Selective sweep on human amylase genes postdates the split with Neanderthals
Humans have more copies of amylase genes than other primates. It is still poorly understood, however, when the copy number expansion occurred and whether its spread was enhanced by selection. Here we assess amylase copy numbers in a global sample of 480 high coverage genomes and find that regions fl...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
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Nature Publishing Group
2016
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| Online Access: | https://eprints.nottingham.ac.uk/39847/ |
| _version_ | 1848795927472504832 |
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| author | Inchley, Charlotte E. Larbey, Cynthia D.A. Shwan, Nzar A.A. Pagani, Luca Saag, Lauri Antão, Tiago Jacobs, Guy Hudjashov, Georgi Metspalu, Ene Mitt, Mario Eichstaedt, Christina A. Malyarchuk, Boris Derenko, Miroslava Wee, Joseph Abdullah, Syafiq Ricaut, François-Xavier Mormina, Maru Mägi, Reedik Villems, Richard Metspalu, Mait Jones, Martin K. Armour, John A.L. Kivisild, Toomas |
| author_facet | Inchley, Charlotte E. Larbey, Cynthia D.A. Shwan, Nzar A.A. Pagani, Luca Saag, Lauri Antão, Tiago Jacobs, Guy Hudjashov, Georgi Metspalu, Ene Mitt, Mario Eichstaedt, Christina A. Malyarchuk, Boris Derenko, Miroslava Wee, Joseph Abdullah, Syafiq Ricaut, François-Xavier Mormina, Maru Mägi, Reedik Villems, Richard Metspalu, Mait Jones, Martin K. Armour, John A.L. Kivisild, Toomas |
| author_sort | Inchley, Charlotte E. |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | Humans have more copies of amylase genes than other primates. It is still poorly understood, however, when the copy number expansion occurred and whether its spread was enhanced by selection. Here we assess amylase copy numbers in a global sample of 480 high coverage genomes and find that regions flanking the amylase locus show notable depression of genetic diversity both in African and non-African populations. Analysis of genetic variation in these regions supports the model of an early selective sweep in the human lineage after the split of humans from Neanderthals which led to the fixation of multiple copies of AMY1 in place of a single copy. We find evidence of multiple secondary losses of copy number with the highest frequency (52%) of a deletion of AMY2A and associated low copy number of AMY1 in Northeast Siberian populations whose diet has been low in starch content. |
| first_indexed | 2025-11-14T19:39:52Z |
| format | Article |
| id | nottingham-39847 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| last_indexed | 2025-11-14T19:39:52Z |
| publishDate | 2016 |
| publisher | Nature Publishing Group |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-398472020-05-04T18:20:43Z https://eprints.nottingham.ac.uk/39847/ Selective sweep on human amylase genes postdates the split with Neanderthals Inchley, Charlotte E. Larbey, Cynthia D.A. Shwan, Nzar A.A. Pagani, Luca Saag, Lauri Antão, Tiago Jacobs, Guy Hudjashov, Georgi Metspalu, Ene Mitt, Mario Eichstaedt, Christina A. Malyarchuk, Boris Derenko, Miroslava Wee, Joseph Abdullah, Syafiq Ricaut, François-Xavier Mormina, Maru Mägi, Reedik Villems, Richard Metspalu, Mait Jones, Martin K. Armour, John A.L. Kivisild, Toomas Humans have more copies of amylase genes than other primates. It is still poorly understood, however, when the copy number expansion occurred and whether its spread was enhanced by selection. Here we assess amylase copy numbers in a global sample of 480 high coverage genomes and find that regions flanking the amylase locus show notable depression of genetic diversity both in African and non-African populations. Analysis of genetic variation in these regions supports the model of an early selective sweep in the human lineage after the split of humans from Neanderthals which led to the fixation of multiple copies of AMY1 in place of a single copy. We find evidence of multiple secondary losses of copy number with the highest frequency (52%) of a deletion of AMY2A and associated low copy number of AMY1 in Northeast Siberian populations whose diet has been low in starch content. Nature Publishing Group 2016-11-17 Article PeerReviewed Inchley, Charlotte E., Larbey, Cynthia D.A., Shwan, Nzar A.A., Pagani, Luca, Saag, Lauri, Antão, Tiago, Jacobs, Guy, Hudjashov, Georgi, Metspalu, Ene, Mitt, Mario, Eichstaedt, Christina A., Malyarchuk, Boris, Derenko, Miroslava, Wee, Joseph, Abdullah, Syafiq, Ricaut, François-Xavier, Mormina, Maru, Mägi, Reedik, Villems, Richard, Metspalu, Mait, Jones, Martin K., Armour, John A.L. and Kivisild, Toomas (2016) Selective sweep on human amylase genes postdates the split with Neanderthals. Scientific Reports, 6 . p. 37198. ISSN 2045-2322 http://www.nature.com/articles/srep37198 doi:10.1038/srep37198 doi:10.1038/srep37198 |
| spellingShingle | Inchley, Charlotte E. Larbey, Cynthia D.A. Shwan, Nzar A.A. Pagani, Luca Saag, Lauri Antão, Tiago Jacobs, Guy Hudjashov, Georgi Metspalu, Ene Mitt, Mario Eichstaedt, Christina A. Malyarchuk, Boris Derenko, Miroslava Wee, Joseph Abdullah, Syafiq Ricaut, François-Xavier Mormina, Maru Mägi, Reedik Villems, Richard Metspalu, Mait Jones, Martin K. Armour, John A.L. Kivisild, Toomas Selective sweep on human amylase genes postdates the split with Neanderthals |
| title | Selective sweep on human amylase genes postdates the split with Neanderthals |
| title_full | Selective sweep on human amylase genes postdates the split with Neanderthals |
| title_fullStr | Selective sweep on human amylase genes postdates the split with Neanderthals |
| title_full_unstemmed | Selective sweep on human amylase genes postdates the split with Neanderthals |
| title_short | Selective sweep on human amylase genes postdates the split with Neanderthals |
| title_sort | selective sweep on human amylase genes postdates the split with neanderthals |
| url | https://eprints.nottingham.ac.uk/39847/ https://eprints.nottingham.ac.uk/39847/ https://eprints.nottingham.ac.uk/39847/ |