Transcriptomics

Dataset Information

7

INTRA_specific hybs: A Burst of Segmental Duplications in the African Great Ape Ancestor


ABSTRACT: Wilson and King were among the first to recognize that the extent of phenotypic change between humans and great apes was dissonant with the rate of molecular change. Proteins are virtually identical; cytogenetically there are few rearrangements that distinguish ape-human chromosomes; rates of single-basepair change and retroposon activity have slowed particularly within hominid lineages when compared to rodents or monkeys. Here, we perform a systematic analysis of duplication content of four primate genomes (macaque, orangutan, chimpanzee and human) in an effort to understand the pattern and rates of genomic duplication during hominid evolution. We find that the ancestral branch leading to human and African great apes shows the most significant increase in duplication activity both in terms of basepairs and in terms of events. This duplication acceleration within the ancestral species is significant when compared to lineage-specific rate estimates even after accounting for copy-number polymorphism and homoplasy. We discover striking examples of recurrent and independent gene-containing duplications within the gorilla and chimpanzee that are absent in the human lineage. Our results suggest that the evolutionary properties of copy-number mutation differ significantly from other forms of genetic mutation and, in contrast to the hominid slowdown of single basepair mutations, there has been a genomic burst of duplication activity at this period during human evolution. A total of 8 humans, 8 chimpanzees and 8 orangutans were hybridized against the reference (NA15510, Clint and Susie, respectively).

SUBMITTER: Priscillia Siswara   Lin Chen  Elaine R Mardis  Mario Ventura  Tomas Marques-Bonet  Arcadi Navarro  Carl Baker  Jeffrey M Kidd  Santhosh Girirajan  Zhaoshi Jiang  Tina A Graves  LaDeanna W Hillier  Ray Malfavon-Borja  M_Francesca Cardone  Evan E Eichler  Lucinda A Fulton  Can Alkan  Gozde Aksay  Richard K Wilson  Ze Cheng 

PROVIDER: E-GEOD-13885 | ArrayExpress | 2010-05-22

SECONDARY ACCESSION(S): GSE13885PRJNA114623

REPOSITORIES: GEO, ArrayExpress

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Publications


It is generally accepted that the extent of phenotypic change between human and great apes is dissonant with the rate of molecular change. Between these two groups, proteins are virtually identical, cytogenetically there are few rearrangements that distinguish ape-human chromosomes, and rates of single-base-pair change and retrotransposon activity have slowed particularly within hominid lineages when compared to rodents or monkeys. Studies of gene family evolution indicate that gene loss and gai  ...[more]

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