Saltations of c is-regulatory modules in Canidae and Hominidae
Abstract Dogs, which were segregated from wolves about thirty thousand years ago, show unique human-similar social-cognitive abilities. However, the genomic basis accounting for the phenotypic saltation between dog and wolf remains unclear. We performed a comparative analysis of genome-wide cis-regu...
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| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-08-01
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| Series: | Scientific Reports |
| Subjects: | |
| Online Access: | https://doi.org/10.1038/s41598-025-13034-y |
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| Summary: | Abstract Dogs, which were segregated from wolves about thirty thousand years ago, show unique human-similar social-cognitive abilities. However, the genomic basis accounting for the phenotypic saltation between dog and wolf remains unclear. We performed a comparative analysis of genome-wide cis-regulatory element frequencies (CREF) for five canids: dog, dingo, red fox, dhole, and wolf, along with four hominids. For each species, genome-wide CREFs are organized into a matrix. The species-specific CREF matrix is stratified into multiple dual eigen-modules through robust singular value decomposition. Cross-species comparisons of dual eigen-modules demonstrated that the top three eigen-modules are highly conserved while the fourth and fifth ones underwent a saltation in dogs. The red fox is closest to the degenerate point characterizing the onset of saltation. Gene enrichment analysis and motif analysis revealed that myelination, long-term memory, and cochlear development are significantly enhanced at level four in both humans and dogs, but not in wolves. Cross-family comparisons revealed a more similar cognition-memory module between humans and dogs than between humans and chimpanzees. Not only the presence of cis-elements but also their frequencies are crucial for deciphering the regulatory saltations that characterize a striking convergent evolution of dogs and humans in proximal regulatory sequences. |
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| ISSN: | 2045-2322 |