Revisiting the Evolutionary History of Pigs via De Novo Mutation Rate Estimation in A Three-generation Pedigree
The mutation rate used in the previous analyses of pig evolution and demographics was cursory and hence invited potential bias in inferring evolutionary history. Herein, we estimated the de novo mutation rate of pigs as 3.6 × 10−9 per base per generation using high-quality whole-genome sequencing da...
| Κύριοι συγγραφείς: | , , , |
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| Μορφή: | Άρθρο |
| Γλώσσα: | English |
| Έκδοση: |
Oxford University Press
2022-12-01
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| Σειρά: | Genomics, Proteomics & Bioinformatics |
| Θέματα: | |
| Διαθέσιμο Online: | http://www.sciencedirect.com/science/article/pii/S1672022922000146 |
| _version_ | 1827160753689329664 |
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| author | Mingpeng Zhang Qiang Yang Huashui Ai Lusheng Huang |
| author_facet | Mingpeng Zhang Qiang Yang Huashui Ai Lusheng Huang |
| author_sort | Mingpeng Zhang |
| collection | DOAJ |
| description | The mutation rate used in the previous analyses of pig evolution and demographics was cursory and hence invited potential bias in inferring evolutionary history. Herein, we estimated the de novo mutation rate of pigs as 3.6 × 10−9 per base per generation using high-quality whole-genome sequencing data from nine individuals in a three-generation pedigree through stringent filtering and validation. Using this mutation rate, we re-investigated the evolutionary history of pigs. The estimated divergence time of ∼ 10 kiloyears ago (KYA) between European wild and domesticated pigs was consistent with the domestication time of European pigs based on archaeological evidence. However, other divergence events inferred here were not as ancient as previously described. Our estimates suggest that Sus speciation occurred ∼ 1.36 million years ago (MYA); European wild pigs split from Asian wild pigs only ∼ 219 KYA; and south and north Chinese wild pigs split ∼ 25 KYA. Meanwhile, our results showed that the most recent divergence event between Chinese wild and domesticated pigs occurred in the Hetao Plain, northern China, approximately 20 KYA, supporting the possibly independent domestication in northern China along the middle Yellow River. We also found that the maximum effective population size of pigs was ∼ 6 times larger than estimated before. An archaic migration from other Sus species originating ∼ 2 MYA to European pigs was detected during western colonization of pigs, which may affect the accuracy of previous demographic inference. Our de novo mutation rate estimation and its consequences for demographic history inference reasonably provide a new vision regarding the evolutionary history of pigs. |
| first_indexed | 2024-03-08T06:49:05Z |
| format | Article |
| id | doaj.art-6978d1740f864beb885afe84131b330d |
| institution | Directory Open Access Journal |
| issn | 1672-0229 |
| language | English |
| last_indexed | 2025-03-21T00:18:02Z |
| publishDate | 2022-12-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | Genomics, Proteomics & Bioinformatics |
| spelling | doaj.art-6978d1740f864beb885afe84131b330d2024-08-03T08:59:07ZengOxford University PressGenomics, Proteomics & Bioinformatics1672-02292022-12-0120610401052Revisiting the Evolutionary History of Pigs via De Novo Mutation Rate Estimation in A Three-generation PedigreeMingpeng Zhang0Qiang Yang1Huashui Ai2Lusheng Huang3State Key Laboratory of Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, ChinaState Key Laboratory of Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, ChinaCorresponding authors.; State Key Laboratory of Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, ChinaCorresponding authors.; State Key Laboratory of Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, ChinaThe mutation rate used in the previous analyses of pig evolution and demographics was cursory and hence invited potential bias in inferring evolutionary history. Herein, we estimated the de novo mutation rate of pigs as 3.6 × 10−9 per base per generation using high-quality whole-genome sequencing data from nine individuals in a three-generation pedigree through stringent filtering and validation. Using this mutation rate, we re-investigated the evolutionary history of pigs. The estimated divergence time of ∼ 10 kiloyears ago (KYA) between European wild and domesticated pigs was consistent with the domestication time of European pigs based on archaeological evidence. However, other divergence events inferred here were not as ancient as previously described. Our estimates suggest that Sus speciation occurred ∼ 1.36 million years ago (MYA); European wild pigs split from Asian wild pigs only ∼ 219 KYA; and south and north Chinese wild pigs split ∼ 25 KYA. Meanwhile, our results showed that the most recent divergence event between Chinese wild and domesticated pigs occurred in the Hetao Plain, northern China, approximately 20 KYA, supporting the possibly independent domestication in northern China along the middle Yellow River. We also found that the maximum effective population size of pigs was ∼ 6 times larger than estimated before. An archaic migration from other Sus species originating ∼ 2 MYA to European pigs was detected during western colonization of pigs, which may affect the accuracy of previous demographic inference. Our de novo mutation rate estimation and its consequences for demographic history inference reasonably provide a new vision regarding the evolutionary history of pigs.http://www.sciencedirect.com/science/article/pii/S1672022922000146PigDe novo mutation rateThree-generation pedigreeEvolutionary historyArchaic migration |
| spellingShingle | Mingpeng Zhang Qiang Yang Huashui Ai Lusheng Huang Revisiting the Evolutionary History of Pigs via De Novo Mutation Rate Estimation in A Three-generation Pedigree Genomics, Proteomics & Bioinformatics Pig De novo mutation rate Three-generation pedigree Evolutionary history Archaic migration |
| title | Revisiting the Evolutionary History of Pigs via De Novo Mutation Rate Estimation in A Three-generation Pedigree |
| title_full | Revisiting the Evolutionary History of Pigs via De Novo Mutation Rate Estimation in A Three-generation Pedigree |
| title_fullStr | Revisiting the Evolutionary History of Pigs via De Novo Mutation Rate Estimation in A Three-generation Pedigree |
| title_full_unstemmed | Revisiting the Evolutionary History of Pigs via De Novo Mutation Rate Estimation in A Three-generation Pedigree |
| title_short | Revisiting the Evolutionary History of Pigs via De Novo Mutation Rate Estimation in A Three-generation Pedigree |
| title_sort | revisiting the evolutionary history of pigs via de novo mutation rate estimation in a three generation pedigree |
| topic | Pig De novo mutation rate Three-generation pedigree Evolutionary history Archaic migration |
| url | http://www.sciencedirect.com/science/article/pii/S1672022922000146 |
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