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Title: Bayesian Analysis of Congruence of Core Genes in Prochlorococcus and Synechococcus and Implications on Horizontal Gene Transfer

Journal Article · · PLoS ONE
 [1];  [2];  [3]
  1. Univ. of Tennessee, Knoxville, TN (United States); Univ. of California, Berkeley, CA (United States)
  2. Univ. of California, Berkeley, CA (United States)
  3. Univ. of California, Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
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It is often suggested that horizontal gene transfer is so ubiquitous in microbes that the concept of a phylogenetic tree representing the pattern of vertical inheritance is oversimplified or even positively misleading. “Universal proteins” have been used to infer the organismal phylogeny, but have been criticized as being only the “tree of one percent.” Currently, few options exist for those wishing to rigorously assess how well a universal protein phylogeny, based on a relative handful of well-conserved genes, represents the phylogenetic histories of hundreds of genes. Here, we address this problem by proposing a visualization method and a statistical test within a Bayesian framework. We use the genomes of marine cyanobacteria, a group thought to exhibit substantial amounts of HGT, as a test case. We take 379 orthologous gene families from 28 cyanobacteria genomes and estimate the Bayesian posterior distributions of trees – a “treecloud” – for each, as well as for a concatenated dataset based on putative “universal proteins.” We then calculate the average distance between trees within and between all treeclouds on various metrics and visualize this high-dimensional space with non-metric multidimensional scaling (NMMDS). We show that the tree space is strongly clustered and that the universal protein treecloud is statistically significantly closer to the center of this tree space than any individual gene treecloud. We apply several commonly-used tests for incongruence/HGT and show that they agree HGT is rare in this dataset, but make different choices about which genes were subject to HGT. Our results show that the question of the representativeness of the “tree of one percent” is a quantitative empirical question, and that the phylogenetic central tendency is a meaningful observation even if many individual genes disagree due to the various sources of incongruence.

Research Organization:
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
Sponsoring Organization:
USDOE; National Science Foundation (NSF)
Grant/Contract Number:
AC02-05CH11231; DEB-0919451; MCB-0851070
OSTI ID:
1904063
Journal Information:
PLoS ONE, Vol. 9, Issue 1; ISSN 1932-6203
Publisher:
Public Library of ScienceCopyright Statement
Country of Publication:
United States
Language:
English

References (43)

Lateral gene transfer and the nature of bacterial innovation journal May 2000
Overlapping confidence intervals or standard error intervals: What do they mean in terms of statistical significance? journal October 2003
Taxonomic Sampling, Phylogenetic Accuracy, and Investigator Bias journal March 1998
Reticulate evolution and incomplete lineage sorting among the ponderosa pines journal August 2009
Visualizing and Assessing Phylogenetic Congruence of Core Gene Sets: A Case Study of the γ-Proteobacteria journal February 2006
Null Models for the Number of Evolutionary Steps in a Character on a Phylogenetic Tree journal August 1991
A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach journal May 2001
Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus journal January 2009
Likelihood-Based Tests of Topologies in Phylogenetics journal December 2000
Compositional dissimilarity as a robust measure of ecological distance journal April 1987
CONSEL: for assessing the confidence of phylogenetic tree selection journal December 2001
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing journal March 2002
Search for a 'Tree of Life' in the thicket of the phylogenetic forest journal January 2009
Lateral gene transfer journal April 2011
An Approximately Unbiased Test of Phylogenetic Tree Selection journal May 2002
Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution journal July 2008
Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus journal January 2007
Plastid Genome Phylogeny and a Model of Amino Acid Substitution for Proteins Encoded by Chloroplast DNA journal April 2000
Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events journal August 2006
From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the γ-Proteobacteria journal September 2003
Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference journal August 1999
The integrated microbial genomes (IMG) system journal January 2006
Random Addition Concatenation Analysis: A Novel Approach to the Exploration of Phylogenomic Signal Reveals Strong Agreement between Core and Shell Genomic Partitions in the Cyanobacteria journal November 2011
Genomes as documents of evolutionary history journal April 2010
Transfer of photosynthesis genes to and from Prochlorococcus viruses journal July 2004
Genome evolution in cyanobacteria: The stable core and the variable shell journal February 2008
MAFFT version 5: improvement in accuracy of multiple sequence alignment journal January 2005
Evolution of patterns on Conus shells journal January 2012
Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima journal May 1999
DendroPy: a Python library for phylogenetic computing journal April 2010
MrBayes 3: Bayesian phylogenetic inference under mixed models journal August 2003
The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer journal August 2005
Profile hidden Markov models journal October 1998
Genomes of Stigonematalean Cyanobacteria (Subsection V) and the Evolution of Oxygenic Photosynthesis from Prokaryotes to Plastids journal December 2012
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea journal December 2009
Analysis and Visualization of Tree Space journal June 2005
Bayesian Estimation of Concordance among Gene Trees journal November 2006
The Discovery and Importance of Multiple Islands of Most-Parsimonious Trees journal September 1991
The cyanobacterial genome core and the origin of photosynthesis journal August 2006
An evaluation of the relative robustness of techniques for ecological ordination journal April 1987
Eradicating Typological Thinking in Prokaryotic Systematics and Evolution journal January 2009
Null Models for the Number of Evolutionary Steps in a Character on a Phylogenetic tree journal August 1991
Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus journal January 2005

Cited By (1)

Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite journal April 2015

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
phylogenetic analysis
phylogenetics
horizontal gene transfer
synechococcus
cyanobacteria
genomics
sequence alignment
evolutionary genetics