Lineage-specific gene duplication and loss in human and great ape evolution.
Given that gene duplication is a major driving force of evolutionary change and the key mechanism underlying the emergence of new genes and biological processes, this study sought to use a novel genome-wide approach to identify genes that have undergone lineage-specific duplications or contractions among several hominoid lineages. Interspecies cDNA array-based comparative genomic hybridization was used to individually compare copy number variation for 39,711 cDNAs, representing 29,619 human genes, across five hominoid species, including human. We identified 1,005 genes, either as isolated genes or in clusters positionally biased toward rearrangement-prone genomic regions, that produced relative hybridization signals unique to one or more of the hominoid lineages. Measured as a function of the evolutionary age of each lineage, genes showing copy number expansions were most pronounced in human (134) and include a number of genes thought to be involved in the structure and function of the brain. This work represents, to our knowledge, the first genome-wide gene-based survey of gene duplication across hominoid species. The genes identified here likely represent a significant majority of the major gene copy number changes that have occurred over the past 15 million years of human and great ape evolution and are likely to underlie some of the key phenotypic characteristics that distinguish these species.
Fortna
Andrew
A
Department of Pharmacology and Human Medical Genetics Program, University of Colorado Health Sciences Center, Denver, Colorado, USA.
Kim
Young
Y
MacLaren
Erik
E
Marshall
Kriste
K
Hahn
Gretchen
G
Meltesen
Lynne
L
Brenton
Matthew
M
Hink
Raquel
R
Burgers
Sonya
S
Hernandez-Boussard
Tina
T
Karimpour-Fard
Anis
A
Glueck
Deborah
D
McGavran
Loris
L
Berry
Rebecca
R
Pollack
Jonathan
J
Sikela
James M
JM
D000818:Animals; D005075:Biological Evolution; D022202:Chromosomes, Artificial, Bacterial; D003001:Cloning, Molecular; D016000:Cluster Analysis; D018076:DNA, Complementary / Q000378:metabolism; D019143:Evolution, Molecular; D051523:Fibroblast Growth Factor 7 / Q000378:metabolism; D020440:Gene Duplication; D014644:Genetic Variation; D016678:Genome; D015186:Hominidae; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D047908:Intracellular Signaling Peptides and Proteins; D008957:Models, Genetic; D008969:Molecular Sequence Data; D005810:Multigene Family; D009693:Nucleic Acid Hybridization; D002679:Pan troglodytes; D011148:Pongo pygmaeus; D011506:Proteins / Q000378:metabolism; D012091:Repetitive Sequences, Nucleic Acid; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D013045:Species Specificity
D018076:DNA, Complementary; C496453:FGF7 protein, human; D047908:Intracellular Signaling Peptides and Proteins; D011506:Proteins; C407225:SPRY3 protein, human; D051523:Fibroblast Growth Factor 7