Genome-scale evolution in local populations of wild chimpanzees
Abstract Analysis of genome-scale evolution has been difficult in large, endangered animals because opportunities to collect high-quality genetic samples are limited. There is a need for novel field-friendly, cost-effective genetic techniques. This study conducted an exome-wide analysis of a total o...
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Nature Portfolio
2025-01-01
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| Online Access: | https://doi.org/10.1038/s41598-024-84163-z |
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| author | Takashi Hayakawa Takushi Kishida Yasuhiro Go Eiji Inoue Eri Kawaguchi Tomoyuki Aizu Hinako Ishizaki Atsushi Toyoda Asao Fujiyama Tetsuro Matsuzawa Chie Hashimoto Takeshi Furuichi Kiyokazu Agata |
| author_facet | Takashi Hayakawa Takushi Kishida Yasuhiro Go Eiji Inoue Eri Kawaguchi Tomoyuki Aizu Hinako Ishizaki Atsushi Toyoda Asao Fujiyama Tetsuro Matsuzawa Chie Hashimoto Takeshi Furuichi Kiyokazu Agata |
| author_sort | Takashi Hayakawa |
| collection | DOAJ |
| description | Abstract Analysis of genome-scale evolution has been difficult in large, endangered animals because opportunities to collect high-quality genetic samples are limited. There is a need for novel field-friendly, cost-effective genetic techniques. This study conducted an exome-wide analysis of a total of 42 chimpanzees (Pan troglodytes) across six African regions, providing insights into population discrimination techniques. Wild chimpanzee DNA was extracted noninvasively from collected fecal samples using the lysis-buffer storage method. To target genome-scale regions of host DNA, exome-capture sequencing was performed using cost-effective baits originally designed for humans (closely related to chimpanzees). Multivariate analysis effectively discriminated differences in local populations, aiding in the identification of samples’ geographical origins. Exome-wide heterozygosity was negatively correlated significantly with genome-wide nonsynonymous–synonymous substitution ratios, suggesting that mutation loads exist at the local population level. Exome sequences revealed functional diversity and protein-coding gene divergence. Segregating pseudogenes were comprehensively annotated, with many being population-specific and others shared among populations. Focusing on multicopy chemosensory receptor genes, the segregating pseudogenes OR7D4 (an olfactory receptor) and TAS2R42 (a bitter taste receptor) were shared among western and eastern chimpanzees. Overall, our analytical framework offers ecological insights into chimpanzees and may be applicable to other organisms. |
| format | Article |
| id | doaj-art-50a28e44dc1747f7bcde723dfb417669 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-50a28e44dc1747f7bcde723dfb4176692025-01-05T12:18:31ZengNature PortfolioScientific Reports2045-23222025-01-0115111610.1038/s41598-024-84163-zGenome-scale evolution in local populations of wild chimpanzeesTakashi Hayakawa0Takushi Kishida1Yasuhiro Go2Eiji Inoue3Eri Kawaguchi4Tomoyuki Aizu5Hinako Ishizaki6Atsushi Toyoda7Asao Fujiyama8Tetsuro Matsuzawa9Chie Hashimoto10Takeshi Furuichi11Kiyokazu Agata12Faculty of Environmental Earth Science, Hokkaido UniversityCollege of Bioresource Sciences, Nihon UniversityGraduate School of Information Science, University of HyogoFaculty of Science, Toho UniversityCenter for iPS Cell Research and Application, Kyoto UniversityDepartment of Genomics and Evolutionary Biology, National Institute of GeneticsDepartment of Genomics and Evolutionary Biology, National Institute of GeneticsDepartment of Genomics and Evolutionary Biology, National Institute of GeneticsAdvanced Genomics Center, National Institute of GeneticsDepartment of Pedagogy, Chubu Gakuin UniversityWildlife Research Center, Kyoto UniversityWildlife Research Center, Kyoto UniversityLaboratory for Regenerative Biology, National Institute for Basic BiologyAbstract Analysis of genome-scale evolution has been difficult in large, endangered animals because opportunities to collect high-quality genetic samples are limited. There is a need for novel field-friendly, cost-effective genetic techniques. This study conducted an exome-wide analysis of a total of 42 chimpanzees (Pan troglodytes) across six African regions, providing insights into population discrimination techniques. Wild chimpanzee DNA was extracted noninvasively from collected fecal samples using the lysis-buffer storage method. To target genome-scale regions of host DNA, exome-capture sequencing was performed using cost-effective baits originally designed for humans (closely related to chimpanzees). Multivariate analysis effectively discriminated differences in local populations, aiding in the identification of samples’ geographical origins. Exome-wide heterozygosity was negatively correlated significantly with genome-wide nonsynonymous–synonymous substitution ratios, suggesting that mutation loads exist at the local population level. Exome sequences revealed functional diversity and protein-coding gene divergence. Segregating pseudogenes were comprehensively annotated, with many being population-specific and others shared among populations. Focusing on multicopy chemosensory receptor genes, the segregating pseudogenes OR7D4 (an olfactory receptor) and TAS2R42 (a bitter taste receptor) were shared among western and eastern chimpanzees. Overall, our analytical framework offers ecological insights into chimpanzees and may be applicable to other organisms.https://doi.org/10.1038/s41598-024-84163-zChimpanzeeLocal populationHeterozygosityPseudogeneOlfactory receptorBitter taste receptor |
| spellingShingle | Takashi Hayakawa Takushi Kishida Yasuhiro Go Eiji Inoue Eri Kawaguchi Tomoyuki Aizu Hinako Ishizaki Atsushi Toyoda Asao Fujiyama Tetsuro Matsuzawa Chie Hashimoto Takeshi Furuichi Kiyokazu Agata Genome-scale evolution in local populations of wild chimpanzees Scientific Reports Chimpanzee Local population Heterozygosity Pseudogene Olfactory receptor Bitter taste receptor |
| title | Genome-scale evolution in local populations of wild chimpanzees |
| title_full | Genome-scale evolution in local populations of wild chimpanzees |
| title_fullStr | Genome-scale evolution in local populations of wild chimpanzees |
| title_full_unstemmed | Genome-scale evolution in local populations of wild chimpanzees |
| title_short | Genome-scale evolution in local populations of wild chimpanzees |
| title_sort | genome scale evolution in local populations of wild chimpanzees |
| topic | Chimpanzee Local population Heterozygosity Pseudogene Olfactory receptor Bitter taste receptor |
| url | https://doi.org/10.1038/s41598-024-84163-z |
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