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1. The Beaker Phenomenon and the genomic transformation of Northwest Europe

Author

Olalde, I., Brace, S., Allentoft, M., Armit, I., Kristiansen, K., Rohland, N., Mallick, S., Booth, T., Szécsényi-Nagy, A., Mittnik, A., Altena, E., Lipson, M., Lazaridis, I., Patterson, N., Broomandkhoshbacht, N., Diekmann, Y., Faltyskova, Z., Fernandes, D., Ferry, M., Harney, E., de Knijff, P., Michel, M., Oppenheimer, J., Stewardson, K., Barclay, A., Alt, K., Fernández, A., Bánffy, E., Bernabò-Brea, M., Billoin, D., Blasco, C., Bonsall, C., Bonsall, L., Allen, T., Büster, L., Carver, S., Navarro, L., Craig, O., Cook, G., Cunliffe, B., Denaire, A., Dinwiddy, K., Dodwell, N., Ernée, M., Evans, C., Kuchařík, M., Farré, J., Fokkens, H., Fowler, C., Gazenbeek, M., Pena, R., Haber-Uriarte, M., Haduch, E., Hey, G., Jowett, N., Knowles, T., Massy, K., Pfrengle, S., Lefranc, P., Lemercier, O., Lefebvre, A., Maurandi, J., Majó, T., McKinley, J., McSweeney, K., Gusztáv, M., Modi, A., Kulcsár, G., Kiss, V., Czene, A., Patay, R., Endródi, A., Köhler, K., Hajdu, T., Cardoso, J., Liesau, C., Pearson, M., Włodarczak, P., Price, T., Prieto, P., Rey, P., Ríos, P., Risch, R., Guerra, M., Schmitt, A., Serralongue, J., Silva, A., Smrčka, V., Vergnaud, L., Zilhão, J., Caramelli, D., Higham, T., Heyd, V., Sheridan, A., Sjögren, K., Thomas, M., Stockhammer, P., Pinhasi, R., Krause, J., Haak, W., Barnes, I., Lalueza-Fox, C., and Reich, D.

Published
2017

2. A recent bottleneck of Y chromosome diversity coincides with a global change in culture

Author

Karmin M., Saag L., Vicente M., Wilson Sayres M., Järve M., Talas U., Rootsi S., Ilumäe A., Mägi R., Mitt M., Pagani L., Puurand T., Faltyskova Z., Clemente F., Cardona A., Metspalu E., Sahakyan H., Yunusbayev B., Hudjashov G., DeGiorgio M., Loogväli E., Eichstaedt C., Eelmets M., Chaubey G., Tambets K., Litvinov S., Mormina M., Xue Y., Ayub Q., Zoraqi G., Korneliussen T., Akhatova F., Lachance J., Tishkoff S., Momynaliev K., Ricaut F., Kusuma P., Razafindrazaka H., Pierron D., Cox M., Sultana G., Willerslev R., Muller C., Westaway M., Lambert D., Skaro V., Kovačević L., Turdikulova S., Dalimova D., Khusainova R., Trofimova N., Akhmetova V., Khidiyatova I., Lichman D., Isakova J., Pocheshkhova E., Sabitov Z., Barashkov N., Nymadawa P., Mihailov E., Seng J., Evseeva I., Migliano A., Abdullah S., Andriadze G., Primorac D., Atramentova L., Utevska O., Yepiskoposyan L., Marjanović D., Kushniarevich A., and Behar D.

Abstract

© 2015 Karmin et al. It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

Published
2015

3. A recent bottleneck of Y chromosome diversity coincides with a global change in culture

Author

Karmin, M., Saag, L., Vicente, M., Wilson Sayres, M.A., Jarve, M., Talas, U.G., Rootsi, S., Ilumae, A.M., Magi, R., Mitt, M., Pagani, L., Puurand, T., Faltyskova, Z., Clemente, F., Cardona, A., Metspalu, E., Sahakyan, H., Yunusbayev, B., Hudjashov, G., DeGiorgio, M., Loogvali, E.L., Eichstaedt, C., Eelmets, M., Chaubey, G., Tambets, K., Litvinov, S., Mormina, M., Xue, Y., Ayub, Q., Zoraqi, G., Korneliussen, T.S., Akhatova, F., Lachance, J., Tishkoff, S., Momynaliev, K., Ricaut, F.X., Kusuma, P., Razafindrazaka, H., Pierron, D., Cox, M.P., Sultana, G.N., Willerslev, R., Muller, C., Westaway, M., Lambert, D., Skaro, V., Kovacevic, L., Turdikulova, S., Dalimova, D., Khusainova, R., Trofimova, N., Akhmetova, V., Khidiyatova, I., Lichman, D.V., Isakova, J., Pocheshkhova, E., Sabitov, Z., Barashkov, N.A., Nymadawa, P., Mihailov, E., Seng, J.W., Evseeva, I., Migliano, A.B., Abdullah, S., Andriadze, G., Primorac, D., Atramentova, L., Utevska, O., Yepiskoposyan, L., Marjanovic, D., Kushniarevich, A., Behar, D.M., Gilissen, C., Vissers, L., Veltman, J.A., Balanovska, E., Derenko, M., Malyarchuk, B., Metspalu, A., Fedorova, S., Eriksson, A., Manica, A., Mendez, F.L., Karafet, T.M., Veeramah, K.R., Bradman, N., Hammer, M.F., Osipova, L.P., Balanovsky, O., Khusnutdinova, E.K., Johnsen, K., Remm, M., Thomas, M.G., Tyler-Smith, C., Underhill, P.A., Willerslev, E., Nielsen, R., Metspalu, M., Villems, R., Kivisild, T., Karmin, M., Saag, L., Vicente, M., Wilson Sayres, M.A., Jarve, M., Talas, U.G., Rootsi, S., Ilumae, A.M., Magi, R., Mitt, M., Pagani, L., Puurand, T., Faltyskova, Z., Clemente, F., Cardona, A., Metspalu, E., Sahakyan, H., Yunusbayev, B., Hudjashov, G., DeGiorgio, M., Loogvali, E.L., Eichstaedt, C., Eelmets, M., Chaubey, G., Tambets, K., Litvinov, S., Mormina, M., Xue, Y., Ayub, Q., Zoraqi, G., Korneliussen, T.S., Akhatova, F., Lachance, J., Tishkoff, S., Momynaliev, K., Ricaut, F.X., Kusuma, P., Razafindrazaka, H., Pierron, D., Cox, M.P., Sultana, G.N., Willerslev, R., Muller, C., Westaway, M., Lambert, D., Skaro, V., Kovacevic, L., Turdikulova, S., Dalimova, D., Khusainova, R., Trofimova, N., Akhmetova, V., Khidiyatova, I., Lichman, D.V., Isakova, J., Pocheshkhova, E., Sabitov, Z., Barashkov, N.A., Nymadawa, P., Mihailov, E., Seng, J.W., Evseeva, I., Migliano, A.B., Abdullah, S., Andriadze, G., Primorac, D., Atramentova, L., Utevska, O., Yepiskoposyan, L., Marjanovic, D., Kushniarevich, A., Behar, D.M., Gilissen, C., Vissers, L., Veltman, J.A., Balanovska, E., Derenko, M., Malyarchuk, B., Metspalu, A., Fedorova, S., Eriksson, A., Manica, A., Mendez, F.L., Karafet, T.M., Veeramah, K.R., Bradman, N., Hammer, M.F., Osipova, L.P., Balanovsky, O., Khusnutdinova, E.K., Johnsen, K., Remm, M., Thomas, M.G., Tyler-Smith, C., Underhill, P.A., Willerslev, E., Nielsen, R., Metspalu, M., Villems, R., and Kivisild, T.

Abstract

Contains fulltext : 153022.pdf (publisher's version ) (Open Access), It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

Published
2015

5. A recent bottleneck of Y chromosome diversity coincides with a global change in culture

Author

Karmin M., Saag L., Vicente M., Wilson Sayres M., Järve M., Talas U., Rootsi S., Ilumäe A., Mägi R., Mitt M., Pagani L., Puurand T., Faltyskova Z., Clemente F., Cardona A., Metspalu E., Sahakyan H., Yunusbayev B., Hudjashov G., DeGiorgio M., Loogväli E., Eichstaedt C., Eelmets M., Chaubey G., Tambets K., Litvinov S., Mormina M., Xue Y., Ayub Q., Zoraqi G., Korneliussen T., Akhatova F., Lachance J., Tishkoff S., Momynaliev K., Ricaut F., Kusuma P., Razafindrazaka H., Pierron D., Cox M., Sultana G., Willerslev R., Muller C., Westaway M., Lambert D., Skaro V., Kovačević L., Turdikulova S., Dalimova D., Khusainova R., Trofimova N., Akhmetova V., Khidiyatova I., Lichman D., Isakova J., Pocheshkhova E., Sabitov Z., Barashkov N., Nymadawa P., Mihailov E., Seng J., Evseeva I., Migliano A., Abdullah S., Andriadze G., Primorac D., Atramentova L., Utevska O., Yepiskoposyan L., Marjanović D., Kushniarevich A., Behar D., Karmin M., Saag L., Vicente M., Wilson Sayres M., Järve M., Talas U., Rootsi S., Ilumäe A., Mägi R., Mitt M., Pagani L., Puurand T., Faltyskova Z., Clemente F., Cardona A., Metspalu E., Sahakyan H., Yunusbayev B., Hudjashov G., DeGiorgio M., Loogväli E., Eichstaedt C., Eelmets M., Chaubey G., Tambets K., Litvinov S., Mormina M., Xue Y., Ayub Q., Zoraqi G., Korneliussen T., Akhatova F., Lachance J., Tishkoff S., Momynaliev K., Ricaut F., Kusuma P., Razafindrazaka H., Pierron D., Cox M., Sultana G., Willerslev R., Muller C., Westaway M., Lambert D., Skaro V., Kovačević L., Turdikulova S., Dalimova D., Khusainova R., Trofimova N., Akhmetova V., Khidiyatova I., Lichman D., Isakova J., Pocheshkhova E., Sabitov Z., Barashkov N., Nymadawa P., Mihailov E., Seng J., Evseeva I., Migliano A., Abdullah S., Andriadze G., Primorac D., Atramentova L., Utevska O., Yepiskoposyan L., Marjanović D., Kushniarevich A., and Behar D.

Abstract

© 2015 Karmin et al. It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

6. A recent bottleneck of Y chromosome diversity coincides with a global change in culture

Author

Karmin M., Saag L., Vicente M., Wilson Sayres M., Järve M., Talas U., Rootsi S., Ilumäe A., Mägi R., Mitt M., Pagani L., Puurand T., Faltyskova Z., Clemente F., Cardona A., Metspalu E., Sahakyan H., Yunusbayev B., Hudjashov G., DeGiorgio M., Loogväli E., Eichstaedt C., Eelmets M., Chaubey G., Tambets K., Litvinov S., Mormina M., Xue Y., Ayub Q., Zoraqi G., Korneliussen T., Akhatova F., Lachance J., Tishkoff S., Momynaliev K., Ricaut F., Kusuma P., Razafindrazaka H., Pierron D., Cox M., Sultana G., Willerslev R., Muller C., Westaway M., Lambert D., Skaro V., Kovačević L., Turdikulova S., Dalimova D., Khusainova R., Trofimova N., Akhmetova V., Khidiyatova I., Lichman D., Isakova J., Pocheshkhova E., Sabitov Z., Barashkov N., Nymadawa P., Mihailov E., Seng J., Evseeva I., Migliano A., Abdullah S., Andriadze G., Primorac D., Atramentova L., Utevska O., Yepiskoposyan L., Marjanović D., Kushniarevich A., Behar D., Karmin M., Saag L., Vicente M., Wilson Sayres M., Järve M., Talas U., Rootsi S., Ilumäe A., Mägi R., Mitt M., Pagani L., Puurand T., Faltyskova Z., Clemente F., Cardona A., Metspalu E., Sahakyan H., Yunusbayev B., Hudjashov G., DeGiorgio M., Loogväli E., Eichstaedt C., Eelmets M., Chaubey G., Tambets K., Litvinov S., Mormina M., Xue Y., Ayub Q., Zoraqi G., Korneliussen T., Akhatova F., Lachance J., Tishkoff S., Momynaliev K., Ricaut F., Kusuma P., Razafindrazaka H., Pierron D., Cox M., Sultana G., Willerslev R., Muller C., Westaway M., Lambert D., Skaro V., Kovačević L., Turdikulova S., Dalimova D., Khusainova R., Trofimova N., Akhmetova V., Khidiyatova I., Lichman D., Isakova J., Pocheshkhova E., Sabitov Z., Barashkov N., Nymadawa P., Mihailov E., Seng J., Evseeva I., Migliano A., Abdullah S., Andriadze G., Primorac D., Atramentova L., Utevska O., Yepiskoposyan L., Marjanović D., Kushniarevich A., and Behar D.

Abstract

© 2015 Karmin et al. It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

7. Author Correction: Ancient genomes indicate population replacement in Early Neolithic Britain.

Author

Brace S, Diekmann Y, Booth TJ, van Dorp L, Faltyskova Z, Rohland N, Mallick S, Olalde I, Ferry M, Michel M, Oppenheimer J, Broomandkhoshbacht N, Stewardson K, Martiniano R, Walsh S, Kayser M, Charlton S, Hellenthal G, Armit I, Schulting R, Craig OE, Sheridan A, Pearson MP, Stringer C, Reich D, Thomas MG, and Barnes I

Abstract

In the version of this Article originally published, there were errors in the colour ordering of the legend in Fig. 5b, and in the positions of the target and surrogate populations in Fig. 5c. This has now been corrected. The conclusions of the study are in no way affected. The errors have been corrected in the HTML and PDF versions of the article.

Published
2019
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8. Ancient genomes indicate population replacement in Early Neolithic Britain.

Author

Brace S, Diekmann Y, Booth TJ, van Dorp L, Faltyskova Z, Rohland N, Mallick S, Olalde I, Ferry M, Michel M, Oppenheimer J, Broomandkhoshbacht N, Stewardson K, Martiniano R, Walsh S, Kayser M, Charlton S, Hellenthal G, Armit I, Schulting R, Craig OE, Sheridan A, Parker Pearson M, Stringer C, Reich D, Thomas MG, and Barnes I

Subjects
Europe, Humans, Population Dynamics, United Kingdom, DNA, Ancient, Genome
Abstract

The roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Aegean ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers. Neolithic cultures first appear in Britain circa 4000 BC, a millennium after they appeared in adjacent areas of continental Europe. The pattern and process of this delayed British Neolithic transition remain unclear. We assembled genome-wide data from 6 Mesolithic and 67 Neolithic individuals found in Britain, dating 8500-2500 BC. Our analyses reveal persistent genetic affinities between Mesolithic British and Western European hunter-gatherers. We find overwhelming support for agriculture being introduced to Britain by incoming continental farmers, with small, geographically structured levels of hunter-gatherer ancestry. Unlike other European Neolithic populations, we detect no resurgence of hunter-gatherer ancestry at any time during the Neolithic in Britain. Genetic affinities with Iberian Neolithic individuals indicate that British Neolithic people were mostly descended from Aegean farmers who followed the Mediterranean route of dispersal. We also infer considerable variation in pigmentation levels in Europe by circa 6000 BC.

Published
2019
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9. Ancient human parallel lineages within North America contributed to a coastal expansion.

Author

Scheib CL, Li H, Desai T, Link V, Kendall C, Dewar G, Griffith PW, Mörseburg A, Johnson JR, Potter A, Kerr SL, Endicott P, Lindo J, Haber M, Xue Y, Tyler-Smith C, Sandhu MS, Lorenz JG, Randall TD, Faltyskova Z, Pagani L, Danecek P, O'Connell TC, Martz P, Boraas AS, Byrd BF, Leventhal A, Cambra R, Williamson R, Lesage L, Holguin B, Ygnacio-De Soto E, Rosas J, Metspalu M, Stock JT, Manica A, Scally A, Wegmann D, Malhi RS, and Kivisild T

Subjects
California, Humans, Ontario, Biological Evolution, Emigration and Immigration, Genome, Human, Population genetics
Abstract

Little is known regarding the first people to enter the Americas and their genetic legacy. Genomic analysis of the oldest human remains from the Americas showed a direct relationship between a Clovis-related ancestral population and all modern Central and South Americans as well as a deep split separating them from North Americans in Canada. We present 91 ancient human genomes from California and Southwestern Ontario and demonstrate the existence of two distinct ancestries in North America, which possibly split south of the ice sheets. A contribution from both of these ancestral populations is found in all modern Central and South Americans. The proportions of these two ancestries in ancient and modern populations are consistent with a coastal dispersal and multiple admixture events., (Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Published
2018
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10. Erratum: The Beaker phenomenon and the genomic transformation of northwest Europe.

Author

Olalde I, Brace S, Allentoft ME, Armit I, Kristiansen K, Booth T, Rohland N, Mallick S, Szécsényi-Nagy A, Mittnik A, Altena E, Lipson M, Lazaridis I, Harper TK, Patterson N, Broomandkhoshbacht N, Diekmann Y, Faltyskova Z, Fernandes D, Ferry M, Harney E, de Knijff P, Michel M, Oppenheimer J, Stewardson K, Barclay A, Alt KW, Liesau C, Ríos P, Blasco C, Miguel JV, García RM, Fernández AA, Bánffy E, Bernabò-Brea M, Billoin D, Bonsall C, Bonsall L, Allen T, Büster L, Carver S, Navarro LC, Craig OE, Cook GT, Cunliffe B, Denaire A, Dinwiddy KE, Dodwell N, Ernée M, Evans C, Kuchařík M, Farré JF, Fowler C, Gazenbeek M, Pena RG, Haber-Uriarte M, Haduch E, Hey G, Jowett N, Knowles T, Massy K, Pfrengle S, Lefranc P, Lemercier O, Lefebvre A, Martínez CH, Olmo VG, Ramírez AB, Maurandi JL, Majó T, McKinley JI, McSweeney K, Mende BG, Modi A, Kulcsár G, Kiss V, Czene A, Patay R, Endrődi A, Köhler K, Hajdu T, Szeniczey T, Dani J, Bernert Z, Hoole M, Cheronet O, Keating D, Velemínský P, Dobeš M, Candilio F, Brown F, Fernández RF, Herrero-Corral AM, Tusa S, Carnieri E, Lentini L, Valenti A, Zanini A, Waddington C, Delibes G, Guerra-Doce E, Neil B, Brittain M, Luke M, Mortimer R, Desideri J, Besse M, Brücken G, Furmanek M, Hałuszko A, Mackiewicz M, Rapiński A, Leach S, Soriano I, Lillios KT, Cardoso JL, Pearson MP, Włodarczak P, Price TD, Prieto P, Rey PJ, Risch R, Guerra MAR, Schmitt A, Serralongue J, Silva AM, Smrčka V, Vergnaud L, Zilhão J, Caramelli D, Higham T, Thomas MG, Kennett DJ, Fokkens H, Heyd V, Sheridan A, Sjögren KG, Stockhammer PW, Krause J, Pinhasi R, Haak W, Barnes I, Lalueza-Fox C, and Reich D

Abstract

This corrects the article DOI: 10.1038/nature25738.

Published
2018
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11. The Beaker phenomenon and the genomic transformation of northwest Europe.

Author

Olalde I, Brace S, Allentoft ME, Armit I, Kristiansen K, Booth T, Rohland N, Mallick S, Szécsényi-Nagy A, Mittnik A, Altena E, Lipson M, Lazaridis I, Harper TK, Patterson N, Broomandkhoshbacht N, Diekmann Y, Faltyskova Z, Fernandes D, Ferry M, Harney E, de Knijff P, Michel M, Oppenheimer J, Stewardson K, Barclay A, Alt KW, Liesau C, Ríos P, Blasco C, Miguel JV, García RM, Fernández AA, Bánffy E, Bernabò-Brea M, Billoin D, Bonsall C, Bonsall L, Allen T, Büster L, Carver S, Navarro LC, Craig OE, Cook GT, Cunliffe B, Denaire A, Dinwiddy KE, Dodwell N, Ernée M, Evans C, Kuchařík M, Farré JF, Fowler C, Gazenbeek M, Pena RG, Haber-Uriarte M, Haduch E, Hey G, Jowett N, Knowles T, Massy K, Pfrengle S, Lefranc P, Lemercier O, Lefebvre A, Martínez CH, Olmo VG, Ramírez AB, Maurandi JL, Majó T, McKinley JI, McSweeney K, Mende BG, Modi A, Kulcsár G, Kiss V, Czene A, Patay R, Endrődi A, Köhler K, Hajdu T, Szeniczey T, Dani J, Bernert Z, Hoole M, Cheronet O, Keating D, Velemínský P, Dobeš M, Candilio F, Brown F, Fernández RF, Herrero-Corral AM, Tusa S, Carnieri E, Lentini L, Valenti A, Zanini A, Waddington C, Delibes G, Guerra-Doce E, Neil B, Brittain M, Luke M, Mortimer R, Desideri J, Besse M, Brücken G, Furmanek M, Hałuszko A, Mackiewicz M, Rapiński A, Leach S, Soriano I, Lillios KT, Cardoso JL, Pearson MP, Włodarczak P, Price TD, Prieto P, Rey PJ, Risch R, Rojo Guerra MA, Schmitt A, Serralongue J, Silva AM, Smrčka V, Vergnaud L, Zilhão J, Caramelli D, Higham T, Thomas MG, Kennett DJ, Fokkens H, Heyd V, Sheridan A, Sjögren KG, Stockhammer PW, Krause J, Pinhasi R, Haak W, Barnes I, Lalueza-Fox C, and Reich D

Subjects
Chromosomes, Human, Y genetics, DNA, Ancient, Europe, Gene Pool, Genetics, Population, Haplotypes, History, Ancient, Humans, Male, Spatio-Temporal Analysis, Cultural Evolution history, Genome, Human genetics, Genomics, Human Migration history
Abstract

From around 2750 to 2500 bc, Bell Beaker pottery became widespread across western and central Europe, before it disappeared between 2200 and 1800 bc. The forces that propelled its expansion are a matter of long-standing debate, and there is support for both cultural diffusion and migration having a role in this process. Here we present genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 individuals associated with Beaker-complex artefacts. We detected limited genetic affinity between Beaker-complex-associated individuals from Iberia and central Europe, and thus exclude migration as an important mechanism of spread between these two regions. However, migration had a key role in the further dissemination of the Beaker complex. We document this phenomenon most clearly in Britain, where the spread of the Beaker complex introduced high levels of steppe-related ancestry and was associated with the replacement of approximately 90% of Britain's gene pool within a few hundred years, continuing the east-to-west expansion that had brought steppe-related ancestry into central and northern Europe over the previous centuries.

Published
2018
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12. A recent bottleneck of Y chromosome diversity coincides with a global change in culture.

Author

Karmin M, Saag L, Vicente M, Wilson Sayres MA, Järve M, Talas UG, Rootsi S, Ilumäe AM, Mägi R, Mitt M, Pagani L, Puurand T, Faltyskova Z, Clemente F, Cardona A, Metspalu E, Sahakyan H, Yunusbayev B, Hudjashov G, DeGiorgio M, Loogväli EL, Eichstaedt C, Eelmets M, Chaubey G, Tambets K, Litvinov S, Mormina M, Xue Y, Ayub Q, Zoraqi G, Korneliussen TS, Akhatova F, Lachance J, Tishkoff S, Momynaliev K, Ricaut FX, Kusuma P, Razafindrazaka H, Pierron D, Cox MP, Sultana GN, Willerslev R, Muller C, Westaway M, Lambert D, Skaro V, Kovačevic L, Turdikulova S, Dalimova D, Khusainova R, Trofimova N, Akhmetova V, Khidiyatova I, Lichman DV, Isakova J, Pocheshkhova E, Sabitov Z, Barashkov NA, Nymadawa P, Mihailov E, Seng JW, Evseeva I, Migliano AB, Abdullah S, Andriadze G, Primorac D, Atramentova L, Utevska O, Yepiskoposyan L, Marjanovic D, Kushniarevich A, Behar DM, Gilissen C, Vissers L, Veltman JA, Balanovska E, Derenko M, Malyarchuk B, Metspalu A, Fedorova S, Eriksson A, Manica A, Mendez FL, Karafet TM, Veeramah KR, Bradman N, Hammer MF, Osipova LP, Balanovsky O, Khusnutdinova EK, Johnsen K, Remm M, Thomas MG, Tyler-Smith C, Underhill PA, Willerslev E, Nielsen R, Metspalu M, Villems R, and Kivisild T

Subjects
Base Sequence, DNA, Mitochondrial genetics, Genetic Variation genetics, Genetics, Population, Haplotypes genetics, Humans, Male, Models, Genetic, Phylogeny, Sequence Analysis, DNA, Chromosomes, Human, Y genetics, Evolution, Molecular, Racial Groups genetics
Abstract

It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males., (© 2015 Karmin et al.; Published by Cold Spring Harbor Laboratory Press.)

Published
2015
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13. A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations.

Author

Clemente FJ, Cardona A, Inchley CE, Peter BM, Jacobs G, Pagani L, Lawson DJ, Antão T, Vicente M, Mitt M, DeGiorgio M, Faltyskova Z, Xue Y, Ayub Q, Szpak M, Mägi R, Eriksson A, Manica A, Raghavan M, Rasmussen M, Rasmussen S, Willerslev E, Vidal-Puig A, Tyler-Smith C, Villems R, Nielsen R, Metspalu M, Malyarchuk B, Derenko M, and Kivisild T

Abstract

Arctic populations live in an environment characterized by extreme cold and the absence of plant foods for much of the year and are likely to have undergone genetic adaptations to these environmental conditions in the time they have been living there. Genome-wide selection scans based on genotype data from native Siberians have previously highlighted a 3 Mb chromosome 11 region containing 79 protein-coding genes as the strongest candidates for positive selection in Northeast Siberians. However, it was not possible to determine which of the genes might be driving the selection signal. Here, using whole-genome high-coverage sequence data, we identified the most likely causative variant as a nonsynonymous G>A transition (rs80356779; c.1436C>T [p.Pro479Leu] on the reverse strand) in CPT1A, a key regulator of mitochondrial long-chain fatty-acid oxidation. Remarkably, the derived allele is associated with hypoketotic hypoglycemia and high infant mortality yet occurs at high frequency in Canadian and Greenland Inuits and was also found at 68% frequency in our Northeast Siberian sample. We provide evidence of one of the strongest selective sweeps reported in humans; this sweep has driven this variant to high frequency in circum-Arctic populations within the last 6-23 ka despite associated deleterious consequences, possibly as a result of the selective advantage it originally provided to either a high-fat diet or a cold environment., (Copyright © 2014 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)

Published
2014
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