The Origins of Genome Complexity

  title={The Origins of Genome Complexity},
  author={Michael Lynch and John S. Conery},
  pages={1401 - 1404}
Complete genomic sequences from diverse phylogenetic lineages reveal notable increases in genome complexity from prokaryotes to multicellular eukaryotes. The changes include gradual increases in gene number, resulting from the retention of duplicate genes, and more abrupt increases in the abundance of spliceosomal introns and mobile genetic elements. We argue that many of these modifications emerged passively in response to the long-term population-size reductions that accompanied increases in… 

Streamlining and simplification of microbial genome architecture.

  • M. Lynch
  • Biology
    Annual review of microbiology
  • 2006
This hypothesis provides a potentially unifying explanation for the continuity in genomic scaling from prokaryotes to multicellular eukaryotes, the divergent patterns of mitochondrial evolution in animals and land plants, and various aspects of genomic modification in microbial endosymbionts.

[Recent progress in plant genome size evolution].

The evolutionary direction of plant genome size is discussed, which tends to favor larger genomes with deletion mechanisms acting to only attenuate genome expansion but not reverse.

Evolution of Genome Size

Fine-scale investigation of the mutational and population-genetic properties of both small and large insertions and deletions should help advance the understanding of how and why genome size evolution has occurred.


It is shown that episodes of fixation of duplications in mitochondrial genomes of the gecko Heteronotia binoei and mantellid frogs coincide with reductions in the ability of selection to purge slightly deleterious mutations.

Mutation Pressure and the Evolution of Organelle Genomic Architecture

Observations provide support for the hypothesis that the fundamental features of genome evolution are largely defined by the relative power of two nonadaptive forces: random genetic drift and mutation pressure.

Reductive genome evolution at both ends of the bacterial population size spectrum

This Opinion article discusses the different hypotheses that have been proposed to account for this reductive genome evolution at both ends of the bacterial population size spectrum.

The mode and tempo of genome size evolution in eukaryotes.

It is shown that the rate of genome size evolution is proportional to genome size, with the fastest rates occurring in the largest genomes, indicating that over long time scales, proportional change is the dominant and universal mode of genome-size evolution in eukaryotes.

The Evolution of Bacterial Genome Architecture

Bacteria with small effective population sizes typically have the smallest genomes, but some marine bacteria counter this near-universal trend: despite having immense population sizes, selection, not drift, acts to reduce genome size in response to metabolic constraints in their nutrient-limited environment.

The evolutionary dynamics of transposable elements in eukaryote genomes.

The sequencing of a multitude of eukaryote genomes has revealed some striking differences in the abundance and diversity of TEs, and the importance of drift in shaping genomic architecture is emphasized.



The evolution of spliceosomal introns.

Intron evolution as a population-genetic process

  • M. Lynch
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 2002
This study provides a second example of a mechanism whereby genomic complexity originates passively as a “pathological” response to small population size, and raises difficulties for the idea that ancient introns played a major role in the origin of genes by exon shuffling.

The evolutionary fate and consequences of duplicate genes.

Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species.

Intron–Genome Size Relationship on a Large Evolutionary Scale

In contrast to previous reports, avian introns were not found to be significantly shorter than introns of mammals, although avian genomes are smaller than genomes of mammals on average by about a factor of 2.5.

Preservation of duplicate genes by complementary, degenerative mutations.

Focusing on the regulatory complexity of eukaryotic genes, it is shown how complementary degenerative mutations in different regulatory elements of duplicated genes can facilitate the preservation of both duplicates, thereby increasing long-term opportunities for the evolution of new gene functions.

The probability of preservation of a newly arisen gene duplicate.

This work examines the influence of various aspects of gene structure, mutation rates, degree of linkage, and population size on the joint fate of a newly arisen duplicate gene and its ancestral locus.

The evolutionary demography of duplicate genes

The origin of a new function appears to be a very rare fate for a duplicate gene through the generation of microchromosomal rearrangements through reciprocal silencing of alternative copies, which can lead to the passive origin of post-zygotic reproductive barriers in descendant lineages of incipient species.

Gene expression and molecular evolution.

  • H. Akashi
  • Biology
    Current opinion in genetics & development
  • 2001

High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups.

The results strongly suggest that the high rate of DNA loss is a general feature of Drosophila and not a peculiar property of a particular stretch of DNA in a particular species group.