Nucleic Acids Research Advance Access originally published online on February 12, 2009
Nucleic Acids Research 2009 37(4):1011-1034; doi:10.1093/nar/gkp089
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2009, Vol. 37, No. 4 1011-1034
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Survey and Summary |
Darwinian evolution in the light of genomics
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
*To whom correspondence should be addressed. Tel: 301 496 2477 (Ext 294); Fax: 30 480 9241; Email: koonin{at}ncbi.nlm.nih.gov
Received January 9, 2009. Revised January 30, 2009. Accepted February 4, 2009.
Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or ‘forest’ of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  L. Boto Horizontal gene transfer in evolution: facts and challenges Proc R Soc B, March 22, 2010; 277(1683): 819 - 827. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. Martin Evolutionary origins of metabolic compartmentalization in eukaryotes Phil Trans R Soc B, March 12, 2010; 365(1541): 847 - 855. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. K. Aziz, M. Breitbart, and R. A. Edwards Transposases are the most abundant, most ubiquitous genes in nature Nucleic Acids Res., March 9, 2010; (2010) gkq140v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Carmel and E. V. Koonin A Universal Nonmonotonic Relationship between Gene Compactness and Expression Levels in Multicellular Eukaryotes Gen Biol Evol, March 1, 2010; 2009(0): 382 - 390. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. X. Chan, R. G. Beiko, A. E. Darling, and M. A. Ragan Lateral Transfer of Genes and Gene Fragments in Prokaryotes Gen Biol Evol, March 1, 2010; 2009(0): 429 - 438. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. W. Bloomquist and M. A. Suchard Unifying Vertical and Nonvertical Evolution: A Stochastic ARG-based Framework Syst Biol, January 1, 2010; 59(1): 27 - 41. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Carter and G. Drouin The Evolutionary Rates of Eukaryotic RNA Polymerases and of Their Transcription Factors Are Affected by the Level of Concerted Evolution of the Genes They Transcribe Mol. Biol. Evol., November 1, 2009; 26(11): 2515 - 2520. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E.V. Koonin, Y.I. Wolf, and P. Puigbo The Phylogenetic Forest and the Quest for the Elusive Tree of Life Cold Spring Harb Symp Quant Biol, August 17, 2009; (2009) sqb.2009.74.006v1. [Abstract] [PDF]
|
|
|
|
 |
|
 D. Y. Lee and K. C. P. Li Systems Diagnostics: The Systems Approach to Molecular Imaging Am. J. Roentgenol., August 1, 2009; 193(2): 287 - 294. [Abstract] [Full Text] [PDF]
|
|