A burst of segmental duplications in the genome of the African great ape ancestor.
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 gain are enriched within the primate lineage. Here, we perform a systematic analysis of duplication content of four primate genomes (macaque, orang-utan, 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 base pairs 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-base-pair mutations, there has been a genomic burst of duplication activity at this period during human evolution.
Marques-Bonet
Tomas
T
Department of Genome Sciences, University of Washington and the Howard Hughes Medical Institute, Seattle, Washington 98195, USA.
Kidd
Jeffrey M
JM
Ventura
Mario
M
Graves
Tina A
TA
Cheng
Ze
Z
Hillier
LaDeana W
LW
Jiang
Zhaoshi
Z
Baker
Carl
C
Malfavon-Borja
Ray
R
Fulton
Lucinda A
LA
Alkan
Can
C
Aksay
Gozde
G
Girirajan
Santhosh
S
Siswara
Priscillia
P
Chen
Lin
L
Cardone
Maria Francesca
MF
Navarro
Arcadi
A
Mardis
Elaine R
ER
Wilson
Richard K
RK
Eichler
Evan E
EE
D000349:Africa; D000818:Animals; D051079:Catarrhini / Q000145:classification / Q000235:genetics*; D002874:Chromosome Mapping; D019143:Evolution, Molecular; D020440:Gene Duplication; D016678:Genome / Q000235:genetics*; D006801:Humans; D011110:Polymorphism, Genetic; D015203:Reproducibility of Results