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...
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ftunivcam:oai:www.repository.cam.ac.uk:1810/263928 2024-02-04T09:58:23+01:00 Selective sweep on human amylase genes postdates the split with Neanderthals Inchley, CE Larbey, CDA Shwan, NAA Pagani, L Saag, L Antão, T Jacobs, G Hudjashov, G Metspalu, E Mitt, M Eichstaedt, CA Malyarchuk, B Derenko, M Wee, J Abdullah, S Ricaut, F-X Mormina, M Mägi, R Villems, R Metspalu, M Jones, MK Armour, JAL Kivisild, T 2016-11-17 application/pdf https://www.repository.cam.ac.uk/handle/1810/263928 https://doi.org/10.17863/CAM.9304 eng eng Nature Publishing Group http://dx.doi.org/10.1038/srep37198 Scientific Reports https://www.repository.cam.ac.uk/handle/1810/263928 doi:10.17863/CAM.9304 Attribution 4.0 International http://creativecommons.org/licenses/by/4.0/ Amylases Animals Evolution Molecular Female Gene Dosage Genetic Variation Genome Human Humans Male Neanderthals Article 2016 ftunivcam https://doi.org/10.17863/CAM.9304 2024-01-11T23:24:25Z 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. This research was supported by European Research Council Starting Investigator grant FP7-261213 (T.K., C.E.I., L.P., T.E.), Estonian Research Infrastructure Roadmap grant no. 373 3.2.0304.11-0312, the European Union European Regional Development Fund Centre of Excellence in Genomics to the Estonian Biocentre and Estonian Institutional Research grant IUT24-1 (T.K., L.S., G.H., M.M. and R.V.); French Ministry of Foreign and European Affairs and French ANR grant number ANR-14-CE31-0013-01 (F.-X.R.); Program of the RAS Presidium “Basic research for the development of the Russian Arctic” (B.M.). Article in Journal/Newspaper Arctic Apollo - University of Cambridge Repository Arctic |
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Open Polar |
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Apollo - University of Cambridge Repository |
op_collection_id |
ftunivcam |
language |
English |
topic |
Amylases Animals Evolution Molecular Female Gene Dosage Genetic Variation Genome Human Humans Male Neanderthals |
spellingShingle |
Amylases Animals Evolution Molecular Female Gene Dosage Genetic Variation Genome Human Humans Male Neanderthals Inchley, CE Larbey, CDA Shwan, NAA Pagani, L Saag, L Antão, T Jacobs, G Hudjashov, G Metspalu, E Mitt, M Eichstaedt, CA Malyarchuk, B Derenko, M Wee, J Abdullah, S Ricaut, F-X Mormina, M Mägi, R Villems, R Metspalu, M Jones, MK Armour, JAL Kivisild, T Selective sweep on human amylase genes postdates the split with Neanderthals |
topic_facet |
Amylases Animals Evolution Molecular Female Gene Dosage Genetic Variation Genome Human Humans Male Neanderthals |
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. This research was supported by European Research Council Starting Investigator grant FP7-261213 (T.K., C.E.I., L.P., T.E.), Estonian Research Infrastructure Roadmap grant no. 373 3.2.0304.11-0312, the European Union European Regional Development Fund Centre of Excellence in Genomics to the Estonian Biocentre and Estonian Institutional Research grant IUT24-1 (T.K., L.S., G.H., M.M. and R.V.); French Ministry of Foreign and European Affairs and French ANR grant number ANR-14-CE31-0013-01 (F.-X.R.); Program of the RAS Presidium “Basic research for the development of the Russian Arctic” (B.M.). |
format |
Article in Journal/Newspaper |
author |
Inchley, CE Larbey, CDA Shwan, NAA Pagani, L Saag, L Antão, T Jacobs, G Hudjashov, G Metspalu, E Mitt, M Eichstaedt, CA Malyarchuk, B Derenko, M Wee, J Abdullah, S Ricaut, F-X Mormina, M Mägi, R Villems, R Metspalu, M Jones, MK Armour, JAL Kivisild, T |
author_facet |
Inchley, CE Larbey, CDA Shwan, NAA Pagani, L Saag, L Antão, T Jacobs, G Hudjashov, G Metspalu, E Mitt, M Eichstaedt, CA Malyarchuk, B Derenko, M Wee, J Abdullah, S Ricaut, F-X Mormina, M Mägi, R Villems, R Metspalu, M Jones, MK Armour, JAL Kivisild, T |
author_sort |
Inchley, CE |
title |
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_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_sort |
selective sweep on human amylase genes postdates the split with neanderthals |
publisher |
Nature Publishing Group |
publishDate |
2016 |
url |
https://www.repository.cam.ac.uk/handle/1810/263928 https://doi.org/10.17863/CAM.9304 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_relation |
https://www.repository.cam.ac.uk/handle/1810/263928 doi:10.17863/CAM.9304 |
op_rights |
Attribution 4.0 International http://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.17863/CAM.9304 |
_version_ |
1789962818984869888 |