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RESOURCE: DupMasker: A tool for annotating primate segmental duplications
- Zhaoshi Jiang,
- Robert Hubley,
- Arian Smit,
- and Evan E. Eichler
Genome Res. August 2008 18: 1362-1368; Published in Advance May 23, 2008, doi:10.1101/gr.078477.108
.... ↵ She, X. , Liu, G. , Ventura, M. , Zhao, S. , Misceo, D. , Roberto, R. , Cardone, M.F. , Rocchi, M. , Green, E.D. , Archidiacano, N. , et al. ( 2006 ) A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal...
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LETTER: Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions
- Stefan Kirsch,
- Claudia Münch,
- Zhaoshi Jiang,
- Ze Cheng,
- Lin Chen,
- Christiane Batz,
- Evan E. Eichler,
- and Werner Schempp
Genome Res. July 2008 18: 1030-1042; Published in Advance April 29, 2008, doi:10.1101/gr.076711.108
...-chromosomal segmental duplications. A multi-step process is depicted leading to the current distribution pattern of duplicated sequences on the Y chromosomes of the great and lesser apes. Serial intrachromosomal duplicative transpositions and chromosomal rearrangements generated a mosaic pattern on all great ape Y...
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LETTER: Segmental duplications and evolutionary plasticity at tumor chromosome break-prone regions
- Eva Darai-Ramqvist,
- Agneta Sandlund,
- Stefan Müller,
- George Klein,
- Stefan Imreh,
- and Maria Kost-Alimova
Genome Res. March 2008 18: 370-379; Published in Advance January 29, 2008, doi:10.1101/gr.7010208
...in inversions during primate evolution; 10 were reused by breaks during mammalian evolution; 14 showed copy number polymorphism in man. TBSD sites showed an increase in satellite repeats, retrotransposed sequences, and other segmental duplications. We propose that the instability of these sites stems from...
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Research: Evolutionary dynamism of the primate LRRC37 gene family
- Giuliana Giannuzzi,
- Priscillia Siswara,
- Maika Malig,
- Tomas Marques-Bonet,
- NISC Comparative Sequencing Program,
- James C. Mullikin,
- Mario Ventura,
- and Evan E. Eichler
Genome Res. January 2013 23: 46-59; Published in Advance October 11, 2012, doi:10.1101/gr.138842.112
...that the human and great ape s show a two- to threefold enrichment of interspersed segmental duplications when compared to macaque and nonprimate mammalian lineages (Bailey and Eichler 2006; She et al. 2006; Marques-Bonet et al. 2009). In these s, intrachromosomal segmental duplications have amosaic structure...
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Letter: Comparative analysis of Alu repeats in primate genomes
- George E. Liu,
- Can Alkan,
- Lu Jiang,
- Shaying Zhao,
- and Evan E. Eichler
Genome Res. May 2009 19: 876-885; doi:10.1101/gr.083972.108
...subfamily. Liu et al. 884 Genome Research www..org shows elevated substitution rates and a great-ape expansion of intrachromosomal duplications. Genome Res. 16: 576–583. Shen, M.R., Batzer, M.A., and Deininger, P.L. 1991. Evolution of the master Alu gene(s). J. Mol. Evol. 33: 311–320. Smit, A.F. 1999...
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ARTICLE: Gene copy number variation spanning 60 million years of human and primate evolution
- Laura Dumas,
- Young H. Kim,
- Anis Karimpour-Fard,
- Michael Cox,
- Janet Hopkins,
- Jonathan R. Pollack,
- and James M. Sikela
Genome Res. September 2007 17: 1266-1277; Published in Advance July 31, 2007, doi:10.1101/gr.6557307
...that were predicted to have increased in humans and the great apes relative to the other primates tested, events that would be expected to have occurred 13–18 Mya. Finally, 105 genes showed elevations in copy number in human and ape species relative to monkeys and prosimians, events that, by parsimony, can...
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ARTICLE: Copy number variation and evolution in humans and chimpanzees
- George H. Perry,
- Fengtang Yang,
- Tomas Marques-Bonet,
- Carly Murphy,
- Tomas Fitzgerald,
- Arthur S. Lee,
- Courtney Hyland,
- Anne C. Stone,
- Matthew E. Hurles,
- Chris Tyler-Smith,
- Evan E. Eichler,
- Nigel P. Carter,
- Charles Lee,
- and Richard Redon
Genome Res. November 2008 18: 1698-1710; Published in Advance September 4, 2008, doi:10.1101/gr.082016.108
...architectures of juxtaposed duplicated segments, where intra- and interchromosomal SDs overlap within and around core duplications ( Jiang et al. 2007 ). Of the 139 common CNVRs that overlapped SDs, 126 (91%) were associated with intrachromosomal SD paralogs, including 87 CNVRs (69%) that also overlapped...
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LETTER: Reduced purifying selection prevails over positive selection in human copy number variant evolution
- Duc-Quang Nguyen,
- Caleb Webber,
- Jayne Hehir-Kwa,
- Rolph Pfundt,
- Joris Veltman,
- and Chris P. Ponting
Genome Res. November 2008 18: 1711-1723; Published in Advance August 7, 2008, doi:10.1101/gr.077289.108
...trends that emerge are that regions showing elevated G+C content give rise to larger CNVs and more frequently overlap with sequence-similar segmental duplications. Such regions also exhibit tendencies to be gene rich and to accumulate more nucleotide substitutions and interspecies synteny breakpoints...
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PERSPECTIVE: Ancestral genomes reconstruction: An integrated, multi-disciplinary approach is needed
- Mariano Rocchi,
- Nicoletta Archidiacono,
- and Roscoe Stanyon
Genome Res. December 2006 16: 1441-1444; Published in Advance October 19, 2006, doi:10.1101/gr.5687906
.... , Liu, G. , Ventura, M. , Zhao, S. , Misceo, D. , Roberto, R. , Cardone, M.F. , Rocchi, M. , Green, E.D. , Archidiacono, N. , et al. ( 2006 ) A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplications...
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Letter: Adaptive evolution of young gene duplicates in mammals
- Mira V. Han,
- Jeffery P. Demuth,
- Casey L. McGrath,
- Claudio Casola,
- and Matthew W. Hahn
Genome Res. May 2009 19: 859-867; doi:10.1101/gr.085951.108
...in neuronal and cognitive functions. Our results imply that genome scans for selection that ignore duplicated loci are missing a large fraction of all adaptive substitutions. The results are also in agreement with the classical model of evolution by gene duplication, supporting a common role...

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