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What Is The Tree of Life?

  • Authors: W. Ford Doolittle , Tyler D. P. Brunet
  • Published in PLoS Genetics: April 14, 2016

Abstract

A universal Tree of Life (TOL) has long been a goal of molecular phylogeneticists, but reticulation at the level of genes and possibly at the levels of cells and species renders any simple interpretation of such a TOL, especially as applied to prokaryotes, problematic.

Introduction

“One of the several ways in which microbiology puts the neo-Darwinian synthesis in jeopardy is by the threatening to ‘uproot the Tree of Life’. Lateral gene transfer (LGT) is much more frequent than most biologists would have imageind up until about 20 years ago, so phylogenetic trees based on sequences of different prokayrotic genes are often different. How to tease out from such conflicting data something that might correspond to a single, universal Tree of Life becomes problematic. Moreover, since many important evolutionary transitions involve lineage fusions at one level or another, the aptness of a tree (a pattern of successive bifurcations) as a summary of life’s history is uncertain.

Darwin’s Tree of Life Hypothesis

  • “Before 1859, hierarchical (tree-like) patterns of organismal relationships were commonly drawn and taken to mirror some natural order, most likely divine. What Darwin gave us when he published The Origin of Species was a nontheistic reason for the discoverability and utility of such classifications.”
  • Darwin wrote ‘Community of descent is the hidden bond which naturalists have been unconsciously seeking, and not some unknown plan of creation.’
  • “There was to be an actual TOL whose ‘ramifying branches may well represent the classification of all extinct and living species in groups subordinate to groups’.”
  • Bapteste and Doolittle have called this claim by Darwin his “TOL Hypothesis”–that is, that the tree-like pattern of relationships recognized by systematists reflects an underlying tree-like evolutionary process.
  • “After Darwin, classifications were most often assumed without proof to be evolutionary: phenetics was taken to be identical to phylogenetics…Not much could be done to improve on this as long as the methods of comparative biology (mostly anatomical) remained the basis for classification, as they had been for centuries.”
  • BUT…“in the mid-1960s, molecular sequencing (First rRNA, then genes, and now complete genomes) appeared to offer a way out of such circularity, a possible independent proof of the TOL hypothesis.
  • Zuckerkandl and Pauling famously wrote: ‘…molecular phylogenetic trees should in principle be definable in terms of molecular information alone. It will be determined to what extent the phylogenetic tree, as derived from molecular data in complete independendence of organismal biology, coincices with the tree constructed on the basis of organismal biology…[and thus]…If the two trees are mostly in agreement with the topology of the branching, the best available single proof of the reality of macro-evolution would be furnished.’

Nearly Universal Trees and the Statistical Tree of Life

  • See p. 3 for following terms.
    • TOL = Tree of Life
    • FOL = Forest of Life
    • 102 NUTs = Nearly Universal Trees
    • STOL = the Statistical Tree of Life
    • Complexity hypothesis (p. 3 of 7)
      • “The complexity hypothesis is the notion that genes whos products interact with the products of many others will have so many coevolved molecular dependencies that [those genes’] function in a distantly related cellular environment is impaired.”
      • Therefore, “connectivity (as defined by the number of protein-protein interactions)…is the key determinnat and there are highly connected systems other than translation in many cells.”
      • “So it may be equally relevant that translation and transciption are conservative and essential cellular activites, while may frequently transferred genes unction in “optional” metabolic systems, representing alternative and therefore evolutionarily more changeable ways cells can make livings.”

Pangenomics

  • count of “core genes” and similarity/difference of gene complements across various species in the genus Escherichia as compared to non bacteria.