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Background  Low nucleotide divergence between human and chimpanzee does not sufficiently explain the species-specific morphological, physiological and behavioral traits. As gene duplication is a major prerequisite for the emergence of new genes and novel biological processes, comparative studies of human and chimpanzee duplicated genes may assist in understanding the mechanisms behind primate evolution. We addressed the divergence between human and chimpanzee duplicated genomic regions by using Luteinizing Hormone Beta ( LHB )/Chorionic Gonadotropin Beta ( CGB ) gene cluster as a model. The placental  CGB  genes that are essential for implantation have evolved from an ancestral pituitary  LHB  gene by duplications in the primate lineage.    Results  We shotgun sequenced and compared the human (45,165 bp) and chimpanzee (39,876 bp)  LHB/CGB  regions and hereby present evidence for structural variation resulting in discordant number of  CGB  genes (6 in human, 5 in chimpanzee). The scenario of species-specific parallel duplications was supported (i) as the most parsimonious solution requiring the least rearrangement events to explain the interspecies structural differences; (ii) by the phylogenetic trees constructed with fragments of intergenic regions; (iii) by the sequence similarity calculations. Across the orthologous regions of  LHB/CGB  cluster, substitutions and indels contributed approximately equally to the interspecies divergence and the distribution of nucleotide identity was correlated with the regional repeat content. Intraspecies gene conversion may have shaped the  LHB/CGB  gene cluster. The substitution divergence (1.8–2.59%) exceeded two-three fold the estimates for single-copy loci and the fraction of transversional mutations was increased compared to the unique sequences (43% versus ~30%). Despite the high sequence identity among  LHB/CGB  genes, there are signs of functional differentiation among the gene copies. Estimates for d n /d s  rate ratio suggested a purifying selection on  LHB  and  CGB8 , and a positive evolution of  CGB1 .    Conclusion  If generalized, our data suggests that in addition to species-specific deletions and duplications, parallel duplication events may have contributed to genetic differences separating humans from their closest relatives. Compared to unique genomic segments, duplicated regions are characterized by high divergence promoted by intraspecies gene conversion and species-specific chromosomal rearrangements, including the alterations in gene copy number.

High divergence in primate-specific duplicated regions: Human and chimpanzee Chorionic Gonadotropin Betagenes