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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Nature Portfolio
2025-08-01
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| Online Access: | https://doi.org/10.1038/s41598-025-13034-y |
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| author | Jianhui Shi Linting Wang Lei M. Li |
| author_facet | Jianhui Shi Linting Wang Lei M. Li |
| author_sort | Jianhui Shi |
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| description | 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. |
| format | Article |
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| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-08-01 |
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| spelling | doaj-art-e6f93c3fffda4cebb6ea9510d09887d92025-08-20T03:46:01ZengNature PortfolioScientific Reports2045-23222025-08-0115112010.1038/s41598-025-13034-ySaltations of c is-regulatory modules in Canidae and HominidaeJianhui Shi0Linting Wang1Lei M. Li2State Key Laboratory of Mathematical Science, Academy of Mathematics and Systems Science, Chinese Academy of SciencesState Key Laboratory of Mathematical Science, Academy of Mathematics and Systems Science, Chinese Academy of SciencesState Key Laboratory of Mathematical Science, Academy of Mathematics and Systems Science, Chinese Academy of SciencesAbstract 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.https://doi.org/10.1038/s41598-025-13034-yCis-regulatory moduleSaltationCan-SINE elementCognitionEmergenceSingular value decomposition |
| spellingShingle | Jianhui Shi Linting Wang Lei M. Li Saltations of c is-regulatory modules in Canidae and Hominidae Scientific Reports Cis-regulatory module Saltation Can-SINE element Cognition Emergence Singular value decomposition |
| title | Saltations of c is-regulatory modules in Canidae and Hominidae |
| title_full | Saltations of c is-regulatory modules in Canidae and Hominidae |
| title_fullStr | Saltations of c is-regulatory modules in Canidae and Hominidae |
| title_full_unstemmed | Saltations of c is-regulatory modules in Canidae and Hominidae |
| title_short | Saltations of c is-regulatory modules in Canidae and Hominidae |
| title_sort | saltations of c is regulatory modules in canidae and hominidae |
| topic | Cis-regulatory module Saltation Can-SINE element Cognition Emergence Singular value decomposition |
| url | https://doi.org/10.1038/s41598-025-13034-y |
| work_keys_str_mv | AT jianhuishi saltationsofcisregulatorymodulesincanidaeandhominidae AT lintingwang saltationsofcisregulatorymodulesincanidaeandhominidae AT leimli saltationsofcisregulatorymodulesincanidaeandhominidae |