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Segmental duplications and the evolution of the primate genome

Nature Reviews Genetics volume 3, pages 65–72 (2002)Cite this article

Abstract

Initial human genome sequence analysis has revealed large segments of nearly identical sequence in particular chromosomal regions. The recent origin of these segments and their abundance (∼5%) has challenged investigators to elucidate their underlying mechanism and role in primate genome evolution. Although the precise fraction is unknown, some of these duplicated segments have recently been shown to be associated with rapid gene innovation and chromosomal rearrangement in the genomes of man and the great apes.

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Figure 1: Model of segmental duplication.
Figure 2: Primate phylogeny.
Figure 3: Sequence similarity among human segmental duplications.
Figure 4: Duplication-driven chromosomal rearrangements.
Figure 5: Positive selection for the morpheus gene family among primates.

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Acknowledgements

This work is supported by the National Institutes of Health, the Department of Energy and the Charles B. Wang Foundation.

Author information

Authors and Affiliations

  1. Department of Genetics and Center for Human Genetics, School of Medicine and University Hospitals of Cleveland, Case Western Reserve University, Cleveland, 44106, Ohio, USA

    Rhea Vallente Samonte & Evan E. Eichler

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  1. Rhea Vallente Samonte
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  2. Evan E. Eichler
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Correspondence to Evan E. Eichler.

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DATABASES

LocusLink 

ABCD1

CMT1A

ECP

NPIP

SLC6A8 

OMIM 

Charcot–Marie–Tooth neuropathy type 1A

Williams–Beuren syndrome 

UniGene 

Hs.135840

LINKS

AF132984

Glossary

DOMAIN ACCRETION

The evolution of larger multidomain proteins by the addition of DNA segments that encode distinct structural domains.

G4 DNA

G-quartet or quadruplex DNA structure formed in vitro by DNA oligonucleotides with repeats that contain three or more consecutive guanines. In the mammalian genome, such regions (for example, telomeres, rDNA and immunoglobulin heavy-chain segments) have specialized recombination properties.

HOMINOID

A primate superfamily that includes the great ape species and humans (hominids).

L1 ELEMENT

A family of long, interspersed repeat elements (LINE1) that is still actively retrotransposing in the mammalian genome.

NEGATIVE SELECTION

A process in which the effective rate of synonymous change exceeds that of amino-acid replacement between homologous genes. It can occur when most non-synonymous changes in the gene are selectively deleterious and decrease the fitness of the species.

PARACENTRIC INVERSION

A structural chromosome alteration that results from breakage, inversion and reinsertion of a fragment of a chromosomal arm.

PERICENTRIC INVERSION

A structural chromosome alteration that results from breakage, inversion and reinsertion of a fragment that spans the centromere.

POSITIVE SELECTION

A process in which the effective rate of amino-acid replacement exceeds that of synonymous change between homologous genes. It can occur when non-synonymous changes in the gene are selectively advantageous and increase the fitness of the species.

PROGENITOR LOCUS

Ancestral locus from which the first segmental duplication is generated.

STASIPATRIC SPECIATION

Emergence of a new species as a consequence of chromosomal rearrangement and genetic isolation due to reduced fecundity and/or fertility of the hybrid species.

STRUCTURAL POLYMORPHISM

A large (usually greater than a few kilobases) chromosomal rearrangement (deletion, duplication or inversion) that is inherited and is polymorphic in a species. If such polymorphisms are cytogenetically visible, they are termed 'heteromorphisms'.

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Samonte, R., Eichler, E. Segmental duplications and the evolution of the primate genome. Nat Rev Genet 3, 65–72 (2002). https://doi.org/10.1038/nrg705

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