Selective sweep on human amylase genes postdates the split with Neanderthals

Charlotte E. Inchley; Cynthia D. A. Larbey; Nzar A. A. Shwan; Luca Pagani; Lauri Saag; Tiago Antão; Guy Jacobs; Georgi Hudjashov; Ene Metspalu; Mario Mitt; Christina A. Eichstaedt; Boris Malyarchuk; Miroslava Derenko; Joseph Wee; Syafiq Abdullah; François-Xavier Ricaut; Maru Mormina; Reedik Mägi; Richard Villems; Mait Metspalu; Martin K. Jones; John A. L. Armour; Toomas Kivisild

doi:10.1038/srep37198

Selective sweep on human amylase genes postdates the split with Neanderthals

Charlotte E. Inchley, Cynthia D. A. Larbey, Nzar A. A. Shwan, Luca Pagani, Lauri Saag, Tiago Antão, Guy Jacobs, Georgi Hudjashov, Ene Metspalu, Mario Mitt, Christina A. Eichstaedt, Boris Malyarchuk, Miroslava Derenko, Joseph Wee, Syafiq Abdullah, François-Xavier Ricaut, Maru Mormina, Reedik Mägi, Richard Villems, Mait MetspaluMartin K. Jones, John A. L. Armour, Toomas Kivisild

University of Winchester

Research output: Contribution to journal › Article › peer-review

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Abstract

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.

Original language	English
Journal	Scientific Reports
Volume	6
Issue number	37198
DOIs	https://doi.org/10.1038/srep37198
Publication status	Published - 17 Nov 2016

Keywords

Evolutionary genetics
Population genetics

Access to Document

10.1038/srep37198

PDFAccepted author manuscript, 686 KBLicence: CC BY-NC-ND

Cite this

Inchley, C. E., Larbey, C. D. A., Shwan, N. A. A., Pagani, L., Saag, L., Antão, T., Jacobs, G., Hudjashov, G., Metspalu, E., Mitt, M., Eichstaedt, C. A., Malyarchuk, B., Derenko, M., Wee, J., Abdullah, S., Ricaut, F-X., Mormina, M., Mägi, R., Villems, R., ... Kivisild, T. (2016). Selective sweep on human amylase genes postdates the split with Neanderthals. Scientific Reports, 6(37198). https://doi.org/10.1038/srep37198

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. In: Scientific Reports. 2016 ; Vol. 6, No. 37198.

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title = "Selective sweep on human amylase genes postdates the split with Neanderthals",

abstract = "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.",

keywords = "Evolutionary genetics, Population genetics",

author = "Inchley, {Charlotte E.} and Larbey, {Cynthia D. A.} and Shwan, {Nzar A. A.} and Luca Pagani and Lauri Saag and Tiago Ant{\~a}o and Guy Jacobs and Georgi Hudjashov and Ene Metspalu and Mario Mitt and Eichstaedt, {Christina A.} and Boris Malyarchuk and Miroslava Derenko and Joseph Wee and Syafiq Abdullah and Fran{\c c}ois-Xavier Ricaut and Maru Mormina and Reedik M{\"a}gi and Richard Villems and Mait Metspalu and Jones, {Martin K.} and Armour, {John A. L.} and Toomas Kivisild",

year = "2016",

month = nov,

day = "17",

doi = "10.1038/srep37198",

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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, 'Selective sweep on human amylase genes postdates the split with Neanderthals', Scientific Reports, vol. 6, no. 37198. https://doi.org/10.1038/srep37198

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.

In: Scientific Reports, Vol. 6, No. 37198, 17.11.2016.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - Selective sweep on human amylase genes postdates the split with Neanderthals

AU - Inchley, Charlotte E.

AU - Larbey, Cynthia D. A.

AU - Shwan, Nzar A. A.

AU - Pagani, Luca

AU - Saag, Lauri

AU - Antão, Tiago

AU - Jacobs, Guy

AU - Hudjashov, Georgi

AU - Metspalu, Ene

AU - Mitt, Mario

AU - Eichstaedt, Christina A.

AU - Malyarchuk, Boris

AU - Derenko, Miroslava

AU - Wee, Joseph

AU - Abdullah, Syafiq

AU - Ricaut, François-Xavier

AU - Mormina, Maru

AU - Mägi, Reedik

AU - Villems, Richard

AU - Metspalu, Mait

AU - Jones, Martin K.

AU - Armour, John A. L.

AU - Kivisild, Toomas

PY - 2016/11/17

Y1 - 2016/11/17

N2 - 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.

AB - 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.

KW - Evolutionary genetics

KW - Population genetics

U2 - 10.1038/srep37198

DO - 10.1038/srep37198

M3 - Article

VL - 6

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

IS - 37198

ER -