The life and death of gene families

@article{Demuth2009TheLA,
  title={The life and death of gene families},
  author={Jeffery P. Demuth and Matthew W. Hahn},
  journal={BioEssays},
  year={2009},
  volume={31}
}
One of the unique insights provided by the growing number of fully sequenced genomes is the pervasiveness of gene duplication and gene loss. Indeed, several metrics now suggest that rates of gene birth and death per gene are only 10–40% lower than nucleotide substitutions per site, and that per nucleotide, the consequent lineage‐specific expansion and contraction of gene families may play at least as large a role in adaptation as changes in orthologous sequences. While gene family evolution is… 
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References

SHOWING 1-10 OF 117 REFERENCES
Estimating the tempo and mode of gene family evolution from comparative genomic data.
TLDR
A model of stochastic birth and death for gene family evolution is used and it is shown that it can be efficiently applied to multispecies genome comparisons and offers both the opportunity to identify large-scale patterns in genome evolution and the ability to make stronger inferences regarding the role of natural selection.
Gene Family Evolution across 12 Drosophila Genomes
TLDR
The results demonstrate that the apparent stasis in total gene number among species has masked rapid turnover in individual gene gain and loss, and it is likely that this genomic revolving door has played a large role in shaping the morphological, physiological, and metabolic differences among species.
The Evolution of Mammalian Gene Families
TLDR
Analysis of the gene families contained within the whole genomes of human, chimpanzee, mouse, rat, and dog finds that more than half of the 9,990 families present in the mammalian common ancestor have either expanded or contracted along at least one lineage.
The evolutionary demography of duplicate genes
TLDR
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.
Positive selection of a gene family during the emergence of humans and African apes
TLDR
The rapidity and bias for amino-acid-altering nucleotide changes suggest adaptive evolution of the morpheus gene family during the emergence of humans and African apes.
Accelerated Rate of Gene Gain and Loss in Primates
TLDR
Using a novel method that allows estimation of rate heterogeneity among lineages, it is found that the rate of gene turnover in humans is more than 2.5 times faster than in other mammals and may be due to both mutational and selective forces.
Lineage-specific gene expansions in bacterial and archaeal genomes.
TLDR
Analysis of 21 completely sequenced prokaryotic genomes shows that lineage-specific expansions comprise a substantial fraction (approximately 5%-33%) of their coding capacities, and a positive correlation exists between the fraction of the genes taken up by lineage- specific expansions and the total number of genes in a genome.
Birth and death of orphan genes in Rickettsia.
TLDR
This analysis demonstrates that gene sequences present in the common ancestor can be inferred even in cases when no full-length open reading frame is present in any of the contemporary species.
Modeling gene and genome duplications in eukaryotes.
TLDR
An evolutionary model that simulates the duplication dynamics of genes, considering genome-wide duplication events and a continuous mode of gene duplication is presented and it is shown that gene loss is strikingly different for large-scale and small-scale duplication Events and highly biased toward certain functional classes.
Gene family evolution and homology: genomics meets phylogenetics.
TLDR
It is shown how the phylogenetic approach makes possible novel kinds of comparative analysis, including detection of domain shuffling and lateral gene transfer, reconstruction of the evolutionary diversification of gene families, tracing of evolutionary change in protein function at the amino acid level, and prediction of structure-function relationships.
...
1
2
3
4
5
...