Indels in the Evolution of the Human and Chimpanzee Genomes


Mutations in the deoxyribonucleic acid (DNA) cause genomic divergence between species and provide a starting point for evolutionary change. There are several sources of sequence variation and here we will focus on insertions and deletions (indels). Such events occur frequently in genomic alignments of humans and chimpanzees and the indel divergence is estimated to 3–5%. In this article, we will discuss some causes behind indels and the possible impact of indels on the evolution of primate genomes. In addition, we will provide some examples of indels that may affect protein function as well as alternative splicing.

Keywords: indels; primate evolution; chimpanzee; genome; divergence; alternative splicing

Figure 1.

Species tree. The divergence time for humans and chimpanzees has been estimated to 5–7 million years ago (MYA) (Glazko and Nei, ; Kumar et al., ), humans and gorillas to 6–8 MYA, humans and orangutans to 12–15 MYA and humans and macaques to 21–25 MYA (Glazko and Nei, ). The divergence time between the common chimpanzee and the bonobo is approximately 2 MYA (Yu et al., ).

Figure 2.

Fusion of the MICA and MICB genes. Schematic representation of the deletion between the MICA and MICB genes, resulting in a fused MICA/B gene in the chimpanzee lineages. Both genes contain 6 exons that are denoted E1–E6. The breakpoint cannot be precisely determined but is predicted to be located around the fourth intron of MICB and at the end of the second intron of MICA (Anzai et al., ). The deletion has been dated to be at least 2 and probably less than 5–7 million years old (de Groot et al., ).

Figure 3.

Deletion leading to a gain of transcripts in the human PIGP gene. (a) There are six translated human transcripts for PIGP in the VEGA database (VEGA transcripts IDs are given in parentheses). In one of the human transcripts (PIGP‐VI) there is a 1 bp deletion in the first exon. Comparative sequence analysis shows that the deletion removes an ancestral stop codon and thus a novel human transcript is gained. Note that the exonic sequence containing the deletion is only used in the sixth transcript and thus the deletion does not affect the remaining transcripts. The box represents a partial alignment of the human and chimpanzee exon 1 sequences. An arrow indicates the human deletion and an asterisk denotes the stop codon in the chimpanzee sequence. (b) Species tree (not drawn to scale) illustrating the relationship between human (H), chimpanzee (C), bonobo (B), gorilla (G), Rhesus macaque (M) and dog (D). The star indicates the time point of the deletion. The deletion has not been found in any other of the examined mammals and it is therefore likely that the transcript originated in the human lineage.

Figure 4.

Insertion leading to a gain of transcripts in the human FAM3B gene. (a) FAM3B has four human‐translated transcripts annotated in the VEGA database (VEGA transcripts IDs are given in parentheses). There is a 10 bp insertion in the second exon of the human FAM3B‐IV transcripts that seems to remove an ancestral stop codon. This exon is unique for the FAM3B‐IV transcript and therefore the insertion does not affect the other transcripts. The box represents a partial alignment of the human and chimpanzee exon 2 sequences. Dashes indicate a 10 bp gap in the alignment and the asterisk denotes the stop codon in the chimpanzee. (b) Species tree (not drawn to scale) illustrating the relationship between human (H), chimpanzee (C), bonobo (B), gorilla (G), Rhesus macaque (M) and dog (D). The analysis implies that the fourth transcript (FAM3B‐IV) was gained in the human lineage. The insertion is indicated with a square in the phylogenetic tree.



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Further Reading

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Wetterbom, Anna, Cavelier, Lucia, and Bergström, Tomas F(Jul 2008) Indels in the Evolution of the Human and Chimpanzee Genomes. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0020851]