly embargoed until publication in a peer-reviewed journal/book):

 

  • v3 (14/07/2017): .pdf
  • v2 (03/04/2017): .pdf
  • v1 (24/02/2015): .doc
  • View this project on GitHub

Detection of molecular convergence – literature review

In prep. (v2 – 21 April 2015)

Abstract

Convergent evolution is a process by which neutral evolutionary processes and adaptive natural selection in response to niche specialisation lead to similar forms arising in unrelated taxa. Phenotypic convergence has been appreciated for well over a century (recognised as a confounding factor in morphological cladistics). Recently several studies have demonstrated that convergent-type signals exist in some molecular datasets. Extending these studies to genome scale data presents substantial challenges and opportunities. This chapter reviews the definition of convergence (compared to parallelism), and the biological interpretation of apparently convergent molecular data. Recent methodological developments and applications are examined and future problems outlined. These include suitable null and alternative models, and the role of multiple test phylogenies in convergence detection by the congruence / phylogeny support method.

 

Manuscripts in progress (all rights reserved – you may not copy or distribute these files; content and conclusions subject to change; strictly embargoed until publication in a peer-reviewed journal/book):

 

  • v1 (10/04/2015): .doc
  • v2 (21/04/2015): .doc